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.
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.
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.
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.
5167032
AGILE: a general approach to detect transitions in evolving data streams
In many applications such as e-commerce, system diagnosis and telecommunication services, data arrives in streams at a high speed. It is common that the underlying process generating the stream may change over time, either as a result of the fundamental evolution or in response to some external stimulus. Detecting these changes is a very challenging problem of great practical importance. The overall volume of the stream usually far exceeds the available main memory and access to the data stream is typically performed via a linear scan in ascending order of the indices of the records. In this paper, we propose a novel approach, AGILE, to monitor streaming data and to detect distinguishable transitions of the underlying processes. AGILE has many advantages over the traditional Hidden Markov Model, e.g., AGILE only requires one scan of the data.
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.
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.
30881426
Constraint-Based Graph Mining in Large Database
Currently, constraints are increasingly considered as a kind of means of user- or expert-control for filtering those unsatisfied and redundant patterns rapidly during the web mining process. Recent work has highlighted the importance of constraint-based mining paradigm in the context of frequent itemsets, sequences, and many other interesting patterns in large database. However, it is still not clear how to push various constraints systematically into graph mining process. In this paper, we categorize various graph-based constraints into several major classes and develop a framework CabGin (i.e. C onstr a int- b ased G raph M in ing) to push them into mining process by their categories. Non-monotonic aggregates like average also can be pushed into CabGin with minor revision. Experimental results show that CabGin can prunes a large search space effectively by pushing graph-based constraints into mining process.
32724421
An Efficient Algorithm of Frequent Connected Subgraph Extraction
Mining frequent patterns from datasets is one of the key success stories of data mining research. Currently, most of the works focus on independent data, 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 in this paper. We 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 Topology, which can mine these graphs efficiently, has been proposed. We evaluate the performance of the algorithm 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.
15012785
An area-reduced scheme for modulo 2/sup n/-1 addition/subtraction
In this paper, we present a versatile area-reduced scheme for modulo 2/sup n/-1 adders and subtracters using a MUX-based increment/decrement algorithm. A FPGA-based comparison of the proposed modulo adder and the conventional modulo adder designs is carried out. The implementation results show that the proposed adder reduces the area close to 30% compared with the modulo adder of Bayoumi et al. The delay and the power are also reduced around 10%. In addition, it is also shown that the proposed design requires less hardware resources than the parallel-prefix modulo adder of Kalampoukas et al. while providing a comparable operation speed.
32534487
Image Segmentation That Merges Together Boundary and Region Information
Segmentation is a classical yet important problem in vision. Most of the previous works are either region-based or boundary-based. The two approaches own complementary merits - while the region-based one always produces closed boundaries, the boundary-based one involves primarily local operations and avoids the complexity of deciding how homogeneous a region and how inhomogeneous neighboring regions should be. In this paper, we propose a new solution mechanism that makes use of both cues. We use the boundary processing and a particular field model to come up with a number of coarse, initial closed boundaries about the image first. Such coarse boundaries will then, through an adaptation of the Four Color Theorem, serve as the initialization to a level-set method-based minimization that acts on the intensity distribution of the image, and allows the final crispy segmentation result to emerge. Compared with the existing solutions, our method requires no initialization from the user, and the automatically extracted closed contours do provide guidance to derive more optimal and smoother segmentation result. Experimental results with some benchmarking image-sets show that the proposed solution could deliver accurate segmentation boundary.