{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import os\n", "import sys\n", "import time\n", "import subprocess\n", "import logging\n", "import warnings\n", "import gc\n", "import numpy as np\n", "import pandas as pd\n", "import seaborn as sns\n", "import matplotlib.pyplot as plt\n", "import matplotlib.patches as mpatches\n", "from concurrent.futures import ProcessPoolExecutor, as_completed" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "from rdkit import Chem\n", "from rdkit.Chem import AllChem, DataStructs, Draw\n", "from rdkit import RDConfig\n", "from rdkit.Chem import Descriptors, rdMolDescriptors, Lipinski, rdDistGeom, rdPartialCharges\n", "from rdkit.Chem.AllChem import GetMorganGenerator\n", "from rdkit.DataStructs.cDataStructs import ConvertToNumpyArray\n", "from rdkit.Avalon.pyAvalonTools import GetAvalonFP" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "import tensorflow as tf\n", "from tensorflow import keras\n", "from tensorflow.keras import layers\n", "from tensorflow.keras.models import Sequential\n", "from tensorflow.keras.layers import Dense, Dropout, Activation\n", "from tensorflow.keras.regularizers import l2\n", "from tensorflow.keras.optimizers import Adam\n", "from tensorflow.keras import regularizers" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "from sklearn.model_selection import train_test_split\n", "from sklearn.linear_model import Ridge\n", "from sklearn.ensemble import RandomForestRegressor\n", "from sklearn.neural_network import MLPRegressor\n", "from sklearn.svm import SVR\n", "from sklearn.metrics import r2_score, mean_absolute_error, mean_squared_error, root_mean_squared_error" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "import optuna\n", "from optuna.trial import TrialState\n", "from optuna.integration import TFKerasPruningCallback" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "from extra_code.feature_search import search_data_descriptor_compress" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "tf.keras.backend.clear_session()\n", "gpus = tf.config.experimental.list_physical_devices('GPU')\n", "if gpus:\n", " try:\n", " for gpu in gpus:\n", " tf.config.experimental.set_memory_growth(gpu, True)\n", " except RuntimeError as e:\n", " print(e)" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "target_path = \"result/4_ANO_feature\"\n", "os.makedirs(target_path, exist_ok=True)" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [], "source": [ "data_ws = pd.read_csv('./data/ws496_logS.csv', dtype={'SMILES': 'string'})\n", "smiles_ws = data_ws['SMILES']\n", "y_ws = data_ws.iloc[:, 2]\n", "\n", "data_delaney = pd.read_csv('./data/delaney-processed.csv', dtype={'smiles': 'string'})\n", "smiles_de = data_delaney['smiles']\n", "y_de = data_delaney.iloc[:, 1]\n", "\n", "data_lovric2020 = pd.read_csv('./data/Lovric2020_logS0.csv', dtype={'isomeric_smiles': 'string'})\n", "smiles_lo = data_lovric2020['isomeric_smiles']\n", "y_lo = data_lovric2020.iloc[:, 1]\n", "\n", "data_huuskonen = pd.read_csv('./data/huusk.csv', dtype={'SMILES': 'string'})\n", "smiles_hu = data_huuskonen['SMILES']\n", "y_hu = data_huuskonen.iloc[:, -1].astype('float')" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [], "source": [ "def mol3d(mol):\n", " mol = Chem.AddHs(mol)\n", " optimization_methods = [\n", " (AllChem.EmbedMolecule, (mol, AllChem.ETKDGv3()), {}),\n", " (AllChem.UFFOptimizeMolecule, (mol,), {'maxIters': 200}),\n", " (AllChem.MMFFOptimizeMolecule, (mol,), {'maxIters': 200})\n", " ]\n", "\n", " for method, args, kwargs in optimization_methods:\n", " try:\n", " method(*args, **kwargs)\n", " if mol.GetNumConformers() > 0:\n", " return mol\n", " except ValueError as e:\n", " print(f\"Error: {e} - Trying next optimization method [{method}]\")\n", "\n", " print(f\"Invalid mol for 3d {'\\033[94m'}{Chem.MolToSmiles(mol)}{'\\033[0m'} - No conformer generated\")\n", " return None" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [], "source": [ "def convert_smiles_to_mol(smiles, fail_folder=None, index=None, yvalue=None):\n", " mol = Chem.MolFromSmiles(smiles)\n", " if mol is None:\n", " print(f\"[convert_smiles_to_mol] Cannot convert {smiles} to Mols\")\n", " return None, {\"smiles\": smiles, \"y_value\": yvalue, \"error\": \"Invalid SMILES\"}\n", "\n", " try:\n", " Chem.Kekulize(mol, clearAromaticFlags=True)\n", " isomeric_smiles = Chem.MolToSmiles(mol, isomericSmiles=True)\n", " mol = Chem.MolFromSmiles(isomeric_smiles)\n", " except Exception as e:\n", " print(f\"[convert_smiles_to_mol] failed {smiles} isomeric_smiles by {e}\")\n", " if fail_folder and index is not None:\n", " img_path = os.path.join(fail_folder, f\"mol_{index}.png\")\n", " img = Draw.MolToImage(mol)\n", " img.save(img_path)\n", " return None, {\"smiles\": smiles, \"y_value\": yvalue, \"error\": f\"Isomeric SMILES error: {e}\"}\n", "\n", " try:\n", " Chem.SanitizeMol(mol)\n", " except Exception as e:\n", " print(f\"[convert_smiles_to_mol] failed {smiles} SanitizeMol by {e}\")\n", " if fail_folder and index is not None:\n", " img_path = os.path.join(fail_folder, f\"mol_{index}.png\")\n", " img = Draw.MolToImage(mol)\n", " img.save(img_path)\n", " return None, {\"smiles\": smiles, \"y_value\": yvalue, \"error\": f\"SanitizeMol error: {e}\"}\n", "\n", " return mol, None" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [], "source": [ "def process_smiles(smiles, yvalue, fail_folder, index):\n", " mol, error = convert_smiles_to_mol(smiles, fail_folder, index, yvalue)\n", " if error:\n", " return None, None, error\n", "\n", " mol_3d = mol3d(mol)\n", " if mol_3d:\n", " return smiles, yvalue, None\n", " else:\n", " img_path = os.path.join(fail_folder, f\"mol_{index}.png\")\n", " img = Draw.MolToImage(mol)\n", " img.save(img_path)\n", " return None, None, {\"smiles\": smiles, \"y_value\": yvalue}\n", "\n", "def process_dataset(smiles_list, y_values, dataset_name, target_path=\"result\", max_workers=None):\n", " start = time.time()\n", " valid_smiles, valid_y = [], []\n", " error_smiles_list = []\n", " fail_folder = f\"{target_path}/failed/{dataset_name}\"\n", " os.makedirs(fail_folder, exist_ok=True)\n", "\n", " with ProcessPoolExecutor(max_workers=max_workers) as executor:\n", " futures = [\n", " executor.submit(process_smiles, smiles, yvalue, fail_folder, i)\n", " for i, (smiles, yvalue) in enumerate(zip(smiles_list, y_values))\n", " ]\n", " for future in as_completed(futures):\n", " smiles, yvalue, error = future.result()\n", " if error:\n", " error_smiles_list.append(error)\n", " elif smiles is not None and yvalue is not None:\n", " valid_smiles.append(smiles)\n", " valid_y.append(yvalue)\n", "\n", " if error_smiles_list:\n", " error_df = pd.DataFrame(error_smiles_list)\n", " error_df.to_csv(os.path.join(fail_folder, \"failed_smiles.csv\"), index=False)\n", " print(f\" [{dataset_name:<10}] : {time.time()-start:.4f} sec\")\n", " return valid_smiles, valid_y" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "smiles_ws, y_ws = process_dataset(smiles_ws, y_ws, \"ws496\", target_path)\n", "smiles_de, y_de = process_dataset(smiles_de, y_de, \"delaney\", target_path)\n", "smiles_lo, y_lo = process_dataset(smiles_lo, y_lo, \"Lovric2020_logS0\", target_path)\n", "smiles_hu, y_hu = process_dataset(smiles_hu, y_hu, \"huusk\", target_path)" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [], "source": [ "LEN_OF_FF = 2048\n", "LEN_OF_MA = 167\n", "LEN_OF_AV = 512" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [], "source": [ "def get_fingerprints(mol):\n", " if mol is None:\n", " return None, None, None\n", " \n", " morgan_generator = GetMorganGenerator(radius=2, fpSize=LEN_OF_FF)\n", " ecfp = morgan_generator.GetFingerprint(mol)\n", " ecfp_array = np.zeros((LEN_OF_FF,),dtype=int)\n", " DataStructs.ConvertToNumpyArray(ecfp, ecfp_array)\n", " \n", " maccs = Chem.rdMolDescriptors.GetMACCSKeysFingerprint(mol)\n", "\n", " avalon_fp = GetAvalonFP(mol)\n", " avalon_array = np.zeros((LEN_OF_AV,),dtype=int)\n", " DataStructs.ConvertToNumpyArray(avalon_fp, avalon_array)\n", " \n", " return ecfp_array, maccs, avalon_array\n", "\n", "def fp_converter(data, use_parallel=True):\n", " mols = [Chem.MolFromSmiles(smi) for smi in data]\n", " \n", " if use_parallel:\n", " try: \n", " with ProcessPoolExecutor() as executor:\n", " results = list(executor.map(get_fingerprints, mols))\n", " except Exception as e:\n", " print(f\"Parallel processing failed due to: {e}. Falling back to sequential processing.\")\n", " use_parallel = False\n", " \n", " if not use_parallel:\n", " results = [get_fingerprints(mol) for mol in mols]\n", " \n", " ECFP, MACCS, AvalonFP = zip(*results)\n", " \n", " ECFP_container = np.vstack([arr for arr in ECFP if arr is not None])\n", " MACCS_container = np.zeros((len(MACCS), LEN_OF_MA), dtype=int)\n", " AvalonFP_container = np.vstack([arr for arr in AvalonFP if arr is not None])\n", "\n", " for i, fp in enumerate(MACCS):\n", " if fp is not None:\n", " DataStructs.ConvertToNumpyArray(fp, MACCS_container[i])\n", " \n", " return mols, ECFP_container, MACCS_container, AvalonFP_container" ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [], "source": [ "mol_ws, x_ws, MACCS_ws, AvalonFP_ws = fp_converter(smiles_ws,target_path)\n", "mol_de, x_de, MACCS_de, AvalonFP_de = fp_converter(smiles_de,target_path)\n", "mol_lo, x_lo, MACCS_lo, AvalonFP_lo = fp_converter(smiles_lo,target_path)\n", "mol_hu, x_hu, MACCS_hu, AvalonFP_hu = fp_converter(smiles_hu,target_path)" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [], "source": [ "def concatenate_to_numpy(*dataframes):\n", " numpy_arrays = [df.to_numpy() if isinstance(df, pd.DataFrame) else df for df in dataframes]\n", " if not all(isinstance(arr, np.ndarray) for arr in numpy_arrays):\n", " raise ValueError(\"All inputs must be either pandas DataFrame or numpy array\")\n", " return np.concatenate(numpy_arrays, axis=1)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "group_nws = concatenate_to_numpy(x_ws, MACCS_ws, AvalonFP_ws)\n", "group_nde = concatenate_to_numpy(x_de, MACCS_de, AvalonFP_de)\n", "group_nlo = concatenate_to_numpy(x_lo, MACCS_lo, AvalonFP_lo)\n", "group_nhu = concatenate_to_numpy(x_hu, MACCS_hu, AvalonFP_hu)\n", "del x_ws, MACCS_ws, AvalonFP_ws\n", "del x_de, MACCS_de, AvalonFP_de\n", "del x_lo, MACCS_lo, AvalonFP_lo\n", "del x_hu, MACCS_hu, AvalonFP_hu\n", "gc.collect()" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [], "source": [ "import logging\n", "import warnings\n", "\n", "os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'\n", "os.environ['CUDA_VISIBLE_DEVICES'] = '0'\n", "os.environ['TF_GPU_ALLOCATOR'] = 'cuda_malloc_async'\n", "os.environ['CUDA_DEVICE_ORDER'] = 'PCI_BUS_ID'\n", "os.environ['TF_XLA_FLAGS'] = '--tf_xla_auto_jit=2 --tf_xla_enable_xla_devices'\n", "os.environ['XLA_FLAGS'] = '--xla_gpu_cuda_data_dir=/usr/local/cuda --xla_gpu_force_compilation_parallelism=1'\n", "os.environ['TF_FORCE_GPU_ALLOW_GROWTH'] = 'true'\n", "os.environ['TF_ENABLE_ONEDNN_OPTS'] = '0'\n", "os.environ['TF_NUMA_NODES'] = '1'\n", "\n", "warnings.filterwarnings('ignore')\n", "\n", "warnings.simplefilter(action='ignore', category=FutureWarning)\n", "\n", "logging.getLogger('tensorflow').setLevel(logging.ERROR)\n", "\n", "tf.get_logger().setLevel('ERROR')\n", "tf.autograph.set_verbosity(0)\n", "\n", "def suppress_warnings(condition=True):\n", " if condition:\n", " logging.getLogger('tensorflow').setLevel(logging.ERROR)\n", " os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'\n", " else:\n", " logging.getLogger('tensorflow').setLevel(logging.WARNING)\n", " os.environ['TF_CPP_MIN_LOG_LEVEL'] = '0'\n", "\n", "suppress_warnings(condition=True)" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [], "source": [ "BATCHSIZE = 32\n", "EPOCHS = 1000\n", "lr = 0.001\n", "decay = 0.00001" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [], "source": [ "\n", "# Colab\n", "# def new_model():\n", "# model = tf.keras.Sequential([\n", "# tf.keras.layers.Dense(\n", "# units=1024,\n", "# activation='relu',\n", "# kernel_initializer='glorot_uniform',\n", "# kernel_regularizer=regularizers.l2(decay)),\n", "# tf.keras.layers.Dropout(0.2),\n", "# tf.keras.layers.Dense(\n", "# units=469,\n", "# activation='relu',\n", "# kernel_initializer='glorot_uniform',\n", "# kernel_regularizer=regularizers.l2(decay)),\n", "# tf.keras.layers.Dropout(0.2),\n", "# tf.keras.layers.Dense(units=1)\n", "# ])\n", "# model.compile(optimizer=tf.keras.optimizers.Adam(learning_rate=lr),\n", "# loss=tf.keras.losses.MeanSquaredError(),\n", "# metrics=[tf.keras.losses.MeanSquaredError(),\n", "# tf.keras.losses.MeanAbsoluteError(),\n", "# tf.keras.metrics.RootMeanSquaredError()])\n", "# return model\n", "\n", "def new_inference_model(input_dim):\n", " model = tf.keras.Sequential([\n", " layers.Input(shape=(input_dim,)),\n", " layers.Dense(\n", " units=1024,\n", " activation='relu',\n", " kernel_initializer='glorot_uniform',\n", " kernel_regularizer=regularizers.l2(decay)),\n", " layers.Dropout(0.2),\n", " layers.Dense(\n", " units=469,\n", " activation='relu',\n", " kernel_initializer='glorot_uniform',\n", " kernel_regularizer=regularizers.l2(decay)),\n", " layers.Dropout(0.2),\n", " layers.Dense(units=1)\n", " ])\n", " model.compile(optimizer=tf.keras.optimizers.Adam(learning_rate=lr),\n", " loss=tf.keras.losses.MeanSquaredError(),\n", " metrics=[tf.keras.losses.MeanSquaredError(),\n", " tf.keras.losses.MeanAbsoluteError(),\n", " tf.keras.metrics.RootMeanSquaredError()])\n", " return model\n", "\n", "def save_model(x_data):\n", " model_path = \"save_model/full_model.keras\"\n", " if not os.path.exists(model_path):\n", " try:\n", " model = new_inference_model(x_data.shape[1])\n", " os.makedirs(\"save_model\", exist_ok=True)\n", " model.save(model_path)\n", " print(f\"Model successfully saved to {model_path}\")\n", " except Exception as e:\n", " print(f\"Error saving model: {e}\")\n", " else:\n", " print(f\"Model already exists at {model_path}\")\n", " os.remove(model_path)\n", " save_model(x_data)" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [], "source": [ "# # Colab\n", "# def preprocess_data(xtr, ytr):\n", "# dataset = tf.data.Dataset.from_tensor_slices((xtr, ytr))\n", "# dataset = dataset.shuffle(buffer_size=len(xtr)).batch(BATCHSIZE).prefetch(tf.data.AUTOTUNE)\n", "# return dataset\n", "\n", "# cb = tf.keras.callbacks.EarlyStopping(\n", "# monitor='loss', \n", "# patience=10,\n", "# restore_best_weights=True,\n", "# # min_delta=0.001,\n", "# mode='min',\n", "# verbose=1\n", "# )" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [], "source": [ "# # Colab\n", "# def objective_ws_fea(trial):\n", "# r2_result = 0.0\n", "# new_x = search_data_descriptor_compress(trial, group_nws, mol_ws, 'ws496')\n", "# new_x = np.nan_to_num(new_x, nan=0.0, posinf=0.0, neginf=0.0).astype('float')\n", "# y_true = np.asarray(y_ws).astype('float')\n", "# model = new_model()\n", "# xtr, xte, ytr, yte = train_test_split(new_x, y_true, test_size=0.2, random_state=42)\n", "# train_dataset = preprocess_data(xtr, ytr)\n", "# model.fit(train_dataset, epochs=EPOCHS, callbacks=[cb,TFKerasPruningCallback(trial,'loss')], verbose=0)\n", "# ypred = model.predict(xte, verbose=0)\n", "# try:\n", "# r2_result = r2_score(yte, ypred)\n", "# print(f\"r2 score: {r2_result:.4f}\")\n", "# except Exception as e:\n", "# print(f\"Error occured: {e}\")\n", "# return r2_result\n", " " ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [], "source": [ "# # Colab\n", "# def objective_de_fea(trial):\n", "# r2_result = 0.0\n", "# new_x = search_data_descriptor_compress(trial, group_nde, mol_de, 'delaney')\n", "# new_x = np.nan_to_num(new_x, nan=0.0, posinf=0.0, neginf=0.0).astype('float')\n", "# y_true = np.asarray(y_de).astype('float')\n", "# model = new_model()\n", "# xtr, xte, ytr, yte = train_test_split(new_x, y_true, test_size=0.2, random_state=42)\n", "# train_dataset = preprocess_data(xtr, ytr)\n", "# model.fit(train_dataset, epochs=EPOCHS, callbacks=[cb,TFKerasPruningCallback(trial,'loss')], verbose=0)\n", "# ypred = model.predict(xte, verbose=0)\n", "# try:\n", "# r2_result = r2_score(yte, ypred)\n", "# print(f\"r2 score: {r2_result:.4f}\")\n", "# except Exception as e:\n", "# print(f\"Error occured: {e}\")\n", "# return r2_result\n", " " ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [], "source": [ "# # Colab\n", "# def objective_lo_fea(trial):\n", "# r2_result = 0.0\n", "# new_x = search_data_descriptor_compress(trial, group_nlo, mol_lo, 'lovric')\n", "# new_x = np.nan_to_num(new_x, nan=0.0, posinf=0.0, neginf=0.0).astype('float')\n", "# y_true = np.asarray(y_lo).astype('float')\n", "# model = new_model()\n", "# xtr, xte, ytr, yte = train_test_split(new_x, y_true, test_size=0.2, random_state=42)\n", "# train_dataset = preprocess_data(xtr, ytr)\n", "# model.fit(train_dataset, epochs=EPOCHS, callbacks=[cb,TFKerasPruningCallback(trial,'loss')], verbose=0)\n", "# ypred = model.predict(xte, verbose=0)\n", "# try:\n", "# r2_result = r2_score(yte, ypred)\n", "# print(f\"r2 score: {r2_result:.4f}\")\n", "# except Exception as e:\n", "# print(f\"Error occured: {e}\")\n", "# return r2_result\n", " " ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [], "source": [ "# # Colab\n", "# def objective_hu_fea(trial):\n", "# r2_result = 0.0\n", "# new_x = search_data_descriptor_compress(trial, group_nhu, mol_hu, 'huusk')\n", "# new_x = np.nan_to_num(new_x, nan=0.0, posinf=0.0, neginf=0.0).astype('float')\n", "# y_true = np.asarray(y_hu).astype('float')\n", "# model = new_model()\n", "# xtr, xte, ytr, yte = train_test_split(new_x, y_true, test_size=0.2, random_state=42)\n", "# train_dataset = preprocess_data(xtr, ytr)\n", "# model.fit(train_dataset, epochs=EPOCHS, callbacks=[cb,TFKerasPruningCallback(trial,'loss')], verbose=0)\n", "# ypred = model.predict(xte, verbose=0)\n", "# try:\n", "# r2_result = r2_score(yte, ypred)\n", "# print(f\"r2 score: {r2_result:.4f}\")\n", "# except Exception as e:\n", "# print(f\"Error occured: {e}\")\n", "# return r2_result\n", " " ] }, { "cell_type": "code", "execution_count": 27, "metadata": {}, "outputs": [], "source": [ "def objective_ws_fea(trial):\n", " try:\n", " new_x = search_data_descriptor_compress(trial, group_nws, mol_ws, 'ws496')\n", " new_x = np.nan_to_num(new_x, nan=0.0, posinf=0.0, neginf=0.0).astype('float')\n", " y_true = np.asarray(y_ws).astype('float')\n", " np.save('new_fps.npy', new_x)\n", " np.save('y_true.npy', y_true)\n", " \n", " save_model(new_x)\n", "\n", " result = subprocess.run(['python3', './extra_code/learning_process.py', \n", " str(BATCHSIZE), str(EPOCHS), \n", " str(lr),\n", " 'new_fps.npy', 'y_true.npy'],\n", " stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)\n", "\n", " if result.stderr:\n", " filtered_stderr = '\\n'.join([line for line in result.stderr.split('\\n') if \"could not open file to read NUMA node\" not in line and \"Your kernel may have been built without NUMA support\" not in line])\n", " if filtered_stderr:\n", " print(f\"Error in subprocess: {filtered_stderr}\", file=sys.stderr)\n", "\n", " for line in result.stdout.splitlines():\n", " if \"R2\" in line:\n", " if \"(prune)\" in line:\n", " print(f\"Pruning trial due to poor R2: {line}\")\n", " r2_result = 0.0\n", " trial.report(r2_result, step=0)\n", " raise optuna.exceptions.TrialPruned()\n", " else:\n", " r2_result = float(line.split(\":\")[1].strip())\n", " print(f\"R2 score: {r2_result}\")\n", " trial.report(r2_result, step=0)\n", "\n", " if trial.should_prune():\n", " raise optuna.exceptions.TrialPruned()\n", "\n", " except Exception as e:\n", " print(f\"Exception occurred: {e}\", file=sys.stderr)\n", " r2_result = 0.0\n", "\n", " gc.collect()\n", "\n", " return r2_result" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [], "source": [ "def objective_de_fea(trial):\n", " try:\n", " new_x = search_data_descriptor_compress(trial, group_nde, mol_de, 'delaney')\n", " new_x = np.nan_to_num(new_x, nan=0.0, posinf=0.0, neginf=0.0).astype('float')\n", " y_true = np.asarray(y_de).astype('float')\n", " np.save('new_fps.npy', new_x)\n", " np.save('y_true.npy', y_true)\n", " \n", " save_model(new_x)\n", "\n", " r2_result = 0.0\n", " \n", " result = subprocess.run(['python3', './extra_code/learning_process.py',\n", " str(BATCHSIZE), str(EPOCHS), \n", " str(lr),\n", " 'new_fps.npy', 'y_true.npy'],\n", " stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)\n", "\n", " if result.stderr:\n", " filtered_stderr = '\\n'.join([line for line in result.stderr.split('\\n') if \"could not open file to read NUMA node\" not in line and \"Your kernel may have been built without NUMA support\" not in line])\n", " if filtered_stderr:\n", " print(f\"Error in subprocess: {filtered_stderr}\", file=sys.stderr)\n", "\n", " for line in result.stdout.splitlines():\n", " if \"R2\" in line:\n", " if \"(prune)\" in line:\n", " print(f\"Pruning trial due to poor R2: {line}\")\n", " r2_result = 0.0\n", " trial.report(r2_result, step=0)\n", " raise optuna.exceptions.TrialPruned()\n", " else:\n", " r2_result = float(line.split(\":\")[1].strip())\n", " print(f\"R2 score: {r2_result}\")\n", " trial.report(r2_result, step=0)\n", "\n", " if trial.should_prune():\n", " raise optuna.exceptions.TrialPruned()\n", "\n", " except Exception as e:\n", " print(f\"Exception occurred: {e}\", file=sys.stderr)\n", " r2_result = 0.0\n", "\n", " gc.collect()\n", "\n", " return r2_result" ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [], "source": [ "def objective_lo_fea(trial):\n", " try:\n", " new_x = search_data_descriptor_compress(trial, group_nlo, mol_lo, 'lovrics')\n", " new_x = np.nan_to_num(new_x, nan=0.0, posinf=0.0, neginf=0.0).astype('float')\n", " y_true = np.asarray(y_lo).astype('float')\n", " np.save('new_fps.npy', new_x)\n", " np.save('y_true.npy', y_true)\n", " \n", " save_model(new_x)\n", " \n", " r2_result = 0.0\n", "\n", " result = subprocess.run(['python3', './extra_code/learning_process.py',\n", " str(BATCHSIZE), str(EPOCHS), \n", " str(lr),\n", " 'new_fps.npy', 'y_true.npy'],\n", " stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)\n", "\n", " if result.stderr:\n", " filtered_stderr = '\\n'.join([line for line in result.stderr.split('\\n') if \"could not open file to read NUMA node\" not in line and \"Your kernel may have been built without NUMA support\" not in line])\n", " if filtered_stderr:\n", " print(f\"Error in subprocess: {filtered_stderr}\", file=sys.stderr)\n", "\n", " for line in result.stdout.splitlines():\n", " if \"R2\" in line:\n", " if \"(prune)\" in line:\n", " print(f\"Pruning trial due to poor R2: {line}\")\n", " r2_result = 0.0\n", " trial.report(r2_result, step=0)\n", " raise optuna.exceptions.TrialPruned()\n", " else:\n", " r2_result = float(line.split(\":\")[1].strip())\n", " print(f\"R2 score: {r2_result}\")\n", " trial.report(r2_result, step=0)\n", "\n", " if trial.should_prune():\n", " raise optuna.exceptions.TrialPruned()\n", "\n", " except Exception as e:\n", " print(f\"Exception occurred: {e}\", file=sys.stderr)\n", " r2_result = 0.0\n", "\n", " gc.collect()\n", "\n", " return r2_result" ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [], "source": [ "def objective_hu_fea(trial):\n", " try:\n", " new_x = search_data_descriptor_compress(trial, group_nhu, mol_hu, 'huusken')\n", " new_x = np.nan_to_num(new_x, nan=0.0, posinf=0.0, neginf=0.0).astype('float')\n", " y_true = np.asarray(y_hu).astype('float')\n", " np.save('new_fps.npy', new_x)\n", " np.save('y_true.npy', y_true)\n", " save_model(new_x)\n", " \n", " r2_result = 0.0\n", "\n", " result = subprocess.run(['python3', './extra_code/learning_process.py',\n", " str(BATCHSIZE), str(EPOCHS), \n", " str(lr),\n", " 'new_fps.npy', 'y_true.npy'],\n", " stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)\n", "\n", " if result.stderr:\n", " filtered_stderr = '\\n'.join([line for line in result.stderr.split('\\n') if \"could not open file to read NUMA node\" not in line and \"Your kernel may have been built without NUMA support\" not in line])\n", " if filtered_stderr:\n", " print(f\"Error in subprocess: {filtered_stderr}\", file=sys.stderr)\n", "\n", " for line in result.stdout.splitlines():\n", " if \"R2\" in line:\n", " if \"(prune)\" in line:\n", " print(f\"Pruning trial due to poor R2: {line}\")\n", " r2_result = 0.0\n", " trial.report(r2_result, step=0)\n", " raise optuna.exceptions.TrialPruned()\n", " else:\n", " r2_result = float(line.split(\":\")[1].strip())\n", " print(f\"R2 score: {r2_result}\")\n", " trial.report(r2_result, step=0)\n", "\n", " if trial.should_prune():\n", " raise optuna.exceptions.TrialPruned()\n", "\n", " except Exception as e:\n", " print(f\"Exception occurred: {e}\", file=sys.stderr)\n", " r2_result = 0.0\n", "\n", " gc.collect()\n", "\n", " return r2_result" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [], "source": [ "storage = optuna.storages.RDBStorage(url=\"sqlite:///ano_analysis.db\", engine_kwargs={\"connect_args\": {\"timeout\": 10000}})\n", "# storage_urls = \"postgresql+psycopg2://postgres:{pwd}}@localhost:{num}}\"\n", "# storage = optuna.storages.RDBStorage(url=storage_urls)" ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [], "source": [ "TRIALS=100" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [], "source": [ "# try:\n", "# optuna.delete_study(study_name=\"ANO_ws_feature\", storage=storage)\n", "# optuna.delete_study(study_name=\"ANO_de_feature\", storage=storage)\n", "# optuna.delete_study(study_name=\"ANO_lo_feature\", storage=storage)\n", "# optuna.delete_study(study_name=\"ANO_hu_feature\", storage=storage)\n", "# except:\n", "# pass\n", "\n", "# try:\n", "# optuna.delete_study(study_name=\"ANO_ws_feature_fixed\", storage=storage)\n", "# optuna.delete_study(study_name=\"ANO_de_feature_fixed\", storage=storage)\n", "# optuna.delete_study(study_name=\"ANO_lo_feature_fixed\", storage=storage)\n", "# optuna.delete_study(study_name=\"ANO_hu_feature_fixed\", storage=storage)\n", "# except:\n", "# pass" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# study_ws_fea = optuna.create_study(study_name='ANO_ws_feature', storage=storage, direction=\"maximize\", pruner=optuna.pruners.SuccessiveHalvingPruner(reduction_factor=64, min_early_stopping_rate=10),load_if_exists=True) \n", "study_ws_fea = optuna.create_study(study_name='ANO_ws_feature', storage=storage, direction=\"maximize\", pruner=optuna.pruners.HyperbandPruner(min_resource=100,max_resource=1000,reduction_factor=3), load_if_exists=True)\n", "study_ws_fea.optimize(objective_ws_fea, n_trials=TRIALS)\n", "pruned_trials_ws_fea = study_ws_fea.get_trials(deepcopy=False, states=[TrialState.PRUNED])\n", "complete_trials_ws_fea = study_ws_fea.get_trials(deepcopy=False, states=[TrialState.COMPLETE])\n", "# 124m 43.4s - Trial 100" ] }, { "cell_type": "code", "execution_count": 36, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991009.518635 3878091 service.cc:146] XLA service 0x564effc2bbc0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991009.518679 3878091 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991009.644367 3878091 service.cc:146] XLA service 0x564effc02a40 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991009.644398 3878091 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991012.421072 3878199 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n", "[I 2024-10-27 10:03:47,160] Trial 300 finished with value: 0.901129 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.901129\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991049.863457 3878984 service.cc:146] XLA service 0x55a289630ac0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991049.863495 3878984 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991049.991176 3878984 service.cc:146] XLA service 0x55a2895ff900 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991049.991209 3878984 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991052.744126 3879098 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n", "[I 2024-10-27 10:04:27,535] Trial 301 finished with value: 0.929339 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.929339\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991090.658611 3879973 service.cc:146] XLA service 0x55e7004c4f40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991090.658679 3879973 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991090.783672 3879973 service.cc:146] XLA service 0x55e70049ce00 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991090.783724 3879973 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991093.538169 3880086 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.903158\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:05:11,123] Trial 302 finished with value: 0.903158 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991131.940927 3880900 service.cc:146] XLA service 0x564516eb6f30 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991131.940990 3880900 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991132.074329 3880900 service.cc:146] XLA service 0x564516deab00 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991132.074363 3880900 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991134.916294 3881008 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.940769\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:06:02,882] Trial 303 finished with value: 0.940769 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 0, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991187.178975 3882511 service.cc:146] XLA service 0x55f899995d20 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991187.179022 3882511 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991187.309350 3882511 service.cc:146] XLA service 0x55f8999b0020 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991187.309384 3882511 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991190.389431 3882617 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.95655\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:06:45,859] Trial 304 finished with value: 0.95655 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991228.720289 3883517 service.cc:146] XLA service 0x55661d6eba40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991228.720322 3883517 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991228.845907 3883517 service.cc:146] XLA service 0x55661d651030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991228.845954 3883517 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991231.673025 3883623 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n", "[I 2024-10-27 10:07:29,661] Trial 305 finished with value: 0.857592 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.857592\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991270.758201 3884733 service.cc:146] XLA service 0x55d28a890070 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991270.758274 3884733 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991270.880669 3884733 service.cc:146] XLA service 0x55d28a747c30 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991270.880704 3884733 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991273.730364 3884836 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.950647\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:08:10,913] Trial 306 finished with value: 0.950647 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991315.798150 3885774 service.cc:146] XLA service 0x55957cedda40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991315.798194 3885774 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991315.920185 3885774 service.cc:146] XLA service 0x55957ce43030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991315.920219 3885774 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991318.788098 3885885 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.925352\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:08:55,087] Trial 307 finished with value: 0.925352 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991360.259539 3886804 service.cc:146] XLA service 0x55d885c4d3e0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991360.259624 3886804 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991360.803471 3886804 service.cc:146] XLA service 0x55d885b80d90 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991360.803505 3886804 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991364.224580 3886914 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.921063\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:09:42,558] Trial 308 finished with value: 0.921063 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 1, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991400.779214 3887787 service.cc:146] XLA service 0x5565ad279a40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991400.779297 3887787 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991400.930404 3887787 service.cc:146] XLA service 0x5565ad1df030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991400.930441 3887787 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991405.076940 3887892 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.940509\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:10:26,225] Trial 309 finished with value: 0.940509 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 0, 'AUTOCORR2D': 0, 'BCUT2D': 0, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991451.142117 3889227 service.cc:146] XLA service 0x55762dae1f30 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991451.142154 3889227 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991451.266905 3889227 service.cc:146] XLA service 0x55762da81f30 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991451.266937 3889227 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991455.763269 