biomedicalinformaticsgroup/cadmus

A full-text article retrieval pipeline for biomedical literature.

Language: Python - Size: 404 KB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 17 - Forks: 2

dmis-lab/bioner-generalization

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

Language: Python - Size: 5.65 MB - Last synced: 18 days ago - Pushed: over 1 year ago - Stars: 6 - Forks: 1

dmis-lab/bc7-chem-id

DMIS at BioCreative VII NLMChem Track

Language: Python - Size: 2.1 MB - Last synced: 18 days ago - Pushed: 7 months ago - Stars: 5 - Forks: 1

ncbi-nlp/BioSentVec

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

Language: Jupyter Notebook - Size: 28.3 KB - Last synced: 18 days ago - Pushed: 10 months ago - Stars: 555 - Forks: 96

ncbi-nlp/BLUE_Benchmark

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

Language: Python - Size: 85 KB - Last synced: 18 days ago - Pushed: over 2 years ago - Stars: 276 - Forks: 40

DUTIR-BioNLP/Taiyi-LLM

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

Language: Python - Size: 10.9 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 116 - Forks: 17

bionlplab/bioc

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

Language: Python - Size: 442 KB - Last synced: 21 days ago - Pushed: 9 months ago - Stars: 28 - Forks: 11

cambridgeltl/cometa

Corpus of Online Medical EnTities: the cometA corpus

Language: Jupyter Notebook - Size: 367 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 45 - Forks: 6

PKPDAI/PKDocClassifier

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

Language: Python - Size: 8.42 MB - Last synced: 18 days ago - Pushed: 4 months ago - Stars: 16 - Forks: 7

ncbi-nlp/PhenoTagger

PhenoTagger

Language: GAP - Size: 69 MB - Last synced: 18 days ago - Pushed: 4 months ago - Stars: 48 - Forks: 11

mobashgr/WeLT

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

Language: Python - Size: 156 KB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 2 - Forks: 1

leebird/bionlp17

Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction

Language: Python - Size: 11.4 MB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 10 - Forks: 6

Rostlab/nalaf

NLP framework in python for entity recognition and relationship extraction

Language: Python - Size: 32 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 111 - Forks: 26

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: 10 days ago - Pushed: about 1 year ago - Stars: 154 - Forks: 30

jakelever/pubrunner

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

Language: Python - Size: 565 KB - Last synced: 2 months ago - Pushed: almost 4 years ago - Stars: 41 - Forks: 6

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: 3 months ago - Pushed: about 1 year ago - Stars: 152 - Forks: 29

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: 2 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

DUTIR-BioNLP/PhenoTagger-Updates

PhenoTagger_v1.2

Language: GAP - Size: 72.1 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 2 - Forks: 1

jakelever/biowordlists

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

Language: Python - Size: 128 KB - Last synced: 4 months ago - Pushed: about 1 year ago - Stars: 15 - Forks: 4

biomedicalinformaticsgroup/pm_abs_extr

This repository automatically requests and extracts abstract from PubMed.

Language: Python - Size: 11.7 KB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

phanxuanphucnd/BioNLP-2023

BioNLP Workshop 2023 and Shared Tasks @ ACL 2023

Language: Python - Size: 21.6 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 3 - Forks: 0

ylaboratory/flambe

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

Language: Jupyter Notebook - Size: 109 KB - Last synced: 4 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

jakelever/cancermine

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

Language: R - Size: 3.47 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 39 - Forks: 7

hu-ner/huner

Named Entity Recognition for biomedical entities

Language: Python - Size: 372 KB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 47 - Forks: 10

Bohdan-Khomtchouk/biosemble

AI assembly of bioNLP wordnets

Language: Python - Size: 6.32 MB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 19 - Forks: 3

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: 8 months ago - Pushed: over 1 year ago - Stars: 0 - 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: 8 months ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 0

Anthony9624/Various-documents

Various documents for deep Learning(Continually updated)

Size: 670 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 1

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: 8 months ago - Pushed: 8 months ago - Stars: 135 - Forks: 25

gsarti/covid-papers-browser

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

Language: CSS - Size: 10.7 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 180 - Forks: 27

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: 7 months ago - Pushed: over 1 year ago - Stars: 50 - Forks: 19

biomedicalinformaticsgroup/ParallelPyMetaMap

This code is to run MetaMap in parallel using Python.

Language: Python - Size: 65.4 KB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 8 - Forks: 0

uashogeschoolutrecht/PhenoTagger_MP Fork of ncbi-nlp/PhenoTagger

PhenoTagger_MP

Language: Python - Size: 9.88 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 1 - Forks: 1

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

Size: 173 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 48 - Forks: 9

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: 9 months ago - Pushed: 12 months ago - Stars: 15 - Forks: 5

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: 10 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

xiongshufeng/Resources Fork of WILAB-HIT/Resources

Language: Batchfile - Size: 14.3 MB - Last synced: 10 months ago - Pushed: about 6 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: 10 months ago - Pushed: almost 6 years ago - Stars: 0 - 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: 10 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

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

Language: Python - Size: 25.4 MB - Last synced: 10 months ago - Pushed: 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: 10 months ago - Pushed: almost 6 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: 10 months ago - Pushed: over 5 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: 10 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

jakelever/civicmine

Text mining cancer biomarkers for the CIVIC database

Language: Python - Size: 1.49 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 20 - Forks: 2

ncbi/AIONER

AIONER

Language: Python - Size: 20.8 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 15 - Forks: 4

abachaa/MEDIQA2021

Language: Python - Size: 2.47 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 18 - Forks: 4

ncbi/SpeciesAssignment

SpeciesAssignment

Language: Python - Size: 891 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 4 - Forks: 4

ncbi-nlp/PubTator-Covid19

Size: 70.3 KB - Last synced: 18 days ago - Pushed: about 4 years ago - Stars: 4 - Forks: 2

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: about 1 year ago - Pushed: over 1 year ago - Stars: 43 - Forks: 5

phosseini/CREST

A Causal Relation Schema for Text

Language: Jupyter Notebook - Size: 56.9 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 30 - Forks: 7

datquocnguyen/BioPosDep

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

Language: Python - Size: 65 MB - Last synced: about 1 year ago - Pushed: about 5 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: about 1 year ago - Pushed: over 3 years ago - Stars: 29 - Forks: 9

ProjectDossier/MedVid2022

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

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

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

NCBI Disease corpus

Language: Jupyter Notebook - Size: 443 KB - Last synced: over 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

jakelever/VERSE

Vancouver Event and Relation System for Extraction

Language: Python - Size: 141 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 13 - Forks: 7

jakelever/tumorantigens

Text mining tumor antigens for cancer immunotherapy research

Language: Python - Size: 12.7 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0