MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
bioel/__init__.py
bioel/dataset.py
bioel/evaluate.py
bioel/linking_eval.py
bioel/logger.py
bioel/model.py
bioel/ontology.py
bioel.egg-info/PKG-INFO
bioel.egg-info/SOURCES.txt
bioel.egg-info/dependency_links.txt
bioel.egg-info/not-zip-safe
bioel.egg-info/requires.txt
bioel.egg-info/top_level.txt
bioel/models/__init__.py
bioel/models/arboel/__init__.py
bioel/models/arboel/Crossencoder/__init__.py
bioel/models/arboel/Crossencoder/crossencoder.py
bioel/models/arboel/Crossencoder/eeval_cluster_linking.py
bioel/models/arboel/Crossencoder/train_crossencoder_mst.py
bioel/models/arboel/Crossencoder/original/__init__.py
bioel/models/arboel/Crossencoder/original/crossencoder.py
bioel/models/arboel/Crossencoder/original/data_process.py
bioel/models/arboel/Crossencoder/original/evaluate_crossencoder.py
bioel/models/arboel/Crossencoder/original/my_train_cross.py
bioel/models/arboel/Crossencoder/original/train_cross.py
bioel/models/arboel/biencoder/__init__.py
bioel/models/arboel/biencoder/evaluate_biencoder.py
bioel/models/arboel/biencoder/train_biencoder.py
bioel/models/arboel/biencoder/data/BiEncoderLightningDataModule.py
bioel/models/arboel/biencoder/data/__init__.py
bioel/models/arboel/biencoder/data/data_process.py
bioel/models/arboel/biencoder/data/data_utils.py
bioel/models/arboel/biencoder/model/BiEncoderLightningModule.py
bioel/models/arboel/biencoder/model/__init__.py
bioel/models/arboel/biencoder/model/biencoder.py
bioel/models/arboel/biencoder/model/eval_biencoder.py
bioel/models/arboel/biencoder/model/eval_cluster_linking.py
bioel/models/arboel/biencoder/model/special_partition/special_partition.c
bioel/models/arboel/biencoder/model/special_partition/special_partition.pyx
bioel/models/arboel/crossencoder/__init__.py
bioel/models/arboel/crossencoder/evaluate_crossencoder.py
bioel/models/arboel/crossencoder/train_crossencoder.py
bioel/models/arboel/crossencoder/data/CrossEncoderLightningDataModule.py
bioel/models/arboel/crossencoder/data/__init__.py
bioel/models/arboel/crossencoder/data/top_cands.py
bioel/models/arboel/crossencoder/model/CrossEncoderLightningModule.py
bioel/models/arboel/crossencoder/model/__init__.py
bioel/models/arboel/crossencoder/model/crossencoder.py
bioel/models/biogenel/LightningDataModule.py
bioel/models/biogenel/LightningModule.py
bioel/models/biogenel/__init__.py
bioel/models/biogenel/data_processing.py
bioel/models/biogenel/eval_biogenel_biobart.py
bioel/models/biogenel/train_biogenel_biobart.py
bioel/models/biogenel/trainer.py
bioel/models/biogenel/utils.py
bioel/models/biogenel/fairseq_beam/__init__.py
bioel/models/biogenel/fairseq_beam/search.py
bioel/models/biogenel/fairseq_beam/sequence_generator.py
bioel/models/biogenel/fairseq_beam/sequence_scorer.py
bioel/models/biogenel/models/__init__.py
bioel/models/biogenel/models/bart_model.py
bioel/models/biogenel/models/beam_scorer.py
bioel/models/biogenel/models/prompt_bart.py
bioel/models/biogenel/models/prompt_t5.py
bioel/models/biogenel/trie/__init__.py
bioel/models/biogenel/trie/create_trie_and_target_kb.py
bioel/models/biogenel/trie/trie.py
bioel/models/krissbert/__init__.py
bioel/models/krissbert/evaluate.py
bioel/models/krissbert/train.py
bioel/models/krissbert/data/__init__.py
bioel/models/krissbert/data/utils.py
bioel/models/krissbert/model/__init__.py
bioel/models/krissbert/model/model.py
bioel/models/sapbert/__init__.py
bioel/models/sapbert/evaluate.py
bioel/models/sapbert/train.py
bioel/models/sapbert/utils.py
bioel/models/sapbert/data/__init__.py
bioel/models/sapbert/data/data_processing.py
bioel/models/sapbert/data/lightingDataModule.py
bioel/models/sapbert/data/utils.py
bioel/models/sapbert/model/__init__.py
bioel/models/sapbert/model/metric_learning.py
bioel/models/sapbert/model/model_wrapper.py
bioel/models/scispacy/__init__.py
bioel/models/scispacy/candidate_generation.py
bioel/models/scispacy/entity_linking.py
bioel/models/scispacy/evaluate.py
bioel/models/scispacy/model.py
bioel/models/scispacy/scispacy_embeddings.py
bioel/utils/__init__.py
bioel/utils/bigbio_utils.py
bioel/utils/dataset_consts.py
bioel/utils/file_cache.py
bioel/utils/obo_utils.py
bioel/utils/statistics.py
bioel/utils/umls_utils.py
tests/__init__.py
tests/test_model.py
tests/test_ontology.py
tests/test_scispacy.py