chemprop
latest
Contents:
Requirements
Installation
Tutorial
Web Interface
Data
Features
Models
Training and Predicting
Hyperparameter Optimization
Interpretation
Command Line Arguments
Neural Network Utility Functions
Utility Functions
Scikit-Learn Models
Useful Scripts
chemprop
Index
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Index
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A
activate_dropout() (in module chemprop.nn_utils)
activation (chemprop.args.TrainArgs attribute)
adding_bond_types (chemprop.args.TrainArgs property)
adding_h (chemprop.args.TrainArgs attribute)
aggregation (chemprop.args.TrainArgs attribute)
aggregation_norm (chemprop.args.TrainArgs attribute)
atom_bond_data_weights() (chemprop.data.data.MoleculeDataset method)
atom_constraints (chemprop.args.TrainArgs property)
atom_descriptor_scaling (chemprop.args.TrainArgs property)
atom_descriptors (chemprop.args.CommonArgs attribute)
atom_descriptors() (chemprop.data.data.MoleculeDataset method)
atom_descriptors_path (chemprop.args.CommonArgs attribute)
atom_descriptors_size (chemprop.args.CommonArgs property)
atom_descriptors_size() (chemprop.data.data.MoleculeDataset method)
atom_features() (chemprop.data.data.MoleculeDataset method)
(in module chemprop.features.featurization)
atom_features_size (chemprop.args.CommonArgs property)
atom_features_size() (chemprop.data.data.MoleculeDataset method)
atom_features_zeros() (in module chemprop.features.featurization)
atom_messages (chemprop.args.TrainArgs attribute)
AtomBondScaler (class in chemprop.data.scaler)
B
batch_graph() (chemprop.data.data.MoleculeDataset method)
batch_size (chemprop.args.CommonArgs attribute)
(chemprop.args.InterpretArgs attribute)
BatchMolGraph (class in chemprop.features.featurization)
bias (chemprop.args.TrainArgs attribute)
bias_solvent (chemprop.args.TrainArgs attribute)
bond_constraints (chemprop.args.TrainArgs property)
bond_descriptor_scaling (chemprop.args.TrainArgs property)
bond_descriptors (chemprop.args.CommonArgs attribute)
bond_descriptors() (chemprop.data.data.MoleculeDataset method)
bond_descriptors_path (chemprop.args.CommonArgs attribute)
bond_descriptors_size (chemprop.args.CommonArgs property)
bond_descriptors_size() (chemprop.data.data.MoleculeDataset method)
bond_features() (chemprop.data.data.MoleculeDataset method)
(in module chemprop.features.featurization)
bond_features_size (chemprop.args.CommonArgs property)
bond_features_size() (chemprop.data.data.MoleculeDataset method)
bond_types (chemprop.data.data.MoleculeDatapoint property)
(chemprop.data.data.MoleculeDataset property)
build_lr_scheduler() (in module chemprop.utils)
build_optimizer() (in module chemprop.utils)
C
c_puct (chemprop.args.InterpretArgs attribute)
cache_cutoff (chemprop.args.TrainArgs attribute)
cache_graph() (in module chemprop.data.data)
cache_mol() (in module chemprop.data.data)
calibration_atom_descriptors_path (chemprop.args.PredictArgs attribute)
calibration_bond_descriptors_path (chemprop.args.PredictArgs attribute)
calibration_features_path (chemprop.args.PredictArgs attribute)
calibration_interval_percentile (chemprop.args.PredictArgs attribute)
calibration_method (chemprop.args.PredictArgs attribute)
calibration_path (chemprop.args.PredictArgs attribute)
calibration_phase_features_path (chemprop.args.PredictArgs attribute)
checkpoint_dir (chemprop.args.CommonArgs attribute)
(chemprop.args.SklearnPredictArgs attribute)
checkpoint_frzn (chemprop.args.TrainArgs attribute)
checkpoint_path (chemprop.args.CommonArgs attribute)
(chemprop.args.SklearnPredictArgs attribute)
checkpoint_paths (chemprop.args.CommonArgs attribute)
(chemprop.args.SklearnPredictArgs attribute)
chemprop.args
module
chemprop.data.data
module
chemprop.data.scaffold
module
chemprop.data.scaler
module
