OpenRaiser/Intern-Atlas huggingface dataset:
DDTS: A Practical System Testing Framework for Scientific Software
Venue: arXiv cs.SE 2014
Year: 2014

Many scientific-software projects test their codes inadequately, or not at all. Despite its well-known benefits, adopting routine testing is often not easy. Development teams may have doubts about establishing effective test procedures, writing test software, or handling the ever-growing complexity of test cases. They may need to run (and test) on restrictive HPC platforms. They almost certainly face time and budget pressures that can keep testing languishing near the bottom of their to-do lists. This paper presents DDTS, a framework for building test suite applications, designed to fit scientific-software projects' requirements. DDTS aims to simplify introduction of rigorous testing, and to ease growing pains as needs mature. It decomposes the testing problem into practical, intuitive phases; makes configuration and extension easy; is portable and suitable to HPC platforms; and exploits parallelism. DDTS is currently used for automated regression and developer pre-commit testing for several scientific-software projects with disparate testing requirements.
Algorithms for Maximum Agreement Forest of Multiple General Trees
Venue: arXiv cs.DS 2014
Year: 2014

The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work about the Maf problem are mainly on two binary phylogenetic trees or two general (i.e., binary and non-binary) phylogenetic trees. In this paper, we study the more general version of the problem: the Maf problem on multiple general phylogenetic trees. We present a parameterized algorithm of running time $O(3^k n^2m)$ and a 3-approximation algorithm for the Maf problem on multiple rooted general phylogenetic trees, and a parameterized algorithm of running time $O(4^k n^2m)$ and a 4-approximation algorithm for the Maf problem on multiple unrooted general phylogenetic trees. We also implement the parameterized algorithm and approximation algorithm for the Maf problem on multiple rooted general phylogenetic trees, and test them on simulated data and biological data.
Age of Big Data and Smart Cities: Privacy Trade-Off
Venue: arXiv cs.CY 2014
Year: 2014

Data will soon become one of the most precious treasures we have ever had, 43 trillion gigabytes of data will be created by 2020 according to a study made by Mckinsey Global Institute, it is estimated that 2.3 trillion gigabytes of data is created each day and most companies in the US have 100.000 gigabytes of data stored. Data is recorded, stored and analyzed to enable technology and services that the world relies on every day, this technology is getting smarter and we will be soon living in a world of smart services or what is called smart cities. This article presents an overview of the topic pointing to its actual status and forecasting the crucial roles it will play in the future, we will define big data analytics and smart cities and talk about their potential contributions in changing our way of living and finally we will discuss the possible down side of this upcoming technologies and how it can fool us, violate our privacy and turn us into puppets or technology slaves.
On the Optimal Precoding for MIMO Gaussian Wire-Tap Channels
Venue: arXiv cs.IT 2014
Year: 2014

We consider the problem of finding secrecy rate of a multiple-input multiple-output (MIMO) wire-tap channel. A transmitter, a legitimate receiver, and an eavesdropper are all equipped with multiple antennas. The channel states from the transmitter to the legitimate user and to the eavesdropper are assumed to be known at the transmitter. In this contribution, we address the problem of finding the optimal precoder/transmit covariance matrix maximizing the secrecy rate of the given wiretap channel. The problem formulation is shown to be equivalent to a difference of convex functions programming problem and an efficient algorithm for addressing this problem is developed.
Entropy of Overcomplete Kernel Dictionaries
Venue: arXiv cs.IT 2014
Year: 2014

In signal analysis and synthesis, linear approximation theory considers a linear decomposition of any given signal in a set of atoms, collected into a so-called dictionary. Relevant sparse representations are obtained by relaxing the orthogonality condition of the atoms, yielding overcomplete dictionaries with an extended number of atoms. More generally than the linear decomposition, overcomplete kernel dictionaries provide an elegant nonlinear extension by defining the atoms through a mapping kernel function (e.g., the gaussian kernel). Models based on such kernel dictionaries are used in neural networks, gaussian processes and online learning with kernels. The quality of an overcomplete dictionary is evaluated with a diversity measure the distance, the approximation, the coherence and the Babel measures. In this paper, we develop a framework to examine overcomplete kernel dictionaries with the entropy from information theory. Indeed, a higher value of the entropy is associated to a further uniform spread of the atoms over the space. For each of the aforementioned diversity measures, we derive lower bounds on the entropy. Several definitions of the entropy are examined, with an extensive analysis in both the input space and the mapped feature space.
On the Importance of Registers for Computability
Venue: arXiv cs.DC 2014
Year: 2014

