Publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2026

  1. ICML-W
    CLAMP: A Mechanistic Probe of Regulatory Structure in Foundation Models under Single-Cell Perturbations
    Amaya Gallagher-Syed, Aaron Wenteler, Sebastian A. Martinez, and Gregory Slabaugh
    In ICML 2026 Workshop on Generative and Agentic AI for Biology, 2026
    Spotlight
  2. Preprint
    ProtoPathway: Biologically Structured Prototype-Pathway Fusion for Multimodal Cancer Survival Prediction
    Amaya Gallagher-Syed, Myles J. Lewis, Michael R. Barnes, and Gregory Slabaugh
    2026
    Under review

2025

  1. ICML
    PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction
    Aaron Wenteler, Martina Occhetta, Nikhil Branson, Magdalena Huebner, Victor Curean, William Dee, William Connell, Alex Hawkins-Hooker, Pui Chung, Yasha Ektefaie, C. M. Cordova, and Amaya Gallagher-Syed
    In International Conference on Machine Learning (ICML), 2025
  2. CVPR
    BioX-CPath: Biologically-driven Explainable Diagnostics for Multistain IHC Computational Pathology
    Amaya Gallagher-Syed, Henry Senior, Omnia Alwazzan, Elena Pontarini, Michele Bombardieri, Costantino Pitzalis, Myles J. Lewis, Michael R. Barnes, Luca Rossi, and Gregory Slabaugh
    In IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2025
  3. Lancet Rheum.
    Machine learning to classify the focus score and Sjögren’s disease using digitalised salivary gland biopsies: a retrospective cohort study
    Jonathan Duquesne, Lucas Basseto, Camille Claye, Michael Barnes, Elena Pontarini, Amaya Gallagher-Syed, and  others
    The Lancet Rheumatology, 2025

2024

  1. NeurIPS-W
    Going Beyond H&E and Oncology: How Do Histopathology Foundation Models Perform for Multi-stain IHC and Immunology?
    Amaya Gallagher-Syed, Elena Pontarini, Myles J. Lewis, Michael R. Barnes, and Gregory Slabaugh
    In NeurIPS 2024 Workshop on Advancements in Medical Foundation Models (AIM-FM), 2024
    arXiv
  2. Preprint
    Multimodal Outer Arithmetic Block Dual Fusion of Whole Slide Images and Omics Data for Precision Oncology
    Omnia Alwazzan, Amaya Gallagher-Syed, Thomas O. Millner, Sebastian Brandner, Ioannis Patras, Silvia Marino, and Gregory Slabaugh
    arXiv preprint arXiv:2411.17418, 2024
    arXiv

2023

  1. BMVC
    Multi-Stain Self-Attention Graph Multiple Instance Learning Pipeline for Histopathology Whole Slide Images
    Amaya Gallagher-Syed, Luca Rossi, Felice Rivellese, Costantino Pitzalis, Myles J. Lewis, Michael R. Barnes, and Gregory Slabaugh
    In 34th British Machine Vision Conference (BMVC), 2023

2022

  1. Sci. Data
    RA-MAP, molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients
    RA-MAP Consortium
    Scientific Data, 2022