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Streaming graph challenge: stochastic block partition

September 12, 2017
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Conference Paper
Author:
Edward K. Kao
…
Published in:
HPEC 2017: IEEE Conf. on High Performance Extreme Computing, 12-14 September 2017.
Topic:
supercomputing
R&D area:
R&D group:

Summary

An important objective for analyzing real-world graphs is to achieve scalable performance on large, streaming graphs. A challenging and relevant example is the graph partition problem. As a combinatorial problem, graph partition is NP-hard, but existing relaxation methods provide reasonable approximate solutions that can be scaled for large graphs. Competitive benchmarks and challenges have proven to be an effective means to advance state-of-the-art performance and foster community collaboration. This paper describes a graph partition challenge with a baseline partition algorithm of sub-quadratic complexity. The algorithm employs rigorous Bayesian inferential methods based on a statistical model that captures characteristics of the real-world graphs. This strong foundation enables the algorithm to address limitations of well-known graph partition approaches such as modularity maximization. This paper describes various aspects of the challenge including: (1) the data sets and streaming graph generator, (2) the baseline partition algorithm with pseudocode, (3) an argument for the correctness of parallelizing the Bayesian inference, (4) different parallel computation strategies such as node-based parallelism and matrix-based parallelism, (5) evaluation metrics for partition correctness and computational requirements, (6) preliminary timing of a Python-based demonstration code and the open source C++ code, and (7) considerations for partitioning the graph in streaming fashion. Data sets and source code for the algorithm as well as metrics, with detailed documentation are available at GraphChallenge.org.
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Summary

An important objective for analyzing real-world graphs is to achieve scalable performance on large, streaming graphs. A challenging and relevant example is the graph partition problem. As a combinatorial problem, graph partition is NP-hard, but existing relaxation methods provide reasonable approximate solutions that can be scaled for large graphs. Competitive...

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Streaming graph challenge: stochastic block partition

SoK: cryptographically protected database search

May 22, 2017
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Conference Paper
Author:
Benjamin W. Fuller
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Published in:
IEEE Symp. on Security and Privacy, 22-26 May 2017.
Topic:
cryptography
R&D area:
R&D group:

Summary

Protected database search systems cryptographically isolate the roles of reading from, writing to, and administering the database. This separation limits unnecessary administrator access and protects data in the case of system breaches. Since protected search was introduced in 2000, the area has grown rapidly, systems are offered by academia, start-ups, and established companies. However, there is no best protected search system or set of techniques. Design of such systems is a balancing act between security, functionality, performance, and usability. This challenge is made more difficult by ongoing database specialization, as some users will want the functionality of SQL, NoSQL, or NewSQL databases. This database evolution will continue, and the protected search community should be able to quickly provide functionality consistent with newly invented databases. At the same time, the community must accurately and clearly characterize the tradeoffs between different approaches. To address these challenges, we provide the following contributions:(1) An identification of the important primitive operations across database paradigms. We find there are a small number of base operations that can be used and combined to support a large number of database paradigms.(2) An evaluation of the current state of protected search systems in implementing these base operations. This evaluation describes the main approaches and tradeoffs for each base operation. Furthermore, it puts protected search in the context of unprotected search, identifying key gaps in functionality.(3) An analysis of attacks against protected search for different base queries.(4) A roadmap and tools for transforming a protected search system into a protected database, including an open-source performance evaluation platform and initial user opinions of protected search.
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Summary

Protected database search systems cryptographically isolate the roles of reading from, writing to, and administering the database. This separation limits unnecessary administrator access and protects data in the case of system breaches. Since protected search was introduced in 2000, the area has grown rapidly, systems are offered by academia, start-ups...

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SoK: cryptographically protected database search

Detecting virus exposure during the pre-symptomatic incubation period using physiological data

March 3, 2017
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Journal Article
Author:
Lauren Milechin
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Published in:
Science Translational Medicine (submitted), 3 March 2017.
Topic:
detection systems
R&D area:
R&D group:

Summary

Early pathogen exposure detection allows better patient care and faster implementation of public health measures (patient isolation, contact tracing). Existing exposure detection most frequently relies on overt clinical symptoms, namely fever, during the infectious prodromal period. We have developed a robust machine learning method to better detect asymptomatic states during the incubation period using subtle, sub-clinical physiological markers. Using high-resolution physiological data from non-human primate studies of Ebola and Marburg viruses, we pre-processed the data to reduce short-term variability and normalize diurnal variations, then provided these to a supervised random forest classification algorithm. In most subjects detection is achieved well before the onset of fever; subject cross-validation lead to 52±14h mean early detection (at >0.90 area under the receiver-operating characteristic curve). Cross-cohort tests across pathogens and exposure routes also lead to successful early detection (28±16h and 43±22h, respectively). We discuss which physiological indicators are most informative for early detection and options for extending this capability to lower data resolution and wearable, non-invasive sensors.
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Summary

Early pathogen exposure detection allows better patient care and faster implementation of public health measures (patient isolation, contact tracing). Existing exposure detection most frequently relies on overt clinical symptoms, namely fever, during the infectious prodromal period. We have developed a robust machine learning method to better detect asymptomatic states during...