chemprop.data.utils
module
chemprop.features.features_generators
module
chemprop.features.featurization
module
chemprop.features.utils
module
chemprop.hyperparameter_optimization
module
chemprop.interpret
module
chemprop.models.model
module
chemprop.models.mpn
module
chemprop.nn_utils
module
chemprop.sklearn_predict
module
chemprop.sklearn_train
module
chemprop.train.cross_validate
module
chemprop.train.evaluate
module
chemprop.train.make_predictions
module
chemprop.train.predict
module
chemprop.train.run_training
module
chemprop.train.train
module
chemprop.utils
module
chemprop_hyperopt() (in module chemprop.hyperparameter_optimization)
chemprop_interpret() (in module chemprop.interpret)
chemprop_predict() (in module chemprop.train.make_predictions)
chemprop_train() (in module chemprop.train.cross_validate)
ChempropModel (class in chemprop.interpret)
class_balance (chemprop.args.TrainArgs attribute)
class_weight (chemprop.args.SklearnTrainArgs attribute)
CommonArgs (class in chemprop.args)
compute_gnorm() (in module chemprop.nn_utils)
compute_pnorm() (in module chemprop.nn_utils)
config_path (chemprop.args.TrainArgs attribute)
config_save_path (chemprop.args.HyperoptArgs attribute)
configure() (chemprop.args.CommonArgs method)
conformal_alpha (chemprop.args.PredictArgs attribute)
constraints() (chemprop.data.data.MoleculeDataset method)
constraints_path (chemprop.args.CommonArgs attribute)
construct_molecule_batch() (in module chemprop.data.data)
create_encoder() (chemprop.models.model.MoleculeModel method)
create_ffn() (chemprop.models.model.MoleculeModel method)
create_logger() (in module chemprop.utils)
cross_validate() (in module chemprop.train.cross_validate)
crossval_index_dir (chemprop.args.TrainArgs attribute)
crossval_index_file (chemprop.args.TrainArgs attribute)
crossval_index_sets (chemprop.args.TrainArgs property)
cuda (chemprop.args.CommonArgs property)
D
data_path (chemprop.args.InterpretArgs attribute)
(chemprop.args.TrainArgs attribute)
data_weights() (chemprop.data.data.MoleculeDataset method)
data_weights_path (chemprop.args.TrainArgs attribute)
dataset_type (chemprop.args.TrainArgs attribute)
depth (chemprop.args.TrainArgs attribute)
depth_solvent (chemprop.args.TrainArgs attribute)
device (chemprop.args.CommonArgs property)
drop_extra_columns (chemprop.args.PredictArgs attribute)
dropout (chemprop.args.TrainArgs attribute)
dropout_sampling_size (chemprop.args.PredictArgs attribute)
E
empty_cache (chemprop.args.CommonArgs attribute)
empty_cache() (in module chemprop.data.data)
ensemble_size (chemprop.args.PredictArgs property)
(chemprop.args.TrainArgs attribute)
ensemble_variance (chemprop.args.PredictArgs attribute)
epochs (chemprop.args.TrainArgs attribute)
evaluate() (in module chemprop.train.evaluate)
evaluate_predictions() (in module chemprop.train.evaluate)
evaluation_methods (chemprop.args.PredictArgs attribute)
evaluation_scores_path (chemprop.args.PredictArgs attribute)
evidential_regularization (chemprop.args.TrainArgs attribute)
explicit_h (chemprop.args.TrainArgs attribute)
extend_features() (chemprop.data.data.MoleculeDatapoint method)
extra_metrics (chemprop.args.TrainArgs attribute)
extract_subgraph() (in module chemprop.interpret)
F
features() (chemprop.data.data.MoleculeDataset method)
features_generator (chemprop.args.CommonArgs attribute)
features_only (chemprop.args.TrainArgs attribute)
features_path (chemprop.args.CommonArgs attribute)
features_scaling (chemprop.args.CommonArgs property)
features_size (chemprop.args.TrainArgs property)
features_size() (chemprop.data.data.MoleculeDataset method)
Featurization_parameters (class in chemprop.features.featurization)
ffn_hidden_size (chemprop.args.TrainArgs attribute)
ffn_num_layers (chemprop.args.TrainArgs attribute)
