With the emergence of social networks and computational biology, more data are in the forms of multi-labeled graphs, where a vertex has multiple labels. Since most algorithms focus only on single labeled graphs, these algorithms perform inefficiently when applied to multi-labeled graphs. In this paper, we investigate the problem of subgraph indexing and matching in the multi-labeled graphs. The label set on a vertex is transformed into a high dimensional box. The R-tree is employed to store and index these boxes. The vertex matching problem can be transformed into spatial range queries on the high dimensional space. In addition, we study two types of queries: location and existence queries. In this paper, detailed algorithms are provided to process these two types of queries. Real and synthetic data sets are employed to demonstrate the efficiency and effectiveness of our subgraph indexing and query processing methods.

Graphs can represent a large number of data types, e.g., online social networks, internet links, procedure dependency graphs, etc. The need for indexing massive graphs is an urgent research problem of great practical importance. The main challenge is the size. Each graph may contain at least tens of millions vertices. The working memory may not be able to store the database graph due to its large size, which increases the processing time significantly.

We present a powerful and efficient approach to the problem of propagating a bug fix to all the locations in a code base to which it applies. Our approach represents bug and fix patterns as subgraphs of a system dependence graph, and it employs a fast, index-based subgraph matching algorithm to discover unfixed bug-pattern instances remaining in a code base. We have also developed a graphical tool to help programmers specify bug patterns and fix patterns easily. We evaluated our approach by applying it to bug fixes in four large open-source projects. The results indicate that the approach exhibits good recall and precision and excellent efficiency.

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.

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.

We propose a novel representative based subgraph mining model. A series of standards and methods are proposed to select invariants. Patterns are mapped into invariant vectors in a multidimensional space. To find qualified patterns, only a subset of frequent patterns is generated as representatives, such that every frequent pattern is close to one of the representative patterns while representative patterns are distant from each other. We devise the RING algorithm, integrating the representative selection into the pattern mining process. Meanwhile, we use R-trees to assist this mining process. Last but not least, a large number of real and synthetic datasets are employed for the empirical study, which show the benefits of the representative model and the efficiency of the RING algorithm.

MOTIVATION: The goal of motif discovery is to detect novel, unknown, and important signals from biology sequences. In most models, the importance of a motif is equal to the sum of the similarity of every single position. In 2006, Song et al. introduced Aggregated Related Column Score (ARCS) measure which includes correlation information to the evaluation of motif importance. The paper showed that the ARCS measure is superior to other measures. Due to the complicated nature of the ARCS motif model, we cannot directly apply existing sequential motif discovery methods to find motifs with high ARCS values. RESULTS: This article presents a novel mining algorithm, ARCS-Motif, to discover related sequential motifs in biological sequences. ARCS-Motif is applied to 400 PROSITE datasets and compared with five alternative methods (CONSENSUS, Gibbs sampler, MEME, SPLASH and DIALIGN-TX). ARCS-Motif outperforms all the methods in accuracy, and most of the methods in efficiency. Although SPLASH has better efficiency than ARCS-Motif, ARCS-Motif has much better accuracy than SPLASH. On average, ARCS-Motif is able to produce the motifs which are at least 10% better than the best of the alternative methods. Among the 400 PROSITE datasets, ARCS-Motif produces the best motifs for more than 200 families. Other than SPLASH, the execution time of ARCS-Motif is less than a third of that of the fastest alternative method and its execution time grows at the slowest rate with respect to the number of sequences and the average sequence among all methods.

BACKGROUND: Clustering is a popular data exploration technique widely used in microarray data analysis. Most conventional clustering algorithms, however, generate only one set of clusters independent of the biological context of the analysis. This is often inadequate to explore data from different biological perspectives and gain new insights. We propose a new clustering model that can generate multiple versions of different clusters from a single dataset, each of which highlights a different aspect of the given dataset. RESULTS: By applying our SigCalc algorithm to three yeast Saccharomyces cerevisiae datasets we show two results. First, we show that different sets of clusters can be generated from the same dataset using different sets of landmark genes. Each set of clusters groups genes differently and reveals new biological associations between genes that were not apparent from clustering the original microarray expression data. Second, we show that many of these new found biological associations are common across datasets. These results also provide strong evidence of a link between the choice of landmark genes and the new biological associations found in gene clusters. CONCLUSION: We have used the SigCalc algorithm to project the microarray data onto a completely new subspace whose co-ordinates are genes (called landmark genes), known to belong to a Biological Process. The projected space is not a true vector space in mathematical terms. However, we use the term subspace to refer to one of virtually infinite numbers of projected spaces that our proposed method can produce. By changing the biological process and thus the landmark genes, we can change this subspace. We have shown how clustering on this subspace reveals new, biologically meaningful clusters which were not evident in the clusters generated by conventional methods. The R scripts (source code) are freely available under the GPL license. The source code is available [see Additional File 1] as additional material, and the latest version can be obtained at http://www4.ncsu.edu/~pchopra/landmarks.html. The code is under active development to incorporate new clustering methods and analysis.

