Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Klindt, David A, Hyvärinen, Aapo, Levy, Axel, Miolane, Nina, Poitevin, Frédéric (July 2024) Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations. Frontiers in Molecular Biosciences, 11. p. 1393564. ISSN 2296-889X

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Abstract

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > computational biology > algorithms bioinformatics > computational biology bioinformatics > computational biology > algorithms > machine learning
CSHL Authors:	Klindt, David
Communities:	CSHL labs > Klindt lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	8 July 2024
Date Deposited:	30 Jul 2024 12:53
Last Modified:	30 Jul 2024 12:53
PMCID:	PMC11263974
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41626

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