Add contribute md #20
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pat-jj
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Nov 15, 2022
pat-jj
approved these changes
Nov 15, 2022
ycq091044
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Nov 16, 2022
* unify sample api * basemodel tmp commit * rnn tmp commit * cnn tmp commit * retain tmp commit * transformer tmp commit * micron tmp commit * add ddi to atc * update ccs code names * use gamenet ddi calculation (bottom-40) * gamenet tmp commit * update gamenet * tmp safedrug commit * tmp classicml, utils, tokenizer * prepare to merge * wrap up models * update doc in data.py * update medcode * update data.py docstring * split source and target kwargs for map * add doc for medcode * minor change in data.py * update datasets * fix example in data.py * move hash_str to datasets.utils * rename models/dev to models/test * update metrics * clean up trainer * fix logging bug * clean up general dl models * clean up drug rec models * switch to double quotation * fixed warning in safedrug * unify docstring * clean up tasks; need to further explain usage * move collate_fn_dict to datasets * DLTrainer -> Trainer * add urgent todo in splitter.py * logging.info -> logging.debug * exclude: visits without condition, procedure, or drug code * only show the distribution for top-10 tokens * use pr_auc_samples as default metrics for multilabel * update examples * update doc * update readme * update doc * auto print dataset.stat() * stat bug fixed for empty list * add examples in fn: is_homo_list and list_nested_level * more comments added in base_dataset.py * wrap sum() into fn flatten_list * new tutorials, sampledatasets (#21) * move collate_fn_dict to datasets * advanced tutorial: define your own healthcare task * move 'parse_tables' to BaseDataset * create patients inside of _parse_basi_info * add advanced turorial 2: Fit your dataset into our pipeline * add advanced tutorial 3; add SampleDataset * minor bug * update following comments * remove optional for samples in SampleDataset * remove get_label_distribution * remove start argument in sum * add inference func to trainer * minor change to index Co-authored-by: zzachw <[email protected]> * Add contribute md (#20) * Create CONTRIBUTING.md * update contribute.md * update contribute.md Co-authored-by: rkalahasty <[email protected]> * update leaderboard * Fix leaderboard and add advanced tutorial 4 (#23) * update leaderboard * fix index.rst * add requirements * build rtd * fix rtd requirements versions * rtd bug fix * add tutorial 4 * use self.__class__.__name__ as dataset_name * follow comment: add dataset_name back; add visit_id_to_patient_id to eicu Co-authored-by: Patrick Jiang <[email protected]> Co-authored-by: zzachw <[email protected]> Co-authored-by: Zhenbang Wu <[email protected]> Co-authored-by: rkalahasty <[email protected]> Co-authored-by: Patrick Jiang <[email protected]>
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