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)
[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.
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.
PheSeq, A Bayesian Deep Learning Model to Enhance and Interpret the Gene Disease Association Studies
Fine-tune with TEA
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.
About Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning
An agentic AI research analyst for medical literature. Built with IBM watsonx.ai, Hybrid Search, TableRAG, and Streamlit, and containerized for IBM Cloud Code Engine.
End-to-end NER and RE pipeline for biomedical texts focusing on the gut-brain axis using BERT, BioBERT, and PubMedBERT.
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