Index

A

add_age() (med.Model method) add_cols() (med.Mat method) add_data() (AlgoMarker.AlgoMarker method), [1] add_feature_generator() (med.Model method) add_feature_generator_to_set() (med.Model method) add_feature_generators() (med.Model method) add_feature_processor_to_set() (med.Model method) add_file() (med.Logger method) add_gender() (med.Model method) add_imputers() (med.Model method) add_normalizers() (med.Model method) add_pre_processors_json_string_to_model() (med.Model method) add_process_to_set() (med.Model method) add_rep_processor_to_set() (med.Model method) add_rows() (med.Mat method) AlgoMarker module

AlgoMarker (class in AlgoMarker) append() (med.Samples method) (med.SampleVectorAdaptor method) append_samples() (med.Features method) append_vec() (med.SampleVectorAdaptor method) apply() (med.Model method) apply_feature_processors() (med.Model method) asSerializable() (med.FeatureAttr method) (med.Features method) (med.IdSamples method) (med.Mat method) (med.Model method) (med.Predictor method) (med.Sample method) (med.SampleFilter method) (med.Samples method) attributes (med.Features property) avg (med.Mat property)

B

bias (ETL_Infra.unit_conversions.SuggestionResult attribute) big_files_fetcher() (in module data_fetcher.files_fetcher)

Bootstrap (class in med) bootstrap_cohort() (med.Bootstrap method)

C

calc_contribs() (med.Model method) calc_feature_contribs_conditional() (med.Model method) calculate() (AlgoMarker.AlgoMarker method), [1] clear() (med.Features method) (med.Mat method) (med.Model method) (med.PidRepository method) (med.Samples method) (med.Split method)

clear_data() (AlgoMarker.AlgoMarker method), [1] collect_and_add_virtual_signals() (med.Model method) CommonLib (class in med) create_index() (med.MedConvert method) create_rep() (med.MedConvert method) create_request_json() (AlgoMarker.AlgoMarker static method) create_train_signal() (in module ETL_Infra.etl_process) current_median (ETL_Infra.unit_conversions.SuggestionResult attribute)

D

data (med.Features property) data_fetcher.db_fetcher module data_fetcher.files_fetcher module date() (med.Sig method) days() (med.Sig method) DB_Access (class in data_fetcher) db_fetcher() (in module data_fetcher.db_fetcher) denorm_mean (med.FeatureAttr property) denorm_sdv (med.FeatureAttr property)

description (ETL_Infra.unit_conversions.SuggestionResult attribute) dict (med.PidRepository property) dict_name() (med.PidRepository method) dict_prep_sets_lookup_table() (med.PidRepository method) dict_section_id() (med.PidRepository method) Dictionary (class in med) dilute() (med.Samples method) discovery() (AlgoMarker.AlgoMarker method), [1] dispose() (AlgoMarker.AlgoMarker method), [1] distance (ETL_Infra.unit_conversions.SuggestionResult attribute) dprint_process() (med.Model method)

E

ETL_Infra.etl_process module ETL_Infra.unit_conversions module

expected_median (ETL_Infra.unit_conversions.SuggestionResult attribute) export_to_numpy() (med.PidRepository method) export_to_sample_vec() (med.Samples method)

F

factor (ETL_Infra.unit_conversions.SuggestionResult attribute) FeatureAttr (class in med) Features (class in med) features (med.Model property) features_count (med.Predictor property) files_fetcher() (in module data_fetcher.files_fetcher) filter() (med.Features method) (med.SampleFilter method) filter_rep_processors() (med.Model method)

find_best_unit_suggestion() (in module ETL_Infra.unit_conversions) find_best_unit_suggestion_to_group() (in module ETL_Infra.unit_conversions) finish_load_data() (med.PidRepository method) finish_prepare_load() (in module ETL_Infra.etl_process) fit_for_repository() (med.Model method) free() (med.PidRepository method) from_name() (med.SampleFilter static method) from_name_params() (med.SampleFilter static method) from_type() (med.SampleFilter static method) from_type_params() (med.SampleFilter static method)

