The paper introduces scalable Graph Transformers for classifying healthy versus tumor epithelial cells in whole-slide images of cutaneous squamous cell carcinoma. By constructing a full‑WSI cell graph and incorporating morphological, texture, and neighboring cell class features, the proposed SGFormer and DIFFormer models outperform traditional image‑based methods, achieving balanced accuracies above 85% on single‑WSI tests and 83.6% on multi‑WSI evaluations. The study demonstrates that preserving tissue‑level context through graph representations improves classification of morphologically similar cell types.
By Lucas Sanc\'er\'e, No\'emie Moreau, Katarzyna Bozek
arXiv:2609.26073v1 Announce Type: new
Abstract: Pathology foundation models (PFMs) provide strong tile-level representations but remain difficult to interpret at the cellular and microenvironmental s...
By Yuxiang Xiao, Zhiwei Chen, Dan Dai, Wei Li, Tianyang Zhang, Yakun Ju, Yang Hu, Kaixiang Yang
arXiv:2608. 16810v1 Announce Type: cross Abstract: Identifying and representing object instances such as cells or nuclei is a common task in microscopy image analysis.
By Ziwen Liu, Martin Weigert
arXiv:2608. 06037v1 Announce Type: new Abstract: Relational inductive biases are essential for capturing structural dependencies among data.
By Rafa{\l} Buler (Gda\'nsk University of Technology), Jakub Buler (Gda\'nsk University of Technology), Maciej Bobowicz (Medical University of Gda\'nsk), Micha{\l} Grochowski (Gda\'nsk University of Technology)
SpaFactor is a lightweight framework that predicts spatial gene expression from hematoxylin and eosin images by fusing central spot visuals with multiscale neighborhood context. It uses a residual MLP to map tissue microenvironment to low‑dimensional latent gene programs, which are decoded into coordinated multi‑gene predictions. Across five public cohorts, SpaFactor outperforms existing methods, especially for spatially variable genes, and better recovers biologically organized spatial patterns.
By Shiting Ruan, Xitong Ling, Qiming He, Ziyou Yan, Huaitian Yuan, Tian Guan, Ying Xiao, Xu Guan, Yonghong He
The paper introduces a biology-informed heterogeneous graph representation that models retinal vessel segments, intercapillary areas, and the foveal avascular zone to predict diabetic retinopathy stages from OCTA images. This graph-based approach reframes staging as a graph-level classification task solved with a graph neural network, achieving AUC-ROC values up to 84% and outperforming biomarker-based classifiers, CNNs, and vision transformers. The method also provides detailed, interpretable explanations by precisely localizing abnormal vessels and non-perfusion areas.
By Laurin Lux, Alexander H. Berger, Maria Romeo Tricas, Richard Rosen, Alaa E. Fayed, Sobha Sivaprasada, Linus Kreitner, Jonas Weidner, Martin J. Menten, Daniel Rueckert, Johannes C. Paetzold