diff --git a/training/hyper/hyper_mp_perovskites.py b/training/hyper/hyper_mp_perovskites.py index 4036ff16..a295cd90 100644 --- a/training/hyper/hyper_mp_perovskites.py +++ b/training/hyper/hyper_mp_perovskites.py @@ -79,13 +79,15 @@ "config": { "name": "PAiNN", "inputs": [ - {"shape": [None], "name": "node_number", "dtype": "float32", "ragged": True}, + {"shape": [None], "name": "node_number", "dtype": "int64", "ragged": True}, {"shape": [None, 3], "name": "node_coordinates", "dtype": "float32", "ragged": True}, {"shape": [None, 2], "name": "range_indices", "dtype": "int64", "ragged": True}, {'shape': (None, 3), 'name': "range_image", 'dtype': 'int64', 'ragged': True}, {'shape': (3, 3), 'name': "graph_lattice", 'dtype': 'float32', 'ragged': False} ], - "input_embedding": {"node": {"input_dim": 95, "output_dim": 128}}, + "input_tensor_type": "ragged", + "input_embedding": None, + "input_node_embedding": {"input_dim": 95, "output_dim": 128}, "equiv_initialize_kwargs": {"dim": 3, "method": "eye"}, "bessel_basis": {"num_radial": 20, "cutoff": 5.0, "envelope_exponent": 5}, "pooling_args": {"pooling_method": "mean"}, @@ -109,11 +111,12 @@ ] }, "compile": { - "optimizer": {"class_name": "Adam", "config": {"lr": 1e-04}}, # "clipnorm": 100.0, "clipvalue": 100.0} + "optimizer": {"class_name": "Adam", "config": {"learning_rate": 1e-04}}, + # "clipnorm": 100.0, "clipvalue": 100.0} "loss": "mean_absolute_error" }, "scaler": { - "class_name": "StandardScaler", + "class_name": "StandardLabelScaler", "module_name": "kgcnn.data.transform.scaler.standard", "config": {"with_std": True, "with_mean": True, "copy": True} }, @@ -133,7 +136,300 @@ "info": { "postfix": "", "postfix_file": "", - "kgcnn_version": "2.2.3" + "kgcnn_version": "4.0.0" + } + }, + "Megnet.make_crystal_model": { + "model": { + "module_name": "kgcnn.literature.Megnet", + "class_name": "make_crystal_model", + "config": { + 'name': "Megnet", + 'inputs': [ + {'shape': (None,), 'name': "node_number", 'dtype': 'int64', 'ragged': True}, + {'shape': (None, 3), 'name': "node_coordinates", 'dtype': 'float32', 'ragged': True}, + {'shape': (None, 2), 'name': "range_indices", 'dtype': 'int64', 'ragged': True}, + {'shape': [1], 'name': "charge", 'dtype': 'float32', 'ragged': False}, + {'shape': (None, 3), 'name': "range_image", 'dtype': 'int64', 'ragged': True}, + {'shape': (3, 3), 'name': "graph_lattice", 'dtype': 'float32', 'ragged': False} + ], + "input_tensor_type": "ragged", + 'input_embedding': None, + "input_node_embedding": {"input_dim": 95, "output_dim": 64}, + # "input_edge_embedding": {"input_dim": 100, "output_dim": 64}, + "make_distance": True, "expand_distance": True, + 'gauss_args': {"bins": 25, "distance": 5, "offset": 0.0, "sigma": 0.4}, + 'meg_block_args': {'node_embed': [64, 32, 32], 'edge_embed': [64, 32, 32], + 'env_embed': [64, 32, 32], 'activation': 'kgcnn>softplus2'}, + 'set2set_args': {'channels': 16, 'T': 3, "pooling_method": "sum", "init_qstar": "0"}, + 'node_ff_args': {"units": [64, 32], "activation": "kgcnn>softplus2"}, + 'edge_ff_args': {"units": [64, 32], "activation": "kgcnn>softplus2"}, + 'state_ff_args': {"units": [64, 32], "activation": "kgcnn>softplus2"}, + 'nblocks': 3, 'has_ff': True, 'dropout': None, 'use_set2set': True, + 'verbose': 10, + 'output_embedding': 'graph', + 'output_mlp': {"use_bias": [True, True, True], "units": [32, 16, 