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AmayaGS/README.md

Hiya 👋 I'm Amaya 🦖

I work at the intersection of AI and biology!

I've developed interpretable deep learning algorithms for biomedical data, with expertise in histopathology and transcriptomics for biomarker discovery and patient stratification in cancer and immunology.

I'm now focusing on modelling cell-cell interactions, biology Foundation models and information propagation in biological systems ✨ 💫

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  1. ProtoPathway ProtoPathway Public

    Interpretable multimodal cancer survival prediction from whole slide images and bulk transcriptomics, with prototype-pathway cross-modal attention.

    Python 6

  2. BioX-CPath BioX-CPath Public

    A biologically interpretable graph neural network for multistain computational pathology - CVPR 2025

    Python 28 1

  3. aaronwtr/PertEval aaronwtr/PertEval Public

    Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.

    Python 37 8

  4. ImmunoHistoBench ImmunoHistoBench Public

    A benchmark of histopathology Foundation Models on multi-stain Immunohistochemistry immune datasets AIM-FM workshop @ NeurIPS 24

    Python 11

  5. MUSTANG MUSTANG Public

    Multi-stain graph self attention multiple instance learning for histopathology Whole Slide Images - BMVC 2023

    Python 14 1

  6. WSI_Segmentation WSI_Segmentation Public

    Automated segmentation of H&E and Immunohistochemistry stained synovial tissue in histopathology Whole Slide Images - MIUA 2023

    Python 6