Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology

Oren Kraus, Kian Kenyon-Dean, Saber Saberian, Maryam Fallah, Peter McLean, Jess Leung, Vasudev Sharma, Ayla Khan, Jia Balakrishnan, Safiye Celik, Dominique Beaini, Maciej Sypetkowski, Chi Vicky Cheng, Kristen Morse, Maureen Makes, Ben Mabey, Berton Earnshaw; Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2024, pp. 11757-11768

Abstract


Featurizing microscopy images for use in biological research remains a significant challenge especially for large-scale experiments spanning millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond.

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[bibtex]
@InProceedings{Kraus_2024_CVPR, author = {Kraus, Oren and Kenyon-Dean, Kian and Saberian, Saber and Fallah, Maryam and McLean, Peter and Leung, Jess and Sharma, Vasudev and Khan, Ayla and Balakrishnan, Jia and Celik, Safiye and Beaini, Dominique and Sypetkowski, Maciej and Cheng, Chi Vicky and Morse, Kristen and Makes, Maureen and Mabey, Ben and Earnshaw, Berton}, title = {Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology}, booktitle = {Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)}, month = {June}, year = {2024}, pages = {11757-11768} }