@misc{Lie, type = {Master Thesis}, author = {Lie, Han Cheng}, title = {A Meshless Method for Conformational Analysis}, language = {en} } @article{LieSullivan, author = {Lie, Han Cheng and Sullivan, T. J.}, title = {Cameron--Martin theorems for sequences of Cauchy-distributed random variables}, series = {arXiv}, journal = {arXiv}, pages = {1608.03784}, abstract = {Given a sequence of Cauchy-distributed random variables defined by a sequence of location parameters and a sequence of scale parameters, we consider another sequence of random variables that is obtained by perturbing the location or scale parameter sequences. Using a result of Kakutani on equivalence of infinite product measures, we provide sufficient conditions for the equivalence of laws of the two sequences.}, language = {en} } @misc{LieSullivan, author = {Lie, Han Cheng and Sullivan, T. J.}, title = {Cameron--Martin theorems for sequences of Cauchy-distributed random variables}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60230}, abstract = {Given a sequence of Cauchy-distributed random variables defined by a sequence of location parameters and a sequence of scale parameters, we consider another sequence of random variables that is obtained by perturbing the location or scale parameter sequences. Using a result of Kakutani on equivalence of infinite product measures, we provide sufficient conditions for the equivalence of laws of the two sequences.}, language = {en} } @misc{QuerLie, author = {Quer, Jannes and Lie, Han Cheng}, title = {Some connections between importance sampling and enhanced sampling methods in molecular dynamics}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-64289}, abstract = {Enhanced sampling methods play an important role in molecular dynamics, because they enable the collection of better statistics of rare events that are important in many physical phenomena. We show that many enhanced sampling methods can be viewed as methods for performing importance sampling, by identifying important correspondences between the language of molecular dynamics and the language of probability theory. We illustrate these connections by highlighting the similarities between the rare event simulation method of Hartmann and Sch{\"u}tte (J. Stat. Mech. Theor. Exp., 2012), and the enhanced sampling method of Valsson and Parrinello (Phys. Rev. Lett. 113, 090601). We show that the idea of changing a probability measure is fundamental to both enhanced sampling and importance sampling.}, language = {en} } @phdthesis{Lie, author = {Lie, Han Cheng}, title = {On a strongly convex approximation of a stochastic optimal control problem for importance sampling of metastable diffusions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-fudissthesis000000101680-4}, language = {en} } @misc{LieSullivanTeckentrup, author = {Lie, Han Cheng and Sullivan, T. J. and Teckentrup, Aretha}, title = {Random forward models and log-likelihoods in Bayesian inverse problems}, series = {SIAM/ASA Journal on Uncertainty Quantification}, volume = {6}, journal = {SIAM/ASA Journal on Uncertainty Quantification}, number = {4}, issn = {1438-0064}, doi = {10.1137/18M1166523}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66324}, pages = {1600 -- 1629}, abstract = {We consider the use of randomised forward models and log-likelihoods within the Bayesian approach to inverse problems. Such random approximations to the exact forward model or log-likelihood arise naturally when a computationally expensive model is approximated using a cheaper stochastic surrogate, as in Gaussian process emulation (kriging), or in the field of probabilistic numerical methods. We show that the Hellinger distance between the exact and approximate Bayesian posteriors is bounded by moments of the difference between the true and approximate log-likelihoods. Example applications of these stability results are given for randomised misfit models in large data applications and the probabilistic solution of ordinary differential equations.}, language = {en} } @article{LieSullivanStuart, author = {Lie, Han Cheng and Sullivan, T. J. and Stuart, Andrew}, title = {Strong convergence rates of probabilistic integrators for ordinary differential equations}, series = {Statistics and Computing}, volume = {29}, journal = {Statistics and Computing}, number = {6}, doi = {10.1007/s11222-019-09898-6}, pages = {1265 -- 1283}, abstract = {Probabilistic integration of a continuous dynamical system is a way of systematically introducing model error, at scales no larger than errors inroduced by standard numerical discretisation, in order to enable thorough exploration of possible responses of the system to inputs. It is thus a potentially useful approach in a number of applications such as forward uncertainty quantification, inverse problems, and data assimilation. We extend the convergence analysis of probabilistic integrators for deterministic ordinary differential equations, as proposed by Conrad et al.\ (\textit{Stat.\ Comput.}, 2016), to establish mean-square convergence in the uniform norm on discrete- or continuous-time solutions under relaxed regularity assumptions on the driving vector fields and their induced flows. Specifically, we show that randomised high-order integrators for globally Lipschitz flows and randomised Euler integrators for dissipative vector fields with polynomially-bounded local Lipschitz constants all have the same mean-square convergence rate as their deterministic counterparts, provided that the variance of the integration noise is not of higher order than the corresponding deterministic integrator.