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Detecting virus exposure during the pre-symptomatic incubation period using physiological data

SIAM data mining "brings it" to annual meeting

February 17, 2017
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Project Report
Author:
Jeremy Kepner
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Published in:
MIT Lincoln Laboratory Report 113081
Topic:
big data
R&D area:
R&D group:

Summary

The Data Mining Activity Group is one of SIAM's most vibrant and dynamic activity groups. To better share our enthusiasm for data mining with the broader SIAM community, our activity group organized six minisymposia at the 2016 Annual Meeting. These minisymposia included 48 talks organized by 11 SIAM members.
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Summary

The Data Mining Activity Group is one of SIAM's most vibrant and dynamic activity groups. To better share our enthusiasm for data mining with the broader SIAM community, our activity group organized six minisymposia at the 2016 Annual Meeting. These minisymposia included 48 talks organized by 11 SIAM members.

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SIAM data mining "brings it" to annual meeting

Learning by doing, High Performance Computing education in the MOOC era

January 17, 2017
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Journal Article
Author:
Julia Mullen
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Published in:
J. Parallel Distrib. Comput., Vol. 105, July 2017, pp. 105-15.
Topic:
high performance computing
R&D area:
R&D group:

Summary

The High Performance Computing (HPC) community has spent decades developing tools that teach practitioners to harness the power of parallel and distributed computing. To create scalable and flexible educational experiences for practitioners in all phases of a career, we turn to Massively Open Online Courses (MOOCs). We detail the design of a unique self-paced online course that incorporates a focus on parallel solutions, personalization, and hands-on practice to familiarize student-users with their target system. Course material is presented through the lens of common HPC use cases and the strategies for parallelizing them. Using personalized paths, we teach researchers how to recognize the alignment between scientific applications and traditional HPC use cases, so they can focus on learning the parallelization strategies key to their workplace success. At the conclusion of their learning path, students should be capable of achieving performance gains on their HPC system.
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Summary

The High Performance Computing (HPC) community has spent decades developing tools that teach practitioners to harness the power of parallel and distributed computing. To create scalable and flexible educational experiences for practitioners in all phases of a career, we turn to Massively Open Online Courses (MOOCs). We detail the design...

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Learning by doing, High Performance Computing education in the MOOC era

Side channel authenticity discriminant analysis for device class identification

September 25, 2016
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Conference Paper
Author:
Eric A. Koziel
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Published in:
ICIP: 2016 IEEE Int. Conf. on Image Processing, 25-28 September 2016.
Topic:
systems architecture
R&D area:
R&D group:

Summary

Counterfeit microelectronics present a significant challenge to commercial and defense supply chains. Many modern anti-counterfeit strategies rely on manufacturer cooperation to include additional identification components. We instead propose Side Channel Authenticity Discriminant Analysis (SICADA) to leverage physical phenomena manifesting from device operation to match suspect parts to a class of authentic parts. This paper examines the extent that power dissipation information can be used to separate unique classes of devices. A methodology for distinguishing device types is presented and tested on both simulation data of a custom circuit and empirical measurements of Microchip dsPIC33F microcontrollers. Experimental results show that power side channels contain significant distinguishing information to identify parts as authentic or suspect counterfeit.
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Summary

Counterfeit microelectronics present a significant challenge to commercial and defense supply chains. Many modern anti-counterfeit strategies rely on manufacturer cooperation to include additional identification components. We instead propose Side Channel Authenticity Discriminant Analysis (SICADA) to leverage physical phenomena manifesting from device operation to match suspect parts to a class of...

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Side channel authenticity discriminant analysis for device class identification

Enhancing HPC security with a user-based firewall

September 13, 2016
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Conference Paper
Author:
Andrew J. Prout
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Published in:
HPEC 2016: IEEE Conf. on High Performance Extreme Computing, 13-15 September 2016.
Topic:
high performance computing
R&D area:
R&D group:

