atomsciΒΆ
- pipeline package
- Submodules
- pipeline.chem_diversity module
- pipeline.compare_models module
copy_best_filesystem_models()
del_ignored_params()
extract_collection_perf_metrics()
extract_model_and_feature_parameters()
get_best_models_info()
get_best_perf_table()
get_collection_datasets()
get_dataset_models()
get_filesystem_models()
get_filesystem_perf_results()
get_multitask_perf_from_files()
get_multitask_perf_from_files_new()
get_multitask_perf_from_tracker()
get_summary_metadata_table()
get_summary_perf_tables()
get_tarball_perf_table()
get_training_datasets()
get_training_perf_table()
num_trainable_parameters_from_file()
- pipeline.dist_metrics module
- pipeline.diversity_plots module
- pipeline.feature_importance module
- pipeline.hyper_perf_plots module
- pipeline.model_pipeline module
ModelPipeline
ModelPipeline.calc_train_dset_pair_dis()
ModelPipeline.create_model_metadata()
ModelPipeline.create_prediction_metadata()
ModelPipeline.get_metrics()
ModelPipeline.load_featurize_data()
ModelPipeline.predict_embedding()
ModelPipeline.predict_full_dataset()
ModelPipeline.predict_on_dataframe()
ModelPipeline.predict_on_smiles()
ModelPipeline.run_predictions()
ModelPipeline.save_metrics()
ModelPipeline.save_model_metadata()
ModelPipeline.split_dataset()
ModelPipeline.train_model()
build_dataset_name()
build_tarball_name()
calc_AD_kmean_dist()
calc_AD_kmean_local_density()
create_prediction_pipeline()
create_prediction_pipeline_from_file()
ensemble_predict()
load_from_tracker()
main()
regenerate_results()
retrain_model()
run_models()
- pipeline.model_tracker module
- pipeline.parameter_parser module
AutoArgumentAdder
all_auto_arguments()
all_auto_float_lists()
all_auto_int_lists()
all_auto_lists()
dict_to_list()
extract_featurizer_params()
extract_model_params()
flatten_dict()
get_parser()
is_list()
is_list_float()
is_list_int()
is_primative_type()
list_defaults()
main()
make_dataset_key_absolute()
parse_command_line()
parse_config_file()
parse_namespace()
postprocess_args()
primative_type_only()
prune_defaults()
remove_unrecognized_arguments()
strip_optional()
to_str()
wrapper()
- pipeline.perf_data module
- pipeline.perf_plots module
- pipeline.predict_from_model module
- Module contents
- utils package
- Submodules
- utils.compare_splits_plots module
- utils.curate_data module
add_classification_column()
aggregate_assay_data()
average_and_remove_duplicates()
create_new_rows_for_extra_results()
filter_in_by_column_values()
filter_in_out_by_column_values()
filter_out_by_column_values()
filter_out_comments()
freq_table()
get_rdkit_smiles_parent()
labeled_freq_table()
mle_censored_mean()
remove_outlier_replicates()
replicate_rmsd()
set_group_permissions()
summarize_data()
xc50topxc50_for_nm()
- utils.data_curation_functions module
atom_curation()
atom_curation_excape()
compute_negative_log_responses()
convert_IC50_to_pIC50()
down_select()
exclude_organometallics()
filter_dtc_data()
get_smiles_4dtc_data()
get_smiles_dtc_data()
get_smiles_excape_data()
ic50topic50()
is_organometallic()
set_data_root()
standardize_relations()
upload_df_dtc_base_smiles_all()
upload_df_dtc_mleqonly()
upload_df_dtc_mleqonly_class()
upload_df_dtc_smiles()
upload_df_dtc_smiles_regr_all_class()
upload_df_excape_mleqonly()
upload_df_excape_mleqonly_class()
upload_df_excape_smiles()
upload_file_dtc_raw_data()
upload_file_dtc_smiles_regr_all()
upload_file_excape_raw_data()
- utils.datastore_functions module
bulk_export_kv_for_files()
bulk_update_kv()
check_key_val()
config_client()
copy_datasets_to_bucket()
dataset_key_exists()
filter_datasets_interactive()
get_key_val()
get_keyval()
initialize_model_tracker()
key_exists()
list_key_values()
repeat_defined_search()
retrieve_bucket_names()
retrieve_columns_from_dataset()
retrieve_dataset_by_dataset_oid()
retrieve_dataset_by_datasetkey()
retrieve_keys()
retrieve_values_for_key()
search_datasets_by_key_value()
search_files_interactive()
string_to_dict()
string_to_list()
summarize_datasets()
update_distribution_kv()
update_kv()
upload_df_to_DS()
upload_file_to_DS()
upload_pickle_to_DS()
- utils.hyperparam_search_wrapper module
GeometricSearch
GridSearch
HyperOptSearch
HyperparameterSearch
HyperparameterSearch.already_run()
HyperparameterSearch.assemble_layers()
HyperparameterSearch.build_jobs()
HyperparameterSearch.filter_jobs()
HyperparameterSearch.generate_assay_list()
HyperparameterSearch.generate_combo()
HyperparameterSearch.generate_combos()
HyperparameterSearch.generate_maestro_commands()
HyperparameterSearch.generate_param_combos()
HyperparameterSearch.generate_searches()
HyperparameterSearch.generate_split_shortlist()
HyperparameterSearch.generate_split_shortlist_file()
HyperparameterSearch.get_dataset_metadata()
HyperparameterSearch.get_shortlist_df()
HyperparameterSearch.return_split_uuid()
HyperparameterSearch.return_split_uuid_file()
HyperparameterSearch.run_search()
HyperparameterSearch.split_and_save_dataset()
HyperparameterSearch.submit_jobs()
RandomSearch
UserSpecifiedSearch
build_hyperopt_search_domain()
build_search()
gen_maestro_command()
get_num_params()
main()
parse_params()
permutate_NNlayer_combo_params()
reformat_filter_dict()
run_cmd()
run_command()
- utils.many_to_one module
- utils.model_file_reader module
ModelFileReader
ModelFileReader.get_dataset_key()
ModelFileReader.get_descriptor_type()
ModelFileReader.get_featurizer()
ModelFileReader.get_id_col()
ModelFileReader.get_model_info()
ModelFileReader.get_model_parameters()
ModelFileReader.get_model_type()
ModelFileReader.get_model_uuid()
ModelFileReader.get_response_cols()
ModelFileReader.get_smiles_col()
ModelFileReader.get_split_csv()
ModelFileReader.get_split_strategy()
ModelFileReader.get_split_uuid()
ModelFileReader.get_splitter()
ModelFileReader.get_splitting_parameters()
ModelFileReader.get_training_dataset()
ModelFileReader.get_version()
get_multiple_models_metadata()
main()
- utils.model_retrain module
- utils.model_version_utils module
- utils.pubchem_utils module
- utils.rdkit_easy module
- utils.split_response_dist_plots module
- utils.struct_utils module
- Module contents