http://www.mdpi.com/journal/algorithms Latest open access articles published in Algorithms at http://www.mdpi.com/journal/algorithms http://www.mdpi.com/1999-4893/6/2/371 In the stable marriage problem, any instance admits the so-called man-optimal stable matching, in which every man is assigned the best possible partner. However, there are instances for which all men receive low-ranked partners even in the man-optimal stable matching. In this paper we consider the problem of improving the man-optimal stable matching by changing only one man’s preference list. We show that the optimization variant and the decision variant of this problem can be solved in time O(n3) and O(n2), respectively, where n is the number of men (women) in an input. We further extend the problem so that we are allowed to change k men’s preference lists. We show that the problem is W[1]-hard with respect to the parameter k and give O(n2k+1)-time and O(nk+1)-time exact algorithms for the optimization and decision variants, respectively. Finally, we show that the problems become easy when k = n; we give O(n2.5 log n)-time and O(n2)-time algorithms for the optimization and decision variants, respectively. Algorithms 2013-05-28 6 2 Article 10.3390/a6020371 371 382 1999-4893 2013-05-28 doi: 10.3390/a6020371 Takao Inoshita Robert Irving Kazuo Iwama Shuichi Miyazaki Takashi Nagase http://www.mdpi.com/1999-4893/6/2/352 In biology, the notion of degenerate pattern plays a central role for describing various phenomena. For example, protein active site patterns, like those contained in the PROSITE database, e.g., [FY ]DPC[LIM][ASG]C[ASG], are, in general, represented by degenerate patterns with character classes. Researchers have developed several approaches over the years to discover degenerate patterns. Although these methods have been exhaustively and successfully tested on genomes and proteins, their outcomes often far exceed the size of the original input, making the output hard to be managed and to be interpreted by refined analysis requiring manual inspection. In this paper, we discuss a characterization of degenerate patterns with character classes, without gaps, and we introduce the concept of pattern priority for comparing and ranking different patterns. We define the class of underlying patterns for filtering any set of degenerate patterns into a new set that is linear in the size of the input sequence. We present some preliminary results on the detection of subtle signals in protein families. Results show that our approach drastically reduces the number of patterns in output for a tool for protein analysis, while retaining the representative patterns. Algorithms 2013-05-22 6 2 Article 10.3390/a6020352 352 370 1999-4893 2013-05-22 doi: 10.3390/a6020352 Matteo Comin Davide Verzotto http://www.mdpi.com/1999-4893/6/2/319 The suffix tree is an extremely important data structure in bioinformatics. Classical implementations require much space, which renders them useless to handle large sequence collections. Recent research has obtained various compressed representations for suffix trees, with widely different space-time tradeoffs. In this paper we show how the use of range min-max trees yields novel representations achieving practical space/time tradeoffs. In addition, we show how those trees can be modified to index highly repetitive collections, obtaining the first compressed suffix tree representation that effectively adapts to that scenario. Algorithms 2013-05-21 6 2 Article 10.3390/a6020319 319 351 1999-4893 2013-05-21 doi: 10.3390/a6020319 Andrés Abeliuk Rodrigo Cánovas Gonzalo Navarro http://www.mdpi.com/1999-4893/6/2/309 Data storage is a major and growing part of IT budgets for research since manyyears. Especially in biology, the amount of raw data products is growing continuously,and the advent of the so-called "next-generation" sequencers has made things worse.Affordable prices have pushed scientists to massively sequence whole genomes and to screenlarge cohort of patients, thereby producing tons of data as a side effect. The need formaximally fitting data into the available storage volumes has encouraged and welcomednew compression algorithms and tools. We focus here on state-of-the-art compression toolsand measure their compression performance on ABI SOLiD data. Algorithms 2013-05-21 6 2 Article 10.3390/a6020309 309 318 1999-4893 2013-05-21 doi: 10.3390/a6020309 Tommaso Mazza Stefano Castellana http://www.mdpi.com/1999-4893/6/2/278 In this contribution, a generic two-phase stochastic variable neighborhood approach is applied to nurse rostering problems. The proposed algorithm is used for creating feasible and efficient nurse rosters for many different nurse rostering cases. In order to demonstrate the efficiency and generic applicability of the proposed approach, experiments with real-world input data coming from many different nurse rostering cases have been conducted. The nurse rostering instances used have significant differences in nature, structure, philosophy and the type of hard and soft constraints. Computational results show that the proposed algorithm performs better than six different existing approaches applied to the same nurse rostering input instances using the same evaluation criteria. In addition, in all cases, it manages to reach the best-known fitness achieved in the literature, and in one case, it manages to beat the best-known fitness achieved till now. Algorithms 2013-05-21 6 2 Article 10.3390/a6020278 278 308 1999-4893 2013-05-21 doi: 10.3390/a6020278 Ioannis Solos Ioannis Tassopoulos Grigorios Beligiannis http://www.mdpi.com/1999-4893/6/2/245 This paper is motivated by, but not limited to, the task of scheduling jobs organized in workflows to a computational grid. Due to the dynamic nature of grid computing, more or less permanent replanning is required so that only very limited time is available to come up with a revised plan. To meet the requirements of both users and resource owners, a multi-objective optimization comprising execution time and costs is needed. This paper summarizes our work over the last six years in this field, and reports new results obtained by the combination of heuristics and evolutionary search in an adaptive Memetic Algorithm. We will show how different heuristics contribute to solving varying replanning scenarios and investigate the question of the maximum manageable work load for a grid of growing size starting with a load of 200 jobs and 20 resources up to 7000 jobs and 700 resources. Furthermore, the effect of four different local searchers incorporated into the evolutionary search is studied. We will also report briefly on approaches that failed within the short time frame given for planning. Algorithms 2013-04-22 6 2 Article 10.3390/a6020245 245 277 1999-4893 2013-04-22 doi: 10.3390/a6020245 Wilfried Jakob Sylvia Strack Alexander Quinte Günther Bengel Karl-Uwe Stucky Wolfgang Süß http://www.mdpi.com/1999-4893/6/2/227 Course timetabling is a combinatorial optimization problem and has been confirmed to be an NP-complete problem. Course timetabling problems are different for different universities. The studied university course timetabling problem involves hard constraints such as classroom, class curriculum, and other variables. Concurrently, some soft constraints need also to be considered, including teacher’s preferred time, favorite class time etc. These preferences correspond to satisfaction values obtained via questionnaires. Particle swarm optimization (PSO) is a promising scheme for solving NP-complete problems due to its fast convergence, fewer parameter settings and ability to fit dynamic environmental characteristics. Therefore, PSO was applied towards solving course timetabling problems in this work. To reduce the computational complexity, a timeslot was designated in a particle’s encoding as the scheduling unit. Two types of PSO, the inertia weight version and constriction version, were evaluated. Moreover, an interchange heuristic was utilized to explore the neighboring solution space to improve solution quality. Additionally, schedule conflicts are handled after a solution has been generated. Experimental results demonstrate that the proposed scheme of constriction PSO with interchange heuristic is able to generate satisfactory course timetables that meet the requirements of teachers and classes according to the various applied constraints. Algorithms 2013-04-19 6 2 Article 10.3390/a6020227 227 244 1999-4893 2013-04-19 doi: 10.3390/a6020227 Ruey-Maw Chen Hsiao-Fang Shih http://www.mdpi.com/1999-4893/6/2/197 The Internet of Things (IoT) refers to the Internet-like structure of billions of interconnected constrained devices, denoted as “smart objects”. Smart objects have limited capabilities, in terms of computational power and memory, and might be battery-powered devices, thus raising the need to adopt particularly energy efficient technologies. Among the most notable challenges that building interconnected smart objects brings about, there are standardization and interoperability. The use of IP has been foreseen as the standard for interoperability for smart objects. As billions of smart objects are expected to come to life and IPv4 addresses have eventually reached depletion, IPv6 has been identified as a candidate for smart-object communication. The deployment of the IoT raises many security issues coming from (i) the very nature of smart objects, e.g., the adoption of lightweight cryptographic algorithms, in terms of processing and memory requirements; and (ii) the use of standard protocols, e.g., the need to minimize the amount of data exchanged between nodes. This paper provides a detailed overview of the security challenges related to the deployment of smart objects. Security protocols at network, transport, and application layers are discussed, together with lightweight cryptographic algorithms proposed to be used instead of conventional and demanding ones, in terms of computational resources. Security aspects, such as key distribution and security bootstrapping, and application scenarios, such as secure data aggregation and service authorization, are also discussed. Algorithms 2013-04-02 6 2 Article 10.3390/a6020197 197 226 1999-4893 2013-04-02 doi: 10.3390/a6020197 Simone Cirani Gianluigi Ferrari Luca Veltri http://www.mdpi.com/1999-4893/6/1/169 Portfolio optimization is one of the problems most frequently encountered by financial practitioners. The main goal of this paper is to fill a gap in the literature by providing a well-documented, step-by-step open-source implementation of Critical Line Algorithm (CLA) in scientific language. The code is implemented as a Python class object, which allows it to be imported like any other Python module, and integrated seamlessly with pre-existing code. We discuss the logic behind CLA following the algorithm’s decision flow. In addition, we developed several utilities that support finding answers to recurrent practical problems. We believe this publication will offer a better alternative to financial practitioners, many of whom are currently relying on generic-purpose optimizers which often deliver suboptimal solutions. The source code discussed in this paper can be downloaded at the authors’ websites (see Appendix). Algorithms 2013-03-22 6 1 Article 10.3390/a6010169 169 196 1999-4893 2013-03-22 doi: 10.3390/a6010169 David Bailey Marcos López de Prado http://www.mdpi.com/1999-4893/6/1/161 We extend the stable flow model of Fleiner to multicommodity flows. In addition to the preference lists of agents on trading partners for each commodity, every trading pair has a preference list on the commodities that the seller can sell to the buyer. A blocking walk (with respect to a certain commodity) may include saturated arcs, provided