ncbi-nlp/BioSentVec

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

Language: Jupyter Notebook - Size: 28.3 KB - Last synced at: 12 months ago - Pushed at: almost 2 years ago - Stars: 567 - Forks: 97

ncbi-nlp/BLUE_Benchmark

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

Language: Python - Size: 85 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 276 - Forks: 40

gsarti/covid-papers-browser

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

Language: CSS - Size: 10.7 MB - Last synced at: 4 months ago - Pushed at: about 3 years ago - Stars: 182 - Forks: 27

cambridgeltl/sapbert

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

Language: Python - Size: 102 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 162 - Forks: 32

jakelever/kindred

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

Language: Python - Size: 2.38 MB - Last synced at: 17 days ago - Pushed at: over 2 years ago - Stars: 156 - Forks: 31

DUTIR-BioNLP/Taiyi-LLM

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

Language: Python - Size: 11.1 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 150 - Forks: 25

abachaa/Existing-Medical-QA-Datasets

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

Size: 26.4 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 135 - Forks: 25

Rostlab/nalaf

NLP framework in python for entity recognition and relationship extraction

Language: Python - Size: 32 MB - Last synced at: 27 days ago - Pushed at: over 2 years ago - Stars: 115 - Forks: 26

ncbi/AIONER

AIONER

Language: Python - Size: 20.8 MB - Last synced at: 21 days ago - Pushed at: about 1 year ago - Stars: 55 - Forks: 17

cambridgeltl/cometa

Corpus of Online Medical EnTities: the cometA corpus

Language: Jupyter Notebook - Size: 367 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 50 - Forks: 6

abachaa/MEDIQA2019

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

Language: Python - Size: 2.43 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 50 - Forks: 19

ncbi-nlp/PhenoTagger

PhenoTagger

Language: GAP - Size: 69 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 48 - Forks: 11

yuzhimanhua/LM-LSTM-CRF Fork of LiyuanLucasLiu/LM-LSTM-CRF

Size: 173 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 48 - Forks: 9

hu-ner/huner

Named Entity Recognition for biomedical entities

Language: Python - Size: 372 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 47 - Forks: 10

medmcqa/medmcqa

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

Language: Jupyter Notebook - Size: 655 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 43 - Forks: 5

phosseini/CREST

A Causal Relation Schema for Text

Language: Python - Size: 56.9 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 42 - Forks: 9

jakelever/pubrunner

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

Language: Python - Size: 565 KB - Last synced at: 2 days ago - Pushed at: about 5 years ago - Stars: 42 - Forks: 6

jakelever/cancermine

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

Language: R - Size: 3.47 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 39 - Forks: 7

bionlplab/bioc

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

Language: Python - Size: 442 KB - Last synced at: 13 days ago - Pushed at: almost 2 years ago - Stars: 33 - Forks: 11

datquocnguyen/BioPosDep

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

Language: Python - Size: 65 MB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 32 - Forks: 5

bionlp-hzau/BioNLP-Corpus

Repository used to collect biomedical corpus on the Internet!

Size: 28.2 MB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 29 - Forks: 9

abachaa/MEDIQA2021

Language: Python - Size: 1.82 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 23 - Forks: 4

biomedicalinformaticsgroup/cadmus

A full-text article retrieval pipeline for biomedical literature.

Language: Python - Size: 271 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 20 - Forks: 2

jakelever/civicmine

Text mining cancer biomarkers for the CIVIC database

Language: Python - Size: 1.49 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 20 - Forks: 2

Bohdan-Khomtchouk/biosemble

AI assembly of bioNLP wordnets

Language: Python - Size: 6.32 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 19 - Forks: 3

PKPDAI/PKDocClassifier

Binary classifier to identify scientific publications reporting pharmacokinetic parameters estimated in vivo

Language: Python - Size: 8.42 MB - Last synced at: 24 days ago - Pushed at: over 1 year ago - Stars: 18 - Forks: 8

suamin/MIL-RBERT

MIL-RBERT: A Data-driven Approach for Noise Reduction in Distantly Supervised Biomedical Relation Extraction (BioNLP @ ACL 2020)

Language: Python - Size: 139 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 15 - Forks: 5

jakelever/biowordlists

Biomedical wordlists (of drugs, genes, etc) for several text mining projects

Language: Python - Size: 128 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 4

jakelever/VERSE

Vancouver Event and Relation System for Extraction

Language: Python - Size: 141 KB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 13 - Forks: 7

leebird/bionlp17

Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction

Language: Python - Size: 11.4 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 10 - Forks: 6

biomedicalinformaticsgroup/ParallelPyMetaMap

This code is to run MetaMap in parallel using Python.

Language: Python - Size: 65.4 KB - Last synced at: 9 months ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 0

ncbi/SpeciesAssignment

SpeciesAssignment

Language: Python - Size: 891 KB - Last synced at: 21 days ago - Pushed at: almost 3 years ago - Stars: 7 - Forks: 4

Anthony9624/Various-documents

Various documents for deep Learning(Continually updated)

Size: 670 MB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 7 - Forks: 1

dmis-lab/bioner-generalization

How Do Your Biomedical Named Entity Recognition Models Generalize to Novel Entities?

