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@ncbi-nlp

NLM BioNLP Research Group (PI: Zhiyong Lu)

These tools are the results of research conducted in the Computational Biology Branch, NLM/NCBI.

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  1. BioSentVec BioSentVec Public

    BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences

    Jupyter Notebook 616 100

  2. bluebert bluebert Public

    BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).

    Python 600 80

  3. BLUE_Benchmark BLUE_Benchmark Public

    BLUE benchmark consists of five different biomedicine text-mining tasks with ten corpora.

    Python 297 41

  4. TrialGPT TrialGPT Public

    Code and data for TrialGPT.

    Python 173 76

  5. NegBio NegBio Public

    📰 High-performance tool for negation and uncertainty detection in radiology reports

    Python 169 42

  6. BioWordVec BioWordVec Public

    Python 153 30

Repositories

Showing 10 of 44 repositories
  • LLM-Medicine-Primer Public
    ncbi-nlp/LLM-Medicine-Primer's past year of commit activity
    26 7 0 0 Updated Jul 27, 2026
  • cell-o1 Public

    Code and data for Cell-o1.

    ncbi-nlp/cell-o1's past year of commit activity
    Python 29 7 1 0 Updated Jul 22, 2026
  • DrugKLM Public
    ncbi-nlp/DrugKLM's past year of commit activity
    Python 3 3 0 1 Updated Jul 16, 2026
  • Trial-Recommendation-Framework Public
    ncbi-nlp/Trial-Recommendation-Framework's past year of commit activity
    Python 0 0 0 0 Updated Jun 30, 2026
  • Gene-R1 Public
    ncbi-nlp/Gene-R1's past year of commit activity
    Python 0 0 0 0 Updated Jun 23, 2026
  • MLLM4BioMed Public

    Multimodal Large Language Models in Biomedicine and Healthcare. Summaries and Guidelines of multimodal LLMs deployed in biomedicine.

    ncbi-nlp/MLLM4BioMed's past year of commit activity
    Python 8 2 0 0 Updated May 22, 2026
  • cGSA Public
    ncbi-nlp/cGSA's past year of commit activity
    Python 2 0 0 0 Updated Jan 8, 2026
  • FAIR-SMART Public
    ncbi-nlp/FAIR-SMART's past year of commit activity
    Java 2 1 0 0 Updated Jan 6, 2026
  • GeneAgent Public

    The code for gene set analysis by accessing domain databases

    ncbi-nlp/GeneAgent's past year of commit activity
    Python 120 16 4 1 Updated Dec 25, 2025
  • MedCalc-Bench Public

    [NeurIPS 2024 Datasets and Benchmark Track Oral] MedCalc-Bench: Evaluating Large Language Models for Medical Calculations

    ncbi-nlp/MedCalc-Bench's past year of commit activity
    Python 96 21 2 0 Updated Dec 18, 2025
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