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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
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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.
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.
2768791
Finding representative set from massive data
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.
14969897
Dynamic adaptive file management in a local area network
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.
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.
35803772
Approximate range–sum query answering on data cubes with probabilistic guarantees
Approximate range aggregate queries are one of the most frequent and useful kinds of queries for Decision Support Systems (DSS), as they are widely used in many data analysis tasks. Traditionally, sampling-based techniques have been proposed to tackle this problem. However, their effectiveness degrade when the underlying data distribution is skewed. Another approach based on the outlier management can limit the effect of data skews but fails to address other requirements of approximate range aggregate queries, such as error guarantees and query processing efficiency. In this paper, we present a technique that provides approximate answers to range aggregate queries on OLAP data cubes efficiently, with theoretical guarantees on the errors. Our basic idea is to build different data structures to manage outliers and the rest of the data. Carefully chosen outliers are organized in a quad-tree based indexing data structure to provide efficient access for query processing. A query-workload adaptive, tree-like synopsis data structure, called TunablePartition-Tree (TP-Tree), is proposed to organize samples extracted from non-outlier data. Our experiments clearly demonstrate the merits of our technique, by comparing with previous well-known techniques.
18265885
Identifying intrusions in computer networks with principal component analysis
Most current anomaly intrusion detection systems (IDSs) detect computer network behavior as normal or abnormal but cannot identify the type of attacks. Moreover, most current intrusion detection methods cannot process large amounts of audit data for real-time operation. In this paper, we propose a novel method for intrusion identification in computer networks based on principal component analysis (PCA). Each network connection is transformed into an input data vector. PCA is employed to reduce the dimensionality of the data vectors and identification is handled in a low dimensional space with high efficiency and low use of system resources. The normal behavior is profiled based on normal data for anomaly detection and models of each type of attack are built based on attack data for intrusion identification. The distance between a vector and its reconstruction onto those reduced subspaces representing the different types of attacks and normal activities is used for identification. The method is tested with network data from MIT Lincoln labs for the 1998 DARPA intrusion detection evaluation program and testing results show that the model is promising in terms of identification accuracy and computational efficiency for real-time intrusion identification.
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.
45794206
Rational Quadratic Parameterizations of Quadrics
Every irreducible quadric in E3 has infinitely many different rational quadratic parameterizations. These parameterizations and the relationships between them are investigated. It is shown that every faithful rational quadratic parameterization of a quadric can be generated by a stereographic projection from a point on the quadric, called the center of projection (COP). Two such parameterizations for the same quadric are related by a rational linear reparameterization if they have the same COP; otherwise they are related by a rational quadratic reparameterization. We also consider unfaithful parameterizations for which, in general, a one-to-one correspondence between points on the surface and parameters in the plane does not exist. It is shown that all unfaithful rational quadratic parameterizations of a properly degenerate quadric can be characterized by a simple canonical form, and there exist no unfaithful rational quadratic parameterizations for a nondegenerate quadric. In addition, given a faithful rational quadratic parameterization of a quadric, a new technique is presented to compute its base points and inversion formula. These results are applied to solve the problems of parameterizing the intersection of two quadrics and reparameterizing a given quadric parameterization with respect to a different COP without implicitization.
20701407
A General Structure of Feedback Shift Registers for Built-In Self Test
A mixed-type feedback shift register (MFSR) is simi lar to a linear feedback shift register (LFSR) except that the connection between two consecutive flip-flops (F/F's) may be through the Q or output, and an extra inver ter may exist at the input to the first flip-flop (stage) of the register. In this p aper, we exploit the properties of MFSR's and show that by using an MFSR based pseudorandom pattern generator (PRPG) or multiple input signature analyzer (MISA), several good features for built-in self test can be obtained. Specifically w e show that: (1) for any given initial seed, an MFSR always exists that can generate the s ame serial output sequence as can an LFSR with the same characteristic polynomial and any initial seed; (2) for any MFSR, we can always find an initial seed for this M FSR such that it can generate the same serial output sequence as can an LFSR with the same characteristic polynomial and any initial seed; and (3) for any given initial seed and any test response to be compressed, an MFSR based MISA can usually be found that will result in any required final signature. If such an MFSR cannot b e found for a specific initial seed and a specific test response sequence, we show that by simply adding one arbitrary dummy pattern to the test response, one can always find the required MFSR. We also show that if the characteristic polynomial of the MFSR based MISA can be chosen freely, it is almost guaranteed that a feasi ble MFSR can be found without adding any dummy patterns to the test response. Fo r example, for a 16-stage MISA, the probability that a feasible MFSR does not exist is less than 2-32768.