{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,19]],"date-time":"2024-08-19T14:40:21Z","timestamp":1724078421452},"reference-count":65,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,12,18]],"date-time":"2020-12-18T00:00:00Z","timestamp":1608249600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,12,18]],"date-time":"2020-12-18T00:00:00Z","timestamp":1608249600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["CRC 1114"],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"crossref","award":["CRC 1114"],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Nonlinear Sci"],"published-print":{"date-parts":[[2021,2]]},"abstract":"Abstract<\/jats:title>We present a novel kernel-based machine learning algorithm for identifying the low-dimensional geometry of the effective dynamics of high-dimensional multiscale stochastic systems. Recently, the authors developed a mathematical framework for the computation of optimal reaction coordinates of such systems that is based on learning a parameterization of a low-dimensional transition manifold in a certain function space. In this article, we enhance this approach by embedding and learning this transition manifold in a reproducing kernel Hilbert space, exploiting the favorable properties of kernel embeddings. Under mild assumptions on the kernel, the manifold structure is shown to be preserved under the embedding, and distortion bounds can be derived. This leads to a more robust and more efficient algorithm compared to the previous parameterization approaches.<\/jats:p>","DOI":"10.1007\/s00332-020-09668-z","type":"journal-article","created":{"date-parts":[[2020,12,18]],"date-time":"2020-12-18T12:03:37Z","timestamp":1608293017000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Dimensionality Reduction of Complex Metastable Systems via Kernel Embeddings of Transition Manifolds"],"prefix":"10.1007","volume":"31","author":[{"given":"Andreas","family":"Bittracher","sequence":"first","affiliation":[]},{"given":"Stefan","family":"Klus","sequence":"additional","affiliation":[]},{"given":"Boumediene","family":"Hamzi","sequence":"additional","affiliation":[]},{"given":"P\u00e9ter","family":"Koltai","sequence":"additional","affiliation":[]},{"given":"Christof","family":"Sch\u00fctte","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,12,18]]},"reference":[{"issue":"6","key":"9668_CR1","doi-asserted-by":"crossref","first-page":"3026","DOI":"10.1016\/j.aim.2011.08.003","volume":"228","author":"I Abraham","year":"2011","unstructured":"Abraham, I., Bartal, Y., Neiman, O.: Advances in metric embedding theory. Adv. Math. 228(6), 3026\u20133126 (2011)","journal-title":"Adv. Math."},{"issue":"4","key":"9668_CR2","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/0167-7152(94)00085-M","volume":"22","author":"JR Baxter","year":"1995","unstructured":"Baxter, J.R., Rosenthal, J.S.: Rates of convergence for everywhere-positive Markov chains. Stat. Probab. Lett. 22(4), 333\u2013338 (1995)","journal-title":"Stat. Probab. Lett."},{"issue":"1","key":"9668_CR3","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-E","volume":"91","author":"H Berendsen","year":"1995","unstructured":"Berendsen, H., van der Spoel, D., van Drunen, R.: Gromacs: a message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91(1), 43\u201356 (1995)","journal-title":"Comput. Phys. Commun."},{"issue":"1","key":"9668_CR4","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.acha.2015.01.001","volume":"40","author":"T Berry","year":"2016","unstructured":"Berry, T., Harlim, J.: Variable bandwidth diffusion kernels. Appl. Comput. Harmonic Anal. 40(1), 68\u201396 (2016)","journal-title":"Appl. Comput. Harmonic Anal."