Writhe-Based Polymer Link Classification Using Machine Learning

Abstract:Unique and rapid classification of knots and links is an open mathematical problem that is relevant to a range of (bio)physical systems, including polymer melts, DNA, and proteins. In this paper, we explore a data-driven approach to the classification problem of link topology. Extending the framework introduced in Ref. 1 (Sleiman et al, 2024 Soft Matter, 20(1), pp.71-78), we show that a feedforward neural network trained on the writhe density matrix classifies thermally equilibrated configurations of the first six prime links with 97% accuracy. We demonstrate that this accuracy remains high across a range of temperatures and lengths of link components, while rapidly deteriorating with the addition of topology-altering Gaussian noise; a result consistent with the writhe density matrix containing features sensitive to topology. Our results show that neural networks based on the writhe density matrix efficiently classify two-component links, establishing machine learning as a promising tool for rapid classification of more complex link topologies, e.g. Borromean rings and multi-component links, as the computational cost of exact numerical calculation of topological invariants becomes prohibitive.

Geometric Topology (math.GT); Soft Condensed Matter (cond-mat.soft); Machine Learning (cs.LG)

arXiv:2607.20657 [math.GT]

(or arXiv:2607.20657v1 [math.GT] for this version)

https://doi.org/10.48550/arXiv.2607.20657 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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