that a positive amount of less preferred commodity is traded along the arc. We prove that a stable multicommodity flow always exists, although it is PPAD-hard to find one. Algorithms 2013-03-18 6 1 Article 10.3390/a6010161 161 168 1999-4893 2013-03-18 doi: 10.3390/a6010161 Tamás Király Júlia Pap http://www.mdpi.com/1999-4893/6/1/136 Image reconstruction is a key component in many medical imaging modalities. The problem of image reconstruction can be viewed as a special inverse problem where the unknown image pixel intensities are estimated from the observed measurements. Since the measurements are usually noise contaminated, statistical reconstruction methods are preferred. In this paper we review some non-negatively constrained simultaneous iterative algorithms for maximum penalized likelihood reconstructions, where all measurements are used to estimate all pixel intensities in each iteration. Algorithms 2013-03-12 6 1 Review 10.3390/a6010136 136 160 1999-4893 2013-03-12 doi: 10.3390/a6010136 Jun Ma http://www.mdpi.com/1999-4893/6/1/119 The maximum common connected edge subgraph problem is to find a connected graph with the maximum number of edges that is isomorphic to a subgraph of each of the two input graphs, where it has applications in pattern recognition and chemistry. This paper presents a dynamic programming algorithm for the problem when the two input graphs are outerplanar graphs of a bounded vertex degree, where it is known that the problem is NP-hard, even for outerplanar graphs of an unbounded degree. Although the algorithm repeatedly modifies input graphs, it is shown that the number of relevant subproblems is polynomially bounded, and thus, the algorithm works in polynomial time. Algorithms 2013-02-18 6 1 Article 10.3390/a6010119 119 135 1999-4893 2013-02-18 doi: 10.3390/a6010119 Tatsuya Akutsu Takeyuki Tamura http://www.mdpi.com/1999-4893/6/1/100 The eccentricity of a node in a graph is defined as the length of a longest shortest path starting at that node. The eccentricity distribution over all nodes is a relevant descriptive property of the graph, and its extreme values allow the derivation of measures such as the radius, diameter, center and periphery of the graph. This paper describes two new methods for computing the eccentricity distribution of large graphs such as social networks, web graphs, biological networks and routing networks.We first propose an exact algorithm based on eccentricity lower and upper bounds, which achieves significant speedups compared to the straightforward algorithm when computing both the extreme values of the distribution as well as the eccentricity distribution as a whole. The second algorithm that we describe is a hybrid strategy that combines the exact approach with an efficient sampling technique in order to obtain an even larger speedup on the computation of the entire eccentricity distribution. We perform an extensive set of experiments on a number of large graphs in order to measure and compare the performance of our algorithms, and demonstrate how we can efficiently compute the eccentricity distribution of various large real-world graphs. Algorithms 2013-02-18 6 1 Article 10.3390/a6010100 100 118 1999-4893 2013-02-18 doi: 10.3390/a6010100 Frank Takes Walter Kosters http://www.mdpi.com/1999-4893/6/1/84 We study the problem of finding the minimum-length curvature constrained closed path through a set of regions in the plane. This problem is referred to as the Dubins Traveling Salesperson Problem with Neighborhoods (DTSPN). An algorithm is presented that uses sampling to cast this infinite dimensional combinatorial optimization problem as a Generalized Traveling Salesperson Problem (GTSP) with intersecting node sets. The GTSP is then converted to an Asymmetric Traveling Salesperson Problem (ATSP) through a series of graph transformations, thus allowing the use of existing approximation algorithms. This algorithm is shown to perform no worse than the best existing DTSPN algorithm and is shown to perform significantly better when the regions overlap. We report on the application of this algorithm to route an Unmanned Aerial Vehicle (UAV) equipped with a radio to collect data from sparsely deployed ground sensors in a field demonstration of autonomous detection, localization, and verification of multiple acoustic events. Algorithms 2013-02-04 6 1 Article 10.3390/a6010084 84 99 1999-4893 2013-02-04 doi: 10.3390/a6010084 Jason Isaacs João Hespanha http://www.mdpi.com/1999-4893/6/1/60 A graph is said to be an intersection graph if there is a set of objects such that each vertex corresponds to an object and two vertices are adjacent if and only if the corresponding objects have a nonempty intersection. There are several natural graph classes that have geometric intersection representations. The geometric representations sometimes help to prove tractability/intractability of problems on graph classes. In this paper, we show some results proved by using geometric representations. Algorithms 2013-01-25 6 1 Article 10.3390/a6010060 60 83 1999-4893 2013-01-25 doi: 10.3390/a6010060 Ryuhei Uehara http://www.mdpi.com/1999-4893/6/1/43 The dominating set problem is a core NP-hard problem in combinatorial optimization and graph theory, and has many important applications. Baker [JACM 41,1994] introduces a k-outer planar graph decomposition-based framework for designing polynomial time approximation scheme (PTAS) for a class of NP-hard problems in planar graphs. It is mentioned that the framework can be applied to obtain an O(2ckn) time, c is a constant, (1+1/k)-approximation algorithm for the planar dominating set problem. We show that the approximation ratio achieved by the mentioned application of the framework is not bounded by any constant for the planar dominating set problem. We modify the application of the framework to give a PTAS for the planar dominating set problem. With k-outer planar graph decompositions, the modified PTAS has an approximation ratio (1 + 2/k). Using 2k-outer planar graph decompositions, the modified PTAS achieves the approximation ratio (1+1/k) in O(22ckn) time. We report a computational study on the modified PTAS. Our results show that the modified PTAS is practical. Algorithms 2013-01-21 6 1 Article 10.3390/a6010043 43 59 1999-4893 2013-01-21 doi: 10.3390/a6010043 Marjan Marzban Qian-Ping Gu http://www.mdpi.com/1999-4893/6/1/29 The wide utilization of Wireless Sensor Networks (WSNs) is obstructed by the severely limited energy constraints of the individual sensor nodes. This is the reason why a large part of the research in WSNs focuses on the development of energy efficient routing protocols. In this paper, a new protocol called Equalized Cluster Head Election Routing Protocol (ECHERP), which pursues energy conservation through balanced clustering, is proposed. ECHERP models the network as a linear system and, using the Gaussian elimination algorithm, calculates the combinations of nodes that can be chosen as cluster heads in order to extend the network lifetime. The performance evaluation of ECHERP is carried out through simulation tests, which evince the effectiveness of this protocol in terms of network energy efficiency when compared against other well-known protocols. Algorithms 2013-01-18 6 1 Article 10.3390/a6010029 29 42 1999-4893 2013-01-18 doi: 10.3390/a6010029 Stefanos Nikolidakis Dionisis Kandris Dimitrios Vergados Christos Douligeris http://www.mdpi.com/1999-4893/6/1/12 Principal Component Analysis (PCA) is widely used for identifying the major components of statistically distributed point clouds. Robust versions of PCA, often based in part on the ℓ1 norm (rather than the ℓ2 norm), are increasingly used, especially for point clouds with many outliers. Neither standard PCA nor robust PCAs can provide, without additional assumptions, reliable information for outlier-rich point clouds and for distributions with several main directions (spokes). We carry out a fundamental and complete reformulation of the PCA approach in a framework based exclusively on the ℓ1 norm and heavy-tailed distributions. The ℓ1 Major Component Detection and Analysis (ℓ1 MCDA) that we propose can determine the main directions and the radial extent of 2D data from single or multiple superimposed Gaussian or heavy-tailed distributions without and with patterned artificial outliers (clutter). In nearly all cases in the computational results, 2D ℓ1 MCDA has accuracy superior to that of standard PCA and of two robust PCAs, namely, the projection-pursuit method of Croux and Ruiz-Gazen and the ℓ1 factorization method of Ke and Kanade. (Standard PCA is, of course, superior to ℓ1 MCDA for Gaussian-distributed point clouds.) The computing time of ℓ1 MCDA is competitive with the computing times of the two robust PCAs. Algorithms 2013-01-17 6 1 Article 10.3390/a6010012 12 28 1999-4893 2013-01-17 doi: 10.3390/a6010012 Ye Tian Qingwei Jin John Lavery Shu-Cherng Fang http://www.mdpi.com/1999-4893/6/1/1 The problem of finding the maximum number of vertex-disjoint uni-color paths in an edge-colored graph has been recently introduced in literature, motivated by applications in social network analysis. In this paper we investigate the approximation and parameterized complexity of the problem. First, we show that, for any constant ε > 0, the problem is not approximable within factor c1-ε, where c is the number of colors, and that the corresponding decision problem is W[1]-hard when parametrized by the number of disjoint paths. Then, we present a fixed-parameter algorithm for the problem parameterized by the number and the length of the disjoint paths. Algorithms 2012-12-27 6 1 Article 10.3390/a6010001 1 11 1999-4893 2012-12-27 doi: 10.3390/a6010001 Paola Bonizzoni Riccardo Dondi Yuri Pirola http://www.mdpi.com/1999-4893/5/4/654 A zero-suppressed binary decision diagram (ZDD) is a graph representation suitable for handling sparse set families. Given a ZDD representing a set family, we present an efficient algorithm to discover a hidden structure, called a co-occurrence relation, on the ground set. This computation can be done in time complexity that is related not to the number of sets, but to some feature values of the ZDD. We furthermore introduce a conditional co-occurrence relation and present an extraction algorithm, which enables us to discover further structural information. Algorithms 2012-12-13 5 4 Article 10.3390/a5040654 654 667 1999-4893 2012-12-13 doi: 10.3390/a5040654 Takahisa Toda http://www.mdpi.com/1999-4893/5/4/636 The aim of this work is the extraction of edges from Magnetic Resonance Imaging (MRI) and Diffusion Tensor Imaging (DTI) images by a deformable contour procedure, using an external force field derived from an anisotropic flow. Moreover, we introduce a divergence map in order to check the convergence of the process. As we know from vector calculus, divergence is a measure of the magnitude of a vector field convergence at a given point. Thus by means level curves of the divergence map, we have automatically selected an initial contour for the deformation process. If the initial curve includes the areas from which the vector field diverges, it will be able to push the curve towards the edges. Furthermore the divergence map highlights the presence of curves pointing to the most significant geometric parts of boundaries corresponding to high curvature values. In this way, the skeleton of the extracted object will be rather well defined and may subsequently be employed in shape analysis and morphological studies. Algorithms 2012-12-13 5 4 Article 10.3390/a5040636 636 653 1999-4893 2012-12-13 doi: 10.3390/a5040636 Donatella Giuliani http://www.mdpi.com/1999-4893/5/4/629 Random graphs are matrices with independent 0–1 elements with probabilities determined by a