arXiv subjects

Yiying Tong

Publications and source records attributed to Yiying Tong.

25 records · Page 2Linked to original sources

arXiv2018

Parallel Transport Unfolding: A Connection-based Manifold Learning Approach

Manifold learning offers nonlinear dimensionality reduction of high-dimensional datasets. In this paper, we bring geometry processing to bear on manifold learning by introducing a new approach based on metric connection for generating a quasi-isometric, low-dimensional mapping from a sparse and irregular sampling of an arbitrary manifold embedded in a high-dimensional space. Geodesic distances of discrete paths over the input pointset are evaluated through "parallel transport unfolding" (PTU) to offer robustness to poor sampling and arbitrary topology. Our new geometric procedure exhibits the same strong resilience to noise as one of the staples of manifold learning, the Isomap algorithm, as it also exploits all pairwise geodesic distances to compute a low-dimensional embedding. While Isomap is limited to geodesically-convex sampled domains, parallel transport unfolding does not suffer from this crippling limitation, resulting in an improved robustness to irregularity and voids in the sampling. Moreover, it involves only simple linear algebra, significantly improves the accuracy of all pairwise geodesic distance approximations, and has the same computational complexity as Isomap. Finally, we show that our connection-based distance estimation can be used for faster variants of Isomap such as L-Isomap.

cs.LG↗

arXiv2018

Divide-and-Conquer Strategy for Large-Scale Eulerian Solvent Excluded Surface

Motivation: Surface generation and visualization are some of the most important tasks in biomolecular modeling and computation. Eulerian solvent excluded surface (ESES) software provides analytical solvent excluded surface (SES) in the Cartesian grid, which is necessary for simulating many biomolecular electrostatic and ion channel models. However, large biomolecules and/or fine grid resolutions give rise to excessively large memory requirements in ESES construction. We introduce an out-of-core and parallel algorithm to improve the ESES software. Results: The present approach drastically improves the spatial and temporal efficiency of ESES. The memory footprint and time complexity are analyzed and empirically verified through extensive tests with a large collection of biomolecule examples. Our results show that our algorithm can successfully reduce memory footprint through a straightforward divide-and-conquer strategy to perform the calculation of arbitrarily large proteins on a typical commodity personal computer. On multi-core computers or clusters, our algorithm can reduce the execution time by parallelizing most of the calculation as disjoint subproblems. Various comparisons with the state-of-the-art Cartesian grid based SES calculation were done to validate the present method and show the improved efficiency. This approach makes ESES a robust software for the construction of analytical solvent excluded surfaces. Availability and implementation: http://weilab.math.msu.edu/ESES.

q-bio.QM↗

arXiv2015

Subdivision based Isogeometric Analysis technique for Electric Field Integral Equations for Simply Connected Structures

The analysis of electromagnetic scattering has long been performed on a discrete representation of the geometry. This representation is typically continuous but {\em not} differentiable. The need to define physical quantities on this geometric representation has led to development of sets of basis functions that need to satisfy constraints at the boundaries of the elements/tesselations (viz., continuity of normal or tangential components across element boundaries). For electromagnetics, these result in either curl/div-conforming basis sets. The geometric representation used for analysis is in stark contrast with that used for design, wherein the surface representation is higher order differentiable. Using this representation for {\em both} geometry and physics on geometry has several advantages, and is eludicated in Hughes et al., Isogeometric analysis: CAD, finite elements, NURBS, exact geometry and mesh refinement, Computer Methods in Applied Mechanics and Engineering 194 (39-41) (2005). Until now, a bulk of the literature on isogeometric methods have been limited to solid mechanics, with some effort to create NURBS based basis functions for electromagnetic analysis. In this paper, we present the first complete isogeometry solution methodology for the electric field integral equation as applied to simply connected structures. This paper systematically proceeds through surface representation using subdivision, definition of vector basis functions on this surface, to fidelity in the solution of integral equations. We also present techniques to stabilize the solution at low frequencies, and impose a Calderón preconditioner. Several results presented serve to validate the proposed approach as well as demonstrate some of its capabilities.