filter_invalid_smiles() (in module chemprop.data.utils)
final_lr (chemprop.args.TrainArgs attribute)
find_clusters() (in module chemprop.interpret)
fingerprint() (chemprop.models.model.MoleculeModel method)
fit() (chemprop.data.scaler.AtomBondScaler method)
(chemprop.data.scaler.StandardScaler method)
folds_file (chemprop.args.TrainArgs attribute)
forward() (chemprop.models.model.MoleculeModel method)
(chemprop.models.mpn.MPN method)
(chemprop.models.mpn.MPNEncoder method)
freeze_first_only (chemprop.args.TrainArgs attribute)
frzn_ffn_layers (chemprop.args.TrainArgs attribute)
G
generate_scaffold() (in module chemprop.data.scaffold)
get_a2a() (chemprop.features.featurization.BatchMolGraph method)
get_activation_function() (in module chemprop.nn_utils)
get_atom_fdim() (in module chemprop.features.featurization)
get_available_features_generators() (in module chemprop.features.features_generators)
get_b2b() (chemprop.features.featurization.BatchMolGraph method)
get_b2br() (chemprop.features.featurization.BatchMolGraph method)
get_bond_fdim() (in module chemprop.features.featurization)
get_checkpoint_paths() (in module chemprop.args)
get_class_sizes() (in module chemprop.data.utils)
get_components() (chemprop.features.featurization.BatchMolGraph method)
get_constraints() (in module chemprop.data.utils)
get_data() (in module chemprop.data.utils)
get_data_from_smiles() (in module chemprop.data.utils)
get_data_weights() (in module chemprop.data.utils)
get_features_generator() (in module chemprop.features.features_generators)
get_header() (in module chemprop.data.utils)
get_inequality_targets() (in module chemprop.data.utils)
get_invalid_smiles_from_file() (in module chemprop.data.utils)
get_invalid_smiles_from_list() (in module chemprop.data.utils)
get_lr() (chemprop.nn_utils.NoamLR method)
get_mixed_task_names() (in module chemprop.data.utils)
get_smiles() (in module chemprop.data.utils)
get_task_names() (in module chemprop.data.utils)
gpu (chemprop.args.CommonArgs attribute)
grad_clip (chemprop.args.TrainArgs attribute)
gt_targets (chemprop.data.data.MoleculeDataLoader property)
gt_targets() (chemprop.data.data.MoleculeDataset method)
H
hidden_size (chemprop.args.TrainArgs attribute)
hidden_size_solvent (chemprop.args.TrainArgs attribute)
hyperopt() (in module chemprop.hyperparameter_optimization)
hyperopt_checkpoint_dir (chemprop.args.HyperoptArgs attribute)
hyperopt_seed (chemprop.args.HyperoptArgs attribute)
HyperoptArgs (class in chemprop.args)
I
ignore_columns (chemprop.args.TrainArgs attribute)
ignore_nan_metrics (chemprop.args.TrainArgs attribute)
impute_mode (chemprop.args.SklearnTrainArgs attribute)
impute_sklearn() (in module chemprop.sklearn_train)
index_select_ND() (in module chemprop.nn_utils)
individual_ensemble_predictions (chemprop.args.PredictArgs attribute)
init_lr (chemprop.args.TrainArgs attribute)
initialize_weights() (in module chemprop.nn_utils)
interpret() (in module chemprop.interpret)
InterpretArgs (class in chemprop.args)
inverse_transform() (chemprop.data.scaler.AtomBondScaler method)
(chemprop.data.scaler.StandardScaler method)
is_adding_hs() (in module chemprop.features.featurization)
is_atom_bond_targets (chemprop.args.TrainArgs attribute)
(chemprop.data.data.MoleculeDataset property)
is_explicit_h() (in module chemprop.features.featurization)
is_keeping_atom_map() (in module chemprop.features.featurization)
is_mol() (in module chemprop.features.featurization)
is_reaction() (in module chemprop.features.featurization)
iter_size (chemprop.data.data.MoleculeDataLoader property)
K
keeping_atom_map (chemprop.args.TrainArgs attribute)
L
load_args() (in module chemprop.utils)
load_checkpoint() (in module chemprop.utils)
load_data() (in module chemprop.train.make_predictions)
load_features() (in module chemprop.features.utils)