1], + "activation": ['kgcnn>softplus2', 'kgcnn>softplus2', 'linear']} + } + }, + "training": { + "cross_validation": {"class_name": "KFold", + "config": {"n_splits": 5, "random_state": 42, "shuffle": True}}, + "fit": { + "batch_size": 32, "epochs": 1000, "validation_freq": 10, "verbose": 2, + "callbacks": [ + {"class_name": "kgcnn>LinearLearningRateScheduler", "config": { + "learning_rate_start": 0.0005, "learning_rate_stop": 0.5e-05, "epo_min": 100, "epo": 1000, + "verbose": 0} + } + ] + }, + "compile": { + "optimizer": {"class_name": "Adam", "config": {"learning_rate": 0.0005}}, + "loss": "mean_absolute_error" + }, + "scaler": { + "class_name": "StandardLabelScaler", + "module_name": "kgcnn.data.transform.scaler.standard", + "config": {"with_std": True, "with_mean": True, "copy": True} + }, + "multi_target_indices": None + }, + "data": { + "dataset": { + "class_name": "MatProjectPerovskitesDataset", + "module_name": "kgcnn.data.datasets.MatProjectPerovskitesDataset", + "config": {}, + "methods": [ + {"map_list": {"method": "set_range_periodic", "max_distance": 5.0}} + ] + }, + "data_unit": "eV/unit_cell" + }, + "info": { + "postfix": "", + "postfix_file": "", + "kgcnn_version": "4.0.0" + } + }, + "DimeNetPP.make_crystal_model": { + "model": { + "class_name": "make_crystal_model", + "module_name": "kgcnn.literature.DimeNetPP", + "config": { + "name": "DimeNetPP", + "inputs": [{"shape": [None], "name": "node_number", "dtype": "int64", "ragged": True}, + {"shape": [None, 3], "name": "node_coordinates", "dtype": "float32", "ragged": True}, + {"shape": [None, 2], "name": "range_indices", "dtype": "int64", "ragged": True}, + {"shape": [None, 2], "name": "angle_indices", "dtype": "int64", "ragged": True}, + {'shape': (None, 3), 'name': "range_image", 'dtype': 'int64', 'ragged': True}, + {'shape': (3, 3), 'name': "graph_lattice", 'dtype': 'float32', 'ragged': False} + ], + "input_tensor_type": "ragged", + "input_embedding": None, + "input_node_embedding": {"input_dim": 95, "output_dim": 128, + "embeddings_initializer": {"class_name": "RandomUniform", + "config": {"minval": -1.7320508075688772, + "maxval": 1.7320508075688772}}}, + "emb_size": 128, "out_emb_size": 256, "int_emb_size": 64, "basis_emb_size": 8, + "num_blocks": 4, "num_spherical": 7, "num_radial": 6, + "cutoff": 5.0, "envelope_exponent": 5, + "num_before_skip": 1, "num_after_skip": 2, "num_dense_output": 3, + "num_targets": 1, "extensive": False, "output_init": "zeros", + "activation": "swish", "verbose": 10, + "output_embedding": "graph", + "use_output_mlp": False, + "output_mlp": {}, + } + }, + "training": { + "cross_validation": {"class_name": "KFold", + "config": {"n_splits": 5, "random_state": 42, "shuffle": True}}, + "fit": { + "batch_size": 16, "epochs": 780, "validation_freq": 10, "verbose": 2, "callbacks": [], + "validation_batch_size": 8 + }, + "compile": { + "optimizer": { + "class_name": "Adam", + "config": { + "learning_rate": { + "class_name": "kgcnn>LinearWarmupExponentialDecay", "config": { + "learning_rate": 0.001, "warmup_steps": 3000.0, "decay_steps": 4000000.0, + "decay_rate": 0.01 + } + }, + "use_ema": True, + "amsgrad": True, + } + }, + "loss": "mean_absolute_error" + }, + "scaler": { + "class_name": "StandardLabelScaler", + "module_name": "kgcnn.data.transform.scaler.standard", + "config": {"with_std": True, "with_mean": True, "copy": True} + }, + "multi_target_indices": None + }, + "data": { + "dataset": { + "class_name": "MatProjectPerovskitesDataset", + "module_name": "kgcnn.data.datasets.MatProjectPerovskitesDataset", + "config": {}, + "methods": [ + {"map_list": {"method": "set_range_periodic", "max_distance": 5.0, "max_neighbours": 17}}, + {"map_list": {"method": "set_angle", "allow_multi_edges": True, "allow_reverse_edges": True}} + ] + }, + }, + "info": { + "postfix": "", + "postfix_file": "", + "kgcnn_version": "4.0.0" + } + }, + "CGCNN.make_crystal_model": { + "model": { + "class_name": "make_crystal_model", + "module_name": "kgcnn.literature.CGCNN", + "config": { + 'name': 'CGCNN', + 'inputs': [ + {'shape': (None,), 'name': 'node_number', 'dtype': 'int64', 'ragged': True}, + {'shape': (None, 3), 'name': 'node_frac_coordinates', 'dtype': 'float64', 'ragged': True}, + {'shape': (None, 2), 'name': 'range_indices', 'dtype': 'int64', 'ragged': True}, + {'shape': (3, 3), 'name': 'graph_lattice', 'dtype': 'float64', 'ragged': False}, + {'shape': (None, 3), 'name': 'range_image', 'dtype': 'float32', 'ragged': True}, + # For `representation="asu"`: + # {'shape': (None, 1), 'name': 'multiplicities', 'dtype': 'float32', 'ragged': True}, + # {'shape': (None, 4, 4), 'name': 'symmops', 'dtype': 'float64', 'ragged': True}, + ], + "input_tensor_type": "ragged", + 'input_node_embedding': {'input_dim': 95, 'output_dim': 64}, + 'representation': 'unit', # None, 'asu' or 'unit' + 'expand_distance': True, + 'make_distances': True, + 'gauss_args': {'bins': 60, 'distance': 6, 'offset': 0.0, 'sigma': 0.4}, + 'conv_layer_args': { + 'units': 128, + 'activation_s': 'kgcnn>shifted_softplus', + 'activation_out': 'kgcnn>shifted_softplus', + 'batch_normalization': True, + }, + 'node_pooling_args': {'pooling_method': 'mean'}, + 'depth': 4, + 'output_mlp': {'use_bias': [True, True, False], 'units': [128, 64, 1], + 'activation': ['kgcnn>shifted_softplus', 'kgcnn>shifted_softplus', 'linear']}, + } + }, + "training": { + "cross_validation": {"class_name": "KFold", + "config": {"n_splits": 5, "random_state": 42, "shuffle": True}}, + "fit": { + "batch_size": 128, "epochs": 1000, "validation_freq": 10, "verbose": 2, + "callbacks": [ + {"class_name": "kgcnn>LinearLearningRateScheduler", "config": { + "learning_rate_start": 1e-03, "learning_rate_stop": 1e-05, "epo_min": 500, "epo": 1000, + "verbose": 0} + } + ] + }, + "compile": { + "optimizer": {"class_name": "Adam", "config": {"learning_rate": 1e-03}}, + "loss": "mean_absolute_error" + }, + "scaler": { + "class_name": "StandardLabelScaler", + "module_name": "kgcnn.data.transform.scaler.standard", + "config": {"with_std": True, "with_mean": True, "copy": True} + }, + "multi_target_indices": None + }, + "data": { + "dataset": { + "class_name": "MatProjectPerovskitesDataset", + "module_name": "kgcnn.data.datasets.MatProjectPerovskitesDataset", + "config": {}, + "methods": [ + {"map_list": {"method": "set_range_periodic", "max_distance": 6.0}} + ] + }, + "data_unit": "eV/unit_cell" + }, + "info": { + "postfix": "", + "postfix_file": "", + "kgcnn_version": "4.0.0" + } + }, + "NMPN.make_crystal_model": { + "model": { + "class_name": "make_crystal_model", + "module_name": "kgcnn.literature.NMPN", + "config": { + "name": "NMPN", + "inputs": [ + {"shape": [None], "name": "node_number", "dtype": "int64", "ragged": True}, + {"shape": [None, 