G

generate_all_features() (med.Model method) generate_labs_mapping_and_units_config() (in module ETL_Infra.etl_process) get_all_features_names() (med.Model method) get_as_matrix() (med.Features method) get_attributes() (med.Samples method) get_categs() (med.Samples method) get_cohort_from_arg() (med.Bootstrap method) get_col() (med.Mat method) get_cols_avg_std() (med.Mat method) get_crc() (med.Features method) get_feature_names() (med.Features method) get_ids() (med.Samples method) get_lut_from_regex() (med.PidRepository method) get_max_serial_id_cnt() (med.Features method) get_members_to_all_sets() (med.Dictionary method) get_name() (AlgoMarker.AlgoMarker method)

get_numpy_copy() (med.Mat method) get_numpy_view_unsafe() (med.Mat method) get_pid_len() (med.Features method) get_pid_pos() (med.Features method) get_plotly_js() (in module plot_graph) get_predictions_size() (med.Samples method) get_preds() (med.Samples method) get_required_signal_names() (med.Model method) get_row() (med.Mat method) get_samples() (med.Features method) get_sig() (med.PidRepository method) get_str_attributes() (med.Samples method) get_sub_mat() (med.Mat method) get_sub_mat_by_flags() (med.Mat method) get_y() (med.Samples method) global_serial_id_cnt (med.Features property) group_size (ETL_Infra.unit_conversions.SuggestionResult attribute)

H

hours() (med.Sig method)

I

id (med.IdSamples property) (med.Sample property) id() (med.Dictionary method) IdSamples (class in med) idSamples (med.Samples property) import_from_sample_vec() (med.Samples method) imputed (med.FeatureAttr property) init() (med.PidRepository method) init_all_files() (med.Logger method) init_all_levels() (med.Logger method) init_all_samples() (med.Features method) init_file() (med.Logger method)

init_from_json_file() (med.Model method) init_from_json_file_with_alterations() (med.Model method) init_from_str() (med.Bootstrap method) init_level() (med.Logger method) init_load_params() (med.MedConvert method) init_out() (med.Logger method) init_pid_pos_len() (med.Features method) insert_preds() (med.Samples method) insert_samples() (med.Features method) insertRec() (med.Samples method) is_categorical() (med.PidRepository method) is_valid() (med.Mat method)

L

learn() (med.Model method) (med.Predictor method) learn_and_apply_feature_processors() (med.Model method) learn_feature_generators() (med.Model method) learn_feature_processors() (med.Model method) learn_rep_processors() (med.Model method) list_directory_files() (in module data_fetcher.files_fetcher) list_signals() (med.PidRepository method)

load() (med.Mat method) load_from_json() (med.PidRepository method) load_from_json_str() (med.PidRepository method) load_numpy() (med.Mat method) load_transposed() (med.Mat method) loadsig() (med.PidRepository method) loadsig_pids() (med.PidRepository method) Logger (class in med) logger_use_stdout() (in module med)

M

make_predictor() (med.Model method) (med.Predictor static method) map_and_fix_units() (in module ETL_Infra.etl_process) Mat (class in med) med module MedConvert (class in med) MEDPY__from_df() (med.Samples method) MEDPY__from_df_adaptor() (med.Samples method) MEDPY__to_df() (med.Samples method) MEDPY_GET_attributes() (med.Features method) MEDPY_GET_avg() (med.Mat method) MEDPY_GET_data() (med.Features method) MEDPY_GET_denorm_mean() (med.FeatureAttr method) MEDPY_GET_denorm_sdv() (med.FeatureAttr method) MEDPY_GET_features() (med.Model method) MEDPY_GET_features_count() (med.Predictor method) MEDPY_GET_global_serial_id_cnt() (med.Features static method) MEDPY_GET_id() (med.IdSamples method) (med.Sample method) MEDPY_GET_idSamples() (med.Samples method) MEDPY_GET_imputed() (med.FeatureAttr method) MEDPY_GET_missing_value() (med.Mat method) MEDPY_GET_model_features() (med.Predictor method) MEDPY_GET_nbootstrap() (med.Bootstrap method) MEDPY_GET_ncols() (med.Mat method) MEDPY_GET_Normalize_Cols() (med.Mat static method) MEDPY_GET_normalize_for_learn() (med.Predictor method) MEDPY_GET_normalize_for_predict() (med.Predictor method) MEDPY_GET_Normalize_Rows() (med.Mat static method) MEDPY_GET_normalize_y_for_learn() (med.Predictor method) MEDPY_GET_normalized() (med.FeatureAttr method) MEDPY_GET_normalized_flag() (med.Mat method) MEDPY_GET_nrows() (med.Mat method) MEDPY_GET_nsplits() (med.Split method) MEDPY_GET_outcome() (med.Sample method) MEDPY_GET_outcomeTime() (med.Sample method) MEDPY_GET_pid2split() (med.Split method) MEDPY_GET_pid_pos_len() (med.Features method) MEDPY_GET_pids() (med.PidRepository method) MEDPY_GET_prediction() (med.Sample method) MEDPY_GET_ROC_max_diff_working_point() (med.Bootstrap method) MEDPY_GET_ROC_score_bins() (med.Bootstrap method) MEDPY_GET_ROC_score_min_samples() (med.Bootstrap method) MEDPY_GET_ROC_score_resolution() (med.Bootstrap method) MEDPY_GET_ROC_use_score_working_points() (med.Bootstrap method) MEDPY_GET_ROC_working_point_FPR() (med.Bootstrap method) MEDPY_GET_ROC_working_point_PR() (med.Bootstrap method) MEDPY_GET_ROC_working_point_Score() (med.Bootstrap method) MEDPY_GET_ROC_working_point_SENS() (med.Bootstrap method) MEDPY_GET_ROC_working_point_TOPN() (med.Bootstrap method) MEDPY_GET_row_ids() (med.Mat method) MEDPY_GET_sample_per_pid() (med.Bootstrap method) MEDPY_GET_samples() (med.Features method) (med.IdSamples method) MEDPY_GET_signals() (med.Mat method) MEDPY_GET_split() (med.IdSamples method) (med.Sample method) MEDPY_GET_std() (med.Mat method) MEDPY_GET_tags() (med.Features method)

