62615149
Mining Asynchronous Periodic Patterns in Time Series Data
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.
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
11001109
DynamO: Dynamic Objects with Persistent Storage
In light of advances in processor and networking technology, especially the emergence of network attached disks, the traditional client-server architecture becomes suboptimal for many computation/data intensive applications, e.g., data mining, scientiic computing, image processing, etc. In this paper, we introduce a revised architecture for this kind of application: the dynamic object server environment (DynamO). The main innovation of this architecture is that the functionality of a persistent storage server is divided into modules which are dynamically migrated to the client on demand. Also, data is transfered directly to the client's cache from network-attached disks, thus avoiding multiple copies from a disk to the server buuer to the network and the client. In this way, a client only places a small load on the server, and also avoids the I/O bottleneck on the server. Furthermore, DynamO employs a distributed cache management allowing several clients to share the in-memory data by using the concept of \who uses it, serves it to others". We show via simulation models how this architecture increases the system's adaptability, scalability and cost performance.
28890
Extension of Lower Probabilities and Coherence of Belief Measures
Coherence is an important concept which is introduced and discussed in a new mathematics branch, Imprecise Probability Theory. By using the Choquet integral, belief measures can be extended to be coherent lower previsions on the linear space consisting of all bounded functions. As a special case, we establish that all belief measures are coherent imprecise probabilities.
14797393
A system for analyzing and indexing human-motion databases
We demonstrate a data-driven approach for representing, compressing, and indexing human-motion databases. Our modeling approach is based on piecewise-linear components that are determined via a divisive clustering method. Selection of the appropriate linear model is determined automatically via a classifier using a subspace of the most significant, or principle features (markers). We show that, after offline training, our model can accurately estimate and classify human motions. We can also construct indexing structures for motion sequences according to their transition trajectories through these linear components. Our method not only provides indices for whole and/or partial motion sequences, but also serves as a compressed representation for the entire motion database. Our method also tends to be immune to temporal variations, and thus avoids the expense of time-warping.
19971560
Successfully Adopting IT for Social Welfare Program Management
In DGO 2003, we first introduced the long-standing Work First project that is inter-disciplinary between social work and computer science at the University of North Carolina at Chapel Hill (UNC-CH) with the collaboration of the North Carolina Department of Health and Human Services (NC DHHS). Based on the success in our Work First project, the NC DHHS and UNC-CH have extended the collaboration to work on a similar project to assist in the evaluation of changes to the Food Stamp employment and training (E&T) program in North Carolina. In this paper, we reflect on our experience to discuss some important aspects of successfully adopting information technology in government agencies in order to replicate them in the new Food Stamp project.
3251955
Containment join size estimation: models and methods
Recent years witnessed an increasing interest in researches in XML, partly due to the fact that XML has now become the de facto standard for data interchange over the internet. A large amount of work has been reported on XML storage models and query processing techniques. However, few works have addressed issues of XML query optimization. In this paper, we report our study on one of the challenges in XML query optimization: containment join size estimation. Containment join is well accepted as an important operation in XML query processing. Estimating the size of its results is no doubt essential to generate efficient XML query processing plans. We propose two models, the interval model and the position model, and a set of estimation methods based on these two models. Comprehensive performance studies were conducted. The results not only demonstrate the advantages of our new algorithms over existing algorithms, but also provide valuable insights into the tradeoff among various parameters.
83220
Defending against wormhole attacks in mobile ad hoc networks
In ad hoc networks, malicious nodes can deploy wormhole attacks to fabricate a false scenario on the proximity relationship among mobile nodes. A classification of the attacks according to the format of the wormholes is proposed. This forms a basis to identify the detection capability of various approaches. An analysis shows that earlier approaches focus on the prevention of wormholes among neighbors that trust each other. As a more generic approach, we present an end-to-end scheme that can detect wormholes on a multi-hop route. Only the trust between the source and the destination is assumed. The mechanism uses geographic information to detect anomalies in neighbor relations and node movements. To reduce the computation and storage overhead, we present a scheme called cell-based open tunnel avoidance (COTA) to manage the information. COTA requires a constant space for every node on the path and the computation overhead increases linearly to the number of detection packets. We prove that the savings do not deteriorate the detection capability. Various schemes to control communication overhead are studied. The simulation and experiments on real devices show that the proposed mechanism can be combined with existent routing protocols to defend against wormhole attacks. Copyright © 2006 John Wiley & Sons, Ltd.
9604504
Bloom Histogram: Path Selectivity Estimation for XML Data with Updates
Cost-based XML query optimization calls for accurate estimation of the selectivity of path expressions. Some other interactive and internet applications can also benefit from such estimations. While there are a number of estimation techniques proposed in the literature, almost none of them has any guarantee on the estimation accuracy within a given space limit. In addition, most of them assume that the XML data are more or less static, i.e., with few updates. In this paper, we present a framework for XML path selectivity estimation in a dynamic context. Specifically, we propose a novel data structure, bloom histogram, to approximate XML path frequency distribution within a small space budget and to estimate the path selectivity accurately with the bloom histogram. We obtain the upper bound of its estimation error and discuss the trade-offs between the accuracy and the space limit. To support updates of bloom histograms efficiently when underlying XML data change, a dynamic summary layer is used to keep exact or more detailed XML path information. We demonstrate through our extensive experiments that the new solution can achieve significantly higher accuracy with an even smaller space than the previous methods in both static and dynamic environments.
15982467
On intrinsic representations of 3D polygons for shape blending
Abstract An intrinsic representation of a geometric object comprises a set of parameters that are invariant under Euclidean transformations and determine the shape and size of the object uniquely. Unlike the case of a two-dimensional polygon which has essentially only one intrinsic representation, a three-dimensional (3D) polygon allows several variations. We study three different intrinsic representations of a 3D polygon, focusing on properties regarding their applications in shape blending. We show that only one of these representations, which is a natural extension to the intrinsic functions of a 3D differentiable curve, is suitable for shape blending, while the others lead to discontinuous shape transformation. Detailed discussions about the evaluation criteria, numerical sensitivity, and an inherent difficulty in shape blending of 3D polygons are also presented.
3126850
Recent innovations in speech-to-text transcription at SRI-ICSI-UW
We summarize recent progress in automatic speech-to-text transcription at SRI, ICSI, and the University of Washington. The work encompasses all components of speech modeling found in a state-of-the-art recognition system, from acoustic features, to acoustic modeling and adaptation, to language modeling. In the front end, we experimented with nonstandard features, including various measures of voicing, discriminative phone posterior features estimated by multilayer perceptrons, and a novel phone-level macro-averaging for cepstral normalization. Acoustic modeling was improved with combinations of front ends operating at multiple frame rates, as well as by modifications to the standard methods for discriminative Gaussian estimation. We show that acoustic adaptation can be improved by predicting the optimal regression class complexity for a given speaker. Language modeling innovations include the use of a syntax-motivated almost-parsing language model, as well as principled vocabulary-selection techniques. Finally, we address portability issues, such as the use of imperfect training transcripts, and language-specific adjustments required for recognition of Arabic and Mandarin