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ML and DL are revolutionising our abilities to analyse biomedical images. Among other host-pathogen interactions may be readily deciphered from microscopy data using convolutional neural networks (CNN). We demonstrate in several studies how the definition of novel ML/DL tasks may aid in studying infection and disease phenotypes. Specifically, ML/DL algorithms may allow unambiguous scoring of virus-infected and uninfected cells in the absence of specific labelling. Accompanied by interpretability approaches, the ability of CNN to learn representations, without explicit feature engineering, may allow for uncovering yet unknown phenotypes in microscopy. Furthermore, we demonstrate novel ML/DL approaches to simplified 3D microscopy acquisition using conventional 2D hardware. Finally, we demonstrate how generative AI can be applied to tasks like image reconstruction and resolution enhancement in fluorescence and brightfield microscopy. Taken together, we show novel approaches to established algorithms in Computer Vision and Data Science. Applied to microscopy data, these approaches allow for the extraction of observations from datasets large enough to not be suitable for manual analysis. We argue that this shows that reformulating conventional ML/DL tasks to answer biological questions may facilitate novel discoveries in Infection and Disease Biology.
| References | 1. Li, Rui, Mikhail Kudryashev, and Artur Yakimovich. "A weak-labelling and deep learning approach for in-focus object segmentation in 3D widefield microscopy." Scientific Reports 13, no. 1 (2023): 12275.; 2. Li, Rui, Gabriel della Maggiora, Vardan Andriasyan, Anthony Petkidis, Artsemi Yushkevich, Mikhail Kudryashev, and Artur Yakimovich. "Microscopy image reconstruction with physics-informed denoising diffusion probabilistic model." arXiv preprint arXiv:2306.02929 (2023). |
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| Acknowledgement of financial support | This work was partially funded by the Center for Advanced Systems Understanding (CASUS) which is financed by Germany’s Federal Ministry of Education and Research (BMBF) and by the Saxon Ministry for Science, Culture, and Tourism (SMWK) with tax funds on the basis of the budget approved by the Saxon State Parliament. The authors acknowledge the financial support by the Federal Ministry of Education and Research of Germany and by Sächsische Staatsministerium für Wissenschaft, Kultur und Tourismus in the programme Center of Excellence for AI-research “Center for Scalable Data Analytics and Artificial Intelligence Dresden/Leipzig”, project identification number: ScaDS.AI. |