small number of parameters. One of the oldest models is the Rasch model where the odds are ratios of positive numbers scaling the rows and columns. Later Persi Diaconis with his coworkers rediscovered the model for symmetric matrices and called the model beta. Here we give goodness-of-fit tests for the model and extend the model to a version of the block model introduced by Holland, Laskey and Leinhard. Algorithms 2012-12-06 5 4 Article 10.3390/a5040629 629 635 1999-4893 2012-12-06 doi: 10.3390/a5040629 Villõ Csiszár Péter Hussami János Komlós Tamás Móri Lídia Rejtõ Gábor Tusnády http://www.mdpi.com/1999-4893/5/4/604 The C library libkww provides functions to compute the Kohlrausch–Williams– Watts function, i.e., the Laplace–Fourier transform of the stretched (or compressed) exponential function exp(-tβ ) for exponents β between 0.1 and 1.9 with double precision. Analytic error bounds are derived for the low and high frequency series expansions. For intermediate frequencies, the numeric integration is enormously accelerated by using the Ooura–Mori double exponential transformation. The primitive of the cosine transform needed for the convolution integrals is also implemented. The software is hosted at http://apps.jcns.fz-juelich.de/kww; version 3.0 is deposited as supplementary material to this article. Algorithms 2012-11-22 5 4 Article 10.3390/a5040604 604 628 1999-4893 2012-11-22 doi: 10.3390/a5040604 Joachim Wuttke http://www.mdpi.com/1999-4893/5/4/588 We present a new method for automatic detection of peaks in noisy periodic and quasi-periodic signals. The new method, called automatic multiscale-based peak detection (AMPD), is based on the calculation and analysis of the local maxima scalogram, a matrix comprising the scale-dependent occurrences of local maxima. The usefulness of the proposed method is shown by applying the AMPD algorithm to simulated and real-world signals. Algorithms 2012-11-21 5 4 Article 10.3390/a5040588 588 603 1999-4893 2012-11-21 doi: 10.3390/a5040588 Felix Scholkmann Jens Boss Martin Wolf http://www.mdpi.com/1999-4893/5/4/545 We investigate a number of recently reported exact algorithms for the maximum clique problem. The program code is presented and analyzed to show how small changes in implementation can have a drastic effect on performance. The computational study demonstrates how problem features and hardware platforms influence algorithm behaviour. The effect of vertex ordering is investigated. One of the algorithms (MCS) is broken into its constituent parts and we discover that one of these parts frequently degrades performance. It is shown that the standard procedure used for rescaling published results (i.e., adjusting run times based on the calibration of a standard program over a set of benchmarks) is unsafe and can lead to incorrect conclusions being drawn from empirical data. Algorithms 2012-11-19 5 4 Article 10.3390/a5040545 545 587 1999-4893 2012-11-19 doi: 10.3390/a5040545 Patrick Prosser http://www.mdpi.com/1999-4893/5/4/529 Regularized Heaviside and Dirac delta function are used in several fields of computational physics and mechanics. Hence the issue of the quadrature of integrals of discontinuous and singular functions arises. In order to avoid ad-hoc quadrature procedures, regularization of the discontinuous and the singular fields is often carried out. In particular, weight functions of the signed distance with respect to the discontinuity interface are exploited. Tornberg and Engquist (Journal of Scientific Computing, 2003, 19: 527–552) proved that the use of compact support weight function is not suitable because it leads to errors that do not vanish for decreasing mesh size. They proposed the adoption of non-compact support weight functions. In the present contribution, the relationship between the Fourier transform of the weight functions and the accuracy of the regularization procedure is exploited. The proposed regularized approach was implemented in the eXtended Finite Element Method. As a three-dimensional example, we study a slender solid characterized by an inclined interface across which the displacement is discontinuous. The accuracy is evaluated for varying position of the discontinuity interfaces with respect to the underlying mesh. A procedure for the choice of the regularization parameters is proposed. Algorithms 2012-11-07 5 4 Article 10.3390/a5040529 529 544 1999-4893 2012-11-07 doi: 10.3390/a5040529 Elena Benvenuti Giulio Ventura Nicola Ponara http://www.mdpi.com/1999-4893/5/4/521 The minimax algorithm, also called the negamax algorithm, remains today the most widely used search technique for two-player perfect-information games. However, minimaxing has been shown to be susceptible to game tree pathology, a paradoxical situation in which the accuracy of the search can decrease as the height of the tree increases. Althöfer’s alternative minimax algorithm has been proven to be invulnerable to pathology. However, it has not been clear whether alpha-beta pruning, a crucial component of practical game programs, could be applied in the context of Alhöfer’s algorithm. In this brief paper, we show how alpha-beta pruning can be adapted to Althöfer’s algorithm. Algorithms 2012-11-05 5 4 Article 10.3390/a5040521 521 528 1999-4893 2012-11-05 doi: 10.3390/a5040521 Ashraf M. Abdelbar http://www.mdpi.com/1999-4893/5/4/506 In this paper we present the PHOCS-2 algorithm, which extracts a “Predicted Hierarchy Of ClassifierS”. The extracted hierarchy helps us to enhance performance of flat classification. Nodes in the hierarchy contain classifiers. Each intermediate node corresponds to a set of classes and each leaf node corresponds to a single class. In the PHOCS-2 we make estimation for each node and achieve more precise computation of false positives, true positives and false negatives. Stopping criteria are based on the results of the flat classification. The proposed algorithm is validated against nine datasets. Algorithms 2012-10-23 5 4 Article 10.3390/a5040506 506 520 1999-4893 2012-10-23 doi: 10.3390/a5040506 German Sapozhnikov Alexander Ulanov http://www.mdpi.com/1999-4893/5/4/490 Data can be represented in many different ways within a particular document or set of documents. Hence, attempts to automatically process the relationships between documents or determine the relevance of certain document objects can be problematic. In this study, we have developed software to automatically catalog objects contained in HTML files for patents granted by the United States Patent and Trademark Office (USPTO). Once these objects are recognized, the software creates metadata that assigns a data type to each document object. Such metadata can be easily processed and analyzed for subsequent text mining tasks. Specifically, document similarity and clustering techniques were applied to a subset of the USPTO document collection. Although our preliminary results demonstrate that tables and numerical data do not provide quantifiable value to a document’s content, the stage for future work in measuring the importance of document objects within a large corpus has been set. Algorithms 2012-10-22 5 4 Article 10.3390/a5040490 490 505 1999-4893 2012-10-22 doi: 10.3390/a5040490 Denise R. Koessler Benjamin W. Martin Bruce E. Kiefer Michael W. Berry http://www.mdpi.com/1999-4893/5/4/469 We propose using side information to further inform anomaly detection algorithms of the semantic context of the text data they are analyzing, thereby considering both divergence from the statistical pattern seen in particular datasets and divergence seen from more general semantic expectations. Computational experiments show that our algorithm performs as expected on data that reflect real-world events with contextual ambiguity, while replicating conventional clustering on data that are either too specialized or generic to result in contextual information being actionable. These results suggest that our algorithm could potentially reduce false positive rates in existing anomaly detection systems. Algorithms 2012-10-19 5 4 Article 10.3390/a5040469 469 489 1999-4893 2012-10-19 doi: 10.3390/a5040469 Amogh Mahapatra Nisheeth Srivastava Jaideep Srivastava http://www.mdpi.com/1999-4893/5/4/449 Forecasting the unit cost of every product type in a factory is an important task. However, it is not easy to deal with the uncertainty of the unit cost. Fuzzy collaborative forecasting is a very effective treatment of the uncertainty in the distributed environment. This paper presents some linear fuzzy collaborative forecasting models to predict the unit cost of a product. In these models, the experts’ forecasts differ and therefore need to be aggregated through collaboration. According to the experimental results, the effectiveness of forecasting the unit cost was considerably improved through collaboration. Algorithms 2012-10-15 5 4 Article 10.3390/a5040449 449 468 1999-4893 2012-10-15 doi: 10.3390/a5040449 Toly Chen http://www.mdpi.com/1999-4893/5/4/433 Imperialist Competitive Algorithm (ICA) is a new population-based evolutionary algorithm. It divides its population of solutions into several sub-populations, and then searches for the optimal solution through two operations: assimilation and competition. The assimilation operation moves each non-best solution (called colony) in a sub-population toward the best solution (called imperialist) in the same sub-population. The competition operation removes a colony from the weakest sub-population and adds it to another sub-population. Previous work on ICA focuses mostly on improving the assimilation operation or replacing the assimilation operation with more powerful meta-heuristics, but none focuses on the improvement of the competition operation. Since the competition operation simply moves a colony (i.e., an inferior solution) from one sub-population to another sub-population, it incurs weak interaction among these sub-populations. This work proposes Interaction Enhanced ICA that strengthens the interaction among the imperialists of all sub-populations. The performance of Interaction Enhanced ICA is validated on a set of benchmark functions for global optimization. The results indicate that the performance of Interaction Enhanced ICA is superior to that of ICA and its existing variants. Algorithms 2012-10-15 5 4 Article 10.3390/a5040433 433 448 1999-4893 2012-10-15 doi: 10.3390/a5040433 Jun-Lin Lin Yu-Hsiang Tsai Chun-Ying Yu Meng-Shiou Li http://www.mdpi.com/1999-4893/5/4/421 We present evidence that one can calculate generically combinatorially expensive Lp and lp averages, 0 < p < 1, in polynomial time by restricting the data to come from a wide class of statistical distributions. Our approach differs from the approaches in the previous literature, which are based on a priori sparsity requirements or on accepting a local minimum as a replacement for a global minimum. The functionals by which Lp averages are calculated are not convex but are radially monotonic and the functionals by which lp averages are calculated are nearly so, which are the keys to solvability in polynomial time. Analytical results for symmetric, radially monotonic univariate distributions are presented. An algorithm for univariate lp averaging is presented. Computational results for a Gaussian distribution, a class of symmetric heavy-tailed distributions and a class of asymmetric heavy-tailed distributions are presented. Many phenomena in human-based areas are increasingly known to be represented by data that have large numbers of outliers and belong to very heavy-tailed distributions. When tails of distributions are so heavy that even medians (L1 and l1 averages) do not exist, one needs to consider using lp minimization principles with 0 < p < 1. Algorithms 2012-10-05 5 4 Article 10.3390/a5040421 