MEDPY_GET_time() (med.Sample method) MEDPY_GET_time_unit() (med.Features method) (med.Samples method) MEDPY_GET_transpose_for_learn() (med.Predictor method) MEDPY_GET_transpose_for_predict() (med.Predictor method) MEDPY_GET_transposed_flag() (med.Mat method) MEDPY_GET_verbosity() (med.Model method) MEDPY_GET_weights() (med.Features method) MEDPY_SET_denorm_mean() (med.FeatureAttr method) MEDPY_SET_denorm_sdv() (med.FeatureAttr method) MEDPY_SET_features_count() (med.Predictor method) MEDPY_SET_global_serial_id_cnt() (med.Features static method) MEDPY_SET_id() (med.IdSamples method) (med.Sample method) MEDPY_SET_imputed() (med.FeatureAttr method) MEDPY_SET_missing_value() (med.Mat method) MEDPY_SET_model_features() (med.Predictor method) MEDPY_SET_nbootstrap() (med.Bootstrap method) MEDPY_SET_normalize_for_learn() (med.Predictor method) MEDPY_SET_normalize_for_predict() (med.Predictor method) MEDPY_SET_normalize_y_for_learn() (med.Predictor method) MEDPY_SET_normalized() (med.FeatureAttr method) MEDPY_SET_normalized_flag() (med.Mat method) MEDPY_SET_outcome() (med.Sample method) MEDPY_SET_outcomeTime() (med.Sample method) MEDPY_SET_prediction() (med.Sample method) MEDPY_SET_ROC_max_diff_working_point() (med.Bootstrap method) MEDPY_SET_ROC_score_bins() (med.Bootstrap method) MEDPY_SET_ROC_score_min_samples() (med.Bootstrap method) MEDPY_SET_ROC_score_resolution() (med.Bootstrap method) MEDPY_SET_ROC_use_score_working_points() (med.Bootstrap method) MEDPY_SET_ROC_working_point_FPR() (med.Bootstrap method) MEDPY_SET_ROC_working_point_PR() (med.Bootstrap method) MEDPY_SET_ROC_working_point_Score() (med.Bootstrap method) MEDPY_SET_ROC_working_point_SENS() (med.Bootstrap method) MEDPY_SET_ROC_working_point_TOPN() (med.Bootstrap method) MEDPY_SET_row_ids() (med.Mat method) MEDPY_SET_sample_per_pid() (med.Bootstrap method) MEDPY_SET_split() (med.IdSamples method) (med.Sample method) MEDPY_SET_time() (med.Sample method) MEDPY_SET_time_unit() (med.Features method) (med.Samples method) MEDPY_SET_transpose_for_learn() (med.Predictor method) MEDPY_SET_transpose_for_predict() (med.Predictor method) MEDPY_SET_transposed_flag() (med.Mat method) MEDPY_SET_verbosity() (med.Model method) minutes() (med.Sig method) missing_value (med.Mat property) Model (class in med) model_features (med.Predictor property) ModelStage (class in med) module AlgoMarker data_fetcher.db_fetcher data_fetcher.files_fetcher ETL_Infra.etl_process ETL_Infra.unit_conversions med plot_graph months() (med.Sig method)

N

name() (med.Dictionary method) nbootstrap (med.Bootstrap property) ncols (med.Mat property) normalize() (med.Mat method) (med.Samples method) normalize_for_learn (med.Predictor property) normalize_for_predict (med.Predictor property)

normalize_y_for_learn (med.Predictor property) normalized (med.FeatureAttr property) normalized_flag (med.Mat property) nrows (med.Mat property) nSamples() (med.Samples method) nsplits (med.Split property) nSplits() (med.Samples method) (med.SampleVectorAdaptor method)

