OpenRaiser/Intern-Atlas huggingface dataset:
Toward a Research Software Security Maturity Model
Venue: arXiv cs.CR 2013
Year: 2013

In its Vision and Strategy for Software for Science, Engineering, and Education the NSF states that it will invest in activities that: "Recognize that software strategies must include the secure and reliable deployment and operation of services, for example by campuses or national facilities or industry, where identity, authentication, authorization and assurance are crucial operational capabilities." and "Result in high-quality, usable, secure, vulnerability-free, sustainable, robust, well-tested, and maintainable/evolvable software; and which promotes the sustainability of solid and useful on-going investments." Such statements evidence that security should indeed be a first-class consideration of the software ecosystem. In this position paper, we share some thoughts related to research software security. Our thoughts are based on the observation that security is not a binary, all-or-nothing attribute, but a range of practices and requirements depending on how the software is expected to be deployed and used. We propose that the community leverage the concept of a maturity model, and work to agree on a research software security maturity model. This model would categorize different sets of security needs of the deployment community, and provide software developers a roadmap for advancing the security maturity of their software. The intent of this paper is not to express such a comprehensive maturity model, but instead to start a conversation and set some initial requirements.
Experiences from Software Engineering of Large Scale AMR Multiphysics Code Frameworks
Venue: arXiv cs.CE 2013
Year: 2013

Among the present generation of multiphysics HPC simulation codes there are many that are built upon general infrastructural frameworks. This is especially true of the codes that make use of structured adaptive mesh refinement (SAMR) because of unique demands placed on the housekeeping aspects of the code. They have varying degrees of abstractions between the infrastructure such as mesh management and IO and the numerics of the physics solvers. In this experience report we summarize the experiences and lessons learned from two of such major software efforts, FLASH and Chombo.
Enabling Reproducible Science with VisTrails
Venue: arXiv cs.SE 2013
Year: 2013

With the increasing amount of data and use of computation in science, software has become an important component in many different domains. Computing is now being used more often and in more aspects of scientific work including data acquisition, simulation, analysis, and visualization. To ensure reproducibility, it is important to capture the different computational processes used as well as their executions. VisTrails is an open-source scientific workflow system for data analysis and visualization that seeks to address the problem of integrating varied tools as well as automatically documenting the methods and parameters employed. Growing from a specific project need to supporting a wide array of users required close collaborations in addition to new research ideas to design a usable and efficient system. The VisTrails project now includes standard software processes like unit testing and developer documentation while serving as a base for further research. In this paper, we describe how VisTrails has developed and how our efforts in structuring and advertising the system have contributed to its adoption in many domains.
#Santiago is not #Chile, or is it? A Model to Normalize Social Media Impact
Venue: arXiv cs.SI 2013
Year: 2013

Online social networks are known to be demographically biased. Currently there are questions about what degree of representativity of the physical population they have, and how population biases impact user-generated content. In this paper we focus on centralism, a problem affecting Chile. Assuming that local differences exist in a country, in terms of vocabulary, we built a methodology based on the vector space model to find distinctive content from different locations, and use it to create classifiers to predict whether the content of a micro-post is related to a particular location, having in mind a geographically diverse selection of micro-posts. We evaluate them in a case study where we analyze the virtual population of Chile that participated in the Twitter social network during an event of national relevance: the municipal (local governments) elections held in 2012. We observe that the participating virtual population is spatially representative of the physical population, implying that there is centralism in Twitter. Our classifiers out-perform a non geographically-diverse baseline at the regional level, and have the same accuracy at a provincial level. However, our approach makes assumptions that need to be tested in multi-thematic and more general datasets. We leave this for future work.
Aggregate-Max Nearest Neighbor Searching in the Plane
Venue: arXiv cs.CG 2013
Year: 2013

We study the aggregate/group nearest neighbor searching for the MAX operator in the plane. For a set $P$ of $n$ points and a query set $Q$ of $m$ points, the query asks for a point of $P$ whose maximum distance to the points in $Q$ is minimized. We present data structures for answering such queries for both $L_1$ and $L_2$ distance measures. Previously, only heuristic and approximation algorithms were given for both versions. For the $L_1$ version, we build a data structure of O(n) size in $O(n\log n)$ time, such that each query can be answered in $O(m+\log n)$ time. For the $L_2$ version, we build a data structure in $O(n\log n)$ time and $O(n\log \log n)$ space, such that each query can be answered in $O(m\sqrt{n}\log^{O(1)} n)$ time, and alternatively, we build a data structure in $O(n^{2+ε})$ time and space for any $ε>0$, such that each query can be answered in $O(m\log n)$ time. Further, we extend our result for the $L_1$ version to the top-$k$ queries where each query asks for the $k$ points of $P$ whose maximum distances to $Q$ are the smallest for any $k$ with $1\leq k\leq n$: We build a data structure of O(n) size in $O(n\log n)$ time, such that each top-$k$ query can be answered in $O(m+k\log n)$ time.
Sustainable Software Development for Next-Gen Sequencing (NGS) Bioinformatics on Emerging Platforms
Venue: arXiv cs.CE 2013
Year: 2013

DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between the potential of this technology and the development of computational methods to realize this potential. Bridging this gap holds possibilities for broad impacts toward multiple grand challenges and offers unprecedented opportunities for software innovation and research. We argue that NGS-enabled applications need a critical mass of sustainable software to benefit from emerging computing platforms' transformative potential. Accumulating the necessary critical mass will require leaders in computational biology, bioinformatics, computer science, and computer engineering work together to identify core opportunity areas, critical software infrastructure, and software sustainability challenges. Furthermore, due to the quickly changing nature of both bioinformatics software and accelerator technology, we conclude that creating sustainable accelerated bioinformatics software means constructing a sustainable bridge between the two fields. In particular, sustained collaboration between domain developers and technology experts is needed to develop the accelerated kernels, libraries, frameworks and middleware that could provide the needed flexible link from NGS bioinformatics applications to emerging platforms.
Timing estimation in distributed sensor and control systems with central processing
Venue: arXiv cs.SY 2013
Year: 2013

We consider the problem of estimating timing of measurements and actuation in distributed sensor and control systems with central processing. The focus is on direct timing estimation for scenarios where clock synchronization is not feasible or desirable. Models of the timing and central and peripheral time stamps are motivated and derived from underlying clock and communication delay definitions and models. Heuristics for constructing a system time is presented and it is outlined how the joint timing and the plant state estimation can be handled. For a simple set of underlying clock and communication delay models, inclusion of peripheral unit time stamps is shown to reduce jitter, and it is argued that in general it will give significant jitter reduction. Finally, a numerical example is given of a contemporary system design.
Software Autotuning for Sustainable Performance Portability
Venue: arXiv cs.PF 2013
Year: 2013

Scientific software applications are increasingly developed by large interdiscplinary teams operating on functional modules organized around a common software framework, which is capable of integrating new functional capabilities without modifying the core of the framework. In such environment, software correctness and modularity take precedence at the expense of code performance, which is an important concern during execution on supercomputing facilities, where the allocation of core-hours is a valuable resource. To alleviate the performance problems, we propose automated performance tuning (autotuning) of software to extract the maximum performance on a given hardware platform and to enable performance portability across heterogeneous hardware platforms. The resulting code remains generic without committing to a particular software stack and yet is compile-time specializable for maximal sustained performance.
Regret-Based Multi-Agent Coordination with Uncertain Task Rewards
Venue: arXiv cs.AI 2013
Year: 2013

Many multi-agent coordination problems can be represented as DCOPs. Motivated by task allocation in disaster response, we extend standard DCOP models to consider uncertain task rewards where the outcome of completing a task depends on its current state, which is randomly drawn from unknown distributions. The goal of solving this problem is to find a solution for all agents that minimizes the overall worst-case loss. This is a challenging problem for centralized algorithms because the search space grows exponentially with the number of agents and is nontrivial for standard DCOP algorithms we have. To address this, we propose a novel decentralized algorithm that incorporates Max-Sum with iterative constraint generation to solve the problem by passing messages among agents. By so doing, our approach scales well and can solve instances of the task allocation problem with hundreds of agents and tasks.
Plug-and-play distributed state estimation for linear systems
Venue: arXiv cs.SY 2013
Year: 2013

This paper proposes a state estimator for large-scale linear systems described by the interaction of state-coupled subsystems affected by bounded disturbances. We equip each subsystem with a Local State Estimator (LSE) for the reconstruction of the subsystem states using pieces of information from parent subsystems only. Moreover we provide conditions guaranteeing that the estimation errors are confined into prescribed polyhedral sets and converge to zero in absence of disturbances. Quite remarkably, the design of an LSE is recast into an optimization problem that requires data from the corresponding subsystem and its parents only. This allows one to synthesize LSEs in a Plug-and-Play (PnP) fashion, i.e. when a subsystem gets added, the update of the whole estimator requires at most the design of an LSE for the subsystem and its parents. Theoretical results are backed up by numerical experiments on a mechanical system.
A Direct Power Controlled and Series Compensated EHV Transmission Line
Venue: arXiv cs.SY 2013
Year: 2013