load_frzn_model() (in module chemprop.utils)
load_model() (in module chemprop.train.make_predictions)
load_scalers() (in module chemprop.utils)
load_task_names() (in module chemprop.utils)
load_valid_atom_or_bond_features() (in module chemprop.features.utils)
log_dir (chemprop.args.HyperoptArgs attribute)
log_frequency (chemprop.args.TrainArgs attribute)
log_scaffold_stats() (in module chemprop.data.scaffold)
loss_function (chemprop.args.TrainArgs attribute)
lt_targets (chemprop.data.data.MoleculeDataLoader property)
lt_targets() (chemprop.data.data.MoleculeDataset method)
M
make_mols() (in module chemprop.data.data)
make_predictions() (in module chemprop.train.make_predictions)
makedirs() (in module chemprop.utils)
manual_trial_dirs (chemprop.args.HyperoptArgs attribute)
map_reac_to_prod() (in module chemprop.features.featurization)
mask() (chemprop.data.data.MoleculeDataset method)
max_atoms (chemprop.args.InterpretArgs attribute)
max_data_size (chemprop.args.CommonArgs attribute)
max_lr (chemprop.args.TrainArgs attribute)
max_molwt (chemprop.data.data.MoleculeDatapoint property)
mcts() (in module chemprop.interpret)
mcts_rollout() (in module chemprop.interpret)
MCTSNode (class in chemprop.interpret)
metric (chemprop.args.TrainArgs attribute)
metrics (chemprop.args.TrainArgs property)
min_atoms (chemprop.args.InterpretArgs attribute)
minimize_score (chemprop.args.TrainArgs property)
model_type (chemprop.args.SklearnTrainArgs attribute)
module
chemprop.args
chemprop.data.data
chemprop.data.scaffold
chemprop.data.scaler
chemprop.data.utils
chemprop.features.features_generators
chemprop.features.featurization
chemprop.features.utils
chemprop.hyperparameter_optimization
chemprop.interpret
chemprop.models.model
chemprop.models.mpn
chemprop.nn_utils
chemprop.sklearn_predict
chemprop.sklearn_train
chemprop.train.cross_validate
chemprop.train.evaluate
chemprop.train.make_predictions
chemprop.train.predict
chemprop.train.run_training
chemprop.train.train
chemprop.utils
mol (chemprop.data.data.MoleculeDatapoint property)
mol2graph() (in module chemprop.features.featurization)
MoleculeDataLoader (class in chemprop.data.data)
MoleculeDatapoint (class in chemprop.data.data)
MoleculeDataset (class in chemprop.data.data)
MoleculeModel (class in chemprop.models.model)
MoleculeSampler (class in chemprop.data.data)
MolGraph (class in chemprop.features.featurization)
mols() (chemprop.data.data.MoleculeDataset method)
morgan_binary_features_generator() (in module chemprop.features.features_generators)
morgan_counts_features_generator() (in module chemprop.features.features_generators)
MPN (class in chemprop.models.mpn)
mpn_shared (chemprop.args.TrainArgs attribute)
MPNEncoder (class in chemprop.models.mpn)
multi_task_sklearn() (in module chemprop.sklearn_train)
multiclass_num_classes (chemprop.args.TrainArgs attribute)
multitask_mean() (in module chemprop.utils)
N
no_adding_bond_types (chemprop.args.TrainArgs attribute)
no_atom_descriptor_scaling (chemprop.args.TrainArgs attribute)
no_bond_descriptor_scaling (chemprop.args.TrainArgs attribute)
no_cache_mol (chemprop.args.CommonArgs attribute)
no_cuda (chemprop.args.CommonArgs attribute)
no_features_scaling (chemprop.args.CommonArgs attribute)
no_shared_atom_bond_ffn (chemprop.args.TrainArgs attribute)
NoamLR (class in chemprop.nn_utils)
normalize_atom_bond_targets() (chemprop.data.data.MoleculeDataset method)
normalize_features() (chemprop.data.data.MoleculeDataset method)
normalize_targets() (chemprop.data.data.MoleculeDataset method)
num_bits (chemprop.args.SklearnTrainArgs attribute)
num_folds (chemprop.args.TrainArgs attribute)
num_iters (chemprop.args.HyperoptArgs attribute)
num_lrs (chemprop.args.TrainArgs property)
num_tasks (chemprop.args.TrainArgs property)
num_tasks() (chemprop.data.data.MoleculeDatapoint method)