},{"issue":"19","key":"9668_CR5","doi-asserted-by":"crossref","first-page":"6732","DOI":"10.1073\/pnas.0408098102","volume":"102","author":"RB Best","year":"2005","unstructured":"Best, R.B., Hummer, G.: Reaction coordinates and rates from transition paths. Proc. Natl. Acad. Sci. 102(19), 6732\u20136737 (2005)","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"2","key":"9668_CR6","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1007\/s00332-017-9415-0","volume":"28","author":"A Bittracher","year":"2017","unstructured":"Bittracher, A., Koltai, P., Klus, S., Banisch, R., Dellnitz, M., Sch\u00fctte, C.: Transition manifolds of complex metastable systems: theory and data-driven computation of effective dynamics. J. Nonlinear Sci. 28(2), 471\u2013512 (2017)","journal-title":"J. Nonlinear Sci."},{"issue":"15","key":"9668_CR7","doi-asserted-by":"crossref","first-page":"154103","DOI":"10.1063\/1.5035183","volume":"149","author":"A Bittracher","year":"2018","unstructured":"Bittracher, A., Banisch, R., Sch\u00fctte, C.: Data-driven computation of molecular reaction coordinates. J. Chem. Phys. 149(15), 154103 (2018)","journal-title":"J. Chem. Phys."},{"key":"9668_CR8","doi-asserted-by":"crossref","unstructured":"Bouvrie, J., Hamzi, B.: Balanced reduction of nonlinear control systems in reproducing kernel Hilbert space. In: Proceedings of 48th Annual Allerton Conference on Communication, Control, and Computing, pp. 294\u2013301 (2010)","DOI":"10.1109\/ALLERTON.2010.5706920"},{"issue":"1","key":"9668_CR9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3934\/jcd.2017001","volume":"4","author":"J Bouvrie","year":"2017","unstructured":"Bouvrie, J., Hamzi, B.: Kernel methods for the approximation of some key quantities of nonlinear systems. J. Comput. Dyn. 4(1), 1\u201319 (2017)","journal-title":"J. Comput. Dyn."},{"issue":"4","key":"9668_CR10","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1137\/14096815X","volume":"55","author":"J Bouvrie","year":"2017","unstructured":"Bouvrie, J., Hamzi, B.: Kernel methods for the approximation of nonlinear systems. SIAM J. Control Optim. 55(4), 2460\u20132492 (2017)","journal-title":"SIAM J. Control Optim."},{"issue":"1","key":"9668_CR11","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.sbi.2010.10.006","volume":"21","author":"G Bowman","year":"2011","unstructured":"Bowman, G., Volez, V., Pande, V.S.: Taming the complexity of protein folding. Curr. Opin. Struct. Biol. 21(1), 4\u201311 (2011)","journal-title":"Curr. Opin. Struct. Biol."},{"key":"9668_CR12","series-title":"Advances in Experimental Medicine and Biology","volume-title":"An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation","year":"2014","unstructured":"Bowman, G.R., Pande, V.S., No\u00e9, F. (eds.): An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. Advances in Experimental Medicine and Biology, vol. 797. Springer, Berlin (2014)"},{"issue":"13","key":"9668_CR13","doi-asserted-by":"crossref","first-page":"6369","DOI":"10.1073\/pnas.90.13.6369","volume":"90","author":"CJ Camacho","year":"1993","unstructured":"Camacho, C.J., Thirumalai, D.: Kinetics and thermodynamics of folding in model proteins. Proc. Natl. Acad. Sci. 90(13), 6369\u20136372 (1993)","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"50","key":"9668_CR14","doi-asserted-by":"crossref","first-page":"19487","DOI":"10.1021\/jp048540w","volume":"108","author":"DS Chekmarev","year":"2004","unstructured":"Chekmarev, D.S., Ishida, T., Levy, R.M.: Long-time conformational transitions of alanine dipeptide in aqueous solution: continuous and discrete-state kinetic models. J. Phys. Chem. B 108(50), 19487\u201319495 (2004)","journal-title":"J. Phys. Chem. B"},{"issue":"2","key":"9668_CR15","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1137\/070696325","volume":"7","author":"RR Coifman","year":"2008","unstructured":"Coifman, R.R., Kevrekidis, I.G., Lafon, S., Maggioni, M., Nadler, B.: Diffusion maps, reduction coordinates, and low dimensional representation of stochastic systems. Multiscale Model. Simul. 