Investigating the Impact of Histopathological Foundation Models on Regressive Prediction of Homologous Recombination Deficiency
This work addresses the need for more precise and transferable biomarker prediction in AI-driven precision oncology, though it represents an incremental application of existing foundation models to a specific medical regression task.
The researchers evaluated five histopathological foundation models for predicting continuous homologous recombination deficiency (HRD) scores from whole slide images across breast, endometrial, and lung cancer cohorts, finding they consistently outperformed contrastive learning baselines in accuracy and generalization while also proposing an upsampling strategy that improved recall and balanced accuracy for underrepresented patient populations.
Foundation models pretrained on large-scale histopathology data have found great success in various fields of computational pathology, but their impact on regressive biomarker prediction remains underexplored. In this work, we systematically evaluate histopathological foundation models for regression-based tasks, demonstrated through the prediction of homologous recombination deficiency (HRD) score - a critical biomarker for personalized cancer treatment. Within multiple instance learning frameworks, we extract patch-level features from whole slide images (WSI) using five state-of-the-art foundation models, and evaluate their impact compared to contrastive learning-based features. Models are trained to predict continuous HRD scores based on these extracted features across breast, endometrial, and lung cancer cohorts from two public medical data collections. Extensive experiments demonstrate that models trained on foundation model features consistently outperform the baseline in terms of predictive accuracy and generalization capabilities while exhibiting systematic differences among the foundation models. Additionally, we propose a distribution-based upsampling strategy to mitigate target imbalance in these datasets, significantly improving the recall and balanced accuracy for underrepresented but clinically important patient populations. Furthermore, we investigate the impact of different sampling strategies and instance bagsizes by ablation studies. Our results highlight the benefits of large-scale histopathological pretraining for more precise and transferable regressive biomarker prediction, showcasing its potential to advance AI-driven precision oncology.