physics.comp-ph↗

arXiv2014

Persistent Homology for The Quantitative Prediction of Fullerene Stability

Persistent homology is a relatively new tool often used for \emph{qualitative} analysis of intrinsic topological features in images and data originated from scientific and engineering applications. In this paper, we report novel \emph{quantitative} predictions of the energy and stability of fullerene molecules, the very first attempt in employing persistent homology in this context. The ground-state structures of a series of small fullerene molecules are first investigated with the standard Vietoris-Rips complex. We decipher all the barcodes, including both short-lived local bars and long-lived global bars arising from topological invariants, and associate them with fullerene structural details. By using accumulated bar lengths, we build quantitative models to correlate local and global Betti-2 bars respectively with the heat of formation and total curvature energies of fullerenes. It is found that the heat of formation energy is related to the local hexagonal cavities of small fullerenes, while the total curvature energies of fullerene isomers are associated with their sphericities, which are measured by the lengths of their long-lived Betti-2 bars. Excellent correlation coefficients ($>0.94$) between persistent homology predictions and those of quantum or curvature analysis have been observed. A correlation matrix based filtration is introduced to further verify our findings.

q-bio.BM↗

arXiv2010

Structure-Preserving Discretization of Incompressible Fluids

The geometric nature of Euler fluids has been clearly identified and extensively studied over the years, culminating with Lagrangian and Hamiltonian descriptions of fluid dynamics where the configuration space is defined as the volume-preserving diffeomorphisms, and Kelvin's circulation theorem is viewed as a consequence of Noether's theorem associated with the particle relabeling symmetry of fluid mechanics. However computational approaches to fluid mechanics have been largely derived from a numerical-analytic point of view, and are rarely designed with structure preservation in mind, and often suffer from spurious numerical artifacts such as energy and circulation drift. In contrast, this paper geometrically derives discrete equations of motion for fluid dynamics from first principles in a purely Eulerian form. Our approach approximates the group of volume-preserving diffeomorphisms using a finite dimensional Lie group, and associated discrete Euler equations are derived from a variational principle with non-holonomic constraints. The resulting discrete equations of motion yield a structure-preserving time integrator with good long-term energy behavior and for which an exact discrete Kelvin's circulation theorem holds.

math.DS↗

arXiv2009

Geometric Computational Electrodynamics with Variational Integrators and Discrete Differential Forms

In this paper, we develop a structure-preserving discretization of the Lagrangian framework for electromagnetism, combining techniques from variational integrators and discrete differential forms. This leads to a general family of variational, multisymplectic numerical methods for solving Maxwell's equations that automatically preserve key symmetries and invariants. In doing so, we demonstrate several new results, which apply both to some well-established numerical methods and to new methods introduced here. First, we show that Yee's finite-difference time-domain (FDTD) scheme, along with a number of related methods, are multisymplectic and derive from a discrete Lagrangian variational principle. Second, we generalize the Yee scheme to unstructured meshes, not just in space but in 4-dimensional spacetime. This relaxes the need to take uniform time steps, or even to have a preferred time coordinate at all. Finally, as an example of the type of methods that can be developed within this general framework, we introduce a new asynchronous variational integrator (AVI) for solving Maxwell's equations. These results are illustrated with some prototype simulations that show excellent energy and conservation behavior and lack of spurious modes, even for an irregular mesh with asynchronous time stepping.

math.NA↗

arXiv2008

Variational Integrators for Maxwell's Equations with Sources

In recent years, two important techniques for geometric numerical discretization have been developed. In computational electromagnetics, spatial discretization has been improved by the use of mixed finite elements and discrete differential forms. Simultaneously, the dynamical systems and mechanics communities have developed structure-preserving time integrators, notably variational integrators that are constructed from a Lagrangian action principle. Here, we discuss how to combine these two frameworks to develop variational spacetime integrators for Maxwell's equations. Extending our previous work, which first introduced this variational perspective for Maxwell's equations without sources, we also show here how to incorporate free sources of charge and current.

math.NA↗