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)

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

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.

Implements relation extraction for biomedical texts using Hard Negative Mining to improve accuracy in identifying complex entity relationships. Includes code for data processing, training, and evaluation with BioC-format datasets.

BioCreative VIII track 2

MSR Cambridge Internship Summer 2023

Fine-tune with TEA

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

Graph-based RAG system for biomedical nutrigenetic knowledge discovery. Enables natural language queries on gene-nutrient interactions, supports personalized nutrition counseling, and runs 100% locally with Ollama LLMs and SBERT embeddings.

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

This repo explores token classification for abbreviation and long-form detection using RoBERTa. We evaluate the impact of adding 50% of the PLODv2-filtered dataset, achieving improved F1 and recall. The repo includes methodology, evaluation using seqeval, and confusion matrix analysis.