Data-driven Efficient Solvers and Predictions of Conformational Transitions for Langevin Dynamics on Manifold in High Dimensions

We work on dynamic problems with collected data $\{\mathsf{x}_i\}$ that distributed on a manifold $\mathcal{M}\subset\mathbb{R}^p$. Through the diffusion map, we first learn the reaction coordinates $\{\mathsf{y}_i\}\subset \mathcal{N}$ where $\mathcal{N}$ is a manifold isometrically embedded into an Euclidean space $\mathbb{R}^\ell$ for $\ell \ll p$. The reaction coordinates enable us to obtain an efficient approximation for the dynamics described by a Fokker-Planck equation on the manifold $\mathcal{N}$. By using the reaction coordinates, we propose an implementable, unconditionally stable, data-driven upwind scheme which automatically incorporates the manifold structure of $\mathcal{N}$. Furthermore, we provide a weighted $L^2$ convergence analysis of the upwind scheme to the Fokker-Planck equation. The proposed upwind scheme leads to a Markov chain with transition probability between the nearest neighbor points. We can benefit from such property to directly conduct manifold-related computations such as finding the optimal coarse-grained network and the minimal energy path that represents chemical reactions or conformational changes. To establish the Fokker-Planck equation, we need to acquire information about the equilibrium potential of the physical system on $\mathcal{N}$. Hence, we apply a Gaussian Process regression algorithm to generate equilibrium potential for a new physical system with new parameters. Combining with the proposed upwind scheme, we can calculate the trajectory of the Fokker-Planck equation on $\mathcal{N}$ based on the generated equilibrium potential. Finally, we develop an algorithm to pullback the trajectory to the original high dimensional space as a generative data for the new physical system.Comment: 59 pages, 16 figure

On boundary detection

Given a sample of a random variable supported by a smooth compact manifold $M\subset \mathbb{R}^d$, we propose a test to decide whether the boundary of $M$ is empty or not with no preliminary support estimation. The test statistic is based on the maximal distance between a sample point and the average of its $k_n$-nearest neighbors. We prove that the level of the test can be estimated, that, with probability one, its power is one for $n$ large enough, and that there exists a consistent decision rule. Heuristics for choosing a convenient value for the $k_n$ parameter and identifying observations close to the boundary are also given. We provide a simulation study of the test

An Efficient and Continuous Voronoi Density Estimator

We introduce a non-parametric density estimator deemed Radial Voronoi Density Estimator (RVDE). RVDE is grounded in the geometry of Voronoi tessellations and as such benefits from local geometric adaptiveness and broad convergence properties. Due to its radial definition RVDE is moreover continuous and computable in linear time with respect to the dataset size. This amends for the main shortcomings of previously studied VDEs, which are highly discontinuous and computationally expensive. We provide a theoretical study of the modes of RVDE as well as an empirical investigation of its performance on high-dimensional data. Results show that RVDE outperforms other non-parametric density estimators, including recently introduced VDEs.Comment: 12 page