No abstract available.

Neglected conditions are an important but difficult-to-find class of software defects. This paper presents a novel approach to revealing neglected conditions that integrates static program analysis and advanced data mining techniques to discover implicit conditional rules in a code base and to discover rule violations that indicate neglected conditions. The approach requires the user to indicate minimal constraints on the context of the rules to be sought, rather than specific rule templates. To permit this generality, rules are modeled as graph minors of enhanced procedure dependence graphs (EPDGs), in which control and data dependence edges are augmented by edges representing shared data dependences. A heuristic maximal frequent subgraph mining algorithm is used to extract candidate rules from EPDGs, and a heuristic graph matching algorithm is used to identify rule violations. We also report the results of an empirical study in which the approach was applied to four open source projects (openssl, make, procmail, amaya). These results indicate that the approach is effective and reasonably efficient.

Graphs are widely used to model complex structured data such as XML documents, protein networks, and chemical compounds. One of the fundamental problems in graph databases is efficient search and retrieval of graphs using indexing techniques. In this paper, we study the problem of indexing graph databases using frequent subtrees as indexing structures. Trees can be manipulated efficiently while preserving a lot of structural information of the original graphs. In our proposed method, frequent subtrees of a database are selected as the feature set. To save memory, the set of feature trees is shrunk based on a support threshold function and their discriminative power. A tree-partition based query processing scheme is proposed to perform graph queries. The concept of center distance constraints is introduced to prune the search space. Furthermore, a new algorithm which utilizes the location information of indexing structures is used to perform subgraph isomorphism tests. We apply our method on a wide range of real and synthetic data to demonstrate the usefulness and effectiveness of this approach.

In the recent past, many exact graph mining algorithms have been developed to find frequent patterns in a graph database. However, many networks or graphs generated from biological data and other applications may be incomplete or inaccurate. Hence, it is necessary to design approximate graph mining techniques. In this paper, we will study the problem of approximate graph mining and propose an optimized solution which uses frequent trees and a spanning tree based pre-verification check in the mining process.

Neglected conditions are an important but difficult-to-find class of software defects. This paper presents a novel approach to revealing neglected conditions that integrates static program analysis and advanced data mining techniques to discover implicit conditional rules in a code base and to discover rule violations that indicate neglected conditions. The approach requires the user to indicate minimal constraints on the context of the rules to be sought, rather than specific rule templates. To permit this generality, rules are modeled as graph minors of program dependence graphs, and both frequent itemset mining and frequent subgraph mining algorithms are employed to identify candidate rules. We report the results of an empirical evaluation of the approach in which it was used to discover conditional rules and neglected conditions in ~25,000 lines of source code.

MOTIVATION: Biologists frequently align multiple biological sequences to determine consensus sequences and/or search for predominant residues and conserved regions. Particularly, determining conserved regions in an alignment is one of the most important activities. Since protein sequences are often several-hundred residues or longer, it is difficult to distinguish biologically important conserved regions (motifs or domains) from others. The widely used tools, Logos, Al2co, Confind, and the entropy-based method, often fail to highlight such regions. Thus a computational tool that can highlight biologically important regions accurately will be highly desired. RESULTS: This paper presents a new scoring scheme ARCS (Aggregated Related Column Score) for aligned biological sequences. ARCS method considers not only the traditional character similarity measure but also column correlation. In an extensive experimental evaluation using 533 PROSITE patterns, ARCS is able to highlight the motif regions with up to 77.7% accuracy corresponding to the top three peaks. AVAILABILITY: The source code is available on http://bio.informatics.indiana.edu/projects/arcs and http://goldengate.case.edu/projects/arcs

Relational databases are the most popular repository for structured data, and is thus one of the richest sources of knowledge in the world. In a relational database, multiple relations are linked together via entity-relationship links. Multirelational classification is the procedure of building a classifier based on information stored in multiple relations and making predictions with it. Existing approaches of inductive logic programming (recently, also known as relational mining) have proven effective with high accuracy in multirelational classification. Unfortunately, most of them suffer from scalability problems with regard to the number of relations in databases. In this paper, we propose a new approach, called CrossMine, which includes a set of novel and powerful methods for multirelational classification, including 1) tuple ID propagation, an efficient and flexible method for virtually joining relations, which enables convenient search among different relations, 2) new definitions for predicates and decision-tree nodes, which involve aggregated information to provide essential statistics for classification, and 3) a selective sampling method for improving scalability with regard to the number of tuples. Based on these techniques, we propose two scalable and accurate methods for multirelational classification: CrossMine-Rule, a rule-based method and CrossMine-Tree, a decision-tree-based method. Our comprehensive experiments on both real and synthetic data sets demonstrate the high scalability and accuracy of the CrossMine approach

Data mining research, which focuses on scalable and effective knowledge discovery from databases, can provide timely solutions for the biologists in these aspects. In this article, we aim to provide platform in which various aspects of microarray data analysis is being introduced. We discuss in layman term how microarray datasets are generated and used in biological research. We use example from the real projects that we participate in to illustrate the potential of different technologies. We also discuss existing data mining tools and methods used for analyzing the microarray data sets and their biological implications. We also offer a wide range of analysis tools that can be applied to microarray gene expression analysis. Finally, we present a set of open problems and future research directions for microarray data analysis.

