Popular GitHub Repositories for Biomedical Text Mining

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

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

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.

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

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.

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

Biomedical Relation Extraction with Knowledge Graph-based Recommendations

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

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

Attention-based approach to NIL Entity Linking

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

Implementation of Deep Divergence Event Graph Kernels