3], "name": "node_coordinates", "dtype": "float32", "ragged": True}, + {"shape": [None, 2], "name": "range_indices", "dtype": "int64", "ragged": True}, + {'shape': (None, 3), 'name': "range_image", 'dtype': 'int64', 'ragged': True}, + {'shape': (3, 3), 'name': "graph_lattice", 'dtype': 'float32', 'ragged': False} + ], + "input_tensor_type": "ragged", + "input_embedding": None, + "input_node_embedding": {"input_dim": 95, "output_dim": 64}, + "input_edge_embedding": {"input_dim": 5, "output_dim": 64}, + "set2set_args": {"channels": 32, "T": 3, "pooling_method": "sum", "init_qstar": "0"}, + "pooling_args": {"pooling_method": "segment_mean"}, + "use_set2set": True, + "depth": 3, + "node_dim": 128, + "verbose": 10, + "geometric_edge": True, "make_distance": True, "expand_distance": True, + "output_embedding": "graph", + "output_mlp": {"use_bias": [True, True, False], "units": [25, 25, 1], + "activation": ["selu", "selu", "linear"]}, + } + }, + "training": { + "cross_validation": {"class_name": "KFold", + "config": {"n_splits": 5, "random_state": 42, "shuffle": True}}, + "fit": { + "batch_size": 16, "epochs": 700, "validation_freq": 10, "verbose": 2, + "callbacks": [ + {"class_name": "kgcnn>LinearLearningRateScheduler", "config": { + "learning_rate_start": 1e-04, "learning_rate_stop": 1e-05, "epo_min": 50, "epo": 700, + "verbose": 0 + } + } + ] + }, + "compile": { + "optimizer": {"class_name": "Adam", "config": {"learning_rate": 1e-04}}, + "loss": "mean_absolute_error" + }, + "scaler": { + "class_name": "StandardLabelScaler", + "module_name": "kgcnn.data.transform.scaler.standard", + "config": {"with_std": True, "with_mean": True, "copy": True} + }, + "multi_target_indices": None + }, + "data": { + "dataset": { + "class_name": "MatProjectPerovskitesDataset", + "module_name": "kgcnn.data.datasets.MatProjectPerovskitesDataset", + "config": {}, + "methods": [ + {"map_list": {"method": "set_range_periodic", "max_distance": 5.0}} + ] + }, + }, + "info": { + "postfix": "", + "postfix_file": "", + "kgcnn_version": "4.0.0" } }, } diff --git a/training/hyper/hyper_qm9_energies.py b/training/hyper/hyper_qm9_energies.py index 67b11dca..4482a837 100644 --- a/training/hyper/hyper_qm9_energies.py +++ b/training/hyper/hyper_qm9_energies.py @@ -231,10 +231,13 @@ ], "input_tensor_type": "ragged", "input_embedding": None, + "equiv_initialize_kwargs": {"dim": 3, "method": "eps", "units": 128}, "input_node_embedding": {"input_dim": 95, "output_dim": 128}, "bessel_basis": {"num_radial": 20, "cutoff": 5.0, "envelope_exponent": 5}, - "pooling_args": {"pooling_method": "sum"}, "conv_args": {"units": 128, "cutoff": None}, - "update_args": {"units": 128}, "depth": 3, "verbose": 10, + "pooling_args": {"pooling_method": "sum"}, + "conv_args": {"units": 128, "cutoff": None}, + "update_args": {"units": 128, "add_eps": True}, + "depth": 3, "verbose": 10, "output_embedding": "graph", "output_mlp": {"use_bias": [True, True], "units": [128, 1], "activation": ["swish", "linear"]}, } diff --git a/training/results/MatProjectDielectricDataset/CGCNN_make_crystal_model/CGCNN_MatProjectDielectricDataset_score.yaml b/training/results/MatProjectDielectricDataset/CGCNN_make_crystal_model/CGCNN_MatProjectDielectricDataset_score.yaml new file mode 100644 index 00000000..8ab5c1eb --- /dev/null +++ b/training/results/MatProjectDielectricDataset/CGCNN_make_crystal_model/CGCNN_MatProjectDielectricDataset_score.yaml @@ -0,0 +1,156 @@ +OS: posix_linux +backend: tensorflow +cuda_available: 'True' +data_unit: '' +date_time: '2023-12-22 12:27:35' +device_id: '[LogicalDevice(name=''/device:CPU:0'', device_type=''CPU''), LogicalDevice(name=''/device:GPU:0'', + device_type=''GPU'')]' +device_memory: '[]' +device_name: '[{}, {''compute_capability'': (8, 0), ''device_name'': ''NVIDIA A100 + 80GB PCIe''}]' +epochs: +- 1000 +- 1000 +- 1000 +- 1000 +- 1000 +execute_folds: null +kgcnn_version: 4.0.0 +learning_rate: +- 1.1979999726463575e-05 +- 1.1979999726463575e-05 +- 1.1979999726463575e-05 +- 1.1979999726463575e-05 +- 1.1979999726463575e-05 +loss: +- 0.003908407408744097 +- 0.004692154470831156 +- 0.006342913489788771 +- 0.0035230836365371943 +- 0.009283904917538166 +max_learning_rate: +- 0.0010000000474974513 +- 0.0010000000474974513 +- 0.0010000000474974513 +- 0.0010000000474974513 +- 0.0010000000474974513 +max_loss: +- 0.29928597807884216 +- 0.2982141375541687 +- 0.34784677624702454 +- 0.33266669511795044 +- 0.2964531183242798 +max_scaled_mean_absolute_error: +- 0.6703238487243652 +- 0.6486446857452393 +- 0.6615451574325562 +- 0.6476733088493347 +- 0.6645464301109314 +max_scaled_root_mean_squared_error: +- 2.226531505584717 +- 2.1471033096313477 +- 1.961928367614746 +- 1.9316452741622925 +- 2.2292592525482178 +max_val_loss: +- 0.13875462114810944 +- 0.17157776653766632 +- 0.2204970121383667 +- 0.241636723279953 +- 0.15825790166854858 +max_val_scaled_mean_absolute_error: +- 0.30842339992523193 +- 0.37336939573287964 +- 0.43662363290786743 +- 0.47117704153060913 +- 0.36141663789749146 +max_val_scaled_root_mean_squared_error: +- 1.2602670192718506 +- 1.8693556785583496 +- 3.8716259002685547 +- 2.9088242053985596 +- 2.1601967811584473 +min_learning_rate: +- 1.1979999726463575e-05 +- 1.1979999726463575e-05 +- 1.1979999726463575e-05 +- 1.1979999726463575e-05 +- 1.1979999726463575e-05 +min_loss: +- 0.00390807818621397 +- 0.004692154470831156 +- 0.006342913489788771 +- 0.0035230836365371943 +- 0.009283904917538166 +min_scaled_mean_absolute_error: +- 0.008782914839684963 +- 0.010183566249907017 +- 0.012111489661037922 +- 0.006886749062687159 +- 0.02086334303021431 +min_scaled_root_mean_squared_error: +- 0.13632167875766754 +- 0.12522505223751068 +- 0.190583735704422 +- 0.07955355197191238 +- 0.5195185542106628 +min_val_loss: +- 0.10097754001617432 +- 0.1282927393913269 +- 0.1741935908794403 +- 0.18756960332393646 +- 0.12386748194694519 +min_val_scaled_mean_absolute_error: +- 0.2205708771944046 +- 0.2831050455570221 +- 0.3451306223869324 +- 0.38085973262786865 +- 0.2762523591518402 +min_val_scaled_root_mean_squared_error: +- 1.1485005617141724 +- 1.4987907409667969 +- 2.642016649246216 +- 2.443527936935425 +- 1.123365879058838 +model_class: make_crystal_model +model_name: CGCNN +model_version: '2023-11-28' +multi_target_indices: null +number_histories: 5 +scaled_mean_absolute_error: +- 0.00878499262034893 +- 0.010183566249907017 +- 0.012111489661037922 +- 0.006886749062687159 +- 0.02086334303021431 +scaled_root_mean_squared_error: +- 0.13636255264282227 +- 0.12528164684772491 +- 0.19060498476028442 +- 0.07955954968929291 +- 0.5195185542106628 +seed: 42 +time_list: +- '0:24:17.400906' +- '0:24:19.909013' +- '0:24:28.518577' +- '0:24:28.251962' +- '0:24:04.352241' +val_loss: +- 0.11400707066059113 +- 