(chemprop.data.data.MoleculeDataset method)
num_trees (chemprop.args.SklearnTrainArgs attribute)
num_workers (chemprop.args.CommonArgs attribute)
number_of_atoms (chemprop.data.data.MoleculeDatapoint property)
(chemprop.data.data.MoleculeDataset property)
number_of_bonds (chemprop.data.data.MoleculeDatapoint property)
(chemprop.data.data.MoleculeDataset property)
number_of_molecules (chemprop.args.CommonArgs attribute)
(chemprop.args.SklearnPredictArgs attribute)
(chemprop.data.data.MoleculeDatapoint property)
(chemprop.data.data.MoleculeDataset property)
O
onek_encoding_unk() (in module chemprop.features.featurization)
overwrite_default_atom_features (chemprop.args.TrainArgs attribute)
overwrite_default_bond_features (chemprop.args.TrainArgs attribute)
overwrite_state_dict() (in module chemprop.utils)
P
param_count() (in module chemprop.nn_utils)
param_count_all() (in module chemprop.nn_utils)
phase_features() (chemprop.data.data.MoleculeDataset method)
phase_features_path (chemprop.args.CommonArgs attribute)
predict() (in module chemprop.sklearn_train)
(in module chemprop.train.predict)
predict_and_save() (in module chemprop.train.make_predictions)
predict_sklearn() (in module chemprop.sklearn_predict)
PredictArgs (class in chemprop.args)
preds_path (chemprop.args.PredictArgs attribute)
(chemprop.args.SklearnPredictArgs attribute)
preprocess_smiles_columns() (in module chemprop.data.utils)
process_args() (chemprop.args.CommonArgs method)
(chemprop.args.HyperoptArgs method)
(chemprop.args.InterpretArgs method)
(chemprop.args.PredictArgs method)
(chemprop.args.SklearnPredictArgs method)
(chemprop.args.TrainArgs method)
prop_delta (chemprop.args.InterpretArgs attribute)
property_id (chemprop.args.InterpretArgs attribute)
pytorch_seed (chemprop.args.TrainArgs attribute)
Q
quantile_loss_alpha (chemprop.args.TrainArgs attribute)
quantiles (chemprop.args.TrainArgs property)
quiet (chemprop.args.TrainArgs attribute)
R
radius (chemprop.args.SklearnTrainArgs attribute)
rdkit_2d_features_generator() (in module chemprop.features.features_generators)
rdkit_2d_normalized_features_generator() (in module chemprop.features.features_generators)
reaction (chemprop.args.TrainArgs attribute)
reaction_mode (chemprop.args.TrainArgs attribute)
reaction_mode() (in module chemprop.features.featurization)
reaction_solvent (chemprop.args.TrainArgs attribute)
register_features_generator() (in module chemprop.features.features_generators)
regression_calibrator_metric (chemprop.args.PredictArgs attribute)
reset_features_and_targets() (chemprop.data.data.MoleculeDatapoint method)
(chemprop.data.data.MoleculeDataset method)
reset_featurization_parameters() (in module chemprop.features.featurization)
resume_experiment (chemprop.args.TrainArgs attribute)
rollout (chemprop.args.InterpretArgs attribute)
run_sklearn() (in module chemprop.sklearn_train)
run_training() (in module chemprop.train.run_training)
S
save_checkpoint() (in module chemprop.utils)
save_dir (chemprop.args.TrainArgs attribute)
save_features() (in module chemprop.features.utils)
save_preds (chemprop.args.TrainArgs attribute)
save_smiles_splits (chemprop.args.TrainArgs attribute)
save_smiles_splits() (in module chemprop.utils)
scaffold_split() (in module chemprop.data.scaffold)
scaffold_to_smiles() (in module chemprop.data.scaffold)
search_parameter_keywords (chemprop.args.HyperoptArgs attribute)
seed (chemprop.args.TrainArgs attribute)
separate_test_atom_descriptors_path (chemprop.args.TrainArgs attribute)
separate_test_bond_descriptors_path (chemprop.args.TrainArgs attribute)
separate_test_constraints_path (chemprop.args.TrainArgs attribute)
separate_test_features_path (chemprop.args.TrainArgs attribute)
separate_test_path (chemprop.args.TrainArgs attribute)
