A Spinorial Formulation of the Maximum Clique Problem of a Graph

We present a new formulation of the maximum clique problem of a graph in complex space. We start observing that the adjacency matrix A of a graph can always be written in the form A = B B where B is a complex, symmetric matrix formed by vectors of zero length (null vectors) and the maximum clique problem can be transformed in a geometrical problem for these vectors. This problem, in turn, is translated in spinorial language and we show that each graph uniquely identifies a set of pure spinors, that is vectors of the endomorphism space of Clifford algebras, and the maximum clique problem is formalized in this setting so that, this much studied problem, may take advantage from recent progresses of pure spinor geometry

Computing maximum cliques in B2B_2-EPG graphs

EPG graphs, introduced by Golumbic et al. in 2009, are edge-intersection graphs of paths on an orthogonal grid. The class $B_k$-EPG is the subclass of EPG graphs where the path on the grid associated to each vertex has at most $k$ bends. Epstein et al. showed in 2013 that computing a maximum clique in $B_1$-EPG graphs is polynomial. As remarked in [Heldt et al., 2014], when the number of bends is at least $4$, the class contains $2$-interval graphs for which computing a maximum clique is an NP-hard problem. The complexity status of the Maximum Clique problem remains open for $B_2$ and $B_3$-EPG graphs. In this paper, we show that we can compute a maximum clique in polynomial time in $B_2$-EPG graphs given a representation of the graph. Moreover, we show that a simple counting argument provides a ${2(k+1)}$-approximation for the coloring problem on $B_k$-EPG graphs without knowing the representation of the graph. It generalizes a result of [Epstein et al, 2013] on $B_1$-EPG graphs (where the representation was needed)

QPTAS and Subexponential Algorithm for Maximum Clique on Disk Graphs

A (unit) disk graph is the intersection graph of closed (unit) disks in the plane. Almost three decades ago, an elegant polynomial-time algorithm was found for Maximum Clique on unit disk graphs [Clark, Colbourn, Johnson; Discrete Mathematics '90]. Since then, it has been an intriguing open question whether or not tractability can be extended to general disk graphs. We show the rather surprising structural result that a disjoint union of cycles is the complement of a disk graph if and only if at most one of those cycles is of odd length. From that, we derive the first QPTAS and subexponential algorithm running in time 2^{O~(n^{2/3})} for Maximum Clique on disk graphs. In stark contrast, Maximum Clique on intersection graphs of filled ellipses or filled triangles is unlikely to have such algorithms, even when the ellipses are close to unit disks. Indeed, we show that there is a constant ratio of approximation which cannot be attained even in time 2^{n^{1-epsilon}}, unless the Exponential Time Hypothesis fails

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

Exact Algorithms for Maximum Clique: a computational study

We investigate a number of recently reported exact algorithms for the maximum clique problem (MCQ, MCR, MCS, BBMC). The program code used is presented and critiqued showing how small changes in implementation can have a drastic effect on performance. The computational study demonstrates how problem features and hardware platforms influence algorithm behaviour. The minimum width order (smallest-last) is investigated, and MCS is broken into its consituent parts and we discover that one of these parts degrades performance. It is shown that the standard procedure used for rescaling published results is unsafe.Comment: 40 pages, 14 figures, 10 tables, 12 short java program listings, code afailable to download at http://www.dcs.gla.ac.uk/~pat/maxClique/distribution