7(2), 842\u2013864 (2008)","journal-title":"Multiscale Model. Simul."},{"key":"9668_CR16","unstructured":"Duvenaud, D., Lloyd, J., Grosse, R., Tenenbaum, J., Zoubin, G.: Structure discovery in nonparametric regression through compositional kernel search. In: Dasgupta, S., McAllester, D.: (eds), Proceedings of the 30th International Conference on Machine Learning, Volume\u00a028 of Proceedings of Machine Learning Research, pp. 1166\u20131174, Atlanta, Georgia, USA, 17\u201319 Jun (2013). PMLR"},{"key":"9668_CR17","unstructured":"E, W., Vanden-Eijnden, E.: Towards a theory of transition paths. J. Stat. Phys. 123(3), 503\u2013523 (2006)"},{"key":"9668_CR18","doi-asserted-by":"crossref","unstructured":"E, W., Ren, W., Vanden-Eijnden, E.: String method for the study of rare events. Phys. Rev. B 66, 052301 (2002)","DOI":"10.1103\/PhysRevB.66.052301"},{"key":"9668_CR19","doi-asserted-by":"crossref","unstructured":"E, W., Ren, W., Vanden-Eijnden, E.: Simplified and improved string method for computing the minimum energy paths in barrier-crossing events. J. Chem. Phys. 126(16), 164103 (2007)","DOI":"10.1063\/1.2720838"},{"issue":"5","key":"9668_CR20","doi-asserted-by":"crossref","first-page":"219","DOI":"10.3390\/e19050219","volume":"19","author":"R Elber","year":"2017","unstructured":"Elber, R., Bello-Rivas, J.M., Ma, P., Cardenas, A.E., Fathizadeh, A.: Calculating iso-committor surfaces as optimal reaction coordinates with milestoning. Entropy 19(5), 219 (2017)","journal-title":"Entropy"},{"issue":"10","key":"9668_CR21","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1038\/nphys1713","volume":"6","author":"PL Freddolino","year":"2010","unstructured":"Freddolino, P.L., Harrison, C.B., Liu, Y., Schulten, K.: Challenges in protein folding simulations: timescale, representation, and analysis. Nat. Phys. 6(10), 751 (2010)","journal-title":"Nat. Phys."},{"issue":"13","key":"9668_CR22","doi-asserted-by":"crossref","first-page":"10B603","DOI":"10.1063\/1.3207882","volume":"131","author":"TA Frewen","year":"2009","unstructured":"Frewen, T.A., Hummer, G., Kevrekidis, I.G.: Exploration of effective potential landscapes using coarse reverse integration. J. Chem. Phys. 131(13), 10B603 (2009)","journal-title":"J. Chem. Phys."},{"key":"9668_CR23","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.physd.2016.04.010","volume":"328","author":"G Froyland","year":"2016","unstructured":"Froyland, G., Gottwald, G.A., Hammerlindl, A.: A trajectory-free framework for analysing multiscale systems. Phys. D Nonlinear Phenom. 328, 34\u201343 (2016)","journal-title":"Phys. D Nonlinear Phenom."},{"key":"9668_CR24","unstructured":"Fukumizu, K., Gretton, A., Sun, X., Sch\u00f6lkopf, B.: Kernel measures of conditional dependence. In: Proceedings of the 20th International Conference on Neural Information Processing Systems, NIPS\u201907, pp. 489\u2013496 (2007)"},{"issue":"3","key":"9668_CR25","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1515\/jib-2012-201","volume":"9","author":"P Gaspar","year":"2012","unstructured":"Gaspar, P., Carbonell, J., Oliveira, J.L.: On the parameter optimization of support vector machines for binary classification. J. Integr. Bioinform. 9(3), 33\u201343 (2012)","journal-title":"J. Integr. Bioinform."