17437497
Enhanced biclustering on expression data
Microarrays are one of the latest breakthroughs in experimental molecular biology, which provide a powerful tool by which the expression patterns of thousands of genes can be monitored simultaneously and are already producing huge amount of valuable data. The concept of bicluster was introduced by Cheng and Church (2000) to capture the coherence of a subset of genes and a subset of conditions. A set of heuristic algorithms were also designed to either find one bicluster or a set of biclusters, which consist of iterations of masking null values and discovered biclusters, coarse and fine node deletion, node addition, and the inclusion of inverted data. These heuristics inevitably suffer from some serious drawback. The masking of null values and discovered biclusters with random numbers may result in the phenomenon of random interference which in turn impacts the discovery of high quality biclusters. To address this issue and to further accelerate the biclustering process, we generalize the model of bicluster to incorporate null values and propose a probabilistic algorithm (FLOC) that can discover a set of k possibly overlapping biclusters simultaneously. Furthermore, this algorithm can easily be extended to support additional features that suit different requirements at virtually little cost. Experimental study on the yeast gene expression data shows that the FLOC algorithm can offer substantial improvements over the previously proposed algorithm.
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.
2548187
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 rep and max 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
5788516
Efficient genome ancestry inference in complex pedigrees with inbreeding
Motivation: High-density SNP data of model animal resources provides opportunities for fine-resolution genetic variation studies. These genetic resources are generated through a variety of breeding schemes that involve multiple generations of matings derived from a set of founder animals. In this article, we investigate the problem of inferring the most probable ancestry of resulting genotypes, given a set of founder genotypes. Due to computational difficulty, existing methods either handle only small pedigree data or disregard the pedigree structure. However, large pedigrees of model animal resources often contain repetitive substructures that can be utilized in accelerating computation. Results: We present an accurate and efficient method that can accept complex pedigrees with inbreeding in inferring genome ancestry. Inbreeding is a commonly used process in generating genetically diverse and reproducible animals. It is often carried out for many generations and can account for most of the computational complexity in real-world model animal pedigrees. Our method builds a hidden Markov model that derives the ancestry probabilities through inbreeding process without explicit modeling in every generation. The ancestry inference is accurate and fast, independent of the number of generations, for model animal resources such as the Collaborative Cross (CC). Experiments on both simulated and real CC data demonstrate that our method offers comparable accuracy to those methods that build an explicit model of the entire pedigree, but much better scalability with respect to the pedigree size. Contact: weiwang@cs.unc.edu
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.
7408751
Quantitative Association Analysis Using Tree Hierarchies
Association analysis arises in many important applications such as bioinformatics and business intelligence. Given a large collection of measurements over a set of samples, association analysis aims to find dependencies of target variables to subsets of measurements. Most previous algorithms adopt a two-stage approach; they first group samples based on the similarity in the subset of measurements, and then they examine the association between these groups and the specified target variables without considering the inter-group similarities or alternative groupings. This can lead to cases where the strength of association depends significantly on arbitrary clustering choices. In this paper, we propose a tree-based method for quantitative association analysis. Tree hierarchies derived from sample similarities represent many possible sample groupings. They also provide a natural way to incorporate domain knowledge such as ontologies and to identify and remove outliers. Given a tree hierarchy, our association analysis evaluates all possible groupings and selects the one with strongest association to the target variable. We introduce an efficient algorithm, TreeQA, to systematically explore the search-space of all possible groupings in a set of input trees, with integrated permutation tests. Experimental results show that TreeQA is able to handlelarge-scale association analysis very efficiently and is more effective and robust in association analysis than previous methods.
207162632
Utility-based anonymization for privacy preservation with less information loss
Privacy becomes a more and more serious concern in applications involving microdata. Recently, efficient anonymization has attracted much research work. Most of the previous methods use global recoding, which maps the domains of the quasi-identifier attributes to generalized or changed values. However, global recoding may not always achieve effective anonymization in terms of discernability and query answering accuracy using the anonymized data. Moreover, anonymized data is often used for analysis. As well accepted in many analytical applications, different attributes in a data set may have different utility in the analysis. The utility of attributes has not been considered in the previous methods.
 In this paper, we study the problem of utility-based anonymization. First, we propose a simple framework to specify utility of attributes. The framework covers both numeric and categorical data. Second, we develop two simple yet efficient heuristic local recoding methods for utility-based anonymization. Our extensive performance study using both real data sets and synthetic data sets shows that our methods outperform the state-of-the-art multidimensional global recoding methods in both discernability and query answering accuracy. Furthermore, our utility-based method can boost the quality of analysis using the anonymized data.
