Frequent Subgraph Mining in Outerplanar Graphs

In recent years there has been an increased interest in frequent pattern discovery in large databases of graph structured objects. While the frequent connected subgraph mining problem for tree datasets can be solved in incremental polynomial time, it becomes intractable for arbitrary graph databases. Existing approaches have therefore resorted to various heuristic strategies and restrictions of the search space, but have not identified a practically relevant tractable graph class beyond trees. In this paper, we define the class of so called tenuous outerplanar graphs, a strict generalization of trees, develop a frequent subgraph mining algorithm for tenuous outerplanar graphs that works in incremental polynomial time, and evaluate the algorithm empirically on the NCI molecular graph dataset

Frequent Subgraph Mining in Outerplanar Graphs

In recent years there has been an increased interest in frequent pattern discovery in large databases of graph structured objects. While the frequent connected subgraph mining problem for tree datasets can be solved in incremental polynomial time, it becomes intractable for arbitrary graph databases. Existing approaches have therefore resorted to various heuristic strategies and restrictions of the search space, but have not identified a practically relevant tractable graph class beyond trees. In this paper, we define the class of so called tenuous outerplanar graphs, a strict generalization of trees, develop a frequent subgraph mining algorithm for tenuous outerplanar graphs that works in incremental polynomial time, and evaluate the algorithm empirically on the NCI molecular graph dataset

FS^3: A Sampling based method for top-k Frequent Subgraph Mining

Mining labeled subgraph is a popular research task in data mining because of its potential application in many different scientific domains. All the existing methods for this task explicitly or implicitly solve the subgraph isomorphism task which is computationally expensive, so they suffer from the lack of scalability problem when the graphs in the input database are large. In this work, we propose FS^3, which is a sampling based method. It mines a small collection of subgraphs that are most frequent in the probabilistic sense. FS^3 performs a Markov Chain Monte Carlo (MCMC) sampling over the space of a fixed-size subgraphs such that the potentially frequent subgraphs are sampled more often. Besides, FS^3 is equipped with an innovative queue manager. It stores the sampled subgraph in a finite queue over the course of mining in such a manner that the top-k positions in the queue contain the most frequent subgraphs. Our experiments on database of large graphs show that FS^3 is efficient, and it obtains subgraphs that are the most frequent amongst the subgraphs of a given size

Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments

GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics

Graph data mining is an active research area. Graphs are general modeling tools to organize information from heterogeneous sources and have been applied in many scientific, engineering, and business fields. With the fast accumulation of graph data, building highly accurate predictive models for graph data emerges as a new challenge that has not been fully explored in the data mining community. In this paper, we demonstrate a novel technique called graph pattern diffusion (GPD) kernel. Our idea is to leverage existing frequent pattern discovery methods and to explore the application of kernel classifier (e.g., support vector machine) in building highly accurate graph classification. In our method, we first identify all frequent patterns from a graph database. We then map subgraphs to graphs in the graph database and use a process we call “pattern diffusion” to label nodes in the graphs. Finally, we designed a graph alignment algorithm to compute the inner product of two graphs. We have tested our algorithm using a number of chemical structure data. The experimental results demonstrate that our method is significantly better than competing methods such as those kernel functions based on paths, cycles, and subgraphs

A Survey on Graph Kernels

Graph kernels have become an established and widely-used technique for solving classification tasks on graphs. This survey gives a comprehensive overview of techniques for kernel-based graph classification developed in the past 15 years. We describe and categorize graph kernels based on properties inherent to their design, such as the nature of their extracted graph features, their method of computation and their applicability to problems in practice. In an extensive experimental evaluation, we study the classification accuracy of a large suite of graph kernels on established benchmarks as well as new datasets. We compare the performance of popular kernels with several baseline methods and study the effect of applying a Gaussian RBF kernel to the metric induced by a graph kernel. In doing so, we find that simple baselines become competitive after this transformation on some datasets. Moreover, we study the extent to which existing graph kernels agree in their predictions (and prediction errors) and obtain a data-driven categorization of kernels as result. Finally, based on our experimental results, we derive a practitioner's guide to kernel-based graph classification

