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Parallel vectorized algebraic AES in MATLAB for rapid prototyping of encrypted sensor processing algorithms and database analytics

Published in:
HPEC 2015: IEEE Conf. on High Performance Extreme Computing, 15-17 September 2015.

Summary

The increasing use of networked sensor systems and networked databases has led to an increased interest in incorporating encryption directly into sensor algorithms and database analytics. MATLAB is the dominant tool for rapid prototyping of sensor algorithms and has extensive database analytics capabilities. The advent of high level and high performance Galois Field mathematical environments allows encryption algorithms to be expressed succinctly and efficiently. This work leverages the Galois Field primitives found the MATLAB Communication Toolbox to implement a mode of the Advanced Encrypted Standard (AES) based on first principals mathematics. The resulting implementation requires 100x less code than standard AES implementations and delivers speed that is effective for many design purposes. The parallel version achieves speed comparable to native OpenSSL on a single node and is sufficient for real-time prototyping of many sensor processing algorithms and database analytics.
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Summary

The increasing use of networked sensor systems and networked databases has led to an increased interest in incorporating encryption directly into sensor algorithms and database analytics. MATLAB is the dominant tool for rapid prototyping of sensor algorithms and has extensive database analytics capabilities. The advent of high level and high...

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Using a power law distribution to describe big data

Published in:
HPEC 2015: IEEE Conf. on High Performance Extreme Computing, 15-17 September 2015.

Summary

The gap between data production and user ability to access, compute and produce meaningful results calls for tools that address the challenges associated with big data volume, velocity and variety. One of the key hurdles is the inability to methodically remove expected or uninteresting elements from large data sets. This difficulty often wastes valuable researcher and computational time by expending resources on uninteresting parts of data. Social sensors, or sensors which produce data based on human activity, such as Wikipedia, Twitter, and Facebook have an underlying structure which can be thought of as having a Power Law distribution. Such a distribution implies that few nodes generate large amounts of data. In this article, we propose a technique to take an arbitrary dataset and compute a power law distributed background model that bases its parameters on observed statistics. This model can be used to determine the suitability of using a power law or automatically identify high degree nodes for filtering and can be scaled to work with big data.
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Summary

The gap between data production and user ability to access, compute and produce meaningful results calls for tools that address the challenges associated with big data volume, velocity and variety. One of the key hurdles is the inability to methodically remove expected or uninteresting elements from large data sets. This...

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Computing on Masked Data to improve the security of big data

Published in:
HST 2015, IEEE Int. Conf. on Technologies for Homeland Security, 14-16 April 2015.

Summary

Organizations that make use of large quantities of information require the ability to store and process data from central locations so that the product can be shared or distributed across a heterogeneous group of users. However, recent events underscore the need for improving the security of data stored in such untrusted servers or databases. Advances in cryptographic techniques and database technologies provide the necessary security functionality but rely on a computational model in which the cloud is used solely for storage and retrieval. Much of big data computation and analytics make use of signal processing fundamentals for computation. As the trend of moving data storage and computation to the cloud increases, homeland security missions should understand the impact of security on key signal processing kernels such as correlation or thresholding. In this article, we propose a tool called Computing on Masked Data (CMD), which combines advances in database technologies and cryptographic tools to provide a low overhead mechanism to offload certain mathematical operations securely to the cloud. This article describes the design and development of the CMD tool.
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Summary

Organizations that make use of large quantities of information require the ability to store and process data from central locations so that the product can be shared or distributed across a heterogeneous group of users. However, recent events underscore the need for improving the security of data stored in such...

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Rapid sequence identification of potential pathogens using techniques from sparse linear algebra

Summary

The decreasing costs and increasing speed and accuracy of DNA sample collection, preparation, and sequencing has rapidly produced an enormous volume of genetic data. However, fast and accurate analysis of the samples remains a bottleneck. Here we present D4RAGenS, a genetic sequence identification algorithm that exhibits the Big Data handling and computational power of the Dynamic Distributed Dimensional Data Model (D4M). The method leverages linear algebra and statistical properties to increase computational performance while retaining accuracy by subsampling the data. Two run modes, Fast and Wise, yield speed and precision tradeoffs, with applications in biodefense and medical diagnostics. The D4RAGenS analysis algorithm is tested over several datasets, including three utilized for the Defense Threat Reduction Agency (DTRA) metagenomic algorithm contest.
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Summary

The decreasing costs and increasing speed and accuracy of DNA sample collection, preparation, and sequencing has rapidly produced an enormous volume of genetic data. However, fast and accurate analysis of the samples remains a bottleneck. Here we present D4RAGenS, a genetic sequence identification algorithm that exhibits the Big Data handling...

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Using a big data database to identify pathogens in protein data space [e-print]

Summary

Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors/false negatives), or scale poorly on large datasets. This paper explores using big data database technologies to characterize very large metagenomic DNA sequences in protein space, with the ultimate goal of rapid pathogen identification in patient samples. Our approach uses the abilities of a big data databases to hold large sparse associative array representations of genetic data to extract statistical patterns about the data that can be used in a variety of ways to improve identification algorithms.
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Summary

Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors/false negatives), or scale poorly on large datasets. This paper explores using big data database technologies to characterize very large metagenomic DNA sequences in protein space, with the ultimate...

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Computing on masked data: a high performance method for improving big data veracity

Published in:
HPEC 2014: IEEE Conf. on High Performance Extreme Computing, 9-11 September 2014.

