def cross_validate(
args: TrainArgs, train_func: Callable[[TrainArgs, MoleculeDataset, Logger],
Dict[str, List[float]]]
) -> Tuple[float, float]:
"""
Runs k-fold cross-validation.
For each of k splits (folds) of the data, trains and tests a model on that split
and aggregates the performance across folds.
:param args: A :class:`~chemprop.args.TrainArgs` object containing arguments for
loading data and training the Chemprop model.
:param train_func: Function which runs training.
:return: A tuple containing the mean and standard deviation performance across folds.
"""
logger = create_logger(name=TRAIN_LOGGER_NAME,
save_dir=args.save_dir,
quiet=args.quiet)
if logger is not None:
debug, info = logger.debug, logger.info
else:
debug = info = print
# Initialize relevant variables
init_seed = args.seed
save_dir = args.save_dir
args.task_names = get_task_names(path=args.data_path,
smiles_columns=args.smiles_columns,
target_columns=args.target_columns,
ignore_columns=args.ignore_columns)
# Print command line
debug('Command line')
debug(f'python {" ".join(sys.argv)}')
# Print args
debug('Args')
debug(args)
# Save args
makedirs(args.save_dir)
args.save(os.path.join(args.save_dir, 'args.json'))
# Get data
debug('Loading data')
data = get_data(path=args.data_path,
args=args,
logger=logger,
skip_none_targets=True)
validate_dataset_type(data, dataset_type=args.dataset_type)
args.features_size = data.features_size()
if args.atom_descriptors == 'descriptor':
args.atom_descriptors_size = data.atom_descriptors_size()
args.ffn_hidden_size += args.atom_descriptors_size
elif args.atom_descriptors == 'feature':
args.atom_features_size = data.atom_features_size()
set_extra_atom_fdim(args.atom_features_size)
debug(f'Number of tasks = {args.num_tasks}')
# Run training on different random seeds for each fold
all_scores = defaultdict(list)
for fold_num in range(args.num_folds):
info(f'Fold {fold_num}')
args.seed = init_seed + fold_num
args.save_dir = os.path.join(save_dir, f'fold_{fold_num}')
makedirs(args.save_dir)
data.reset_features_and_targets()
model_scores = train_func(args, data, logger)
for metric, scores in model_scores.items():
all_scores[metric].append(scores)
all_scores = dict(all_scores)
# Convert scores to numpy arrays
for metric, scores in all_scores.items():
all_scores[metric] = np.array(scores)
# Report results
info(f'{args.num_folds}-fold cross validation')
# Report scores for each fold
for fold_num in range(args.num_folds):
for metric, scores in all_scores.items():
info(
f'\tSeed {init_seed + fold_num} ==> test {metric} = {np.nanmean(scores[fold_num]):.6f}'
)
if args.show_individual_scores:
for task_name, score in zip(args.task_names, scores[fold_num]):
info(
f'\t\tSeed {init_seed + fold_num} ==> test {task_name} {metric} = {score:.6f}'
)
# Report scores across folds
for metric, scores in all_scores.items():
avg_scores = np.nanmean(
scores, axis=1) # average score for each model across tasks
mean_score, std_score = np.nanmean(avg_scores), np.nanstd(avg_scores)
info(f'Overall test {metric} = {mean_score:.6f} +/- {std_score:.6f}')
if args.show_individual_scores:
for task_num, task_name in enumerate(args.task_names):
info(
f'\tOverall test {task_name} {metric} = '
f'{np.nanmean(scores[:, task_num]):.6f} +/- {np.nanstd(scores[:, task_num]):.6f}'
)
# Save scores
with open(os.path.join(save_dir, TEST_SCORES_FILE_NAME), 'w') as f:
writer = csv.writer(f)
header = ['Task']
for metric in args.metrics:
header += [f'Mean {metric}', f'Standard deviation {metric}'] + \
[f'Fold {i} {metric}' for i in range(args.num_folds)]
writer.writerow(header)
for task_num, task_name in enumerate(args.task_names):
