├── .gitignore ├── LICENSE ├── README.md ├── code ├── PMC-Patients_collection │ ├── PMC-Patients_collection │ │ ├── add_annotations.py │ │ ├── add_citation.py │ │ ├── annotate.py │ │ ├── extractor.py │ │ └── filters.py │ ├── PMC-Patients_stat │ │ ├── MeSH_humans.py │ │ ├── basic_stat.py │ │ ├── human_rel_stat.py │ │ ├── humans_stat.py │ │ └── relation_stat.py │ ├── PMC_OA_utils │ │ ├── Mesh_tree.py │ │ ├── PMC_OA_meta.py │ │ ├── extract_PMC_cites.py │ │ └── extract_PMC_keywords.py │ ├── README.md │ ├── pubmed_extractors │ │ ├── extract_cites.py │ │ ├── extract_mesh.py │ │ └── extract_title_abstract.py │ └── xml_utils.py └── downstream_task │ ├── README.md │ ├── baseline │ ├── PAR │ │ ├── BM25 │ │ │ ├── add_index.py │ │ │ └── query.py │ │ ├── Dense │ │ │ ├── dataloader.py │ │ │ ├── generate_embeddings.py │ │ │ ├── main.py │ │ │ ├── model.py │ │ │ └── sbert.py │ │ ├── NN │ │ │ └── NN.py │ │ ├── RRF │ │ │ └── RRF.py │ │ └── generate_human_eval.py │ └── PPR │ │ ├── BM25 │ │ ├── add_index.py │ │ ├── full_query.py │ │ └── query.py │ │ ├── Dense │ │ ├── dataloader.py │ │ ├── generate_embeddings.py │ │ ├── generate_full.py │ │ ├── main.py │ │ ├── model.py │ │ └── sbert.py │ │ ├── NN │ │ └── NN.py │ │ ├── RRF │ │ └── RRF.py │ │ └── generate_human_eval.py │ └── dataset_construction │ ├── PAR_stat.py │ ├── PPR_stat.py │ ├── consistency_with_human.py │ ├── dataset_split.py │ └── generate_PAR.py ├── datasets └── README.md └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhao-zy15/PMC-Patients/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhao-zy15/PMC-Patients/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: 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