An algorithm for optimal transport between a simplex soup and a point cloud

We propose a numerical method to find the optimal transport map between a measure supported on a lower-dimensional subset of R^d and a finitely supported measure. More precisely, the source measure is assumed to be supported on a simplex soup, i.e. on a union of simplices of arbitrary dimension between 2 and d. As in [Aurenhammer, Hoffman, Aronov, Algorithmica 20 (1), 1998, 61--76] we recast this optimal transport problem as the resolution of a non-linear system where one wants to prescribe the quantity of mass in each cell of the so-called Laguerre diagram. We prove the convergence with linear speed of a damped Newton's algorithm to solve this non-linear system. The convergence relies on two conditions: (i) a genericity condition on the point cloud with respect to the simplex soup and (ii) a (strong) connectedness condition on the support of the source measure defined on the simplex soup. Finally, we apply our algorithm in R^3 to compute optimal transport plans between a measure supported on a triangulation and a discrete measure. We also detail some applications such as optimal quantization of a probability density over a surface, remeshing or rigid point set registration on a mesh

Light in Power: A General and Parameter-free Algorithm for Caustic Design

We present in this paper a generic and parameter-free algorithm to efficiently build a wide variety of optical components, such as mirrors or lenses, that satisfy some light energy constraints. In all of our problems, one is given a collimated or point light source and a desired illumination after reflection or refraction and the goal is to design the geometry of a mirror or lens which transports exactly the light emitted by the source onto the target. We first propose a general framework and show that eight different optical component design problems amount to solving a light energy conservation equation that involves the computation of visibility diagrams. We then show that these diagrams all have the same structure and can be obtained by intersecting a 3D Power diagram with a planar or spherical domain. This allows us to propose an efficient and fully generic algorithm capable to solve these eight optical component design problems. The support of the prescribed target illumination can be a set of directions or a set of points located at a finite distance. Our solutions satisfy design constraints such as convexity or concavity. We show the effectiveness of our algorithm on simulated and fabricated examples

Intersection of paraboloids and application to Minkowski-type problems

In this article, we study the intersection (or union) of the convex hull of N confocal paraboloids (or ellipsoids) of revolution. This study is motivated by a Minkowski-type problem arising in geometric optics. We show that in each of the four cases, the combinatorics is given by the intersection of a power diagram with the unit sphere. We prove the complexity is O(N) for the intersection of paraboloids and Omega(N^2) for the intersection and the union of ellipsoids. We provide an algorithm to compute these intersections using the exact geometric computation paradigm. This algorithm is optimal in the case of the intersection of ellipsoids and is used to solve numerically the far-field reflector problem

Robust Geometry Estimation using the Generalized Voronoi Covariance Measure

The Voronoi Covariance Measure of a compact set K of R^d is a tensor-valued measure that encodes geometric information on K and which is known to be resilient to Hausdorff noise but sensitive to outliers. In this article, we generalize this notion to any distance-like function delta and define the delta-VCM. We show that the delta-VCM is resilient to Hausdorff noise and to outliers, thus providing a tool to estimate robustly normals from a point cloud approximation. We present experiments showing the robustness of our approach for normal and curvature estimation and sharp feature detection

Properties of Gauss digitized sets and digital surface integration

International audienceThis paper presents new topological and geometrical properties of Gauss digitizations of Euclidean shapes, most of them holding in arbitrary dimension $d$. We focus on $r$-regular shapes sampled by Gauss digitization at gridstep $h$. The digitized boundary is shown to be close to the Euclidean boundary in the Hausdorff sense, the minimum distance $\frac{\sqrt{d}}{2}h$ being achieved by the projection map $\xi$ induced by the Euclidean distance. Although it is known that Gauss digitized boundaries may not be manifold when $d \ge 3$, we show that non-manifoldness may only occur in places where the normal vector is almost aligned with some digitization axis, and the limit angle decreases with $h$. We then have a closer look at the projection of the digitized boundary onto the continuous boundary by $\xi$. We show that the size of its non-injective part tends to zero with $h$. This leads us to study the classical digital surface integration scheme, which allocates a measure to each surface element that is proportional to the cosine of the angle between an estimated normal vector and the trivial surface element normal vector. We show that digital integration is convergent whenever the normal estimator is multigrid convergent, and we explicit the convergence speed. Since convergent estimators are now available in the litterature, digital integration provides a convergent measure for digitized objects

