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@ncbi-nlp NLM BioNLP Research Group (PI: Zhiyong Lu)

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    44 repositories

    • Gene-R1

      Public
      Python
      •0•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • MLLM4BioMed

      Public
      Multimodal Large Language Models in Biomedicine and Healthcare. Summaries and Guidelines of multimodal LLMs deployed in biomedicine.
      Python
      •1•6•0•0•Updated May 22, 2026May 22, 2026

    • DrugKLM

      Public
      Python
      •3•3•0•1•Updated Apr 2, 2026Apr 2, 2026

    • Med-V1

      Public
      Python
      •
      Other
      •0•13•0•0•Updated Mar 12, 2026Mar 12, 2026

    • cGSA

      Public
      Python
      •0•1•0•0•Updated Jan 8, 2026Jan 8, 2026

    • FAIR-SMART

      Public
      Java
      •1•2•0•0•Updated Jan 6, 2026Jan 6, 2026

    • GeneAgent

      Public
      The code for gene set analysis by accessing domain databases
      Python
      •
      Other
      •17•114•4•1•Updated Dec 25, 2025Dec 25, 2025

    • LLM-Medicine-Primer

      Public
      Other
      •3•10•0•0•Updated Dec 21, 2025Dec 21, 2025

    • MedCalc-Bench

      Public
      [NeurIPS 2024 Datasets and Benchmark Track Oral] MedCalc-Bench: Evaluating Large Language Models for Medical Calculations
      Python
      •21•92•2•0•Updated Dec 18, 2025Dec 18, 2025

    • cell-o1

      Public
      Code and data for Cell-o1.
      Python
      •
      Other
      •7•28•1•0•Updated Sep 19, 2025Sep 19, 2025

    • BioREDirect

      Public
      Python
      •0•12•0•0•Updated Aug 20, 2025Aug 20, 2025

    • Clinical-Tool-Learning

      Public
      Python
      •
      Other
      •5•26•0•0•Updated Aug 10, 2025Aug 10, 2025

    • DeepSeeNet

      Public
      :eyes: DeepSeeNet is a deep learning framework for classifying patient-based age-related macular degeneration severity in retinal color fundus photographs.
      Python
      •
      Other
      •30•65•2•0•Updated Jul 25, 2025Jul 25, 2025

    • deepseenet-plus

      Public
      Python
      •1•1•1•1•Updated Jul 25, 2025Jul 25, 2025

    • adversarial-manipulations

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Jul 24, 2025Jul 24, 2025

    • TrialGPT

      Public
      Code and data for TrialGPT.
      Python
      •
      Other
      •72•160•5•2•Updated Jan 24, 2025Jan 24, 2025

    • Calculator-Recommendation

      Public
      MedQA-Calc is a benchmarking dataset designed to assess the capability of LLMs to recommend clinical calculators
      Python
      •
      Other
      •0•3•0•0•Updated Oct 22, 2024Oct 22, 2024

    • EnzChemRED

      Public
      2•1•0•0•Updated Sep 17, 2024Sep 17, 2024

    • Unmasking-GPT-Bias

      Public
      Jupyter Notebook
      •0•3•0•0•Updated Sep 4, 2024Sep 4, 2024

    • Deep-RPD-Net

      Public
      Python
      •1•0•0•0•Updated Aug 30, 2024Aug 30, 2024

    • PhenoTagger

      Public
      PhenoTagger
      hpobionlpphenotype-concept-recognition
      hpobionlpphenotype-concept-recognition
      GAP
      •
      MIT License
      •16•65•1•0•Updated Jan 24, 2024Jan 24, 2024

    • TeamTat

      Public
      Text annotation tool for team collaboration
      JavaScript
      •
      MIT License
      •13•43•9•8•Updated Jan 10, 2024Jan 10, 2024

    • NCBITextLib

      Public
      Software library for building a large-scale data infrastructure for text mining
      C++
      •
      Other
      •4•9•1•1•Updated Jan 7, 2024Jan 7, 2024

    • Medical-Imaging-Causal-Fairness

      Public
      Python
      •
      Other
      •0•2•0•0•Updated Jan 4, 2024Jan 4, 2024

    • BioWordVec

      Public
      Python
      •
      Other
      •30•153•1•1•Updated Nov 30, 2023Nov 30, 2023

    • pubtator-gpt

      Public
      3•33•0•0•Updated Nov 30, 2023Nov 30, 2023

    • PhenoRerank

      Public
      Python
      •2•2•2•0•Updated Aug 24, 2023Aug 24, 2023

    • BioSentVec

      Public
      BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences
      natural-language-processingword-embeddingspubmed
      natural-language-processingword-embeddingspubmedfasttextmimic-iiibionlpsentence-similaritysentence-embeddingssent2vec
      Jupyter Notebook
      •
      Other
      •99•616•13•1•Updated Aug 15, 2023Aug 15, 2023

    • NegBio

      Public
      :newspaper: High-performance tool for negation and uncertainty detection in radiology reports
      nlpreportsclinical-notes
      nlpreportsclinical-notesclinical-researchclincalclincal-nlp
      Python
      •
      Other
      •42•166•7•4•Updated Jul 16, 2023Jul 16, 2023

    • bluebert

      Public
      BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).
      natural-language-processingpubmedmimic-iii
      natural-language-processingpubmedmimic-iiilanguage-modelbertpubmed-abstractsbert-model
      Python
      •
      Other
      •80•595•5•1•Updated Mar 25, 2023Mar 25, 2023
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