52059378
A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression
This paper studies the problem of building multiclass classifiers for tissue classification based on gene expression. The recent development of microarray technologies has enabled biologists to quantify gene expression of tens of thousands of genes in a single experiment. Biologists have begun collecting gene expression for a large number of samples. One of the urgent issues in the use of microarray data is to develop methods for characterizing samples based on their gene expression. The most basic step in the research direction is binary sample classification, which has been studied extensively over the past few years. This paper investigates the next step-multiclass classification of samples based on gene expression. The characteristics of expression data (e.g. large number of genes with small sample size) makes the classification problem more challenging. The process of building multiclass classifiers is divided into two components: (i) selection of the features (i.e. genes) to be used for training and testing and (ii) selection of the classification method. This paper compares various feature selection methods as well as various state-of-the-art classification methods on various multiclass gene expression datasets. Our study indicates that multiclass classification problem is much more difficult than the binary one for the gene expression datasets. The difficulty lies in the fact that the data are of high dimensionality and that the sample size is small. The classification accuracy appears to degrade very rapidly as the number of classes increases. In particular, the accuracy was very low regardless of the choices of the methods for large-class datasets (e.g. NCI60 and GCM). While increasing the number of samples is a plausible solution to the problem of accuracy degradation, it is important to develop algorithms that are able to analyze effectively multiple-class expression data for these special datasets.
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.
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.
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.
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.
2644770
Pulse: A Dynamic Deadlock Detection Mechanism Using Speculative Execution
Deadlock can occur wherever multiple processes interact. Most existing static and dynamic deadlock detection tools focus on simple types of deadlock, such as those caused by incorrect ordering of lock acquisitions. In this paper, we propose Pulse, a novel operating system mechanism that dynamically detects various types of deadlock in application programs. Pulse runs as a system daemon. Periodically, it scans the system for processes that have been blocked for a long time (e.g., waiting on I/O events). To determine if these processes are deadlocked, Pulse speculatively executes them ahead to discover their dependences. Based on this information, it constructs a general resource graph and detects deadlock by checking if the graph contains cycles. The ability to look into the future allows Pulse to detect deadlocks involving consumable resources, such as synchronization semaphores and pipes, which no existing tools can detect. We evaluate Pulse by showing that it can detect deadlocks in the classical dining-philosophers and smokers problems. Furthermore, we show that Pulse can detect a well-known deadlock scenario, which is widely referred to as a denial-of-service vulnerability, in the Apache web server. Our results show that Pulse can detect all these deadlocks within three seconds, and it introduces little performance overhead to normal applications that do not deadlock.
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.
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.
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
3381503
Finite-alphabet information and multivariate blind deconvolution and identification of linear systems
This article addresses the problem of estimating a multivariate linear system from its output when the input is an unobservable sequence of random vectors with finite-alphabet distribution. By explicitly utilizing the finite-alphabet property, an estimation method is proposed under the traditional inverse filtering paradigm as a generalization of a univariate method that has been studied previously. Identifiability of multivariate systems by the proposed method is proved mathematically under very mild conditions that can be satisfied even if the input is nonstationary and has both cross-channel and serial statistical dependencies. Statistical super-efficiency in estimating both parametric and nonparametric systems is also established for an alphabet-based cost function.