Mixing Histopathology Prototypes into Robust Slide-Level Representations for Cancer Subtyping

• URL: http://arxiv.org/abs/2310.12769v1
• Date: Thu, 19 Oct 2023 14:15:20 GMT
• Title: Mixing Histopathology Prototypes into Robust Slide-Level Representations for Cancer Subtyping
• Authors: Joshua Butke, Noriaki Hashimoto, Ichiro Takeuchi, Hiroaki Miyoshi, Koichi Ohshima, Jun Sakuma
• Abstract summary: Whole-slide image analysis via the means of computational pathology often relies on processing tessellated gigapixel images with only slide-level labels available. Applying multiple instance learning-based methods or transformer models is computationally expensive as each image, all instances have to be processed simultaneously. TheMixer is an under-explored alternative model to common vision transformers, especially for large-scale datasets.
• Score: 19.577541771516124
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Whole-slide image analysis via the means of computational pathology often relies on processing tessellated gigapixel images with only slide-level labels available. Applying multiple instance learning-based methods or transformer models is computationally expensive as, for each image, all instances have to be processed simultaneously. The MLP-Mixer is an under-explored alternative model to common vision transformers, especially for large-scale datasets. Due to the lack of a self-attention mechanism, they have linear computational complexity to the number of input patches but achieve comparable performance on natural image datasets. We propose a combination of feature embedding and clustering to preprocess the full whole-slide image into a reduced prototype representation which can then serve as input to a suitable MLP-Mixer architecture. Our experiments on two public benchmarks and one inhouse malignant lymphoma dataset show comparable performance to current state-of-the-art methods, while achieving lower training costs in terms of computational time and memory load. Code is publicly available at https://github.com/butkej/ProtoMixer.

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