Ανάλυση πρωτεΐνης σε πλέγμα

Σημείωση: διατίθεται συμπληρωματικό υλικό σε ξεχωριστό αρχείο

On Sparse Hitting Sets: From Fair Vertex Cover to Highway Dimension

We consider the Sparse Hitting Set (Sparse-HS) problem, where we are given a set system (V,?,?) with two families ?,? of subsets of the universe V. The task is to find a hitting set for ? that minimizes the maximum number of elements in any of the sets of ?. This generalizes several problems that have been studied in the literature. Our focus is on determining the complexity of some of these special cases of Sparse-HS with respect to the sparseness k, which is the optimum number of hitting set elements in any set of ? (i.e., the value of the objective function). For the Sparse Vertex Cover (Sparse-VC) problem, the universe is given by the vertex set V of a graph, and ? is its edge set. We prove NP-hardness for sparseness k ? 2 and polynomial time solvability for k = 1. We also provide a polynomial-time 2-approximation algorithm for any k. A special case of Sparse-VC is Fair Vertex Cover (Fair-VC), where the family ? is given by vertex neighbourhoods. For this problem it was open whether it is FPT (or even XP) parameterized by the sparseness k. We answer this question in the negative, by proving NP-hardness for constant k. We also provide a polynomial-time (2-1/k)-approximation algorithm for Fair-VC, which is better than any approximation algorithm possible for Sparse-VC or the Vertex Cover problem (under the Unique Games Conjecture). We then switch to a different set of problems derived from Sparse-HS related to the highway dimension, which is a graph parameter modelling transportation networks. In recent years a growing literature has shown interesting algorithms for graphs of low highway dimension. To exploit the structure of such graphs, most of them compute solutions to the r-Shortest Path Cover (r-SPC) problem, where r > 0, ? contains all shortest paths of length between r and 2r, and ? contains all balls of radius 2r. It is known that there is an XP algorithm that computes solutions to r-SPC of sparseness at most h if the input graph has highway dimension h. However it was not known whether a corresponding FPT algorithm exists as well. We prove that r-SPC and also the related r-Highway Dimension (r-HD) problem, which can be used to formally define the highway dimension of a graph, are both W[1]-hard. Furthermore, by the result of Abraham et al. [ICALP 2011] there is a polynomial-time O(log k)-approximation algorithm for r-HD, but for r-SPC such an algorithm is not known. We prove that r-SPC admits a polynomial-time O(log n)-approximation algorithm

On a class of covering problems with variable capacities in wireless networks

We consider the problem of allocating clients to base stations in wireless networks. Two design decisions are the location of the base stations, and the power levels of the base stations. We model the interference, due to the increased power usage resulting in greater serving radius, as capacities that are non-increasing with respect to the covering radius. Clients have demands that are not necessarily uniform and the capacity of a facility limits the total demand that can be served by the facility. We consider three models. In the first model, the location of the base stations and the clients are fixed, and the problem is to determine the serving radius for each base station so as to serve a set of clients with maximum total profit subject to the capacity constraints of the base stations. In the second model, each client has an associated demand in addition to its profit. A fixed number of facilities have to be opened from a candidate set of locations. The goal is to serve clients so as to maximize the profit subject to the capacity constraints. In the third model, the location and the serving radius of the base stations are to be determined. There are costs associated with opening the base stations, and the goal is to open a set of base stations of minimum total cost so as to serve the entire demand subject to the capacity constraints at the base stations. We show that for the first model the problem is NP-complete even when there are only two choices for the serving radius, and the capacities are 1, 2. For the second model, we give a 1/2 approximation algorithm. For the third model, we give a column generation procedure for solving the standard linear programming model, and a randomized rounding procedure. We establish the efficacy of the column generation based rounding scheme on randomly generated instances

Algorithms & experiments for the protein chain lattice fitting problem

ix, 47 leaves ; 29 cm.This study seeks to design algorithms that may be used to determine if a given lattice is a good approximation to a given rigid protein structure. Ideal lattice models discovered using our techniques may then be used in algorithms for protein folding and inverse protein folding. In this study we develop methods based on dynamic programming and branch and bound in an effort to identify “ideal” lattice models. To further our understanding of the concepts behind the methods we have utilized a simple cubic lattice for our analysis. The algorithms may be adapted to work on any lattice. We describe two algorithms. One for aligning the protein backbone to the lattice as a walk. This algorithm runs in polynomial time. The second algorithm for aligning a protein backbone as a path to the lattice. Both the algorithms seek to minimize the CRMS deviation of the alignment. The second problem was recently shown to be NP-Complete, hence it is highly unlikely that an efficient algorithm exists. The first algorithm gives a lower bound on the optimal solution to the second problem, and can be used in a branch and bound procedure. Further, we perform an empirical evaluation of our algorithm on proteins from the Protein Data Bank (PDB)