BERN2: an advanced neural biomedical namedentity recognition and normalization tool
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Updated
Mar 28, 2024 - Python
BERN2: an advanced neural biomedical namedentity recognition and normalization tool
A neural named entity recognition and multi-type normalization tool for biomedical text mining
Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)
A novel medical large language model family with 13/70B parameters, which have SOTA performances on various medical tasks
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
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.
A Silver Standard Corpus of Human Phenotype-Gene Relations
[COLING22] Text-to-Text Extraction and Verbalization of Biomedical Event Graphs
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.
Official implementation of PPI Relation Extraction (IEEE BigData 2022)
K-RET: Knowledgeable Biomedical Relation Extraction System
SciLK: a Scientific natural Language Toolkit
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