Exploring Low-Rank Property in Multiple Instance Learning for Whole Slide Image Classification

Abstract

The classification of gigapixel-sized whole slide images (WSIs) with slide-level labels can be formulated as a multiple-instance-learning (MIL) problem. State-of-the-art models often consist of two decoupled parts: local feature embedding with a pre-trained model followed by a global feature aggregation network for classification. We leverage the properties of the apparent similarity in high-resolution WSIs, which essentially exhibit \textit{low-rank} structures in the data manifold, to develop a novel MIL with a boost in both feature embedding and feature aggregation. We extend the contrastive learning with a pathology-specific Low-Rank Constraint (LRC) for feature embedding to pull together samples (i.e., patches) belonging to the same pathological tissue in the low-rank subspace and simultaneously push apart those from different latent subspaces. At the feature aggregation stage, we introduce an iterative low-rank attention MIL (ILRA-MIL) model to aggregate features with low-rank learnable latent vectors to model global interactions among all instances. We highlight the importance of instance correlation modeling but refrain from directly using the transformer encoder considering the $O(n^2)$ complexity. ILRA-MIL with LRC pre-trained features achieves strong empirical results across various benchmarks, including (i) 96.49\% AUC on the CAMELYON16 for binary metastasis classification, (ii) 97.63\% AUC on the TCGA-NSCLC for lung cancer subtyping, and (iii) 0.6562 kappa on the large-scale PANDA dataset for prostate cancer classification. The code is available at https://github.com/jinxixiang/low_rank_wsi.