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@ncbi-nlp

NLM/NCBI 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 587 100

  2. bluebert bluebert Public

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

    Python 568 81

  3. BLUE_Benchmark BLUE_Benchmark Public

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

    Python 291 41

  4. NegBio NegBio Public

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

    Python 159 42

  5. BioWordVec BioWordVec Public

    Python 147 30

  6. TrialGPT TrialGPT Public

    Code and data for TrialGPT.

    Python 78 34

Repositories

Showing 10 of 36 repositories
  • GeneAgent Public

    Codebase of GeneAgent, a language agent for gene set analysis.

    ncbi-nlp/GeneAgent’s past year of commit activity
    Python 0 0 0 0 Updated Mar 7, 2025
  • BioREDirect Public
    ncbi-nlp/BioREDirect’s past year of commit activity
    Python 5 0 0 0 Updated Jan 27, 2025
  • TrialGPT Public

    Code and data for TrialGPT.

    ncbi-nlp/TrialGPT’s past year of commit activity
    Python 78 34 1 1 Updated Jan 24, 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 45 9 0 0 Updated Jan 12, 2025
  • LLM-Medicine-Primer Public
    ncbi-nlp/LLM-Medicine-Primer’s past year of commit activity
    4 1 0 0 Updated Oct 24, 2024
  • Calculator-Recommendation Public

    MedQA-Calc is a benchmarking dataset designed to assess the capability of LLMs to recommend clinical calculators

    ncbi-nlp/Calculator-Recommendation’s past year of commit activity
    Python 1 0 0 0 Updated Oct 22, 2024
  • deepseenet-plus Public
    ncbi-nlp/deepseenet-plus’s past year of commit activity
    Python 0 0 0 0 Updated Oct 14, 2024
  • Clinical-Tool-Learning Public
    ncbi-nlp/Clinical-Tool-Learning’s past year of commit activity
    Python 2 0 0 0 Updated Oct 9, 2024
  • EnzChemRED Public
    ncbi-nlp/EnzChemRED’s past year of commit activity
    0 0 0 0 Updated Sep 17, 2024
  • Unmasking-GPT-Bias Public
    ncbi-nlp/Unmasking-GPT-Bias’s past year of commit activity
    Jupyter Notebook 3 0 0 0 Updated Sep 4, 2024
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