421 432 1999-4893 2012-10-05 doi: 10.3390/a5040421 John E. Lavery http://www.mdpi.com/1999-4893/5/4/398 In this paper we demonstrate a family of metrics for estimating the quality of a text summary relative to one or more human-generated summaries. The improved metrics are based on features automatically computed from the summaries to measure content and linguistic quality. The features are combined using one of three methods—robust regression, non-negative least squares, or canonical correlation, an eigenvalue method. The new metrics significantly outperform the previous standard for automatic text summarization evaluation, ROUGE. Algorithms 2012-09-26 5 4 Article 10.3390/a5040398 398 420 1999-4893 2012-09-26 doi: 10.3390/a5040398 Peter A. Rankel John M. Conroy Judith D. Schlesinger http://www.mdpi.com/1999-4893/5/3/379 Monitoring data streams in a distributed system has attracted considerable interest in recent years. The task of feature selection (e.g., by monitoring the information gain of various features) requires a very high communication overhead when addressed using straightforward centralized algorithms. While most of the existing algorithms deal with monitoring simple aggregated values such as frequency of occurrence of stream items, motivated by recent contributions based on geometric ideas we present an alternative approach. The proposed approach enables monitoring values of an arbitrary threshold function over distributed data streams through stream dependent constraints applied separately on each stream. We report numerical experiments on a real-world data that detect instances where communication between nodes is required, and compare the approach and the results to those recently reported in the literature. Algorithms 2012-09-18 5 3 Article 10.3390/a5030379 379 397 1999-4893 2012-09-18 doi: 10.3390/a5030379 Yaakov Malinovsky Jacob Kogan http://www.mdpi.com/1999-4893/5/3/364 When an event occurs in the real world, numerous news reports describing this event start to appear on different news sites within a few minutes of the event occurrence. This may result in a huge amount of information for users, and automated processes may be required to help manage this information. In this paper, we describe a clustering system that can cluster news reports from disparate sources into event-centric clusters—i.e., clusters of news reports describing the same event. A user can identify any RSS feed as a source of news he/she would like to receive and our clustering system can cluster reports received from the separate RSS feeds as they arrive without knowing the number of clusters in advance. Our clustering system was designed to function well in an online incremental environment. In evaluating our system, we found that our system is very good in performing fine-grained clustering, but performs rather poorly when performing coarser-grained clustering. Algorithms 2012-08-24 5 3 Article 10.3390/a5030364 364 378 1999-4893 2012-08-24 doi: 10.3390/a5030364 Joel Azzopardi Christopher Staff http://www.mdpi.com/1999-4893/5/3/330 An algorithm that forecasts volcanic activity using an event tree decision making framework and logistic regression has been developed, characterized, and validated. The suite of empirical models that drive the system were derived from a sparse and geographically diverse dataset comprised of source modeling results, volcano monitoring data, and historic information from analog volcanoes. Bootstrapping techniques were applied to the training dataset to allow for the estimation of robust logistic model coefficients. Probabilities generated from the logistic models increase with positive modeling results, escalating seismicity, and rising eruption frequency. Cross validation yielded a series of receiver operating characteristic curves with areas ranging between 0.78 and 0.81, indicating that the algorithm has good forecasting capabilities. Our results suggest that the logistic models are highly transportable and can compete with, and in some cases outperform, non-transportable empirical models trained with site specific information. Algorithms 2012-08-22 5 3 Article 10.3390/a5030330 330 363 1999-4893 2012-08-22 doi: 10.3390/a5030330 William N. Junek Linwood W. Jones Mark T. Woods http://www.mdpi.com/1999-4893/5/3/318 Segmentation of clinically relevant regions from potentially noisy images represents a significant challenge in the field of mammography. We propose novel approaches based on the WaveCluster clustering algorithm for segmenting both the breast profile in the presence of significant acquisition noise and segmenting regions of interest (ROIs) within the breast. Using prior manual segmentations performed by domain experts as ground truth data, we apply our method to 150 film mammograms with significant acquisition noise from the University of South Florida’s Digital Database for Screening Mammography. We then apply a similar segmentation procedure to detect the position and extent of suspicious regions of interest. Our approach was able to segment the breast profile from all 150 images, leaving minor residual noise adjacent to the breast in three. Performance on ROI extraction was also excellent, with 81% sensitivity and 0.96 false positives per image when measured against manually segmented ground truth ROIs. When not utilizing image morphology, our approach ran in linear time with the input size. These results highlight the potential of WaveCluster as a useful addition to the mammographic segmentation repertoire. Algorithms 2012-08-10 5 3 Article 10.3390/a5030318 318 329 1999-4893 2012-08-10 doi: 10.3390/a5030318 Michael Barnathan http://www.mdpi.com/1999-4893/5/2/304 Predicting the price of a dynamic random access memory (DRAM) product is a critical task to the manufacturer. However, it is not easy to contend with the uncertainty of the price. In order to effectively predict the price of a DRAM product, an agent-based fuzzy collaborative intelligence approach is proposed in this study. In the agent-based fuzzy collaborative intelligence approach, each agent uses a fuzzy neural network to predict the DRAM price based on its view. The agent then communicates its view and forecasting results to other agents with the aid of an automatic collaboration mechanism. According to the experimental results, the overall performance was improved through the agents’ collaboration. Algorithms 2012-05-24 5 2 Article 10.3390/a5020304 304 317 1999-4893 2012-05-24 doi: 10.3390/a5020304 Toly Chen http://www.mdpi.com/1999-4893/5/2/289 Cloud computing is an emerging technology where IT resources are virtualized to users as a set of a unified computing resources on a pay per use basis. The resources are dynamically chosen to satisfy a user Service Level Agreement and a required level of performance. Divisible load applications occur in many scientific and engineering applications and can easily be mapped to a Cloud using a master-worker pattern. However, those applications pose challenges to obtain the required performance. We model divisible load applications tasks processing on a set of cloud resources. We derive a novel model and formulas for computing the blocking probability in the system. The formulas are useful to analyze and predict the behavior of a divisible load application on a chosen set of resources to satisfy a Service Level Agreement before the implementation phase, thus saving time and platform energy. They are also useful as a dynamic feedback to a cloud scheduler for optimal scheduling. We evaluate the model in a set of illustrative scenarios. Algorithms 2012-05-11 5 2 Article 10.3390/a5020289 289 303 1999-4893 2012-05-11 doi: 10.3390/a5020289 Leila Ismail Liren Zhang http://www.mdpi.com/1999-4893/5/2/273 Imaginary cubes are three dimensional objects which have square silhouette projections in three orthogonal ways just as a cube has. In this paper, we study imaginary cubes and present assembly puzzles based on them. We show that there are 16 equivalence classes of minimal convex imaginary cubes, among whose representatives are a hexagonal bipyramid imaginary cube and a triangular antiprism imaginary cube. Our main puzzle is to put three of the former and six of the latter pieces into a cube-box with an edge length of twice the size of the original cube. Solutions of this puzzle are based on remarkable properties of these two imaginary cubes, in particular, the possibility of tiling 3D Euclidean space. Algorithms 2012-05-09 5 2 Article 10.3390/a5020273 273 288 1999-4893 2012-05-09 doi: 10.3390/a5020273 Hideki Tsuiki http://www.mdpi.com/1999-4893/5/2/261 A disentanglement puzzle consists of mechanically interlinked pieces, and the puzzle is solved by disentangling one piece from another set of pieces. A string puzzle consists of strings entangled with one or more wooden pieces. We consider the generalized string puzzle problem whose input is the layout of strings and a wooden board with holes embedded in the 3-dimensional Euclidean space. We present a polynomial-time transformation from an arbitrary instance ƒ of the 3SAT problem to a string puzzle s such that ƒ is satisfiable if and only if s is solvable. Therefore, the generalized string puzzle problem is NP-hard. Algorithms 2012-04-13 5 2 Article 10.3390/a5020261 261 272 1999-4893 2012-04-13 doi: 10.3390/a5020261 Chuzo Iwamoto Kento Sasaki Kenichi Morita http://www.mdpi.com/1999-4893/5/2/236 Deduplication in storage systems has gained momentum recently for its capability in reducing data footprint. However, deduplication introduces challenges to storage management as storage objects (e.g., files) are no longer independent from each other due to content sharing between these storage objects. In this paper, we present a graph-based framework to address the challenges of storage management due to deduplication. Specifically, we model content sharing among storage objects by content sharing graphs (CSG), and apply graph-based algorithms to two real-world storage management use cases for deduplication-enabled storage systems. First, a quasi-linear algorithm was developed to partition deduplication domains with a minimal amount of deduplication loss (i.e., data replicated across partitioned domains) in commercial deduplication-enabled storage systems, whereas in general the partitioning problem is NP-complete. For a real-world trace of 3 TB data with 978 GB of removable duplicates, the proposed algorithm can partition the data into 15 balanced partitions with only 54 GB of deduplication loss, that is, a 5% deduplication loss. Second, a quick and accurate method to query the deduplicated size for a subset of objects in deduplicated storage systems was developed. For the same trace of 3 TB data, the optimized graph-based algorithm can complete the query in 2.6 s, which is less than 1% of that of the traditional algorithm based on the deduplication metadata. Algorithms 2012-04-10 5 2 Article 10.3390/a5020236 236 260 1999-4893 2012-04-10 doi: 10.3390/a5020236 Maohua Lu Cornel Constantinescu Prasenjit Sarkar http://www.mdpi.com/1999-4893/5/2/214 Grammar-based compression is a well-studied technique to construct a context-free grammar (CFG) deriving a given text uniquely. In this work, we propose an online algorithm for grammar-based compression. Our algorithm guarantees O(log2 n)- approximation ratio for the minimum grammar size, where n is an input size, and it runs in input linear time and output linear space. In addition, we propose a practical encoding, which transforms a restricted CFG into a more compact representation. Experimental results by comparison with standard compressors demonstrate that our algorithm is especially effective for highly repetitive text. Algorithms 2012-04-10 5 2 Article 10.3390/a5020214 214 235 1999-4893 2012-04-10 doi: 