ATOM Data-Driven Modeling Pipeline
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ATOM Data-Driven Modeling Pipeline
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A
accumulate() (pipeline.perf_data.EpochManager method)
accumulate_preds() (pipeline.perf_data.ClassificationPerfData method)
(pipeline.perf_data.HybridPerfData method)
(pipeline.perf_data.KFoldClassificationPerfData method)
(pipeline.perf_data.KFoldRegressionPerfData method)
(pipeline.perf_data.PerfData method)
(pipeline.perf_data.RegressionPerfData method)
(pipeline.perf_data.SimpleClassificationPerfData method)
(pipeline.perf_data.SimpleHybridPerfData method)
(pipeline.perf_data.SimpleRegressionPerfData method)
add_classification_column() (in module utils.curate_data)
aggregate_assay_data() (in module utils.curate_data)
atom_curation() (in module utils.data_curation_functions)
atom_curation_excape() (in module utils.data_curation_functions)
average_and_remove_duplicates() (in module utils.curate_data)
B
base_feature_importance() (in module pipeline.feature_importance)
base_mol_from_inchi() (in module utils.struct_utils)
base_mol_from_smiles() (in module utils.struct_utils)
base_smiles_from_inchi() (in module utils.struct_utils)
base_smiles_from_smiles() (in module utils.struct_utils)
build_dataset_name() (in module pipeline.model_pipeline)
build_tarball_name() (in module pipeline.model_pipeline)
C
calc_AD_kmean_dist() (in module pipeline.model_pipeline)
calc_AD_kmean_local_density() (in module pipeline.model_pipeline)
calc_dist_diskdataset() (in module pipeline.chem_diversity)
calc_dist_feat_array() (in module pipeline.chem_diversity)
calc_dist_smiles() (in module pipeline.chem_diversity)
calc_summary() (in module pipeline.chem_diversity)
calc_train_dset_pair_dis() (pipeline.model_pipeline.ModelPipeline method)
canonical_tautomers_from_smiles() (in module utils.struct_utils)
check_version_compatible() (in module utils.model_version_utils)
ClassificationPerfData (class in pipeline.perf_data)
cluster_permutation_importance() (in module pipeline.feature_importance)
compute() (pipeline.perf_data.EpochManager method)
(pipeline.perf_data.EpochManagerKFold method)
compute_negative_log_responses() (in module utils.data_curation_functions)
compute_perf_metrics() (pipeline.perf_data.HybridPerfData method)
(pipeline.perf_data.KFoldClassificationPerfData method)
(pipeline.perf_data.KFoldRegressionPerfData method)
(pipeline.perf_data.PerfData method)
(pipeline.perf_data.RegressionPerfData method)
(pipeline.perf_data.SimpleClassificationPerfData method)
(pipeline.perf_data.SimpleHybridPerfData method)
(pipeline.perf_data.SimpleRegressionPerfData method)
convert_IC50_to_pIC50() (in module utils.data_curation_functions)
convert_metadata() (in module pipeline.model_tracker)
copy_best_filesystem_models() (in module pipeline.compare_models)
create_model_metadata() (pipeline.model_pipeline.ModelPipeline method)
create_new_rows_for_extra_results() (in module utils.curate_data)
create_perf_data() (in module pipeline.perf_data)
create_prediction_metadata() (pipeline.model_pipeline.ModelPipeline method)
create_prediction_pipeline() (in module pipeline.model_pipeline)
create_prediction_pipeline_from_file() (in module pipeline.model_pipeline)
D
DatastoreInsertionException
del_ignored_params() (in module pipeline.compare_models)
display_feature_clusters() (in module pipeline.feature_importance)
dist_hist_plot() (utils.compare_splits_plots.SplitStats method)
dist_hist_train_v_test_plot() (utils.compare_splits_plots.SplitStats method)
dist_hist_train_v_valid_plot() (utils.compare_splits_plots.SplitStats method)
diversity_plots() (in module pipeline.diversity_plots)
down_select() (in module utils.data_curation_functions)
download_activitytype() (in module utils.pubchem_utils)
download_bioactivity_assay() (in module utils.pubchem_utils)
download_dose_response_from_bioactivity() (in module utils.pubchem_utils)
download_SID_from_bioactivity_assay() (in module utils.pubchem_utils)
download_smiles() (in module utils.pubchem_utils)
draw_structure() (in module utils.struct_utils)
E
ensemble_predict() (in module pipeline.model_pipeline)
EpochManager (class in pipeline.perf_data)
EpochManagerKFold (class in pipeline.perf_data)
exclude_organometallics() (in module utils.data_curation_functions)
