‌Navigating the MIL Trade-Off: Flexible Pooling for Whole Slide Image Classification

Hossein Jafarinia, Danial Hamdi, Amirhossein Alamdar, Elahe Zahiri, Soroush Vafaie Tabar, Alireza Alipanah, Nahal Mirzaie, Saeed Razavi, Amir Najafi, Mohammad Hossein Rohban

Keywords: Whole Slide Image, Self-Supervised Learning, Multiple Instance Learning, Data Augmentation

Abstract: Multiple Instance Learning (MIL) is a standard weakly supervised approach for Whole Slide Image (WSI) classification, where performance hinges on both feature representation and MIL pooling strategies. Recent research has predominantly focused on Transformer-based architectures adapted for WSIs. However, we argue that this trend faces a fundamental limitation: data scarcity. In typical settings, Transformer models yield only marginal gains without access to large-scale datasets—resources that are virtually inaccessible to all but a few well-funded research labs. Motivated by this, we revisit simple, non-attention MIL with unsupervised slide features and analyze temperature-$\beta$-controlled log-sum-exp (LSE) pooling. For slides partitioned into $N$ patches, we theoretically show that LSE has a smooth transition at a critical $\beta_{\mathrm{crit}}=\mathcal{O}(\log N)$ threshold, interpolating between mean-like aggregation (stable, better generalization but less sensitive) and max-like aggregation (more sensitive but looser generalization bounds). Grounded in this analysis, we introduce Maxsoft—a novel MIL pooling function that enables flexible control over this trade-off, allowing adaptation to specific tasks and datasets. To further tackle real-world deployment challenges such as specimen heterogeneity, we propose PerPatch augmentation—a simple yet effective technique that enhances model robustness. Empirically, Maxsoft achieves state-of-the-art performance in low-data regimes across four major benchmarks (CAMELYON16, CAMELYON17, TCGA-Lung, and SICAP-MIL), often matching or surpassing large-scale foundation models. When combined with PerPatch augmentation, this performance is further improved through increased robustness. Code is available at \href{https://github.com/jafarinia/maxsoft}{\texttt{https://github.com/jafarinia/maxsoft}}

Primary Area: Machine learning for sciences (e.g. climate, health, life sciences, physics, social sciences)

Submission Number: 26125