Summary

High Performance Computing (HPC) systems traditionally allow their users unrestricted use of their internal network. While this network is normally controlled enough to guarantee privacy without the need for encryption, it does not provide a method to authenticate peer connections. Protocols built upon this internal network, such as those used in MPI, Lustre, Hadoop, or Accumulo, must provide their own authentication at the application layer. Many methods have been employed to perform this authentication, such as operating system privileged ports, Kerberos, munge, TLS, and PKI certificates. However, support for all of these methods requires the HPC application developer to include support and the user to configure and enable these services. The user-based firewall capability we have prototyped enables a set of rules governing connections across the HPC internal network to be put into place using Linux netfilter. By using an operating system-level capability, the system is not reliant on any developer or user actions to enable security. The rules we have chosen and implemented are crafted to not impact the vast majority of users and be completely invisible to them. Additionally, we have measured the performance impact of this system under various workloads.
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Summary

High Performance Computing (HPC) systems traditionally allow their users unrestricted use of their internal network. While this network is normally controlled enough to guarantee privacy without the need for encryption, it does not provide a method to authenticate peer connections. Protocols built upon this internal network, such as those used...

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Enhancing HPC security with a user-based firewall

Julia implementation of the Dynamic Distributed Dimensional Data Model

September 13, 2016
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Conference Paper
Author:
null
…
Published in:
HPEC 2016: IEEE Conf. on High Performance Extreme Computing, 13-15 September 2016.
Topic:
high performance computing
R&D area:
R&D group:

Summary

Julia is a new language for writing data analysis programs that are easy to implement and run at high performance. Similarly, the Dynamic Distributed Dimensional Data Model (D4M) aims to clarify data analysis operations while retaining strong performance. D4M accomplishes these goals through a composable, unified data model on associative arrays. In this work, we present an implementation of D4M in Julia and describe how it enables and facilitates data analysis. Several experiments showcase scalable performance in our new Julia version as compared to the original Matlab implementation.
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Summary

Julia is a new language for writing data analysis programs that are easy to implement and run at high performance. Similarly, the Dynamic Distributed Dimensional Data Model (D4M) aims to clarify data analysis operations while retaining strong performance. D4M accomplishes these goals through a composable, unified data model on associative...

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Julia implementation of the Dynamic Distributed Dimensional Data Model

Benchmarking the Graphulo processing framework

September 13, 2016
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Conference Paper
Author:
Vijay N. Gadepally
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Published in:
HPEC 2016: IEEE Conf. on High Performance Extreme Computing, 13-15 September 2016.
Topic:
high performance computing
R&D area:
R&D group:

Summary

Graph algorithms have wide applicability to a variety of domains and are often used on massive datasets. Recent standardization efforts such as the GraphBLAS are designed to specify a set of key computational kernels that hardware and software developers can adhere to. Graphulo is a processing framework that enables GraphBLAS kernels in the Apache Accumulo database. In our previous work, we have demonstrated a core Graphulo operation that performs large scale multiplication operations of database tables called TableMult. In this article, we present results of scaling the Graphulo engine to larger problems and scalablity when using greater number of resources. Specifically, we present the results of two experiments that demonstrate Graphulo scaling performance as linear with the number of available resources. The first experiment demonstrates cluster processing rates through Graphulo's TableMult operator on two large graphs, scaled between 2^17 and 2^19 vertices. The second experiment uses TableMult to extract a random set of rows from a large graph (2^19 nodes) to simulate a cued graph analytic. These benchmarking results are of relevance to Graphulo users who wish to apply Graphulo to their graph problems.
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Summary

Graph algorithms have wide applicability to a variety of domains and are often used on massive datasets. Recent standardization efforts such as the GraphBLAS are designed to specify a set of key computational kernels that hardware and software developers can adhere to. Graphulo is a processing framework that enables GraphBLAS...

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Benchmarking the Graphulo processing framework

High-throughput ingest of data provenance records in Accumulo

September 13, 2016
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Conference Paper
Author:
Thomas M. Moyer
…
Published in:
HPEC 2016: IEEE Conf. on High Performance Extreme Computing, 13-15 September 2016.
Topic:
supercomputing
R&D area:
R&D group:

Summary

Whole-system data provenance provides deep insight into the processing of data on a system, including detecting data integrity attacks. The downside to systems that collect whole-system data provenance is the sheer volume of data that is generated under many heavy workloads. In order to make provenance metadata useful, it must be stored somewhere where it can be queried. This problem becomes even more challenging when considering a network of provenance-aware machines all collecting this metadata. In this paper, we investigate the use of D4M and Accumulo to support high-throughput data ingest of whole-system provenance data. We find that we are able to ingest 3,970 graph components per second. Centrally storing the provenance metadata allows us to build systems that can detect and respond to data integrity attacks that are captured by the provenance system.
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Summary

Whole-system data provenance provides deep insight into the processing of data on a system, including detecting data integrity attacks. The downside to systems that collect whole-system data provenance is the sheer volume of data that is generated under many heavy workloads. In order to make provenance metadata useful, it must...

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High-throughput ingest of data provenance records in Accumulo
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