MIL vs. Aggregation: Evaluating Patient-Level Survival Prediction Strategies Using Graph-Based Learning

Abstract: Oncologists often rely on a multitude of data, including whole-slide images (WSIs), to guide therapeutic decisions, aiming for the best patient outcome. However, predicting the prognosis of cancer patients can be a challenging task due to tumor heterogeneity and intra-patient variability, and the complexity of analyzing WSIs. These images are extremely large, containing billions of pixels, making direct processing computationally expensive and requiring specialized methods to extract relevant information. Additionally, multiple WSIs from the same patient may capture different tumor regions, some being more informative than others. This raises a fundamental question: Should we use all WSIs to characterize the patient, or should we identify the most representative slide for prognosis? Our work seeks to answer this question by performing a comparison of various strategies for predicting survival at the WSI and patient level. The former treats each WSI as an independent sample, mimicking the strategy adopted in other works, while the latter comprises methods to either aggregate the predictions of the several WSIs or automatically identify the most relevant slide using multiple-instance learning (MIL). Additionally, we evaluate different Graph Neural Networks architectures under these strategies. We conduct our experiments using the MMIST-ccRCC dataset, which comprises patients with clear cell renal cell carcinoma (ccRCC). Our results show that MIL-based selection improves accuracy, suggesting that choosing the most representative slide benefits survival prediction.