10.3390/a5020214 Shirou Maruyama Hiroshi Sakamoto Masayuki Takeda http://www.mdpi.com/1999-4893/5/2/176 Link puzzles involve finding paths or a cycle in a grid that satisfy given local and global properties. This paper proposes algorithms that enumerate solutions and instances of two link puzzles, Slitherlink and Numberlink, by zero-suppressed binary decision diagrams (ZDDs). A ZDD is a compact data structure for a family of sets provided with a rich family of set operations, by which, for example, one can easily extract a subfamily satisfying a desired property. Thanks to the nature of ZDDs, our algorithms offer a tool to assist users to design instances of those link puzzles. Algorithms 2012-04-05 5 2 Article 10.3390/a5020176 176 213 1999-4893 2012-04-05 doi: 10.3390/a5020176 Ryo Yoshinaka Toshiki Saitoh Jun Kawahara Koji Tsuruma Hiroaki Iwashita Shin-ichi Minato http://www.mdpi.com/1999-4893/5/1/158 Tantrix (Tantrix R ⃝ is a registered trademark of Colour of Strategy Ltd. in New Zealand, and of TANTRIX JAPAN in Japan, respectively, under the license of M. McManaway, the inventor.) is a puzzle to make a loop by connecting lines drawn on hexagonal tiles, and the objective of this research is to solve it by a computer. For this purpose, we first give a problem setting of solving Tantrix as making a loop on a given fixed board. We then formulate it as an integer program by describing the rules of Tantrix as its constraints, and solve it by a mathematical programming solver to have a solution. As a result, we establish a formulation that can solve Tantrix of moderate size, and even when the solutions are invalid only by elementary constraints, we achieved it by introducing additional constraints and re-solve it. By this approach we succeeded to solve Tantrix of size up to 60. Algorithms 2012-03-22 5 1 Article 10.3390/a5010158 158 175 1999-4893 2012-03-22 doi: 10.3390/a5010158 Fumika Kino Yushi Uno http://www.mdpi.com/1999-4893/5/1/148 Suppose there is a collection of n simple polygons in the plane, none of which overlap each other. The polygons are interlocked if no subset can be separated arbitrarily far from the rest. It is natural to ask the characterization of the subsets that makes the set of interlocked polygons free (not interlocked). This abstracts the essence of a kind of sliding block puzzle. We show that any monotone Boolean function ƒ on n variables can be described by m = O(n) interlocked polygons. We also show that the decision problem that asks if given polygons are interlocked is PSPACE-complete. Algorithms 2012-03-19 5 1 Article 10.3390/a5010148 148 157 1999-4893 2012-03-19 doi: 10.3390/a5010148 Erik D. Demaine Martin L. Demaine Ryuhei Uehara http://www.mdpi.com/1999-4893/5/1/113 In this paper, we integrate a grid system and a wireless network to present a convenient computational service system, called the Semi-Preemptive Computational Service system (SePCS for short), which provides users with a wireless access environment and through which a user can share his/her resources with others. In the SePCS, each node is dynamically given a score based on its CPU level, available memory size, current length of waiting queue, CPU utilization and bandwidth. With the scores, resource nodes are classified into three levels. User requests based on their time constraints are also classified into three types. Resources of higher levels are allocated to more tightly constrained requests so as to increase the total performance of the system. To achieve this, a resource broker with the Semi-Preemptive Algorithm (SPA) is also proposed. When the resource broker cannot find suitable resources for the requests of higher type, it preempts the resource that is now executing a lower type request so that the request of higher type can be executed immediately. The SePCS can be applied to a Vehicular Ad Hoc Network (VANET), users of which can then exploit the convenient mobile network services and the wireless distributed computing. As a result, the performance of the system is higher than that of the tested schemes. Algorithms 2012-03-14 5 1 Article 10.3390/a5010113 113 147 1999-4893 2012-03-14 doi: 10.3390/a5010113 Fang-Yie Leu Keng-Yen Chao Ming-Chang Lee Jia-Chun Lin http://www.mdpi.com/1999-4893/5/1/98 In this note we illustrate and develop further with mathematics and examples, the work on successive standardization (or normalization) that is studied earlier by the same authors in [1] and [2]. Thus, we deal with successive iterations applied to rectangular arrays of numbers, where to avoid technical difficulties an array has at least three rows and at least three columns. Without loss, an iteration begins with operations on columns: first subtract the mean of each column; then divide by its standard deviation. The iteration continues with the same two operations done successively for rows. These four operations applied in sequence completes one iteration. One then iterates again, and again, and again, ... In [1] it was argued that if arrays are made up of real numbers, then the set for which convergence of these successive iterations fails has Lebesgue measure 0. The limiting array has row and column means 0, row and column standard deviations 1. A basic result on convergence given in [1] is true, though the argument in [1] is faulty. The result is stated in the form of a theorem here, and the argument for the theorem is correct. Moreover, many graphics given in [1] suggest that except for a set of entries of any array with Lebesgue measure 0, convergence is very rapid, eventually exponentially fast in the number of iterations. Because we learned this set of rules from Bradley Efron, we call it “Efron’s algorithm”. More importantly, the rapidity of convergence is illustrated by numerical examples. Algorithms 2012-02-29 5 1 Article 10.3390/a5010098 98 112 1999-4893 2012-02-29 doi: 10.3390/a5010098 Richard A. Olshen Bala Rajaratnam http://www.mdpi.com/1999-4893/5/1/76 Air-borne and space-borne acquired hyperspectral images are used to recognize objects and to classify materials on the surface of the earth. The state of the art compressor for lossless compression of hyperspectral images is the Spectral oriented Least SQuares (SLSQ) compressor (see [1–7]). In this paper we discuss hyperspectral image compression: we show how to visualize each band of a hyperspectral image and how this visualization suggests that an appropriate band ordering can lead to improvements in the compression process. In particular, we consider two important distance measures for band ordering: Pearson’s Correlation and Bhattacharyya distance, and report on experimental results achieved by a Java-based implementation of SLSQ. Algorithms 2012-02-20 5 1 Article 10.3390/a5010076 76 97 1999-4893 2012-02-20 doi: 10.3390/a5010076 Raffaele Pizzolante Bruno Carpentieri http://www.mdpi.com/1999-4893/5/1/56 This paper presents a genetic-based control scheme that not only utilizes evolutionary characteristics to find the signal acquisition parameters, but also employs an adaptive scheme to control the search space and avoid the genetic control converging to local optimal value so as to acquire the desired signal precisely and rapidly. Simulations and experiment results show that the proposed method can improve the precision of signal parameters and take less signal acquisition time than traditional serial search methods for global navigation satellite system (GNSS) signals. Algorithms 2012-02-17 5 1 Article 10.3390/a5010056 56 75 1999-4893 2012-02-17 doi: 10.3390/a5010056 Chung-Liang Chang Ho-Nien Shou http://www.mdpi.com/1999-4893/5/1/50 Building on results from data compression, we prove nearly tight bounds on how well sequences of length n can be predicted in terms of the size σ of the alphabet and the length k of the context considered when making predictions. We compare the performance achievable by an adaptive predictor with no advance knowledge of the sequence, to the performance achievable by the optimal static predictor using a table listing the frequency of each (k + 1)-tuple in the sequence. We show that, if the elements of the sequence are chosen uniformly at random, then an adaptive predictor can compete in the expected case if k ≤ logσ n – 3 – ε, for a constant ε > 0, but not if k ≥ logσ n. Algorithms 2012-02-17 5 1 Article 10.3390/a5010050 50 55 1999-4893 2012-02-17 doi: 10.3390/a5010050 Travis Gagie http://www.mdpi.com/1999-4893/5/1/30 We review the state of the art in DNA microarray image compression and provide original comparisons between standard and microarray-specific compression techniques that validate and expand previous work. First, we describe the most relevant approaches published in the literature and classify them according to the stage of the typical image compression process where each approach makes its contribution, and then we summarize the compression results reported for these microarray-specific image compression schemes. In a set of experiments conducted for this paper, we obtain new results for several popular image coding techniques that include the most recent coding standards. Prediction-based schemes CALIC and JPEG-LS are the best-performing standard compressors, but are improved upon by the best microarray-specific technique, Battiato’s CNN-based scheme. Algorithms 2012-02-14 5 1 Article 10.3390/a5010030 30 49 1999-4893 2012-02-14 doi: 10.3390/a5010030 Miguel Hernández-Cabronero Ian Blanes Michael W. Marcellin Joan Serra-Sagristà http://www.mdpi.com/1999-4893/5/1/18 In this paper, we consider the following sliding puzzle called torus puzzle. In an m by n board, there are mn pieces numbered from 1 to mn. Initially, the pieces are placed in ascending order. Then they are scrambled by rotating the rows and columns without the player’s knowledge. The objective of the torus puzzle is to rearrange the pieces in ascending order by rotating the rows and columns. We provide a solution to this puzzle. In addition, we provide lower and upper bounds on the number of steps for solving the puzzle. Moreover, we consider a variant of the torus puzzle in which each piece is colored either black or white, and we present a hardness result for solving it. Algorithms 2012-01-13 5 1 Article 10.3390/a5010018 18 29 1999-4893 2012-01-13 doi: 10.3390/a5010018 Kazuyuki Amano Yuta Kojima Toshiya Kurabayashi Keita Kurihara Masahiro Nakamura Ayaka Omi Toshiyuki Tanaka Koichi Yamazaki http://www.mdpi.com/1999-4893/5/1/1 We present tools that can be used within a larger system referred to as a passive assistant. The system receives information from a mobile device, as well as information from an image database such as Google Street View, and employs image processing to provide useful information about a local urban environment to a user who is visually impaired. The first stage acquires and computes accurate location information, the second stage performs texture and color analysis of a scene, and the third stage provides specific object recognition and navigation information. These second and third stages rely on compression-based tools (dimensionality reduction, vector quantization, and coding) that are enhanced by knowledge of (approximate) location of objects. Algorithms 2012-01-10 5 1 Article 10.3390/a5010001 1 17 1999-4893 2012-01-10 doi: 10.3390/a5010001 Antonella Di Lillo Ajay Daptardar Kevin Thomas James A. Storer Giovanni Motta http://www.mdpi.com/1999-4893/4/4/307 For fixed k ≥ 2 and fixed data alphabet of cardinality m, the hierarchical type class of a data string of length n = kj for some j ≥ 1 is formed by permuting the string in all possible ways under permutations arising from the isomorphisms of the unique finite rooted tree of depth j which has n leaves and k children for each non-leaf vertex. Suppose the data strings in a hierarchical