3889331 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.894207\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:11:13,004] Trial 310 finished with value: 0.894207 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991498.598796 3890315 service.cc:146] XLA service 0x55ad0232ea30 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991498.598861 3890315 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991498.767379 3890315 service.cc:146] XLA service 0x55ad02294020 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991498.767420 3890315 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991504.631469 3890420 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.948552\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:12:04,487] Trial 311 finished with value: 0.948552 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991548.095158 3891537 service.cc:146] XLA service 0x55fd6bcaebd0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991548.095196 3891537 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991548.235867 3891537 service.cc:146] XLA service 0x55fd6bc7da90 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991548.235895 3891537 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991553.470302 3891646 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.895575\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:12:50,958] Trial 312 finished with value: 0.895575 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991598.160773 3892758 service.cc:146] XLA service 0x56263e784a40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991598.160835 3892758 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991598.301029 3892758 service.cc:146] XLA service 0x56263e6ea030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991598.301070 3892758 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991601.403319 3892864 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.918338\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:13:40,020] Trial 313 finished with value: 0.918338 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991643.108005 3893789 service.cc:146] XLA service 0x562e6a405880 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991643.108044 3893789 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991643.233399 3893789 service.cc:146] XLA service 0x562e6a381f00 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991643.233434 3893789 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991646.312847 3893895 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.946533\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:14:25,291] Trial 314 finished with value: 0.946533 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991690.778341 3894999 service.cc:146] XLA service 0x56439fa6d950 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991690.778427 3894999 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991690.907297 3894999 service.cc:146] XLA service 0x56439fa3c790 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991690.907332 3894999 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991693.970012 3895109 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.905433\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:15:10,871] Trial 315 finished with value: 0.905433 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991736.224593 3896200 service.cc:146] XLA service 0x55cdb0cf09c0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991736.224644 3896200 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991736.348410 3896200 service.cc:146] XLA service 0x55cdb0d26980 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991736.348438 3896200 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991739.574187 3896303 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.958766\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:16:01,902] Trial 316 finished with value: 0.958766 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991785.018276 3897795 service.cc:146] XLA service 0x558d5e6573f0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991785.018325 3897795 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991785.197187 3897795 service.cc:146] XLA service 0x558d5e5f5ae0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991785.197226 3897795 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991790.418473 3897907 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.940516\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:16:47,480] Trial 317 finished with value: 0.940516 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991833.613780 3898979 service.cc:146] XLA service 0x55921684ca40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991833.613817 3898979 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991833.745934 3898979 service.cc:146] XLA service 0x5592167b2030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991833.745964 3898979 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991836.822015 3899091 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.901428\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:17:34,521] Trial 318 finished with value: 0.901428 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991880.184545 3900176 service.cc:146] XLA service 0x562d0841afe0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991880.184594 3900176 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991881.051304 3900176 service.cc:146] XLA service 0x562d0845c1c0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991881.051344 3900176 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991884.137711 3900286 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.95056\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:18:22,863] Trial 319 finished with value: 0.95056 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991928.487981 3901284 service.cc:146] XLA service 0x5614d3f12e20 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991928.488017 3901284 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991928.612716 3901284 service.cc:146] XLA service 0x5614d3e7bbe0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991928.612756 3901284 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991931.768846 3901387 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.95756\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:19:10,757] Trial 320 finished with value: 0.95756 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729991976.204145 3902788 service.cc:146] XLA service 0x5572ed5fb190 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991976.204204 3902788 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729991976.361713 3902788 service.cc:146] XLA service 0x5572ed52eb40 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729991976.361745 3902788 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729991979.502145 3902897 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.897826\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:19:59,066] Trial 321 finished with value: 0.897826 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992022.727292 3903914 service.cc:146] XLA service 0x56132b90ee00 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992022.727338 3903914 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992022.867332 3903914 service.cc:146] XLA service 0x56132b7c69c0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992022.867369 3903914 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992025.926202 3904024 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.867705\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:20:44,531] Trial 322 finished with value: 0.867705 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992068.952008 3904889 service.cc:146] XLA service 0x55dda0617ad0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992068.952046 3904889 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992069.083546 3904889 service.cc:146] XLA service 0x55dda05ef670 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992069.083576 3904889 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992072.187516 3905001 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.930565\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:21:28,754] Trial 323 finished with value: 0.930565 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 0, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992114.456489 3905846 service.cc:146] XLA service 0x5577da9bf9c0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992114.456528 3905846 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992114.653841 3905846 service.cc:146] XLA service 0x5577da9f5980 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992114.653870 3905846 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992117.837518 3905957 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.908159\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:22:17,990] Trial 324 finished with value: 0.908159 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992157.703260 3907164 service.cc:146] XLA service 0x562e5a5b7f80 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992157.703310 3907164 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992157.842371 3907164 service.cc:146] XLA service 0x562e5ad83a90 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992157.842404 3907164 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992160.987027 3907267 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.924949\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:23:00,080] Trial 325 finished with value: 0.924949 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992203.622615 3908227 service.cc:146] XLA service 0x5597e6b61480 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992203.622658 3908227 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992203.757656 3908227 service.cc:146] XLA service 0x5597e6b30720 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992203.757763 3908227 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992206.963853 3908336 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.886879\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:23:44,185] Trial 326 finished with value: 0.886879 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992249.904975 3909206 service.cc:146] XLA service 0x5624980bbc70 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992249.905010 3909206 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992250.036827 3909206 service.cc:146] XLA service 0x56249808ab30 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992250.036860 3909206 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992253.229694 3909316 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.929457\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:24:32,771] Trial 327 finished with value: 0.929457 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992295.761765 3910405 service.cc:146] XLA service 0x55a862fe51c0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992295.761835 3910405 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992295.916351 3910405 service.cc:146] XLA service 0x55a862fb2e60 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992295.916383 3910405 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992299.077273 3910510 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.945218\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:25:18,779] Trial 328 finished with value: 0.945218 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992344.633154 3911553 service.cc:146] XLA service 0x557669b5e110 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992344.633214 3911553 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992344.779463 3911553 service.cc:146] XLA service 0x557669b9f2f0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992344.779497 3911553 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992347.921873 3911658 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.922527\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:26:03,796] Trial 329 finished with value: 0.922527 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992389.113544 3912402 service.cc:146] XLA service 0x56447ddc5160 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992389.113581 3912402 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992389.241908 3912402 service.cc:146] XLA service 0x56447dcf8b10 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992389.241941 3912402 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992392.305742 3912509 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.912883\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:26:51,809] Trial 330 finished with value: 0.912883 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992436.037044 3913618 service.cc:146] XLA service 0x55a0b98bfe50 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992436.037081 3913618 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992436.160848 3913618 service.cc:146] XLA service 0x55a0b98fae20 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992436.160882 3913618 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992441.437749 3913721 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.888361\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:27:37,989] Trial 331 finished with value: 0.888361 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 0, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992482.697187 3914450 service.cc:146] XLA service 0x55dfda653630 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992482.697244 3914450 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992482.832208 3914450 service.cc:146] XLA service 0x55dfda621560 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992482.832242 3914450 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992486.211339 3914554 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.907563\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:28:23,883] Trial 332 finished with value: 0.907563 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992527.556615 3915715 service.cc:146] XLA service 0x55f01bd23e10 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992527.556672 3915715 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992527.700354 3915715 service.cc:146] XLA service 0x55f01bcfac90 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992527.700391 3915715 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992530.610230 3915816 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n", "[I 2024-10-27 10:29:09,897] Trial 333 finished with value: 0.95294 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.95294\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992570.590102 3916972 service.cc:146] XLA service 0x555d6d2a2cd0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992570.590161 3916972 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992570.732617 3916972 service.cc:146] XLA service 0x555d6d271b90 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992570.732650 3916972 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992576.035974 3917078 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n", "[I 2024-10-27 10:29:52,592] Trial 334 finished with value: 0.916996 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 0, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.916996\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992622.045816 3917978 service.cc:146] XLA service 0x55e8120b9ba0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992622.045874 3917978 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992622.172564 3917978 service.cc:146] XLA service 0x55e811ff4fd0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992622.172596 3917978 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992631.310743 3918083 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.883163\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:30:51,540] Trial 335 finished with value: 0.883163 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992676.086016 3919015 service.cc:146] XLA service 0x5614880dca40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992676.086171 3919015 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992676.246044 3919015 service.cc:146] XLA service 0x561488042030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992676.246094 3919015 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992681.825142 3919126 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.914016\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:31:40,631] Trial 336 finished with value: 0.914016 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992727.294146 3920327 service.cc:146] XLA service 0x559f3ff0f390 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992727.294185 3920327 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992727.501672 3920327 service.cc:146] XLA service 0x559f3fe4b8b0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992727.501710 3920327 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992730.641778 3920437 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.938009\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:32:30,669] Trial 337 finished with value: 0.938009 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992775.147658 3921495 service.cc:146] XLA service 0x5602b1f68ac0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992775.147702 3921495 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992775.277359 3921495 service.cc:146] XLA service 0x5602b1f37980 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992775.277391 3921495 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992778.287566 3921602 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n", "[I 2024-10-27 10:33:17,599] Trial 338 finished with value: 0.884827 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.884827\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992825.386450 3922636 service.cc:146] XLA service 0x5633b60feba0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992825.386496 3922636 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992825.509898 3922636 service.cc:146] XLA service 0x5633b61134e0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992825.509928 3922636 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992828.319915 3922745 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.963535\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:34:05,940] Trial 339 finished with value: 0.963535 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992870.936657 3924081 service.cc:146] XLA service 0x561fb19b3b00 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992870.936702 3924081 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992871.117604 3924081 service.cc:146] XLA service 0x561fb2100770 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992871.117632 3924081 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992874.250062 3924191 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n", "[I 2024-10-27 10:34:52,159] Trial 340 finished with value: 0.893933 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 112 with value: 0.973052.