arXiv Machine Learning By Taoyong Cui, Xi Wang, Zonghang Li, Jinchao Ding, Lingsen You, Yuzhi Xu, Wanghan Xu, Fang Wu, Kejun Ying, Wanli Ouyang, Pheng Ann Heng, Ling Yang, Zhenfei Yin, Yingcheng Wu

An immune world model for multiscale forecasting and therapeutic hypothesis generation

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arXiv Machine Learning
Sep 18

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

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.

By Yuheng Liang, Lucy Chhuo, Ahmadreza Argha, Nona Farbehi, Lu Chen, Roohallah Alizadehsani, Mehdi Hosseinzadeh, Min Yang, Thantrira Porntaveetusm, Youqiong Ye, Hamid Alinejad-Rokny
arXiv Machine Learning
4d ago

Estimating the Causal Effects of T Cell Receptors

The paper introduces a method for estimating the causal effects of T cell receptor (TCR) sequences on patient outcomes using observational TCR sequencing and clinical data. It corrects for unobserved confounders by leveraging the pre-selection TCR repertoire generated through V(D)J recombination as a natural experiment, and employs permutation‑invariant neural networks to scale to millions of sequences. The approach is validated on semisynthetic data and applied to COVID‑19 severity, identifying TCRs that are observed in patients, bind SARS‑CoV‑2 antigens in vitro, and positively influence clinical outcomes.

By Eli N. Weinstein, Elizabeth B. Wood, David M. Blei
arXiv Computation and Language
Sep 18

JEPA-Anything: Learning Predictive Models across Different Worlds

JEPA-Anything is a domain‑agnostic framework that uses orthogonal predictive factorization (OPF) to decompose latent targets into complementary factors, learn them via dedicated pathways, and recombine them for shared prediction. The method is evaluated across seven diverse domains—vision, biology, clinical trajectories, control, molecular dynamics, physical fields, and weather—showing improvements on 10 dynamics tasks, reduced error on Interventional Pong, and lowest one‑step and 100‑step molecular errors among compared methods. Experimental validation includes a factor‑nominated biological intervention that succeeded in cell co‑cultures, organoids, tumor fragments, and mice, and latent orbital modes that recover the Keplerian scaling exponent.

By Taoyong Cui, Zhongyao Wang, Xinyue Xu, Weiyang Liu, Zhaochen Yu, Yuying Zhang, Qiang Gao, Mengyue Yang, Wanli Ouyang, Pheng Ann Heng, Yingcheng Wu, Zhenfei Yin, Ling Yang
arXiv AI
Jul 22

Biological Amnesia in ICU Time-Series Prediction: A Drift-Adaptive Two-Stream Architecture with Temporal Retrieval

arXiv:2607. 19020v1 Announce Type: cross Abstract: Background: Clinical decision support systems degrade silently as treatment protocols evolve, yet standard adaptation methods treat models as monolithic blocks, unable to distinguish stable patient physiology from shifting institutional practice.

By Fatema Ferdous Tamanna, K. M. Merajul Arefin, Md. Abdul Masud