Adaptive Patching for High-resolution Image Segmentation with Transformers

Enzhi Zhang, Isaac Lyngaas, Peng Chen, Xiao Wang, Jun Igarashi, Yuankai Huo, Masaharu Munetomo, Mohamed Wahib

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Attention-based models are proliferating in the space of image analytics, including segmentation. The standard method of feeding images to transformer encoders is to divide the images into patches and then feed the patches to the model as a linear sequence of tokens. For high-resolution images, e.g. microscopic pathology images, the quadratic compute and memory cost prohibits the use of an attention-based model, if we are to use smaller patch sizes that are favorable in segmentation. The solution is to either use custom complex multi-resolution models or approximate attention schemes. We take inspiration from Adapative Mesh Refinement (AMR) methods in HPC by adaptively patching the images, as a pre-processing step, based on the image details to reduce the number of patches being fed to the model, by orders of magnitude. This method has a negligible overhead, and works seamlessly with any attention-based model, i.e. it is a pre-processing step that can be adopted by any attention-based model without friction. We demonstrate superior segmentation quality over SoTA segmentation models for real-world pathology datasets while gaining a geomean speedup of 6.9 × for resolutions up to 64 K2, on up to 2,048 GPUs.

Original languageEnglish
Title of host publicationProceedings of SC 2024
Subtitle of host publicationInternational Conference for High Performance Computing, Networking, Storage and Analysis
PublisherIEEE Computer Society
ISBN (Electronic)9798350352917
DOIs
StatePublished - 2024
Event2024 International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2024 - Atlanta, United States
Duration: Nov 17 2024Nov 22 2024

Publication series

NameInternational Conference for High Performance Computing, Networking, Storage and Analysis, SC
ISSN (Print)2167-4329
ISSN (Electronic)2167-4337

Conference

Conference2024 International Conference for High Performance Computing, Networking, Storage and Analysis, SC 2024
Country/TerritoryUnited States
CityAtlanta
Period11/17/2411/22/24

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