Graph theoretic methods for the analysis of structural relationships in biological macromolecules

Subgraph isomorphism and maximum common subgraph isomorphism algorithms from graph theory provide an effective and an efficient way of identifying structural relationships between biological macromolecules. They thus provide a natural complement to the pattern matching algorithms that are used in bioinformatics to identify sequence relationships. Examples are provided of the use of graph theory to analyze proteins for which three-dimensional crystallographic or NMR structures are available, focusing on the use of the Bron-Kerbosch clique detection algorithm to identify common folding motifs and of the Ullmann subgraph isomorphism algorithm to identify patterns of amino acid residues. Our methods are also applicable to other types of biological macromolecule, such as carbohydrate and nucleic acid structures

Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis

This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work

Fast Search for Dynamic Multi-Relational Graphs

Acting on time-critical events by processing ever growing social media or news streams is a major technical challenge. Many of these data sources can be modeled as multi-relational graphs. Continuous queries or techniques to search for rare events that typically arise in monitoring applications have been studied extensively for relational databases. This work is dedicated to answer the question that emerges naturally: how can we efficiently execute a continuous query on a dynamic graph? This paper presents an exact subgraph search algorithm that exploits the temporal characteristics of representative queries for online news or social media monitoring. The algorithm is based on a novel data structure called the Subgraph Join Tree (SJ-Tree) that leverages the structural and semantic characteristics of the underlying multi-relational graph. The paper concludes with extensive experimentation on several real-world datasets that demonstrates the validity of this approach.Comment: SIGMOD Workshop on Dynamic Networks Management and Mining (DyNetMM), 201

Malware Classification based on Call Graph Clustering

Each day, anti-virus companies receive tens of thousands samples of potentially harmful executables. Many of the malicious samples are variations of previously encountered malware, created by their authors to evade pattern-based detection. Dealing with these large amounts of data requires robust, automatic detection approaches. This paper studies malware classification based on call graph clustering. By representing malware samples as call graphs, it is possible to abstract certain variations away, and enable the detection of structural similarities between samples. The ability to cluster similar samples together will make more generic detection techniques possible, thereby targeting the commonalities of the samples within a cluster. To compare call graphs mutually, we compute pairwise graph similarity scores via graph matchings which approximately minimize the graph edit distance. Next, to facilitate the discovery of similar malware samples, we employ several clustering algorithms, including k-medoids and DBSCAN. Clustering experiments are conducted on a collection of real malware samples, and the results are evaluated against manual classifications provided by human malware analysts. Experiments show that it is indeed possible to accurately detect malware families via call graph clustering. We anticipate that in the future, call graphs can be used to analyse the emergence of new malware families, and ultimately to automate implementation of generic detection schemes.Comment: This research has been supported by TEKES - the Finnish Funding Agency for Technology and Innovation as part of its ICT SHOK Future Internet research programme, grant 40212/0

RASCAL: calculation of graph similarity using maximum common edge subgraphs

A new graph similarity calculation procedure is introduced for comparing labeled graphs. Given a minimum similarity threshold, the procedure consists of an initial screening process to determine whether it is possible for the measure of similarity between the two graphs to exceed the minimum threshold, followed by a rigorous maximum common edge subgraph (MCES) detection algorithm to compute the exact degree and composition of similarity. The proposed MCES algorithm is based on a maximum clique formulation of the problem and is a significant improvement over other published algorithms. It presents new approaches to both lower and upper bounding as well as vertex selection

Graph Homomorphism Revisited for Graph Matching

In a variety of emerging applications one needs to decide whether a graph G matches another G p , i.e. , whether G has a topological structure similar to that of G p . The traditional notions of graph homomorphism and isomorphism often fall short of capturing the structural similarity in these applications. This paper studies revisions of these notions, providing a full treatment from complexity to algorithms. (1) We propose p-homomorphism (p -hom) and 1-1 p -hom, which extend graph homomorphism and subgraph isomorphism, respectively, by mapping edges from one graph to paths in another, and by measuring the similarity of nodes . (2) We introduce metrics to measure graph similarity, and several optimization problems for p -hom and 1-1 p -hom. (3) We show that the decision problems for p -hom and 1-1 p -hom are NP-complete even for DAGs, and that the optimization problems are approximation-hard. (4) Nevertheless, we provide approximation algorithms with provable guarantees on match quality. We experimentally verify the effectiveness of the revised notions and the efficiency of our algorithms in Web site matching, using real-life and synthetic data. </jats:p