arXiv subjects

Johan Vallon-Christersson

Publications and source records attributed to Johan Vallon-Christersson.

2 recordsLinked to original sources

arXiv2026

Evaluation and Prognostic Validation of Deep Regression Models for WSI-Based Gene-Expression Prediction

Gene-expression profiling is widely used in research and central to many areas of precision oncology, but remains costly and not universally accessible. Recent advances in computational pathology enable prediction of transcriptomic profiles directly from hematoxylin and eosin (H&E)-stained whole-slide images (WSIs), although optimal modeling strategies and clinical relevance remain unclear. In this study, we systematically evaluate deep regression models for WSI-based gene-expression prediction across multiple regression formulations and pathology foundation models (PFMs), and assess whether the resulting predicted transcriptomic signals retain prognostic utility. Across four TCGA datasets, we find that direct regression using attention-based multiple instance learning together with PFM feature extractors provides a strong and computationally efficient baseline, with no consistent benefit from separately training multiple models on subsets of genes. We then externally validate the selected configuration on an independent cohort of 997 breast cancer patients, demonstrating robust generalization for clinically relevant gene sets such as PAM50. To assess clinical relevance, we further evaluate predicted gene-expression scores in two independent population-representative breast cancer cohorts comprising 4,172 patients with survival endpoints, where predicted scores retain prognostic value in both the full patient cohort and the ER+ & HER2- subgroup. Together, these results demonstrate that WSI-based gene-expression prediction can generalize across independent cohorts and recover biologically and clinically meaningful molecular structure, supporting its potential as a scalable approach for transcriptomic phenotyping and risk stratification.

q-bio.GN↗

arXiv2026

Benchmarking Pathology Foundation Models for Breast Cancer Survival Prediction

Pathology foundation models (PFMs) have recently emerged as powerful pretrained encoders for computational pathology, enabling transfer learning across a wide range of downstream tasks. However, systematic comparisons of these models for clinically meaningful prediction problems remain limited, especially in the context of survival prediction under external validation. In this study, we benchmark widely used and recently proposed PFMs for breast cancer survival prediction from whole-slide histopathology images. Using a standardized pipeline based on patch-level feature extraction and a unified survival modeling framework, we evaluate model representations across three independent clinical cohorts comprising more than 5,400 patients with long-term follow-up. Models are trained on one cohort and evaluated on two independent external cohorts, enabling a rigorous assessment of cross-dataset generalization. Overall, H-optimus-1 achieves the strongest survival prediction performance. More broadly, we observe consistent generational improvements across model families, with second-generation PFMs outperforming their first-generation counterparts. However, absolute performance differences between many recent PFMs remain modest, suggesting diminishing returns from further scaling of pretraining data or model size alone. Notably, the compact distilled model H0-mini slightly outperforms its larger teacher model H-optimus-0, despite using fewer than 8% of the parameters and enabling significantly faster feature extraction. Together, these results provide the first large-scale, externally validated benchmark of PFMs for breast cancer survival prediction, and offer practical guidance for efficient deployment of PFMs in clinical workflows.

cs.CV↗