},{"key":"9668_CR26","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1039\/C6FD00120C","volume":"195","author":"GD Ges\u00f9a","year":"2016","unstructured":"Ges\u00f9a, G.D., Leli\u00e8vre, T., Peutreca, D.L., Nectouxa, B.: Jump Markov models and transition state theory: the quasi-stationary distribution approach. Faraday Discuss. 195, 469\u2013495 (2016)","journal-title":"Faraday Discuss."},{"issue":"64","key":"9668_CR27","first-page":"2211","volume":"12","author":"M G\u00f6nen","year":"2011","unstructured":"G\u00f6nen, M., Alpaydin, E.: Multiple kernel learning algorithms. J. Mach. Learn. Res. 12(64), 2211\u20132268 (2011)","journal-title":"J. Mach. Learn. Res."},{"issue":"Mar","key":"9668_CR28","first-page":"723","volume":"13","author":"A Gretton","year":"2012","unstructured":"Gretton, A., Borgwardt, K.M., Rasch, M.J., Sch\u00f6lkopf, B., Smola, A.: A kernel two-sample test. J. Mach. Learn. Res. 13(Mar), 723\u2013773 (2012)","journal-title":"J. Mach. Learn. Res."},{"issue":"5","key":"9668_CR29","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1088\/0951-7715\/12\/5\/303","volume":"12","author":"B Hunt","year":"1999","unstructured":"Hunt, B., Kaloshin, V.: Regularity of embeddings of infinite-dimensional fractal sets into finite-dimensional spaces. Nonlinearity 12(5), 1263\u20131275 (1999)","journal-title":"Nonlinearity"},{"issue":"1","key":"9668_CR30","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1146\/annurev-fluid-121108-145537","volume":"42","author":"R Klein","year":"2010","unstructured":"Klein, R.: Scale-dependent models for atmospheric flows. Annu. Rev. Fluid Mech. 42(1), 249\u2013274 (2010)","journal-title":"Annu. Rev. Fluid Mech."},{"issue":"24","key":"9668_CR31","doi-asserted-by":"crossref","first-page":"244109","DOI":"10.1063\/1.5063533","volume":"149","author":"S Klus","year":"2018","unstructured":"Klus, S., Bittracher, A., Schuster, I., Sch\u00fctte, C.: A kernel-based approach to molecular conformation analysis. J. Chem. Phys. 149(24), 244109 (2018)","journal-title":"J. Chem. Phys."},{"key":"9668_CR32","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1007\/s00332-017-9437-7","volume":"28","author":"S Klus","year":"2018","unstructured":"Klus, S., N\u00fcske, F., Koltai, P., Wu, H., Kevrekidis, I., Sch\u00fctte, C., No\u00e9, F.: Data-driven model reduction and transfer operator approximation. J. Nonlinear Sci. 28, 985\u20131010 (2018)","journal-title":"J. Nonlinear Sci."},{"issue":"1","key":"9668_CR33","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/s00332-019-09574-z","volume":"30","author":"S Klus","year":"2020","unstructured":"Klus, S., Schuster, I., Muandet, K.: Eigendecompositions of transfer operators in reproducing kernel Hilbert spaces. J. Nonlinear Sci. 30(1), 283\u2013315 (2020)","journal-title":"J. Nonlinear Sci."},{"issue":"1","key":"9668_CR34","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/BF02289565","volume":"29","author":"JB Kruskal","year":"1964","unstructured":"Kruskal, J.B.: Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika 29(1), 1\u201327 (1964)","journal-title":"Psychometrika"},{"issue":"7","key":"9668_CR35","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1016\/j.neucom.2008.12.017","volume":"72","author":"JA Lee","year":"2009","unstructured":"Lee, J.A., Verleysen, M.: Quality assessment of dimensionality reduction: rank-based criteria. Neurocomputing 72(7), 1431\u20131443 (2009)","journal-title":"Neurocomputing"},{"issue":"2","key":"9668_CR36","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1175\/1520-0469(2003)060<0393:SMMFTT>2.0.CO;2","volume":"60","author":"AJ Majda","year":"2003","unstructured":"Majda, A.J., Klein, R.: Systematic multiscale models for the tropics. J. Atmos. Sci. 60(2), 393\u2013408 (2003)","journal-title":"J. Atmos. Sci."