In the information age, data is pervasive. In some applications, data explosion is a significant phenomenon. The massive data volume poses challenges to both human users and computers. In this project, we propose a new model for identifying representative set from a large database. A representative set is a special subset of the original dataset, which has three main characteristics: It is significantly smaller in size compared to the original dataset. It captures the most information from the original dataset compared to other subsets of the same size. It has low redundancy among the representatives it contains. We use information-theoretic measures such as mutual information and relative entropy to measure the representativeness of the representative set. We first design a greedy algorithm and then present a heuristic algorithm that delivers much better performance. We run experiments on two real datasets and evaluate the effectiveness of our representative set in terms of coverage and accuracy. The experiments show that our representative set attains expected characteristics and captures information more efficiently.

MINING biological data is an emerging area of intersection between data mining and bioinformatics. Bioinformaticians have been working on the research and development of computational methodologies and tools for expanding the use of biological, medical, behavioral, or health-related data. Data mining researchers have been making substantial contribution to the development of models and algorithms to meet challenges posed by the bioinformatics research. Some successful examples are frequent pattern discovery on biological molecules, text mining in biomedical literature, information integration, probabilistic modeling of genome sequences, etc. This special issue of the IEEE Transactions on Knowledge and Data Engineering features a collection of 11 papers, selected from 54 submissions, representing recent advances at the frontier of mining biological data. Mining frequent trees is very useful in bioinformatics applications. The first paper, “Efficiently Mining Frequent Trees in a Forest: Algorithms and Applications” by Mohammed J. Zaki, formulates the problem of mining (embedded) subtrees in a forest of rooted, labeled, and ordered trees. The author presents TreeMiner, a novel algorithm to discover all frequent subtrees in a forest, using a new data structure called scope-list. TreeMiner has been proven to be superior to previous methods such as PatternMatcher and has shown promising results in analyzing RNA structure and phylogenetics data sets. In the second paper, “Frequent Substructure-Based Approaches for Classifying Chemical Compounds” by Mukund Deshpande, Michihiro Kuramochi, Nikil Wale, and George Karypis, the authors devise a substructurebased classification algorithm that decouples the substructure discovery process from the classification model construction and uses frequent subgraph discovery algorithms to find all topological and geometric substructures present in the data set. The advantage of this approach is that, during classification model construction, all relevant substructures are available and thus allow the classifier to intelligently select the most discriminating ones. This approach is employed to build models to correctly assign chemical compounds to various classes of interests, which have many applications in pharmaceutical research and are used extensively at various phases during the drug development process. Glycans, or carbohydrate sugar chains, are regarded as the third class of biological molecules, subsequent to DNA and proteins, and the recent advent of glycome informatics has generated an increasing number of glycan structures and annotation data. Glycans play important roles in the development and functioning of multicellular organisms and their structures can be represented by labeled ordered trees. The third paper, “A Probabilistic Model for Mining Labeled Ordered Trees: Capturing Patterns in Carbohydrate Sugar Chains” byNobuhisaUeda, Kiyoko F. Aoki-Kinoshita, Atsuko Yamaguchi, Tatsuya Akustu, and Hiroshi Mamitsuka, proposes a probabilistic model for mining labeled ordered trees and an EM algorithm for efficient learning. Proteins are the machinery of life. A number of techniques have been developed to classify proteins according to important features in their sequences, secondary structures, or three-dimensional structures. The fourth paper, “Finding Patterns on Protein Surfaces: Algorithms and Applications to Protein Classification” by Xiong Wang, introduces a novel approach to protein classification based on significant geometric patterns on the surface of a protein. The binding in protein-protein interactions exhibits a kind of biochemical stability in cells, which can be described by the mathematical notion of the fixed points. In the fifth paper, “Using Fixed Point Theorems to Model the Binding in Protein-Protein Interactions” by Jinyan Li and Haiquan Li, the authors define a point as a protein motif pair consisting of two traditional protein motifs. They propose a method to discover stable motif pairs of a given function from a large protein interaction sequence data set. With the rapid growth of articles on genomics research, it has become a challenge for biomedical researchers to access this ever-increasing quantity of information to understand the newest discovery of functions of proteins they are studying. To facilitate functional annotation of proteins by utilizing the huge amounts of biomedical literature and transforming the knowledge into easily accessible database formats, the text mining technique thus becomes essential. The sixth paper, “Literature Extraction of Protein Functions Using Sentence Pattern Mining” by Jung-Hsien Chiang and Hsu-Chun Yu, proposes the method of sentence pattern mining to extract protein functions from biomedical literature. Identifying concepts that have already been patented is essential for undertaking new biomedical research. Traditional keyword-based search on patent databases may not be sufficient enough to retrieve all the relevant information, especially for the biomedical domain. The seventh paper, “Information Retrieval and Knowledge Discovery Utilizing a BioMedical Patent Semantic Web” by Sougata Mukherjea, Bhuvan Bamba, and Pankaj Kankar, presents BioPatentMiner, a system that facilitates information retrieval and knowledge discovery from biomedical patents. BioPatentMiner first identifies biological terms IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING, VOL. 17, NO. 8, AUGUST 2005 1019