Tree comparison: enumeration and application to cheminformatics

Graphs are a well-known data structure used in many application domains that rely on relationships between individual entities. Examples are social networks, where the users may be in friendship with each other, road networks, where one-way or bidirectional roads connect crossings, and work package assignments, where workers are assigned to tasks. In chem- and bioinformatics, molecules are often represented as molecular graphs, where vertices represent atoms, and bonds between them are represented by edges connecting the vertices. Since there is an ever-increasing amount of data that can be treated as graphs, fast algorithms are needed to compare such graphs. A well-researched concept to compare two graphs is the maximum common subgraph. On the one hand, this allows finding substructures that are common to both input graphs. On the other hand, we can derive a similarity score from the maximum common subgraph. A practical application is rational drug design which involves molecular similarity searches. In this thesis, we study the maximum common subgraph problem, which entails finding a largest graph, which is isomorphic to subgraphs of two input graphs. We focus on restrictions that allow polynomial-time algorithms with a low exponent. An example is the maximum common subtree of two input trees. We succeed in improving the previously best-known time bound. Additionally, we provide a lower time bound under certain assumptions. We study a generalization of the maximum common subtree problem, the block-and-bridge preserving maximum common induced subgraph problem between outerplanar graphs. This problem is motivated by the application to cheminformatics. First, the vast majority of drugs modeled as molecular graphs is outerplanar, and second, the blocks correspond to the ring structures and the bridges to atom chains or linkers. If we allow disconnected common subgraphs, the problem becomes NP-hard even for trees as input. We propose a second generalization of the maximum common subtree problem, which allows skipping vertices in the input trees while maintaining polynomial running time. Since a maximum common subgraph is not unique in general, we investigate the problem to enumerate all maximum solutions. We do this for both the maximum common subtree problem and the block-and-bridge preserving maximum common induced subgraph problem between outerplanar graphs. An arising subproblem which we analyze is the enumeration of maximum weight matchings in bipartite graphs. We support a weight function between the vertices and edges for all proposed common subgraph methods in this thesis. Thus the objective is to compute a common subgraph of maximum weight. The weights may be integral or real-valued, including negative values. A special case of using such a weight function is computing common subgraph isomorphisms between labeled graphs, where labels between mapped vertices and edges must be equal. An experimental study evaluates the practical running times and the usefulness of our block-and-bridge preserving maximum common induced subgraph algorithm against state of the art algorithms

Comparing graphs

Graphs are a well-studied mathematical concept, which has become ubiquitous to represent structured data in many application domains like computer vision, social network analysis or chem- and bioinformatics. The ever-increasing amount of data in these domains requires to efficiently organize and extract information from large graph data sets. In this context techniques for comparing graphs are fundamental, e.g., in order to obtain meaningful similarity measures between graphs. These are a prerequisite for the application of a variety of data mining algorithms to the domain of graphs. Hence, various approaches to graph comparison evolved and are wide-spread in practice. This thesis is dedicated to two different strategies for comparing graphs: maximum common subgraph problems and graph kernels. We study maximum common subgraph problems, which are based on classical graph-theoretical concepts for graph comparison and are NP-hard in the general case. We consider variants of the maximum common subgraph problem in restricted graph classes, which are highly relevant for applications in cheminformatics. We develop a polynomial-time algorithm, which allows to compute a maximum common subgraph under block and bridge preserving isomorphism in series-parallel graphs. This generalizes the problem of computing maximum common biconnected subgraphs in series-parallel graphs. We show that previous approaches to this problem, which are based on the separators represented by standard graph decompositions, fail. We introduce the concept of potential separators to overcome this issue and use them algorithmically to solve the problem in series-parallel graphs. We present algorithms with improved bounds on running time for the subclass of outerplanar graphs. Finally, we establish a sufficient condition for maximum common subgraph variants to allow derivation of graph distance metrics. This leads to polynomial-time computable graph distance metrics in restricted graph classes. This progress constitutes a step towards solving practically relevant maximum common subgraph problems in polynomial time. The second contribution of this thesis is to graph kernels, which have their origin in specific data mining algorithms. A key property of graph kernels is that they allow to consider a large (possibly infinite) number of features and can support graphs with arbitrary annotation, while being efficiently computable. The main contributions of this part of the thesis are (i) the development of novel graph kernels, which are especially designed for attributed graphs with arbitrary annotations and (ii) the systematic study of implicit and explicit mapping into a feature space for computation of graph kernels w.r.t. its impact on the running time and the ability to consider arbitrary annotations. We propose graph kernels based on bijections between subgraphs and walks of fixed length. In an experimental study we show that these approaches provide a viable alternative to known techniques, in particular for graphs with complex annotations

Frequent subgraph mining in outerplanar graphs

status: publishe

Frequent Subgraph Mining in Outerplanar Graphs

In recent years there has been an increased interest in frequent pattern discovery in large databases of graph structured objects. While the frequent connected subgraph mining problem for tree datasets can be solved in incremental polynomial time, it becomes intractable for arbitrary graph databases. Existing approaches have therefore resorted to various heuristic strategies and restrictions of the search space, but have not identified a practically relevant tractable graph class beyond trees. In this paper, we consider the class of outerplanar graphs, a strict generalization of trees, develop a frequent subgraph mining algorithm for outerplanar graphs, and show that it works in incremental polynomial time for the practically relevant subclass of well-behaved outerplanar graphs, i.e., which have only polynomially many simple cycles. We evaluate the algorithm empirically on chemo- and bioinformatics applications