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Functions162 in github.com/clinicalml/TabLLM

⨍ Functions 162◇ Types & classes 23
↓ 14 callersMethodapply
(self, example)
t-few/src/data/dataset_readers.py:645
↓ 11 callersMethod__init__
(self, config)
t-few/src/data/dataset_readers.py:497
↓ 11 callersMethodsubstitute
(self, mapping, **kwargs)
helper/note_template.py:33
↓ 11 callersFunctiontrain_validation_test_split
(data)
create_external_datasets.py:230
↓ 9 callersMethodread_orig_dataset
Read the original dataset :param split: split of data
t-few/src/data/dataset_readers.py:694
↓ 7 callersMethodclean_note
(note)
helper/note_generator.py:761
↓ 6 callersMethodgenerate_notes_n_important_concepts
(self, **kwargs)
helper/note_generator.py:312
↓ 5 callersFunctionbyte_to_string_columns
(data)
create_external_datasets.py:236
↓ 4 callersFunctioncreate_collate_fn
(pad_token_id, pretrain)
t-few/src/data/data_module.py:184
↓ 4 callersMethodselect_first_concept_occurrence
(concepts, visits)
helper/note_generator.py:677
↓ 4 callersMethodset_absolute_weights
(abs_weight, concepts=None, visits=None)
helper/note_generator.py:664
↓ 3 callersMethod__init__
(self, config, tokenizer, dataset_reader)
t-few/src/data/data_module.py:9
↓ 3 callersMethodadd_temporal_value_to_visits
(visits, temporal, name)
helper/note_generator.py:656
↓ 3 callersFunctionnormalize_examples
(data)
create_external_datasets.py:406
↓ 3 callersMethodpermute_concept
(self, mapping, concept_id)
helper/note_generator.py:272
↓ 3 callersMethodsave_model
(self, finish=False)
t-few/src/models/EncoderDecoder.py:340
↓ 2 callersMethod_sample_few_shot_data
(self, orig_data)
t-few/src/data/dataset_readers.py:206
↓ 2 callersMethodcompute_metric
(self, accumulated)
t-few/src/data/dataset_readers.py:749
↓ 2 callersFunctioncreate_valid_test
(split)
evaluate_external_dataset.py:347
↓ 2 callersFunctionderange
(n)
create_external_datasets.py:96
↓ 2 callersMethodderive_name_pronoun_series
(gender)
helper/note_generator.py:638
↓ 2 callersFunctionencode_categorical
(data)
evaluate_external_dataset.py:326
↓ 2 callersMethodget_eval_template
(self)
t-few/src/data/dataset_readers.py:691
↓ 2 callersMethodget_template
(self, template_idx)
t-few/src/data/dataset_readers.py:145
↓ 2 callersMethodload_model
(self)
t-few/src/models/EncoderDecoder.py:332
↓ 2 callersFunctionload_train_validation_test
(dataset_name, data_dir)
create_external_datasets.py:228
↓ 2 callersFunctionlower_first_char_if_second_low
(s)
helper/note_generator.py:790
↓ 2 callersMethodpredict
Predict the lbl for particular pet :param batch: :param pet: :return:
t-few/src/models/EncoderDecoder.py:131
↓ 2 callersMethodread_few_shot_dataset
(self)
t-few/src/data/dataset_readers.py:183
↓ 2 callersFunctionread_shortened_concepts
(file_name)
helper/note_generator.py:794
↓ 2 callersFunctionremove_constants
(data)
create_external_datasets.py:389
↓ 2 callersFunctionstrip_string_columns
(df)
create_external_datasets.py:289
↓ 2 callersFunctionsubmit_req
(item, model, max_tries=300, sleep_sec=20, yes_no_probability=False)
query_gpt3.py:96
↓ 2 callersMethodvalidation_test_shared_preparation
(self, outputs, output_file)
t-few/src/models/EncoderDecoder.py:245
↓ 1 callersFunction_add_adjusted_col_offsets
Add adjusted column offsets to take into account multi-column cells.
helper/preprocess.py:5
↓ 1 callersFunction_get_heuristic_col_headers
Heuristic to find column headers.
helper/preprocess.py:30
↓ 1 callersFunction_get_heuristic_row_headers
Heuristic to find row headers.
