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
1764796
Mining Approximate Order Preserving Clusters in the Presence of Noise
Subspace clustering has attracted great attention due to its capability of finding salient patterns in high dimensional data. Order preserving subspace clusters have been proven to be important in high throughput gene expression analysis, since functionally related genes are often co-expressed under a set of experimental conditions. Such co-expression patterns can be represented by consistent orderings of attributes. Existing order preserving cluster models require all objects in a cluster have identical attribute order without deviation. However, real data are noisy due to measurement technology limitation and experimental variability which prohibits these strict models from revealing true clusters corrupted by noise. In this paper, we study the problem of revealing the order preserving clusters in the presence of noise. We propose a noise-tolerant model called approximate order preserving cluster (AOPC). Instead of requiring all objects in a cluster have identical attribute order, we require that (1) at least a certain fraction of the objects have identical attribute order; (2) other objects in the cluster may deviate from the consensus order by up to a certain fraction of attributes. We also propose an algorithm to mine AOPC. Experiments on gene expression data demonstrate the efficiency and effectiveness of our algorithm.
7919807
Fastanova: an efficient algorithm for genome-wide association study
Studying the association between quantitative phenotype (such as height or weight) and single nucleotide polymorphisms (SNPs) is an important problem in biology. To understand underlying mechanisms of complex phenotypes, it is often necessary to consider joint genetic effects across multiple SNPs. ANOVA (analysis of variance) test is routinely used in association study. Important findings from studying gene-gene (SNP-pair) interactions are appearing in the literature. However, the number of SNPs can be up to millions. Evaluating joint effects of SNPs is a challenging task even for SNP-pairs. Moreover, with large number of SNPs correlated, permutation procedure is preferred over simple Bonferroni correction for properly controlling family-wise error rate and retaining mapping power, which dramatically increases the computational cost of association study.
 In this paper, we study the problem of finding SNP-pairs that have significant associations with a given quantitative phenotype. We propose an efficient algorithm, FastANOVA, for performing ANOVA tests on SNP-pairs in a batch mode, which also supports large permutation test. We derive an upper bound of SNP-pair ANOVA test, which can be expressed as the sum of two terms. The first term is based on single-SNP ANOVA test. The second term is based on the SNPs and independent of any phenotype permutation. Furthermore, SNP-pairs can be organized into groups, each of which shares a common upper bound. This allows for maximum reuse of intermediate computation, efficient upper bound estimation, and effective SNP-pair pruning. Consequently, FastANOVA only needs to perform the ANOVA test on a small number of candidate SNP-pairs without the risk of missing any significant ones. Extensive experiments demonstrate that FastANOVA is orders of magnitude faster than the brute-force implementation of ANOVA tests on all SNP pairs.
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.
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.
917867
Graph Database Indexing Using Structured Graph Decomposition
We introduce a novel method of indexing graph databases in order to facilitate subgraph isomorphism and similarity queries. The index is comprised of two major data structures. The primary structure is a directed acyclic graph which contains a node for each of the unique, induced subgraphs of the database graphs. The secondary structure is a hash table which cross-indexes each subgraph for fast isomorphic lookup. In order to create a hash key independent of isomorphism, we utilize a code-based canonical representation of adjacency matrices, which we have further refined to improve computation speed. We validate the concept by demonstrating its effectiveness in answering queries for two practical datasets. Our experiments show that for subgraph isomorphism queries, our method outperforms existing methods by more than an order of magnitude.
9041413
Structure-based graph distance measures of high degree of precision
In recent years, evaluating graph distance has become more and more important in a variety of real applications and many graph distance measures have been proposed. Among all of those measures, structure-based graph distance measures have become the research focus due to their independence of the definition of cost functions. However, existing structure-based graph distance measures have low degree of precision because only node and edge information of graphs are employed in these measures. To improve the precision of graph distance measures, we define substructure abundance vector (SAV) to capture more substructure information of a graph. Furthermore, based on SAV, we propose unified graph distance measures which are generalization of the existing structure-based graph distance measures. In general, the unified graph distance measures can evaluate graph distance in much finer grain. We also show that unified graph distance measures based on occurrence mapping and some of their variants are metrics. Finally, we apply the unified graph distance metric and its variants to the population evolution analysis and construct distance graphs of marker networks in three populations, which reflect the single nucleotide polymorphism (SNP) linkage disequilibrium (LD) differences among these populations.
9921122
Probabilistic Skyline Operator over Sliding Windows
Skyline computation has many applications including multi-criteria decision making. In this paper, we study the problem of efficient processing of continuous skyline queries over sliding windows on uncertain data elements regarding given probability thresholds. We first characterize what kind of elements we need to keep in our query computation. Then we show the size of dynamically maintained candidate set and the size of skyline. We develop novel, efficient techniques to process a continuous, probabilistic skyline query. Finally, we extend our techniques to the applications where multiple probability thresholds are given or we want to retrieve "top-k" skyline data objects. Our extensive experiments demonstrate that the proposed techniques are very efficient and handle a high-speed data stream in real time.
5600324
A prediction algorithm for time series based on adaptive model selection
HMM (Hidden Markov model) has been used successfully to analyze various types of time series. To fit time series with HMM, the number of hidden states should be determined before learning other parameters, since it has great impact on the complexity and precision of the fitting HMM. However this becomes too difficult when there is not enough prior knowledge about the observed series, which will lead to the increasing mean error in prediction process. To overcome this shortcoming, a prediction algorithm PAAMS for time series based on adaptive model selection is proposed. In PAAMS, the model can be dynamically updated when the prediction mean error increases. During the update process, an automatic model selection method AMSA is applied to get the best hidden state number and other model parameters. The proposed method AMSA is based on clustering, in which the number of hidden states is considered as the number of clusters. The feasibility and effectiveness of proposed prediction algorithm are explained. Experiments on American stock price data set are done and the results show that the PAAMS algorithm can achieve higher precision than that of previous study on the same data sets based on fixed model techniques.
6315207
Target detection and identification using canonical correlation analysis and subspace partitioning
We present a data-driven approach for target detection and identification based on a linear mixture model. Our aim is to determine the existence of certain targets in a mixture without specific information on the targets or the background, and to identify the targets from a given library. We use the maximum canonical correlation between the target set and the observations as the detection score, and use coefficients of the canonical vector to identify the indices of the present components from the given target library. The performance of the detector is enhanced using subspace partitioning on the target library. Both simulation and experimental results are presented to demonstrate the effectiveness of the proposed method in Raman spectroscopy for detection of surface-deposited chemical agents.
12596805
FMC: An Approach for Privacy Preserving OLAP
To preserve private information while providing thorough analysis is one of the significant issues in OLAP systems. One of the challenges in it is to prevent inferring the sensitive value through the more aggregated non-sensitive data. This paper presents a novel algorithm FMC to eliminate the inference problem by hiding additional data besides the sensitive information itself, and proves that this additional information is both necessary and sufficient. Thus, this approach could provide as much information as possible for users, as well as preserve the security. The strategy does not impact on the online performance of the OLAP system. Systematic analysis and experimental comparison are provided to show the effectiveness and feasibility of FMC.