},{"issue":"1","key":"9668_CR37","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/s41467-017-02388-1","volume":"9","author":"A Mardt","year":"2018","unstructured":"Mardt, A., Pasquali, L., Wu, H., No\u00e9, F.: Vampnets for deep learning of molecular kinetics. Nat. Commun. 9(1), 5 (2018)","journal-title":"Nat. Commun."},{"issue":"2","key":"9668_CR38","first-page":"199","volume":"8","author":"JC Mattingly","year":"2002","unstructured":"Mattingly, J.C., Stuart, A.M.: Geometric ergodicity of some hypo-elliptic diffusions for particle motions. Markov Process. Relat. Fields 8(2), 199\u2013214 (2002)","journal-title":"Markov Process. Relat. Fields"},{"issue":"4","key":"9668_CR39","doi-asserted-by":"crossref","first-page":"44109","DOI":"10.1063\/1.4974306","volume":"146","author":"RT McGibbon","year":"2017","unstructured":"McGibbon, R.T., Husic, B.E., Pande, V.S.: Identification of simple reaction coordinates from complex dynamics. J. Chem. Phys. 146(4), 44109 (2017)","journal-title":"J. Chem. Phys."},{"key":"9668_CR40","doi-asserted-by":"crossref","unstructured":"Melzer, T., Reiter, M., Bischof, H.: Nonlinear feature extraction using generalized canonical correlation analysis. In: Dorffner, G., Bischof, H., Hornik, K. (eds), Artificial Neural Networks\u2014ICANN 2001, pp. 353\u2013360 (2001)","DOI":"10.1007\/3-540-44668-0_50"},{"issue":"441\u2013458","key":"9668_CR41","first-page":"415","volume":"209","author":"J Mercer","year":"1909","unstructured":"Mercer, J.: Functions of positive and negative type, and their connection the theory of integral equations. Philos. Trans. R. Soc. Lond. A Math. Phys. Eng. Sci. 209(441\u2013458), 415\u2013446 (1909)","journal-title":"Philos. Trans. R. Soc. Lond. A Math. Phys. Eng. Sci."},{"issue":"1\u20132","key":"9668_CR42","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1561\/2200000060","volume":"10","author":"K Muandet","year":"2017","unstructured":"Muandet, K., Fukumizu, K., Sriperumbudur, B., Sch\u00f6lkopf, B.: Kernel mean embedding of distributions: a review and beyond. Found. Trends Mach. Learn. 10(1\u20132), 1\u2013141 (2017)","journal-title":"Found. Trends Mach. Learn."},{"issue":"1","key":"9668_CR43","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/anie.198000013","volume":"19","author":"K M\u00fcller","year":"1980","unstructured":"M\u00fcller, K.: Reaction paths on multidimensional energy hypersurfaces. Angewandte Chemie Int. Ed. Engl. 19(1), 1\u201313 (1980)","journal-title":"Angewandte Chemie Int. Ed. Engl."},{"key":"9668_CR44","volume-title":"Topology","author":"JR Munkres","year":"2000","unstructured":"Munkres, J.R.: Topology, 2nd edn. Prentice Hall, Upper Saddle River (2000)","edition":"2"},{"issue":"1","key":"9668_CR45","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.acha.2005.07.004","volume":"21","author":"B Nadler","year":"2006","unstructured":"Nadler, B., Lafon, S., Coifman, R.R., Kevrekidis, I.G.: Diffusion maps, spectral clustering and reaction coordinates of dynamical systems. Appl. Comput. Harmon. Anal. 21(1), 113\u2013127 (2006)","journal-title":"Appl. Comput. Harmon. Anal."},{"issue":"45","key":"9668_CR46","doi-asserted-by":"crossref","first-page":"19011","DOI":"10.1073\/pnas.0905466106","volume":"106","author":"F No\u00e9","year":"2009","unstructured":"No\u00e9, F., Sch\u00fctte, C., Vanden-Eijnden, E., Reich, L., Weikl, T.R.: Constructing the full ensemble of folding pathways from short off-equilibrium simulations. Proc. Natl. Acad. Sci. 106(45), 19011\u201319016 (2009)","journal-title":"Proc. Natl. Acad. Sci."},{"key":"9668_CR47","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.jcp.2019.03.040","volume":"389","author":"H Owhadi","year":"2019","unstructured":"Owhadi, H., Yoo, G.R.: Kernel flows: from learning kernels from data into the abyss. J. Comput. Phys. 389, 22\u201347 (2019)","journal-title":"J. Comput. Phys."