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quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
Vincent Mallet1,2, Michael Nilges1, Guillaume Bouvier1
1Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, C3BI, USR3756, Paris 75015, France.
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.
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