Solving Maximum Clique Problem for Protein Structure Similarity

A basic assumption of molecular biology is that proteins sharing close three-dimensional (3D) structures are likely to share a common function and in most cases derive from a same ancestor. Computing the similarity between two protein structures is therefore a crucial task and has been extensively investigated. Evaluating the similarity of two proteins can be done by finding an optimal one-to-one matching between their components, which is equivalent to identifying a maximum weighted clique in a specific "alignment graph". In this paper we present a new integer programming formulation for solving such clique problems. The model has been implemented using the ILOG CPLEX Callable Library. In addition, we designed a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST (Vector Alignment Search Tool) - a software for aligning protein 3D structures largely used in NCBI (National Center for Biotechnology Information). The original VAST clique solver uses the well known Bron and Kerbosh algorithm (BK). Our computational results on real life protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK for the largest proteins

A Tutorial on Clique Problems in Communications and Signal Processing

Since its first use by Euler on the problem of the seven bridges of K\"onigsberg, graph theory has shown excellent abilities in solving and unveiling the properties of multiple discrete optimization problems. The study of the structure of some integer programs reveals equivalence with graph theory problems making a large body of the literature readily available for solving and characterizing the complexity of these problems. This tutorial presents a framework for utilizing a particular graph theory problem, known as the clique problem, for solving communications and signal processing problems. In particular, the paper aims to illustrate the structural properties of integer programs that can be formulated as clique problems through multiple examples in communications and signal processing. To that end, the first part of the tutorial provides various optimal and heuristic solutions for the maximum clique, maximum weight clique, and $k$-clique problems. The tutorial, further, illustrates the use of the clique formulation through numerous contemporary examples in communications and signal processing, mainly in maximum access for non-orthogonal multiple access networks, throughput maximization using index and instantly decodable network coding, collision-free radio frequency identification networks, and resource allocation in cloud-radio access networks. Finally, the tutorial sheds light on the recent advances of such applications, and provides technical insights on ways of dealing with mixed discrete-continuous optimization problems

A Lagrangian relaxation approach to the edge-weighted clique problem

The $b$-clique polytope $CP^n_b$ is the convex hull of the node and edge incidence vectors of all subcliques of size at most $b$ of a complete graph on $n$ nodes. Including the Boolean quadric polytope $QP^n$ as a special case and being closely related to the quadratic knapsack polytope, it has received considerable attention in the literature. In particular, the max-cut problem is equivalent with optimizing a linear function over $QP^n_n$. The problem of optimizing linear functions over $CP^n_b$ has so far been approached via heuristic combinatorial algorithms and cutting-plane methods. We study the structure of $CP^n_b$ in further detail and present a new computational approach to the linear optimization problem based on Lucena's suggestion of integrating cutting planes into a Lagrangian relaxation of an integer programming problem. In particular, we show that the separation problem for tree inequalities becomes polynomial in our Lagrangian framework. Finally, computational results are presented. \u

Solving MaxSAT and #SAT on structured CNF formulas

In this paper we propose a structural parameter of CNF formulas and use it to identify instances of weighted MaxSAT and #SAT that can be solved in polynomial time. Given a CNF formula we say that a set of clauses is precisely satisfiable if there is some complete assignment satisfying these clauses only. Let the ps-value of the formula be the number of precisely satisfiable sets of clauses. Applying the notion of branch decompositions to CNF formulas and using ps-value as cut function, we define the ps-width of a formula. For a formula given with a decomposition of polynomial ps-width we show dynamic programming algorithms solving weighted MaxSAT and #SAT in polynomial time. Combining with results of 'Belmonte and Vatshelle, Graph classes with structured neighborhoods and algorithmic applications, Theor. Comput. Sci. 511: 54-65 (2013)' we get polynomial-time algorithms solving weighted MaxSAT and #SAT for some classes of structured CNF formulas. For example, we get $O(m^2(m + n)s)$ algorithms for formulas $F$ of $m$ clauses and $n$ variables and size $s$, if $F$ has a linear ordering of the variables and clauses such that for any variable $x$ occurring in clause $C$, if $x$ appears before $C$ then any variable between them also occurs in $C$, and if $C$ appears before $x$ then $x$ occurs also in any clause between them. Note that the class of incidence graphs of such formulas do not have bounded clique-width

A cutting-plane approach to the edge-weighted maximal clique problem

We investigated the computational performance of a cutting-plane algorithm for the problem of determining a maximal subclique in an edge-weighted complete graph. Our numerical results are contrasted with reports on closely related problems for which cutting-plane approaches perform well in instances of moderate size. Somewhat surprisingly, we find that our approach already in the case of n = 15 or N = 25 nodes in the underlying graph typically neither produces an integral solution nor yields a good approximation to the true optimal objective function value. This result seems to shed some doubt on the universal applicability of cuttingplane approaches as an efficient means to solve linear (0, 1)-programming problems of moderate size