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
arXiv:2609.36429v1 Announce Type: new
Abstract: Predicting gene expression from H&E-stained histology images offers a scalable alternative to costly spatial transcriptomics, yet most existing methods...
By Zijun Gao, Chunbin Gu, Jinxi Xiang, Xiangde Luo, Pheng-Ann Heng
Reconstructing lineages from live-imaging microscopy requires linking cell detections across time, including through cell divisions. A common approach is to construct a candidate graph and associate cell segmentations (nodes) across frames.
The paper introduces the Semantic-Aware Subgraph State Space Model (SASG-SSM) for classifying whole slide images in histopathology. It groups spatially connected patches into semantic subgraphs that preserve internal spatial organization, then uses a graph neural network encoder combined with a Mamba-based state space encoder to integrate local and global contextual information. Experiments on four WSI subtyping datasets show consistent performance gains over state‑of‑the‑art methods, with additional robustness in small‑cohort and few‑shot scenarios.
arXiv:2606. 29773v1 Announce Type: new Abstract: Graphs are widely used to model relational systems, with applications in domains such as social networks, finance, and biomedicine.
By Haoxin Sun, Yiqing Lin, Yajun Huang, Chenhui Dong, Mingjun Li, Zhongzhi Zhang
arXiv:2606. 07633v1 Announce Type: cross Abstract: Accurate classification of nuclei subtypes in histopathology images is critical for downstream tasks including tumor grading, immune infiltrate quantification, and prognosis prediction.
By Spoorthi M, Suja Palaniswamy
arXiv:2606. 02602v1 Announce Type: new Abstract: In computational pathology, Whole Slide Images (WSIs) survival analysis is crucial for patient prognosis assessment, but it faces multiple technical challenges.
By Yuanfang Chen, Peiqiang Yan, Yuntao Shou, Qian Zhao, Xiangyong Cao