One of the major challenges in applications related to social networks, computational biology, collaboration networks etc., is to efficiently search for similar patterns in their underlying graphs. These graphs are typically noisy and contain thousands of vertices and millions of edges. In many cases, the graphs are unlabelled and the notion of similarity is also not well defined. We study the problem of searching an induced sub graph in a large target graph that is most similar to the given query graph. We assume that the query graph and target graph are undirected and unlabelled. We use graph let kernels [1] to define graph similarity. Graph let kernels are known to perform better than other kernels in different applications.
With the emergence of new applications, e.g., computational biology, new software engineering techniques, social networks, etc., more data is in the form of graphs. Locating occurrences of a query graph in a large database graph is an important research topic. Due to the existence of noise (e.g., missing edges) in the large database graph, we investigate the problem of approximate subgraph indexing, i.e., finding the occurrences of a query graph in a large database graph with (possible) missing edges. The SAPPER method is proposed to solve this problem. Utilizing the hybrid neighborhood unit structures in the index, SAPPER takes advantage of pre-generated random spanning trees and a carefully designed graph enumeration order. Real and synthetic data sets are employed to demonstrate the efficiency and scalability of our approximate subgraph indexing method. Given a query graph @math q and a data graph @math G, subgraph similarity matching is to retrieve all matches of @math q in @math G with the number of missing edges bounded by a given threshold @math ∈. Many works have been conducted to study the problem of subgraph similarity matching due to its ability to handle applications involved with noisy or erroneous graph data. In practice, a data graph can be extremely large, e.g., a web-scale graph containing hundreds of millions of vertices and billions of edges. The state-of-the-art approaches employ centralized algorithms to process the subgraph similarity queries, and thus, they are infeasible for such a large graph due to the limited computational power and storage space of a centralized server. To address this problem, in this paper, we investigate subgraph similarity matching for a web-scale graph deployed in a distributed environment. We propose distributed algorithms and optimization techniques that exploit the properties of subgraph similarity matching, so that we can well utilize the parallel computing power and lower the communication cost among the distributed data centers for query processing. Specifically, we first relax and decompose @math q into a minimum number of sub-queries. Next, we send each sub-query to conduct the exact matching in parallel. Finally, we schedule and join the exact matches to obtain final query answers. Moreover, our workload-balance strategy further speeds up the query processing. Our experimental results demonstrate the feasibility of our proposed approach in performing subgraph similarity matching over web-scale graph data.  Graph has become increasingly important in modelling complicated structures and schemaless data such as proteins, chemical compounds, and XML documents. Given a graph query, it is desirable to retrieve graphs quickly from a large database via graph-based indices. In this paper, we investigate the issues of indexing graphs and propose a novel solution by applying a graph mining technique. Different from the existing path-based methods, our approach, called gIndex, makes use of frequent substructure as the basic indexing feature. Frequent substructures are ideal candidates since they explore the intrinsic characteristics of the data and are relatively stable to database updates. To reduce the size of index structure, two techniques, size-increasing support constraint and discriminative fragments, are introduced. Our performance study shows that gIndex has 10 times smaller index size, but achieves 3--10 times better performance in comparison with a typical path-based method, GraphGrep. The gIndex approach not only provides and elegant solution to the graph indexing problem, but also demonstrates how database indexing and query processing can benefit form data mining, especially frequent pattern mining. Furthermore, the concepts developed here can be applied to indexing sequences, trees, and other complicated structures as well. Modern search engines answer keyword-based queries extremely efficiently. The impressive speed is due to clever inverted index structures, caching, a domain-independent knowledge of strings, and thousands of machines. Several research efforts have attempted to generalize keyword search to keytree and keygraph searching, because trees and graphs have many applications in next-generation database systems. This paper surveys both algorithms and applications, giving some emphasis to our own work. Complex social and information network search becomes important with a variety of applications. In the core of these applications, lies a common and critical problem: Given a labeled network and a query graph, how to efficiently search the query graph in the target network. The presence of noise and the incomplete knowledge about the structure and content of the target network make it unrealistic to find an exact match. Rather, it is more appealing to find the top-k approximate matches. In this paper, we propose a neighborhood-based similarity measure that could avoid costly graph isomorphism and edit distance computation. Under this new measure, we prove that subgraph similarity search is NP hard, while graph similarity match is polynomial. By studying the principles behind this measure, we found an information propagation model that is able to convert a large network into a set of multidimensional vectors, where