export_model() (in module pipeline.model_tracker)
extract_collection_perf_metrics() (in module pipeline.compare_models)
extract_datastore_model_tarball() (in module pipeline.model_tracker)
extract_model_and_feature_parameters() (in module pipeline.compare_models)
F
filter_dtc_data() (in module utils.data_curation_functions)
filter_in_by_column_values() (in module utils.curate_data)
filter_in_out_by_column_values() (in module utils.curate_data)
filter_out_by_column_values() (in module utils.curate_data)
filter_out_comments() (in module utils.curate_data)
fix_moe_smiles() (in module utils.struct_utils)
freq_table() (in module utils.curate_data)
G
get_ampl_version() (in module utils.model_version_utils)
get_ampl_version_from_dir() (in module utils.model_version_utils)
get_ampl_version_from_json() (in module utils.model_version_utils)
get_ampl_version_from_model() (in module utils.model_version_utils)
get_best_models_info() (in module pipeline.compare_models)
get_best_perf_table() (in module pipeline.compare_models)
get_collection_datasets() (in module pipeline.compare_models)
get_dataset_key() (utils.model_file_reader.ModelFileReader method)
get_dataset_models() (in module pipeline.compare_models)
get_descriptor_type() (utils.model_file_reader.ModelFileReader method)
get_featurizer() (utils.model_file_reader.ModelFileReader method)
get_filesystem_models() (in module pipeline.compare_models)
get_filesystem_perf_results() (in module pipeline.compare_models)
get_full_metadata() (in module pipeline.model_tracker)
get_full_metadata_by_uuid() (in module pipeline.model_tracker)
get_id_col() (utils.model_file_reader.ModelFileReader method)
get_major_version() (in module utils.model_version_utils)
get_metadata_by_uuid() (in module pipeline.model_tracker)
get_metrics() (pipeline.model_pipeline.ModelPipeline method)
get_model_collection_by_uuid() (in module pipeline.model_tracker)
get_model_info() (utils.model_file_reader.ModelFileReader method)
get_model_parameters() (utils.model_file_reader.ModelFileReader method)
get_model_training_data_by_uuid() (in module pipeline.model_tracker)
get_model_type() (utils.model_file_reader.ModelFileReader method)
get_model_uuid() (utils.model_file_reader.ModelFileReader method)
get_multiple_models_metadata() (in module utils.model_file_reader)
get_multitask_perf_from_files() (in module pipeline.compare_models)
get_multitask_perf_from_files_new() (in module pipeline.compare_models)
get_multitask_perf_from_tracker() (in module pipeline.compare_models)
get_pred_values() (pipeline.perf_data.ClassificationPerfData method)
(pipeline.perf_data.HybridPerfData method)
(pipeline.perf_data.KFoldClassificationPerfData method)
(pipeline.perf_data.KFoldRegressionPerfData method)
(pipeline.perf_data.PerfData method)
(pipeline.perf_data.RegressionPerfData method)
(pipeline.perf_data.SimpleClassificationPerfData method)
(pipeline.perf_data.SimpleHybridPerfData method)
(pipeline.perf_data.SimpleRegressionPerfData method)
get_prediction_results() (pipeline.perf_data.ClassificationPerfData method)
(pipeline.perf_data.HybridPerfData method)
(pipeline.perf_data.PerfData method)
(pipeline.perf_data.RegressionPerfData method)
get_rdkit_smiles() (in module utils.struct_utils)
get_rdkit_smiles_parent() (in module utils.curate_data)
get_real_values() (pipeline.perf_data.KFoldClassificationPerfData method)
(pipeline.perf_data.KFoldRegressionPerfData method)
(pipeline.perf_data.PerfData method)
(pipeline.perf_data.SimpleClassificationPerfData method)
(pipeline.perf_data.SimpleHybridPerfData method)
(pipeline.perf_data.SimpleRegressionPerfData method)
get_response_cols() (utils.model_file_reader.ModelFileReader method)
get_score_types() (in module pipeline.hyper_perf_plots)
get_smiles_4dtc_data() (in module utils.data_curation_functions)
get_smiles_col() (utils.model_file_reader.ModelFileReader method)
get_smiles_dtc_data() (in module utils.data_curation_functions)
get_smiles_excape_data() (in module utils.data_curation_functions)
get_split_csv() (utils.model_file_reader.ModelFileReader method)
get_split_labeled_dataset() (in module utils.split_response_dist_plots)
get_split_strategy() (utils.model_file_reader.ModelFileReader method)
get_split_uuid() (utils.model_file_reader.ModelFileReader method)