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.893933\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[W 2024-10-27 10:34:54,769] Trial 341 failed with parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1} because of the following error: KeyboardInterrupt().\n", "Traceback (most recent call last):\n", " File \"/home/arer90/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/_optimize.py\", line 197, in _run_trial\n", " value_or_values = func(trial)\n", " ^^^^^^^^^^^\n", " File \"/tmp/ipykernel_3198053/2020294395.py\", line 3, in objective_de_fea\n", " new_x = search_data_descriptor_compress(trial, group_nde, mol_de, 'delaney')\n", " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", " File \"/home/arer90/Codes/extra_code/feature_search.py\", line 325, in search_data_descriptor_compress\n", " clear_descriptor_memory(descriptor)\n", " File \"/home/arer90/Codes/extra_code/feature_search.py\", line 263, in clear_descriptor_memory\n", " gc.collect()\n", "KeyboardInterrupt\n", "[W 2024-10-27 10:34:54,771] Trial 341 failed with value None.\n" ] }, { "ename": "KeyboardInterrupt", "evalue": "", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", "Cell \u001b[0;32mIn[36], line 3\u001b[0m\n\u001b[1;32m 1\u001b[0m study_de_fea \u001b[38;5;241m=\u001b[39m optuna\u001b[38;5;241m.\u001b[39mcreate_study(study_name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mANO_de_feature\u001b[39m\u001b[38;5;124m'\u001b[39m, storage\u001b[38;5;241m=\u001b[39mstorage, direction\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmaximize\u001b[39m\u001b[38;5;124m\"\u001b[39m, pruner\u001b[38;5;241m=\u001b[39moptuna\u001b[38;5;241m.\u001b[39mpruners\u001b[38;5;241m.\u001b[39mSuccessiveHalvingPruner(reduction_factor\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m64\u001b[39m, min_early_stopping_rate\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m10\u001b[39m),load_if_exists\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m) \n\u001b[1;32m 2\u001b[0m \u001b[38;5;66;03m# study_de_fea = optuna.create_study(study_name='ANO_de_feature', storage=storage, direction=\"maximize\", pruner=optuna.pruners.HyperbandPruner(min_resource=100,max_resource=1000,reduction_factor=3), load_if_exists=True)\u001b[39;00m\n\u001b[0;32m----> 3\u001b[0m study_de_fea\u001b[38;5;241m.\u001b[39moptimize(objective_de_fea, n_trials\u001b[38;5;241m=\u001b[39mTRIALS)\n\u001b[1;32m 4\u001b[0m pruned_trials_de_fea \u001b[38;5;241m=\u001b[39m study_de_fea\u001b[38;5;241m.\u001b[39mget_trials(deepcopy\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, states\u001b[38;5;241m=\u001b[39m[TrialState\u001b[38;5;241m.\u001b[39mPRUNED])\n\u001b[1;32m 5\u001b[0m complete_trials_de_fea \u001b[38;5;241m=\u001b[39m study_de_fea\u001b[38;5;241m.\u001b[39mget_trials(deepcopy\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, states\u001b[38;5;241m=\u001b[39m[TrialState\u001b[38;5;241m.\u001b[39mCOMPLETE])\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/study.py:475\u001b[0m, in \u001b[0;36mStudy.optimize\u001b[0;34m(self, func, n_trials, timeout, n_jobs, catch, callbacks, gc_after_trial, show_progress_bar)\u001b[0m\n\u001b[1;32m 373\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21moptimize\u001b[39m(\n\u001b[1;32m 374\u001b[0m \u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 375\u001b[0m func: ObjectiveFuncType,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 382\u001b[0m show_progress_bar: \u001b[38;5;28mbool\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m,\n\u001b[1;32m 383\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 384\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Optimize an objective function.\u001b[39;00m\n\u001b[1;32m 385\u001b[0m \n\u001b[1;32m 386\u001b[0m \u001b[38;5;124;03m Optimization is done by choosing a suitable set of hyperparameter values from a given\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 473\u001b[0m \u001b[38;5;124;03m If nested invocation of this method occurs.\u001b[39;00m\n\u001b[1;32m 474\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 475\u001b[0m _optimize(\n\u001b[1;32m 476\u001b[0m study\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 477\u001b[0m func\u001b[38;5;241m=\u001b[39mfunc,\n\u001b[1;32m 478\u001b[0m n_trials\u001b[38;5;241m=\u001b[39mn_trials,\n\u001b[1;32m 479\u001b[0m timeout\u001b[38;5;241m=\u001b[39mtimeout,\n\u001b[1;32m 480\u001b[0m n_jobs\u001b[38;5;241m=\u001b[39mn_jobs,\n\u001b[1;32m 481\u001b[0m catch\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mtuple\u001b[39m(catch) \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(catch, Iterable) \u001b[38;5;28;01melse\u001b[39;00m (catch,),\n\u001b[1;32m 482\u001b[0m callbacks\u001b[38;5;241m=\u001b[39mcallbacks,\n\u001b[1;32m 483\u001b[0m gc_after_trial\u001b[38;5;241m=\u001b[39mgc_after_trial,\n\u001b[1;32m 484\u001b[0m show_progress_bar\u001b[38;5;241m=\u001b[39mshow_progress_bar,\n\u001b[1;32m 485\u001b[0m )\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/_optimize.py:63\u001b[0m, in \u001b[0;36m_optimize\u001b[0;34m(study, func, n_trials, timeout, n_jobs, catch, callbacks, gc_after_trial, show_progress_bar)\u001b[0m\n\u001b[1;32m 61\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 62\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m n_jobs \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[0;32m---> 63\u001b[0m _optimize_sequential(\n\u001b[1;32m 64\u001b[0m study,\n\u001b[1;32m 65\u001b[0m func,\n\u001b[1;32m 66\u001b[0m n_trials,\n\u001b[1;32m 67\u001b[0m timeout,\n\u001b[1;32m 68\u001b[0m catch,\n\u001b[1;32m 69\u001b[0m callbacks,\n\u001b[1;32m 70\u001b[0m gc_after_trial,\n\u001b[1;32m 71\u001b[0m reseed_sampler_rng\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m,\n\u001b[1;32m 72\u001b[0m time_start\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 73\u001b[0m progress_bar\u001b[38;5;241m=\u001b[39mprogress_bar,\n\u001b[1;32m 74\u001b[0m )\n\u001b[1;32m 75\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 76\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m n_jobs \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m:\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/_optimize.py:160\u001b[0m, in \u001b[0;36m_optimize_sequential\u001b[0;34m(study, func, n_trials, timeout, catch, callbacks, gc_after_trial, reseed_sampler_rng, time_start, progress_bar)\u001b[0m\n\u001b[1;32m 157\u001b[0m \u001b[38;5;28;01mbreak\u001b[39;00m\n\u001b[1;32m 159\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 160\u001b[0m frozen_trial \u001b[38;5;241m=\u001b[39m _run_trial(study, func, catch)\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 162\u001b[0m \u001b[38;5;66;03m# The following line mitigates memory problems that can be occurred in some\u001b[39;00m\n\u001b[1;32m 163\u001b[0m \u001b[38;5;66;03m# environments (e.g., services that use computing containers such as GitHub Actions).\u001b[39;00m\n\u001b[1;32m 164\u001b[0m \u001b[38;5;66;03m# Please refer to the following PR for further details:\u001b[39;00m\n\u001b[1;32m 165\u001b[0m \u001b[38;5;66;03m# https://github.com/optuna/optuna/pull/325.\u001b[39;00m\n\u001b[1;32m 166\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m gc_after_trial:\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/_optimize.py:248\u001b[0m, in \u001b[0;36m_run_trial\u001b[0;34m(study, func, catch)\u001b[0m\n\u001b[1;32m 241\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m \u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mShould not reach.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 243\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 244\u001b[0m frozen_trial\u001b[38;5;241m.\u001b[39mstate \u001b[38;5;241m==\u001b[39m TrialState\u001b[38;5;241m.\u001b[39mFAIL\n\u001b[1;32m 245\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m func_err \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 246\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(func_err, catch)\n\u001b[1;32m 247\u001b[0m ):\n\u001b[0;32m--> 248\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m func_err\n\u001b[1;32m 249\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m frozen_trial\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/_optimize.py:197\u001b[0m, in \u001b[0;36m_run_trial\u001b[0;34m(study, func, catch)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m get_heartbeat_thread(trial\u001b[38;5;241m.\u001b[39m_trial_id, study\u001b[38;5;241m.\u001b[39m_storage):\n\u001b[1;32m 196\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 197\u001b[0m value_or_values \u001b[38;5;241m=\u001b[39m func(trial)\n\u001b[1;32m 198\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m exceptions\u001b[38;5;241m.\u001b[39mTrialPruned \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 199\u001b[0m \u001b[38;5;66;03m# TODO(mamu): Handle multi-objective cases.\u001b[39;00m\n\u001b[1;32m 200\u001b[0m state \u001b[38;5;241m=\u001b[39m TrialState\u001b[38;5;241m.\u001b[39mPRUNED\n", "Cell \u001b[0;32mIn[28], line 3\u001b[0m, in \u001b[0;36mobjective_de_fea\u001b[0;34m(trial)\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mobjective_de_fea\u001b[39m(trial):\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m----> 3\u001b[0m new_x \u001b[38;5;241m=\u001b[39m search_data_descriptor_compress(trial, group_nde, mol_de, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mdelaney\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 4\u001b[0m new_x \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mnan_to_num(new_x, nan\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0.0\u001b[39m, posinf\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0.0\u001b[39m, neginf\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0.0\u001b[39m)\u001b[38;5;241m.\u001b[39mastype(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfloat\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 5\u001b[0m y_true \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39masarray(y_de)\u001b[38;5;241m.\u001b[39mastype(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfloat\u001b[39m\u001b[38;5;124m'\u001b[39m)\n", "File \u001b[0;32m~/Codes/extra_code/feature_search.py:325\u001b[0m, in \u001b[0;36msearch_data_descriptor_compress\u001b[0;34m(trial, fps, mols, name, target_path, save_res)\u001b[0m\n\u001b[1;32m 323\u001b[0m descriptor \u001b[38;5;241m=\u001b[39m [Chem\u001b[38;5;241m.\u001b[39mLipinski\u001b[38;5;241m.\u001b[39mNumSaturatedRings(alpha) \u001b[38;5;28;01mfor\u001b[39;00m alpha \u001b[38;5;129;01min\u001b[39;00m mols]\n\u001b[1;32m 324\u001b[0m fps \u001b[38;5;241m=\u001b[39m generating_newfps(fps, descriptor, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mNumSaturatedRings\u001b[39m\u001b[38;5;124m'\u001b[39m, save_res)\n\u001b[0;32m--> 325\u001b[0m clear_descriptor_memory(descriptor)\n\u001b[1;32m 326\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m phase15 \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m 327\u001b[0m descriptor \u001b[38;5;241m=\u001b[39m [Chem\u001b[38;5;241m.\u001b[39mLipinski\u001b[38;5;241m.\u001b[39mNumAliphaticRings(alpha) \u001b[38;5;28;01mfor\u001b[39;00m alpha \u001b[38;5;129;01min\u001b[39;00m mols]\n", "File \u001b[0;32m~/Codes/extra_code/feature_search.py:263\u001b[0m, in \u001b[0;36msearch_data_descriptor_compress..clear_descriptor_memory\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m 261\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mclear_descriptor_memory\u001b[39m(descriptor):\n\u001b[1;32m 262\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m descriptor\n\u001b[0;32m--> 263\u001b[0m gc\u001b[38;5;241m.\u001b[39mcollect()\n", "\u001b[0;31mKeyboardInterrupt\u001b[0m: " ] } ], "source": [ "study_de_fea = optuna.create_study(study_name='ANO_de_feature', storage=storage, direction=\"maximize\", pruner=optuna.pruners.SuccessiveHalvingPruner(reduction_factor=64, min_early_stopping_rate=10),load_if_exists=True) \n", "# study_de_fea = optuna.create_study(study_name='ANO_de_feature', storage=storage, direction=\"maximize\", pruner=optuna.pruners.HyperbandPruner(min_resource=100,max_resource=1000,reduction_factor=3), load_if_exists=True)\n", "study_de_fea.optimize(objective_de_fea, n_trials=TRIALS)\n", "pruned_trials_de_fea = study_de_fea.get_trials(deepcopy=False, states=[TrialState.PRUNED])\n", "complete_trials_de_fea = study_de_fea.get_trials(deepcopy=False, states=[TrialState.COMPLETE])\n", "# 148m 31.6s - Trial 100" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [], "source": [ "TRIALS=150" ] }, { "cell_type": "code", "execution_count": 38, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:34:57,866] Using an existing study with name 'ANO_lo_feature' instead of creating a new one.