arXiv subjects

Denis Zorin

Publications and source records attributed to Denis Zorin.

At least 55 records · Page 3Linked to original sources

arXiv2020

Fast Tetrahedral Meshing in the Wild

We propose a new tetrahedral meshing method, fTetWild, to convert triangle soups into high-quality tetrahedral meshes. Our method builds on the TetWild algorithm, replacing the rational triangle insertion with a new incremental approach to construct and optimize the output mesh, interleaving triangle insertion and mesh optimization. Our approach makes it possible to maintain a valid floating-point tetrahedral mesh at all algorithmic stages, eliminating the need for costly constructions with rational numbers used by TetWild, while maintaining full robustness and similar output quality. This allows us to improve on TetWild in two ways. First, our algorithm is significantly faster, with running time comparable to less robust Delaunay-based tetrahedralization algorithms. Second, our algorithm is guaranteed to produce a valid tetrahedral mesh with floating-point vertex coordinates, while TetWild produces a valid mesh with rational coordinates which is not guaranteed to be valid after floating-point conversion. As a trade-off, our algorithm no longer guarantees that all input triangles are present in the output mesh, but in practice, as confirmed by our tests on the Thingi10k dataset, the algorithm always succeeds in inserting all input triangles.

cs.GR↗

arXiv2019

Scalable Simulation of Realistic Volume Fraction Red Blood Cell Flows through Vascular Networks

High-resolution blood flow simulations have potential for developing better understanding biophysical phenomena at the microscale, such as vasodilation, vasoconstriction and overall vascular resistance. To this end, we present a scalable platform for the simulation of red blood cell (RBC) flows through complex capillaries by modeling the physical system as a viscous fluid with immersed deformable particles. We describe a parallel boundary integral equation solver for general elliptic partial differential equations, which we apply to Stokes flow through blood vessels. We also detail a parallel collision avoiding algorithm to ensure RBCs and the blood vessel remain contact-free. We have scaled our code on Stampede2 at the Texas Advanced Computing Center up to 34,816 cores. Our largest simulation enforces a contact-free state between four billion surface elements and solves for three billion degrees of freedom on one million RBCs and a blood vessel composed from two million patches.

cs.CE↗

arXiv2019

A parameteric class of composites with a large achievable range of effective elastic properties

In this paper we investigate numerically an instance of the problem of G-closure for two-dimensional periodic metamaterials. Specifically, we consider composites with isotropic homogenized elasticity tensor, obtained as a mixture of two isotropic materials, focusing on the case of a single material with voids. This problem is important, in particular, in the context of designing small-scale structures for metamaterials in the context of additive fabrication, as this type of metamaterials makes it possible to obtain a range of material properties using a single base material. We demonstrate that two closely related simple parametric families based on the structure proposed by O. Sigmund attain good coverage of the space of isotropic properties satisfying Hashin-Shtrikman bounds. In particular, for positive Poisson ratio, we demonstrate that Hashin-Shtrikman bound can be approximated arbitrarily well, within limits imposed by numerical approximation: a strong evidence that these bounds are achievable in this case. For negative Poisson ratios, we numerically obtain a bound which we hypothesize to be close to optimal, at least for metamaterials with rotational symmetries of a regular triangle tiling.

physics.comp-ph↗

arXiv2019

Perceptual deep depth super-resolution

RGBD images, combining high-resolution color and lower-resolution depth from various types of depth sensors, are increasingly common. One can significantly improve the resolution of depth maps by taking advantage of color information; deep learning methods make combining color and depth information particularly easy. However, fusing these two sources of data may lead to a variety of artifacts. If depth maps are used to reconstruct 3D shapes, e.g., for virtual reality applications, the visual quality of upsampled images is particularly important. The main idea of our approach is to measure the quality of depth map upsampling using renderings of resulting 3D surfaces. We demonstrate that a simple visual appearance-based loss, when used with either a trained CNN or simply a deep prior, yields significantly improved 3D shapes, as measured by a number of existing perceptual metrics. We compare this approach with a number of existing optimization and learning-based techniques.

cs.CV↗

arXiv2019

Gradient Dynamics of Shallow Univariate ReLU Networks

We present a theoretical and empirical study of the gradient dynamics of overparameterized shallow ReLU networks with one-dimensional input, solving least-squares interpolation. We show that the gradient dynamics of such networks are determined by the gradient flow in a non-redundant parameterization of the network function. We examine the principal qualitative features of this gradient flow. In particular, we determine conditions for two learning regimes:kernel and adaptive, which depend both on the relative magnitude of initialization of weights in different layers and the asymptotic behavior of initialization coefficients in the limit of large network widths. We show that learning in the kernel regime yields smooth interpolants, minimizing curvature, and reduces to cubic splines for uniform initializations. Learning in the adaptive regime favors instead linear splines, where knots cluster adaptively at the sample points.

