1043853
Scalable mining of large disk-based graph databases
Mining frequent structural patterns from graph databases is an interesting problem with broad applications. Most of the previous studies focus on pruning unfruitful search subspaces effectively, but few of them address the mining on large, disk-based databases. As many graph databases in applications cannot be held into main memory, scalable mining of large, disk-based graph databases remains a challenging problem. In this paper, we develop an effective index structure, ADI (for <u>ad</u>jacency <u>i</u>ndex), to support mining various graph patterns over large databases that cannot be held into main memory. The index is simple and efficient to build. Moreover, the new index structure can be easily adopted in various existing graph pattern mining algorithms. As an example, we adapt the well-known gSpan algorithm by using the ADI structure. The experimental results show that the new index structure enables the scalable graph pattern mining over large databases. In one set of the experiments, the new disk-based method can mine graph databases with one million graphs, while the original gSpan algorithm can only handle databases of up to 300 thousand graphs. Moreover, our new method is faster than gSpan when both can run in main memory.
8249361
SUDEPHIC: Self-Tuning Density-Based Partitioning and Hierarchical Clustering
Clustering is one of the primary techniques in data mining, for which to find the user expecting result is a major issue. However, to dynamically specify the parameters for clustering algorithms presents an obstacle for users. This paper firstly introduces a novel density-based partitioning and hierarchical algorithm, which makes it easy to employ synthetic feedback mechanism in clustering. Additionally, by investigating into the relation between parameters and the clustering result, we propose a self-tuning technique for the setting of parameters. Meanwhile, the density distribution within a cluster can be expressed in the result for the user to specify the cluster’s feature. The algorithm is both evaluated in theory and practice. It outperforms many existing algorithms both in efficiency and quality.
14792668
Personalization as a service: the architecture and a case study
Cloud computing has become a hot topic in the IT industry. Great efforts have been made to establish cloud computing platforms for enterprise users, mostly small businesses. However, there are few researches about the impact of cloud computing over individual users. In this paper we focus on how to provide personalized services for individual users in the cloud environment. We argue that a personalized cloud service shall compose of two parts. The client side program records user activities on personal de-vices such as PC. Besides that, the user model is also computed on the client side to avoid server overhead. The cloud side program fetches the user model periodically and adjusts its results accordingly. We build a personalized cloud data search engine prototype to prove our idea.
30881426
Constraint-Based Graph Mining in Large Database
Currently, constraints are increasingly considered as a kind of means of user- or expert-control for filtering those unsatisfied and redundant patterns rapidly during the web mining process. Recent work has highlighted the importance of constraint-based mining paradigm in the context of frequent itemsets, sequences, and many other interesting patterns in large database. However, it is still not clear how to push various constraints systematically into graph mining process. In this paper, we categorize various graph-based constraints into several major classes and develop a framework CabGin (i.e. C onstr a int- b ased G raph M in ing) to push them into mining process by their categories. Non-monotonic aggregates like average also can be pushed into CabGin with minor revision. Experimental results show that CabGin can prunes a large search space effectively by pushing graph-based constraints into mining process.
207162632
Utility-based anonymization for privacy preservation with less information loss
Privacy becomes a more and more serious concern in applications involving microdata. Recently, efficient anonymization has attracted much research work. Most of the previous methods use global recoding, which maps the domains of the quasi-identifier attributes to generalized or changed values. However, global recoding may not always achieve effective anonymization in terms of discernability and query answering accuracy using the anonymized data. Moreover, anonymized data is often used for analysis. As well accepted in many analytical applications, different attributes in a data set may have different utility in the analysis. The utility of attributes has not been considered in the previous methods.
 In this paper, we study the problem of utility-based anonymization. First, we propose a simple framework to specify utility of attributes. The framework covers both numeric and categorical data. Second, we develop two simple yet efficient heuristic local recoding methods for utility-based anonymization. Our extensive performance study using both real data sets and synthetic data sets shows that our methods outperform the state-of-the-art multidimensional global recoding methods in both discernability and query answering accuracy. Furthermore, our utility-based method can boost the quality of analysis using the anonymized data.
10409272
Repairing Inconsistent XML Documents
XML document may contain inconsistencies that violate predefined integrity constraints, and there are two basic concepts for this problem: Repair is the data consistent with the integrity constraints, and also minimally differs from the original one. Consistent data is the data common for every possible repair. In this paper, first we give a general constraint model for XML, which can express functional dependencies, keys and multivalued dependencies. Next we provide a repair framework for inconsistent XML document with three basic update operations: node insertion, node deletion and value modification. Following this approach, we introduce the concept of repair for inconsistent XML document, discuss the chase process to generate repairs, and prove some important properties of the chase process. Finally we give a method to obtain the greatest lower bound of all possible repairs, which is sufficient for consistent data.
377228
SPIN: mining maximal frequent subgraphs from graph databases
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.
10178337
Intelligent Sequential Mining Via Alignment: Optimization Techniques for Very Large DB
The shear volume of the results in traditional support based frequent sequential pattern mining methods has led to increasing interest in new intelligent mining methods to find more meaningful and compact results. One such approach is the consensus sequential pattern mining method based on sequence alignment, which has been successfully applied to various areas. However, the current approach to consensus sequential pattern mining has quadratic run time with respect to the database size limiting its application to very large databases. In this paper, we introduce two optimization techniques to reduce the running time significantly. First, we determine the theoretical bound for precision of the proximity matrix and reduce the time spent on calculating the full matrix. Second, we use a sample based iterative clustering method which allows us to use a much faster k-means clustering method with only a minor increase in memory consumption with negligible loss in accuracy.
9528238
A framework for ontology-driven subspace clustering
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.
8630623
Gene ontology friendly biclustering of expression profiles
The soundness of clustering in the analysis of gene expression profiles and gene function prediction is based on the hypothesis that genes with similar expression profiles may imply strong correlations with their functions in the biological activities. Gene ontology (GO) has become a well accepted standard in organizing gene function categories. Different gene function categories in GO can have very sophisticated relationships, such as 'part of' and 'overlapping'. Until now, no clustering algorithm can generate gene clusters within which the relationships can naturally reflect those of gene function categories in the GO hierarchy. The failure in resembling the relationships may reduce the confidence of clustering in gene function prediction. In this paper, we present a new clustering technique, smart hierarchical tendency preserving clustering (SMTP-clustering), based on a bicluster model, tendency preserving cluster (TP-Cluster). By directly incorporating gene ontology information into the clustering process, the SMTP-clustering algorithm yields a TP-cluster tree within which any subtree can be well mapped to a part of the GO hierarchy. Our experiments on yeast cell cycle data demonstrate that this method is efficient and effective in generating the biological relevant TP-clusters.
36057715
Guest Editors' Introduction: Special Issue on Mining Biological Data
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