nonlinear dimensionality reduction

Ferguson, Andrew, Athanassios Panagiotopoulos, Pablo Debenedetti, and Ioannis Kevrekidis. (2011) 2011. “Integrating Diffusion Maps With Umbrella Sampling: Application to Alanine Dipeptide”. Journal of Chemical Physics 134 (13): 135103.

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Sonday, Benjamin, Mikko Haataja, and Ioannis Kevrekidis. (2009) 2009. “Coarse-Graining the Dynamics of a Driven Interface in the Presence of Mobile Impurities: Effective Description via Diffusion Maps”. Physical Review E 80 (3): 031102.

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Dsilva, Carmeline, Bomyi Lim, Hang Lu, Amit Singer, Ioannis Kevrekidis, and Stanislav Shvartsman. (2015) 2015. “Temporal Ordering and Registration of Images in Studies of Developmental Dynamics”. Development 142 (9): 1717-24.

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Sonday, Benjamin, Amit Singer, and Ioannis Kevrekidis. (2013) 2013. “Noisy Dynamic Simulations in the Presence of Symmetry: Data Alignment and Model Reduction”. Computers & Mathematics With Applications 65 (10): 1535-57.

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Ferguson, Andrew, Athanassios Panagiotopoulos, Pablo Debenedetti, and Ioannis Kevrekidis. (2010) 2010. “Systematic Determination of Order Parameters for Chain Dynamics Using Diffusion Maps”. Proceedings of the National Academy of Sciences of the United States of America 107 (31): 13597-602.

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Nedialkova, Lilia, Miguel Amat, Ioannis Kevrekidis, and Gerhard Hummer. (2014) 2014. “Diffusion Maps, Clustering and Fuzzy Markov Modeling in Peptide Folding Transitions”. Journal of Chemical Physics 141 (11): 114102.

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Marschler, Christian, Jens Starke, Ping Liu, and Ioannis Kevrekidis. (2014) 2014. “Coarse-Grained Particle Model for Pedestrian Flow Using Diffusion Maps”. Physical Review E 89 (1): 013304.

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Xue, Yuzhen, Peter Ludovice, Martha Grover, Lilia Nedialkova, Carmeline Dsilva, and Ioannis Kevrekidis. (2013) 2013. “State Reduction in Molecular Simulations”. Computers & Chemical Engineering 51: 102-10.

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Erban, Radek, Thomas Frewen, Xiao Wang, Timothy Elston, Ronald Coifman, Boaz Nadler, and Ioannis Kevrekidis. (2007) 2007. “Variable-Free Exploration of Stochastic Models: A Gene Regulatory Network Example”. Journal of Chemical Physics 126 (15): 155103.

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Kim, Sang Beom, Carmeline Dsilva, Ioannis Kevrekidis, and Pablo Debenedetti. (2015) 2015. “Systematic Characterization of Protein Folding Pathways Using Diffusion Maps: Application to Trp-Cage Miniprotein”. Journal of Chemical Physics 142 (8): 085101.

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Laing, Frewen, and Kevrekidis. (2007) 2007. “Coarse-Grained Dynamics of an Activity Bump in a Neural Field Model”. Nonlinearity 20 (9): 2127-46.

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