O

opposite_transformation (ETL_Infra.unit_conversions.SuggestionResult attribute) outcome (med.Sample property)

outcomeTime (med.Sample property) override_splits() (med.Samples method) (med.SampleVectorAdaptor method)

P

parse_cohort_file() (med.Bootstrap method) parse_cohort_line() (med.Bootstrap method) parse_from_string() (med.Sample method) pid2split (med.Split property) pid_pos_len (med.Features property) PidRepository (class in med) pids (med.PidRepository property) plot_graph module plot_graph() (in module plot_graph)

predict() (med.Predictor method) prediction (med.Sample property) Predictor (class in med) PredictorTypes (class in med) prep_sets_lookup_table() (med.Dictionary method) prepare_dicts() (in module ETL_Infra.etl_process) prepare_final_signals() (in module ETL_Infra.etl_process) print_() (med.Sample method) print_auc_performance() (med.CommonLib static method) print_csv() (med.Features method)

Q

quick_learn_rep_processors() (med.Model method)

R

read_all() (med.PidRepository method) read_all_i() (med.PidRepository method) read_from_bin_file() (med.Mat method) (med.Samples method) read_from_csv_file() (med.Mat method) read_from_csv_mat() (med.Features method) read_from_file() (med.Model method) (med.Samples method) (med.Split method) read_predictor_from_file() (med.CommonLib static method) resize() (med.Mat method)

ROC_max_diff_working_point (med.Bootstrap property) ROC_score_bins (med.Bootstrap property) ROC_score_min_samples (med.Bootstrap property) ROC_score_resolution (med.Bootstrap property) ROC_use_score_working_points (med.Bootstrap property) ROC_working_point_FPR (med.Bootstrap property) ROC_working_point_PR (med.Bootstrap property) ROC_working_point_Score (med.Bootstrap property) ROC_working_point_SENS (med.Bootstrap property) ROC_working_point_TOPN (med.Bootstrap property) row_ids (med.Mat property)

S

same_as() (med.IdSamples method) (med.Samples method) Sample (class in med) sample_per_pid (med.Bootstrap property) SampleFilter (class in med) Samples (class in med) samples (med.Features property) (med.IdSamples property) SampleVectorAdaptor (class in med) section_id() (med.Dictionary method) set_as_matrix() (med.Features method) set_predictor() (med.Model method) set_samples() (med.Samples method) set_signals() (med.Mat method) set_split() (med.IdSamples method) set_time_unit() (med.Features method)

set_val() (med.Mat method) shuffleMatrix() (med.CommonLib static method) Sig (class in med) sig_description() (med.PidRepository method) sig_id() (med.PidRepository method) sig_type() (med.PidRepository method) signals (med.Mat property) sort_by_id_date() (med.Samples method) Split (class in med) split (med.IdSamples property) (med.Sample property) split_by_fold() (med.Features method) split_train_test() (med.Samples method) std (med.Mat property) subtract() (med.Samples method) SuggestionResult (class in ETL_Infra.unit_conversions) switch_to_in_mem() (med.PidRepository method)

T

tags (med.Features property) target_unit (ETL_Infra.unit_conversions.SuggestionResult attribute) test() (med.Mat method) thisown (med.Bootstrap property) (med.CommonLib property) (med.Dictionary property) (med.FeatureAttr property) (med.Features property) (med.IdSamples property) (med.Logger property) (med.Mat property) (med.MedConvert property) (med.Model property) (med.ModelStage property) (med.PidRepository property) (med.Predictor property) (med.PredictorTypes property) (med.Sample property) (med.SampleFilter property) (med.Samples property) (med.SampleVectorAdaptor property) (med.Sig property) (med.Split property) (med.Time property)

Time (class in med) time (med.Sample property) time() (med.Sig method) time_unit (med.Features property) (med.Samples property) timeU() (med.Sig method) transpose() (med.Mat method) transpose_for_learn (med.Predictor property) transpose_for_predict (med.Predictor property) transposed_flag (med.Mat property) try_get_quantile() (in module ETL_Infra.unit_conversions)

U

uget() (med.PidRepository method)

V

val() (med.Sig method) verbosity (med.Model property)

version() (med.Features method) (med.Samples method)

W

weights (med.Features property) write_as_csv_mat() (med.Features method) write_feature_matrix() (med.Model method) write_predictor_to_file() (med.Predictor method) write_to_bin_file() (med.Mat method) (med.Samples method)

write_to_csv_file() (med.Mat method) write_to_file() (med.Model method) (med.Samples method) (med.Split method) write_to_string() (med.Sample method)

Y

years() (med.Sig method)

Z

zero() (med.Mat method)