Most of today's structured data is stored in relational databases. Such a database consists of multiple relations which are linked together conceptually via entity-relationship links in the design of relational database schemas. Multirelational classification can be widely used in many disciplines, such as financial decision-making, medical research, and geographical applications. However, most classification approaches only work on single "flat" data relations. It is usually difficult to convert multiple relations into a single flat relation without either introducing huge, undesirable "universal relation" or losing essential information. Previous works using inductive logic programming approaches (recently also known as relational mining) have proven effective with high accuracy in multi-relational classification. Unfortunately, they suffer from poor scalability w.r.t. the number of relations and the number of attributes in databases. We propose CrossMine, an efficient and scalable approach for multirelational classification. Several novel methods are developed in CrossMine, including (1) tuple ID propagation, which performs semantics-preserving virtual join to achieve high efficiency on databases with complex schemas, and (2) a selective sampling method, which makes it highly scalable w.r.t. the number of tuples in the databases. Both theoretical backgrounds and implementation techniques of CrossMine are introduced. Our comprehensive experiments on both real and synthetic databases demonstrate the high scalability and accuracy of CrossMine.

In many applications such as e-commerce, system diagnosis and telecommunication services, data arrives in streams at a high speed. It is common that the underlying process generating the stream may change over time, either as a result of the fundamental evolution or in response to some external stimulus. Detecting these changes is a very challenging problem of great practical importance. The overall volume of the stream usually far exceeds the available main memory and access to the data stream is typically performed via a linear scan in ascending order of the indices of the records. In this paper, we propose a novel approach, AGILE, to monitor streaming data and to detect distinguishable transitions of the underlying processes. AGILE has many advantages over the traditional Hidden Markov Model, e.g., AGILE only requires one scan of the data.

One fundamental challenge for mining recurring subgraphs from semi-structured data sets is the overwhelming abundance of such patterns. In large graph databases, the total number of frequent subgraphs can become too large to allow a full enumeration using reasonable computational resources. In this paper, we propose a new algorithm that mines only maximal frequent subgraphs, i.e. subgraphs that are not a part of any other frequent subgraphs. This may exponentially decrease the size of the output set in the best case; in our experiments on practical data sets, mining maximal frequent subgraphs reduces the total number of mined patterns by two to three orders of magnitude.Our method first mines all frequent trees from a general graph database and then reconstructs all maximal subgraphs from the mined trees. Using two chemical structure benchmarks and a set of synthetic graph data sets, we demonstrate that, in addition to decreasing the output size, our algorithm can achieve a five-fold speed up over the current state-of-the-art subgraph mining algorithms.

Due to the advances in positioning technologies, the real time information of moving objects becomes increasingly available, which has posed new challenges to the database research. As a long-standing technique to identify overall distribution patterns in data, clustering has achieved brilliant successes in analyzing static datasets. In this paper, we study the problem of clustering moving objects, which could catch interesting pattern changes during the motion process and provide better insight into the essence of the mobile data points. In order to catch the spatial-temporal regularities of moving objects and handle large amounts of data, micro-clustering [20] is employed. Efficient techniques are proposed to keep the moving micro-clusters geographically small. Important events such as the collisions among moving micro-clusters are also identified. In this way, high quality moving micro-clusters are dynamically maintained, which leads to fast and competitive clustering result at any given time instance. We validate our approaches with a through experimental evaluation, where orders of magnitude improvement on running time is observed over normal K-Means clustering method [14].

Traditional clustering is a descriptive task that seeks to identify homogeneous groups of objects based on the values of their attributes. While domain knowledge is always the best way to justify clustering, few clustering algorithms have ever take domain knowledge into consideration. In this paper, the domain knowledge is represented by hierarchical ontology. We develop a framework by directly incorporating domain knowledge into clustering process, yielding a set of clusters with strong ontology implication. During the clustering process, ontology information is utilized to efficiently prune the exponential search space of the subspace clustering algorithms. Meanwhile, the algorithm generates automatical interpretation of the clustering result by mapping the natural hierarchical organized subspace clusters with significant categorical enrichment onto the ontology hierarchy. Our experiments on a set of gene expression data using gene ontology demonstrate that our pruning technique driven by ontology significantly improve the clustering performance with minimal degradation of the cluster quality. Meanwhile, many hierarchical organizations of gene clusters corresponding to a sub-hierarchies in gene ontology were also successfully captured.