},{"issue":"17","key":"9668_CR48","doi-asserted-by":"crossref","first-page":"174105","DOI":"10.1063\/1.3565032","volume":"134","author":"J-H Prinz","year":"2011","unstructured":"Prinz, J.-H., Wu, H., Sarich, M., Keller, B., Senne, M., Held, M., Chodera, J.D., Sch\u00fctte, C., No\u00e9, F.: Markov models of molecular kinetics: generation and validation. J. Chem. Phys. 134(17), 174105 (2011)","journal-title":"J. Chem. Phys."},{"issue":"5500","key":"9668_CR49","doi-asserted-by":"crossref","first-page":"2323","DOI":"10.1126\/science.290.5500.2323","volume":"290","author":"ST Roweis","year":"2000","unstructured":"Roweis, S.T., Saul, L.K.: Nonlinear dimensionality reduction by locally linear embedding. Science 290(5500), 2323\u20132326 (2000)","journal-title":"Science"},{"issue":"2","key":"9668_CR50","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1080\/10618600.1992.10477008","volume":"1","author":"MJ Schervish","year":"1992","unstructured":"Schervish, M.J., Carlin, B.P.: On the convergence of successive substitution sampling. J. Comput. Graph. Stat. 1(2), 111\u2013127 (1992)","journal-title":"J. Comput. Graph. Stat."},{"key":"9668_CR51","doi-asserted-by":"crossref","DOI":"10.7551\/mitpress\/4175.001.0001","volume-title":"Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond","author":"B Sch\u00f6lkopf","year":"2001","unstructured":"Sch\u00f6lkopf, B., Smola, A.J.: Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond. MIT Press, Cambridge (2001)"},{"issue":"5","key":"9668_CR52","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1162\/089976698300017467","volume":"10","author":"B Sch\u00f6lkopf","year":"1998","unstructured":"Sch\u00f6lkopf, B., Smola, A., M\u00fcller, K.-R.: Nonlinear component analysis as a kernel eigenvalue problem. Neural Comput. 10(5), 1299\u20131319 (1998)","journal-title":"Neural Comput."},{"issue":"4","key":"9668_CR53","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1007\/s11222-015-9558-5","volume":"25","author":"B Sch\u00f6lkopf","year":"2015","unstructured":"Sch\u00f6lkopf, B., Muandet, K., Fukumizu, K., Harmeling, S., Peters, J.: Computing functions of random variables via reproducing kernel Hilbert space representations. Stat. Comput. 25(4), 755\u2013766 (2015)","journal-title":"Stat. Comput."},{"key":"9668_CR54","volume-title":"Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches. Number 24 in Courant Lecture Notes","author":"C Sch\u00fctte","year":"2013","unstructured":"Sch\u00fctte, C., Sarich, M.: Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches. Number 24 in Courant Lecture Notes. American Mathematical Society, Providence (2013)"},{"issue":"2","key":"9668_CR55","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1021\/ct5007357","volume":"11","author":"CR Schwantes","year":"2015","unstructured":"Schwantes, C.R., Pande, V.S.: Modeling molecular kinetics with tICA and the kernel trick. J. Chem. Theory Comput. 11(2), 600\u2013608 (2015)","journal-title":"J. Chem. Theory Comput."},{"issue":"12","key":"9668_CR56","doi-asserted-by":"crossref","first-page":"5568","DOI":"10.1063\/1.479860","volume":"111","author":"PE Smith","year":"1999","unstructured":"Smith, P.E.: The alanine dipeptide free energy surface in solution. J. Chem. Phys. 111(12), 5568\u20135579 (1999)","journal-title":"J. Chem. Phys."