相关论文: Shortest Paths with Pairwise-Distinct Edge Labels:…
The quadratic shortest path problem is the problem of finding a path in a directed graph such that the sum of interaction costs over all pairs of arcs on the path is minimized. We derive several semidefinite programming relaxations for the…
Objective: Modelling the associations from high-throughput experimental molecular data has provided unprecedented insights into biological pathways and signalling mechanisms. Graphical models and networks have especially proven to be useful…
In this thesis, we design algorithms for several NP-hard problems in both worst and beyond worst case settings. In the first part of the thesis, we apply the traditional worst case methodology and design approximation algorithms for the Hub…
We consider the following problem that we call the Shortest Two Disjoint Paths problem: given an undirected graph $G=(V,E)$ with edge weights $w:E \rightarrow \mathbb{R}$, two terminals $s$ and $t$ in $G$, find two internally…
The degree centrality of a node, defined as the number of nodes adjacent to it, is often used as a measure of importance of a node to the structure of a network. This metric can be extended to paths in a network, where the degree centrality…
Shortest path problems are a touchstone for evaluating the computing performance and functional range of novel computing substrates. Much has been published in recent years regarding the use of biocomputers to solve minimal path problems…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
Let G=(V,E)(|V|=n and |E|=m) be an undirected graph with positive edge weights. Let P_{G}(s, t) be a shortest s-t path in G. Let l be the number of edges in P_{G}(s, t). The \emph{Edge Replacement Path} problem is to compute a shortest s-t…
In this survey paper, we will present a number of core algorithmic questions concerning several transitive reduction problems on network that have applications in network synthesis and analysis involving cellular processes. Our starting…
The Constraint Shortest Path (CSP) problem is as follows. An $n$-vertex graph is given, each edge/arc assigned two weights. Let us call them "cost" and "length" for definiteness. Finding a min-cost upper-bounded length path between a given…
Network flow is a powerful mathematical framework to systematically explore the relationship between structure and function in biological, social, and technological networks. We introduce a new pipelining model of flow through networks…
Given a connected, undirected graph whose edges are labelled (or coloured), the minimum labelling spanning tree (MLST) problem seeks a spanning tree whose edges have the smallest number of distinct labels (or colours). In recent work, the…
We consider the parametric shortest paths problem in a linearly interpolated graph. Given two positively-weighted directed graphs $G_0=(V,E,\omega_0)$ and $G_1=(V,E,\omega_1),$ the linearly interpolated graph is the family of graphs…
This paper studies reduced-order modeling of dynamic networks with strongly connected topology. Given a graph clustering of an original complex network, we construct a quotient graph with less number of vertices, where the edge weights are…
Biological and cellular systems are often modeled as graphs in which vertices represent objects of interest (genes, proteins, drugs) and edges represent relational ties among these objects (binds-to, interacts-with, regulates). This…
Shortest path algorithms have played a key role in the past century, paving the way for modern day GPS systems to find optimal routes along static systems in fractions of a second. One application of these algorithms includes optimizing the…
We study a scenario for route planning in road networks, where the objective to be optimized may change between every shortest path query. Since this invalidates many of the known speedup techniques for road networks that are based on…
We study the problem of computing constrained shortest paths for battery electric vehicles. Since battery capacities are limited, fastest routes are often infeasible. Instead, users are interested in fast routes on which the energy…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
We study parameterized versions of classical algorithms for computing shortest-path trees. This is most easily expressed in terms of tropical geometry. Applications include shortest paths in traffic networks with variable link travel times.