Microarray datasets typically contain large number of columns but small number of rows. Association rules have been proved to be useful in analyzing such datasets. However, most existing association rule mining algorithms are unable to efficiently handle datasets with large number of columns. Moreover, the number of association rules generated from such datasets is enormous due to the large number of possible column combinations.In this paper, we describe a new algorithm called FARMER that is specially designed to discover association rules from microarray datasets. Instead of finding individual association rules, FARMER finds interesting rule groups which are essentially a set of rules that are generated from the same set of rows. Unlike conventional rule mining algorithms, FARMER searches for interesting rules in the row enumeration space and exploits all user-specified constraints including minimum support, confidence and chi-square to support efficient pruning. Several experiments on real bioinformatics datasets show that FARMER is orders of magnitude faster than previous association rule mining algorithms.

Microarrays are one of the latest breakthroughs in experimental molecular biology, which provide a powerful tool by which the expression patterns of thousands of genes can be monitored simultaneously and are already producing huge amount of valuable data. The concept of bicluster was introduced by Cheng and Church (2000) to capture the coherence of a subset of genes and a subset of conditions. A set of heuristic algorithms were also designed to either find one bicluster or a set of biclusters, which consist of iterations of masking null values and discovered biclusters, coarse and fine node deletion, node addition, and the inclusion of inverted data. These heuristics inevitably suffer from some serious drawback. The masking of null values and discovered biclusters with random numbers may result in the phenomenon of random interference which in turn impacts the discovery of high quality biclusters. To address this issue and to further accelerate the biclustering process, we generalize the model of bicluster to incorporate null values and propose a probabilistic algorithm (FLOC) that can discover a set of k possibly overlapping biclusters simultaneously. Furthermore, this algorithm can easily be extended to support additional features that suit different requirements at virtually little cost. Experimental study on the yeast gene expression data shows that the FLOC algorithm can offer substantial improvements over the previously proposed algorithm.

Analyzing sequence data has become increasingly important recently in the area of biological sequences, text documents, Web access logs, etc. We investigate the problem of clustering sequences based on their sequential features. As a widely recognized technique, clustering has proven to be very useful in detecting unknown object categories and revealing hidden correlations among objects. One difficulty that prevents clustering from being performed extensively on sequence data (in categorical domain) is the lack of an effective yet efficient similarity measure. Therefore, we propose a novel model (CLUSEQ) for sequence cluster by exploring significant statistical properties possessed by the sequences. The conditional probability distribution (CPD) of the next symbol given a preceding segment is derived and used to characterize sequence behavior and to support the similarity measure. A variation of the suffix tree, namely probabilistic suffix tree, is employed to organize (the significant portion of) the CPD in a concise way. A novel algorithm is devised to efficiently discover clusters with high quality and is able to automatically adjust the number of clusters to its optimal range via a unique combination of successive new cluster generation and cluster consolidation. The performance of CLUSEQ has been demonstrated via extensive experiments on several real and synthetic sequence databases.

The growth of bioinformatics has resulted in datasets with new characteristics. These datasets typically contain a large number of columns and a small number of rows. For example, many gene expression datasets may contain 10,000-100,000 columns but only 100-1000 rows.Such datasets pose a great challenge for existing (closed) frequent pattern discovery algorithms, since they have an exponential dependence on the average row length. In this paper, we describe a new algorithm called CARPENTER that is specially designed to handle datasets having a large number of attributes and relatively small number of rows. Several experiments on real bioinformatics datasets show that CARPENTER is orders of magnitude better than previous closed pattern mining algorithms like CLOSET and CHARM.

Support vector machines (SVMs) have been promising methods for classification and regression analysis because of their solid mathematical foundations which convery several salient properties that other methods hardly provide. However, despite the prominent properties of SVMs, they are not as favored for large-scale data mining as for pattern recognition or machine learning because the training complexity of SVMs is highly dependent on the size of a data set. Many real-world data mining applications involve millions or billions of data records where even multiple scans of the entire data are too expensive to perform. This paper presents a new method, Clustering-Based SVM (CB-SVM), which is specifically designed for handling very large data sets. CB-SVM applies a hierarchical micro-clustering algorithm that scans the entire data set only once to provide an SVM with high quality samples that carry the statistical summaries of the data such that the summaries maximize the benefit of learning the SVM. CB-SVM tries to generate the best SVM boundary for very large data sets given limited amount of resources. Our experiments on synthetic and real data sets show that CB-SVM is highly scalable for very large data sets while also generating high classification accuracy.

In this paper, we focus on mining periodic patterns allowing some degree of imperfection in the form of random replacement from a perfect periodic pattern. In InfoMiner+, we proposed a new metric, namely generalized information gain, to identify patterns with events of vastly different occurrence frequencies and to adjust for the deviation from a pattern. In particular, a penalty is allowed to be associated with gaps between pattern occurrences. This is particularly useful in locating repeats in DNA sequences. In this paper, we present an effective mining algorithm, STAMP, to simultaneously mine significant patterns and the associated subsequences under the model of generalized information gain.

