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67
Partial Least Squares Regression for Graph Mining
"... Attributed graphs are increasingly more common in many application domains such as chemistry, biology and text processing. A central issue in graph mining is how to collect informative subgraph patterns for a given learning task. We propose an iterative mining method based on partial least squares r ..."
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Cited by 32 (5 self)
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Attributed graphs are increasingly more common in many application domains such as chemistry, biology and text processing. A central issue in graph mining is how to collect informative subgraph patterns for a given learning task. We propose an iterative mining method based on partial least squares regression (PLS). To apply PLS to graph data, a sparse version of PLS is developed first and then it is combined with a weighted pattern mining algorithm. The mining algorithm is iteratively called with different weight vectors, creating one latent component per one mining call. Our method, graph PLS, is efficient and easy to implement, because the weight vector is updated with elementary matrix calculations. In experiments, our graph PLS algorithm showed competitive prediction accuracies in many chemical datasets and its efficiency was significantly superior to graph boosting (gBoost) and the naive method based on frequent graph mining.
A Survey of Frequent Subgraph Mining Algorithms
 THE KNOWLEDGE ENGINEERING REVIEW
, 2004
"... Graph mining is an important research area within the domain of data mining. The field of study concentrates on the identification of frequent subgraphs within graph data sets. The research goals are directed at: (i) effective mechanisms for generating candidate subgraphs (without generating duplica ..."
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Cited by 27 (1 self)
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Graph mining is an important research area within the domain of data mining. The field of study concentrates on the identification of frequent subgraphs within graph data sets. The research goals are directed at: (i) effective mechanisms for generating candidate subgraphs (without generating duplicates) and (ii) how best to process the generated candidate subgraphs so as to identify the desired frequent subgraphs in a way that is computationally efficient and procedurally effective. This paper presents a survey of current research in the field of frequent subgraph mining, and proposed solutions to address the main research issues.
Direct mining of discriminative and essential frequent patterns via modelbased search tree
 In KDD
, 2008
"... Frequent patterns provide solutions to datasets that do not have wellstructured feature vectors. However, frequent pattern mining is nontrivial since the number of unique patterns is exponential but many are nondiscriminative and correlated. Currently, frequent pattern mining is performed in two ..."
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Cited by 26 (7 self)
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Frequent patterns provide solutions to datasets that do not have wellstructured feature vectors. However, frequent pattern mining is nontrivial since the number of unique patterns is exponential but many are nondiscriminative and correlated. Currently, frequent pattern mining is performed in two sequential steps: enumerating a set of frequent patterns, followed by feature selection. Although many methods have been proposed in the past few years on how to perform each separate step efficiently, there is still limited success in eventually finding highly compact and discriminative patterns. The culprit is due to the inherent nature of this widely adopted twostep approach. This paper discusses these problems and proposes a new and different method. It builds a decision tree that partitions the data onto different
Nearoptimal supervised feature selection among frequent subgraphs
 IN SIAM INT’L CONF. ON DATA MINING
, 2009
"... Graph classification is an increasingly important step in numerous application domains, such as function prediction of molecules and proteins, computerised scene analysis, and anomaly detection in program flows. Among the various approaches proposed in the literature, graph classification based on f ..."
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Cited by 24 (10 self)
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Graph classification is an increasingly important step in numerous application domains, such as function prediction of molecules and proteins, computerised scene analysis, and anomaly detection in program flows. Among the various approaches proposed in the literature, graph classification based on frequent subgraphs is a popular branch: Graphs are represented as (usually binary) vectors, with components indicating whether a graph contains a particular subgraph that is frequent across the dataset. On large graphs, however, one faces the enormous problem that the number of these frequent subgraphs may grow exponentially with the size of the graphs, but only few of them possess enough discriminative power to make them
Output Space Sampling for Graph Patterns
, 2009
"... Recent interest in graph pattern mining has shifted from finding all frequent subgraphs to obtaining a small subset of frequent subgraphs that are representative, discriminative or significant. The main motivation behind that is to cope with the scalability problem that the graph mining algorithms s ..."
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Cited by 23 (5 self)
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Recent interest in graph pattern mining has shifted from finding all frequent subgraphs to obtaining a small subset of frequent subgraphs that are representative, discriminative or significant. The main motivation behind that is to cope with the scalability problem that the graph mining algorithms suffer when mining databases of large graphs. Another motivation is to obtain a succinct output set that is informative and useful. In the same spirit, researchers also proposed sampling based algorithms that sample the output space of the frequent patterns to obtain representative subgraphs. In this work, we propose a generic sampling framework that is based on MetropolisHastings algorithm to sample the output space of frequent subgraphs. Our experiments on various sampling strategies show the versatility, utility and efficiency of the proposed sampling approach.
GBASE: A Scalable and General Graph Management System
"... Graphs appear in numerous applications including cybersecurity, the Internet, social networks, protein networks, recommendation systems, and many more. Graphs with millions or even billions of nodes and edges are commonplace. How to store such large graphs efficiently? What are the core operations ..."
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Cited by 22 (5 self)
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Graphs appear in numerous applications including cybersecurity, the Internet, social networks, protein networks, recommendation systems, and many more. Graphs with millions or even billions of nodes and edges are commonplace. How to store such large graphs efficiently? What are the core operations/queries on those graph? How to answer the graph queries quickly? We propose GBASE, a scalable and general graph management and mining system. The key novelties lie in 1) our storage and compression scheme for a parallel setting and 2) the carefully chosen graph operations and their efficient implementation. We designed and implemented an instance of GBASE using MAPREDUCE/HADOOP. GBASE provides a parallel indexing mechanism for graph mining operations that both saves storage space, as well as accelerates queries. We ran numerous experiments on real graphs, spanning billions of nodes and edges, and we show that our proposed GBASE is indeed fast, scalable and nimble, with significant savings in space and time.
