Variational approximation of functionals defined on 1-dimensional connected sets: the planar case

In this paper we consider variational problems involving 1-dimensional connected sets in the Euclidean plane, such as the classical Steiner tree problem and the irrigation (Gilbert-Steiner) problem. We relate them to optimal partition problems and provide a variational approximation through Modica-Mortola type energies proving a $\Gamma$-convergence result. We also introduce a suitable convex relaxation and develop the corresponding numerical implementations. The proposed methods are quite general and the results we obtain can be extended to $n$-dimensional Euclidean space or to more general manifold ambients, as shown in the companion paper [11].Comment: 30 pages, 5 figure

A parallel genetic algorithm for the Steiner Problem in Networks

This paper presents a parallel genetic algorithm to the Steiner Problem in Networks. Several previous papers have proposed the adoption of GAs and others metaheuristics to solve the SPN demonstrating the validity of their approaches. This work differs from them for two main reasons: the dimension and the characteristics of the networks adopted in the experiments and the aim from which it has been originated. The reason that aimed this work was namely to build a comparison term for validating deterministic and computationally inexpensive algorithms which can be used in practical engineering applications, such as the multicast transmission in the Internet. On the other hand, the large dimensions of our sample networks require the adoption of a parallel implementation of the Steiner GA, which is able to deal with such large problem instances

A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions

The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the reconstruction of a protein-protein subnetwork that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorithmic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza infection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Performance improvement of an optical network providing services based on multicast

Operators of networks covering large areas are confronted with demands from some of their customers who are virtual service providers. These providers may call for the connectivity service which fulfils the specificity of their services, for instance a multicast transition with allocated bandwidth. On the other hand, network operators want to make profit by trading the connectivity service of requested quality to their customers and to limit their infrastructure investments (or do not invest anything at all). We focus on circuit switching optical networks and work on repetitive multicast demands whose source and destinations are {\em \`a priori} known by an operator. He may therefore have corresponding trees "ready to be allocated" and adapt his network infrastructure according to these recurrent transmissions. This adjustment consists in setting available branching routers in the selected nodes of a predefined tree. The branching nodes are opto-electronic nodes which are able to duplicate data and retransmit it in several directions. These nodes are, however, more expensive and more energy consuming than transparent ones. In this paper we are interested in the choice of nodes of a multicast tree where the limited number of branching routers should be located in order to minimize the amount of required bandwidth. After formally stating the problem we solve it by proposing a polynomial algorithm whose optimality we prove. We perform exhaustive computations to show an operator gain obtained by using our algorithm. These computations are made for different methods of the multicast tree construction. We conclude by giving dimensioning guidelines and outline our further work.Comment: 16 pages, 13 figures, extended version from Conference ISCIS 201

Optimal expression evaluation for data parallel architectures

A data parallel machine represents an array or other composite data structure by allocating one processor (at least conceptually) per data item. A pointwise operation can be performed between two such arrays in unit time, provided their corresponding elements are allocated in the same processors. If the arrays are not aligned in this fashion, the cost of moving one or both of them is part of the cost of the operation. The choice of where to perform the operation then affects this cost. If an expression with several operands is to be evaluated, there may be many choices of where to perform the intermediate operations. An efficient algorithm is given to find the minimum-cost way to evaluate an expression, for several different data parallel architectures. This algorithm applies to any architecture in which the metric describing the cost of moving an array is robust. This encompasses most of the common data parallel communication architectures, including meshes of arbitrary dimension and hypercubes. Remarks are made on several variations of the problem, some of which are solved and some of which remain open