arXiv AI By Yesung Cho, Ji Hwan Park, Chanil Kim, Hyewon Kim, Honglan Li, Yumin Lee, Geongyu Lee, Sujeong Hong, Seong Min Park, Yoonyoung Lee, Hee Sool Rho, Sumin Lee, Amos Chungwon Lee, Changhwan Lee, Hwanyoung Shim, Hyunwook Kim, Hyeji Shin, Sanha Park, Jihoon Yu, Yoon Hee Shin, Sooheon Kim, Hyunjin Park, Seung Min Park, Sangwan Kim, Yujung Kim, Sung-Im Do, Eun-Young Kim, Dongmyung Shin, Jongbae Park, In-Gu Do

Spatial proteomics guided by H&E-based AI reveals recurrence-risk niches in triple-negative breast cancer

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arXiv:2608. 03145v1 Announce Type: new Abstract: Deep learning models can predict cancer recurrence from H&E stained slides, but the localized molecular states underlying these predictions remain largely obscured.

Summary generated by The Flow from the publisher's feed. The full article lives at arXiv AI.

arXiv Machine Learning
Jul 28

INSIGHT: Spatially resolved survival modelling from routine histology crosslinked with molecular profiling reveals prognostic epithelial-immune axes in stage II/III colorectal cancer

arXiv:2512. 22262v2 Announce Type: replace-cross Abstract: Routine histology contains rich prognostic information in stage II/III colorectal cancer, much of which is embedded in complex spatial tissue organisation.

By Piotr Keller, Mark Eastwood, Zedong Hu, Aim\'ee Selten, Ruqayya Awan, Gertjan Rasschaert, Sara Verbandt, Vlad Popovici, Hubert Piessevaux, Hayley T Morris, Petros Tsantoulis, Thomas Alexander McKee, Andr\'e D'Hoore, C\'edric Schraepen, Xavier Sagaert, Gert De Hertogh, Sabine Tejpar, Fayyaz Minhas
arXiv AI
Jun 30

Data-Efficient Multimodal Alignment for Histopathology-based Molecular Prediction

arXiv:2606. 29949v1 Announce Type: cross Abstract: H&E-stained whole-slide images offer cohort-scale availability and rich spatial context but lack molecular specificity, whereas bulk RNA-seq provides transcriptome-wide resolution at high cost with limited archival availability.

By Dominik Winter, Dominik Vonficht, Lo\"ic Le Bescond, Christian Gebbe, Marco Rosati, Richard J. Chen, Markus Schick, Ross Stewart, Nicolas Brieu
arXiv Machine Learning
Jun 5

HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data

arXiv:2506. 11152v4 Announce Type: replace-cross Abstract: Single-cell transcriptomics and proteomics have become a great source for data-driven insights into biology, enabling the use of advanced deep learning methods to understand cellular heterogeneity and gene expression at the single-cell level.

By Hiren Madhu, Jo\~ao Felipe Rocha, Tinglin Huang, Siddharth Viswanath, Smita Krishnaswamy, Rex Ying
arXiv Machine Learning
Jun 3

Spatial Transcriptomics-Guided Alignment Enhances Molecular Profiling in Pathology Foundation Model

arXiv:2606. 03644v1 Announce Type: new Abstract: Comprehensive molecular profiling is essential for modern precision oncology but remains hindered by prohibitive costs, specimen exhaustion, and protracted turnaround times.

By Fengtao Zhou, Yingxue Xu, Zhengyu Zhang, Yihui Wang, Zhengrui Guo, Ling Liang, Jiabo Ma, Cheng Jin, Ziyi Liu, Huajun Zhou, Hongyi Wang, Du Cai, Chenglong Zhao, Xi Wang, Can Yang, Yu Wang, Wenbin Li, Feng Gao, Zhe Wang, Zhenhui Li, Xiuming Zhang, Li Liang, Hao Chen