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

Bioformer: an efficient BERT model for biomedical text mining

[EMNLP 2024] This is the code for our paper "BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers".

This repository contains the code used for distillation and fine-tuning of compact biomedical transformers that have been introduced in the paper "On The Effectiveness of Compact Biomedical Transformers"

Patient Family History extraction tool

BERT-for-BioNLP-OST2019-AGAC-Task2

AGAC-BioNL-OST2009-Task1 BERT+CRF

PheSeq, A Bayesian Deep Learning Model to Enhance and Interpret the Gene Disease Association Studies

Cancer-Alterome is a comprehensive and curated dataset that focuses on the investigation of regulatory events caused by gene alteration in the context of cancer.

BioCreative VIII track 2

MSR Cambridge Internship Summer 2023

About Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning

We present an open-source end-to-end framework for disease-specific knowledge discovery from raw text. This repository includes two annotated datasets focused on Rett syndrome and Alzheimer's disease, designed to detect semantic relations between biomedical entities. Extensive benchmarking explores various relation and entity representations.