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Landmark Diffusion Maps (L-dMaps): Accelerated manifold learning out-of-sample extension

by   Andrew W. Long, et al.
University of Illinois at Urbana-Champaign

Diffusion maps are a nonlinear manifold learning technique based on harmonic analysis of a diffusion process over the data. Out-of-sample extensions with computational complexity O(N), where N is the number of points comprising the manifold, frustrate applications to online learning applications requiring rapid embedding of high-dimensional data streams. We propose landmark diffusion maps (L-dMaps) to reduce the complexity to O(M), where M ≪ N is the number of landmark points selected using pruned spanning trees or k-medoids. Offering (N/M) speedups in out-of-sample extension, L-dMaps enables the application of diffusion maps to high-volume and/or high-velocity streaming data. We illustrate our approach on three datasets: the Swiss roll, molecular simulations of a C_24H_50 polymer chain, and biomolecular simulations of alanine dipeptide. We demonstrate up to 50-fold speedups in out-of-sample extension for the molecular systems with less than 4 manifold reconstruction fidelity relative to calculations over the full dataset.


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Code Repositories


C++ implementation of the Diffusion Map, with Python bindings

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