KarelDO/BioDEX

BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance.

Language: Jupyter Notebook - Size: 22.5 MB - Last synced at: 9 days ago - Pushed at: over 1 year ago - Stars: 51 - Forks: 5

scarandriy/NeuroMine

LLM-powered pipeline for mining and structuring neuroprotective compound data from scientific literature. Includes data extraction, storage, and web-based search.

Language: TypeScript - Size: 3.68 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 0 - Forks: 0

dmis-lab/BERN2

BERN2: an advanced neural biomedical namedentity recognition and normalization tool

Language: Python - Size: 1.77 MB - Last synced at: 12 days ago - Pushed at: about 1 year ago - Stars: 188 - Forks: 43

BIDS-Xu-Lab/Me-LLaMA

A novel medical large language model family with 13/70B parameters, which have SOTA performances on various medical tasks

Language: Python - Size: 229 KB - Last synced at: 12 days ago - Pushed at: 5 months ago - Stars: 149 - Forks: 18

dmis-lab/bern

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

Language: Python - Size: 1010 KB - Last synced at: 7 days ago - Pushed at: about 3 years ago - Stars: 178 - Forks: 43

AstraZeneca/KAZU

Fast, world class biomedical NER

Language: Python - Size: 11.4 MB - Last synced at: 17 days ago - Pushed at: 3 months ago - Stars: 86 - Forks: 8

tznurmin/TEA

Taxonomic Entity Augmentation makes biomedical texts less repetitive

Language: Python - Size: 161 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

biomedicalinformaticsgroup/cadmus

A full-text article retrieval pipeline for biomedical literature.

Language: Python - Size: 271 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 20 - Forks: 2

ncbi/BioConceptVec

Language: Jupyter Notebook - Size: 60.1 MB - Last synced at: 1 day ago - Pushed at: over 5 years ago - Stars: 41 - Forks: 13

ncbi/biocreative_litcovid

Evaluation scripts of the Biocreative LitCovid track

Language: Python - Size: 115 KB - Last synced at: 1 day ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 1

lasigeBioTM/K-RET

K-RET: Knowledgeable Biomedical Relation Extraction System

Language: Python - Size: 4.17 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 9 - Forks: 3

MPKuchciak/PubMedResearch

This repository focuses on processing and analyzing PubMed abstracts to support disease detection, tokenization, and large-scale text mining. It includes workflows for API data collection, tokenization, entity recognition, sentiment analysis, and topic modeling.

Language: Jupyter Notebook - Size: 181 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

lasigeBioTM/NILINKER

Attention-based approach to NIL Entity Linking

Language: Python - Size: 807 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0

bayer-science-for-a-better-life/data2text-bioleaflets

Biomedical Data-to-Text Generation via Fine-Tuning Transformers

Language: Python - Size: 113 KB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 29 - Forks: 3

lavita-ai/medical-ai-atlas

A comprehensive atlas of ML/NLP Tools/Models/Data/Research in Medical/Clinical Domain

Size: 267 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

disi-unibo-nlp/ddegk

Implementation of Deep Divergence Event Graph Kernels

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disi-unibo-nlp/bio-ee-egv

[COLING22] Text-to-Text Extraction and Verbalization of Biomedical Event Graphs

Language: Python - Size: 94 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 0

BaderLab/saber

Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not stable.

Language: Python - Size: 3.85 MB - Last synced at: 27 days ago - Pushed at: almost 5 years ago - Stars: 102 - Forks: 17

yuzhimanhua/Multi-BioNER

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

Language: Python - Size: 157 KB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 129 - Forks: 28

SciCrunch/bio_electra

Bio-Electra - Small and efficient discriminatively pre-trained language representation models for biomedical text mining

Language: Python - Size: 21.2 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 1

yuzhimanhua/PENNER

PENNER: Pattern-enhanced Nested Named Entity Recognition in Biomedical Literature (BIBM'18)

Language: Python - Size: 13.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 10 - Forks: 3

oligogenic/Deep_active_learning_bioRE

Framework to study the use of deep active learning for biomedical relation extraction

Language: Python - Size: 7.97 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

lasigeBioTM/BiOnt

BiOnt: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction

Language: Python - Size: 16 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 26 - Forks: 6

psaegert/pmtrendviz

Unsupervised Discovery Of Trends In Biomedical Research Based On The PubMed Baseline Repository

Language: Python - Size: 500 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

lasigeBioTM/PGR-crowd

A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing

Language: Python - Size: 27.4 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 1

lasigeBioTM/PGR

A Silver Standard Corpus of Human Phenotype-Gene Relations

Language: Python - Size: 4.98 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 3

biomedicalinformaticsgroup/OntoSuite-Miner Fork of hxin/OntoSuite-Miner

An NLP pipeline for annotating ontologies from biomedical corpora

Language: Perl - Size: 80.3 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0

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

skoblov-lab/SciLK

SciLK: a Scientific natural Language Toolkit

Language: Python - Size: 13.4 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 8 - Forks: 2

biomedicalinformaticsgroup/ParallelPyMetaMap

This code is to run MetaMap in parallel using Python.

Language: Python - Size: 65.4 KB - Last synced at: 7 months ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 0

BNLNLP/PPI-Relation-Extraction

Official implementation of PPI Relation Extraction (IEEE BigData 2022)

Language: Python - Size: 20.4 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1

awakenedhaki/navigating-my-reference-manager

Navigating My Reference Manager

Language: R - Size: 66.4 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

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: 2 months ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 1

kuldeep7688/BioMedicalBertNer

Named Entity Recognition using BERT

Language: Python - Size: 48.8 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

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: about 6 years ago - Stars: 32 - Forks: 5

mtpandi/Text-Mining-for-PGx

A Text Mining project applied to PGx-related available literature from PubMed

Language: R - Size: 13.6 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 1

Dimas263/NLP_NER_BERT_BILSTM_CRF_Named_Entity_Recognition

NLP Named Entity Recognition dalam bidang Biomedis, mendeteksi teks dan membuat klasifikasi apakah teks tersebut mempunyai entitas plant atau disease, memberi label pada teks, menguji hubungan entitas plant dan disease, menilai kecocokan antara kedua entitas, membandingkan hasil uji dengan menggunakan models BERT-BILSTM-CRF

Language: Jupyter Notebook - Size: 10.9 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

Dimas263/NLP_NER_BERT_Named_Entity_Recognition

NLP Named Entity Recognition dalam bidang Biomedis, mendeteksi teks dan membuat klasifikasi apakah teks tersebut mempunyai entitas plant atau disease, memberi label pada teks, menguji hubungan entitas plant dan disease, menilai kecocokan antara kedua entitas, membandingkan hasil uji dengan menggunakan models BERT

Language: Jupyter Notebook - Size: 4.03 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

Aequivinius/covid

👑🦠 Annotating PMC and PubMed articles for Covid-related entities

Language: Jupyter Notebook - Size: 13.1 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 1