get_splitter() (utils.model_file_reader.ModelFileReader method)
get_splitting_parameters() (utils.model_file_reader.ModelFileReader method)
get_summary_metadata_table() (in module pipeline.compare_models)
get_summary_perf_tables() (in module pipeline.compare_models)
get_tarball_perf_table() (in module pipeline.compare_models)
get_training_dataset() (utils.model_file_reader.ModelFileReader method)
get_training_datasets() (in module pipeline.compare_models)
get_training_perf_table() (in module pipeline.compare_models)
get_version() (utils.model_file_reader.ModelFileReader method)
get_weights() (pipeline.perf_data.KFoldClassificationPerfData method)
(pipeline.perf_data.KFoldRegressionPerfData method)
(pipeline.perf_data.PerfData method)
(pipeline.perf_data.SimpleClassificationPerfData method)
(pipeline.perf_data.SimpleHybridPerfData method)
(pipeline.perf_data.SimpleRegressionPerfData method)
H
has_nans() (in module utils.many_to_one)
HybridPerfData (class in pipeline.perf_data)
I
ic50topic50() (in module utils.data_curation_functions)
is_organometallic() (in module utils.data_curation_functions)
K
kekulize_smiles() (in module utils.struct_utils)
KFoldClassificationPerfData (class in pipeline.perf_data)
KFoldRegressionPerfData (class in pipeline.perf_data)
L
labeled_freq_table() (in module utils.curate_data)
load_featurize_data() (pipeline.model_pipeline.ModelPipeline method)
load_from_tracker() (in module pipeline.model_pipeline)
M
main() (in module pipeline.model_pipeline)
(in module utils.model_file_reader)
(in module utils.model_retrain)
(in module utils.model_version_utils)
make_all_plots() (utils.compare_splits_plots.SplitStats method)
many_to_one() (in module utils.many_to_one)
many_to_one_df() (in module utils.many_to_one)
ManyToOneException
mcs() (in module pipeline.dist_metrics)
mle_censored_mean() (in module utils.curate_data)
MLMTClientInstantiationException
model_choice_score() (pipeline.perf_data.ClassificationPerfData method)
(pipeline.perf_data.HybridPerfData method)
(pipeline.perf_data.RegressionPerfData method)
ModelFileReader (class in utils.model_file_reader)
ModelPipeline (class in pipeline.model_pipeline)
module
pipeline
pipeline.chem_diversity
pipeline.compare_models
pipeline.dist_metrics
pipeline.diversity_plots
pipeline.feature_importance
pipeline.hyper_perf_plots
pipeline.model_pipeline
pipeline.model_tracker
pipeline.perf_data
pipeline.perf_plots
pipeline.predict_from_model
utils
utils.compare_splits_plots
utils.curate_data
utils.data_curation_functions
utils.many_to_one
utils.model_file_reader
utils.model_retrain
utils.model_version_utils
utils.pubchem_utils
utils.split_response_dist_plots
utils.struct_utils
mol_wt_from_smiles() (in module utils.struct_utils)
mols_from_smiles() (in module utils.struct_utils)
N
NANCompoundIDException
NANSMILESException
negative_predictive_value() (in module pipeline.perf_data)
no_nan_ids_or_smiles() (in module utils.many_to_one)
num_trainable_parameters_from_file() (in module pipeline.compare_models)
O
on_new_best_valid() (pipeline.perf_data.EpochManager method)
P
parse_args() (in module utils.compare_splits_plots)
PerfData (class in pipeline.perf_data)
permutation_feature_importance() (in module pipeline.feature_importance)
pipeline
module
pipeline.chem_diversity
module
pipeline.compare_models
module
pipeline.dist_metrics
module
pipeline.diversity_plots
module
pipeline.feature_importance
module
pipeline.hyper_perf_plots
module
pipeline.model_pipeline
module
pipeline.model_tracker
module
pipeline.perf_data
module
pipeline.perf_plots
module
pipeline.predict_from_model
module
plot_dataset_dist_distr() (in module pipeline.diversity_plots)
plot_feature_importances() (in module pipeline.feature_importance)
plot_nn_perf() (in module pipeline.hyper_perf_plots)
plot_perf_vs_epoch() (in module pipeline.perf_plots)
plot_prec_recall_curve() (in module pipeline.perf_plots)
plot_pred_vs_actual() (in module pipeline.perf_plots)
plot_pred_vs_actual_from_df() (in module pipeline.perf_plots)
plot_pred_vs_actual_from_file() (in module pipeline.perf_plots)
plot_rf_nn_xg_perf() (in module pipeline.hyper_perf_plots)
plot_rf_perf() (in module pipeline.hyper_perf_plots)
plot_ROC_curve() (in module pipeline.perf_plots)
plot_split_perf() (in module pipeline.hyper_perf_plots)