Strong c-concavity and stability in optimal transport

The stability of solutions to optimal transport problems under variation of the measures is fundamental from a mathematical viewpoint: it is closely related to the convergence of numerical approaches to solve optimal transport problems and justifies many of the applications of optimal transport. In this article, we introduce the notion of strong c-concavity, and we show that it plays an important role for proving stability results in optimal transport for general cost functions c. We then introduce a differential criterion for proving that a function is strongly c-concave, under an hypothesis on the cost introduced originally by Ma-Trudinger-Wang for establishing regularity of optimal transport maps. Finally, we provide two examples where this stability result can be applied, for cost functions taking value +$\infty$ on the sphere: the reflector problem and the Gaussian curvature measure prescription problem

Convergence of a Newton algorithm for semi-discrete optimal transport

Many problems in geometric optics or convex geometry can be recast as optimal transport problems and a popular way to solve these problems numerically is to assume that the source probability measure is absolutely continuous while the target measure is finitely supported. We introduce a damped Newton's algorithm for this type of problems, which is experimentally efficient, and we establish its global linear convergence for cost functions satisfying an assumption that appears in the regularity theory for optimal transport

Improved prediction of critical residues for protein function based on network and phylogenetic analyses

BACKGROUND: Phylogenetic approaches are commonly used to predict which amino acid residues are critical to the function of a given protein. However, such approaches display inherent limitations, such as the requirement for identification of multiple homologues of the protein under consideration. Therefore, complementary or alternative approaches for the prediction of critical residues would be desirable. Network analyses have been used in the modelling of many complex biological systems, but only very recently have they been used to predict critical residues from a protein's three-dimensional structure. Here we compare a couple of phylogenetic approaches to several different network-based methods for the prediction of critical residues, and show that a combination of one phylogenetic method and one network-based method is superior to other methods previously employed. RESULTS: We associate a network with each member of a set of proteins for which the three-dimensional structure is known and the critical residues have been previously determined experimentally. We show that several network-based centrality measurements (connectivity, 2-connectivity, closeness centrality, betweenness and cluster coefficient) accurately detect residues critical for the protein's function. Phylogenetic approaches render predictions as reliable as the network-based measurements, although, interestingly, the two general approaches tend to predict different sets of critical residues. Hence we propose a hybrid method that is composed of one network-based calculation – the closeness centrality – and one phylogenetic approach – the Conseq server. This hybrid approach predicts critical residues more accurately than the other methods tested here. CONCLUSION: We show that network analysis can be used to improve the prediction of amino acids critical for protein function, when utilized in combination with phylogenetic approaches. It is proposed that such improvement is due to the complementary nature of these approaches: network-based methods tend to predict as critical those residues that are highly connected and internal (i.e., non-surface), although some surface residues are indeed identified as critical by network analyses; whereas residues chosen by phylogenetic approaches display a lower overall probability of being surface inaccessible

Optimal transport: discretization and algorithms

This chapter describes techniques for the numerical resolution of optimal transport problems. We will consider several discretizations of these problems, and we will put a strong focus on the mathematical analysis of the algorithms to solve the discretized problems. We will describe in detail the following discretizations and corresponding algorithms: the assignment problem and Bertsekas auction's algorithm; the entropic regularization and Sinkhorn-Knopp's algorithm; semi-discrete optimal transport and Oliker-Prussner or damped Newton's algorithm, and finally semi-discrete entropic regularization. Our presentation highlights the similarity between these algorithms and their connection with the theory of Kantorovich duality

Optimal transport: discretization and algorithms

This chapter describes techniques for the numerical resolution of optimal transport problems. We will consider several discretizations of these problems, and we will put a strong focus on the mathematical analysis of the algorithms to solve the discretized problems. We will describe in detail the following discretizations and corresponding algorithms: the assignment problem and Bertsekas auction's algorithm; the entropic regularization and Sinkhorn-Knopp's algorithm; semi-discrete optimal transport and Oliker-Prussner or damped Newton's algorithm, and finally semi-discrete entropic regularization. Our presentation highlights the similarity between these algorithms and their connection with the theory of Kantorovich duality