Periodicy detection in time series data is a challenging problem of great importance in many applications. Most previous work focused on mining synchronous periodic patterns and did not recognize the misaligned presence of a pattern due to the intervention of random noise. In this paper, we propose a more flexible model of asynchronous periodic pattern that may be present only within a subsequence and whose occurrences may be shifted due to disturbance. Two parameters min/spl I.bar/rep and max/spl I.bar/dis are employed to specify the minimum number of repetitions that is required within each segment of nondisrupted pattern occurrences and the maximum allowed disturbance between any two successive valid segments. Upon satisfying these two requirements, the longest valid subsequence of a pattern is returned. A two-phase algorithm is devised to first generate potential periods by distance-based pruning followed by an iterative procedure to derive and validate candidate patterns and locate the longest valid subsequence. We also show that this algorithm cannot only provide linear time complexity with respect to the length of the sequence but also achieve space efficiency.

Analyzing sequence data (particularly in categorical domains) has become increasingly important, partially due to the significant advances in biology and other fields. Examples of sequence data include DNA sequences, unfolded protein sequences, text documents, Web usage data, system traces, etc. Previous work on mining sequence data has mainly focused on frequent pattern discovery. In this project, we focus on the problem of clustering sequence data.

Clustering has been an active research area of great practical importance for recent years. Most previous clustering models have focused on grouping objects with similar values on a (sub)set of dimensions (e.g., subspace cluster) and assumed that every object has an associated value on every dimension (e.g., bicluster). These existing cluster models may not always be adequate in capturing coherence exhibited among objects. Strong coherence may still exist among a set of objects (on a subset of attributes) even if they take quite different values on each attribute and the attribute values are not fully specified. This is very common in many applications including bio-informatics analysis as well as collaborative filtering analysis, where the data may be incomplete and subject to biases. In bio-informatics, a bicluster model has recently been proposed to capture coherence among a subset of the attributes. We introduce a more general model, referred to as the /spl delta/-cluster model, to capture coherence exhibited by a subset of objects on a subset of attributes, while allowing absent attribute values. A move-based algorithm (FLOC) is devised to efficiently produce a near-optimal clustering results. The /spl delta/-cluster model takes the bicluster model as a special case, where the FLOC algorithm performs far superior to the bicluster algorithm. We demonstrate the correctness and efficiency of the /spl delta/-cluster model and the FLOC algorithm on a number of real and synthetic data sets.

In this paper we focus on mining periodic patterns allowing some degree of imperfection in the form of random replacement from a perfect periodic pattern. Information gain was proposed to identify patterns with events of vastly different occurrence frequencies and adjust for deviation from a pattern. However, it does not involve a penalty if there exists some gap between pattern occurrences. In many applications, e.g., bioinformatics, it is important to identify subsequences that a pattern repeats perfectly (or near perfectly). As a solution, we extend the information gain measure to include a penalty for gaps between pattern occurrences. We call this measure generalized information gain. Furthermore, we need to find a subsequence S' such that for a pattern P, the generalized information gain of P in S' is high. This is particularly useful in locating repeats in DNA sequences. In this paper, we developed an effective mining algorithm, InfoMiner+, to simultaneously mine significant patterns and associated subsequences.

In this paper, we investigate in the problem of efficient filtering of a large dataset according to some user specified criterion. A novel paradigm is introduced to allow users to easily integrate their prior knowledge in the mining process and to customize the mining result. The Bayesian Network is chosen as the model to represent user's knowledge due to its rich expressive power, compact representation, and intuitive semantics. However, one difficulty that prevents the Bayesian network model from being applied to large scale databases in a brute-force way is the generally high computational complexity of the inference algorithms. To tackle this challenge, we propose three techniques, namely network pruning of conditional probability, computation reuse by tuple reordering, and early termination, to speed up the process dramatically. It has been demonstrated that our proposed algorithm can save as much as 95% of the execution time empirically.

Clustering is the process of grouping a set of objects into classes of similar objects. Although definitions of similarity vary from one clustering model to another, in most of these models the concept of similarity is based on distances, e.g., Euclidean distance or cosine distance. In other words, similar objects are required to have close values on at least a set of dimensions. In this paper, we explore a more general type of similarity. Under the pCluster model we proposed, two objects are similar if they exhibit a coherent pattern on a subset of dimensions. For instance, in DNA microarray analysis, the expression levels of two genes may rise and fall synchronously in response to a set of environmental stimuli. Although the magnitude of their expression levels may not be close, the patterns they exhibit can be very much alike. Discovery of such clusters of genes is essential in revealing significant connections in gene regulatory networks. E-commerce applications, such as collaborative filtering, can also benefit from the new model, which captures not only the closeness of values of certain leading indicators but also the closeness of (purchasing, browsing, etc.) patterns exhibited by the customers. Our paper introduces an effective algorithm to detect such clusters, and we perform tests on several real and synthetic data sets to show its effectiveness.