plot_split_subset_response_distrs() (in module utils.split_response_dist_plots)
plot_tani_dist_distr() (in module pipeline.diversity_plots)
plot_train_valid_test_scores() (in module pipeline.hyper_perf_plots)
plot_umap_feature_projections() (in module pipeline.perf_plots)
plot_umap_train_set_neighbors() (in module pipeline.perf_plots)
plot_xg_perf() (in module pipeline.hyper_perf_plots)
predict_embedding() (pipeline.model_pipeline.ModelPipeline method)
predict_from_model_file() (in module pipeline.predict_from_model)
predict_from_tracker_model() (in module pipeline.predict_from_model)
predict_full_dataset() (pipeline.model_pipeline.ModelPipeline method)
predict_on_dataframe() (pipeline.model_pipeline.ModelPipeline method)
predict_on_smiles() (pipeline.model_pipeline.ModelPipeline method)
print_stats() (utils.compare_splits_plots.SplitStats method)
R
rdkit_smiles_from_smiles() (in module utils.struct_utils)
regenerate_results() (in module pipeline.model_pipeline)
RegressionPerfData (class in pipeline.perf_data)
remove_outlier_replicates() (in module utils.curate_data)
replicate_rmsd() (in module utils.curate_data)
retrain_model() (in module pipeline.model_pipeline)
rms_error() (in module pipeline.perf_data)
run_models() (in module pipeline.model_pipeline)
run_predictions() (pipeline.model_pipeline.ModelPipeline method)
S
save_figure() (in module utils.compare_splits_plots)
save_metrics() (pipeline.model_pipeline.ModelPipeline method)
save_model() (in module pipeline.model_tracker)
save_model_metadata() (pipeline.model_pipeline.ModelPipeline method)
save_model_tarball() (in module pipeline.model_tracker)
set_data_root() (in module utils.data_curation_functions)
set_group_permissions() (in module utils.curate_data)
set_make_pred() (pipeline.perf_data.EpochManager method)
should_stop() (pipeline.perf_data.EpochManager method)
SimpleClassificationPerfData (class in pipeline.perf_data)
SimpleHybridPerfData (class in pipeline.perf_data)
SimpleRegressionPerfData (class in pipeline.perf_data)
smiles_to_inchi_key() (in module utils.struct_utils)
split() (in module utils.compare_splits_plots)
split_dataset() (pipeline.model_pipeline.ModelPipeline method)
SplitStats (class in utils.compare_splits_plots)
standardize_relations() (in module utils.data_curation_functions)
subset_frac_plot() (utils.compare_splits_plots.SplitStats method)
summarize_data() (in module utils.curate_data)
T
tanimoto() (in module pipeline.dist_metrics)
tanimoto_single() (in module pipeline.dist_metrics)
train_model() (in module utils.model_retrain)
(pipeline.model_pipeline.ModelPipeline method)
train_model_from_tar() (in module utils.model_retrain)
train_model_from_tracker() (in module utils.model_retrain)
train_models_from_dataset_keys() (in module utils.model_retrain)
U
umap_plot() (utils.compare_splits_plots.SplitStats method)
update() (pipeline.perf_data.EpochManager method)
update_epoch() (pipeline.perf_data.EpochManager method)
update_valid() (pipeline.perf_data.EpochManager method)
upload_df_dtc_base_smiles_all() (in module utils.data_curation_functions)
upload_df_dtc_mleqonly() (in module utils.data_curation_functions)
upload_df_dtc_mleqonly_class() (in module utils.data_curation_functions)
upload_df_dtc_smiles() (in module utils.data_curation_functions)
upload_df_dtc_smiles_regr_all_class() (in module utils.data_curation_functions)
upload_df_excape_mleqonly() (in module utils.data_curation_functions)
upload_df_excape_mleqonly_class() (in module utils.data_curation_functions)
upload_df_excape_smiles() (in module utils.data_curation_functions)
upload_distmatrix_to_DS() (in module pipeline.chem_diversity)
upload_file_dtc_raw_data() (in module utils.data_curation_functions)
upload_file_dtc_smiles_regr_all() (in module utils.data_curation_functions)
upload_file_excape_raw_data() (in module utils.data_curation_functions)
utils
module
utils.compare_splits_plots
module
utils.curate_data
module
utils.data_curation_functions
module
utils.many_to_one
module
utils.model_file_reader
module
utils.model_retrain
module
utils.model_version_utils
module
utils.pubchem_utils
module
utils.split_response_dist_plots
module
utils.struct_utils
module
V
validate_version() (in module utils.model_version_utils)
X
xc50topxc50_for_nm() (in module utils.curate_data)
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