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Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations.

ABSTRACT:

Motivation

Computer-aided analysis of biological images typically requires extensive training on large-scale annotated datasets, which is not viable in many situations. In this paper, we present Generative Adversarial Network Discriminator Learner (GAN-DL), a novel self-supervised learning paradigm based on the StyleGAN2 architecture, which we employ for self-supervised image representation learning in the case of fluorescent biological images.

Results

We show that Wasserstein Generative Adversarial Networks enable high-throughput compound screening based on raw images. We demonstrate this by classifying active and inactive compounds tested for the inhibition of SARS-CoV-2 infection in two different cell models: the primary human renal cortical epithelial cells (HRCE) and the African green monkey kidney epithelial cells (VERO). In contrast to previous methods, our deep learning-based approach does not require any annotation, and can also be used to solve subtle tasks it was not specifically trained on, in a self-supervised manner. For example, it can effectively derive a dose-response curve for the tested treatments.

Availability and implementation

Our code and embeddings are available at https://gitlab.com/AlesioRFM/gan-dl StyleGAN2 is available at https://github.com/NVlabs/stylegan2 .

SUBMITTER: Mascolini A

PROVIDER: S-EPMC9308954 | biostudies-literature |

REPOSITORIES: biostudies-literature

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