697583
Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows
MOTIVATION
Typical high-throughput genotyping techniques produce numerous missing calls that confound subsequent analyses, such as disease association studies. Common remedies for this problem include removing affected markers and/or samples or, otherwise, imputing the missing data. On small marker sets imputation is frequently based on a vote of the K-nearest-neighbor (KNN) haplotypes, but this technique is neither practical nor justifiable for large datasets.


RESULTS
We describe a data structure that supports efficient KNN queries over arbitrarily sized, sliding haplotype windows, and evaluate its use for genotype imputation. The performance of our method enables exhaustive exploration over all window sizes and known sites in large (150K, 8.3M) SNP panels. We also compare the accuracy and performance of our methods with competing imputation approaches.


AVAILABILITY
A free open source software package, NPUTE, is available at http://compgen.unc.edu/software, for non-commercial uses.
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.
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
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.
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
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
6717365
Efficient approximate entity extraction with edit distance constraints
Named entity recognition aims at extracting named entities from unstructured text. A recent trend of named entity recognition is finding approximate matches in the text with respect to a large dictionary of known entities, as the domain knowledge encoded in the dictionary helps to improve the extraction performance.
 In this paper, we study the problem of approximate dictionary matching with edit distance constraints. Compared to existing studies using token-based similarity constraints, our problem definition enables us to capture typographical or orthographical errors, both of which are common in entity extraction tasks yet may be missed by token-based similarity constraints. Our problem is technically challenging as existing approaches based on q-gram filtering have poor performance due to the existence of many short entities in the dictionary. Our proposed solution is based on an improved neighborhood generation method employing novel partitioning and prefix pruning techniques. We also propose an efficient document processing algorithm that minimizes unnecessary comparisons and enumerations and hence achieves good scalability. We have conducted extensive experiments on several publicly available named entity recognition datasets. The proposed algorithm outperforms alternative approaches by up to an order of magnitude.
15939515
GraphMiner: a structural pattern-mining system for large disk-based graph databases and its applications
Mining frequent structural patterns from graph databases is an important research problem with broad applications. Recently, we developed an effective index structure, ADI, and efficient algorithms for mining frequent patterns from large, disk-based graph databases [5], as well as constraint-based mining techniques. The techniques have been integrated into a research prototype system--- GraphMiner. In this paper, we describe a demo of GraphMiner which showcases the technical details of the index structure and the mining algorithms including their efficient implementation, the mining performance and the comparison with some state-of-the-art methods, the constraint-based graph-pattern mining techniques and the procedure of constrained graph mining, as well as mining real data sets in novel applications.
7316344
CLINCH: Clustering Incomplete High-Dimensional Data for Data Mining Application
Clustering is a common technique in data mining to discover hidden patterns from massive datasets. With the development of privacy-maintaining data mining application, clustering incomplete high-dimensional data has becoming more and more useful. Motivated by these limits, we develop a novel algorithm CLINCH, which could produce fine clusters on incomplete high-dimensional data space. To handle missing attributes, CLINCH employs a prediction method that can be more precise than traditional techniques. On the other hand, we also introduce an efficient way in which dimensions are processed one by one to attack the “curse of dimensionality”. Experiments show that our algorithm not only outperforms many existing high-dimensional clustering algorithms in scalability and efficiency, but also produces precise results.
2629783
Optimal Rate-Based Image Transmissions via Multiple Paths in Wireless Sensor Network
Many sensor applications such as monitoring and surveillance may require image sensor array to conduct collaborative image transmissions in wireless sensor network (WSN). The large size image transmission in WSN is a bottleneck due to the limited energy resources. In this paper, we propose an optimal scheme for image sensors to utilize inter-sensor correlations to decide transmission patterns based on a multi-level rate-oriented routing (MLRR) routing scheme, which achieves high energy efficiencies and longer network lifetime. This optimization scheme allows each image sensor to transmit optimal fractions of the overlapped images through appropriate multiple rate-oriented routing paths. The simulation results by using GA algorithm show that the proposed image transmission scheme can achieve considerable gains in terms of the WSN energy efficiency and network lifetime extension.