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Embedding undirected graphs in a Euclidean space has many computational benefits. FastMap is an efficient embedding algorithm that facilitates a geometric interpretation of problems posed on undirected graphs. However, Euclidean distances…
Any symmetric affinity function $w: V\times V \to \mathbb{R}_+$ defined on a discrete set $V$ induces Euclidean space structure on $V$. In particular, an undirected graph specified by an affinity (or adjacency) matrix can be considered as a…
In the matching interdiction problem, we are given an undirected graph with weights and interdiction costs on the edges and seek to remove a subset of the edges constrained to some budget, such that the weight of a maximum weight matching…
We investigate a special case of the maximum quadratic assignment problem where one matrix is a product matrix and the other matrix is the distance matrix of a one-dimensional point set. We show that this special case, which we call the…
In this paper we consider the classical problem of computing linear extensions of a given poset which is well known to be a difficult problem. However, in our setting the elements of the poset are multivariate polynomials, and only a small…
The calculation of Euclidean distance between points is generalized to one-dimensional objects such as strings or polymers. Necessary and sufficient conditions for the minimal transformation between two polymer configurations are derived.…
In this paper, we propose a novel approach for manifold learning that combines the Earthmover's distance (EMD) with the diffusion maps method for dimensionality reduction. We demonstrate the potential benefits of this approach for learning…
This paper proposes and illustrates a general framework to integrate the areas of vision research and complex networks. Each image pixel is associated to a network node and the Euclidean distance between the visual properties (e.g.…
Network embedding aims to learn the low-dimensional representations of vertexes in a network, while structure and inherent properties of the network is preserved. Existing network embedding works primarily focus on preserving the…
We define a class of Euclidean distances on weighted graphs, enabling to perform thermodynamic soft graph clustering. The class can be constructed form the "raw coordinates" encountered in spectral clustering, and can be extended by means…
We present a novel technique for encoding and decoding constant weight binary codes that uses a geometric interpretation of the codebook. Our technique is based on embedding the codebook in a Euclidean space of dimension equal to the weight…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Random geometric graphs are random graph models defined on metric measure spaces. A random geometric graph is generated by first sampling points from a metric space and then connecting each pair of sampled points independently with a…
This paper introduces the \emph{$d$-distance matching problem}, in which we are given a bipartite graph $G=(S,T;E)$ with $S=\{s_1,\dots,s_n\}$, a weight function on the edges and an integer $d\in\mathbb Z_+$. The goal is to find a maximum…
Structure-based drug design uses three-dimensional geometric information of macromolecules, such as proteins or nucleic acids, to identify suitable ligands. Geometric deep learning, an emerging concept of neural-network-based machine…
We initiate the study of a fundamental combinatorial problem: Given a capacitated graph $G=(V,E)$, find a shortest walk ("route") from a source $s\in V$ to a destination $t\in V$ that includes all vertices specified by a set…
The planted densest subgraph detection problem refers to the task of testing whether in a given (random) graph there is a subgraph that is unusually dense. Specifically, we observe an undirected and unweighted graph on $n$ vertices. Under…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
Geometric embedding of graphs in a point set in the plane is a well known problem. In this paper, the complexity of a variant of this problem, where the point set is bounded by a simple polygon, is considered. Given a point set in the plane…