type class are losslessly encoded via binary codewords of minimal length. A hierarchical entropy function is a function on the set of m-dimensional probability distributions which describes the asymptotic compression rate performance of this lossless encoding scheme as the data length n is allowed to grow without bound. We determine infinitely many hierarchical entropy functions which are each self-affine. For each such function, an explicit iterated function system is found such that the graph of the function is the attractor of the system. Algorithms 2011-11-01 4 4 Article 10.3390/a4040307 307 333 1999-4893 2011-11-01 doi: 10.3390/a4040307 John Kieffer http://www.mdpi.com/1999-4893/4/4/285 We propose a framework for the exact probabilistic analysis of window-based pattern matching algorithms, such as Boyer–Moore, Horspool, Backward DAWG Matching, Backward Oracle Matching, and more. In particular, we develop an algorithm that efficiently computes the distribution of a pattern matching algorithm’s running time cost (such as the number of text character accesses) for any given pattern in a random text model. Text models range from simple uniform models to higher-order Markov models or hidden Markov models (HMMs). Furthermore, we provide an algorithm to compute the exact distribution of differences in running time cost of two pattern matching algorithms. Methodologically, we use extensions of finite automata which we call deterministic arithmetic automata (DAAs) and probabilistic arithmetic automata (PAAs) [1]. Given an algorithm, a pattern, and a text model, a PAA is constructed from which the sought distributions can be derived using dynamic programming. To our knowledge, this is the first time that substring- or suffix-based pattern matching algorithms are analyzed exactly by computing the whole distribution of running time cost. Experimentally, we compare Horspool’s algorithm, Backward DAWG Matching, and Backward Oracle Matching on prototypical patterns of short length and provide statistics on the size of minimal DAAs for these computations. Algorithms 2011-10-31 4 4 Article 10.3390/a4040285 285 306 1999-4893 2011-10-31 doi: 10.3390/a4040285 Tobias Marschall Sven Rahmann http://www.mdpi.com/1999-4893/4/4/262 The smallest grammar problem—namely, finding a smallest context-free grammar that generates exactly one sequence—is of practical and theoretical importance in fields such as Kolmogorov complexity, data compression and pattern discovery. We propose a new perspective on this problem by splitting it into two tasks: (1) choosing which words will be the constituents of the grammar and (2) searching for the smallest grammar given this set of constituents. We show how to solve the second task in polynomial time parsing longer constituent with smaller ones. We propose new algorithms based on classical practical algorithms that use this optimization to find small grammars. Our algorithms consistently find smaller grammars on a classical benchmark reducing the size in 10% in some cases. Moreover, our formulation allows us to define interesting bounds on the number of small grammars and to empirically compare different grammars of small size. Algorithms 2011-10-26 4 4 Article 10.3390/a4040262 262 284 1999-4893 2011-10-26 doi: 10.3390/a4040262 Rafael Carrascosa François Coste Matthias Gallé Gabriel Infante-Lopez http://www.mdpi.com/1999-4893/4/4/239 Radio Frequency Interference (RFI) detection and mitigation algorithms based on a signal’s spectrogram (frequency and time domain representation) are presented. The radiometric signal’s spectrogram is treated as an image, and therefore image processing techniques are applied to detect and mitigate RFI by two-dimensional filtering. A series of Monte-Carlo simulations have been performed to evaluate the performance of a simple thresholding algorithm and a modified two-dimensional Wiener filter. Algorithms 2011-10-25 4 4 Article 10.3390/a4040239 239 261 1999-4893 2011-10-25 doi: 10.3390/a4040239 Jose Miguel Tarongi Adriano Camps http://www.mdpi.com/1999-4893/4/4/223 In order to be able to capture effects from co-transcriptional folding, we extend stochastic context-free grammars such that the probability of applying a rule can depend on the length of the subword that is eventually generated from the symbols introduced by the rule, and we show that existing algorithms for training and for determining the most probable parse tree can easily be adapted to the extended model without losses in performance. Furthermore, we show that the extended model is suited to improve the quality of predictions of RNA secondary structures. The extended model may also be applied to other fields where stochastic context-free grammars are used like natural language processing. Additionally some interesting questions in the field of formal languages arise from it. Algorithms 2011-10-21 4 4 Article 10.3390/a4040223 223 238 1999-4893 2011-10-21 doi: 10.3390/a4040223 Frank Weinberg Markus E. Nebel http://www.mdpi.com/1999-4893/4/3/200 In an asynchronous data stream, the data items may be out of order with respect to their original timestamps. This paper studies the space complexity required by a data structure to maintain such a data stream so that it can approximate the set of frequent items over a sliding time window with sufficient accuracy. Prior to our work, the best solution is given by Cormode et al. [1], who gave an O (1/ε log W log (εB/ log W) min {log W, 1/ε} log |U|)- space data structure that can approximate the frequent items within an ε error bound, where W and B are parameters of the sliding window, and U is the set of all possible item names. We gave a more space-efficient data structure that only requires O (1/ε log W log (εB/ logW) log log W) space. Algorithms 2011-09-22 4 3 Article 10.3390/a4030200 200 222 1999-4893 2011-09-22 doi: 10.3390/a4030200 Hing-Fung Ting Lap-Kei Lee Ho-Leung Chan Tak-Wah Lam http://www.mdpi.com/1999-4893/4/3/183 We present a survey of results concerning Lempel–Ziv data compression on parallel and distributed systems, starting from the theoretical approach to parallel time complexity to conclude with the practical goal of designing distributed algorithms with low communication cost. Storer’s extension for image compression is also discussed. Algorithms 2011-09-14 4 3 Article 10.3390/a4030183 183 199 1999-4893 2011-09-14 doi: 10.3390/a4030183 Sergio De Agostino http://www.mdpi.com/1999-4893/4/3/155 The European Space Agency (ESA) successfully launched the Soil Moisture and Ocean Salinity (SMOS) mission in November 2, 2009. SMOS uses a new type of instrument, a synthetic aperture radiometer named MIRAS that provides full-polarimetric multi-angular L-band brightness temperatures, from which regular and global maps of Sea Surface Salinity (SSS) and Soil Moisture (SM) are generated. Although SMOS operates in a restricted band (1400–1427 MHz), radio-frequency interference (RFI) appears in SMOS imagery in many areas of the world, and it is an important issue to be addressed for quality SSS and SM retrievals. The impact on SMOS imagery of a sinusoidal RFI source is reviewed, and the problem is illustrated with actual RFI encountered by SMOS. Two RFI detection and mitigation algorithms are developed (dual-polarization and full-polarimetric modes), the performance of the second one has been quantitatively evaluated in terms of probability of detection and false alarm (using a synthetic test scene), and results presented using real dual-polarization and full-polarimetric SMOS imagery. Finally, a statistical analysis of more than 13,000 L1b snap-shots is presented and discussed. Algorithms 2011-08-30 4 3 Article 10.3390/a4030155 155 182 1999-4893 2011-08-30 doi: 10.3390/a4030155 Adriano Camps Jerome Gourrion Jose Miguel Tarongi Mercedes Vall Llossera Antonio Gutierrez Jose Barbosa Rita Castro http://www.mdpi.com/1999-4893/4/2/131 This paper analyzes how recommender systems can be applied to current e-learning systems to guide learners in personalized inclusive e-learning scenarios. Recommendations can be used to overcome current limitations of learning management systems in providing personalization and accessibility features. Recommenders can take advantage of standards-based solutions to provide inclusive support. To this end we have identified the need for developing semantic educational recommender systems, which are able to extend existing learning management systems with adaptive navigation support. In this paper we present three requirements to be considered in developing these semantic educational recommender systems, which are in line with the service-oriented approach of the third generation of learning management systems, namely: (i) a recommendation model; (ii) an open standards-based service-oriented architecture; and (iii) a usable and accessible graphical user interface to deliver the recommendations. Algorithms 2011-07-20 4 2 Article 10.3390/a4030131 131 154 1999-4893 2011-07-20 doi: 10.3390/a4030131 Olga C. Santos Jesus G. Boticario http://www.mdpi.com/1999-4893/4/2/115 Peelle’s Pertinent Puzzle (PPP) was described in 1987 in the context of estimating fundamental parameters that arise in nuclear interaction experiments. In PPP, generalized least squares (GLS) parameter estimates fell outside the range of the data, which has raised concerns that GLS is somehow flawed and has led to suggested alternatives to GLS estimators. However, there have been no corresponding performance comparisons among methods, and one suggested approach involving simulated data realizations is statistically incomplete. Here we provide performance comparisons among estimators, introduce approximate Bayesian computation (ABC) using density estimation applied to simulated data realizations to produce an alternative to the incomplete approach, complete the incompletely specified approach, and show that estimation error in the assumed covariance matrix cannot always be ignored. Algorithms 2011-06-23 4 2 Article 10.3390/a4020115 115 130 1999-4893 2011-06-23 doi: 10.3390/a4020115 Tom Burr Todd Graves Nicolas Hengartner Toshihiko Kawano Feng Pan Patrick Talou http://www.mdpi.com/1999-4893/4/2/87 Two goodness-of-fit tests for copulas are being investigated. The first one deals with the case of elliptical copulas and the second one deals with independent copulas. These tests result from the expansion of the projection pursuit methodology that we will introduce in the present article. This method enables us to determine on which axis system these copulas lie as well as the exact value of these very copulas in the basis formed by the axes previously determined irrespective of their value in their canonical basis. Simulations are also presented as well as an application to real datasets. Algorithms 2011-04-26 4 2 Article 10.3390/a4020087 87 114 1999-4893 2011-04-26 doi: 10.3390/a4020087 Jacques Touboul http://www.mdpi.com/1999-4893/4/2/75 Given a directed graph G with non-negative cost on the arcs, a directed tour cover T of G is a cycle (not necessarily simple) in G such that either head or tail (or both of them) of every arc in G is touched by T. The minimum directed tour cover problem (DToCP), which is to find a directed tour cover of minimum cost, is NP-hard. It is thus interesting to design approximation algorithms with performance guarantee to solve this problem. Although its undirected counterpart (ToCP) has been studied in recent years, in our knowledge, the DToCP remains widely open. In this paper, we give a 2 log2(n)-approximation algorithm for the DToCP. Algorithms 2011-04-20 4 2 Article 10.3390/a4020075 75 86 1999-4893 2011-04-20 doi: 10.3390/a4020075 Viet Hung Nguyen http://www.mdpi.com/1999-4893/4/1/61 The problem of compressed pattern matching, which has recently been treated