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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 Public

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

    Python 144 36

  2. causallib Public

    A Python package for modular causal inference analysis and model evaluations

    Python 762 99

  3. 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 33 14

  4. 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 23 6

Repositories

Showing 10 of 13 repositories
  • causallib Public

    A Python package for modular causal inference analysis and model evaluations

    Python 762 Apache-2.0 99 2 2 Updated Mar 20, 2025
  • Python 0 0 0 0 Updated Mar 20, 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.

    Python 33 Apache-2.0 14 0 4 Updated Mar 17, 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

    Python 9 4 1 0 Updated Mar 14, 2025
  • fuse-drug Public

    FuseMedML based molecular biochemistry library for drug discovery/repurposing

    Python 21 Apache-2.0 5 10 2 Updated Mar 13, 2025
  • gene-benchmark Public

    Benchmark gene representations from different model families

    Jupyter Notebook 10 Apache-2.0 0 2 1 Updated Mar 10, 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.

    Python 23 Apache-2.0 6 0 1 Updated Feb 27, 2025
  • fuse-med-ml Public

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

    Python 144 Apache-2.0 36 24 (4 issues need help) 10 Updated Feb 23, 2025
  • histocartography Public

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

    Python 251 AGPL-3.0 58 17 5 Updated Dec 23, 2023
  • Geno4SD Public

    An python omics data toolkit for the analysis across biological scales

    Jupyter Notebook 10 Apache-2.0 1 0 0 Updated Dec 5, 2023

People

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