Scalable Architecture for Integrated Batch and Streaming Analysis of Big Data

Thesis (Ph.D.) - Indiana University, Computer Sciences, 2015As Big Data processing problems evolve, many modern applications demonstrate special characteristics. Data exists in the form of both large historical datasets and high-speed real-time streams, and many analysis pipelines require integrated parallel batch processing and stream processing. Despite the large size of the whole dataset, most analyses focus on specific subsets according to certain criteria. Correspondingly, integrated support for efficient queries and post- query analysis is required. To address the system-level requirements brought by such characteristics, this dissertation proposes a scalable architecture for integrated queries, batch analysis, and streaming analysis of Big Data in the cloud. We verify its effectiveness using a representative application domain - social media data analysis - and tackle related research challenges emerging from each module of the architecture by integrating and extending multiple state-of-the-art Big Data storage and processing systems. In the storage layer, we reveal that existing text indexing techniques do not work well for the unique queries of social data, which put constraints on both textual content and social context. To address this issue, we propose a flexible indexing framework over NoSQL databases to support fully customizable index structures, which can embed necessary social context information for efficient queries. The batch analysis module demonstrates that analysis workflows consist of multiple algorithms with different computation and communication patterns, which are suitable for different processing frameworks. To achieve efficient workflows, we build an integrated analysis stack based on YARN, and make novel use of customized indices in developing sophisticated analysis algorithms. In the streaming analysis module, the high-dimensional data representation of social media streams poses special challenges to the problem of parallel stream clustering. Due to the sparsity of the high-dimensional data, traditional synchronization method becomes expensive and severely impacts the scalability of the algorithm. Therefore, we design a novel strategy that broadcasts the incremental changes rather than the whole centroids of the clusters to achieve scalable parallel stream clustering algorithms. Performance tests using real applications show that our solutions for parallel data loading/indexing, queries, analysis tasks, and stream clustering all significantly outperform implementations using current state-of-the-art technologies

Parallelizing Windowed Stream Joins in a Shared-Nothing Cluster

The availability of large number of processing nodes in a parallel and distributed computing environment enables sophisticated real time processing over high speed data streams, as required by many emerging applications. Sliding window stream joins are among the most important operators in a stream processing system. In this paper, we consider the issue of parallelizing a sliding window stream join operator over a shared nothing cluster. We propose a framework, based on fixed or predefined communication pattern, to distribute the join processing loads over the shared-nothing cluster. We consider various overheads while scaling over a large number of nodes, and propose solution methodologies to cope with the issues. We implement the algorithm over a cluster using a message passing system, and present the experimental results showing the effectiveness of the join processing algorithm.Comment: 11 page

Mapping Large Scale Research Metadata to Linked Data: A Performance Comparison of HBase, CSV and XML

OpenAIRE, the Open Access Infrastructure for Research in Europe, comprises a database of all EC FP7 and H2020 funded research projects, including metadata of their results (publications and datasets). These data are stored in an HBase NoSQL database, post-processed, and exposed as HTML for human consumption, and as XML through a web service interface. As an intermediate format to facilitate statistical computations, CSV is generated internally. To interlink the OpenAIRE data with related data on the Web, we aim at exporting them as Linked Open Data (LOD). The LOD export is required to integrate into the overall data processing workflow, where derived data are regenerated from the base data every day. We thus faced the challenge of identifying the best-performing conversion approach.We evaluated the performances of creating LOD by a MapReduce job on top of HBase, by mapping the intermediate CSV files, and by mapping the XML output.Comment: Accepted in 0th Metadata and Semantics Research Conferenc

FAST: FAST Analysis of Sequences Toolbox.

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought