Related papers: Cycle-based formulations in Distance Geometry
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
The immersed boundary method is a numerical and mathematical formulation for solving fluid-structure interaction problems. It relies on solving fluid equations on an Eulerian fluid grid and interpolating the resulting velocity back onto…
This work addresses a modification of the random geometric graph (RGG) model by considering a set of points uniformly and independently distributed on the surface of a $(d-1)$-sphere with radius $r$ in a $d-$dimensional Euclidean space,…
To numerically solve a generic elliptic equation on two-dimensional domains with rectangular Cartesian grids, we propose a cut-cell geometric multigrid method that features (1) general algorithmic steps that apply to two-dimensional…
We study stochastic graph optimization problems in a novel distributed setting. As in the standard centralized setting, a random subgraph $G^*$ of a known base graph $G$ is realized by including each edge $e$ independently with a known…
Euclidean distance matrices (EDMs) are a major tool for localization from distances, with applications ranging from protein structure determination to global positioning and manifold learning. They are, however, static objects which serve…
Edit distance is a measurement of similarity between two sequences such as strings, point sequences, or polygonal curves. Many matching problems from a variety of areas, such as signal analysis, bioinformatics, etc., need to be solved in a…
Straight-forward conformation generation models, which generate 3-D structures directly from input molecular graphs, play an important role in various molecular tasks with machine learning, such as 3D-QSAR and virtual screening in drug…
A local weighted discontinuous Galerkin gradient discretization method for solving elliptic equations is introduced. The local scheme is based on a coarse grid and successively improves the solution solving a sequence of local elliptic…
The recently developed 3D graphic statics (3DGS) lacks a rigorous mathematical definition relating the geometrical and topological properties of the reciprocal polyhedral diagrams as well as a precise method for the geometric construction…
This is an expository paper. A $1$-cycle in a graph is a set $C$ of edges such that every vertex is contained in an even number of edges from $C$. E.g., a cycle in the sense of graph theory is a $1$-cycle, but not vice versa. It is easy to…
Discrete forms of the mean and directed curvature are constructed on piecewise flat manifolds, providing local curvature approximations for smooth manifolds embedded in both Euclidean and non-Euclidean spaces. The resulting expressions take…
Graph embeddings, wherein the nodes of the graph are represented by points in a continuous space, are used in a broad range of Graph ML applications. The quality of such embeddings crucially depends on whether the geometry of the space…
We improve the best known upper bound on the number of edges in a unit-distance graph on $n$ vertices for each $n\in\{16,\ldots,30\}$. When $n\leq 21$, our bounds match the best known lower bounds, and we fully enumerate the densest…
The problem of finding multiple simple shortest paths in a weighted directed graph $G=(V,E)$ has many applications, and is considerably more difficult than the corresponding problem when cycles are allowed in the paths. Even for a single…
Symmetry is an important aesthetic criteria in graph drawing and network visualisation. Symmetric graph drawings aim to faithfully represent automorphisms of graphs as geometric symmetries in a drawing. In this paper, we design and…
Geometric consistency, i.e. the preservation of neighbourhoods, is a natural and strong prior in 3D shape matching. Geometrically consistent matchings are crucial for many downstream applications, such as texture transfer or statistical…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
The majority of inverse kinematics (IK) algorithms search for solutions in a configuration space defined by joint angles. However, the kinematics of many robots can also be described in terms of distances between rigidly-attached points,…
We study hyperbolized versions of cohomological equations that appear with cocycles by isometries of the euclidean space. These (hyperbolized versions of) equations have a unique continuous solution. We concentrate in to know whether or not…