26202322
Searching the web using composed pages
Given a user keyword query, current Web search engines return a list of pages ranked by their “goodness” with respect to the query. However, this technique misses results whose contents are distributed across multiple physical pages and are connected via hyperlinks and frames [3]. That is, it is often the case that no single page contains all query keywords. Li et al. [3] make a first step towards this problem by returning a tree of hyperlinked pages that collectively contain all query keywords. The limitation of this approach is that it operates at the page-level granularity, which ignores the specific context where the keywords are found within the pages. More importantly, it is cumbersome for the user to locate the most desirable tree of pages due to the amount of data in each page tree and a large number of page trees.
8121416
Biclustering Protein Complex Interactions with a Biclique Finding Algorithm
Biclustering has many applications in text mining, Web clickstream mining, and bioinformatics. When data entries are binary, the tightest biclusters become bicliques. We propose a flexible and highly efficient algorithm to compute bicliques. We first generalize the Motzkin-Straus formalism for computing the maximal clique from L1 constraint to Lp constraint, which enables us to provide a generalized Motzkin-Straus formalism for computing maximal-edge bicliques. By adjusting parameters, the algorithm can favor biclusters with more rows less columns, or vice verse, thus increasing the flexibility of the targeted biclusters. We then propose an algorithm to solve the generalized Motzkin-Straus optimization problem. The algorithm is provably convergent and has a computational complexity of O(/E/) where /E/ is the number of edges. Using this algorithm, we bicluster the yeast protein complex interaction network. We find that biclustering protein complexes at the protein level does not clearly reflect the functional linkage among protein complexes in many cases, while biclustering at protein domain level can reveal many underlying linkages. We show several new biologically significant results.
654543
A survey on wavelet applications in data mining
Recently there has been significant development in the use of wavelet methods in various data mining processes. However, there has been written no comprehensive survey available on the topic. The goal of this is paper to fill the void. First, the paper presents a high-level data-mining framework that reduces the overall process into smaller components. Then applications of wavelets for each component are reviewd. The paper concludes by discussing the impact of wavelets on data mining research and outlining potential future research directions and applications.
217251
On combining multiple clusterings
Many problems can be reduced to the problem of combining multiple clusterings. In this paper, we first summarize different application scenarios of combining multiple clusterings and provide a new perspective of viewing the problem as a categorical clustering problem. We then show the connections between various consensus and clustering criteria and discuss the complexity results of the problem. Finally we propose a new method to determine the final clustering. Experiments on kinship terms and clustering popular music from heterogeneous feature sets show the effectiveness of combining multiple clusterings.
206784011
The Relationships Among Various Nonnegative Matrix Factorization Methods for Clustering
The nonnegative matrix factorization (NMF) has been shown recently to be useful for clustering and various extensions and variations of NMF have been proposed recently. Despite significant research progress in this area, few attempts have been made to establish the connections between various factorization methods while highlighting their differences. In this paper we aim to provide a comprehensive study on matrix factorization for clustering. In particular, we present an overview and summary on various matrix factorization algorithms and theoretically analyze the relationships among them. Experiments are also conducted to empirically evaluate and compare various factorization methods. In addition, our study also answers several previously unaddressed yet important questions for matrix factorizations including the interpretation and normalization of cluster posterior and the benefits and evaluation of simultaneous clustering. We expect our study would provide good insights on matrix factorization research for clustering.
22622233
Using Uncorrelated Discriminant Analysis for Tissue Classification with Gene Expression Data
The classification of tissue samples based on gene expression data is an important problem in medical diagnosis of diseases such as cancer. In gene expression data, the number of genes is usually very high (in the thousands) compared to the number of data samples (in the tens or low hundreds); that is, the data dimension is large compared to the number of data points (such data is said to be undersampled). To cope with performance and accuracy problems associated with high dimensionality, it is commonplace to apply a preprocessing step that transforms the data to a space of significantly lower dimension with limited loss of the information present in the original data. Linear Discriminant Analysis (LDA) is a well-known technique for dimension reduction and feature extraction, but it is not applicable for undersampled data due to singularity problems associated with the matrices in the underlying representation. This paper presents a dimension reduction and feature extraction scheme, called Uncorrelated Linear Discriminant Analysis (ULDA), for undersampled problems and illustrates its utility on gene expression data. ULDA employs the Generalized Singular Value Decomposition method to handle undersampled data and the features that it produces in the transformed space are uncorrelated, which makes it attractive for gene expression data. The properties of ULDA are established rigorously and extensive experimental results on gene expression data are presented to illustrate its effectiveness in classifying tissue samples. These results provide a comparative study of various state-of-the-art classification methods on well-known gene expression data sets.
