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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 137 34

  2. causallib causallib Public

    A Python package for modular causal inference analysis and model evaluations

    Python 733 97

  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 22 10

  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 15 3

Repositories

Showing 10 of 12 repositories
  • 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 22 Apache-2.0 10 0 2 Updated Nov 14, 2024
  • 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 137 Apache-2.0 34 24 (5 issues need help) 10 Updated Nov 13, 2024
  • fuse-drug Public

    FuseMedML based molecular biochemistry library for drug discovery/repurposing

    BiomedSciAI/fuse-drug’s past year of commit activity
    Python 14 Apache-2.0 5 10 1 Updated Nov 11, 2024
  • gene-benchmark Public

    Benchmark gene representations from different model families

    BiomedSciAI/gene-benchmark’s past year of commit activity
    Jupyter Notebook 5 Apache-2.0 0 0 1 Updated Nov 5, 2024
  • 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 15 Apache-2.0 3 1 0 Updated Nov 1, 2024
  • causallib Public

    A Python package for modular causal inference analysis and model evaluations

    BiomedSciAI/causallib’s past year of commit activity
    Python 733 Apache-2.0 97 2 2 Updated Jul 31, 2024
  • 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 241 AGPL-3.0 57 17 5 Updated Dec 23, 2023
  • Geno4SD Public

    An python omics data toolkit for the analysis across biological scales

    BiomedSciAI/Geno4SD’s past year of commit activity
    Jupyter Notebook 10 Apache-2.0 1 0 0 Updated Dec 5, 2023
  • 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 7 2 0 0 Updated Jul 24, 2023
  • BiomedSciAI/multimodal-models-toolkit’s past year of commit activity
    Jupyter Notebook 7 0 1 0 Updated Jun 23, 2023

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