Solving Maximum Clique Problem for Protein Structure Similarity

Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum weighted clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper we present both a new integer programming formulation for solving such clique problems and a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST, a software for aligning protein 3D structures largely used in the National Center for Biotechnology Information, an original clique solver which uses the well known Bron and Kerbosch algorithm (BK). Our computational results on real protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK.

Remarks on the Balaban Index

In this paper we compute some bounds of the Balaban index and then by means of group action we compute the Balaban index of vertex transitive graphs. ACM Computing Classification System (1998): G.2.2 , F.2.2.

On the Vertex Separation of Cactus Graphs

This paper is part of a work in progress whose goal is to construct a fast, practical algorithm for the vertex separation (VS) of cactus graphs. We prove a \main theorem for cacti", a necessary and sufficient condition for the VS of a cactus graph being k. Further, we investigate the ensuing ramifications that prevent the construction of an algorithm based on that theorem only.

On the Vertex Separation of Maximal Outerplanar Graphs

We investigate the NP-complete problem Vertex Separation (VS) on Maximal Outerplanar Graphs (mops). We formulate and prove a “main theorem for mops”, a necessary and sufficient condition for the vertex separation of a mop being k. The main theorem reduces the vertex separation of mops to a special kind of stretchability, one that we call affixability, of submops.

An Inequality for Generalized Chromatic Graphs

Асен Божилов, Недялко Ненов - Нека G е n-върхов граф и редицата от степените на върховете му е d1, d2, . . . , dn, а V(G) е множеството от върховете на G. Степента на върха v бележим с d(v). Най-малкото естествено число r, за което V(G) има r-разлагане V(G) = V1 ∪ V2 ∪ · · · ∪ Vr, Vi ∩ Vj = ∅, , i 6 = j такова, че d(v) ≤ n − |Vi|, ∀v ∈ Vi, i = 1, 2, . . . , r е означено с ϕ(G). В тази работа доказваме неравенството ...

On a Class of Vertex Folkman Numbers

Let a1 , . . . , ar, be positive integers, i=1 ... r, m = ∑(ai − 1) + 1 and p = max{a1 , . . . , ar }. For a graph G the symbol G → (a1 , . . . , ar ) means that in every r-coloring of the vertices of G there exists a monochromatic ai -clique of color i for some i ∈ {1, . . . , r}. In this paper we consider the vertex Folkman numbers F (a1 , . . . , ar ; m − 1) = min |V (G)| : G → (a1 , . . . , ar ) and Km−1 ⊂ G} We prove that F (a1 , . . . , ar ; m − 1) = m + 6, if p = 3 and m ≧ 6 (Theorem 3) and F (a1 , . . . , ar ; m − 1) = m + 7, if p = 4 and m ≧ 6 (Theorem 4).

Sequences of Maximal Degree Vertices in Graphs

2000 Mathematics Subject Classification: 05C35.

A Linear Time Algorithm for Computing Longest Paths in Cactus Graphs

ACM Computing Classification System (1998): G.2.2.

The Wiener, Eccentric Connectivity and Zagreb Indices of the Hierarchical Product of Graphs

Let G1 = (V1, E1) and G2 = (V2, E2) be two graphs having a distinguished or root vertex, labeled 0. The hierarchical product G2 ⊓ G1 of G2 and G1 is a graph with vertex set V2 × V1. Two vertices y2y1 and x2x1 are adjacent if and only if y1x1 ∈ E1 and y2 = x2; or y2x2 ∈ E2 and y1 = x1 = 0. In this paper, the Wiener, eccentric connectivity and Zagreb indices of this new operation of graphs are computed. As an application, these topological indices for a class of alkanes are computed. ACM Computing Classification System (1998): G.2.2, G.2.3.

On strongly regular graphs with m2 = qm3 and m3 = qm2

2010 Mathematics Subject Classification: 05C50.

On the Asymptotic Behavior of the Ratio between the Numbers of Binary Primitive and Irreducible Polynomials

This work was presented in part at the 8th International Conference on Finite Fields and Applications Fq^8 , Melbourne, Australia, 9-13 July, 2007.

On the 3-Colouring Vertex Folkman Number F(2,2,4)

In this note we prove that F (2, 2, 4) = 13.

Learning Technology in Scheduling Based on the Mixed Graphs

We propose the adaptive algorithm for solving a set of similar scheduling problems using learning technology. It is devised to combine the merits of an exact algorithm based on the mixed graph model and heuristics oriented on the real-world scheduling problems. The former may ensure high quality of the solution by means of an implicit exhausting enumeration of the feasible schedules. The latter may be developed for certain type of problems using their peculiarities. The main idea of the learning technology is to produce effective (in performance measure) and efficient (in computational time) heuristics by adapting local decisions for the scheduling problems under consideration. Adaptation is realized at the stage of learning while solving a set of sample scheduling problems using a branch-and-bound algorithm and structuring knowledge using pattern recognition apparatus.

A Metaheuristic Approach to Solving the Generalized Vertex Cover Problem

AMS Subj. Classification: 90C27, 05C85, 90C59

The Eccentric Connectivity Polynomial of some Graph Operations

The eccentric connectivity index of a graph G, ξ^C, was proposed by Sharma, Goswami and Madan. It is defined as ξ^C(G) = ∑ u ∈ V(G) degG(u)εG(u), where degG(u) denotes the degree of the vertex x in G and εG(u) = Max{d(u, x) | x ∈ V (G)}. The eccentric connectivity polynomial is a polynomial version of this topological index. In this paper, exact formulas for the eccentric connectivity polynomial of Cartesian product, symmetric difference, disjunction and join of graphs are presented.