row = [task_name]
for metric, scores in all_scores.items():
task_scores = scores[:, task_num]
mean, std = np.nanmean(task_scores), np.nanstd(task_scores)
row += [mean, std] + task_scores.tolist()
writer.writerow(row)
# Determine mean and std score of main metric
avg_scores = np.nanmean(all_scores[args.metric], axis=1)
mean_score, std_score = np.nanmean(avg_scores), np.nanstd(avg_scores)
# Optionally merge and save test preds
if args.save_preds:
all_preds = pd.concat([
pd.read_csv(
os.path.join(save_dir, f'fold_{fold_num}', 'test_preds.csv'))
for fold_num in range(args.num_folds)
])
all_preds.to_csv(os.path.join(save_dir, 'test_preds.csv'), index=False)
return mean_score, std_score
def cross_validate(args: TrainArgs,
train_func: Callable[[TrainArgs, MoleculeDataset, Logger], Dict[str, List[float]]]
) -> Tuple[float, float]:
"""
Runs k-fold cross-validation.
For each of k splits (folds) of the data, trains and tests a model on that split
and aggregates the performance across folds.
:param args: A :class:`~chemprop.args.TrainArgs` object containing arguments for
loading data and training the Chemprop model.
:param train_func: Function which runs training.
:return: A tuple containing the mean and standard deviation performance across folds.
"""
logger = create_logger(name=TRAIN_LOGGER_NAME, save_dir=args.save_dir, quiet=args.quiet)
if logger is not None:
debug, info = logger.debug, logger.info
else:
debug = info = print
# Initialize relevant variables
init_seed = args.seed
save_dir = args.save_dir
args.task_names = get_task_names(path=args.data_path, smiles_columns=args.smiles_columns,
target_columns=args.target_columns, ignore_columns=args.ignore_columns)
# Print command line
debug('Command line')
debug(f'python {" ".join(sys.argv)}')
# Print args
debug('Args')
debug(args)
# Save args
makedirs(args.save_dir)
try:
args.save(os.path.join(args.save_dir, 'args.json'))
except subprocess.CalledProcessError:
debug('Could not write the reproducibility section of the arguments to file, thus omitting this section.')
args.save(os.path.join(args.save_dir, 'args.json'), with_reproducibility=False)
# set explicit H option and reaction option
reset_featurization_parameters(logger=logger)
set_explicit_h(args.explicit_h)
set_adding_hs(args.adding_h)
if args.reaction:
set_reaction(args.reaction, args.reaction_mode)
elif args.reaction_solvent:
set_reaction(True, args.reaction_mode)
# Get data
debug('Loading data')
data = get_data(
path=args.data_path,
args=args,
logger=logger,
skip_none_targets=True,
data_weights_path=args.data_weights_path
)
validate_dataset_type(data, dataset_type=args.dataset_type)
args.features_size = data.features_size()
if args.atom_descriptors == 'descriptor':
args.atom_descriptors_size = data.atom_descriptors_size()
args.ffn_hidden_size += args.atom_descriptors_size
elif args.atom_descriptors == 'feature':
args.atom_features_size = data.atom_features_size()
set_extra_atom_fdim(args.atom_features_size)
if args.bond_features_path is not None:
args.bond_features_size = data.bond_features_size()
set_extra_bond_fdim(args.bond_features_size)
debug(f'Number of tasks = {args.num_tasks}')
if args.target_weights is not None and len(args.target_weights) != args.num_tasks:
raise ValueError('The number of provided target weights must match the number and order of the prediction tasks')
# Run training on different random seeds for each fold
all_scores = defaultdict(list)
for fold_num in range(args.num_folds):
info(f'Fold {fold_num}')
args.seed = init_seed + fold_num
args.save_dir = os.path.join(save_dir, f'fold_{fold_num}')
makedirs(args.save_dir)
data.reset_features_and_targets()
