biomedical-text-mining
There are 38 repositories under biomedical-text-mining topic.
dmis-lab/bern
A neural named entity recognition and multi-type normalization tool for biomedical text mining
dmis-lab/BERN2
BERN2: an advanced neural biomedical namedentity recognition and normalization tool
yuzhimanhua/Multi-BioNER
Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)
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.
BIDS-Xu-Lab/Me-LLaMA
A novel medical large language model family with 13/70B parameters, which have SOTA performances on various medical tasks
AstraZeneca/KAZU
Fast, world class biomedical NER
KarelDO/BioDEX
BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World Pharmacovigilance.
datquocnguyen/BioPosDep
Tokenization, sentence segmentation, POS tagging and dependency parsing for biomedical texts (BMC Bioinformatics 2019)
bayer-science-for-a-better-life/data2text-bioleaflets
Biomedical Data-to-Text Generation via Fine-Tuning Transformers
lasigeBioTM/BiOnt
BiOnt: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction
biomedicalinformaticsgroup/cadmus
A full-text article retrieval pipeline for biomedical literature.
disi-unibo-nlp/bio-ee-egv
[COLING22] Text-to-Text Extraction and Verbalization of Biomedical Event Graphs
lasigeBioTM/PGR
A Silver Standard Corpus of Human Phenotype-Gene Relations
vj1494/PipelineIE
PipelineIE is a project that contains a pipeline for information extraction (currently triple) from free text and domain specific text (eg. biomedical domain) and also supports custom models making it flexible to support other domains. It takes care of coreference resolution and entity resolution by also allowing to test with different tools.
yuzhimanhua/PENNER
PENNER: Pattern-enhanced Nested Named Entity Recognition in Biomedical Literature (BIBM'18)
lasigeBioTM/K-RET
K-RET: Knowledgeable Biomedical Relation Extraction System
biomedicalinformaticsgroup/ParallelPyMetaMap
This code is to run MetaMap in parallel using Python.
BNLNLP/PPI-Relation-Extraction
Official implementation of PPI Relation Extraction (IEEE BigData 2022)
lasigeBioTM/K-BiOnt
Biomedical Relation Extraction with Knowledge Graph-based Recommendations
skoblov-lab/SciLK
SciLK: a Scientific natural Language Toolkit
dmis-lab/bioner-generalization
How Do Your Biomedical Named Entity Recognition Models Generalize to Novel Entities?
Aequivinius/covid
👑🦠 Annotating PMC and PubMed articles for Covid-related entities
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
kuldeep7688/BioMedicalBertNer
Named Entity Recognition using BERT
ncbi/biocreative_litcovid
Evaluation scripts of the Biocreative LitCovid track
SciCrunch/bio_electra
Bio-Electra - Small and efficient discriminatively pre-trained language representation models for biomedical text mining
lasigeBioTM/NILINKER
Attention-based approach to NIL Entity Linking
lasigeBioTM/PGR-crowd
A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing
oligogenic/Deep_active_learning_bioRE
Framework to study the use of deep active learning for biomedical relation extraction
psaegert/pmtrendviz
Unsupervised Discovery Of Trends In Biomedical Research Based On The PubMed Baseline Repository
awakenedhaki/navigating-my-reference-manager
Navigating My Reference Manager
biomedicalinformaticsgroup/pm_abs_extr
This repository automatically requests and extracts abstract from PubMed.
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
lavita-ai/medical-ai-atlas
A comprehensive atlas of ML/NLP Tools/Models/Data/Research in Medical/Clinical Domain