All consensus hierarchies in the literature assume that we have, in addition to copies of a given object, an unbounded number of registers. But why do we really need these registers? This paper considers what would happen if one attempts to solve consensus using various objects but without any registers. We show that under a reasonable assumption, objects like queues and stacks cannot emulate the missing registers. We also show that, perhaps surprisingly, initialization, shown to have no computational consequences when registers are readily available, is crucial in determining the synchronization power of objects when no registers are allowed. Finally, we show that without registers, the number of available objects affects the level of consensus that can be solved. Our work thus raises the question of whether consensus hierarchies which assume an unbounded number of registers truly capture synchronization power, and begins a line of research aimed at better understanding the interaction between read-write memory and the powerful synchronization operations available on modern architectures.
When reputation enforces evolutionary cooperation in unreliable MANETs
Venue: arXiv cs.GT 2014
Year: 2014

In self-organized mobile ad hoc networks (MANETs), network functions rely on cooperation of self-interested nodes, where a challenge is to enforce their mutual cooperation. In this paper, we study cooperative packet forwarding in a one-hop unreliable channel which results from loss of packets and noisy observation of transmissions. We propose an indirect reciprocity framework based on evolutionary game theory, and enforce cooperation of packet forwarding strategies in both structured and unstructured MANETs. Furthermore, we analyze the evolutionary dynamics of cooperative strategies, and derive the threshold of benefit-to-cost ratio to guarantee the convergence of cooperation. The numerical simulations verify that the proposed evolutionary game theoretic solution enforces cooperation when the benefit-to-cost ratio of the altruistic exceeds the critical condition. In addition, the network throughput performance of our proposed strategy in structured MANETs is measured, which is in close agreement with that of the full cooperative strategy.
Cuckoo Search Inspired Hybridization of the Nelder-Mead Simplex Algorithm Applied to Optimization of Photovoltaic Cells
Venue: arXiv cs.NE 2014
Year: 2014

A new hybridization of the Cuckoo Search (CS) is developed and applied to optimize multi-cell solar systems; namely multi-junction and split spectrum cells. The new approach consists of combining the CS with the Nelder-Mead method. More precisely, instead of using single solutions as nests for the CS, we use the concept of a simplex which is used in the Nelder-Mead algorithm. This makes it possible to use the flip operation introduces in the Nelder-Mead algorithm instead of the Levy flight which is a standard part of the CS. In this way, the hybridized algorithm becomes more robust and less sensitive to parameter tuning which exists in CS. The goal of our work was to optimize the performance of multi-cell solar systems. Although the underlying problem consists of the minimization of a function of a relatively small number of parameters, the difficulty comes from the fact that the evaluation of the function is complex and only a small number of evaluations is possible. In our test, we show that the new method has a better performance when compared to similar but more compex hybridizations of Nelder-Mead algorithm using genetic algorithms or particle swarm optimization on standard benchmark functions. Finally, we show that the new method outperforms some standard meta-heuristics for the problem of interest.
Combining Technical and Financial Impacts for Countermeasure Selection
Venue: arXiv cs.CR 2014
Year: 2014

Research in information security has generally focused on providing a comprehensive interpretation of threats, vulnerabilities, and attacks, in particular to evaluate their danger and prioritize responses accordingly. Most of the current approaches propose advanced techniques to detect intrusions and complex attacks but few of these approaches propose well defined methodologies to react against a given attack. In this paper, we propose a novel and systematic method to select security countermeasures from a pool of candidates, by ranking them based on the technical and financial impact associated to each alternative. The method includes industrial evaluation and simulations of the impact associated to a given security measure which allows to compute the return on response investment for different candidates. A simple case study is proposed at the end of the paper to show the applicability of the model.
A Weighted Common Subgraph Matching Algorithm
Venue: arXiv cs.DS 2014
Year: 2014

We propose a weighted common subgraph (WCS) matching algorithm to find the most similar subgraphs in two labeled weighted graphs. WCS matching, as a natural generalization of the equal-sized graph matching or subgraph matching, finds wide applications in many computer vision and machine learning tasks. In this paper, the WCS matching is first formulated as a combinatorial optimization problem over the set of partial permutation matrices. Then it is approximately solved by a recently proposed combinatorial optimization framework - Graduated NonConvexity and Concavity Procedure (GNCCP). Experimental comparisons on both synthetic graphs and real world images validate its robustness against noise level, problem size, outlier number, and edge density.
Entropy Dynamics of Community Alignment in the Italian Parliament Time-Dependent Network
Venue: arXiv cs.SI 2014
Year: 2014