}, language = {en} } @article{LieSullivan, author = {Lie, Han Cheng and Sullivan, T. J.}, title = {Equivalence of weak and strong modes of measures on topological vector spaces}, series = {Inverse Problems}, volume = {34}, journal = {Inverse Problems}, number = {11}, doi = {10.1088/1361-6420/aadef2}, pages = {115013}, abstract = {Modes of a probability measure on an infinite-dimensional Banach space X are often defined by maximising the small-radius limit of the ratio of measures of norm balls. Helin and Burger weakened the definition of such modes by considering only balls with centres in proper subspaces of X, and posed the question of when this restricted notion coincides with the unrestricted one. We generalise these definitions to modes of arbitrary measures on topological vector spaces, defined by arbitrary bounded, convex, neighbourhoods of the origin. We show that a coincident limiting ratios condition is a necessary and sufficient condition for the equivalence of these two types of modes, and show that the coincident limiting ratios condition is satisfied in a wide range of topological vector spaces.}, language = {en} } @article{LieSullivan2018, author = {Lie, Han Cheng and Sullivan, T. J.}, title = {Quasi-invariance of countable products of Cauchy measures under non-unitary dilations}, series = {Electronic Communications in Probability}, volume = {23}, journal = {Electronic Communications in Probability}, number = {8}, doi = {10.1214/18-ECP113}, pages = {1 -- 6}, year = {2018}, language = {en} } @misc{BojarovskiHegeLieetal., author = {Bojarovski, Stefan and Hege, Hans-Christian and Lie, Han Cheng and Weber, Marcus}, title = {Topological analysis and visualization of scalar functions characterizing conformational transitions of molecules on multiple time-scales}, series = {Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany}, journal = {Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany}, abstract = {Molecular processes such as protein folding or ligand-receptor-binding can be understood by analyzing the free energy landscape. Those processes are often metastable, i.e. the molecular systems remain in basins around local minima of the free energy landscape, and in rare cases undergo gauche transitions between metastable states by passing saddle-points of this landscape. By discretizing the configuration space, this can be modeled as a discrete Markov process. One way to compute the transition rates between conformations of a molecular system is by utilizing Transition Path Theory and the concept of committor functions. A fundamental problem from the computational point of view is that many time-scales are involved, ranging from 10^(-14) sec for the fastest motion to 10^(-6) sec or more for conformation changes that cause biological effects. The goal of our work is to provide a better understanding of such transitions in configuration space on various time-scales by analyzing characteristic scalar functions topologically and geometrically. We are developing suitable visualization and interaction techniques to support our analysis. For example, we are analyzing a transition rate indicator function by computing and visualizing its Reeb graph together with the sets of molecular states corresponding to maxima of the transition rate indicator function. A particular challenge is the high dimensionality of the domain which does not allow for a straightforward visualization of the function. The computational topology approach to the analysis of the transition rate indicator functions for a molecular system allows to explore different time scales of the system by utilizing coarser or finer topological partitioning of the function. A specific goal is the development of tools for analyzing the hierarchy of these partitionings. This approach tackles the analysis of a complex and sparse dataset from a different angle than the well-known spectral analysis of Markov State Models.}, language = {en} } @inproceedings{TeymurLieSullivanetal., author = {Teymur, Onur and Lie, Han Cheng and Sullivan, T. J. and Calderhead, Ben}, title = {Implicit probabilistic integrators for ODEs}, series = {Advances in Neural Information Processing Systems 31 (NIPS 2018)}, booktitle = {Advances in Neural Information Processing Systems 31 (NIPS 2018)}, language = {en} } @article{LieSullivan, author = {Lie, Han Cheng and Sullivan, T. J.}, title = {Erratum: Equivalence of weak and strong modes of measures on topological vector spaces (2018 Inverse Problems 34 115013)}, series = {Inverse Problems}, volume = {34}, journal = {Inverse Problems}, number = {12}, doi = {10.1088/1361-6420/aae55b}, pages = {129601}, language = {en} } @article{LieSullivanTeckentrup2020, author = {Lie, Han Cheng and Sullivan, T. J. and Teckentrup, Aretha}, title = {Error bounds for some approximate posterior measures in Bayesian inference}, series = {Numerical Mathematics and Advanced Applications ENUMATH 2019}, journal = {Numerical Mathematics and Advanced Applications ENUMATH 2019}, publisher = {Springer}, doi = {10.1007/978-3-030-55874-1_26}, pages = {275 -- 283}, year = {2020}, language = {en} } @article{AyanbayevKlebanovLieetal., author = {Ayanbayev, Birzhan and Klebanov, Ilja and Lie, Han Cheng and Sullivan, T. J.