quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
Vincent Mallet, Michaël Nilges, Guillaume Bouvier
Abstract
SUMMARY: We implemented the Self-Organizing Maps algorithm running efficiently on GPUs, and also provide several clustering methods of the resulting maps. We provide scripts and a use case to cluster macro-molecular conformations generated by molecular dynamics simulations. AVAILABILITY AND IMPLEMENTATION: The method is available on GitHub and distributed as a pip package.
Topics & Concepts
Computer scienceCluster analysisScripting languageCluster (spacecraft)Molecular dynamicsMacroComputational scienceR packageDynamics (music)Parallel computingTheoretical computer scienceArtificial intelligenceProgramming languageChemistryComputational chemistryPhysicsAcousticsProtein Structure and DynamicsMachine Learning in Materials ScienceTheoretical and Computational Physics