14135377
Utility-based anonymization using local recoding
Privacy becomes a more and more serious concern in applications involving microdata. Recently, efficient anonymization has attracted much research work. Most of the previous methods use global recoding, which maps the domains of the quasi-identifier attributes to generalized or changed values. However, global recoding may not always achieve effective anonymization in terms of discernability and query answering accuracy using the anonymized data. Moreover, anonymized data is often for analysis. As well accepted in many analytical applications, different attributes in a data set may have different utility in the analysis. The utility of attributes has not been considered in the previous methods.In this paper, we study the problem of utility-based anonymization. First, we propose a simple framework to specify utility of attributes. The framework covers both numeric and categorical data. Second, we develop two simple yet efficient heuristic local recoding methods for utility-based anonymization. Our extensive performance study using both real data sets and synthetic data sets shows that our methods outperform the state-of-the-art multidimensional global recoding methods in both discernability and query answering accuracy. Furthermore, our utility-based method can boost the quality of analysis using the anonymized data.
20581508
Scheduling sensor activity for information coverage of discrete targets in sensor networks
In this paper, we study the problem of scheduling sensor activity to cover a set of targets with known locations such that all targets can be monitored all the time and the network can operate as long as possible. A solution to this scheduling problem is to partition all sensors into some sensor covers such that each cover can monitor all targets and the covers are activated sequentially. In this paper, we propose to provide information coverage instead of the conventional sensing disk coverage for target. The notion of information coverage is based on estimation theory to exploit the collaborative nature of geographically distributed sensors. Due to the use of information coverage, a target that is not within the sensing disk of any single sensor can still be considered to be monitored (information covered) by the cooperation of more than one sensor. This change of the problem settings complicates the solutions compared to that by using a disk coverage model. We first define the target information coverage (TIC) problem and prove its NP-completeness. We then propose a heuristic to approximately solve our problem. Simulation results show that our heuristic is better than an existing algorithm and is close to the upper bound when only the sensing disk coverage model is used. Furthermore, simulation results also show that the network lifetime can be significantly improved by using the notion of information coverage compared with that by using the conventional definition of sensing disk coverage. Copyright © 2008 John Wiley & Sons, Ltd.
6659460
Generalized Riordan arrays
In this paper, we generalize the concept of Riordan array. A generalized Riordan array with respect to c"n is an infinite, lower triangular array determined by the pair (g(t),f(t)) and has the generic element d"n","k=[t^n/c"n]g(t)(f(t))^k/c"k, where c"n is a fixed sequence of non-zero constants with c"0=1. We demonstrate that the generalized Riordan arrays have similar properties to those of the classical Riordan arrays. Based on the definition, the iteration matrices related to the Bell polynomials are special cases of the generalized Riordan arrays and the set of iteration matrices is a subgroup of the Riordan group. We also study the relationships between the generalized Riordan arrays and the Sheffer sequences and show that the Riordan group and the group of Sheffer sequences are isomorphic. From the Sheffer sequences, many special Riordan arrays are obtained. Additionally, we investigate the recurrence relations satisfied by the elements of the Riordan arrays. Based on one of the recurrences, some matrix factorizations satisfied by the Riordan arrays are presented. Finally, we give two applications of the Riordan arrays, including the inverse relations problem and the connection constants problem.
24887227
Cross-layer routing optimization in multirate wireless sensor networks for distributed source coding based applications
The advancement in distributed source coding (DSC) for mission-driven wireless sensor networks (WSNs) has opened a new vista for its wide applications in multiple correlated sensor networks such as real time target tracking and environment monitoring. The features of the DSC applications offer many potential opportunities for sensor networks to utilize multirate transmissions for network performance enhancement. In this paper, we propose a methodology for cross-layer optimization between routing and DSC in WSNs, and we introduce a multirate based routing scheme for mission-driven DSC applications that can considerably extend network lifetime. The proposed scheme adopts the rate assignment based on residual energy and employs a joint rate and energy scheduling mechanism to meet the end-to-end transmission rate demand, information precision requirement, and energy constraints in the networks adopting DSC. This approach is different from the traditional multirate research in link adaptation, where the focus was to increase channel throughput based on rate adaptation from variable channel conditions. The objective of this work is not to utilize multirate for increasing channel throughput, but to exploit multirate capability for routing optimization in DSC based applications with consideration for energy consumption. We also introduce the concept of "Energy Usage Scheduling (EUS)" to optimize the energy usage based on the rate constraints and DSC application needs. Simulation results show that the proposed scheme can achieve a significantly longer network lifetime than that reported in the literature.