cs.LG↗

arXiv2019

ABC: A Big CAD Model Dataset For Geometric Deep Learning

We introduce ABC-Dataset, a collection of one million Computer-Aided Design (CAD) models for research of geometric deep learning methods and applications. Each model is a collection of explicitly parametrized curves and surfaces, providing ground truth for differential quantities, patch segmentation, geometric feature detection, and shape reconstruction. Sampling the parametric descriptions of surfaces and curves allows generating data in different formats and resolutions, enabling fair comparisons for a wide range of geometric learning algorithms. As a use case for our dataset, we perform a large-scale benchmark for estimation of surface normals, comparing existing data driven methods and evaluating their performance against both the ground truth and traditional normal estimation methods.

cs.GR↗

arXiv2019

Structurally optimized shells

Shells, i.e., objects made of a thin layer of material following a surface, are among the most common structures in use. They are highly efficient, in terms of material required to maintain strength, but also prone to deformation and failure. We introduce an efficient method for reinforcing shells, that is, adding material to the shell to increase its resilience to external loads. Our goal is to produce a reinforcement structure of minimal weight. It has been demonstrated that optimal reinforcement structures may be qualitatively different, depending on external loads and surface shape. In some cases, it naturally consists of discrete protruding ribs; in other cases, a smooth shell thickness variation allows to save more material. Most previously proposed solutions, starting from classical Michell trusses, are not able to handle a full range of shells (e.g., are restricted to self-supporting structures) or are unable to reproduce this range of behaviors, resulting in suboptimal structures. We propose a new method that works for any input surface with any load configurations, taking into account both in-plane (tensile/compression) and out-of-plane (bending) forces. By using a more precise volume model, we are capable of producing optimized structures with the full range of qualitative behaviors. Our method includes new algorithms for determining the layout of reinforcement structure elements, and an efficient algorithm to optimize their shape, minimizing a non-linear non-convex functional at a fraction of the cost and with better optimality compared to standard solvers. We demonstrate the optimization results for a variety of shapes, and the improvements it yields in the strength of 3D-printed objects.

cs.GR↗

arXiv2019

Deep Geometric Prior for Surface Reconstruction

The reconstruction of a discrete surface from a point cloud is a fundamental geometry processing problem that has been studied for decades, with many methods developed. We propose the use of a deep neural network as a geometric prior for surface reconstruction. Specifically, we overfit a neural network representing a local chart parameterization to part of an input point cloud using the Wasserstein distance as a measure of approximation. By jointly fitting many such networks to overlapping parts of the point cloud, while enforcing a consistency condition, we compute a manifold atlas. By sampling this atlas, we can produce a dense reconstruction of the surface approximating the input cloud. The entire procedure does not require any training data or explicit regularization, yet, we show that it is able to perform remarkably well: not introducing typical overfitting artifacts, and approximating sharp features closely at the same time. We experimentally show that this geometric prior produces good results for both man-made objects containing sharp features and smoother organic objects, as well as noisy inputs. We compare our method with a number of well-known reconstruction methods on a standard surface reconstruction benchmark.

cs.CV↗

arXiv2019

Poly-Spline Finite Element Method

We introduce an integrated meshing and finite element method pipeline enabling black-box solution of partial differential equations in the volume enclosed by a boundary representation. We construct a hybrid hexahedral-dominant mesh, which contains a small number of star-shaped polyhedra, and build a set of high-order basis on its elements, combining triquadratic B-splines, triquadratic hexahedra (27 degrees of freedom), and harmonic elements. We demonstrate that our approach converges cubically under refinement, while requiring around 50% of the degrees of freedom than a similarly dense hexahedral mesh composed of triquadratic hexahedra. We validate our approach solving Poisson's equation on a large collection of models, which are automatically processed by our algorithm, only requiring the user to provide boundary conditions on their surface.

math.NA↗

arXiv2018

Parallel contact-aware simulations of deformable particles in 3D Stokes flow

We present a parallel-scalable method for simulating non-dilute suspensions of deformable particles immersed in Stokesian fluid in three dimensions. A critical component in these simulations is robust and accurate collision handling. This work complements our previous work [L. Lu, A. Rahimian, and D. Zorin. Contact-aware simulations of particulate Stokesian suspensions. Journal of Computational Physics 347C: 160-182] by extending it to 3D and by introducing new parallel algorithms for collision detection and handling. We use a well-established boundary integral formulation with spectral Galerkin method to solve the fluid flow. The key idea is to ensure an interference-free particle configuration by introducing explicit contact constraints into the system. While such constraints are typically unnecessary in the formulation they make it possible to eliminate catastrophic loss of accuracy in the discretized problem by preventing contact explicitly. The incorporation of contact constraints results in a significant increase in stable time-step size for locally-implicit time-stepping and a reduction in the necessary number of discretization points for stability. Our method maintains the accuracy of previous methods at a significantly lower cost for dense suspensions and the time step size is independent from the volume fraction. Our method permits simulations with high volume fractions; we report results with up to 60% volume fraction. We demonstrated the parallel scaling of the algorithms on up to 16K CPU cores.

