Computing and Information Systems - Research Publications
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ItemThe use of online social networking for higher education from an activity theory perspective(National Taiwan University, 2010-12-01)
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ItemLocal network Voronoi diagrams(ACM, 2010)Continuous queries in road networks have gained significant research interests due to advances in GIS and mobile computing. Consider the following scenario: "A driver uses a networked GPS navigator to monitor five nearest gas stations in a road network." The main challenge of processing such a moving query is how to efficiently monitor network distances of the k nearest and possible resultant objects. To enable result monitoring in real-time, researchers have devised techniques which utilize precomputed distances and results, e.g., the network Voronoi diagram (NVD). However, the main drawback of preprocessing is that it requires access to all data objects and network nodes, which means that it is not suitable for large datasets in many real life situations. The best existing method to monitor kNN results without precomputation relies on executions of snapshot queries at network nodes encountered by the query point. This method results in repetitive distance evaluation over the same or similar sets of nodes. In this paper, we propose a method called the local network Voronoi diagram (LNVD) to compute query answers for a small area around the query point. As a result, our method requires neither precomputation nor distance evaluation at every intersection. According to our extensive analysis and experimental results, our method significantly outperforms the best existing method in terms of data access and computation costs.
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ItemShared artefacts as participatory Babel fish(ACM, 2010-12-01)
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Itemis-rSNP: a novel technique for in silico regulatory SNP detection(OXFORD UNIV PRESS, 2010-09)MOTIVATION: Determining the functional impact of non-coding disease-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) is challenging. Many of these SNPs are likely to be regulatory SNPs (rSNPs): variations which affect the ability of a transcription factor (TF) to bind to DNA. However, experimental procedures for identifying rSNPs are expensive and labour intensive. Therefore, in silico methods are required for rSNP prediction. By scoring two alleles with a TF position weight matrix (PWM), it can be determined which SNPs are likely rSNPs. However, predictions in this manner are noisy and no method exists that determines the statistical significance of a nucleotide variation on a PWM score. RESULTS: We have designed an algorithm for in silico rSNP detection called is-rSNP. We employ novel convolution methods to determine the complete distributions of PWM scores and ratios between allele scores, facilitating assignment of statistical significance to rSNP effects. We have tested our method on 41 experimentally verified rSNPs, correctly predicting the disrupted TF in 28 cases. We also analysed 146 disease-associated SNPs with no known functional impact in an attempt to identify candidate rSNPs. Of the 11 significantly predicted disrupted TFs, 9 had previous evidence of being associated with the disease in the literature. These results demonstrate that is-rSNP is suitable for high-throughput screening of SNPs for potential regulatory function. This is a useful and important tool in the interpretation of GWAS. AVAILABILITY: is-rSNP software is available for use at: www.genomics.csse.unimelb.edu.au/is-rSNP.
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ItemMIRAGAA-a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer(OXFORD UNIV PRESS, 2010-01-15)MOTIVATION: Cancer evolves through microevolution where random lesions that provide the biggest advantage to cancer stand out in their frequent occurrence in multiple samples. At the same time, a gene function can be changed by aberration of the corresponding gene or modification of microRNA (miRNA) expression, which attenuates the gene. In a large number of cancer samples, these two mechanisms might be distributed in a coordinated and almost mutually exclusive manner. Understanding this coordination may assist in identifying changes which significantly produce the same functional impact on cancer phenotype, and further identify genes that are universally required for cancer. Present methodologies for finding aberrations usually analyze single datasets, which cannot identify such pairs of coordinating genes and miRNAs. RESULTS: We have developed MIRAGAA, a statistical approach, to assess the coordinated changes of genome copy numbers and miRNA expression. We have evaluated MIRAGAA on The Cancer Genome Atlas (TCGA) Glioblastoma Multiforme datasets. In these datasets, a number of genome regions coordinating with different miRNAs are identified. Although well known for their biological significance, these genes and miRNAs would be left undetected for being less significant if the two datasets were analyzed individually. AVAILABILITY AND IMPLEMENTATION: The source code, implemented in R and java, is available from our project web site at http://www.csse.unimelb.edu.au/~rgaire/MIRAGAA/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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ItemIndex compression using 64-bit words(WILEY, 2010-02)
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ItemThe hvtree: A memory hierarchy aware version index(Association for Computing Machinery (ACM), 2010-01-01)The huge amount of temporal data generated from many important applications call for a highly efficient and scalable version index. The TSB-tree has the potential of large scalability due to its unique feature of progressive migration of data to larger mediums. However, its traditional design optimized for two levels of the memory hierarchy (the main memory and the hard disk) undermines its potential for high efficiency in face of today's advances in hardware, especially CPU/cache speed and memory size. We propose a novel version index structure called the HV-tree. Different from all previous version index structures, the HV-tree has nodes of different sizes, each optimized for a level of the memory hierarchy. As data migrates to different levels of the memory hierarchy, the HV-tree will adjust the node size automatically to exploit the best performance of all levels of the memory hierarchy. Moreover, the HV-tree has a unique chain mechanism to maximally keep recent data in higher levels of the memory hierarchy. As a result, HV-tree is several times faster than the TSB-tree for point queries (query with single key and single time value), and up to 1000 times faster than the TSB-tree for key-range and time-range queries.
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ItemEfficient Set Intersection for Inverted Indexing(ASSOC COMPUTING MACHINERY, 2010-12)Conjunctive Boolean queries are a key component of modern information retrieval systems, especially when Web-scale repositories are being searched. A conjunctive query q is equivalent to a | q |-way intersection over ordered sets of integers, where each set represents the documents containing one of the terms, and each integer in each set is an ordinal document identifier. As is the case with many computing applications, there is tension between the way in which the data is represented, and the ways in which it is to be manipulated. In particular, the sets representing index data for typical document collections are highly compressible, but are processed using random access techniques, meaning that methods for carrying out set intersections must be alert to issues to do with access patterns and data representation. Our purpose in this article is to explore these trade-offs, by investigating intersection techniques that make use of both uncompressed “integer” representations, as well as compressed arrangements. We also propose a simple hybrid method that provides both compact storage, and also faster intersection computations for conjunctive querying than is possible even with uncompressed representations.
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