Evolutionary multi-objective design of autoencoders for compact representation of histopathology whole slide images

Abstract

The recent success of deep learning coincides with the surge of digital pathology as an effect of the pandemic. However, processing a massive volume of gigapixel histopathology images is daunting. Hence, establishing compact image representations for efficient computational pathology becomes paramount. Deep autoencoders have been frequently used to compress feature vectors extracted from pre-trained networks. However, the topology of autoencoders is generally set heuristically. In this paper, we propose a multi-objective evolutionary framework as a bi-level optimization scheme in which the outer level evolves autoencoders for the goal of dimension reduction while the inner level is to optimize their weights for training. Throughout the evolution process, multiple minimization objectives such as complexity, classification error, and code size are considered. These objectives can obtain compressed models to generate a very small set of deep features with the highest classification accuracy. We use images from The Cancer Genome Atlas (TCGA) repository provided by the National Cancer Institute to train and validate our optimization framework. We increased the classification accuracy by 8% while the image representation is 46,000 times shorter. We apply the framework to demonstrate higher accuracy, substantial memory reduction and faster processing for image retrieval compared to SOTA.