14562465
Bioinformatics on Embedded Systems: A Case Study of Computational Biology Applications on VLIW Architecture
Bioinformatics applications represent the increasingly important workloads. Their characteristics and implications on the underlying hardware design, however, are largely unknown. Currently, biological data processing ubiquitously relies on the high-end systems equipped with expensive, general-purpose processors. The future generation of bioinformatics requires the more flexible and cost-effective computing platforms to meet its rapidly growing market. The programmable, application-specific embedded systems appear to be an attractive solution in terms of easy of programming, design cost, power, portability and time-to-market. The first step towards such systems is to characterize bioinformatics applications on the target architecture. Such studies can help in understanding the design issues and the trade-offs in specializing hardware and software systems to meet the needs of bioinformatics market. This paper evaluates several representative bioinformatics tools on the VLIW based embedded systems. We investigate the basic characteristics of the benchmarks, impact of function units, the efficiency of VLIW execution, cache behavior and the impact of compiler optimizations. The architectural implications observed from this study can be applied to the design optimizations. To the best of our knowledge, this is one of the first such studies that have ever been attempted.
25228668
A joint estimation approach for two-tone image deblurring by blind deconvolution
A new statistical method is proposed for deblurring two-tone images, i.e., images with two unknown grey levels, that are blurred by an unknown linear filter. The key idea of the proposed method is to adjust a deblurring filter until its output becomes two tone. Two optimization criteria are proposed for the adjustment of the deblurring filter. A three-step iterative algorithm (TSIA) is also proposed to minimize the criteria. It is proven mathematically that by minimizing either of the criteria, the original (nonblurred) image, along with the blur filter, will be recovered uniquely (only with possible scale/shift ambiguities) at high SNR. The recovery is guaranteed not only for i.i.d. images but also for correlated and nonstationary images. It does not require a priori knowledge of the statistical parameters or the tone values of the original image; neither does it require a priori knowledge of the phase or other special information (e.g., FIR, symmetry, nonnegativity, etc.) about the blur filter. Numerical experiments are carried out to test the method on synthetic and real images.
2911701
Workload characterization of bioinformatics applications
The exponential growth in the amount of genomic information has spurred growing interest in large scale analysis of genetic data. Bioinformatics applications represent the increasingly important workloads. However, very few results on the behavior of these applications running on the state-of-the-art microprocessor and systems have been published. This paper proposes a suite of widely used bioinformatics applications and studies the execution characteristics of these benchmarks on a representative architecture-the Intel Pentium 4. To understand the impacts and implications of bioinformatics workloads on the microprocessor designs, we contrast the characteristics of bioinformatics workloads and the widely used SPEC 2000 integer benchmarks.
16509721
A location system using asynchronous distributed sensors
This paper describes a location system using an asynchronous distributed sensor network. The sensors' clocks operate independently and are not explicitly synchronized. The motion of the source, or the object, between two emitted pulses will cause the inter-arrival time of these two pulses at each sensor to vary. This inter-arrival time is a function of the source location and motion and is independent of the clock offsets among sensors. Thus, the independently calculated time-difference-of-arrival (TDOA) of successive pulses at each sensor provides a reliable source of information to estimate the source position as well as its motion. The Cramer-Rao lower bound (CRLB) is derived to assess the performance of the proposed method and to show that its performance can approach that of a synchronous network given a sufficient number of sensors and moderate source movement. Some sub-optimal but effective source trajectory tracking methods are proposed which further relax the assumption of source motion between consecutive pulses. The simulation results show that the proposed estimation and tracking methods are quite good.
10443056
A large, fast instruction window for tolerating cache misses
Instruction window size is an important design parameter for many modern processors. Large instruction windows offer the potential advantage of exposing large amounts of instruction level parallelism. Unfortunately naively scaling conventional window designs can significantly degrade clock cycle time, undermining the benefits of increased parallelism.This paper presents a new instruction window design targeted at achieving the latency tolerance of large windows with the clock cycle time of small windows. The key observation is that instructions dependent on a long latency operation (e.g., cache miss) cannot execute until that source operation completes. These instructions are moved out of the conventional, small, issue queue to a much larger waiting instruction buffer (WIB). When the long latency operation completes, the instructions are reinserted into the issue queue. In this paper, we focus specifically on load cache misses and their dependent instructions. Simulations reveal that, for an 8-way processor, a 2K-entry WIB with a 32-entry issue queue can achieve speedups of 20%, 84%, and 50% over a conventional 32-entry issue queue for a subset of the SPEC CINT2000, SPEC CFP2000, and Olden benchmarks, respectively.