SemiSupervised Feature Selection for Graph Classification ABSTRACT
"... The problem of graph classification has attracted great interest in the last decade. Current research on graph classification assumes the existence of large amounts of labeled training graphs. However, in many applications, the labels of graph data are very expensive or difficult to obtain, while th ..."
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Cited by 14 (5 self)
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The problem of graph classification has attracted great interest in the last decade. Current research on graph classification assumes the existence of large amounts of labeled training graphs. However, in many applications, the labels of graph data are very expensive or difficult to obtain, while there are often copious amounts of unlabeled graph data available. In this paper, we study the problem of semisupervised feature selection for graph classification and propose a novel solution, called gSSC, to efficiently search for optimal subgraph features with labeled and unlabeled graphs. Different from existing feature selection methods in vector spaces which assume the feature set is given, we perform semisupervised feature selection for graph data in a progressive way together with the subgraph feature mining process. We derive a feature evaluation criterion, named gSemi, to estimate the usefulness of subgraph features based upon both labeled and unlabeled graphs. Then we propose a branchandbound algorithm to efficiently search for optimal subgraph features by judiciously pruning the subgraph search space. Empirical studies on several realworld tasks demonstrate that our semisupervised feature selection approach can effectively boost graph classification performances with semisupervised feature selection and is very efficient by pruning the subgraph search space using both labeled and unlabeled graphs.
Towards proximity pattern mining in large graphs
 In Proceedings of the 2010 ACM SIGMOD International Conference on Management of data. SIGMOD ’10. ACM
, 2010
"... Mining graph patterns in large networks is critical to a variety of applications such as malware detection and biological module discovery. However, frequent subgraphs are often ineffective to capture association existing in these applications, due to the complexity of isomorphism testing and the ..."
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Cited by 13 (3 self)
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Mining graph patterns in large networks is critical to a variety of applications such as malware detection and biological module discovery. However, frequent subgraphs are often ineffective to capture association existing in these applications, due to the complexity of isomorphism testing and the inelastic pattern definition. In this paper, we introduce proximity pattern which is a significant departure from the traditional concept of frequent subgraphs. Defined as a set of labels that cooccur in neighborhoods, proximity pattern blurs the boundary between itemset and structure. It relaxes the rigid structure constraint of frequent subgraphs, while introducing connectivity to frequent itemsets. Therefore, it can benefit from both: efficient mining in itemsets and structure proximity from graphs. We developed two models to define proximity patterns. The second one, called Normalized Probabilistic Association (NmPA), is able to transform a complex graph mining problem to a simplified probabilistic itemset mining problem, which can be solved efficiently by a modified FPtree algorithm, called pFP. NmPA and pFP are evaluated on reallife social and intrusion networks. Empirical results show that it not only finds interesting patterns that are ignored by the existing approaches, but also achieves high performance for finding proximity patterns in largescale graphs.
Multilabel feature selection for graph classification
 In Proceedings of the 10th IEEE International Conference on Data Mining
, 2010
"... Abstract—Nowadays, the classification of graph data has become an important and active research topic in the last decade, which has a wide variety of real world applications, e.g. drug activity predictions and kinase inhibitor discovery. Current research on graph classification focuses on singlelabe ..."
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Cited by 11 (4 self)
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Abstract—Nowadays, the classification of graph data has become an important and active research topic in the last decade, which has a wide variety of real world applications, e.g. drug activity predictions and kinase inhibitor discovery. Current research on graph classification focuses on singlelabel settings. However, in many applications, each graph data can be assigned with a set of multiple labels simultaneously. Extracting good features using multiple labels of the graphs becomes an important step before graph classification. In this paper, we study the problem of multilabel feature selection for graph classification and propose a novel solution, called gMLC, to efficiently search for optimal subgraph features for graph objects with multiple labels. Different from existing feature selection methods in vector spaces which assume the feature set is given, we perform multilabel feature selection for graph data in a progressive way together with the subgraph feature mining process. We derive an evaluation criterion, named gHSIC, to estimate the dependence between subgraph features and multiple labels of graphs. Then a branchandbound algorithm is proposed to efficiently search for optimal subgraph features by judiciously pruning the subgraph search space using multiple labels. Empirical studies on realworld tasks demonstrate that our feature selection approach can effectively boost multilabel graph classification performances and is more efficient by pruning the subgraph search space using multiple labels. Keywordsfeature selection; graph classification; multilabel learning. I.
GAIA: Graph Classification Using Evolutionary Computation
"... Discriminative subgraphs are widely used to define the feature space for graph classification in large graph databases. Several scalable approaches have been proposed to mine discriminative subgraphs. However, their intensive computation needs prevent them from mining large databases. We propose an ..."
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Cited by 11 (1 self)
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Discriminative subgraphs are widely used to define the feature space for graph classification in large graph databases. Several scalable approaches have been proposed to mine discriminative subgraphs. However, their intensive computation needs prevent them from mining large databases. We propose an efficient method GAIA for mining discriminative subgraphs for graph classification in large databases. Our method employs a novel subgraph encoding approach to support an arbitrary subgraph pattern exploration order and explores the subgraph pattern space in a process resembling biological evolution. In this manner, GAIA is able to find discriminative subgraph patterns much faster than other algorithms. Additionally, we take advantage of parallel computing to further improve the quality of resulting patterns. In the end, we employ sequential coverage to generate association rules as graph classifiers using patterns mined by GAIA. Extensive experiments have been performed to analyze the performance of GAIA and to compare it with two other stateoftheart approaches. GAIA outperforms the other approaches both in terms of classification accuracy and runtime efficiency.