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@BiomedSciAI

BiomedSciAI

BiomedSciAI

🙋‍♀️ What is BiomedSciAI?

Our mission is to accelerate scientific discovery in Biomedical Sciences through a variety of tools that can help scientists do their research quicker and more effectively.

Whether you use population-scale data like EHRs, body-part data like medical imaging, subcellullar-scale data like spatially resolved omics, or a combination of various modalities, we host tools that will help you make the most out of it.

🌈 How can I get involved?

If you want to contribute and get involved check out the guidelines of the repository of your interest and our code of conduct.

👩‍💻 How can I use it?

We have plenty of stuff you can do with BiomedSciAI. A good starting point is to check out the pinned repositories. You can find all implementation details and some examples in the docs.

Try out the examples in the repositories that we prepared for various applications.

Pinned Loading

  1. fuse-med-ml fuse-med-ml Public

    A python framework accelerating ML based discovery in the medical field by encouraging code reuse. Batteries included :)

    Python 151 37

  2. causallib causallib Public

    A Python package for modular causal inference analysis and model evaluations

    Python 799 106

  3. biomed-multi-alignment biomed-multi-alignment Public

    We introduce ibm/biomed.omics.bl.sm.ma-ted-458m. A biomedical foundation model trained over 2 billion biological samples across multiple modalities, including proteins, small molecules, and single-…

    Python 39 17

  4. biomed-multi-view biomed-multi-view Public

    This repository contains the implementation of the Multi-view Molecular Embedding with Late Fusion (MMELON) architecture. MMELON combines molecular representations from three views — image, graph, …

    Python 40 10

  5. biomed-multi-omic biomed-multi-omic Public

    Build foundation model for RNA or DNA data

    Jupyter Notebook 52 11

Repositories

Showing 10 of 14 repositories
  • biomed-multi-omic Public

    Build foundation model for RNA or DNA data

    BiomedSciAI/biomed-multi-omic’s past year of commit activity
    Jupyter Notebook 52 Apache-2.0 11 0 1 Updated Dec 4, 2025
  • fuse-med-ml Public

    A python framework accelerating ML based discovery in the medical field by encouraging code reuse. Batteries included :)

    BiomedSciAI/fuse-med-ml’s past year of commit activity
    Python 151 Apache-2.0 37 24 (4 issues need help) 11 Updated Nov 24, 2025
  • biomed-multi-alignment Public

    We introduce ibm/biomed.omics.bl.sm.ma-ted-458m. A biomedical foundation model trained over 2 billion biological samples across multiple modalities, including proteins, small molecules, and single-cell gene data.

    BiomedSciAI/biomed-multi-alignment’s past year of commit activity
    Python 39 Apache-2.0 17 1 2 Updated Oct 29, 2025
  • biomed-llm Public

    Representation Alignment of Biomedical Modalities to LLMs for Multi-Modal Reasoning

    BiomedSciAI/biomed-llm’s past year of commit activity
    0 Apache-2.0 0 0 0 Updated Oct 2, 2025
  • fuse-drug Public

    FuseMedML based molecular biochemistry library for drug discovery/repurposing

    BiomedSciAI/fuse-drug’s past year of commit activity
    Python 23 Apache-2.0 5 10 2 Updated Sep 21, 2025
  • biomed-multi-view Public

    This repository contains the implementation of the Multi-view Molecular Embedding with Late Fusion (MMELON) architecture. MMELON combines molecular representations from three views — image, graph, and text —to learn a joint embedding that can be finetuned for downstream tasks in chemical and biological property prediction.

    BiomedSciAI/biomed-multi-view’s past year of commit activity
    Python 40 Apache-2.0 10 4 2 Updated Jun 4, 2025
  • gene-benchmark Public

    Benchmark gene representations from different model families

    BiomedSciAI/gene-benchmark’s past year of commit activity
    Jupyter Notebook 14 Apache-2.0 1 2 1 Updated May 29, 2025
  • causallib Public

    A Python package for modular causal inference analysis and model evaluations

    BiomedSciAI/causallib’s past year of commit activity
    Python 799 Apache-2.0 106 2 2 Updated Apr 6, 2025
  • r-BRICS Public

    Revised breaking of retrosynthetically interesting chemical substructures (r-BRICS) – a revised BRICS module based on rdKit that breaks ring structures and carbon chains

    BiomedSciAI/r-BRICS’s past year of commit activity
    Python 14 4 1 0 Updated Mar 14, 2025
  • histocartography Public

    A standardized Python API with necessary preprocessing, machine learning and explainability tools to facilitate graph-analytics in computational pathology.

    BiomedSciAI/histocartography’s past year of commit activity
    Python 261 AGPL-3.0 61 18 5 Updated Dec 23, 2023