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Preprints, Working Papers, ... (Preprint) Year : 2023

Analyzing multimodal probability measures with autoencoders


Finding collective variables to describe some important coarse-grained information on physical systems, in particular metastable states, remains a key issue in molecular dynamics. Recently, machine learning techniques have been intensively used to complement and possibly bypass expert knowledge in order to construct collective variables. Our focus here is on neural network approaches based on autoencoders. We study some relevant mathematical properties of the loss function considered for training autoencoders, and provide physical interpretations based on conditional variances and minimum energy paths. We also consider various extensions in order to better describe physical systems, by incorporating more information on transition states at saddle points, and/or allowing for multiple decoders in order to describe several transition paths. Our results are illustrated on toy two dimensional systems and on alanine dipeptide.

Dates and versions

hal-04230596 , version 1 (06-10-2023)



Tony Lelièvre, Thomas Pigeon, Gabriel Stoltz, Wei Zhang. Analyzing multimodal probability measures with autoencoders. 2023. ⟨hal-04230596⟩
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