Language: Python - Size: 5.65 MB - Last synced at: 11 days ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 1

dmis-lab/bc7-chem-id

DMIS at BioCreative VII NLMChem Track

Language: Python - Size: 2.1 MB - Last synced at: 11 days ago - Pushed at: 11 months ago - Stars: 5 - Forks: 1

allenai/TOPICAL

:magic_wand::page_facing_up: TOPICAL: TOPIC pages AutomagicaLly

Language: Python - Size: 428 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 0

DUTIR-BioNLP/PhenoTagger-Updates

An Improved Method for Phenotype Concept Recognition Using Rich HPO Information

Language: GAP - Size: 77.1 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 4 - Forks: 1

ylaboratory/flambe

datasets for tissue and tool named entity recognition, annotation files for biological workflow extraction, and disambiguation files

Language: Jupyter Notebook - Size: 117 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 1

miladnouriezade/Ktrain-BioBert_NER

This repository contains data and BioBert based NER model monologg/biobert_v1.1_pubmed from community-uploaded Hugging Face models for detecting entities such as chemical and disease.

Language: Python - Size: 50.1 MB - Last synced at: 4 months ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 0

ncbi-nlp/PubTator-Covid19

Size: 70.3 KB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 2

phanxuanphucnd/BioNLP-2023

BioNLP Workshop 2023 and Shared Tasks @ ACL 2023

Language: Python - Size: 21.6 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

mobashgr/WeLT

A cost-sensitive BERT that handles the class imbalance for the task of biomedical NER.

Language: Python - Size: 156 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

shitohana/ezmetaserver

EzMetaServer is a comprehensive platform for fetching and analyzing biological and biomedical metadata. It provides a unified interface to access NCBI databases and extract named entities from biomedical text.

Language: Python - Size: 25.4 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

JULIELab/gepi

GePI (GEne - Protein Interactions) is a web portal for quick and convenient access to gene - protein interaction mentions automatically extracted from the biomedical literature, i.e. PubMed and PubMed Central (Open Access Subset).

Language: JavaScript - Size: 156 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

qanastek/BioCreative-VII-Track-5

[BioCreative VII] Track 5 - LitCovid track Multi-label topic classification for COVID-19 literature annotation

Language: Python - Size: 20.4 MB - Last synced at: 5 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 1

biomedicalinformaticsgroup/pm_abs_extr

This repository automatically requests and extracts abstract from PubMed.

Language: Python - Size: 11.7 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

uashogeschoolutrecht/PhenoTagger_MP Fork of ncbi-nlp/PhenoTagger

PhenoTagger_MP

Language: Python - Size: 9.88 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

ProjectDossier/MedVid2022

[bioNLP 2022] DoSSIER at MedVidQA 2022: Text-based Approaches to Medical Video Answer Localization Problem

Language: Python - Size: 429 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

jakelever/tumorantigens

Text mining tumor antigens for cancer immunotherapy research

Language: Python - Size: 12.7 KB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

xiongshufeng/Multi-BioNER Fork of yuzhimanhua/Multi-BioNER

Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)

Language: Python - Size: 74.1 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

sirisacademic/AIObioEnts

AIObioEnts, and all-in-one biomedical named-entity recognition following the all-in-one NER scheme

Language: Python - Size: 42.7 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

DgoMndez/DL-patogen-colab-DIIC

Estudio del carácter patogénico de variantes humanas mediante deep learning. Fine-tuning de BERT para la representación de enfermedades: un método de aprendizaje sobre datasets de textos biomédicos.

Language: Jupyter Notebook - Size: 101 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

miladnouriezade/HUNER-evaluation

This repository stands for applying and evaluating HUNER pre-trained model ("disease_all") on "BC5CDR-Disease" data set .

Language: Python - Size: 1.75 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

nettargets/ncbi-disease Fork of openbiocorpora/ncbi-disease

NCBI Disease corpus

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nettargets/bern Fork of dmis-lab/bern

A neural named entity recognition and multi-type normalization tool for biomedical text mining

Language: Python - Size: 994 KB - Last synced at: 8 months ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

xiongshufeng/DDI-extraction-through-LSTM Fork of sunilitggu/DDI-extraction-through-LSTM

DDI Extraction from Biomedical text using LSTM network

Language: Python - Size: 232 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

xiongshufeng/Transfer-Learning-BNER-Bioinformatics-2018 Fork of BaderLab/Transfer-Learning-BNER-Bioinformatics-2018

This repository contains supplementary data, and links to the model and corpora used for the paper: Transfer learning for biomedical named entity recognition with neural networks.

Language: Python - Size: 112 MB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

xiongshufeng/HSCRF-pytorch Fork of ZhixiuYe/HSCRF-pytorch

ACL 2018: Hybrid semi-Markov CRF for Neural Sequence Labeling (http://aclweb.org/anthology/P18-2038)

Language: Python - Size: 1000 KB - Last synced at: almost 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

xiongshufeng/NeuroNER Fork of Franck-Dernoncourt/NeuroNER

Named-entity recognition using neural networks. Easy-to-use and state-of-the-art results.

Language: Python - Size: 121 MB - Last synced at: almost 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

xiongshufeng/Resources Fork of WILAB-HIT/Resources

Language: Batchfile - Size: 14.3 MB - Last synced at: almost 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

xiongshufeng/crnn-relation-classification Fork of desh2608/crnn-relation-classification

Tensorflow implementation of the Convolutional Recurrent Neural Network model with max pooling and attentive pooling, for relation classification on biomedical text.

Language: Python - Size: 12.7 KB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

xiongshufeng/MTL-Bioinformatics-2016 Fork of cambridgeltl/MTL-Bioinformatics-2016

Language: Python - Size: 25.4 MB - Last synced at: almost 2 years ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0