7426538
Biclustering in gene expression data by tendency
The advent of DNA microarray technologies has revolutionized the experimental study of gene expression. Clustering is the most popular approach of analyzing gene expression data and has indeed proven to be successful in many applications. Our work focuses on discovering a subset of genes which exhibit similar expression patterns along a subset of conditions in the gene expression matrix. Specifically, we are looking for the order preserving clusters (OP-cluster), in each of which a subset of genes induce a similar linear ordering along a subset of conditions. The pioneering work of the OPSM model, which enforces the strict order shared by the genes in a cluster, is included in our model as a special case. Our model is more robust than OPSM because similarly expressed conditions are allowed to form order equivalent groups and no restriction is placed on the order within a group. Guided by our model, we design and implement a deterministic algorithm, namely OPC-tree, to discover OP-clusters. Experimental study on two real datasets demonstrates the effectiveness of the algorithm in the application of tissue classification and cell cycle identification. In addition, a large percentage of OP-clusters exhibit significant enrichment of one or more function categories, which implies that OP-clusters indeed carry significant biological relevance.
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
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
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.
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.
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.
3416923
Efficient Computation of the Skyline Cube
Skyline has been proposed as an important operator for multi-criteria decision making, data mining and visualization, and user-preference queries. In this paper. we consider the problem of efficiently computing a SKYCUBE, which consists of skylines of all possible non-empty subsets of a given set of dimensions. While existing skyline computation algorithms can be immediately extended to computing each skyline query independently, such "shared-nothing" algorithms are inefficient. We develop several computation sharing strategies based on effectively identifying the computation dependencies among multiple related skyline queries. Based on these sharing strategies, two novel algorithms, Bottom-Up and Top-Down algorithms, are proposed to compute SKYCUBE efficiently. Finally, our extensive performance evaluations confirm the effectiveness of the sharing strategies. It is shown that new algorithms significantly outperform the naive ones.
19790030
Extracting frequent connected subgraphs from large graph sets
Mining frequent patterns from datasets is one of the key success of data mining research. Currently, most of the studies focus on the data sets in which the elements are independent, such as the items in the marketing basket. However, the objects in the real world often have close relationship with each other. How to extract frequent patterns from these relations is the objective of this paper. The authors use graphs to model the relations, and select a simple type for analysis. Combining the graph theory and algorithms to generate frequent patterns, a new algorithm called Topology, which can mine these graphs efficiently, has been proposed. The performance of the algorithm is evaluated by doing experiments with synthetic datasets and real data. The experimental results show that Topology can do the job well. At the end of this paper, the potential improvement is mentioned.
518796
Performance Analysis of Multi-hop IEEE 802.11 DCF Backhaul Networks
Because of the wide deployment of 802.11 equipments in the past decade, current applications are not limited anymore to only single access points (AP) deployments for indoor usage, but have been extended to multi-hop networks to fulfill the need of high speed connectivity in mobile environments, where the analysis of multi-hop networks is extremely complicated. The behavior of an AP is dependent not only on its neighborspsila behavior, but also on the behavior of other hidden nodes. In this paper, we provide an accurate and verified multi-hop wireless backhaul analysis for performance of IEEE 802.11 DCF in terms of the channel throughput using a static channel error rate. The model is based on analysis of a single hop communications for evaluating the multi-hop wireless backhaul networks. We utilized our existing 3.5-mile Federal Railroad Administration (FRA) test bed on the BNSF railroad track in Nebraska to validate the model. Our field measurements and simulation results show that our proposed model is accurate.
6000340
Probabilistic Reverse Nearest Neighbor Queries on Uncertain Data
Uncertain data are inherent in various important applications and reverse nearest neighbor (RNN) query is an important query type for many applications. While many different types of queries have been studied on uncertain data, there is no previous work on answering RNN queries on uncertain data. In this paper, we formalize probabilistic reverse nearest neighbor query that is to retrieve the objects from the uncertain data that have higher probability than a given threshold to be the RNN of an uncertain query object. We develop an efficient algorithm based on various novel pruning approaches that solves the probabilistic RNN queries on multidimensional uncertain data. The experimental results demonstrate that our algorithm is even more efficient than a sampling-based approximate algorithm for most of the cases and is highly scalable.