publications

2025

1. 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

   IEEE Conference on Computer Vision and Pattern Recognition, 2025
2. 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, 2025

2024

1. 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, and  others

   bioRxiv, 2024
2. 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

   NeurIPS 2024 AIM-FM Workshop, 2024

2023

1. 

   Multi-Stain Self-Attention Graph Multiple Instance Learning Pipeline for Histopathology Whole Slide Images

   Amaya Gallagher-Syed, Luca Rossi, Felice Rivellese, Costantino Pitzalis, Myles Lewis, Michael Barnes, and Gregory Slabaugh

   In 34th British Machine Vision Conference 2023, BMVC 2023, Aberdeen, UK, November 20-24, 2023, 2023

2. 

   OP0232 deep learning accurately predicts focus score and diagnosis of primary sjögren syndrome using labial salivary gland biopsies

   L Basseto, J Duquesne, V Bouget, M Barnes, E Pontarini, A Gallagher-Syed, M Bombardieri, B Fisher, S Nayar, C Adam, and  others

   Annals of the Rheumatic Diseases, 2023

2022

1. RA-MAP, molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients

   Scientific data, 2022

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