Use of a weighted matching algorithm to sequence clusters in spatial join processing

One of the most expensive operations in a spatial database is spatial join processing. This study focuses on how to improve the performance of such processing. The main objective is to reduce the Input/Output (I/O) cost of the spatial join process by using a technique called cluster-scheduling. Generally, the spatial join is processed in two steps, namely filtering and refinement. The cluster-scheduling technique is performed after the filtering step and before the refinement step and is part of the housekeeping phase. The key point of this technique is to realise order wherein two consecutive clusters in the sequence have maximal overlapping objects. However, finding the maximal overlapping order has been shown to be Nondeterministic Polynomial-time (NP)-complete. This study proposes an algorithm to provide approximate maximal overlapping (AMO) order in a Cluster Overlapping (CO) graph. The study proposes the use of an efficient maximum weighted matching algorithm to solve the problem of finding AMO order. As a result, the I/O cost in spatial join processing can be minimised

Efficient Subgraph Matching on Billion Node Graphs

The ability to handle large scale graph data is crucial to an increasing number of applications. Much work has been dedicated to supporting basic graph operations such as subgraph matching, reachability, regular expression matching, etc. In many cases, graph indices are employed to speed up query processing. Typically, most indices require either super-linear indexing time or super-linear indexing space. Unfortunately, for very large graphs, super-linear approaches are almost always infeasible. In this paper, we study the problem of subgraph matching on billion-node graphs. We present a novel algorithm that supports efficient subgraph matching for graphs deployed on a distributed memory store. Instead of relying on super-linear indices, we use efficient graph exploration and massive parallel computing for query processing. Our experimental results demonstrate the feasibility of performing subgraph matching on web-scale graph data.Comment: VLDB201

SVS-JOIN : efficient spatial visual similarity join for geo-multimedia

In the big data era, massive amount of multimedia data with geo-tags has been generated and collected by smart devices equipped with mobile communications module and position sensor module. This trend has put forward higher request on large-scale geo-multimedia retrieval. Spatial similarity join is one of the significant problems in the area of spatial database. Previous works focused on spatial textual document search problem, rather than geo-multimedia retrieval. In this paper, we investigate a novel geo-multimedia retrieval paradigm named spatial visual similarity join (SVS-JOIN for short), which aims to search similar geo-image pairs in both aspects of geo-location and visual content. Firstly, the definition of SVS-JOIN is proposed and then we present the geographical similarity and visual similarity measurement. Inspired by the approach for textual similarity join, we develop an algorithm named SVS-JOIN B by combining the PPJOIN algorithm and visual similarity. Besides, an extension of it named SVS-JOIN G is developed, which utilizes spatial grid strategy to improve the search efficiency. To further speed up the search, a novel approach called SVS-JOIN Q is carefully designed, in which a quadtree and a global inverted index are employed. Comprehensive experiments are conducted on two geo-image datasets and the results demonstrate that our solution can address the SVS-JOIN problem effectively and efficiently

Temporal Stream Algebra

Data stream management systems (DSMS) so far focus on event queries and hardly consider combined queries to both data from event streams and from a database. However, applications like emergency management require combined data stream and database queries. Further requirements are the simultaneous use of multiple timestamps after different time lines and semantics, expressive temporal relations between multiple time-stamps and exible negation, grouping and aggregation which can be controlled, i. e. started and stopped, by events and are not limited to fixed-size time windows. Current DSMS hardly address these requirements. This article proposes Temporal Stream Algebra (TSA) so as to meet the afore mentioned requirements. Temporal streams are a common abstraction of data streams and data- base relations; the operators of TSA are generalizations of the usual operators of Relational Algebra. A in-depth 'analysis of temporal relations guarantees that valid TSA expressions are non-blocking, i. e. can be evaluated incrementally. In this respect TSA differs significantly from previous algebraic approaches which use specialized operators to prevent blocking expressions on a "syntactical" level

A New Design for Open and Scalable Collaboration of Independent Databases in Digitally Connected Enterprises

“Digitally connected enterprises” refers to e-business, global supply chains, and other new business designs of the Knowledge Economy; all of which require open and scalable information supply chains across independent enterprises. Connecting proprietarily designed and controlled enterprise databases in these information supply chains is a critical success factor for them. Previous connection designs tend to rely on “hard-coded” regimes, which do not respond well to disruptions (including changes and failures), and do not afford these enterprises sufficient flexibility to join simultaneously in multiple supply chain regimes and share information for the benefit of all. The paper develops a new design: It combines matchmaking with global database query, and thereby supports the interoperation of independent databases to form on-demand information supply chains. The design provides flexible (re-)configuration to decrease the impact of disruption, and proactive control to increase collaboration and information sharing. More broadly, the papers results contribute to a new Information System design method for massively extended enterprises, and facilitate new business designs using digital connections at the level of databases

Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for similar to 25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.U.S. National Institutes of Health R00-GM087550U.S. National Science Foundation (NSF) DEB-0515729NSF BEACON Center for the Study of Evolution in Action DBI-0939454Cancer Prevention & Research Institute of Texas (CPRIT) RP130124University of Texas at Austin startup fundsUniversity of Texas at AustinCPRIT Cancer Research TraineeshipMolecular Bioscience

Improved single-swab sample preparation for recovering bacterial and phage DNA from human skin and wound microbiomes.

BackgroundCharacterization of the skin and wound microbiome is of high biomedical interest, but is hampered by the low biomass of typical samples. While sample preparation from other microbiomes (e.g., gut) has been the subject of extensive optimization, procedures for skin and wound microbiomes have received relatively little attention. Here we describe an improved method for obtaining both phage and microbial DNA from a single skin or wound swab, characterize the yield of DNA in model samples, and demonstrate the utility of this approach with samples collected from a wound clinic.ResultsWe find a substantial improvement when processing wound samples in particular; while only one-quarter of wound samples processed by a traditional method yielded sufficient DNA for downstream analysis, all samples processed using the improved method yielded sufficient DNA. Moreover, for both skin and wound samples, community analysis and viral reads obtained through deep sequencing of clinical swab samples showed significant improvement with the use of the improved method.ConclusionUse of this method may increase the efficiency and data quality of microbiome studies from low-biomass samples