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.
Simulation-based inference (SBI) with machine learning is an increasingly important tool for solving inverse problems in science and engineering, including parameter inference and the inversion of detector effects. We provide an overview of the Bayesian and frequentist statistica…
Double Machine Learning (DML) is a popular approach for treatment effect estimation in various settings, which allows a wide range of flexible machine learning methods to be used for nuisance parameter estimation while preserving valid inference. In practice, however, applied res…
Machine-learning surrogates of physical systems face a paradox: explainable models facing the challenge of expressivity to capture complex nonlinear flows, whereas expressive deep surrogates match high-fidelity simulations only through massive parameterisations that turn the lear…
We introduce implicit machine learning force fields (I-MLFFs), which replace explicit stacks of neural network layers with self-consistent fixed-point equations. In molecular simulations, this formulation enables intermediate representations to be reused across successive timeste…
Previous work has shown that the simple dataflow primitives of the Lustre language allow the natural, semantically unambiguous, and compact representation of machine learning (ML) applications, including models featuring complex conditional execution and recurrent state. The Lust…
Scaling semiconductor quantum dot arrays toward fault-tolerant quantum computing requires efficient tuneup of spin qubits, a process that depends on the analysis of charge stability maps (CSMs) and remains largely manual. While machine learning has been widely applied to CSM anal…