Pattern discovery in long sequences is of great importance in many applications including computational biology study, consumer behavior analysis, system performance analysis, etc. In a noisy environment, an observed sequence may not accurately reflect the underlying behavior. For example, in a protein sequence, the amino acid N is likely to mutate to D with little impact to the biological function of the protein. It would be desirable if the occurrence of D in the observation can be related to a possible mutation from N in an appropriate manner. Unfortunately, the support measure (i.e., the number of occurrences) of a pattern does not serve this purpose. In this paper, we introduce the concept of compatibility matrix as the means to provide a probabilistic connection from the observation to the underlying true value. A new metric match is also proposed to capture the "real support" of a pattern which would be expected if a noise-free environment is assumed. In addition, in the context we address, a pattern could be very long. The standard pruning technique developed for the market basket problem may not work efficiently. As a result, a novel algorithm that combines statistical sampling and a new technique (namely border collapsing) is devised to discover long patterns in a minimal number of scans of the sequence database with sufficiently high confidence. Empirical results demonstrate the robustness of the match model (with respect to the noise) and the efficiency of the probabilistic algorithm.

Data mining has been an area of increasing interest. The association rule discovery problem in particular has been widely studied. However, there are still some unresolved problems. For example, research on mining patterns in the evolution of numerical attributes is still lacking. This is both a challenging problem and one with significant practical applications in business, science, and medicine. In this paper we present a temporal association rule model for evolving numerical attributes. Metrics for qualifying a temporal association rule include the familiar measures of support and strength used in traditional association rule mining and a new metric called density. The density metric not only gives us a way to extract the rules that best represent the data, but also provides an effective mechanism to prune the search space. An efficient algorithm is devised for mining temporal association rules, which utilizes all three thresholds (especially the strength) to prune the search space drastically. Moreover, the resulting rules are represented in a concise manner via rule sets to reduce the output size. Experimental results on real and synthetic data sets demonstrate the efficiency of our algorithm.

Discovery of periodic patterns in time series data has become an active research area with many applications. These patterns can be hierarchical in nature, where a higher level pattern may consist of repetitions of lower level patterns. Unfortunately, the presence of noise may prevent these higher level patterns from being recognized in the sense that two portions (of a data sequence) that support the same (high level) pattern may have different layouts of occurrences of basic symbols. There may not exist any common representation in terms of raw symbol combinations; and hence such (high level) patterns may not be expressed by any previous model (defined on raw symbols or symbol combinations) and would not be properly recognized by any existing method. In this paper, we propose a novel model, namely meta-pattern, to capture these high level patterns. As a more flexible model, the number of potential meta-patterns could be very large. A substantial difficulty is how to identify the proper pattern candidates. However the well-known a priori properly is not able to provide sufficient pruning power. A new property, namely component location, is identified and used to conduct candidate generation so that an efficient computation-based mining algorithm can be developed. We apply our algorithm to real and synthetic sequences and interesting patterns are discovered.

In this paper, we focus on mining surprising periodic patterns in a sequence of events. In many applications, e.g., computational biology, an infrequent pattern is still considered very significant if its actual occurrence frequency exceeds the prior expectation by a large margin. The traditional metric, such as support, is not necessarily the ideal model to measure this kind of surprising patterns because it treats all patterns equally in the sense that every occurrence carries the same weight towards the assessment of the significance of a pattern regardless of the probability of occurrence. A more suitable measurement, information, is introduced to naturally value the degree of surprise of each occurrence of a pattern as a continuous and monotonically decreasing function of its probability of occurrence. This would allow patterns with vastly different occurrence probabilities to be handled seamlessly. As the accumulated degree of surprise of all repetitions of a pattern, the concept of information gain is proposed to measure the overall degree of surprise of the pattern within a data sequence. The bounded information gain property is identified to tackle the predicament caused by the violation of the downward closure property by the information gain measure and in turn provides an efficient solution to this problem. Empirical tests demonstrate the efficiency and the usefulness of the proposed model.

In light of advances in processor and networking technology, especially the emergence of network attached disks, the traditional client-server architecture of file systems has become suboptimal for many computation/data intensive applications. We introduce a revised architecture for file management employing network attached storage: the dynamic file server environment (Dynamo). Dynamo introduces two main architectural innovations: to provide high scalability, the file management functions are mainly performed cooperatively by the clients in the system. Furthermore, data is transferred directly to the client's cache from network-attached disks, thus avoiding copies from a disk to the server buffer and then over the network to the client. Secondly, Dynamo uses a cooperative cache management which employs a decentralized lottery-based page replacement strategy. We show via performance benchmarks run on the Dynamo system and simulation results how this architecture increases the system's adaptability, scalability and cost performance.

