Learning Binary and Sparse Permutation-Invariant Representations for Fast and Memory Efficient Whole Slide Image Search

Abstract: Learning suitable Whole slide images (WSIs) representations for efficient retrieval systems is a non-trivial task. The WSI embeddings obtained from current methods are in Euclidean space not ideal for efficient WSI retrieval. Furthermore, most of the current methods require high GPU memory due to the simultaneous processing of multiple sets of patches. To address these challenges, we propose a novel framework for learning binary and sparse WSI representations utilizing a deep generative modelling and the Fisher Vector. We introduce new loss functions for learning sparse and binary permutation-invariant WSI representations that employ instance-based training achieving better memory efficiency. The learned WSI representations are validated on The Cancer Genomic Atlas (TCGA) and Liver-Kidney-Stomach (LKS) datasets. The proposed method outperforms Yottixel (a recent search engine for histopathology images) both in terms of retrieval accuracy and speed. Further, we achieve competitive performance against SOTA on the public benchmark LKS dataset for WSI classification.