Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles. Preclinical transfer-learning models can simulate drug-induced expression changes but are often hard to interpret and unstable, whereas knowledge-graph methods provide mechanistic context yet remain static and fail to capture drug-induced transcriptomic perturbation dynamics.
arXiv:2607. 04557v1 Announce Type: cross Abstract: Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles.
By Dongmin Bang, Sugyun An, Inyoung Sung, Ilho Yun, Sun Kim, Sangseon Lee
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:2510.06113v2 Announce Type: replace
Abstract: Survival analysis plays a vital role in making clinical decisions. However, the models currently in use are often difficult to interpret, which red...
By Shuo Jiang, Zhuwen Chen, Liaoman Xu, Yanming Zhu, Changmiao Wang, Jiong Zhang, Feiwei Qin, Yifei Chen, Zhu Zhu
arXiv:2607. 04912v1 Announce Type: cross Abstract: In patients with breast cancer, pathological complete response (pCR) has been established as a clinically meaningful surrogate marker for long-term outcomes.
By Johannes Kiechle, Richard Osuala, Daniel M. Lang, Stefan M. Fischer, Ivana Jan\'i\v{c}kov\'a, Karim Lekadir, Julia A. Schnabel, Jan C. Peeken
arXiv:2610.07694v1 Announce Type: new
Abstract: The integrative analysis of histopathological Whole-Slide Images (WSIs) and transcriptomic profiles holds significant promise for cancer survival predi...
By Tao Zhou, Ying Hu, Huazhu Fu, Yi Zhou, Xiao-Jun Wu, Haibin Ling
arXiv:2606. 17115v1 Announce Type: cross Abstract: Foundation models (FMs) have emerged as powerful representation extractors for medical data, yet their generalizability to datasets under distribution shift remains underexplored.
By Jingyu Hu, Giuseppe Tripodi, Reed Naidoo, Sarah F. McGough, Tapabrata Chakraborti
arXiv:2610.03693v1 Announce Type: new
Abstract: Scarcity of labeled data limits development of deep learning biomarkers in oncology. We develop a two-stage AI model predicting pathological complete r...
By Jungkyu Park, Dhruva Biswas, Joseph Cappadona, Cerise Tang, Ken G. Zeng, Bartosz Machura, Chuwen Liu, Paolo Tarantino, Coral Omene, Francisco J. Esteva, Rohit Bhargava, Marcin Braun, Kamila Pa\'zdzierz, Jakub Czerwi\'nski, Hanna Roma\'nska-Knight, Albert Grinshpun, Bareket Daniel, Michele Buchinger, Frederick Howard, Piotr Wysocki, Brie Chun, Freya Schnabel, Rich Caruana, Jan Witowski, Krzysztof J. Geras
arXiv:2606. 09898v1 Announce Type: new Abstract: Cancer treatment planning requires decisions across multiple clinical dimensions at once.
By Sujoy Banik, Sayantan Chakraborty, Boishakhi Das Toma, Zainab Ghafoor, Ushashi Bhattacharjee, Koushik Howlader, Tirtho Roy
The paper presents a newly curated, multi-center, multi-modal, and longitudinal lung cancer dataset comprising 1,365 patients with whole-slide images, CT scans, PET scans, structured clinical data, transcriptomics, and follow-up information. The dataset features substantial, non-uniform missingness across modalities, making it ideal for evaluating robust multi-modal fusion strategies. Benchmarks on 12‑month overall survival, disease‑specific survival, and longitudinal hazard prediction demonstrate that integrating complementary modalities consistently outperforms uni-modal approaches, even under severe missing data.
By Rita Cordeiro Mendes, Maria Rita Fonseca Verdelho, Carlos Santiago, Catarina Barata
arXiv:2512.08029v4 Announce Type: replace
Abstract: Clinical decision-making in oncology requires forecasting how disease evolves under treatment, yet most AI systems remain static predictors that ca...
By Tianxingjian Ding, Yuanhao Zou, Chen Chen, Mubarak Shah, Yu Tian
MultiSigBERT is a unified framework that performs multimodal sequential survival modeling in oncology by integrating narrative clinical reports, numerical measurements, and structured variables. The method converts free-text reports into sentence embeddings, compresses them with modality-specific PCA, and concatenates them with structured covariates to create joint temporal trajectories. These trajectories are encoded using the Signature transform from Rough Paths theory, and the resulting high-dimensional features are fed into a LASSO-regularized Cox model, achieving a concordance index of 0.743 on an independent test set of over 2,500 patients.
By Paul Minchella, St\'ephane Chr\'etien, Guillaume Metzler, Lo\"ic Verlingue, R\'emi Vaucher