The Hausdorff distance between some sets of points

Hausdorff distance can be used in various areas, where the problems of shape matching and comparison appear. We look at the Hausdorff distance between two hyperspheres in (mathbb{R}^n). With respect to different geometric objects, the Hausdorff distance between a segment and a hypersphere in (mathbb{R}^n) is given, too. Using the Mahalanobis distance, a modified Hausdorff distance between a segment and an ellipse in the plane, and generally between a segment and a hyper-ellipsoid in (mathbb{R}^n) is adopted. Finally, the modified Hausdorff distance between ellipses is obtained

Adaptive Geometry Images for Remeshing

Geometry images are a kind of completely regular remeshing methods for mesh representation. Traditional geometry images have difficulties in achieving optimal reconstruction errors and preserving manually selected geometric details, due to the limitations of parametrization methods. To solve two issues, we propose two adaptive geometry images for remeshing triangular meshes. The first scheme produces geometry images with the minimum Hausdorff error by finding the optimization direction for sampling points based on the Hausdorff distance between the original mesh and the reconstructed mesh. The second scheme produces geometry images with higher reconstruction precision over the manually selected region-of-interest of the input mesh, by increasing the number of sampling points over the region-of-interest. Experimental results show that both schemes give promising results compared with traditional parametrization-based geometry images

Novel semi-metrics for multivariate change point analysis and anomaly detection

This paper proposes a new method for determining similarity and anomalies between time series, most practically effective in large collections of (likely related) time series, by measuring distances between structural breaks within such a collection. We introduce a class of \emph{semi-metric} distance measures, which we term \emph{MJ distances}. These semi-metrics provide an advantage over existing options such as the Hausdorff and Wasserstein metrics. We prove they have desirable properties, including better sensitivity to outliers, while experiments on simulated data demonstrate that they uncover similarity within collections of time series more effectively. Semi-metrics carry a potential disadvantage: without the triangle inequality, they may not satisfy a "transitivity property of closeness." We analyse this failure with proof and introduce an computational method to investigate, in which we demonstrate that our semi-metrics violate transitivity infrequently and mildly. Finally, we apply our methods to cryptocurrency and measles data, introducing a judicious application of eigenvalue analysis.Comment: Accepted manuscript. Minor edits since v2. Equal contribution from first two author

Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways

Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transition paths. As such paths are curves in a high-dimensional space, they have been difficult to compare quantitatively, a prerequisite to, for instance, assess the quality of different sampling algorithms. The Path Similarity Analysis (PSA) approach alleviates these difficulties by utilizing the full information in 3N-dimensional trajectories in configuration space. PSA employs the Hausdorff or Fr\'echet path metrics---adopted from computational geometry---enabling us to quantify path (dis)similarity, while the new concept of a Hausdorff-pair map permits the extraction of atomic-scale determinants responsible for path differences. Combined with clustering techniques, PSA facilitates the comparison of many paths, including collections of transition ensembles. We use the closed-to-open transition of the enzyme adenylate kinase (AdK)---a commonly used testbed for the assessment enhanced sampling algorithms---to examine multiple microsecond equilibrium molecular dynamics (MD) transitions of AdK in its substrate-free form alongside transition ensembles from the MD-based dynamic importance sampling (DIMS-MD) and targeted MD (TMD) methods, and a geometrical targeting algorithm (FRODA). A Hausdorff pairs analysis of these ensembles revealed, for instance, that differences in DIMS-MD and FRODA paths were mediated by a set of conserved salt bridges whose charge-charge interactions are fully modeled in DIMS-MD but not in FRODA. We also demonstrate how existing trajectory analysis methods relying on pre-defined collective variables, such as native contacts or geometric quantities, can be used synergistically with PSA, as well as the application of PSA to more complex systems such as membrane transporter proteins.Comment: 9 figures, 3 tables in the main manuscript; supplementary information includes 7 texts (S1 Text - S7 Text) and 11 figures (S1 Fig - S11 Fig) (also available from journal site

A Constrained Resampling Strategy for Mesh Improvement

In many geometry processing applications, it is required to improve an initial mesh in terms of multiple quality objectives. Despite the availability of several mesh generation algorithms with provable guarantees, such generated meshes may only satisfy a subset of the objectives. The conflicting nature of such objectives makes it challenging to establish similar guarantees for each combination, e.g., angle bounds and vertex count. In this paper, we describe a versatile strategy for mesh improvement by interpreting quality objectives as spatial constraints on resampling and develop a toolbox of local operators to improve the mesh while preserving desirable properties. Our strategy judiciously combines smoothing and transformation techniques allowing increased flexibility to practically achieve multiple objectives simultaneously.  We apply our strategy to both planar and surface meshes demonstrating how to simplify Delaunay meshes while preserving element quality, eliminate all obtuse angles in a complex mesh, and maximize the shortest edge length in a Voronoi tessellation far better than the state-of-the-art

Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways

abstract: Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational geometry) to quantify the degree of similarity between piecewise-linear curves. It thus completely avoids relying on projections into low dimensional spaces, as used in traditional approaches. To elucidate the principles of PSA, we quantified the effect of path roughness induced by thermal fluctuations using a toy model system. Using, as an example, the closed-to-open transitions of the enzyme adenylate kinase (AdK) in its substrate-free form, we compared a range of protein transition path-generating algorithms. Molecular dynamics-based dynamic importance sampling (DIMS) MD and targeted MD (TMD) and the purely geometric FRODA (Framework Rigidity Optimized Dynamics Algorithm) were tested along with seven other methods publicly available on servers, including several based on the popular elastic network model (ENM). PSA with clustering revealed that paths produced by a given method are more similar to each other than to those from another method and, for instance, that the ENM-based methods produced relatively similar paths. PSA applied to ensembles of DIMS MD and FRODA trajectories of the conformational transition of diphtheria toxin, a particularly challenging example, showed that the geometry-based FRODA occasionally sampled the pathway space of force field-based DIMS MD. For the AdK transition, the new concept of a Hausdorff-pair map enabled us to extract the molecular structural determinants responsible for differences in pathways, namely a set of conserved salt bridges whose charge-charge interactions are fully modelled in DIMS MD but not in FRODA. PSA has the potential to enhance our understanding of transition path sampling methods, validate them, and to provide a new approach to analyzing conformational transitions.The article is published at http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.100456