Scan-Invariant Mamba With Differentiated Sequence Contrastive Learning in Computational Pathology

Multiple instance learning (MIL) is a commonly used paradigm for histopathological analysis due to the ultra-high resolution and coarse-grained labels of Whole Slide Images (WSIs). Recent studies apply Mamba architecture to WSI classification by modeling MIL as long-sequence tasks, but a key discrepancy remains: Mamba's output is sensitive to scanning modes, whereas MIL requires scan-invariant predictions. To address this problem, we propose Scan-invariant Mamba with Differentiated Sequence Contrastive Learning (SMDC-MIL), a novel Mamba-based MIL approach enabling bag-level feature learning independent of input modes. Our method mitigates scanning-mode impacts and adapts Mamba to learn the bag discrimination features that are independent of the input mode via two innovations: 1) a differentiated sequence generation mechanism that employs instance rearrangement, augmentation, and masking to simulate real-world scanning variations by maximizing differences in sequence order, length, and composition from the same WSI; and 2) a differentiated sequence contrastive learning architecture that enforces consistent bag-level representations and predictions across diverse sequences using the same Mamba model, guiding it to prioritize scan-invariant discriminative features. Experimental results on 4 computational pathology tasks and 10 datasets demonstrate that our SMDC-MIL achieves state-of-the-art performance compared to other methods. The corresponding code is available at https://github.com/LianYueZ/SMDCMIL.git.