├── .gitignore ├── LICENSE.txt ├── README.md ├── chat_templates ├── README.md ├── alpaca.jinja ├── amberchat.jinja ├── chatml.jinja ├── chatqa.jinja ├── falcon-instruct.jinja ├── gemma-it.jinja ├── llama-2-chat.jinja ├── llama-3-instruct.jinja ├── mistral-instruct.jinja ├── openchat-3.5.jinja ├── phi-3.jinja ├── saiga.jinja ├── solar-instruct.jinja ├── vicuna.jinja └── zephyr.jinja ├── images ├── dataset.png ├── logo.png └── model.png ├── poster.pdf ├── resource ├── CCSCM.csv ├── ICD10CM_to_CCSCM.csv ├── ICD9CM_to_CCSCM.csv └── hcup_ccs_2015_definitions.yaml ├── sample_data ├── qa_event_subset.jsonl └── qa_note_subset.jsonl ├── slides.pdf └── src ├── dataset ├── collator.py └── dataset.py ├── eval ├── eval.ipynb ├── query_gpt4.ipynb ├── query_llemr.ipynb └── summary_eval.ipynb ├── model ├── init_llemr.py ├── modeling_dummy.py ├── modeling_llemr.py └── utils.py ├── preprocess ├── 01_cohort_selection.ipynb ├── 02_event_hosp_diagnoses_icd.ipynb ├── 02_event_hosp_labevents.ipynb ├── 02_event_hosp_microbiologyevents.ipynb ├── 02_event_hosp_prescriptions.ipynb ├── 02_event_hosp_transfers.ipynb ├── 02_event_icu_chartevents.ipynb ├── 02_event_icu_inputevents.ipynb ├── 02_event_icu_outputevents.ipynb ├── 02_event_icu_procedureevents.ipynb ├── 02_event_static.ipynb ├── 03_merge_events.ipynb ├── 04_generate_qa_note.ipynb ├── 04_paraphrase_qa_event.ipynb ├── 04_template_qa_event.ipynb ├── 05_data_split.ipynb ├── 06_precompute_event_embeddings.py └── precompute_event_embeddings.sh ├── train ├── ds_zero2_no_offload.json ├── train.py └── train.sh └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zzachw/llemr/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zzachw/llemr/HEAD/LICENSE.txt 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