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992930.427725 3925119 service.cc:146] XLA service 0x5555a8b30040 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992930.427764 3925119 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992930.549627 3925119 service.cc:146] XLA service 0x5555a8a6bf70 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992930.549665 3925119 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992933.407998 3925223 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.6111\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:35:49,550] Trial 3 finished with value: 0.6111 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 1, 'Ipc': 0, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 0, 'InertialShapeFactor': 0, 'Eccentricity': 0, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 1, 'RDF': 1, 'MORSE': 0, 'WHIM': 1, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729992976.468944 3926102 service.cc:146] XLA service 0x555da3d76ae0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992976.468993 3926102 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729992976.631333 3926102 service.cc:146] XLA service 0x555da3d4d960 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729992976.631370 3926102 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729992979.639721 3926211 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.665943\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:36:39,054] Trial 4 finished with value: 0.665943 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 1, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 0, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 0, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 1, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993024.681819 3927341 service.cc:146] XLA service 0x55aa56eaf3e0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993024.681888 3927341 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993024.845132 3927341 service.cc:146] XLA service 0x55aa56de2d90 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993024.845160 3927341 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993028.042739 3927446 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.713339\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:37:26,788] Trial 5 finished with value: 0.713339 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 1, 'NumHAcceptors': 1, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 0, 'FractionCSP3': 1, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 0, 'InertialShapeFactor': 0, 'Eccentricity': 0, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 1, 'RDF': 1, 'MORSE': 0, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993076.351628 3928738 service.cc:146] XLA service 0x559d154d5940 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993076.351681 3928738 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993076.488517 3928738 service.cc:146] XLA service 0x559d154a4780 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993076.488550 3928738 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993079.508727 3928848 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.781681\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:38:18,737] Trial 6 finished with value: 0.781681 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993119.134274 3930020 service.cc:146] XLA service 0x55e4e6eed9c0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993119.134319 3930020 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993119.284837 3930020 service.cc:146] XLA service 0x55e4e6f23980 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993119.284874 3930020 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993122.252171 3930129 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.725071\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:39:01,506] Trial 7 finished with value: 0.725071 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 0, 'BertzCT': 1, 'Ipc': 0, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 0, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 0, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 1, 'AUTOCORR3D': 1, 'RDF': 0, 'MORSE': 0, 'WHIM': 1, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993167.586394 3931552 service.cc:146] XLA service 0x55c68396eb50 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993167.586441 3931552 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993167.707478 3931552 service.cc:146] XLA service 0x55c68393d990 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993167.707505 3931552 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993170.641906 3931662 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.731387\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:39:48,661] Trial 8 finished with value: 0.731387 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 1, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 1, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 1, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 0, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 1, 'RDF': 0, 'MORSE': 0, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993216.358614 3933216 service.cc:146] XLA service 0x55f2934a0c30 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993216.358685 3933216 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993216.479294 3933216 service.cc:146] XLA service 0x55f2934df8e0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993216.479339 3933216 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993219.395547 3933323 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.762563\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:40:40,340] Trial 9 finished with value: 0.762563 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 1, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 1, 'NOCount': 0, 'RingCount': 1, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 1, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 0, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 0, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 1, 'AUTOCORR3D': 1, 'RDF': 0, 'MORSE': 0, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993267.148442 3934929 service.cc:146] XLA service 0x563835c5ba40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993267.148497 3934929 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993267.287713 3934929 service.cc:146] XLA service 0x563835bc1030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993267.287758 3934929 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993270.260464 3935030 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.687833\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:41:27,216] Trial 10 finished with value: 0.687833 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 1, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 0, 'BCUT2D': 0, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 0, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 1, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993317.114148 3936375 service.cc:146] XLA service 0x55e1937565e0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993317.114189 3936375 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993317.244978 3936375 service.cc:146] XLA service 0x55e1936e4dd0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993317.245023 3936375 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993320.004518 3936484 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.748738\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:42:18,269] Trial 11 finished with value: 0.748738 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 0, 'RadiusOfGyration': 0, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993370.450775 3937958 service.cc:146] XLA service 0x55a31378bda0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993370.450821 3937958 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993370.576177 3937958 service.cc:146] XLA service 0x55a3135e0c40 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993370.576209 3937958 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993373.405117 3938061 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.735083\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:43:08,949] Trial 12 finished with value: 0.735083 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993422.310806 3939213 service.cc:146] XLA service 0x55db4a7ffcd0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993422.310855 3939213 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993422.440473 3939213 service.cc:146] XLA service 0x55db49e04390 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993422.440508 3939213 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993425.723559 3939317 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.686333\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:44:05,516] Trial 13 finished with value: 0.686333 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 0, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993470.235134 3940500 service.cc:146] XLA service 0x55fa739618e0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993470.235187 3940500 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993470.361622 3940500 service.cc:146] XLA service 0x55fa738c6ed0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993470.361660 3940500 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993473.383033 3940609 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.712349\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:44:50,277] Trial 14 finished with value: 0.712349 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993516.649403 3941779 service.cc:146] XLA service 0x563b7a54ea40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993516.649438 3941779 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993516.774245 3941779 service.cc:146] XLA service 0x563b7a4b4030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993516.774276 3941779 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993519.625113 3941882 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.750515\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:45:38,737] Trial 15 finished with value: 0.750515 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 0, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993577.700374 3943199 service.cc:146] XLA service 0x558af476c5c0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993577.700418 3943199 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993577.840414 3943199 service.cc:146] XLA service 0x558af479c3a0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993577.840459 3943199 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993580.807099 3943304 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.733632\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:46:36,993] Trial 16 finished with value: 0.733632 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993632.507571 3944374 service.cc:146] XLA service 0x55b0cad36bb0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993632.507620 3944374 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993632.646289 3944374 service.cc:146] XLA service 0x55b0cad05a70 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993632.646324 3944374 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993635.675326 3944478 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.789597\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:47:34,177] Trial 17 finished with value: 0.789597 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993684.921690 3945868 service.cc:146] XLA service 0x55b49ec45110 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993684.921728 3945868 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993685.044260 3945868 service.cc:146] XLA service 0x55b49ec862f0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993685.044292 3945868 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993687.763661 3945983 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.74738\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:48:22,687] Trial 18 finished with value: 0.74738 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 1, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 0, 'RadiusOfGyration': 0, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 1, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993730.261411 3947063 service.cc:146] XLA service 0x5565cd15e940 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993730.261443 3947063 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993730.409868 3947063 service.cc:146] XLA service 0x5565cd12d780 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993730.409901 3947063 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993733.128959 3947173 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.736633\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:49:10,947] Trial 19 finished with value: 0.736633 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993780.084209 3948419 service.cc:146] XLA service 0x55c71b16a630 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993780.084245 3948419 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993780.211626 3948419 service.cc:146] XLA service 0x55c71b138560 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993780.211656 3948419 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993782.968434 3948529 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.713683\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:49:58,642] Trial 20 finished with value: 0.713683 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993826.372730 3949829 service.cc:146] XLA service 0x55b48be82a40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993826.372831 3949829 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993826.500685 3949829 service.cc:146] XLA service 0x55b48bde8030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993826.500722 3949829 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993829.220354 3949939 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.759597\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:50:44,774] Trial 21 finished with value: 0.759597 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 1, 'NumHAcceptors': 1, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 1, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 0, 'Asphericity': 1, 'PBF': 0, 'RadiusOfGyration': 0, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 1, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993871.466854 3951198 service.cc:146] XLA service 0x55806db589e0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993871.466893 3951198 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993871.593062 3951198 service.cc:146] XLA service 0x55806da94940 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993871.593096 3951198 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993874.343192 3951306 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.735784\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:51:31,028] Trial 22 finished with value: 0.735784 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993920.861295 3952232 service.cc:146] XLA service 0x55b3957ec9c0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993920.861328 3952232 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993920.986591 3952232 service.cc:146] XLA service 0x55b3957bb800 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993920.986623 3952232 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993923.736186 3952347 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.710556\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:52:19,589] Trial 23 finished with value: 0.710556 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729993969.425872 3953628 service.cc:146] XLA service 0x55f2b4d0cdf0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993969.425913 3953628 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729993969.554583 3953628 service.cc:146] XLA service 0x55f2b4bc49b0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729993969.554626 3953628 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729993972.349660 3953737 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.456082\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:53:08,664] Trial 24 finished with value: 0.456082 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994014.278032 3954456 service.cc:146] XLA service 0x5564b1652a40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994014.278087 3954456 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994014.406905 3954456 service.cc:146] XLA service 0x5564b15b8030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994014.406936 3954456 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994017.176928 3954569 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.790012\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:53:54,817] Trial 25 finished with value: 0.790012 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994064.353067 3955853 service.cc:146] XLA service 0x557bc131a0c0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994064.353108 3955853 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994064.485514 3955853 service.cc:146] XLA service 0x557bc12f1a10 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994064.485551 3955853 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994067.268622 3955961 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.672312\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:54:42,663] Trial 26 finished with value: 0.672312 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994109.594790 3957133 service.cc:146] XLA service 0x56012b8c3760 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994109.594843 3957133 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994109.718036 3957133 service.cc:146] XLA service 0x56012b71e780 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994109.718067 3957133 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994112.454192 3957242 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.742336\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:55:29,890] Trial 27 finished with value: 0.742336 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994159.340007 3958243 service.cc:146] XLA service 0x55984d3c3b50 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994159.340050 3958243 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994159.468604 3958243 service.cc:146] XLA service 0x55984d392a10 