ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy

Abstract

Deriving insights from experimentally generated datasets requires methods that can account for random and systematic measurement errors and remove them in order to accurately represent the underlying effects of the conditions being tested. Here we present a framework for pretraining on large-scale microscopy datasets that includes three steps: (1) curating a set of diverse and self-consistent training samples, (2) scaling training of an appropriate foundation model architecture on this dataset, (3) evaluating intermediate layers of the trained model to identify the best representation for downstream tasks. Using this strategy, we present the largest foundation model for cell microscopy data to our knowledge, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome relationship recall, batch correction replicate consistency, and compound-gene activity prediction benchmarks.