sophisticated indexing and similarity search algorithms are available. The proposed method, called Ness (Neighborhood Based Similarity Search), is appropriate for graphs with low automorphism and high noise, which are common in many social and information networks. Ness is not only efficient, but also robust against structural noise and information loss. Empirical results show that it can quickly and accurately find high-quality matches in large networks, with negligible cost. Currently, a huge amount of biological data can be naturally represented by graphs, e.g., protein interaction networks, gene regulatory networks, etc. The need for indexing large graphs is an urgent research problem of great practical importance. The main challenge is size. Each graph may contain thousands (or more) vertices. Most of the previous work focuses on indexing a set of small or medium sized database graphs (with only tens of vertices) and finding whether a query graph occurs in any of these. In this paper, we are interested in finding all the matches of a query graph in a given large graph of thousands of vertices, which is a very important task in many biological applications. This increases the complexity significantly. We propose a novel distance measurement which reintroduces the idea of frequent substructures in a single large graph. We devise the novel structure distance based approach (GADDI) to efficiently find matches of the query graph. GADDI is further optimized by the use of a dynamic matching scheme to minimize redundant calculations. Last but not least, a number of real and synthetic data sets are used to evaluate the efficiency and scalability of our proposed method. Network querying is a growing domain with vast applications ranging from screening compounds against a database of known molecules to matching sub-networks across species. Graph indexing is a powerful method for searching a large database of graphs. Most graph indexing methods to date tackle the exact matching (isomorphism) problem, limiting their applicability to specific instances in which such matches exist. Here we provide a novel graph indexing method to cope with the more general, inexact matching problem. Our method, SIGMA, builds on approximating a variant of the set-cover problem that concerns overlapping multi-sets. We extensively test our method and compare it to a baseline method and to the state-of-the-art Grafil. We show that SIGMA outperforms both, providing higher pruning power in all the tested scenarios. It is increasingly common to find real-life data represented as networks of labeled, heterogeneous entities. To query these networks, one often needs to identify the matches of a given query graph in a (typically large) network modeled as a target graph. Due to noise and the lack of fixed schema in the target graph, the query graph can substantially differ from its matches in the target graph in both structure and node labels, thus bringing challenges to the graph querying tasks. In this paper, we propose NeMa (Network Match), a neighborhood-based subgraph matching technique for querying real-life networks. (1) To measure the quality of the match, we propose a novel subgraph matching cost metric that aggregates the costs of matching individual nodes, and unifies both structure and node label similarities. (2) Based on the metric, we formulate the minimum cost subgraph matching problem. Given a query graph and a target graph, the problem is to identify the (top-k) matches of the query graph with minimum costs in the target graph. We show that the problem is NP-hard, and also hard to approximate. (3) We propose a heuristic algorithm for solving the problem based on an inference model. In addition, we propose optimization techniques to improve the efficiency of our method. (4) We empirically verify that NeMa is both effective and efficient compared to the keyword search and various state-of-the-art graph querying techniques. Structured data including sets, sequences, trees and graphs, pose significant challenges to fundamental aspects of data management such as efficient storage, indexing, and similarity search. With the fast accumulation of graph databases, similarity search in graph databases has emerged as an important research topic. Graph similarity search has applications in a wide range of domains including cheminformatics, bioinformatics, sensor network management, social network management, and XML documents, among others. Most of the current graph indexing methods focus on subgraph query processing, i.e. determining the set of database graphs that contains the query graph and hence do not directly support similarity search. In data mining and machine learning, various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models for supervised learning, graph kernel functions have (i) high computational complexity and (ii) non-trivial difficulty to be indexed in a graph database. Our objective is to bridge graph kernel function and similarity search in graph databases by proposing (i) a novel kernel-based similarity measurement and (ii) an efficient indexing structure for graph data management. Our method of similarity measurement builds upon local features extracted from each node and their neighboring nodes in graphs. A hash table is utilized to support efficient storage and fast search of the extracted local features. Using the hash table, a graph kernel function is defined to capture the intrinsic similarity of graphs and for fast similarity query processing. We have implemented our method, which we have named G-hash, and have demonstrated its utility on large chemical graph databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Most importantly, the new similarity measurement and the index structure is scalable to large database with smaller indexing size, faster indexing construction time, and faster query processing time as compared to state-of-the-art indexing methods such as C-tree, gIndex, and GraphGrep.