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:2603. 11872v3 Announce Type: replace-cross Abstract: Translating single-cell RNA sequencing (scRNA-seq) data into mechanistic biological hypotheses remains a critical bottleneck, as agentic AI systems lack direct access to transcriptomic representations while expression foundation models remain opaque to natural language.
By Omar Coser
arXiv:2606. 26563v1 Announce Type: cross Abstract: Single-cell studies require analysts to convert raw measurements into specific biological claims through multi-step workflows and integration of metadata, assay context, and auxiliary evidence.
By Ian Diks, Zhen Yang, Arjun Banerjee, Tim Proctor, Kenny Workman
arXiv:2608.24688v1 Announce Type: new
Abstract: Precision oncology necessitates a longitudinal model of patient state that captures cancer evolution and treatment over time, integrating multimodal ob...
By Eugene Vorontsov, Yi Kan Wang, Alican Bozkurt, Adam Casson, Ludmila Tydlitatova, Michal Zelechowski, Ezra E. W. Cohen, Jyoti D. Patel, Max Banaszak, Caitlin McWilliams, Shane Colley, Kate Sasser, Ryan Fukushima, Eric Lefkofsky, Razik Yousfi, Siqi Liu
arXiv:2607. 23821v1 Announce Type: new Abstract: Identifying therapeutic target genes from single-cell RNA sequencing (scRNA-seq) data remains a fundamental challenge in translational biology.
By Shuyu Chen, Chen Zhu, Ye Zhang, Yang Li, Qiqi Xie, Haohan Wang
The paper introduces Conserved Immune Topology (CIT), a lightweight spatial representation that enhances cross‑cancer MSI‑H prediction by augmenting pathology foundation‑model embeddings with immune‑related descriptors. CIT identifies immune‑associated tiles via unsupervised clustering and encodes features such as tertiary lymphoid structures, peritumoral immune reactions, tumor‑infiltrating lymphocyte density, and immune‑tumor mixing, all without requiring annotations or target‑domain data. In cross‑site and cross‑cancer experiments on CPTAC‑COAD and TCGA‑STAD cohorts, CIT improved zero‑shot TransMIL AUC from 0.6627 to 0.7161, demonstrating that spatial immune topology can provide an organ‑invariant representation for MSI‑H prediction.
By Dasari Naga Raju