math.NA↗

arXiv2018

Seamless Parametrization with Arbitrarily Prescribed Cones

Seamless global parametrization of surfaces is a key operation in geometry processing, e.g. for high-quality quad mesh generation. A common approach is to prescribe the parametric domain structure, in particular the locations of parametrization singularities (cones), and solve a non-convex optimization problem minimizing a distortion measure, with local injectivity imposed through either constraints or barrier terms. In both cases, an initial valid parametrization is essential to serve as feasible starting point for obtaining an optimized solution. While convexified versions of the constraints eliminate this initialization requirement, they narrow the range of solutions, causing some problem instances that actually do have a solution to become infeasible. We demonstrate that for arbitrary given sets of topologically admissible parametric cones with prescribed curvature, a global seamless parametrization always exists (with the exception of one well-known case). Importantly, our proof is constructive and directly leads to a general algorithm for computing such parametrizations. Most distinctively, this algorithm is bootstrapped with a convex optimization problem (solving for a conformal map), in tandem with a simple linear equation system (determining a seamless modification of this map). This initial map can then serve as valid starting point and be optimized with respect to application specific distortion measures using existing injectivity preserving methods.

cs.GR↗

arXiv2018

Surface Networks

We study data-driven representations for three-dimensional triangle meshes, which are one of the prevalent objects used to represent 3D geometry. Recent works have developed models that exploit the intrinsic geometry of manifolds and graphs, namely the Graph Neural Networks (GNNs) and its spectral variants, which learn from the local metric tensor via the Laplacian operator. Despite offering excellent sample complexity and built-in invariances, intrinsic geometry alone is invariant to isometric deformations, making it unsuitable for many applications. To overcome this limitation, we propose several upgrades to GNNs to leverage extrinsic differential geometry properties of three-dimensional surfaces, increasing its modeling power. In particular, we propose to exploit the Dirac operator, whose spectrum detects principal curvature directions --- this is in stark contrast with the classical Laplace operator, which directly measures mean curvature. We coin the resulting models \emph{Surface Networks (SN)}. We prove that these models define shape representations that are stable to deformation and to discretization, and we demonstrate the efficiency and versatility of SNs on two challenging tasks: temporal prediction of mesh deformations under non-linear dynamics and generative models using a variational autoencoder framework with encoders/decoders given by SNs.

stat.ML↗

arXiv2017

On Discrete Conformal Seamless Similarity Maps

An algorithm for the computation of global discrete conformal parametrizations with prescribed global holonomy signatures for triangle meshes was recently described in [Campen and Zorin 2017]. In this paper we provide a detailed analysis of convergence and correctness of this algorithm. We generalize and extend ideas of [Springborn et al. 2008] to show a connection of the algorithm to Newton's algorithm applied to solving the system of constraints on angles in the parametric domain, and demonstrate that this system can be obtained as a gradient of a convex energy.

cs.GR↗

arXiv2016

What Lies Beneath the Surface: Topological-Shape Optimization With the Kernel-Independent Fast Multipole Method

The paper presents a new method for shape and topology optimization based on an efficient and scalable boundary integral formulation for elasticity. To optimize topology, our approach uses iterative extraction of isosurfaces of a topological derivative. The numerical solution of the elasticity boundary value problem at every iteration is performed with the boundary element formulation and the kernel-independent fast multipole method. Providing excellent single node performance, scalable parallelization and the best available asymptotic complexity, our method is among the fastest optimization tools available today. The performance of our approach is studied on few illustrative examples, including the optimization of engineered constructions for the minimum compliance and the optimization of the microstructure of a metamaterial for the desired macroscopic tensor of elasticity.

