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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 590 100

  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 292 41

  4. NegBio NegBio Public

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

    Python 160 42

  5. BioWordVec BioWordVec Public

    Python 148 30

  6. TrialGPT TrialGPT Public

    Code and data for TrialGPT.

    Python 86 37

Repositories

Showing 10 of 36 repositories
  • GeneAgent Public

    The code for gene set analysis by accessing domain databases

    Python 0 0 0 0 Updated Mar 13, 2025
  • BioREDirect Public
    Python 5 0 0 0 Updated Jan 27, 2025
  • TrialGPT Public

    Code and data for TrialGPT.

    Python 86 37 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

    Python 48 9 1 0 Updated Jan 12, 2025
  • 5 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

    Python 1 0 0 0 Updated Oct 22, 2024
  • Python 0 0 0 0 Updated Oct 14, 2024
  • Python 2 0 0 0 Updated Oct 9, 2024
  • EnzChemRED Public
    1 0 0 0 Updated Sep 17, 2024
  • Jupyter Notebook 3 0 0 0 Updated Sep 4, 2024

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