},{"key":"9668_CR57","doi-asserted-by":"crossref","unstructured":"Smola, A., Gretton, A., Song, L., Sch\u00f6lkopf, B.: A Hilbert space embedding for distributions. In: Proceedings of the 18th International Conference on Algorithmic Learning Theory, pp. 13\u201331. Springer-Verlag (2007)","DOI":"10.1007\/978-3-540-75225-7_5"},{"issue":"15","key":"9668_CR58","doi-asserted-by":"crossref","first-page":"5860","DOI":"10.1063\/1.471317","volume":"104","author":"ND Socci","year":"1996","unstructured":"Socci, N.D., Onuchic, J.N., Wolynes, P.G.: Diffusive dynamics of the reaction coordinate for protein folding funnels. J. Chem. Phys. 104(15), 5860\u20135868 (1996)","journal-title":"J. Chem. Phys."},{"key":"9668_CR59","first-page":"1517","volume":"11","author":"BK Sriperumbudur","year":"2010","unstructured":"Sriperumbudur, B.K., Gretton, A., Fukumizu, K., Sch\u00f6lkopf, B., Lanckriet, G.R.: Hilbert space embeddings and metrics on probability measures. J. Mach. Learn. Res. 11, 1517\u20131561 (2010)","journal-title":"J. Mach. Learn. Res."},{"key":"9668_CR60","volume-title":"Support Vector Machines","author":"I Steinwart","year":"2008","unstructured":"Steinwart, I., Christmann, A.: Support Vector Machines, 1st edn. Springer, New York (2008)","edition":"1"},{"issue":"19","key":"9668_CR61","doi-asserted-by":"crossref","first-page":"194103","DOI":"10.1063\/1.3130083","volume":"130","author":"E Vanden-Eijnden","year":"2009","unstructured":"Vanden-Eijnden, E., Venturoli, M.: Revisiting the finite temperature string method for the calculation of reaction tubes and free energies. J. Chem. Phys. 130(19), 194103 (2009)","journal-title":"J. Chem. Phys."},{"key":"9668_CR62","doi-asserted-by":"crossref","DOI":"10.4324\/9780203767719","volume-title":"Multidimensional Scaling: History, Theory, and Applications","author":"FW Young","year":"2013","unstructured":"Young, F.W.: Multidimensional Scaling: History, Theory, and Applications. Psychology Press, New York (2013)"},{"key":"9668_CR63","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1039\/C6FD00147E","volume":"195","author":"W Zhang","year":"2016","unstructured":"Zhang, W., Hartmann, C., Sch\u00fctte, C.: Effective dynamics along given reaction coordinates, and reaction rate theory. Faraday Discuss. 195, 365\u2013394 (2016)","journal-title":"Faraday Discuss."},{"key":"9668_CR64","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1103\/PhysRev.124.983","volume":"124","author":"R Zwanzig","year":"1961","unstructured":"Zwanzig, R.: Memory effects in irreversible thermodynamics. Phys. Rev. 124, 983\u2013992 (1961)","journal-title":"Phys. Rev."},{"key":"9668_CR65","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780195140187.001.0001","volume-title":"Nonequilibrium Statistical Mechanics","author":"R Zwanzig","year":"2001","unstructured":"Zwanzig, R.: Nonequilibrium Statistical Mechanics. Oxford University Press, Oxford (2001)"}],"container-title":["Journal of Nonlinear Science"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00332-020-09668-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00332-020-09668-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00332-020-09668-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,19]],"date-time":"2024-08-19T14:06:27Z","timestamp":1724076387000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00332-020-09668-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12,18]]},"references-count":65,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,2]]}},"alternative-id":["9668"],"URL":"https:\/\/doi.org\/10.1007\/s00332-020-09668-z","relation":{},"ISSN":["0938-8974","1432-1467"],"issn-type":[{"type":"print","value":"0938-8974"},{"type":"electronic","value":"1432-1467"}],"subject":[],"published":{"date-parts":[[2020,12,18]]},"assertion":[{"value":"31 May 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 November 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 December 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"3"}}