Complex institutions are typically characterized by meso-scale structures which are fundamental for the successful coordination of multiple agents. Here we introduce a framework to study the temporal dynamics of the node-community relationship based on the concept of community alignment, a measure derived from the modularity matrix that defines the alignment of a node with respect to the core of its community. The framework is applied to the 16th legislature of the Italian Parliament to study the dynamic relationship in voting behavior between Members of the Parliament (MPs) and their political parties. As a novel contribution, we introduce two entropy-based measures that capture politically interesting dynamics: the group alignment entropy (over a single snapshot), and the node alignment entropy (over multiple snapshots). We show that significant meso-scale changes in the time-dependent network structures can be detected by a combination of the two measures. We observe a steady growth of the group alignment entropy after a major internal conflict in the ruling majority and a different distribution of nodes alignment entropy after the government transition.
CUR Algorithm for Partially Observed Matrices
Venue: arXiv cs.LG 2014
Year: 2014

CUR matrix decomposition computes the low rank approximation of a given matrix by using the actual rows and columns of the matrix. It has been a very useful tool for handling large matrices. One limitation with the existing algorithms for CUR matrix decomposition is that they need an access to the {\it full} matrix, a requirement that can be difficult to fulfill in many real world applications. In this work, we alleviate this limitation by developing a CUR decomposition algorithm for partially observed matrices. In particular, the proposed algorithm computes the low rank approximation of the target matrix based on (i) the randomly sampled rows and columns, and (ii) a subset of observed entries that are randomly sampled from the matrix. Our analysis shows the relative error bound, measured by spectral norm, for the proposed algorithm when the target matrix is of full rank. We also show that only $O(n r\ln r)$ observed entries are needed by the proposed algorithm to perfectly recover a rank $r$ matrix of size $n\times n$, which improves the sample complexity of the existing algorithms for matrix completion. Empirical studies on both synthetic and real-world datasets verify our theoretical claims and demonstrate the effectiveness of the proposed algorithm.
A Survey on Software Testing Techniques using Genetic Algorithm
Venue: arXiv cs.SE 2014
Year: 2014

The overall aim of the software industry is to ensure delivery of high quality software to the end user. To ensure high quality software, it is required to test software. Testing ensures that software meets user specifications and requirements. However, the field of software testing has a number of underlying issues like effective generation of test cases, prioritisation of test cases etc which need to be tackled. These issues demand on effort, time and cost of the testing. Different techniques and methodologies have been proposed for taking care of these issues. Use of evolutionary algorithms for automatic test generation has been an area of interest for many researchers. Genetic Algorithm (GA) is one such form of evolutionary algorithms. In this research paper, we present a survey of GA approach for addressing the various issues encountered during software testing.
On Covering a Solid Sphere with Concentric Spheres in ${\mathbb Z}^3$
Venue: arXiv cs.CG 2014
Year: 2014

We show that a digital sphere, constructed by the circular sweep of a digital semicircle (generatrix) around its diameter, consists of some holes (absentee-voxels), which appear on its spherical surface of revolution. This incompleteness calls for a proper characterization of the absentee-voxels whose restoration will yield a complete spherical surface without any holes. In this paper, we present a characterization of such absentee-voxels using certain techniques of digital geometry and show that their count varies quadratically with the radius of the semicircular generatrix. Next, we design an algorithm to fill these absentee-voxels so as to generate a spherical surface of revolution, which is more realistic from the viewpoint of visual perception. We further show that covering a solid sphere by a set of complete spheres also results in an asymptotically larger count of absentees, which is cubic in the radius of the sphere. The characterization and generation of complete solid spheres without any holes can also be accomplished in a similar fashion. We furnish test results to substantiate our theoretical findings.
Approximate k-flat Nearest Neighbor Search
Venue: arXiv cs.CG 2014
Year: 2014

Let $k$ be a nonnegative integer. In the approximate $k$-flat nearest neighbor ($k$-ANN) problem, we are given a set $P \subset \mathbb{R}^d$ of $n$ points in $d$-dimensional space and a fixed approximation factor $c > 1$. Our goal is to preprocess $P$ so that we can efficiently answer approximate $k$-flat nearest neighbor queries: given a $k$-flat $F$, find a point in $P$ whose distance to $F$ is within a factor $c$ of the distance between $F$ and the closest point in $P$. The case $k = 0$ corresponds to the well-studied approximate nearest neighbor problem, for which a plethora of results are known, both in low and high dimensions. The case $k = 1$ is called approximate line nearest neighbor. In this case, we are aware of only one provably efficient data structure, due to Andoni, Indyk, Krauthgamer, and Nguyen. For $k \geq 2$, we know of no previous results. We present the first efficient data structure that can handle approximate nearest neighbor queries for arbitrary $k$. We use a data structure for $0$-ANN-queries as a black box, and the performance depends on the parameters of the $0$-ANN solution: suppose we have an $0$-ANN structure with query time $O(n^ρ)$ and space requirement $O(n^{1+σ})$, for $ρ, σ> 0$. Then we can answer $k$-ANN queries in time $O(n^{k/(k + 1 - ρ) + t})$ and space $O(n^{1+σk/(k + 1 - ρ)} + n\log^{O(1/t)} n)$. Here, $t > 0$ is an arbitrary constant and the $O$-notation hides exponential factors in $k$, $1/t$, and $c$ and polynomials in $d$. Our new data structures also give an improvement in the space requirement over the previous result for $1$-ANN: we can achieve near-linear space and sublinear query time, a further step towards practical applications where space constitutes the bottleneck.
On Octonary Codes and their Covering Radii
Venue: arXiv cs.IT 2014
Year: 2014

