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

BERN2: an advanced neural biomedical namedentity recognition and normalization tool

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

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.

Fast, world class biomedical NER

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

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

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

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

BiOnt: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction

A full-text article retrieval pipeline for biomedical literature.

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

A Silver Standard Corpus of Human Phenotype-Gene Relations

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

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.

Biomedical Relation Extraction with Knowledge Graph-based Recommendations

SciLK: a Scientific natural Language Toolkit

Official implementation of PPI Relation Extraction (IEEE BigData 2022)