in many papers dealing with free text, is extended to structured files, specifically to dictionaries, which appear in any full-text retrieval system. The prefix-omission method is combined with Huffman coding and a new variant based on Fibonacci codes is presented. Experimental results suggest that the new methods are often preferable to earlier ones, in particular for small files which are typical for dictionaries, since these are usually kept in small chunks. Algorithms 2011-03-22 4 1 Article 10.3390/a4010061 61 74 1999-4893 2011-03-22 doi: 10.3390/a4010061 Shmuel T. Klein Dana Shapira http://www.mdpi.com/1999-4893/4/1/40 Several variants of the edit distance problem with block deletions are considered. Polynomial time optimal algorithms are presented for the edit distance with block deletions allowing character insertions and character moves, but without block moves. We show that the edit distance with block moves and block deletions is NP-complete (Nondeterministic Polynomial time problems in which any given solution to such problem can be verified in polynomial time, and any NP problem can be converted into it in polynomial time), and that it can be reduced to the problem of non-recursive block moves and block deletions within a constant factor. Algorithms 2011-03-07 4 1 Article 10.3390/a4010040 40 60 1999-4893 2011-03-07 doi: 10.3390/a4010040 Dana Shapira James A. Storer http://www.mdpi.com/1999-4893/4/1/28 Generalized least squares (GLS) for model parameter estimation has a long and successful history dating to its development by Gauss in 1795. Alternatives can outperform GLS in some settings, and alternatives to GLS are sometimes sought when GLS exhibits curious behavior, such as in Peelle’s Pertinent Puzzle (PPP). PPP was described in 1987 in the context of estimating fundamental parameters that arise in nuclear interaction experiments. In PPP, GLS estimates fell outside the range of the data, eliciting concerns that GLS was somehow flawed. These concerns have led to suggested alternatives to GLS estimators. This paper defends GLS in the PPP context, investigates when PPP can occur, illustrates when PPP can be beneficial for parameter estimation, reviews optimality properties of GLS estimators, and gives an example in which PPP does occur. Algorithms 2011-02-15 4 1 Article 10.3390/a4010028 28 39 1999-4893 2011-02-15 doi: 10.3390/a4010028 Tom Burr Toshihiko Kawano Patrick Talou Feng Pan Nicolas Hengartner http://www.mdpi.com/1999-4893/4/1/16 Several measurements are used to describe the behavior of a diabetic patient’s blood glucose. We describe a new, wavelet-based algorithm that indicates a new measurement called a PLA index could be used to quantify the variability or predictability of blood glucose. This wavelet-based approach emphasizes the shape of a blood glucose graph. Using continuous glucose monitors (CGMs), this measurement could become a new tool to classify patients based on their blood glucose behavior and may become a new method in the management of diabetes. Algorithms 2011-02-15 4 1 Article 10.3390/a4010016 16 27 1999-4893 2011-02-15 doi: 10.3390/a4010016 Edward Aboufadel Robert Castellano Derek Olson http://www.mdpi.com/1999-4893/4/1/1 Chris Langton proposed a model of an artificial life that he named “ant”: an agent- called ant- that is over a square of a grid moves by turning to the left (or right) accordingly to black (or white) color of the square where it is heading, and the square then reverses its color. Bunimovich and Troubetzkoy proved that an ant’s trajectory is always unbounded, or equivalently, there exists no repeatable configuration of the ant’s system. On the other hand, by introducing a new type of color where the ant goes straight ahead and the color never changes, repeatable configurations are known to exist. In this paper, we prove that determining whether a given finite configuration of generalized Langton’s ant is repeatable or not is PSPACE-hard. We also prove the PSPACE-hardness of the ant’s problem on a hexagonal grid. Algorithms 2011-01-28 4 1 Article 10.3390/a4010001 1 15 1999-4893 2011-01-28 doi: 10.3390/a4010001 Tatsuie Tsukiji Takeo Hagiwara http://www.mdpi.com/1999-4893/3/4/329 Increasingly encompassing models have been suggested for our world. Theories range from generally accepted to increasingly speculative to apparently bogus. The progression of theories from ego- to geo- to helio-centric models to universe and multiverse theories and beyond was accompanied by a dramatic increase in the sizes of the postulated worlds, with humans being expelled from their center to ever more remote and random locations. Rather than leading to a true theory of everything, this trend faces a turning point after which the predictive power of such theories decreases (actually to zero). Incorporating the location and other capacities of the observer into such theories avoids this problem and allows to distinguish meaningful from predictively meaningless theories. This also leads to a truly complete theory of everything consisting of a (conventional objective) theory of everything plus a (novel subjective) observer process. The observer localization is neither based on the controversial anthropic principle, nor has it anything to do with the quantum-mechanical observation process. The suggested principle is extended to more practical (partial, approximate, probabilistic, parametric) world models (rather than theories of everything). Finally, I provide a justification of Ockham’s razor, and criticize the anthropic principle, the doomsday argument, the no free lunch theorem, and the falsifiability dogma. Algorithms 2010-09-29 3 4 Article 10.3390/a3040329 329 350 1999-4893 2010-09-29 doi: 10.3390/a3040329 Marcus Hutter http://www.mdpi.com/1999-4893/3/3/311 We compare univariate L1 interpolating splines calculated on 5-point windows, on 7-point windows and on global data sets using four different spline functionals, namely, ones based on the second derivative, the first derivative, the function value and the antiderivative. Computational results indicate that second-derivative-based 5-point-window L1 splines preserve shape as well as or better than the other types of L1 splines. To calculate second-derivative-based 5-point-window L1 splines, we introduce an analysis-based, parallelizable algorithm. This algorithm is orders of magnitude faster than the previously widely used primal affine algorithm. Algorithms 2010-08-20 3 3 Article 10.3390/a3030311 311 328 1999-4893 2010-08-20 doi: 10.3390/a3030311 Lu Yu Qingwei Jin John E. Lavery Shu-Cherng Fang http://www.mdpi.com/1999-4893/3/3/294 We present a car traffic simulation prototype for complex networks, that is formed by a collection of roads and junctions. Traffic load evolution is described by a model based on fluid dynamic conservation laws, deduced from conservation of the number of cars. The model contains some additional hypothesis in order to reproduce specific car traffic features such as route based car distribution at nodes and the presence of right-of-way at the crossroads. A complete implementation of this model is then presented, together with computational results on case studies. Algorithms 2010-08-09 3 3 Article 10.3390/a3030294 294 310 1999-4893 2010-08-09 doi: 10.3390/a3030294 Massimiliano Caramia Ciro D’Apice Benedetto Piccoli Antonino Sgalambro http://www.mdpi.com/1999-4893/3/3/276 We analytically investigate univariate C1 continuous cubic L1 interpolating splines calculated by minimizing an L1 spline functional based on the second derivative on 5-point windows. Specifically, we link geometric properties of the data points in the windows with linearity, convexity and oscillation properties of the resulting L1 spline. These analytical results provide the basis for a computationally efficient algorithm for calculation of L1 splines on 5-point windows. Algorithms 2010-07-30 3 3 Article 10.3390/a3030276 276 293 1999-4893 2010-07-30 doi: 10.3390/a3030276 Qingwei Jin John E. Lavery Shu-Cherng Fang http://www.mdpi.com/1999-4893/3/3/265 The metric average is a binary operation between sets in Rn which is used in the approximation of set-valued functions. We introduce an algorithm that applies tools of computational geometry to the computation of the metric average of 2D sets with piecewise linear boundaries. Algorithms 2010-07-26 3 3 Article 10.3390/a3030265 265 275 1999-4893 2010-07-26 doi: 10.3390/a3030265 Shay Kels Nira Dyn Evgeny Lipovetsky http://www.mdpi.com/1999-4893/3/3/260 Ray J. Solomonoff died on December 7, 2009, in Cambridge, Massachusetts, of complications of a stroke caused by an aneurism in his head. Ray was the first inventor of Algorithmic Information Theory which deals with the shortest effective description length of objects and is commonly designated by the term “Kolmogorov complexity.” In the 1950s Solomonoff was one of the first researchers to treat probabilistic grammars and the associated languages. He treated probabilistic Artificial Intelligence (AI) when “probabilistic” was unfashionable, and treated questions of machine learning early on. But his greatest contribution is the creation of Algorithmic Information Theory. [...] Algorithms 2010-07-20 3 3 Obituary 10.3390/a3030260 260 264 1999-4893 2010-07-20 doi: 10.3390/a3030260 Paul M.B. Vitanyi http://www.mdpi.com/1999-4893/3/3/255 Ray Solomonoff was always inventive. As a child, he had a lab in his parent's cellar in Cleveland and a secret air hole to vent the smoke from his experiments. He gave his friend Marvin Minsky a so-called "Hurry" clock — a clock labeled "HURRY" that ran very fast. Helped by a friend, he built a year round house in N.H. He put in thick insulation, enabling him to heat the house with two rows of light bulbs along the ceiling. I met Ray shortly after he finished this house, in 1969. I knew about foraging, so I showed him edible plants like Indian Cucumber Root. He was so happy: it was as if we found a fountain of champagne. [...] Algorithms 2010-07-20 3 3 Obituary 10.3390/a30302555 255 259 1999-4893 2010-07-20 doi: 10.3390/a30302555 Grace Solomonoff http://www.mdpi.com/1999-4893/3/3/244 We analyze further the Magnus-Derek game, a two-player game played on a round table with n positions. The players jointly control the movement of a token. One player, Magnus, aims to maximize the number of positions visited while minimizing the number of rounds. The other player, Derek, attempts to minimize the number of visited positions. We present a new strategy for Magnus that succeeds in visiting the maximal number of positions in 3(n – 1) rounds, which is the optimal number of rounds up to a constant factor. Algorithms 2010-07-15 3 3 Article 10.3390/a3030244 244 254 1999-4893 2010-07-15 doi: 10.3390/a3030244 Nedev http://www.mdpi.com/1999-4893/3/3/224 The algorithm of Lenstra, Lenstra, and Lovász (LLL) transforms a given integer lattice basis into a reduced basis. Storjohann improved the worst case complexity of LLL algorithms by a factor of O(n) using modular arithmetic. Koy and Schnorr developed a segment-LLL basis reduction algorithm that generates lattice basis satisfying a weaker condition than the LLL reduced basis with O(n) improvement than the LLL algorithm. In this paper we combine Storjohann’s modular arithmetic approach with the segment-LLL approach to further improve the worst case complexity of the segment-LLL algorithms by a factor of n0.5. Algorithms 2010-07-12 3 3 Article 10.3390/a3030224 224 243 1999-4893 2010-07-12 doi: 10.3390/a3030224 Mehrotra Li http://www.mdpi.com/1999-4893/3/3/216 This brief note presents an algorithm to solve ordinary stochastic differential equations (SDEs). The algorithm is based on the joint solution of a system of two partial differential equations and provides strong solutions for