helper/preprocess.py:21
↓ 1 callersFunctionadd_gpt3_zero_shot_predictions
(dataset, task, data_dir)
evaluate_external_dataset.py:427
↓ 1 callersFunctioncollect_exp_scores
(exp_name_template, datasets)
t-few/src/scripts/get_results_table.py:11
↓ 1 callersFunctioncollect_exp_scores
(exp_name_template, datasets)
t-few/src/scripts/get_result_table.py:11
↓ 1 callersFunctioncompute_metric
(clf_in, X, y)
evaluate_external_dataset.py:232
↓ 1 callersFunctionentry_to_text
(note)
create_external_datasets.py:196
↓ 1 callersFunctionevaluate_model
(seed, model, metric, parameters, X_train, y_train, X_valid, y_valid, X_test, y_test)
evaluate_external_dataset.py:211
↓ 1 callersMethodget_answer_choices_list
(self, example)
t-few/src/data/dataset_readers.py:673
↓ 1 callersFunctionget_light_gbm
()
evaluate_external_dataset.py:220
↓ 1 callersFunctionget_lr
()
evaluate_external_dataset.py:214
↓ 1 callersFunctionget_tabpfn
()
evaluate_external_dataset.py:228
↓ 1 callersMethodget_template
(self, template_idx)
t-few/src/data/dataset_readers.py:477
↓ 1 callersMethodget_train_template
(self)
t-few/src/data/dataset_readers.py:688
↓ 1 callersFunctionget_xgboost
()
evaluate_external_dataset.py:223
↓ 1 callersFunctionis_custom_task
(cfg)
t-few/src/data/dataset_readers.py:31
↓ 1 callersFunctionmain
()
create_external_datasets.py:47
↓ 1 callersFunctionmain
()
evaluate_external_dataset.py:25
↓ 1 callersFunctionmain
()
query_gpt3.py:155
↓ 1 callersFunctionmake_result_table
(args)
t-few/src/scripts/get_results_table.py:10
↓ 1 callersFunctionmake_result_table
(args)
t-few/src/scripts/get_result_table.py:10
↓ 1 callersFunctionoutput_linear_classifier_features
(examples, output_dir, dataset)
create_external_datasets.py:388
↓ 1 callersFunctionparse_args
()
create_external_datasets.py:511
↓ 1 callersFunctionparse_args
()
evaluate_external_dataset.py:452
↓ 1 callersFunctionparse_args
()
query_gpt3.py:34
↓ 1 callersMethodparse_data
Parse data into separate dataframes for visits, non-temporal and temporal dataframes.
helper/note_generator.py:685
↓ 1 callersFunctionparse_expname
(fname)
t-few/src/scripts/get_results_table.py:25
↓ 1 callersFunctionparse_expname
(fname)
t-few/src/scripts/get_result_table.py:25
↓ 1 callersFunctionpost_request
(example, model, yes_no_probability=False)
query_gpt3.py:50
↓ 1 callersFunctionpr_auc_score
(labels, probabilities)
t-few/src/data/dataset_readers.py:337
↓ 1 callersFunctionprepare_data
(dataset_name, model_name, dataset, enc=None, scale=True)
evaluate_external_dataset.py:300
↓ 1 callersFunctionpreprocess
(example)
helper/preprocess.py:4
↓ 1 callersFunctionread_dataset
(task, input_file)
query_gpt3.py:122
↓ 1 callersFunctionread_last_eval
(fname)
t-few/src/scripts/get_results_table.py:18
↓ 1 callersFunctionread_last_eval
(fname)
t-few/src/scripts/get_result_table.py:18
↓ 1 callersFunctionread_orig_dataset
(orig_data, seed, split)
evaluate_external_dataset.py:367
↓ 1 callersMethodread_orig_dataset
Read the original dataset :param split: split of data
t-few/src/data/dataset_readers.py:168
↓ 1 callersFunctionremove_columns
(data_dict, columns)
evaluate_external_dataset.py:301
↓ 1 callersFunctionremove_constants
(data)
evaluate_external_dataset.py:304
↓ 1 callersFunctionreplace_age_nans
(data)
evaluate_external_dataset.py:312
↓ 1 callersFunctionresult_str
(acc_list)
t-few/src/scripts/get_results_table.py:34
↓ 1 callersFunctionresult_str
(acc_list)
t-few/src/scripts/get_result_table.py:34
↓ 1 callersFunctionsample_few_shot_data
(orig_data, num_shot, few_shot_random_seed)
evaluate_external_dataset.py:384
↓ 1 callersFunctionshuffle_dataset
(dataset)
create_external_datasets.py:103
↓ 1 callersFunctiontable_to_text
(note)
create_external_datasets.py:179
↓ 1 callersFunctionunpack_example
(example, task)
query_gpt3.py:46
↓ 1 callersFunctionwrite_into_table
(name, value)
create_external_datasets.py:170
Method__getitem__
(self, key)
t-few/src/data/data_module.py:85
Method__getitem__
(self, key)
t-few/src/data/data_module.py:165
Method__init__
(self, template, prefixes=None, suffixes=None, defaults=None, pre=None, post=None, fns=None)
helper/note_template.py:7
Method__init__
Parse data of a OMOP cohort into class structures.
helper/note_generator.py:101
Method__init__
(self, dataset, templates, tokenizer, add_special_tokens=True)
t-few/src/data/data_module.py:75
Method__init__
(self, config, tokenizer, dataset_reader)
t-few/src/data/data_module.py:127
Method__init__
(self, dataset, templates, tokenizer)
t-few/src/data/data_module.py:156
Method__init__
:param config:
t-few/src/data/dataset_readers.py:134
Method__init__
(self, config)
t-few/src/data/dataset_readers.py:222
Method__init__
(self, config)
t-few/src/data/dataset_readers.py:343
Method__init__
(self, config)
t-few/src/data/dataset_readers.py:366
Method__init__
(self, config)
t-few/src/data/dataset_readers.py:379
Method__init__
(self, config)
t-few/src/data/dataset_readers.py:392
Method__init__
(self, config)
t-few/src/data/dataset_readers.py:405
Method__init__
(self, config)
t-few/src/data/dataset_readers.py:410
Method__init__
(self, config)
t-few/src/data/dataset_readers.py:415
Method__init__
(self, config)
t-few/src/data/dataset_readers.py:469
Method__init__
(self, config)
t-few/src/data/dataset_readers.py:474
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