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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 594 100

  2. bluebert bluebert Public

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

    Python 573 82

  3. BLUE_Benchmark BLUE_Benchmark Public

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

    Python 296 41

  4. NegBio NegBio Public

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

    Python 164 43

  5. BioWordVec BioWordVec Public

    Python 152 30

  6. TrialGPT TrialGPT Public

    Code and data for TrialGPT.

    Python 117 55

Repositories

Showing 10 of 38 repositories
  • DeepSeeNet Public

    👀 DeepSeeNet is a deep learning framework for classifying patient-based age-related macular degeneration severity in retinal color fundus photographs.

    ncbi-nlp/DeepSeeNet’s past year of commit activity
    Python 63 30 2 1 Updated Jul 25, 2025
  • deepseenet-plus Public
    ncbi-nlp/deepseenet-plus’s past year of commit activity
    Python 0 0 1 0 Updated Jul 25, 2025
  • adversarial-manipulations Public
    ncbi-nlp/adversarial-manipulations’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Jul 24, 2025
  • BioREDirect Public
    ncbi-nlp/BioREDirect’s past year of commit activity
    Python 9 0 0 0 Updated Jul 15, 2025
  • cell-o1 Public

    Code and data for Cell-o1.

    ncbi-nlp/cell-o1’s past year of commit activity
    Python 19 1 0 0 Updated Jul 14, 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 69 13 0 0 Updated Jul 13, 2025
  • Clinical-Tool-Learning Public
    ncbi-nlp/Clinical-Tool-Learning’s past year of commit activity
    Python 5 1 0 0 Updated Jun 16, 2025
  • GeneAgent Public

    The code for gene set analysis by accessing domain databases

    ncbi-nlp/GeneAgent’s past year of commit activity
    Python 37 3 0 0 Updated Mar 13, 2025
  • TrialGPT Public

    Code and data for TrialGPT.

    ncbi-nlp/TrialGPT’s past year of commit activity
    Python 117 55 0 2 Updated Jan 24, 2025
  • LLM-Medicine-Primer Public
    ncbi-nlp/LLM-Medicine-Primer’s past year of commit activity
    5 1 0 0 Updated Oct 24, 2024
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