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994159.468639 3958243 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994162.300366 3958351 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.769052\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:56:18,471] Trial 28 finished with value: 0.769052 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994202.922835 3959784 service.cc:146] XLA service 0x55b3947ede30 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994202.922893 3959784 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994203.044694 3959784 service.cc:146] XLA service 0x55b3946e60e0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994203.044744 3959784 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994205.721633 3959891 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.650223\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:57:00,017] Trial 29 finished with value: 0.650223 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994247.409801 3960757 service.cc:146] XLA service 0x563bfe8e8ba0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994247.409840 3960757 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994247.537404 3960757 service.cc:146] XLA service 0x563bfe823fd0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994247.537435 3960757 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994250.231932 3960865 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n", "[I 2024-10-27 10:57:47,176] Trial 30 finished with value: 0.686447 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 1, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 1, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 0, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 1, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 0, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.686447\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994299.287508 3961866 service.cc:146] XLA service 0x5651247d2a50 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994299.287577 3961866 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994299.422173 3961866 service.cc:146] XLA service 0x565123dd7df0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994299.422207 3961866 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994302.117953 3961976 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.691319\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:58:37,691] Trial 31 finished with value: 0.691319 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994344.541496 3963324 service.cc:146] XLA service 0x55d7f2478de0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994344.541617 3963324 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994344.664858 3963324 service.cc:146] XLA service 0x55d7f244fc60 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994344.664889 3963324 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994347.292985 3963440 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.688873\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 10:59:24,609] Trial 32 finished with value: 0.688873 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994390.818671 3964410 service.cc:146] XLA service 0x5633ecc61170 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994390.818729 3964410 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994390.947512 3964410 service.cc:146] XLA service 0x5633ecb94b20 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994390.947544 3964410 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994393.742316 3964517 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.738052\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:00:11,534] Trial 33 finished with value: 0.738052 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994438.701616 3965817 service.cc:146] XLA service 0x55fdb9214a40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994438.701672 3965817 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994438.831013 3965817 service.cc:146] XLA service 0x55fdb917a030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994438.831046 3965817 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994441.723927 3965933 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.767346\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:00:57,809] Trial 34 finished with value: 0.767346 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994482.025024 3967329 service.cc:146] XLA service 0x55cc8ddd3b70 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994482.025091 3967329 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994482.149105 3967329 service.cc:146] XLA service 0x55cc8dbc9430 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994482.149138 3967329 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994484.811305 3967438 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.751077\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:01:42,888] Trial 35 finished with value: 0.751077 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 0, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 1, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994526.988161 3968678 service.cc:146] XLA service 0x55b5092c49a0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994526.988235 3968678 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994527.111140 3968678 service.cc:146] XLA service 0x55b5091ffdd0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994527.111171 3968678 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994529.923309 3968787 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.719502\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:02:26,576] Trial 36 finished with value: 0.719502 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 0, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994572.514228 3969627 service.cc:146] XLA service 0x55ae640553d0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994572.514283 3969627 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994572.647323 3969627 service.cc:146] XLA service 0x55ae6402d330 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994572.647355 3969627 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994575.270764 3969737 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.688653\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:03:10,400] Trial 37 finished with value: 0.688653 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 1, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 0, 'InertialShapeFactor': 0, 'Eccentricity': 0, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 1, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994613.599033 3970910 service.cc:146] XLA service 0x559a3f6b4880 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994613.599100 3970910 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994613.719580 3970910 service.cc:146] XLA service 0x559a3f68c1d0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994613.719607 3970910 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994616.357572 3971021 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.720587\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:03:51,679] Trial 38 finished with value: 0.720587 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 1, 'NOCount': 0, 'RingCount': 1, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 0, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 0, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994655.294031 3972182 service.cc:146] XLA service 0x562216330080 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994655.294074 3972182 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994655.422473 3972182 service.cc:146] XLA service 0x5622163079d0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994655.422504 3972182 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994658.110715 3972291 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.659888\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:04:35,929] Trial 39 finished with value: 0.659888 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 1, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 1, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 0, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 1, 'RDF': 0, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994708.660297 3973358 service.cc:146] XLA service 0x55a0d38bda40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994708.660339 3973358 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994708.790697 3973358 service.cc:146] XLA service 0x55a0d3823030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994708.790733 3973358 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994711.535491 3973467 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.701053\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:05:28,298] Trial 40 finished with value: 0.701053 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994750.378272 3975001 service.cc:146] XLA service 0x5558231d3590 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994750.378315 3975001 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994750.512730 3975001 service.cc:146] XLA service 0x5558231a2830 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994750.512763 3975001 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994753.258257 3975114 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.742663\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:06:09,039] Trial 41 finished with value: 0.742663 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 1, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 1, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 0, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 1, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 0, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 1, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 0, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994798.523735 3976435 service.cc:146] XLA service 0x55bf50692ac0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994798.523769 3976435 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994798.657880 3976435 service.cc:146] XLA service 0x55bf504e7960 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994798.657909 3976435 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994801.422897 3976542 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.746899\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:06:59,190] Trial 42 finished with value: 0.746899 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994849.673986 3977907 service.cc:146] XLA service 0x55e90f5c3880 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994849.674053 3977907 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994849.796256 3977907 service.cc:146] XLA service 0x55e90f53ff00 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994849.796287 3977907 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994852.516234 3978017 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.77308\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:07:48,465] Trial 43 finished with value: 0.77308 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994898.051194 3979199 service.cc:146] XLA service 0x561083aee830 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994898.051250 3979199 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994898.173883 3979199 service.cc:146] XLA service 0x561082f72f00 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994898.173925 3979199 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994900.901112 3979309 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.740479\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:08:39,080] Trial 44 finished with value: 0.740479 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994948.625762 3980615 service.cc:146] XLA service 0x5633e10e3f30 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994948.625805 3980615 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994948.754030 3980615 service.cc:146] XLA service 0x5633e1125110 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994948.754063 3980615 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729994951.593458 3980723 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.714658\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:09:27,337] Trial 45 finished with value: 0.714658 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729994998.081058 3982012 service.cc:146] XLA service 0x556169920b90 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994998.081120 3982012 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729994998.199509 3982012 service.cc:146] XLA service 0x556169775a30 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729994998.199557 3982012 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995000.959041 3982122 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.705781\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:10:17,992] Trial 46 finished with value: 0.705781 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995045.765544 3983029 service.cc:146] XLA service 0x55ecc278f4b0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995045.765595 3983029 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995045.887842 3983029 service.cc:146] XLA service 0x55ecc1d92df0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995045.887868 3983029 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995048.715035 3983142 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.689885\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:11:06,879] Trial 47 finished with value: 0.689885 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995097.065998 3984609 service.cc:146] XLA service 0x55bca1fccf40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995097.066049 3984609 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995097.198266 3984609 service.cc:146] XLA service 0x55bca1fa4e00 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995097.198298 3984609 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995100.019741 3984716 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.778711\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:11:55,122] Trial 48 finished with value: 0.778711 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 0, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995144.490749 3985768 service.cc:146] XLA service 0x555d93d2ae30 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995144.490812 3985768 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995144.605750 3985768 service.cc:146] XLA service 0x555d93c230e0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995144.605791 3985768 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995147.405358 3985883 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.685821\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:12:44,765] Trial 49 finished with value: 0.685821 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 1, 'Ipc': 0, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 0, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 0, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 0, 'InertialShapeFactor': 1, 'Eccentricity': 0, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 1, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995186.654658 3986968 service.cc:146] XLA service 0x5575d6c88ea0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995186.654701 3986968 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995186.778086 3986968 service.cc:146] XLA service 0x5575d472f800 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995186.778124 3986968 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995191.453194 3987076 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.766241\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:13:27,356] Trial 50 finished with value: 0.766241 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 1, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 0, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995235.684672 3988378 service.cc:146] XLA service 0x5635dbe823d0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995235.684714 3988378 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995235.814666 3988378 service.cc:146] XLA service 0x5635dbe51670 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995235.814692 3988378 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995238.535491 3988493 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.767288\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:14:17,303] Trial 51 finished with value: 0.767288 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 1, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 0, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 0, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 1, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995283.820402 3989992 service.cc:146] XLA service 0x5558148a4ff0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995283.820461 3989992 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995283.944764 3989992 service.cc:146] XLA service 0x555813e70d00 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995283.944801 3989992 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995286.689705 3990099 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.701542\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:15:04,933] Trial 52 finished with value: 0.701542 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 0, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995335.005269 3991630 service.cc:146] XLA service 0x55bf44aad690 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995335.005306 3991630 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995335.130074 3991630 service.cc:146] XLA service 0x55bf44991dc0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995335.130106 3991630 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995337.894968 3991739 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.703612\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:15:54,110] Trial 53 finished with value: 0.703612 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995382.313944 3993111 service.cc:146] XLA service 0x55aa35973bb0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995382.313988 3993111 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995382.463266 3993111 service.cc:146] XLA service 0x55aa35942a70 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995382.463299 3993111 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995385.218499 3993226 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.770365\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:16:43,191] Trial 54 finished with value: 0.770365 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 0, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995431.287716 3994602 service.cc:146] XLA service 0x55dafd5b44f0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995431.287751 3994602 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995431.412351 3994602 service.cc:146] XLA service 0x55dafd582420 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995431.412379 3994602 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995434.196076 3994712 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.716392\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:17:29,813] Trial 55 finished with value: 0.716392 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995479.992707 3995871 service.cc:146] XLA service 0x55556e9d2490 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995479.992740 3995871 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995480.119132 3995871 service.cc:146] XLA service 0x55556e9a03c0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995480.119163 3995871 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995482.871406 3995986 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.703284\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:18:21,743] Trial 56 finished with value: 0.703284 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995528.610138 3997667 service.cc:146] XLA service 0x55e6e799fed0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995528.610180 3997667 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995528.736450 3997667 service.cc:146] XLA service 0x55e6e7857a90 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995528.736481 3997667 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995533.364859 3997783 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.718837\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:19:10,256] Trial 57 finished with value: 0.718837 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995580.409100 3999395 service.cc:146] XLA service 0x56107eff3490 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995580.409134 3999395 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995580.536260 3999395 service.cc:146] XLA service 0x56107efc13c0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995580.536311 3999395 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995583.320553 3999505 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.765037\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:20:00,440] Trial 58 finished with value: 0.765037 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 0, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729995625.837207 4000599 service.cc:146] XLA service 0x5632e7e3fa40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995625.837247 4000599 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729995625.966373 4000599 service.cc:146] XLA service 0x5632e7da5030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729995625.966412 4000599 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729995628.694750 4000709 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.751952\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:20:46,958] Trial 59 finished with value: 0.751952 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.843203.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[W 2024-10-27 11:21:33,186] Trial 60 failed with parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 1, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 1, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1} because of the following error: KeyboardInterrupt().\n", "Traceback (most recent call last):\n", " File \"/home/arer90/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/_optimize.py\", line 197, in _run_trial\n", " value_or_values = func(trial)\n", " ^^^^^^^^^^^\n", " File \"/tmp/ipykernel_3198053/1450763917.py\", line 13, in objective_lo_fea\n", " result = subprocess.run(['python3', './extra_code/learning_process.py',\n", " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", " File \"/home/arer90/miniconda3/envs/ai/lib/python3.12/subprocess.py\", line 550, in run\n", " stdout, stderr = process.communicate(input, timeout=timeout)\n", " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", " File \"/home/arer90/miniconda3/envs/ai/lib/python3.12/subprocess.py\", line 1209, in communicate\n", " stdout, stderr = self._communicate(input, endtime, timeout)\n", " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", " File \"/home/arer90/miniconda3/envs/ai/lib/python3.12/subprocess.py\", line 2113, in _communicate\n", " ready = selector.select(timeout)\n", " ^^^^^^^^^^^^^^^^^^^^^^^^\n", " File \"/home/arer90/miniconda3/envs/ai/lib/python3.12/selectors.py\", line 415, in select\n", " fd_event_list = self._selector.poll(timeout)\n", " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n", "KeyboardInterrupt\n", "[W 2024-10-27 11:21:33,196] Trial 60 failed with value None.\n" ] }, { "ename": "KeyboardInterrupt", "evalue": "", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", "Cell \u001b[0;32mIn[38], line 3\u001b[0m\n\u001b[1;32m 1\u001b[0m study_lo_fea \u001b[38;5;241m=\u001b[39m optuna\u001b[38;5;241m.\u001b[39mcreate_study(study_name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mANO_lo_feature\u001b[39m\u001b[38;5;124m'\u001b[39m, storage\u001b[38;5;241m=\u001b[39mstorage, direction\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmaximize\u001b[39m\u001b[38;5;124m\"\u001b[39m, pruner\u001b[38;5;241m=\u001b[39moptuna\u001b[38;5;241m.\u001b[39mpruners\u001b[38;5;241m.\u001b[39mSuccessiveHalvingPruner(reduction_factor\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m64\u001b[39m, min_early_stopping_rate\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m10\u001b[39m),load_if_exists\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m) \n\u001b[1;32m 2\u001b[0m \u001b[38;5;66;03m# study_lo_fea = optuna.create_study(study_name='ANO_lo_feature', storage=storage, direction=\"maximize\", pruner=optuna.pruners.HyperbandPruner(min_resource=100,max_resource=1000,reduction_factor=3), load_if_exists=True)\u001b[39;00m\n\u001b[0;32m----> 3\u001b[0m study_lo_fea\u001b[38;5;241m.\u001b[39moptimize(objective_lo_fea, n_trials\u001b[38;5;241m=\u001b[39mTRIALS)\n\u001b[1;32m 4\u001b[0m pruned_trials_lo_fea \u001b[38;5;241m=\u001b[39m study_lo_fea\u001b[38;5;241m.\u001b[39mget_trials(deepcopy\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, states\u001b[38;5;241m=\u001b[39m[TrialState\u001b[38;5;241m.\u001b[39mPRUNED])\n\u001b[1;32m 5\u001b[0m complete_trials_lo_fea \u001b[38;5;241m=\u001b[39m study_lo_fea\u001b[38;5;241m.\u001b[39mget_trials(deepcopy\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, states\u001b[38;5;241m=\u001b[39m[TrialState\u001b[38;5;241m.\u001b[39mCOMPLETE])\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/study.py:475\u001b[0m, in \u001b[0;36mStudy.optimize\u001b[0;34m(self, func, n_trials, timeout, n_jobs, catch, callbacks, gc_after_trial, show_progress_bar)\u001b[0m\n\u001b[1;32m 373\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21moptimize\u001b[39m(\n\u001b[1;32m 374\u001b[0m \u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 375\u001b[0m func: ObjectiveFuncType,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 382\u001b[0m show_progress_bar: \u001b[38;5;28mbool\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m,\n\u001b[1;32m 383\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 384\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Optimize an objective function.\u001b[39;00m\n\u001b[1;32m 385\u001b[0m \n\u001b[1;32m 386\u001b[0m \u001b[38;5;124;03m Optimization is done by choosing a suitable set of hyperparameter values from a given\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 473\u001b[0m \u001b[38;5;124;03m If nested invocation of this method occurs.\u001b[39;00m\n\u001b[1;32m 474\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 475\u001b[0m _optimize(\n\u001b[1;32m 476\u001b[0m study\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 477\u001b[0m func\u001b[38;5;241m=\u001b[39mfunc,\n\u001b[1;32m 478\u001b[0m n_trials\u001b[38;5;241m=\u001b[39mn_trials,\n\u001b[1;32m 479\u001b[0m timeout\u001b[38;5;241m=\u001b[39mtimeout,\n\u001b[1;32m 480\u001b[0m n_jobs\u001b[38;5;241m=\u001b[39mn_jobs,\n\u001b[1;32m 481\u001b[0m catch\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mtuple\u001b[39m(catch) \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(catch, Iterable) \u001b[38;5;28;01melse\u001b[39;00m (catch,),\n\u001b[1;32m 482\u001b[0m callbacks\u001b[38;5;241m=\u001b[39mcallbacks,\n\u001b[1;32m 483\u001b[0m gc_after_trial\u001b[38;5;241m=\u001b[39mgc_after_trial,\n\u001b[1;32m 484\u001b[0m show_progress_bar\u001b[38;5;241m=\u001b[39mshow_progress_bar,\n\u001b[1;32m 485\u001b[0m )\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/_optimize.py:63\u001b[0m, in \u001b[0;36m_optimize\u001b[0;34m(study, func, n_trials, timeout, n_jobs, catch, callbacks, gc_after_trial, show_progress_bar)\u001b[0m\n\u001b[1;32m 61\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 62\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m n_jobs \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[0;32m---> 63\u001b[0m _optimize_sequential(\n\u001b[1;32m 64\u001b[0m study,\n\u001b[1;32m 65\u001b[0m func,\n\u001b[1;32m 66\u001b[0m n_trials,\n\u001b[1;32m 67\u001b[0m timeout,\n\u001b[1;32m 68\u001b[0m catch,\n\u001b[1;32m 69\u001b[0m callbacks,\n\u001b[1;32m 70\u001b[0m gc_after_trial,\n\u001b[1;32m 71\u001b[0m reseed_sampler_rng\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m,\n\u001b[1;32m 72\u001b[0m time_start\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 73\u001b[0m progress_bar\u001b[38;5;241m=\u001b[39mprogress_bar,\n\u001b[1;32m 74\u001b[0m )\n\u001b[1;32m 75\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 76\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m n_jobs \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m:\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/_optimize.py:160\u001b[0m, in \u001b[0;36m_optimize_sequential\u001b[0;34m(study, func, n_trials, timeout, catch, callbacks, gc_after_trial, reseed_sampler_rng, time_start, progress_bar)\u001b[0m\n\u001b[1;32m 157\u001b[0m \u001b[38;5;28;01mbreak\u001b[39;00m\n\u001b[1;32m 159\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 160\u001b[0m frozen_trial \u001b[38;5;241m=\u001b[39m _run_trial(study, func, catch)\n\u001b[1;32m 161\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 162\u001b[0m \u001b[38;5;66;03m# The following line mitigates memory problems that can be occurred in some\u001b[39;00m\n\u001b[1;32m 163\u001b[0m \u001b[38;5;66;03m# environments (e.g., services that use computing containers such as GitHub Actions).\u001b[39;00m\n\u001b[1;32m 164\u001b[0m \u001b[38;5;66;03m# Please refer to the following PR for further details:\u001b[39;00m\n\u001b[1;32m 165\u001b[0m \u001b[38;5;66;03m# https://github.com/optuna/optuna/pull/325.\u001b[39;00m\n\u001b[1;32m 166\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m gc_after_trial:\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/_optimize.py:248\u001b[0m, in \u001b[0;36m_run_trial\u001b[0;34m(study, func, catch)\u001b[0m\n\u001b[1;32m 241\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m \u001b[38;5;28;01mFalse\u001b[39;00m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mShould not reach.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 243\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\n\u001b[1;32m 244\u001b[0m frozen_trial\u001b[38;5;241m.\u001b[39mstate \u001b[38;5;241m==\u001b[39m TrialState\u001b[38;5;241m.\u001b[39mFAIL\n\u001b[1;32m 245\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m func_err \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 246\u001b[0m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(func_err, catch)\n\u001b[1;32m 247\u001b[0m ):\n\u001b[0;32m--> 248\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m func_err\n\u001b[1;32m 249\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m frozen_trial\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/site-packages/optuna/study/_optimize.py:197\u001b[0m, in \u001b[0;36m_run_trial\u001b[0;34m(study, func, catch)\u001b[0m\n\u001b[1;32m 195\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m get_heartbeat_thread(trial\u001b[38;5;241m.\u001b[39m_trial_id, study\u001b[38;5;241m.\u001b[39m_storage):\n\u001b[1;32m 196\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 197\u001b[0m value_or_values \u001b[38;5;241m=\u001b[39m func(trial)\n\u001b[1;32m 198\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m exceptions\u001b[38;5;241m.\u001b[39mTrialPruned \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 199\u001b[0m \u001b[38;5;66;03m# TODO(mamu): Handle multi-objective cases.\u001b[39;00m\n\u001b[1;32m 200\u001b[0m state \u001b[38;5;241m=\u001b[39m TrialState\u001b[38;5;241m.\u001b[39mPRUNED\n", "Cell \u001b[0;32mIn[29], line 13\u001b[0m, in \u001b[0;36mobjective_lo_fea\u001b[0;34m(trial)\u001b[0m\n\u001b[1;32m 9\u001b[0m save_model(new_x)\n\u001b[1;32m 11\u001b[0m r2_result \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m0.0\u001b[39m\n\u001b[0;32m---> 13\u001b[0m result \u001b[38;5;241m=\u001b[39m subprocess\u001b[38;5;241m.\u001b[39mrun([\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mpython3\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m./extra_code/learning_process.py\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m 14\u001b[0m \u001b[38;5;28mstr\u001b[39m(BATCHSIZE), \u001b[38;5;28mstr\u001b[39m(EPOCHS), \n\u001b[1;32m 15\u001b[0m \u001b[38;5;28mstr\u001b[39m(lr),\n\u001b[1;32m 16\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mnew_fps.npy\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124my_true.npy\u001b[39m\u001b[38;5;124m'\u001b[39m],\n\u001b[1;32m 17\u001b[0m stdout\u001b[38;5;241m=\u001b[39msubprocess\u001b[38;5;241m.\u001b[39mPIPE, stderr\u001b[38;5;241m=\u001b[39msubprocess\u001b[38;5;241m.\u001b[39mPIPE, text\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m 19\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m result\u001b[38;5;241m.\u001b[39mstderr:\n\u001b[1;32m 20\u001b[0m filtered_stderr \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m.\u001b[39mjoin([line \u001b[38;5;28;01mfor\u001b[39;00m line \u001b[38;5;129;01min\u001b[39;00m result\u001b[38;5;241m.\u001b[39mstderr\u001b[38;5;241m.