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Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
The problem of finding the densest subgraph in a given graph has several applications in graph mining, particularly in areas like social network analysis, protein and gene analyses etc. Depending on the application, finding dense subgraphs…
Graph matching is a fundamental tool in computer vision and pattern recognition. In this paper, we introduce an algorithm for graph matching based on the proximal operator, referred to as differentiable proximal graph matching (DPGM).…
The fundamental inverse problem in distance geometry is the one of finding positions from inter-point distances. The Discretizable Molecular Distance Geometry Problem (DMDGP) is a subclass of the Distance Geometry Problem (DGP) whose search…
Recognition of an adversary's objective is a core problem in physical security and cyber defense. Prior work on target recognition focuses on developing optimal inference strategies given the adversary's operating environment. However, the…
This thesis investigates the use of problem-specific knowledge to enhance a genetic algorithm approach to multiple-choice optimisation problems.It shows that such information can significantly enhance performance, but that the choice of…
A geometric graph is a combinatorial graph, endowed with a geometry that is inherited from its embedding in a Euclidean space. Formulation of a meaningful measure of (dis-)similarity in both the combinatorial and geometric structures of two…
Network optimization has generally been focused on solving network flow problems, but recently there have been investigations into optimizing network characteristics. Optimizing network connectivity to maximize the number of nodes within a…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
The Euclidean distance geometry problem arises in a wide variety of applications, from determining molecular conformations in computational chemistry to localization in sensor networks. When the distance information is incomplete, the…
Managing radio spectrum resources is a crucial issue. The frequency assignment problem (FAP) basically aims to allocate, in an efficient manner, limited number of frequencies to communication links. Geographically close links, however,…
Graphs are widely used to model execution dependencies in applications. In particular, the NP-complete problem of partitioning a graph under constraints receives enormous attention by researchers because of its applicability in…
Similarity graphs are an active research direction for the nearest neighbor search (NNS) problem. New algorithms for similarity graph construction are continuously being proposed and analyzed by both theoreticians and practitioners.…
Given an integer dimension K and a simple, undirected graph G with positive edge weights, the Distance Geometry Problem (DGP) aims to find a realization function mapping each vertex to a coordinate in K-dimensional space such that the…
We propose a heuristic method that generates a graph for order/degree problem. Target graphs of our heuristics have large order (> 4000) and diameter 3. We describe the ob- servation of smaller graphs and basic structure of our heuristics.…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
The orienteering problem is a well-studied and fundamental problem in transportation science. In the problem, we are given a graph with prizes on the nodes and lengths on the edges, together with a budget on the overall tour length. The…
Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies,…
Exploiting geometric structure to improve the asymptotic complexity of discrete assignment problems is a well-studied subject. In contrast, the practical advantages of using geometry for such problems have not been explored. We implement…