├── .gitignore ├── LICENSE ├── README.md ├── checkpoints └── model_log.txt ├── images ├── model.jpg ├── performance.png └── performance_new.png ├── input ├── abbreviation.dict └── number_mapping.txt ├── output ├── adr │ ├── candidates │ │ ├── test_candidates.txt │ │ └── training_aligned_cos_with_mention_candidate.txt │ ├── char_vocabulary.dict │ ├── context │ │ ├── test_mention_context.txt │ │ └── train_mention_context.txt │ ├── embed │ │ └── entity_emb_50.txt │ ├── entity_kb.txt │ ├── mention_entity_prior.txt │ ├── test_data.txt │ ├── train_data.txt │ └── word_vocabulary.dict └── ncbi │ ├── candidates │ ├── test_candidates.txt │ └── training_aligned_cos_with_mention_candidate.txt │ ├── char_vocabulary.dict │ ├── context │ ├── test_mention_context.txt │ └── train_mention_context.txt │ ├── embed │ └── entity_emb_50.txt │ ├── entity_kb.txt │ ├── mention_entity_prior.txt │ ├── test_data.txt │ ├── train_data.txt │ └── word_vocabulary.dict ├── requirements.txt └── source ├── binomial_interval.py ├── build_model.py ├── candidate_sample.py ├── char_model.py ├── data_utils.py ├── debug.py ├── embed.py ├── generate_candidate.py ├── layers.py ├── load_data.py ├── predict.py ├── preprocess_sample.py ├── train.py └── word2vec.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tigerchen52/Biomedical-Entity-Linking/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tigerchen52/Biomedical-Entity-Linking/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tigerchen52/Biomedical-Entity-Linking/HEAD/README.md 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