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"

Systematic evaluation of hallucination risks in Large Language Models (GPT-4, Claude 3, Gemini Pro) for clinical proteomics and mass spectrometry interpretation. Production-ready detection framework with comprehensive benchmarks.

Patient Family History extraction tool

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.

BERT-for-BioNLP-OST2019-AGAC-Task2

RAG pipeline for medical question-answering. Fuses lexical and dense retrieval (MedCPT, Contriever, Specter + FAISS) with OpenAI, Gemini, and HuggingFace LLMs. Supports iterative multi-round reasoning, strict typing, structured observability, and a clean layered architecture

AGAC-BioNL-OST2009-Task1 BERT+CRF

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

MedQA-NLI is a comprehensive medical reasoning dataset comprising 42,889 instances designed for training and evaluating models on natural language inference (NLI) tasks in biomedical domains.

BioGemma — Google Gemma 3 1B fine-tuned on medical/biomedical corpus for clinical NLP tasks

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.

SOEA-Plus (PDEMC): 3-task biomedical metacognition benchmark evaluating LLM metacognitive control across 2 frontier models on 300 real PubMed examples. Reveals the Control Collapse Gap

Core LLM for M.A.R.S. (Model Assisted Review System). Utilizes fine-tuned Llama 3.2 3B to automate biomedical SLR screening with 92.2% accuracy.

Clinical trial document intelligence pipelines using medallion architecture. Classification (87 categories) + NER (8 entity types) on Databricks.