52799543
Fast computation of database operations using graphics processors
We present new algorithms for performing fast computation of several common database operations on commodity graphics processors. Specifically, we consider operations such as conjunctive selections, aggregations, and semi-linear queries, which are essential computational components of typical database, data warehousing, and data mining applications. While graphics processing units (GPUs) have been designed for fast display of geometric primitives, we utilize the inherent pipelining and parallelism, single instruction and multiple data (SIMD) capabilities, and vector processing functionality of GPUs, for evaluating boolean predicate combinations and semi-linear queries on attributes and executing database operations efficiently. Our algorithms take into account some of the limitations of the programming model of current GPUs and perform no data rearrangements. Our algorithms have been implemented on a programmable GPU (e.g. NVIDIA's GeForce FX 5900) and applied to databases consisting of up to a million records. We have compared their performance with an optimized implementation of CPU-based algorithms. Our experiments indicate that the graphics processor available on commodity computer systems is an effective co-processor for performing database operations.
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.
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
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.
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.
9910247
Image Segmentation That Optimizes Global Homogeneity in a Variational Framework
A two-phase segmentation mechanism is described that allows a global homogeneity-related measure to be optimized in a level-set formulation. The mechanism has uniform treatment toward texture, gray level, and color boundaries. Intensities or colors of the image are first coarsely quantized into a number of classes. Then a class map is formed by having each pixel labeled with the class identity its gray or color level is associated with. With this class map, for any segmented region, it can be determined which pixels inside the region belong to which classes, and it can even be calculated how spread-out each of such classes is inside the region. The average spread-size of the classes in the region, in comparison with the size of the region, then constitutes a good measure in evaluating how homogeneous the region is. With the measure, the segmentation problem can be formulated as the optimization of the average homogeneity of the segmented regions. This work contributes chiefly by expressing the above optimization functional in such a way that allows it to be encoded in a variational formulation and that the solution can be reached by the deformation of an active contour. In addition, to solve the problem of multiple optima, this work incorporates an additional geodesic term into the functional of the optimization to maintain the active contour's mobility at even adverse condition of the deformation process. Experimental results on synthetic and real images are presented to demonstrate the performance of the mechanism.
20644298
MASSIVE: a multidisciplinary applications-oriented simulation and visualization environment
The objective of the MASSIVE project is to build a grid platform to enable large-scale and distributed scientific and engineering computations. Its focus is numerical simulation and visualization. This paper addresses a prototype grid utilizing resources at the Center for Engineering and Scientific Computation (CESC) in Zhejiang University (ZJU). This grid is capable of taking a model geometry generated by CAD systems, transferring it to an SGI Onyx 3900 supercomputer where it is meshed. The meshed geometry is then transferred to a Dawning PC cluster where it is used to solve computational fluid dynamics and computational solid mechanics problems and it is finally visualized showing numerical results.
5516407
Condensed cube: an effective approach to reducing data cube size
Pre-computed data cube facilitates OLAP (on-line analytical processing). It is well-known that data cube computation is an expensive operation. While most algorithms have been devoted to optimizing memory management and reducing computation costs, less work has addressed a fundamental issue: the size of a data cube is huge when a large base relation with a large number of attributes is involved. In this paper, we propose a new concept, called a condensed data cube. The condensed cube is of much smaller size than a complete non-condensed cube. More importantly, it is a fully pre-computed cube without compression, and, hence, it requires neither decompression nor further aggregation when answering queries. Several algorithms for computing a condensed cube are proposed. Results of experiments on the effectiveness of condensed data cube are presented, using both synthetic and real-world data. The results indicate that the proposed condensed cube can reduce both the cube size and therefore its computation time.
17409738
Flexible Querying of Personal Information
The amount of personal data that users store and access in personal information systems has grown massively. Simple flexible search tools are a necessity for users to be able to access the data they need. In addition, the file organization that is typical in file systems is not a practical logical view anymore as applications may store information across files, or combine different objects into a single file. Users cannot be expected to know or remember the exact location and specific details about the data they are looking for; search techniques should allow for some approximation during query processing in order to return useful results while accounting for possible errors in the query. We present a scoring framework that takes into account approximation in both the content and structural dimensions of the data. Our query model extends the search to consider information across file boundaries. We implemented a prototype of our search techniques over a real data set and report on our experimental results.