This paper presents the design and analysis of a compensation method with application to a 345 kV 480 MVA three-phase transmission line. The compensator system includes a series injected voltage source converter that minimizes the resonance effects of capacitor line reactance. This creates an ability to compensate for the effects of subsynchronous resonance and thereby increase line loadability and control real and reactive power flows. The granularity of power flow control and simultaneous stabilization is achieved by the method of direct decoupled power control (DPC). The design process is detailed with respect to optimal response characteristics considering variations of line parameters, realistic transformer impedances, and maximum ramp response rates. Line effects are demonstrated in a PLECS model in MATLAB, and compensation control system functionality is verified. A case study is provided of a 345 kV transmission line from an EMTP simulation in PSCAD that accounts for distributed parameter effects that are encountered in physical EHV transmission lines. This demonstrates the improvement in stability to power system transients as well as damping of power system oscillations.
High-level robot programming based on CAD: dealing with unpredictable environments
Venue: arXiv cs.RO 2013
Year: 2013

Purpose - The purpose of this paper is to present a CAD-based human-robot interface that allows non-expert users to teach a robot in a manner similar to that used by human beings to teach each other. Design/methodology/approach - Intuitive robot programming is achieved by using CAD drawings to generate robot programs off-line. Sensory feedback allows minimization of the effects of uncertainty, providing information to adjust the robot paths during robot operation. Findings - It was found that it is possible to generate a robot program from a common CAD drawing and run it without any major concerns about calibration or CAD model accuracy. Research limitations/implications - A limitation of the proposed system has to do with the fact that it was designed to be used for particular technological applications. Practical implications - Since most manufacturing companies have CAD packages in their facilities today, CAD-based robot programming may be a good option to program robots without the need for skilled robot programmers. Originality/value - The paper proposes a new CAD-based robot programming system. Robot programs are directly generated from a CAD drawing running on a commonly available 3D CAD package (Autodesk Inventor) and not from a commercial, computer aided robotics (CAR) software, making it a simple CAD integrated solution. This is a low-cost and low-setup time system where no advanced robot programming skills are required to operate it. In summary, robot programs are generated with a high-level of abstraction from the robot language.
A low-cost laser scanning solution for flexible robotic cells: spray coating
Venue: arXiv cs.RO 2013
Year: 2013

In this paper, an adaptive and low-cost robotic coating platform for small production series is presented. This new platform presents a flexible architecture that enables fast/automatic system adaptive behaviour without human intervention. The concept is based on contactless technology, using artificial vision and laser scanning to identify and characterize different workpieces travelling on a conveyor. Using laser triangulation, the workpieces are virtually reconstructed through a simplified cloud of three-dimensional (3D) points. From those reconstructed models, several algorithms are implemented to extract information about workpieces profile (pattern recognition), size, boundary and pose. Such information is then used to on-line adjust the base robot programmes. These robot programmes are off-line generated from a 3D computer-aided design model of each different workpiece profile. Finally, the robotic manipulator executes the coating process after its base programmes have been adjusted. This is a low-cost and fully autonomous system that allows adapting the robots behaviour to different manufacturing situations. It means that the robot is ready to work over any piece at any time, and thus, small production series can be reduced to as much as a one-object series. No skilled workers and large setup times are needed to operate it. Experimental results showed that this solution proved to be efficient and can be applied not only for spray coating purposes but also for many other industrial processes (automatic manipulation, pick-and-place, inspection, etc.).
Frequency and time domain packet scheduling based on channel prediction with imperfect CQI in LTE
Venue: arXiv cs.NI 2013
Year: 2013

Channel-dependent scheduling of transmission of data packets in a wireless system is based on measurement and feedback of the channel quality. To alleviate the performance degradation due to simultaneous multiple imperfect channel quality information (CQI), a simple and efficient packet scheduling (PS) algorithm is developed in downlink LTE system for real time traffic. A frequency domain channel predictor based on Kalman filter is first developed to restore the true CQI from erroneous channel quality feedback. Then, a time domain grouping technique employing the joint of Proportional Fair (PF) and Modified Largest Weighted Delay First (M-LWDF) algorithms is used. It was proved this proposal achieves better performance in terms of system throughput and packet loss ratio by simulation results.
A Novel Methodology to Overcome Routing Misbehavior in MANET using Retaliation Model
Venue: arXiv cs.NI 2013
Year: 2013