\u001b[39msplit(\u001b[38;5;124m'\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m'\u001b[39m) \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcould not open file to read NUMA node\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m line \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mYour kernel may have been built without NUMA support\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m line])\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/subprocess.py:550\u001b[0m, in \u001b[0;36mrun\u001b[0;34m(input, capture_output, timeout, check, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 548\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m Popen(\u001b[38;5;241m*\u001b[39mpopenargs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs) \u001b[38;5;28;01mas\u001b[39;00m process:\n\u001b[1;32m 549\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 550\u001b[0m stdout, stderr \u001b[38;5;241m=\u001b[39m process\u001b[38;5;241m.\u001b[39mcommunicate(\u001b[38;5;28minput\u001b[39m, timeout\u001b[38;5;241m=\u001b[39mtimeout)\n\u001b[1;32m 551\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m TimeoutExpired \u001b[38;5;28;01mas\u001b[39;00m exc:\n\u001b[1;32m 552\u001b[0m process\u001b[38;5;241m.\u001b[39mkill()\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/subprocess.py:1209\u001b[0m, in \u001b[0;36mPopen.communicate\u001b[0;34m(self, input, timeout)\u001b[0m\n\u001b[1;32m 1206\u001b[0m endtime \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 1208\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 1209\u001b[0m stdout, stderr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_communicate(\u001b[38;5;28minput\u001b[39m, endtime, timeout)\n\u001b[1;32m 1210\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyboardInterrupt\u001b[39;00m:\n\u001b[1;32m 1211\u001b[0m \u001b[38;5;66;03m# https://bugs.python.org/issue25942\u001b[39;00m\n\u001b[1;32m 1212\u001b[0m \u001b[38;5;66;03m# See the detailed comment in .wait().\u001b[39;00m\n\u001b[1;32m 1213\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m timeout \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/subprocess.py:2113\u001b[0m, in \u001b[0;36mPopen._communicate\u001b[0;34m(self, input, endtime, orig_timeout)\u001b[0m\n\u001b[1;32m 2106\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_check_timeout(endtime, orig_timeout,\n\u001b[1;32m 2107\u001b[0m stdout, stderr,\n\u001b[1;32m 2108\u001b[0m skip_check_and_raise\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m 2109\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m( \u001b[38;5;66;03m# Impossible :)\u001b[39;00m\n\u001b[1;32m 2110\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m_check_timeout(..., skip_check_and_raise=True) \u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[1;32m 2111\u001b[0m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfailed to raise TimeoutExpired.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m-> 2113\u001b[0m ready \u001b[38;5;241m=\u001b[39m selector\u001b[38;5;241m.\u001b[39mselect(timeout)\n\u001b[1;32m 2114\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_check_timeout(endtime, orig_timeout, stdout, stderr)\n\u001b[1;32m 2116\u001b[0m \u001b[38;5;66;03m# XXX Rewrite these to use non-blocking I/O on the file\u001b[39;00m\n\u001b[1;32m 2117\u001b[0m \u001b[38;5;66;03m# objects; they are no longer using C stdio!\u001b[39;00m\n", "File \u001b[0;32m~/miniconda3/envs/ai/lib/python3.12/selectors.py:415\u001b[0m, in \u001b[0;36m_PollLikeSelector.select\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 413\u001b[0m ready \u001b[38;5;241m=\u001b[39m []\n\u001b[1;32m 414\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 415\u001b[0m fd_event_list \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_selector\u001b[38;5;241m.\u001b[39mpoll(timeout)\n\u001b[1;32m 416\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mInterruptedError\u001b[39;00m:\n\u001b[1;32m 417\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ready\n", "\u001b[0;31mKeyboardInterrupt\u001b[0m: " ] } ], "source": [ "study_lo_fea = optuna.create_study(study_name='ANO_lo_feature', storage=storage, direction=\"maximize\", pruner=optuna.pruners.SuccessiveHalvingPruner(reduction_factor=64, min_early_stopping_rate=10),load_if_exists=True) \n", "# study_lo_fea = optuna.create_study(study_name='ANO_lo_feature', storage=storage, direction=\"maximize\", pruner=optuna.pruners.HyperbandPruner(min_resource=100,max_resource=1000,reduction_factor=3), load_if_exists=True)\n", "study_lo_fea.optimize(objective_lo_fea, n_trials=TRIALS)\n", "pruned_trials_lo_fea = study_lo_fea.get_trials(deepcopy=False, states=[TrialState.PRUNED])\n", "complete_trials_lo_fea = study_lo_fea.get_trials(deepcopy=False, states=[TrialState.COMPLETE])\n", "# 137m 25.3s - Trial 100" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:21:35,473] Using an existing study with name 'ANO_hu_feature' instead of creating a new one.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "BCUT2D calculation failed: ERROR: No Gasteiger Partial Charge parameters for Element: Sn Mode: sp3\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729996007.302521 4003764 service.cc:146] XLA service 0x55d3e493edc0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729996007.302569 4003764 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729996007.439999 4003764 service.cc:146] XLA service 0x55d3e4915c40 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729996007.440028 4003764 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729996012.288356 4003872 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.848289\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:27:05,030] Trial 2 finished with value: 0.848289 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 1, 'NumHAcceptors': 1, 'NumHDonors': 1, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 1, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 0, 'LabuteASA': 1, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 1, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 0, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 0, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 0, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 1, 'RDF': 1, 'MORSE': 0, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 0 with value: 0.939079.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729996042.982911 4004372 service.cc:146] XLA service 0x561697be9860 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729996042.982962 4004372 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729996043.127021 4004372 service.cc:146] XLA service 0x561697b253e0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729996043.127060 4004372 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729996046.659685 4004479 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.937361\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:27:43,192] Trial 3 finished with value: 0.937361 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 1, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 1, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 1, 'FractionCSP3': 0, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 0, 'BCUT2D': 0, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 0, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 0, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 0 with value: 0.939079.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729996362.176318 4006901 service.cc:146] XLA service 0x55ae3397e660 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729996362.176362 4006901 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729996362.316361 4006901 service.cc:146] XLA service 0x55ae3398d490 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729996362.316415 4006901 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729996365.409047 4007011 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.889872\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:33:01,385] Trial 4 finished with value: 0.889872 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 1, 'NHOHCount': 1, 'NOCount': 1, 'RingCount': 1, 'NumAromaticRings': 0, 'NumSaturatedRings': 0, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 1, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 0, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 0, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 0, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 0, 'AUTOCORR2D': 0, 'BCUT2D': 0, 'Asphericity': 1, 'PBF': 1, 'RadiusOfGyration': 0, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 0, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 0 with value: 0.939079.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "BCUT2D calculation failed: ERROR: No Gasteiger Partial Charge parameters for Element: Sn Mode: sp3\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729996697.985485 4009043 service.cc:146] XLA service 0x557d8e14dee0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729996697.985533 4009043 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729996698.119196 4009043 service.cc:146] XLA service 0x557d8e0b6ca0 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729996698.119253 4009043 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729996701.120181 4009152 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.939862\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:38:36,832] Trial 5 finished with value: 0.939862 and parameters: {'NumRotatableBonds': 0, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 1, 'RingCount': 1, 'NumAromaticRings': 0, 'NumSaturatedRings': 1, 'NumAliphaticRings': 1, 'LabuteASA': 0, 'BalabanJ': 0, 'BertzCT': 1, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 1, 'NumAmideBonds': 0, 'FractionCSP3': 0, 'NumSpiroAtoms': 0, 'NumBridgeheadAtoms': 0, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 0, 'MQNs': 1, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 1, 'PBF': 0, 'RadiusOfGyration': 0, 'InertialShapeFactor': 1, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 0, 'NPR_series[1-2]_ind': 1, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 0, 'WHIM': 0, 'GETAWAY': 1}. Best is trial 5 with value: 0.939862.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "BCUT2D calculation failed: ERROR: No Gasteiger Partial Charge parameters for Element: Sn Mode: sp3\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729997043.906454 4011102 service.cc:146] XLA service 0x559a07dcaa40 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729997043.906513 4011102 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729997044.042250 4011102 service.cc:146] XLA service 0x559a07d30030 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729997044.042288 4011102 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729997047.037883 4011214 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.818023\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:44:21,123] Trial 6 finished with value: 0.818023 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 1, 'NumHAcceptors': 0, 'NumHDonors': 0, 'NumHeteroatoms': 0, 'NumValenceElectrons': 0, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 1, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 0, 'LabuteASA': 1, 'BalabanJ': 0, 'BertzCT': 0, 'Ipc': 1, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 0, 'HallKierAlpha': 0, 'NumAmideBonds': 0, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 1, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 1, 'VSA_EState_Series[1-10]': 1, 'MQNs': 0, 'AUTOCORR2D': 0, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 1, 'RadiusOfGyration': 1, 'InertialShapeFactor': 0, 'Eccentricity': 1, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 1, 'AUTOCORR3D': 1, 'RDF': 0, 'MORSE': 1, 'WHIM': 1, 'GETAWAY': 1}. Best is trial 5 with value: 0.939862.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "BCUT2D calculation failed: ERROR: No Gasteiger Partial Charge parameters for Element: Sn Mode: sp3\n", "Model already exists at save_model/full_model.keras\n", "Model successfully saved to save_model/full_model.keras\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Error in subprocess: WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "WARNING: All log messages before absl::InitializeLog() is called are written to STDERR\n", "I0000 00:00:1729997092.655814 4011838 service.cc:146] XLA service 0x5606bd6ddfc0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729997092.655911 4011838 service.cc:154] StreamExecutor device (0): Host, Default Version\n", "I0000 00:00:1729997092.818595 4011838 service.cc:146] XLA service 0x5606bd595b80 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices:\n", "I0000 00:00:1729997092.818636 4011838 service.cc:154] StreamExecutor device (0): NVIDIA GeForce RTX 3060 Laptop GPU, Compute Capability 8.6\n", "I0000 00:00:1729997096.298232 4011942 device_compiler.h:188] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "R2 score: 0.899125\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[I 2024-10-27 11:45:10,913] Trial 7 finished with value: 0.899125 and parameters: {'NumRotatableBonds': 1, 'HeavyAtomCount': 0, 'NumHAcceptors': 1, 'NumHDonors': 0, 'NumHeteroatoms': 1, 'NumValenceElectrons': 1, 'NHOHCount': 0, 'NOCount': 0, 'RingCount': 0, 'NumAromaticRings': 1, 'NumSaturatedRings': 0, 'NumAliphaticRings': 0, 'LabuteASA': 0, 'BalabanJ': 1, 'BertzCT': 0, 'Ipc': 0, 'kappa_Series[1-3]_ind': 0, 'Chi_Series[13]_ind': 1, 'Phi': 1, 'HallKierAlpha': 0, 'NumAmideBonds': 1, 'FractionCSP3': 1, 'NumSpiroAtoms': 1, 'NumBridgeheadAtoms': 1, 'PEOE_VSA_Series[1-14]_ind': 1, 'SMR_VSA_Series[1-10]_ind': 0, 'SlogP_VSA_Series[1-12]_ind': 1, 'EState_VSA_Series[1-11]_ind': 0, 'VSA_EState_Series[1-10]': 0, 'MQNs': 0, 'AUTOCORR2D': 1, 'BCUT2D': 1, 'Asphericity': 0, 'PBF': 0, 'RadiusOfGyration': 1, 'InertialShapeFactor': 1, 'Eccentricity': 0, 'SpherocityIndex': 1, 'PMI_series[1-3]_ind': 1, 'NPR_series[1-2]_ind': 0, 'AUTOCORR3D': 0, 'RDF': 1, 'MORSE': 0, 'WHIM': 0, 'GETAWAY': 0}. Best is trial 5 with value: 0.939862.\n" ] } ], "source": [ "study_hu_fea = optuna.create_study(study_name='ANO_hu_feature', storage=storage, direction=\"maximize\", pruner=optuna.pruners.SuccessiveHalvingPruner(reduction_factor=64, min_early_stopping_rate=10),load_if_exists=True) \n", "# study_hu_fea = optuna.create_study(study_name='ANO_hu_feature', storage=storage, direction=\"maximize\", pruner=optuna.pruners.HyperbandPruner(min_resource=100,max_resource=1000,reduction_factor=3), load_if_exists=True)\n", "study_hu_fea.optimize(objective_hu_fea, n_trials=TRIALS)\n", "pruned_trials_hu_fea = study_hu_fea.get_trials(deepcopy=False, states=[TrialState.PRUNED])\n", "complete_trials_hu_fea = study_hu_fea.get_trials(deepcopy=False, states=[TrialState.COMPLETE])\n", "# 308m 15.1s - Trial 100" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "print(\"Study statistics: [ws_feature] \")\n", "print(\" Number of finished trials: \", len(study_ws_fea.trials))\n", "print(\" Number of pruned trials: \", len(pruned_trials_ws_fea))\n", "print(\" Number of complete trials: \", len(complete_trials_ws_fea))\n", "print(\"Best trial:\")\n", "trial_ws_fea = study_ws_fea.best_trial\n", "print(\" Value: \", trial_ws_fea.value)\n", "print(\" Params: \")\n", "for key, value in trial_ws_fea.params.items():\n", " print(\" {}: {}\".format(key, value))" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "print(\"Study statistics: [de_feature] \")\n", "print(\" Number of finished trials: \", len(study_de_fea.trials))\n", "print(\" Number of pruned trials: \", len(pruned_trials_de_fea))\n", "print(\" Number of complete trials: \", len(complete_trials_de_fea))\n", "print(\"Best trial:\")\n", "trial_de_fea = study_de_fea.best_trial\n", "print(\" Value: \", trial_de_fea.value)\n", "print(\" Params: \")\n", "for key, value in trial_de_fea.params.items():\n", " print(\" {}: {}\".format(key, value))" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "print(\"Study statistics: [lo_feature] \")\n", "print(\" Number of finished trials: \", len(study_lo_fea.trials))\n", "print(\" Number of pruned trials: \", len(pruned_trials_lo_fea))\n", "print(\" Number of complete trials: \", len(complete_trials_lo_fea))\n", "print(\"Best trial:\")\n", "trial_lo_fea = study_lo_fea.best_trial\n", "print(\" Value: \", trial_lo_fea.value)\n", "print(\" Params: \")\n", "for key, value in trial_lo_fea.params.items():\n", " print(\" {}: {}\".format(key, value))" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "print(\"Study statistics: [hu_feature] \")\n", "print(\" Number of finished trials: \", len(study_hu_fea.trials))\n", "# print(\" Number of pruned trials: \", len(pruned_trials_hu_fea))\n", "# print(\" Number of complete trials: \", len(complete_trials_hu_fea))\n", "print(\"Best trial:\")\n", "trial_hu_fea = study_hu_fea.best_trial\n", "print(\" Value: \", trial_hu_fea.value)\n", "print(\" Params: \")\n", "for key, value in trial_hu_fea.params.items():\n", " print(\" {}: {}\".format(key, value))" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "ai", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.12.2" }, "orig_nbformat": 4 }, "nbformat": 4, "nbformat_minor": 2 }