Automatic biomarker discovery and enrichment with BRAD.

Journal: Bioinformatics (Oxford, England)
PMID: 40323323

Abstract

MOTIVATION: Integrating Large Language Models (LLMs) with research tools presents technical and reproducibility challenges for biomedical research. While commercial artificial intelligence (AI) systems are easy to adopt, they obscure data provenance, lack transparency, and can generates false information, making them unfit for many research problems. To address these challenges, we developed the Bioinformatics Retrieval Augmented Digital (BRAD) agent software system.

Authors

  • Joshua Pickard
    Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
  • Ram Prakash
    Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
  • Marc Andrew Choi
    Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, United States.
  • Natalie Oliven
    Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
  • Cooper Stansbury
    Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
  • Jillian Cwycyshyn
    Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
  • Nicholas Galioto
    Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
  • Alex Gorodetsky
    Department of Aerospace Engineering, University of Michigan, Ann Arbor, MI 48109, United States.
  • Alvaro Velasquez
    Department of Computer Science, University of Colorado Boulder, Boulder, CO 80309, United States.
  • Indika Rajapakse
    Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, United States.

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