math.OC↗

arXiv2016

Contact-aware simulations of particulate Stokesian suspensions

We present an efficient, accurate, and robust method for simulation of dense suspensions of deformable and rigid particles immersed in Stokesian fluid in two dimensions. We use a well-established boundary integral formulation for the problem as the foundation of our approach. This type of formulations, with a high-order spatial discretization and an implicit and adaptive time discretization, have been shown to be able to handle complex interactions between particles with high accuracy. Yet, for dense suspensions, very small time-steps or expensive implicit solves as well as a large number of discretization points are required to avoid non-physical contact and intersections between particles, leading to infinite forces and numerical instability. Our method maintains the accuracy of previous methods at a significantly lower cost for dense suspensions. The key idea is to ensure interference-free configuration by introducing explicit contact constraints into the system. While such constraints are unnecessary in the formulation, in the discrete form of the problem, they make it possible to eliminate catastrophic loss of accuracy by preventing contact explicitly. Introducing contact constraints results in a significant increase in stable time-step size for explicit time-stepping, and a reduction in the number of points adequate for stability.

math.NA↗

arXiv2016

Ubiquitous evaluation of layer potentials using Quadrature by Kernel-Independent Expansion

We introduce a quadrature scheme--QBKIX--for the high-order accurate evaluation of layer potentials associated with general elliptic PDEs near to and on the domain boundary. Relying solely on point evaluations of the underlying kernel, our scheme is essentially PDE-independent; in particular, no analytic expansion nor addition theorem is required. Moreover, it applies to boundary integrals with singular, weakly singular, and hypersingular kernels. Our work builds upon Quadrature by Expansion (QBX), which approximates the potential by an analytic expansion in the neighborhood of each expansion center. In contrast, we use a sum of fundamental solutions lying on a ring enclosing the neighborhood, and solve a small dense linear system for their coefficients to match the potential on a smaller concentric ring. We test the new method with Laplace, Helmholtz, Yukawa, Stokes, and Navier (elastostatic) kernels in two dimensions (2D) using adaptive, panel-based boundary quadratures on smooth and corner domains. Advantages of the algorithm include its relative simplicity of implementation, immediate extension to new kernels, dimension-independence (allowing simple generalization to 3D), and compatibility with fast algorithms such as the kernel-independent FMM.

math.NA↗

arXiv2016

A Tensor-Train accelerated solver for integral equations in complex geometries

We present a framework using the Quantized Tensor Train (QTT) decomposition to accurately and efficiently solve volume and boundary integral equations in three dimensions. We describe how the QTT decomposition can be used as a hierarchical compression and inversion scheme for matrices arising from the discretization of integral equations. For a broad range of problems, computational and storage costs of the inversion scheme are extremely modest $O(\log N)$ and once the inverse is computed, it can be applied in $O(N \log N)$. We analyze the QTT ranks for hierarchically low rank matrices and discuss its relationship to commonly used hierarchical compression techniques such as FMM and HSS. We prove that the QTT ranks are bounded for translation-invariant systems and argue that this behavior extends to non-translation invariant volume and boundary integrals. For volume integrals, the QTT decomposition provides an efficient direct solver requiring significantly less memory compared to other fast direct solvers. We present results demonstrating the remarkable performance of the QTT-based solver when applied to both translation and non-translation invariant volume integrals in 3D. For boundary integral equations, we demonstrate that using a QTT decomposition to construct preconditioners for a Krylov subspace method leads to an efficient and robust solver with a small memory footprint. We test the QTT preconditioners in the iterative solution of an exterior elliptic boundary value problem (Laplace) formulated as a boundary integral equation in complex, multiply connected geometries.

math.NA↗

arXiv2016

A fast platform for simulating flexible fiber suspensions applied to cell mechanics

We present a novel platform for the large-scale simulation of fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space. One of the main motivations for this work is to study the dynamics of fiber assemblies within biological cells. For this, we also incorporate the key biophysical elements that determine the dynamics of these assemblies, which include the polymerization and depolymerization kinetics of fibers, their interactions with molecular motors and other objects, their flexibility, and hydrodynamic coupling. This work, to our knowledge, is the first technique to include many-body hydrodynamic interactions (HIs), and the resulting fluid flows, in cellular fiber assemblies. We use the non-local slender body theory to compute the fluid-structure interactions of the fibers and a second-kind boundary integral formulation for other rigid bodies and the confining boundary. A kernel-independent implementation of the fast multiple method is utilized for efficient evaluation of HIs. The deformation of the fibers is described by the nonlinear Euler--Bernoulli beam theory and their polymerization is modeled by the reparametrization of the dynamic equations in the appropriate non-Lagrangian frame. We use a pseudo-spectral representation of fiber positions and implicit HIs in the time-stepping to resolve large fiber deformations, and to allow time-steps not constrained by temporal stiffness or fiber-fiber interactions. The entire computational scheme is parallelized, which enables simulating assemblies of thousands of fibers. We use our method to investigate two important questions in the mechanics of cell division: (i) the effect of confinement on the hydrodynamic mobility of microtubule asters; and (ii) the dynamics of the positioning of mitotic spindle in complex cell geometries.

math.NA↗