# If resuming experiment, load results from trained models
test_scores_path = os.path.join(args.save_dir, 'test_scores.json')
if args.resume_experiment and os.path.exists(test_scores_path):
print('Loading scores')
with open(test_scores_path) as f:
model_scores = json.load(f)
# Otherwise, train the models
else:
model_scores = train_func(args, data, logger)
for metric, scores in model_scores.items():
all_scores[metric].append(scores)
all_scores = dict(all_scores)
# Convert scores to numpy arrays
for metric, scores in all_scores.items():
all_scores[metric] = np.array(scores)
# Report results
info(f'{args.num_folds}-fold cross validation')
# Report scores for each fold
contains_nan_scores = False
for fold_num in range(args.num_folds):
for metric, scores in all_scores.items():
info(f'\tSeed {init_seed + fold_num} ==> test {metric} = {multitask_mean(scores[fold_num], metric):.6f}')
if args.show_individual_scores:
for task_name, score in zip(args.task_names, scores[fold_num]):
info(f'\t\tSeed {init_seed + fold_num} ==> test {task_name} {metric} = {score:.6f}')
if np.isnan(score):
contains_nan_scores = True
# Report scores across folds
for metric, scores in all_scores.items():
avg_scores = multitask_mean(scores, axis=1, metric=metric) # average score for each model across tasks
mean_score, std_score = np.mean(avg_scores), np.std(avg_scores)
info(f'Overall test {metric} = {mean_score:.6f} +/- {std_score:.6f}')
if args.show_individual_scores:
for task_num, task_name in enumerate(args.task_names):
info(f'\tOverall test {task_name} {metric} = '
f'{np.mean(scores[:, task_num]):.6f} +/- {np.std(scores[:, task_num]):.6f}')
if contains_nan_scores:
info("The metric scores observed for some fold test splits contain 'nan' values. \
This can occur when the test set does not meet the requirements \
for a particular metric, such as having no valid instances of one \
task in the test set or not having positive examples for some classification metrics. \
Before v1.5.1, the default behavior was to ignore nan values in individual folds or tasks \
and still return an overall average for the remaining folds or tasks. The behavior now \
is to include them in the average, converting overall average metrics to 'nan' as well.")
# Save scores
with open(os.path.join(save_dir, TEST_SCORES_FILE_NAME), 'w') as f:
writer = csv.writer(f)
header = ['Task']
for metric in args.metrics:
header += [f'Mean {metric}', f'Standard deviation {metric}'] + \
[f'Fold {i} {metric}' for i in range(args.num_folds)]
writer.writerow(header)
if args.dataset_type == 'spectra': # spectra data type has only one score to report
row = ['spectra']
for metric, scores in all_scores.items():
task_scores = scores[:,0]
mean, std = np.mean(task_scores), np.std(task_scores)
row += [mean, std] + task_scores.tolist()
writer.writerow(row)
else: # all other data types, separate scores by task
for task_num, task_name in enumerate(args.task_names):
row = [task_name]
for metric, scores in all_scores.items():
task_scores = scores[:, task_num]
mean, std = np.mean(task_scores), np.std(task_scores)
row += [mean, std] + task_scores.tolist()
writer.writerow(row)
# Determine mean and std score of main metric
avg_scores = multitask_mean(all_scores[args.metric], metric=args.metric, axis=1)
mean_score, std_score = np.mean(avg_scores), np.std(avg_scores)
# Optionally merge and save test preds
if args.save_preds:
all_preds = pd.concat([pd.read_csv(os.path.join(save_dir, f'fold_{fold_num}', 'test_preds.csv'))
for fold_num in range(args.num_folds)])
all_preds.to_csv(os.path.join(save_dir, 'test_preds.csv'), index=False)
return mean_score, std_score