In this paper, we extend the tradition association rule problem by allowing a weight to be associated with each item in a transaction, to re ect interest/intensity of the item within the transaction.This provides us in turn with an opportunity to associate a weight parameter with each item in the resulting association rule.We call it weighted association rule (WAR).WAR not only improves the con dence of the rules, but also provides a mechanism to do more effective target marketing by identifying or segmenting customers based on their potential degree of loyalty o r v olume of purchases.Our approach mines WARs by rst ignoring the weight and nding the frequent itemsets (via a traditional frequent itemset discovery algorithm), and is followed by i n troducing the weight during the rule generation.It is shown by experimental results that our approach not only results in shorter average execution times, but also produces higher quality results than the generalization of previous known methods on quantitative association rules.

Abstract—Periodicy detection in time series data is a challenging problem of great importance in many applications. Most previous work focused on mining synchronous periodic patterns and did not recognize the misaligned presence of a pattern due to the intervention of random noise. In this paper, we propose a more flexible model of asynchronous periodic pattern that may be present only within a subsequence and whose occurrences may be shifted due to disturbance. Two parameters min rep and max dis are employed to specify the minimum number of repetitions that is required within each segment of nondisrupted pattern occurrences and the maximum allowed disturbance between any two successive valid segments. Upon satisfying these two requirements, the longest valid subsequence of a pattern is returned. A two-phase algorithm is devised to first generate potential periods by distance-based pruning followed by an iterative procedure to derive and validate candidate patterns and locate the longest valid subsequence. We also show that this algorithm cannot only provide linear time complexity with respect to the length of the sequence but also achieve space efficiency. Index Terms—Asynchronous periodic pattern, segment-based approach, partial periodicity. æ 1

With the exponential growth of hosts and traffic workloads on the Internet, collaborative web caching has been recognized as an efficient solution to alleviate web page server bottlenecks and reduce traffic. However, cache discovery, i.e., locating where a page is cached, is a challenging problem, especially in the fast growing World Wide Web environment, where the number of participating proxies can be very large. In this paper, we propose a new scheme which employs proxy affinities to maintain a dynamic distributed collaborative caching infrastructure. Web pages are partitioned into clusters according to proxy reference patterns. All proxies which frequently access some page(s) in the same web page cluster form an “information group”. When web pages belonging to a web page cluster are deleted from or added into a proxy's cache, only proxies in the associated information group are notified. This scheme can be shown to greatly reduce the number of messages and other overhead on individual proxies while maintaining a high cache hit rate. Finally, we employ trace driven simulation to evaluate our web caching scheme using three web access trace logs to verify that our caching structure can provide significant benefits on real workloads.

In light of advances in processor and networking technology, especially the emergence of network attached disks, the traditional client-server architecture of persistent storage systems has become suboptimal for many computation/data intensive applications. In this paper, we introduce a revised architecture for persistent object management employing network attached storage: the dynamic object server environment (Dynamo). Dynamo introduces two main architectural innovations: (1) to provide high scalability, the object management functions are mainly performed cooperatively by the clients in the system. Furthermore, data is transferred directly to the client's cache from network-attached disks, thus avoiding copies from a disk to the server buffer and then over the network to the client. Other systems have an a priori assignment of ‘object management’ functions to specific nodes; (2) Dynamo uses a cooperative cache management which employs a decentralized lottery-based page replacement strategy with a novel technique which attempts to put a page replaced from one node into the cache of another node which is likely to access the page in the near future. We show via performance benchmarks run on the Dynamo system and simulation results how this architecture increases the system's adaptability, scalability and cost performance. Copyright © 2000 John Wiley & Sons, Ltd.

Spatial data mining presents new challenges due to the large size of spatial data, the complexity of spatial data types, and the special nature of spatial access methods. Most research in this area has focused on efficient query processing of static data. This paper introduces an active spatial data mining approach that extends the current spatial data mining algorithms to efficiently support user-defined triggers on dynamically evolving spatial data. To exploit the locality of the effect of an update and the nature of spatial data, we employ a hierarchical structure with associated statistical information at the various levels of the hierarchy and decompose the user-defined trigger into a set of subtriggers associated with cells in the hierarchy. Updates are suspended in the hierarchy until their cumulative effect might cause the trigger to fire. It is shown that this approach achieves three orders of magnitude improvement over the naive approach that reevaluate the condition over the database for each update, while both approaches produce the same result without any delay. Moreover, this scheme can support incremental query processing as well.

Spatial data mining presents new challenges due to the large size of spatial data, the complexity of spatial data types, and the special nature of spatial access methods. Most research in this area has focused on efficient query processing of static data. This paper introduces an active spatial data mining approach which extends the current spatial data mining algorithms to efficiently support user-defined triggers on dynamically evolving spatial data. To exploit the locality of the effect of an update and the nature of spatial data, we employ a hierarchical structure with associated statistical information at the various levels of the hierarchy and decompose the user-defined trigger into a set of sub-triggers associated with cells in the hierarchy. Updates are suspended in the hierarchy until their cumulative effect might cause the trigger to fire. It is shown that this approach achieves three orders of magnitude improvement over the naive approach that re-evaluates the condition over the database for each update, while both approaches produce the same result without any delay. Moreover this scheme can support incremental query processing as well.