2172280
TEAM: efficient two-locus epistasis tests in human genome-wide association study
As a promising tool for identifying genetic markers underlying phenotypic differences, genome-wide association study (GWAS) has been extensively investigated in recent years. In GWAS, detecting epistasis (or gene–gene interaction) is preferable over single locus study since many diseases are known to be complex traits. A brute force search is infeasible for epistasis detection in the genome-wide scale because of the intensive computational burden. Existing epistasis detection algorithms are designed for dataset consisting of homozygous markers and small sample size. In human study, however, the genotype may be heterozygous, and number of individuals can be up to thousands. Thus, existing methods are not readily applicable to human datasets. In this article, we propose an efficient algorithm, TEAM, which significantly speeds up epistasis detection for human GWAS. Our algorithm is exhaustive, i.e. it does not ignore any epistatic interaction. Utilizing the minimum spanning tree structure, the algorithm incrementally updates the contingency tables for epistatic tests without scanning all individuals. Our algorithm has broader applicability and is more efficient than existing methods for large sample study. It supports any statistical test that is based on contingency tables, and enables both family-wise error rate and false discovery rate controlling. Extensive experiments show that our algorithm only needs to examine a small portion of the individuals to update the contingency tables, and it achieves at least an order of magnitude speed up over the brute force approach. Contact: xiang@cs.unc.edu
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
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.
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.
5517318
Power Control for Distributed MAC Protocols in Wireless Ad Hoc Networks
In centralized wireless networks, reducing the transmission power normally leads to higher network transport throughput. In this paper, we investigate power control in a different scenario, where the network adopts distributed MAC layer coordination mechanisms. We first consider widely adopted RTS/CTS based MAC protocols. We show that an optimal power control protocol should use higher transmission power than the "just enough" power in order to improve spatial utilization. The optimal protocol has a minimal transmission floor area of Theta(dijdmax), where dmax is the maximal transmission range and dij is the link length. This surprisingly implies that if a long link is broken into several short links, then the sum of the transmission floors reserved by the short links is still comparable to that reserved by the long link. Thus, using short links does not necessarily lead to higher throughput. Another consequence of this is that, with the optimal RTS/CTS based MAC, rate control can at best provide a factor of 2 improvement in transport throughput. We then extend our results to other distributed MAC protocols which uses physical carrier sensing or busy-tone as the control signal. Our simulation results show that the optimal power controlled scheme outperforms other popular MAC layer power control protocols.
90043
A new approach to design robust backstepping controller for MIMO nonlinear systems with input unmodeled dynamics
In this paper, a new scheme inspired by the idea of decentralized control methodology is proposed to design output feedback controllers for a class of MIMO nonlinear systems with input unmodeled dynamics. With dynamic normalization and backstepping approach, the destabilizing effects of unmodeled dynamics depending on inputs are compensated and global uniform boundedness of all the signals in the closed loop system is established for sufficiently weak input unmodeled dynamics.
7588231
Efficient Algorithms for Mining Maximal Frequent Concatenate Sequences in Biological Datasets
The growth of bioinformatics has resulted in datasets with new characteristics. The DNA sequences typically contain a large number of items. From them biologists assemble a whole genome of species based on frequent concatenate sequences, which ordinarily have hundreds of items. Such datasets pose a great challenge for existing frequent pattern discovery algorithms. Almost all of them are Apriori-like and so have an exponential dependence on the average sequence length. PrefixSpan is the most efficient algorithm, which presented the projection-based sequential pattern-growth approach. However it grows sequential patterns by exploring length-1 frequent patterns and so is not suitable for biological dataset with long frequent concatenate sequences. In this paper, we propose two novel algorithms, called MacosFSpan and MacosVSpan, to mine maximal frequent concatenate sequences. They are specially designed to handle datasets having long frequent concatenate sequences. Our performance study shows that MacosFSpan outperforms the traditional methods with length-1 sequences exploration and MacosVSpan is more efficient than Macos VSpan
47035961
Efficient Algorithms for Node Disjoint Subgraph Homeomorphism Determination
Recently, great efforts have been dedicated to researches on the management of large-scale graph-based data, where node disjoint subgraph homeomorphism relation between graphs has been shown to be more suitable than (sub)graph isomorphism in many cases, especially in those cases where node skipping and node mismatching are desired. However, no efficient algorithm for node disjoint subgraph homeomorphism determination (ndSHD) has been available. In this paper, we propose two computationally efficient ndSHD algorithms based on state spaces searching with backtracking, which employ many heuristics to prune the search spaces. Experimental results on synthetic data sets show that the proposed algorithms are efficient, require relatively little time in most of cases, can scale to large or dense graphs, and can accommodate to more complex fuzzy matching cases.
30440322
A Quantitative Study of Mobility Impact for Real-Time Services on a Wi-Fi Multi-hop Network
In this paper, we analyze the performance of mobile real time services in a large-scale IEEE 802.11 multi-hop network. We present our field measurements with discussion of performance bottlenecks for VoIP services under mobile scenarios. We utilized our test bed which is located in Nebraska and supported by the University of Nebraska-Lincoln (UNL), US Federal Railroads Administrations (FRA), and major US railroad companies. Our UNL-FRA test bed consists of 8 outdoor access point towers, which are deployed along 3.5 mile of BNSF railroad. Passive measurement approaches are taken to ensure the integrity of collected data and multi-layer stream based packet analyzer has been implemented to provide a global view of the entire performance of the monitored network from the physical layer to the application layer. Based on our analysis of collected data, we conclude that in a typical outdoor 802.11 environment similar to our UNL-FRA test bed, uncertain handoff latencies and lack of Quality of Service guarantee are main performance bottlenecks for real-time applications. Furthermore, we discuss the enhancement strategies to support mobility in high-speed railway networks. We believe our work is one of the initial efforts in wireless mobile network field measurement in terms of scale, methodology, and analysis.