separate_test_phase_features_path (chemprop.args.TrainArgs attribute)
separate_val_atom_descriptors_path (chemprop.args.TrainArgs attribute)
separate_val_bond_descriptors_path (chemprop.args.TrainArgs attribute)
separate_val_constraints_path (chemprop.args.TrainArgs attribute)
separate_val_features_path (chemprop.args.TrainArgs attribute)
separate_val_path (chemprop.args.TrainArgs attribute)
separate_val_phase_features_path (chemprop.args.TrainArgs attribute)
set_adding_hs() (in module chemprop.features.featurization)
set_atom_descriptors() (chemprop.data.data.MoleculeDatapoint method)
set_atom_features() (chemprop.data.data.MoleculeDatapoint method)
set_bond_descriptors() (chemprop.data.data.MoleculeDatapoint method)
set_bond_features() (chemprop.data.data.MoleculeDatapoint method)
set_cache_graph() (in module chemprop.data.data)
set_cache_mol() (in module chemprop.data.data)
set_explicit_h() (in module chemprop.features.featurization)
set_extra_atom_fdim() (in module chemprop.features.featurization)
set_extra_bond_fdim() (in module chemprop.features.featurization)
set_features() (chemprop.data.data.MoleculeDatapoint method)
(in module chemprop.train.make_predictions)
set_keeping_atom_map() (in module chemprop.features.featurization)
set_reaction() (in module chemprop.features.featurization)
set_targets() (chemprop.data.data.MoleculeDatapoint method)
(chemprop.data.data.MoleculeDataset method)
shared_atom_bond_ffn (chemprop.args.TrainArgs property)
show_individual_scores (chemprop.args.TrainArgs attribute)
single_task (chemprop.args.SklearnTrainArgs attribute)
single_task_sklearn() (in module chemprop.sklearn_train)
sklearn_predict() (in module chemprop.sklearn_predict)
sklearn_train() (in module chemprop.sklearn_train)
SklearnPredictArgs (class in chemprop.args)
SklearnTrainArgs (class in chemprop.args)
smiles() (chemprop.data.data.MoleculeDataset method)
smiles_columns (chemprop.args.CommonArgs attribute)
(chemprop.args.SklearnPredictArgs attribute)
spectra_activation (chemprop.args.TrainArgs attribute)
spectra_phase_mask_path (chemprop.args.TrainArgs attribute)
spectra_target_floor (chemprop.args.TrainArgs attribute)
split_data() (in module chemprop.data.utils)
split_key_molecule (chemprop.args.TrainArgs attribute)
split_sizes (chemprop.args.TrainArgs attribute)
split_type (chemprop.args.TrainArgs attribute)
StandardScaler (class in chemprop.data.scaler)
startup_random_iters (chemprop.args.HyperoptArgs attribute)
step() (chemprop.nn_utils.NoamLR method)
T
target_columns (chemprop.args.TrainArgs attribute)
target_weights (chemprop.args.TrainArgs attribute)
targets (chemprop.data.data.MoleculeDataLoader property)
targets() (chemprop.data.data.MoleculeDataset method)
task_names (chemprop.args.TrainArgs property)
test (chemprop.args.TrainArgs attribute)
test_fold_index (chemprop.args.TrainArgs attribute)
test_path (chemprop.args.PredictArgs attribute)
(chemprop.args.SklearnPredictArgs attribute)
timeit() (in module chemprop.utils)
train() (in module chemprop.train.train)
train_data_size (chemprop.args.TrainArgs property)
TrainArgs (class in chemprop.args)
transform() (chemprop.data.scaler.AtomBondScaler method)
(chemprop.data.scaler.StandardScaler method)
U
uncertainty_dropout_p (chemprop.args.PredictArgs attribute)
uncertainty_method (chemprop.args.PredictArgs attribute)
undirected (chemprop.args.TrainArgs attribute)
update_prediction_args() (in module chemprop.utils)
use_input_features (chemprop.args.TrainArgs property)
V
val_fold_index (chemprop.args.TrainArgs attribute)
validate_data() (in module chemprop.data.utils)
validate_dataset_type() (in module chemprop.data.utils)
W
warmup_epochs (chemprop.args.TrainArgs attribute)
weights_ffn_num_layers (chemprop.args.TrainArgs attribute)
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