MANET is a cooperative network in which nodes are responsible for forwarding as well as routing. Noncooperation is still a big challenge that certainly degrades the performance and reliability of a MANET. This paper presents a novel methodology to overcome routing misbehavior in MANET using Retaliation Model. In this model node misbehavior is watched and an equivalent misbehavior is given in return. This model employs several parameters such as number of packets forwarded, number of packets received for forwarding, packet forwarding ratio etc. to calculate Grade and Bonus Points. The Grade is used to isolate selfish nodes from the routing paths and the Bonus Points defines the number of packets dropped by an honest node in retaliation over its misconducts. The implementation is done in "GloMoSim" on top of the DSR protocol. We obtained up to 40% packet delivery ratio with a cost of a minimum of 7.5% overhead compared to DSR. To minimize total control traffic overhead we have included the FG Model with our model and it reduces the overhead up to 75%. This model enforces cooperation due to its stricter punishment strategy and justifies its name.
The Cost of an Epidemic over a Complex Network: A Random Matrix Approach
Venue: arXiv cs.SI 2013
Year: 2013

In this paper we quantify the total economic impact of an epidemic over a complex network using tools from random matrix theory. Incorporating the direct and indirect costs of infection, we calculate the disease cost in the large graph limit for an SIS (Susceptible - Infected - Susceptible) infection process. We also give an upper bound on this cost for arbitrary finite graphs and illustrate both calculated costs using extensive simulations on random and real-world networks. We extend these calculations by considering the total social cost of an epidemic, accounting for both the immunization and disease costs for various immunization strategies and determining the optimal immunization. Our work focuses on the transient behavior of the epidemic, in contrast to previous research, which typically focuses on determining the steady-state system equilibrium.
Hardware Support for Address Mapping in PGAS Languages; a UPC Case Study
Venue: arXiv cs.DC 2013
Year: 2013

The Partitioned Global Address Space (PGAS) programming model strikes a balance between the locality-aware, but explicit, message-passing model and the easy-to-use, but locality-agnostic, shared memory model. However, the PGAS rich memory model comes at a performance cost which can hinder its potential for scalability and performance. To contain this overhead and achieve full performance, compiler optimizations may not be sufficient and manual optimizations are typically added. This, however, can severely limit the productivity advantage. Such optimizations are usually targeted at reducing address translation overheads for shared data structures. This paper proposes a hardware architectural support for PGAS, which allows the processor to efficiently handle shared addresses. This eliminates the need for such hand-tuning, while maintaining the performance and productivity of PGAS languages. We propose to avail this hardware support to compilers by introducing new instructions to efficiently access and traverse the PGAS memory space. A prototype compiler is realized by extending the Berkeley Unified Parallel C (UPC) compiler. It allows unmodified code to use the new instructions without the user intervention, thereby creating a real productive programming environment. Two implementations are realized: the first is implemented using the full system simulator Gem5, which allows the evaluation of the performance gain. The second is implemented using a softcore processor Leon3 on an FPGA to verify the implementability and to parameterize the cost of the new hardware and its instructions. The new instructions show promising results for the NAS Parallel Benchmarks implemented in UPC. A speedup of up to 5.5x is demonstrated for unmodified and unoptimized codes. Unoptimized code performance using this hardware was shown to also surpass the performance of manually optimized code by up to 10%.
On Sound Compilation of Reals
Venue: arXiv cs.PL 2013
Year: 2013

Writing accurate numerical software is hard because of many sources of unavoidable uncertainties, including finite numerical precision of implementations. We present a programming model where the user writes a program in a real-valued implementation and specification language that explicitly includes different types of uncertainties. We then present a compilation algorithm that generates a conventional implementation that is guaranteed to meet the desired precision with respect to real numbers. Our verification step generates verification conditions that treat different uncertainties in a unified way and encode reasoning about floating-point roundoff errors into reasoning about real numbers. Such verification conditions can be used as a standardized format for verifying the precision and the correctness of numerical programs. Due to their often non-linear nature, precise reasoning about such verification conditions remains difficult. We show that current state-of-the art SMT solvers do not scale well to solving such verification conditions. We propose a new procedure that combines exact SMT solving over reals with approximate and sound affine and interval arithmetic. We show that this approach overcomes scalability limitations of SMT solvers while providing improved precision over affine and interval arithmetic. Using our initial implementation we show the usefullness and effectiveness of our approach on several examples, including those containing non-linear computation.