arXiv Machine Learning By Yuheng Liang, Lucy Chhuo, Ahmadreza Argha, Nona Farbehi, Lu Chen, Roohallah Alizadehsani, Mehdi Hosseinzadeh, Min Yang, Thantrira Porntaveetusm, Youqiong Ye, Hamid Alinejad-Rokny

Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability

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The study evaluated nine transcriptomic models—five bulk RNA‑seq and four single‑cell RNA‑seq—designed to predict response to immune checkpoint inhibitors. Across independent datasets, bulk models performed near chance while single‑cell models offered only modest gains, and pathway analyses revealed inconsistent biomarker signals. The results highlight the limited cross‑cohort robustness and biological consistency of current transcriptomic ICI predictors.

Machine-generated by The Flow from the publisher's headline and feed description — not written or checked by a human. The full article lives at arXiv Machine Learning.

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.

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arXiv AI
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ELISA: An Interpretable Hybrid Generative AI Agent for Expression-Grounded Discovery in Single-Cell Genomics

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By Omar Coser
arXiv Machine Learning
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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 Computer Vision
Sep 7

Conserved Immune Topology Improves Pathology Foundation Model Generalization for Cross-Cancer MSI-H Prediction

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