}, title = {Γ-convergence of Onsager-Machlup functionals: I. With applications to maximum a posteriori estimation in Bayesian inverse problems}, series = {Inverse Problems}, volume = {38}, journal = {Inverse Problems}, number = {2}, doi = {10.1088/1361-6420/ac3f81}, pages = {32}, language = {en} } @article{AyanbayevKlebanovLieetal., author = {Ayanbayev, Birzhan and Klebanov, Ilja and Lie, Han Cheng and Sullivan, T. J.}, title = {Γ-convergence of Onsager-Machlup functionals: II. Infinite product measures on Banach spaces}, series = {Inverse Problems}, volume = {38}, journal = {Inverse Problems}, number = {2}, doi = {10.1088/1361-6420/ac3f82}, pages = {35}, language = {en} } @article{KoltaiLiePlonka, author = {Koltai, P{\´e}ter and Lie, Han Cheng and Plonka, Martin}, title = {Fr{\´e}chet differentiable drift dependence of Perron-Frobenius and Koopman operators for non-deterministic dynamics}, series = {Nonlinearity}, volume = {32}, journal = {Nonlinearity}, number = {11}, doi = {10.1088/1361-6544/ab1f2a}, pages = {4232 -- 4257}, abstract = {We prove the Fr{\´e}chet differentiability with respect to the drift of Perron-Frobenius and Koopman operators associated to time-inhomogeneous ordinary stochastic differential equations. This result relies on a similar differentiability result for pathwise expectations of path functionals of the solution of the stochastic differential equation, which we establish using Girsanov's formula. We demonstrate the significance of our result in the context of dynamical systems and operator theory, by proving continuously differentiable drift dependence of the simple eigen- and singular values and the corresponding eigen- and singular functions of the stochastic Perron-Frobenius and Koopman operators.}, language = {en} } @article{LieFackeldeyWeber2013, author = {Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus}, title = {A Square Root Approximation of Transition Rates for a Markov State Model}, series = {SIAM. J. Matrix Anal. Appl.}, volume = {34}, journal = {SIAM. J. Matrix Anal. Appl.}, number = {2}, doi = {10.1137/120899959}, pages = {738 -- 756}, year = {2013}, language = {en} } @article{CvetkovicConradLie, author = {Cvetkovic, Nada and Conrad, Tim and Lie, Han Cheng}, title = {A Convergent Discretisation Method for Transition Path Theory for Diffusion Processes}, series = {Multiscale Modeling \& Simulation}, volume = {19}, journal = {Multiscale Modeling \& Simulation}, number = {1}, publisher = {Society for Industrial and Applied Mathematics}, doi = {10.1137/20M1329354}, pages = {242 -- 266}, language = {en} } @misc{LieFackeldeyWeber, author = {Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus}, title = {A square root approximation of transition rates for a Markov State Model}, issn = {1438-0064}, doi = {10.1137/120899959}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42195}, abstract = {Trajectory- or mesh-based methods for analyzing the dynamical behavior of large molecules tend to be impractical due to the curse of dimensionality - their computational cost increases exponentially with the size of the molecule. We propose a method to break the curse by a novel square root approximation of transition rates, Monte Carlo quadrature and a discretization approach based on solving linear programs. With randomly sampled points on the molecular energy landscape and randomly generated discretizations of the molecular configuration space as our initial data, we construct a matrix describing the transition rates between adjacent discretization regions. This transition rate matrix yields a Markov State Model of the molecular dynamics. We use Perron cluster analysis and coarse-graining techniques in order to identify metastable sets in configuration space and approximate the transition rates between the metastable sets. Application of our method to a simple energy landscape on a two-dimensional configuration space provides proof of concept and an example for which we compare the performance of different discretizations. We show that the computational cost of our method grows only polynomially with the size of the molecule. However, finding discretizations of higher-dimensional configuration spaces in which metastable sets can be identified remains a challenge.}, language = {en} } @article{QuerLie, author = {Quer, Jannes and Lie, Han Cheng}, title = {Some connections between importance sampling and enhanced sampling methods in molecular dynamics}, series = {Journal of Chemical Physics}, journal = {Journal of Chemical Physics}, abstract = {Enhanced sampling methods play an important role in molecular dynamics, because they enable the collection of better statistics of rare events that are important in many physical phenomena. We show that many enhanced sampling methods can be viewed as methods for performing importance sampling, by identifying important correspondences between the language of molecular dynamics and the language of probability theory. We illustrate these connections by highlighting the similarities between the rare event simulation method of Hartmann and Sch{\"u}tte (J. Stat. Mech. Theor. Exp., 2012), and the enhanced sampling method of Valsson and Parrinello (Phys. Rev. Lett. 113, 090601). We show that the idea of changing a probability measure is fundamental to both enhanced sampling and importance sampling.}, language = {en} }