0.14116309583187103 +- 0.19164298474788666 +- 0.20423556864261627 +- 0.13235312700271606 +val_scaled_mean_absolute_error: +- 0.2466062605381012 +- 0.3129154443740845 +- 0.3801003396511078 +- 0.4156058132648468 +- 0.29770055413246155 +val_scaled_root_mean_squared_error: +- 1.2402254343032837 +- 1.694710373878479 +- 3.0533506870269775 +- 2.6101980209350586 +- 1.2695704698562622 diff --git a/training/results/MatProjectDielectricDataset/CGCNN_make_crystal_model/CGCNN_hyper.json b/training/results/MatProjectDielectricDataset/CGCNN_make_crystal_model/CGCNN_hyper.json new file mode 100644 index 00000000..0df0d93a --- /dev/null +++ b/training/results/MatProjectDielectricDataset/CGCNN_make_crystal_model/CGCNN_hyper.json @@ -0,0 +1 @@ +{"model": {"class_name": "make_crystal_model", "module_name": "kgcnn.literature.CGCNN", "config": {"name": "CGCNN", "inputs": [{"shape": [null], "name": "node_number", "dtype": "int64", "ragged": true}, {"shape": [null, 3], "name": "node_frac_coordinates", "dtype": "float64", "ragged": true}, {"shape": [null, 2], "name": "range_indices", "dtype": "int64", "ragged": true}, {"shape": [null, 3], "name": "range_image", "dtype": "float32", "ragged": true}, {"shape": [3, 3], "name": "graph_lattice", "dtype": "float64", "ragged": false}], "input_tensor_type": "ragged", "input_node_embedding": {"input_dim": 95, "output_dim": 64}, "representation": "unit", "expand_distance": true, "make_distances": true, "gauss_args": {"bins": 60, "distance": 6, "offset": 0.0, "sigma": 0.4}, "conv_layer_args": {"units": 128, "activation_s": "kgcnn>shifted_softplus", "activation_out": "kgcnn>shifted_softplus", "batch_normalization": true}, "node_pooling_args": {"pooling_method": "mean"}, "depth": 4, "output_mlp": {"use_bias": [true, true, false], "units": [128, 64, 1], "activation": ["kgcnn>shifted_softplus", "kgcnn>shifted_softplus", "linear"]}}}, "training": {"cross_validation": {"class_name": "KFold", "config": {"n_splits": 5, "random_state": 42, "shuffle": true}}, "fit": {"batch_size": 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a/training/results/MatProjectDielectricDataset/DimeNetPP_make_crystal_model/DimeNetPP_MatProjectDielectricDataset_score.yaml b/training/results/MatProjectDielectricDataset/DimeNetPP_make_crystal_model/DimeNetPP_MatProjectDielectricDataset_score.yaml new file mode 100644 index 00000000..57a7c2c6 --- /dev/null +++ b/training/results/MatProjectDielectricDataset/DimeNetPP_make_crystal_model/DimeNetPP_MatProjectDielectricDataset_score.yaml @@ -0,0 +1,138 @@ +OS: posix_linux +backend: tensorflow +cuda_available: 'True' +data_unit: '' +date_time: '2023-12-23 08:04:54' +device_id: '[LogicalDevice(name=''/device:CPU:0'', device_type=''CPU''), LogicalDevice(name=''/device:GPU:0'', + device_type=''GPU'')]' +device_memory: '[]' +device_name: '[{}, {''compute_capability'': (8, 0), ''device_name'': ''NVIDIA A100 + 80GB PCIe''}]' +epochs: +- 780 +- 780 +- 780 +- 780 +- 780 +execute_folds: null +kgcnn_version: 4.0.0 +loss: +- 0.014057300053536892 +- 0.010803972370922565 +- 0.021847454831004143 +- 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+- 1.5344483852386475 +min_val_scaled_root_mean_squared_error: +- 7.693243503570557 +- 4.385979652404785 +- 7.473199844360352 +- 3.0994436740875244 +- 2.897643566131592 +model_class: make_model +model_name: PAiNN +model_version: '2023-10-04' +multi_target_indices: null +number_histories: 5 +scaled_mean_absolute_error: +- 0.5739108324050903 +- 0.6887179613113403 +- 0.5221326351165771 +- 0.41577157378196716 +- 0.7747818231582642 +scaled_root_mean_squared_error: +- 0.7554106712341309 +- 0.8686598539352417 +- 0.6846397519111633 +- 0.5605447888374329 +- 0.9511976838111877 +seed: 42 +time_list: +- '0:47:27.132277' +- '0:47:44.092972' +- '0:47:52.275830' +- '0:48:39.693941' +- '0:48:18.381033' +val_loss: +- 0.007661634124815464 +- 0.006994512863457203 +- 0.006724040489643812 +- 0.006898249499499798 +- 0.0068360986188054085 +val_scaled_mean_absolute_error: +- 1.7198737859725952 +- 1.569486379623413 +- 1.5101431608200073 +- 1.548624873161316 +- 1.5344483852386475 +val_scaled_root_mean_squared_error: +- 8.332200050354004 +- 4.385979652404785 +- 7.6372528076171875 +- 3.0994436740875244 +- 2.897643566131592 diff --git a/training/results/QM7Dataset/PAiNN/PAiNN_hyper.json b/training/results/QM7Dataset/PAiNN/PAiNN_hyper.json new file mode 100644 index 00000000..16f57623 --- /dev/null +++ b/training/results/QM7Dataset/PAiNN/PAiNN_hyper.json @@ -0,0 +1 @@ +{"model": {"class_name": "make_model", "module_name": "kgcnn.literature.PAiNN", "config": {"name": "PAiNN", "inputs": [{"shape": [null], "name": "node_number", "dtype": "int64", "ragged": true}, {"shape": [null, 3], "name": "node_coordinates", "dtype": "float32", "ragged": true}, {"shape": [null, 2], "name": "range_indices", "dtype": "int64", "ragged": true}], "input_tensor_type": "ragged", "input_embedding": null, "input_node_embedding": {"input_dim": 95, "output_dim": 128}, "equiv_initialize_kwargs": {"dim": 3, "method": "eps"}, "bessel_basis": {"num_radial": 20, "cutoff": 5.0, "envelope_exponent": 5}, "pooling_args": {"pooling_method": "sum"}, "conv_args": {"units": 128, "cutoff": null}, "update_args": {"units": 128}, "depth": 3, "verbose": 10, "output_embedding": "graph", "output_mlp": {"use_bias": [true, true], "units": [128, 1], "activation": ["swish", "linear"]}}}, "training": {"fit": {"batch_size": 32, "epochs": 872, "validation_freq": 10, "verbose": 2, "callbacks": []}, "compile": {"optimizer": {"class_name": "Adam", "config": {"learning_rate": {"class_name": "kgcnn>LinearWarmupExponentialDecay", "config": {"learning_rate": 0.001, "warmup_steps": 150.0, "decay_steps": 200000.0, "decay_rate": 0.01}}, "amsgrad": true, "use_ema": true}}, "loss": "mean_absolute_error"}, "scaler": {"class_name": "QMGraphLabelScaler", "config": {"atomic_number": "node_number", "scaler": [{"class_name": "StandardLabelScaler", "config": {"with_std": true, "with_mean": true, "copy": true}}]}}, "multi_target_indices": null}, "data": {"data_unit": "kcal/mol"}, "info": {"postfix": "", "postfix_file": "", "kgcnn_version": "4.0.0"}, "dataset": {"class_name": "QM7Dataset", "module_name": "kgcnn.data.datasets.QM7Dataset", "config": {}, "methods": [{"map_list": {"method": "set_range", "max_distance": 5, "max_neighbours": 10000}}]}} \ No newline at end of file diff --git a/training/results/README.md b/training/results/README.md index 81d1d7ff..07341f8f 100644 --- a/training/results/README.md +++ b/training/results/README.md @@ -57,6 +57,7 @@ ESOL consists of 1128 compounds as smiles and their corresponding water solubili | model | kgcnn | epochs | MAE [log mol/L] | RMSE [log mol/L] | |:------------|:--------|---------:|:-----------------------|:-----------------------| | AttentiveFP | 4.0.0 | 200 | 0.4351 ± 0.0110 | 0.6080 ± 0.0207 | +| CMPNN | 4.0.0 | 600 | 0.5276 ± 0.0154 | 0.7505 ± 0.0189 | | DGIN | 4.0.0 | 300 | 0.4434 ± 0.0252 | 0.6225 ± 0.0420 | | DMPNN | 4.0.0 | 300 | 0.4401 ± 0.0165 | 0.6203 ± 0.0292 | | EGNN | 4.0.0 | 800 | 0.4507 ± 0.0152 | 0.6563 ± 0.0370 | @@ -151,9 +152,13 @@ Energies and forces for molecular dynamics trajectories. All geometries in A, en Materials Project dataset from Matbench with 4764 crystal structures and their corresponding Refractive index (unitless). We use a random 5-fold cross-validation. -| model | kgcnn | epochs | MAE [no unit] | RMSE [no unit] | -|:--------------------------|:--------|---------:|:-----------------------|:-----------------------| -| Schnet.make_crystal_model | 4.0.0 | 800 | **0.3180 ± 0.0359** | **1.8509 ± 0.5854** | +| model | kgcnn | epochs | MAE [no unit] | RMSE [no unit] | +|:-----------------------------|:--------|---------:|:-----------------------|:-----------------------| +| CGCNN.make_crystal_model | 4.0.0 | 1000 | 0.3306 ± 0.0602 | 1.9736 ± 0.7324 | +| DimeNetPP.make_crystal_model | 4.0.0 | 780 | 0.3415 ± 0.0542 | 1.9637 ± 0.6323 | +| Megnet.make_crystal_model | 4.0.0 | 1000 | 0.3362 ± 0.0550 | 2.0156 ± 0.5872 | +| NMPN.make_crystal_model | 4.0.0 | 700 | 0.3289 ± 0.0489 | 1.8770 ± 0.6522 | +| Schnet.make_crystal_model | 4.0.0 | 800 | **0.3180 ± 0.0359** | **1.8509 ± 0.5854** | #### MatProjectEFormDataset @@ -188,6 +193,7 @@ Materials Project dataset from Matbench with 636 crystal structures and their co | CGCNN.make_crystal_model | 4.0.0 | 1000 | 57.6974 ± 18.0803 | 140.6167 ± 44.8418 | | DimeNetPP.make_crystal_model | 4.0.0 | 780 | 50.2880 ± 11.4199 | 126.0600 ± 38.3769 | | Megnet.make_crystal_model | 4.0.0 | 1000 | 51.1735 ± 9.1746 | 123.4178 ± 32.9582 | +| NMPN.make_crystal_model | 4.0.0 | 700 | 59.3986 ± 10.9272 | 139.5943 ± 32.1129 | | PAiNN.make_crystal_model | 4.0.0 | 800 | 49.3889 ± 11.5376 | 121.7087 ± 30.0472 | | Schnet.make_crystal_model | 4.0.0 | 800 | **45.2412 ± 11.6395** | **115.6890 ± 39.0929** | @@ -266,11 +272,15 @@ TUDataset of proteins that are classified as enzymes or non-enzymes. Nodes repre QM7 dataset is a subset of GDB-13. Molecules of up to 23 atoms (including 7 heavy atoms C, N, O, and S), totalling 7165 molecules. We use dataset-specific 5-fold cross-validation. The atomization energies are given in kcal/mol and are ranging from -800 to -2000 kcal/mol). -| model | kgcnn | epochs | MAE [kcal/mol] | RMSE [kcal/mol] | -|:--------|:--------|---------:|:-----------------------|:-----------------------| -| Megnet | 4.0.0 | 800 | **1.5180 ± 0.0802** | **3.0321 ± 0.1936** | -| NMPN | 4.0.0 | 500 | 7.2907 ± 0.9061 | 38.1446 ± 12.1445 | -| Schnet | 4.0.0 | 800 | 3.4313 ± 0.4757 | 10.8978 ± 7.3863 | +| model | kgcnn | epochs | MAE [kcal/mol] | RMSE [kcal/mol] | +|:----------|:--------|---------:|:-----------------------|:-----------------------| +| DimeNetPP | 4.0.0 | 872 | 3.4639 ± 0.2003 | 7.5327 ± 1.8190 | +| EGNN | 4.0.0 | 800 | 1.7300 ± 0.1336 | 5.1268 ± 2.5134 | +| Megnet | 4.0.0 | 800 | 1.5180 ± 0.0802 | 3.0321 ± 0.1936 | +| MXMNet | 4.0.0 | 900 | **1.2431 ± 0.0820** | **2.6694 ± 0.2584** | +| NMPN | 4.0.0 | 500 | 7.2907 ± 0.9061 | 38.1446 ± 12.1445 | +| PAiNN | 4.0.0 | 872 | 1.5765 ± 0.0742 | 5.2705 ± 2.2848 | +| Schnet | 4.0.0 | 800 | 3.4313 ± 0.4757 | 10.8978 ± 7.3863 | #### QM9Dataset