This paper introduces new reduction and torsion codes for an octonary code and determines their basic properties. These could be useful for the classification of self-orthogonal and self dual codes over $\mathbb{Z}_8$. We also focus our attention on covering radius problem of octonary codes. In particular, we determine lower and upper bounds of the covering radius of several classes of Repetition codes, Simplex codes of Type $α$ and Type $β$ and their duals, MacDonald codes, and Reed-Muller codes over $\mathbb{Z}_8$.
A Novel Uncertainty Parameter SR (Signal To Residual Spectrum Ratio) Evaluation Approach For Speech Enhancement
Venue: arXiv cs.SD 2014
Year: 2014

Usually, hearing impaired people use hearing aids which are implemented with speech enhancement algorithms. Estimation of speech and estimation of nose are the components in single channel speech enhancement system. The main objective of any speech enhancement algorithm is estimation of noise power spectrum for non stationary environment. VAD (Voice Activity Detector) is used to identify speech pauses and during these pauses only estimation of noise. MMSE (Minimum Mean Square Error) speech enhancement algorithm did not enhance the intelligibility, quality and listener fatigues are the perceptual aspects of speech. Novel evaluation approach SR (Signal to Residual spectrum ratio) based on uncertainty parameter introduced for the benefits of hearing impaired people in non stationary environments to control distortions. By estimation and updating of noise based on division of original pure signal into three parts such as pure speech, quasi speech and non speech frames based on multiple threshold conditions. Different values of SR and LLR demonstrate the amount of attenuation and amplification distortions. The proposed method will compared with any one method WAT(Weighted Average Technique) Hence by using parameters SR (signal to residual spectrum ratio) and LLR (log like hood ratio), MMSE (Minim Mean Square Error) in terms of segmented SNR and LLR.
A Guide To Deal With Uncertainties In Software Project Management
Venue: arXiv cs.SE 2014
Year: 2014

Various project management approaches do not consider the impact that uncertainties have on the project. The identified threats by uncertainty in a projec day-to-day are real and immediate and the expectations in a project are often high. The project manager faces a dilemma: decisions must be made in the present about future situations which are inherently uncertain. The use of uncertainty management in project can be a determining factor for the project success. This paper presents a systematic review about uncertainties management in software projects and a guide is proposed based on the review. It aims to present the best practices to manage uncertainties in software projects in a structured way including techniques and strategies to uncertainties containment.
An Experimental Evaluation of Performance of A Hadoop Cluster on Replica Management
Venue: arXiv cs.DC 2014
Year: 2014

Hadoop is an open source implementation of the MapReduce Framework in the realm of distributed processing. A Hadoop cluster is a unique type of computational cluster designed for storing and analyzing large data sets across cluster of workstations. To handle massive scale data, Hadoop exploits the Hadoop Distributed File System termed as HDFS. The HDFS similar to most distributed file systems share a familiar problem on data sharing and availability among compute nodes, often which leads to decrease in performance. This paper is an experimental evaluation of Hadoop's computing performance which is made by designing a rack aware cluster that utilizes the Hadoop's default block placement policy to improve data availability. Additionally, an adaptive data replication scheme that relies on access count prediction using Langrange's interpolation is adapted to fit the scenario. To prove, experiments were conducted on a rack aware cluster setup which significantly reduced the task completion time, but once the volume of the data being processed increases there is a considerable cutback in computational speeds due to update cost. Further the threshold level for balance between the update cost and replication factor is identified and presented graphically.
Pheet meets C++11
Venue: arXiv cs.DC 2014
Year: 2014

Pheet is a C++ task-scheduling framework that allows for easy customization of internal data-structures. The implementation was started before the C++11 standard was committed and therefore did not use the new standardized memory model but compiler/platform specific intrinsics for atomic memory operations. This not only makes the implementation harder to port to other compilers or architectures but also suffers from the fact that prior C++ versions did not specify any memory model. In this report I discuss the porting of one of the internal Pheet data structures to the new memory model and provide reasoning about the correctness based on the semantics of the memory consistency model. Using two benchmarks from the Pheet benchmark suite I compare the performance of the original against the new implementation which shows a significant speedup under certain conditions on one of the two test machines.