Summary

The growing gap between data and users calls for innovative tools that address the challenges faced by big data volume, velocity and variety. Along with these standard three V's of big data, an emerging fourth "V" is veracity, which addresses the confidentiality, integrity, and availability of the data. Traditional cryptographic techniques that ensure the veracity of data can have overheads that are too large to apply to big data. This work introduces a new technique called Computing on Masked Data (CMD), which improves data veracity by allowing computations to be performed directly on masked data and ensuring that only authorized recipients can unmask the data. Using the sparse linear algebra of associative arrays, CMD can be performed with significantly less overhead than other approaches while still supporting a wide range of linear algebraic operations on the masked data. Databases with strong support of sparse operations, such as SciDB or Apache Accumulo, are ideally suited to this technique. Examples are shown for the application of CMD to a complex DNA matching algorithm and to database operations over social media data.
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Summary

The growing gap between data and users calls for innovative tools that address the challenges faced by big data volume, velocity and variety. Along with these standard three V's of big data, an emerging fourth "V" is veracity, which addresses the confidentiality, integrity, and availability of the data. Traditional cryptographic...

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Computing on masked data: a high performance method for improving big data veracity

Published in:
HPEC 2014: IEEE Conf. on High Performance Extreme Computing, 9-11 September 2014.

Summary

The growing gap between data and users calls for innovative tools that address the challenges faced by big data volume, velocity and variety. Along with these standard three V's of big data, an emerging fourth "V" is veracity, which addresses the confidentiality, integrity, and availability of the data. Traditional cryptographic techniques that ensure the veracity of data can have overheads that are too large to apply to big data. This work introduces a new technique called Computing on Masked Data (CMD), which improves data veracity by allowing computations to be performed directly on masked data and ensuring that only authorized recipients can unmask the data. Using the sparse linear algebra of associative arrays, CMD can be performed with significantly less overhead than other approaches while still supporting a wide range of linear algebraic operations on the masked data. Databases with strong support of sparse operations, such as SciDB or Apache Accumulo, are ideally suited to this technique. Examples are shown for the application of CMD to a complex DNA matching algorithm and to database operations over social media data.
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Summary

The growing gap between data and users calls for innovative tools that address the challenges faced by big data volume, velocity and variety. Along with these standard three V's of big data, an emerging fourth "V" is veracity, which addresses the confidentiality, integrity, and availability of the data. Traditional cryptographic...

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Big Data dimensional analysis

Published in:
HPEC 2014: IEEE Conf. on High Performance Extreme Computing, 9-11 September 2014.

Summary

The ability to collect and analyze large amounts of data is a growing problem within the scientific community. The growing gap between data and users calls for innovative tools that address the challenges faced by big data volume, velocity and variety. One of the main challenges associated with big data variety is automatically understanding the underlying structures and patterns of the data. Such an understanding is required as a pre-requisite to the application of advanced analytics to the data. Further, big data sets often contain anomalies and errors that are difficult to know a priori. Current approaches to understanding data structure are drawn from the traditional database ontology design. These approaches are effective, but often require too much human involvement to be effective for the volume, velocity and variety of data encountered by big data systems. Dimensional Data Analysis (DDA) is a proposed technique that allows big data analysts to quickly understand the overall structure of a big dataset, determine anomalies. DDA exploits structures that exist in a wide class of data to quickly determine the nature of the data and its statistical anomalies. DDA leverages existing schemas that are employed in big data databases today. This paper presents DDA, applies it to a number of data sets, and measures its performance. The overhead of DDA is low and can be applied to existing big data systems without greatly impacting their computing requirements.
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Summary

The ability to collect and analyze large amounts of data is a growing problem within the scientific community. The growing gap between data and users calls for innovative tools that address the challenges faced by big data volume, velocity and variety. One of the main challenges associated with big data...

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Achieving 100,000,000 database inserts per second using Accumulo and D4M

Summary

The Apache Accumulo database is an open source relaxed consistency database that is widely used for government applications. Accumulo is designed to deliver high performance on unstructured data such as graphs of network data. This paper tests the performance of Accumulo using data from the Graph500 benchmark. The Dynamic Distributed Dimensional Data Model (D4M) software is used to implement the benchmark on a 216-node cluster running the MIT SuperCloud software stack. A peak performance of over 100,000,000 database inserts per second was achieved which is 100x larger than the highest previously published value for any other database. The performance scales linearly with the number of ingest clients, number of database servers, and data size. The performance was achieved by adapting several supercomputing techniques to this application: distributed arrays, domain decomposition, adaptive load balancing, and single-program-multiple-data programming.
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Summary

The Apache Accumulo database is an open source relaxed consistency database that is widely used for government applications. Accumulo is designed to deliver high performance on unstructured data such as graphs of network data. This paper tests the performance of Accumulo using data from the Graph500 benchmark. The Dynamic Distributed...

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Genetic sequence matching using D4M big data approaches

Published in:
HPEC 2014: IEEE Conf. on High Performance Extreme Computing, 9-11 September 2014.

Summary

Recent technological advances in Next Generation Sequencing tools have led to increasing speeds of DNA sample collection, preparation, and sequencing. One instrument can produce over 600 Gb of genetic sequence data in a single run. This creates new opportunities to efficiently handle the increasing workload. We propose a new method of fast genetic sequence analysis using the Dynamic Distributed Dimensional Data Model (D4M) - an associative array environment for MATLAB developed at MIT Lincoln Laboratory. Based on mathematical and statistical properties, the method leverages big data techniques and the implementation of an Apache Acculumo database to accelerate computations one-hundred fold over other methods. Comparisons of the D4M method with the current gold-standard for sequence analysis, BLAST, show the two are comparable in the alignments they find. This paper will present an overview of the D4M genetic sequence algorithm and statistical comparisons with BLAST.
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Summary

Recent technological advances in Next Generation Sequencing tools have led to increasing speeds of DNA sample collection, preparation, and sequencing. One instrument can produce over 600 Gb of genetic sequence data in a single run. This creates new opportunities to efficiently handle the increasing workload. We propose a new method...

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