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ncbi-nlp /BioSentVec

Star590

BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences

natural-language-processing word-embeddings pubmed fasttext mimic-iii bionlp sentence-similarity sentence-embeddings sent2vec

UpdatedAug 15, 2023
Jupyter Notebook

ncbi-nlp /BLUE_Benchmark

Star291

BLUE benchmark consists of five different biomedicine text-mining tasks with ten corpora.

benchmark natural-language-understanding bionlp

UpdatedJan 12, 2022
Python

abachaa /Existing-Medical-QA-Datasets

Star278

Multimodal Question Answering in the Medical Domain: A summary of Existing Datasets and Systems

nlp qa computer-vision vqa question-answering datasets radiology medical-informatics bionlp medical-qa-datasets medical-qa consumer-health-questions

UpdatedOct 17, 2023

medmcqa /medmcqa

Star189

A large-scale (194k), Multiple-Choice Question Answering (MCQA) dataset designed to address realworld medical entrance exam questions.

nlp qa leaderboard dataset question-answering medical-informatics bionlp medical-dataset medical-datasets multiple-choice-question-answering medical-qa-datasets medical-qa medical-question-answering

UpdatedNov 28, 2022
Jupyter Notebook

cambridgeltl /sapbert

Star184

[NAACL'21 & ACL'21] SapBERT: Self-alignment pretraining for BERT & XL-BEL: Cross-Lingual Biomedical Entity Linking.

nlp machine-learning metric-learning representation-learning language-model bert bionlp lexical-semantics contrastive-learning naacl2021 acl2021

UpdatedApr 28, 2023
Python

gsarti /covid-papers-browser

Star182

Browse Covid-19 & SARS-CoV-2 Scientific Papers with Transformers 🦠 📖

search-engine natural-language-processing bionlp biobert scibert covid-19

UpdatedJun 22, 2022
CSS

jakelever /kindred

Star157

A Python biomedical relation extraction package that uses a supervised approach (i.e. needs training data).

python text-mining relation-extraction bionlp

UpdatedMar 12, 2023
Python

DUTIR-BioNLP /Taiyi-LLM

Star147

Biomedical LLM, A Bilingual (Chinese and English) Fine-Tuned Large Language Model for Diverse Biomedical Tasks

bionlp llm

UpdatedMar 12, 2025
Python

Rostlab /nalaf

Star114

NLP framework in python for entity recognition and relationship extraction

python nlp ml pubmed pubmed-central pubmed-parser ner bionlp relationship-extraction

UpdatedDec 8, 2022
Python

ncbi-nlp /PhenoTagger

Star55

PhenoTagger

hpo bionlp phenotype-concept-recognition

UpdatedJan 24, 2024
GAP

ncbi /AIONER

Star52

AIONER

named-entity-recognition ner bionlp

UpdatedJul 25, 2024
Python

abachaa /MEDIQA2019

Star51

Challenge on Textual Inference and Question Entailment in the Medical Domainhttps://sites.google.com/view/mediqa2019

nlp inference question-answering bionlp entailment medical-natural-language-processing

UpdatedJan 27, 2023
Python

cambridgeltl /cometa

Star50

Corpus of Online Medical EnTities: the cometA corpus

nlp machine-learning deep-learning transformer entity-linking bionlp

UpdatedMar 6, 2025
Jupyter Notebook

hu-ner /huner

Star47

Named Entity Recognition for biomedical entities

named-entity-recognition neural-networks corpora ner bionlp

UpdatedJan 11, 2023
Python

phosseini /CREST

Star43

A Causal Relation Schema for Text

nlp natural-language-processing artificial-intelligence dataset semeval causality brat relation-extraction natural-language-understanding bionlp

UpdatedNov 4, 2024
Python

jakelever /pubrunner

Star42

A framework for keeping biomedical text mining result up-to-date

python infrastructure text-mining snakemake pubmed pubmed-central bionlp

UpdatedJul 11, 2020
Python

jakelever /cancermine

Star41

Text-mined knowledgebase for drivers, oncogenes and tumor suppressors in cancer

text-mining cancer precision-medicine bionlp oncogenes tumor-suppressors cancer-driver-genes cancer-types

UpdatedMar 12, 2023
R

datquocnguyen /BioPosDep

Star33

Tokenization, sentence segmentation, POS tagging and dependency parsing for biomedical texts (BMC Bioinformatics 2019)

bioinformatics tokenizer pos-tagging dependency-parsing bionlp segmenter biomedical-text-mining

UpdatedApr 6, 2019
Python

bionlp-hzau /BioNLP-Corpus

Star32

Repository used to collect biomedical corpus on the Internet!

corpus biomedical bionlp

UpdatedSep 24, 2020

bionlplab /bioc

Star31

Data structures and code to read/write BioC XML and Json.

json xml writer reader bioc bionlp

UpdatedAug 21, 2023
Python

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