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.
9813108
CoFD : An Algorithm for Non-distance Based Clustering in High Dimensional Spaces
The clustering problem, which aims at identifying the distribution of patterns and intrinsic correlations in large data sets by partitioning the data points into similarity clusters, has been widely studied. Traditional clustering algorithms use distance functions to measure similarity and are not suitable for high dimensional spaces. In this paper, we propose CoFD algorithm, which is a non-distance based clustering algorithm for high dimensional spaces. Based on the maximum likelihood principle, CoFD is to optimize parameters to maximize the likelihood between data points and the model generated by the parameters. Experimental results on both synthetic data sets and a real data set show the efficiency and effectiveness of CoFD.
14819927
Gene functional classification by semi-supervised learning from heterogeneous data
Gene function discovery is an important and interesting problem in computational analysis of microarray data. In this paper, we investigate the use of a semi-supervised learning algorithm for inferring gene functional classifications from heterogeneous data set consisting of DNA microarray expression measurements and phylogenetic profiles from whole-genome sequence compassions. The semisupervised learning approach aims at minimizing the disagreement between individual models built from each separate information source by employing a co-updating method and making use of both labeled and unlabeled data. Our results suggest that the semisupervised approach could be used for gene functional classification. The data sets and the program code used for the experiments can be accessed from our webpage.
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.
8864863
Integrating Features from Different Sources for Music Information Retrieval
Efficient and intelligent music information retrieval is a very important topic of the 21st century. With the ultimate goal of building personal music information retrieval systems, this paper studies the problem of identifying "similar" artists using both lyrics and acoustic data. In this paper, we present a clustering algorithm that integrates features from both sources to perform bimodal learning. The algorithm is tested on a data set consisting of 570 songs from 53 albums of 41 artists using artist similarity provided by All Music Guide. Experimental results show that the accuracy of artist similarity classifiers can be significantly improved and that artist similarity can be efficiently identified.
1750917
A general model for clustering binary data
Clustering is the problem of identifying the distribution of patterns and intrinsic correlations in large data sets by partitioning the data points into similarity classes. This paper studies the problem of clustering binary data. This is the case for market basket datasets where the transactions contain items and for document datasets where the documents contain "bag of words". The contribution of the paper is three-fold. First a general binary data clustering model is presented. The model treats the data and features equally, based on their symmetric association relations, and explicitly describes the data assignments as well as feature assignments. We characterize several variations with different optimization procedures for the general model. Second, we also establish the connections between our clustering model with other existing clustering methods. Third, we also discuss the problem for determining the number of clusters for binary clustering. Experimental results show the effectiveness of the proposed clustering model.
2949388
Optimal k-Anonymity with Flexible Generalization Schemes through Bottom-up Searching
In recent years, a major thread of research on k-anonymity has focused on developing more flexible generalization schemes that produce higher-quality datasets. In this paper we introduce three new generalization schemes that improve on existing schemes, as well as algorithms enumerating valid generalizations in these schemes. We also introduce a taxonomy for generalization schemes and a new cost metric for measuring information loss. We present a bottom-up search strategy for finding optimal anonymizations. This strategy works particularly well when the value of k is small. We show the feasibility of our approach through experiments on real census data
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.
20811204
Asymptotic analysis of a fast algorithm for efficient multiple frequency estimation
Based on an asymptotic analysis of the contraction mapping (CM) method of Li and Kedem (1993), a bandwidth shrinkage rule is proposed for fast and accurate estimation of the frequencies of multiple sinusoids from noisy measurements. The CM frequency estimates are defined as the fixed points of a contractive mapping formed by the lag-one autocorrelation coefficient calculated from the output. of a parametric filter applied to the observed time series. With bandwidth parameters judiciously chosen according to the asymptotic analysis, the algorithm is shown to be able to accommodate possibly poor initial values of precision O(n/sup -1/3/) and converge to a final estimate whose accuracy is arbitrarily close to O(n/sup -3/2/), the optimal error rate for frequency estimation under the Gaussian assumption. The total computational complexity of the algorithm is shown to be O(n log n), which is comparable to that of n-point fast Fourier transform (FFT). A novelty in the asymptotic analysis is that it accommodates closely spaced frequencies by allowing not only the filter bandwidth but also the frequency separation to be functions of the sample size n. This enables an assessment of the accuracy of the frequency estimates for given bandwidths and initial values in situations where some or all of the frequencies are close to each other.
2949246
t-Closeness: Privacy Beyond k-Anonymity and l-Diversity
The k-anonymity privacy requirement for publishing microdata requires that each equivalence class (i.e., a set of records that are indistinguishable from each other with respect to certain "identifying" attributes) contains at least k records. Recently, several authors have recognized that k-anonymity cannot prevent attribute disclosure. The notion of l-diversity has been proposed to address this; l-diversity requires that each equivalence class has at least l well-represented values for each sensitive attribute. In this paper we show that l-diversity has a number of limitations. In particular, it is neither necessary nor sufficient to prevent attribute disclosure. We propose a novel privacy notion called t-closeness, which requires that the distribution of a sensitive attribute in any equivalence class is close to the distribution of the attribute in the overall table (i.e., the distance between the two distributions should be no more than a threshold t). We choose to use the earth mover distance measure for our t-closeness requirement. We discuss the rationale for t-closeness and illustrate its advantages through examples and experiments.