finite-dimensional systems of SDEs driven by standard Wiener processes and with adapted initial data. Several examples illustrate its use. Algorithms 2010-07-01 3 3 Article 10.3390/a3030216 216 223 1999-4893 2010-07-01 doi: 10.3390/a3030216 Schurz http://www.mdpi.com/1999-4893/3/2/197 This paper is a review which presents and explains the decomposition of graphs by clique minimal separators. The pace is leisurely, we give many examples and figures. Easy algorithms are provided to implement this decomposition. The historical and theoretical background is given, as well as sketches of proofs of the structural results involved. Algorithms 2010-05-14 3 2 Review 10.3390/a3020197 197 215 1999-4893 2010-05-14 doi: 10.3390/a3020197 Berry Pogorelcnik Simonet http://www.mdpi.com/1999-4893/3/2/183 In recent years, many tools have been proposed to reduce programming learning difficulties felt by many students. Our group has contributed to this effort through the development of several tools, such as VIP, SICAS, OOP-Anim, SICAS-COL and H-SICAS. Even though we had some positive results, the utilization of these tools doesn’t seem to significantly reduce weaker student’s difficulties. These students need stronger support to motivate them to get engaged in learning activities, inside and outside classroom. Nowadays, many technologies are available to create contexts that may help to accomplish this goal. We consider that a promising path goes through the integration of solutions. In this paper we analyze the features, strengths and weaknesses of the tools developed by our group. Based on these considerations we present a new environment, integrating different types of pedagogical approaches, resources, tools and technologies for programming learning support. With this environment, currently under development, it will be possible to review contents and lessons, based on video and screen captures. The support for collaborative tasks is another key point to improve and stimulate different models of teamwork. The platform will also allow the creation of various alternative models (learning objects) for the same subject, enabling personalized learning paths adapted to each student knowledge level, needs and preferential learning styles. The learning sequences will work as a study organizer, following a suitable taxonomy, according to student’s cognitive skills. Although the main goal of this environment is to support students with more difficulties, it will provide a set of resources supporting the learning of more advanced topics. Software engineering techniques and representations, object orientation and event programming are features that will be available in order to promote the learning progress of students. Algorithms 2010-04-20 3 2 Article 10.3390/a3020183 183 196 1999-4893 2010-04-20 doi: 10.3390/a3020183 Santos Gomes Mendes http://www.mdpi.com/1999-4893/3/2/168 Both learning how to program and understanding algorithms or data structures are often difficult. This paper presents three complementary approaches that we employ to help our students in learning to program, especially during the first term of their study. We use a web-based programming task database as an easy and risk-free environment for taking the first steps in programming Java. The Animal algorithm visualization system is used to visualize the dynamic behavior of algorithms and data structures. We complement both approaches with tutorial videos on using the Eclipse IDE. We also report on the experiences with this combined approach. Algorithms 2010-04-15 3 2 Article 10.3390/a3020168 168 182 1999-4893 2010-04-15 doi: 10.3390/a3020168 Rößling http://www.mdpi.com/1999-4893/3/2/145 Given a sequence T = t0t1 . . . tn-1 of size n = |T|, with symbols from a fixed alphabet Σ, (|Σ| ≤ n), the suffix array provides a listing of all the suffixes of T in a lexicographic order. Given T, the suffix sorting problem is to construct its suffix array. The direct suffix sorting problem is to construct the suffix array of T directly without using the suffix tree data structure. While algorithims for linear time, linear space direct suffix sorting have been proposed, the actual constant in the linear space is still a major concern, given that the applications of suffix trees and suffix arrays (such as in whole-genome analysis) often involve huge data sets. In this work, we reduce the gap between current results and the minimal space requirement. We introduce an algorithm for the direct suffix sorting problem with worst case time complexity in O(n), requiring only (1 2/3 n log n ¡ n log |Σ| + O(1)) bits in memory space. This implies 5 2/3 n+O(1) bytes for total space requirment, (including space for both the output suffix array and the input sequence T) assuming n ≤ 232, |Σ| ≤ 256, and 4 bytes per integer. The basis of our algorithm is an extension of Shannon-Fano-Elias codes used in source coding and information theory. This is the first time information-theoretic methods have been used as the basis for solving the suffix sorting problem. Algorithms 2010-04-01 3 2 Article 10.3390/a3020145 145 167 1999-4893 2010-04-01 doi: 10.3390/a3020145 Adjeroh Nan http://www.mdpi.com/1999-4893/3/2/125 The present paper describes a novel recognition method of pulmonary nodules (i.e., cancer candidates) in thoracic computed tomography scans by use of three-dimensional spherical and cylindrical models that represent nodules and blood vessels, respectively. The anatomical validity of these object models and their fidelity to computed tomography scans are evaluated based on the Bayes theorem. The nodule recognition is employed by the maximum a posteriori estimation. The proposed method is applied to 26 actual computed tomography scans, and experimental results are shown. Algorithms 2010-03-31 3 2 Article 10.3390/a3020125 125 144 1999-4893 2010-03-31 doi: 10.3390/a3020125 Takizawa Yamamoto Shiina http://www.mdpi.com/1999-4893/3/2/100 Graph search algorithms have exploited graph extremities, such as the leaves of a tree and the simplicial vertices of a chordal graph. Recently, several well-known graph search algorithms have been collectively expressed as two generic algorithms called MLS and MLSM. In this paper, we investigate the properties of the vertex that is numbered 1 by MLS on a chordal graph and by MLSM on an arbitrary graph. We explain how this vertex is an extremity of the graph. Moreover, we show the remarkable property that the minimal separators included in the neighborhood of this vertex are totally ordered by inclusion. Algorithms 2010-03-24 3 2 Article 10.3390/a3020100 100 124 1999-4893 2010-03-24 doi: 10.3390/a3020100 Berry Blair Bordat Simonet http://www.mdpi.com/1999-4893/3/1/92 In this paper, we apply various data mining techniques including continuous numeric and discrete classification prediction models of base oils biodegradability, with emphasis on improving prediction accuracy. The results show that highly biodegradable oils can be better predicted through numeric models. In contrast, classification models did not uncover a similar dichotomy. With the exception of Memory Based Reasoning and Decision Trees, tested classification techniques achieved high classification prediction. However, the technique of Decision Trees helped uncover the most significant predictors. A simple classification rule derived based on this predictor resulted in good classification accuracy. The application of this rule enables efficient classification of base oils into either low or high biodegradability classes with high accuracy. For the latter, a higher precision biodegradability prediction can be obtained using continuous modeling techniques. Algorithms 2010-02-23 3 1 Article 10.3390/algor3010092 92 99 1999-4893 2010-02-23 doi: 10.3390/algor3010092 Sihem Ben Abdelmelek Saloua Saidane Malika Trabelsi http://www.mdpi.com/1999-4893/3/1/76 Algorithm animations typically assist in educational tasks aimed simply at achieving understanding. Potentially, animations could assist in higher levels of cognition, such as the analysis level, but they usually fail in providing this support because they are not flexible or comprehensive enough. In particular, animations of recursion provided by educational systems hardly support the analysis of recursive algorithms. Here we show how to provide full support to the analysis of recursive algorithms. From a technical point of view, animations are enriched with interaction techniques inspired by the information visualization (InfoVis) field. Interaction tasks are presented in seven categories, and deal with both static visualizations and dynamic animations. All of these features are implemented in the SRec system, and visualizations generated by SRec are used to illustrate the article. Algorithms 2010-02-10 3 1 Article 10.3390/a3010076 76 91 1999-4893 2010-02-10 doi: 10.3390/a3010076 J. Ángel Velázquez-Iturbide Antonio Pérez-Carrasco http://www.mdpi.com/1999-4893/3/1/63 If we can use previous knowledge of the source (or the knowledge of a source that is correlated to the one we want to compress) to exploit the compression process then we can have significant gains in compression. By doing this in the fundamental source coding theorem we can substitute entropy with conditional entropy and we have a new theoretical limit that allows for better compression. To do this, when data compression is used for data transmission, we can assume some degree of interaction between the compressor and the decompressor that can allow a more efficient usage of the previous knowledge they both have of the source. In this paper we review previous work that applies interactive approaches to data compression and discuss this possibility. Algorithms 2010-01-29 3 1 Article 10.3390/a3010063 63 75 1999-4893 2010-01-29 doi: 10.3390/a3010063 Bruno Carpentieri http://www.mdpi.com/1999-4893/3/1/44 A new breast cancer detection algorithm, named the “Gabor Cancer Detection” (GCD) algorithm, utilizing Gabor features is proposed. Three major steps are involved in the GCD algorithm, preprocessing, segmentation (generating alarm segments), and classification (reducing false alarms). In preprocessing, a digital mammogram is down-sampled, quantized, denoised and enhanced. Nonlinear diffusion is used for noise suppression. In segmentation, a band-pass filter is formed by rotating a 1-D Gaussian filter (off center) in frequency space, termed as “Circular Gaussian Filter” (CGF). A CGF can be uniquely characterized by specifying a central frequency and a frequency band. A mass or calcification is a space-occupying lesion and usually appears as a bright region on a mammogram. The alarm segments (suspicious to be masses/calcifications) can be extracted out using a threshold that is adaptively decided upon the histogram analysis of the CGF-filtered mammogram. In classification, a Gabor filter bank is formed with five bands by four orientations (horizontal, vertical, 45 and 135 degree) in Fourier frequency domain. For each mammographic image, twenty Gabor-filtered images are produced. A set of edge histogram descriptors (EHD) are then extracted from 20 Gabor images for classification. An EHD signature is computed with four orientations of Gabor images along each band and five EHD signatures are then joined together to form an EHD feature vector of 20 dimensions. With the EHD features, the fuzzy C-means clustering technique and k-nearest neighbor (KNN) classifier are used to reduce the number of false alarms. The experimental results tested on the DDSM database (University of South Florida) show the promises of GCD algorithm in breast cancer detection, which achieved TP (true positive rate) = 90% at FPI (false positives per image) = 1.21 in mass detection; and TP = 93% at FPI = 1.19 in calcification detection. Algorithms 2010-01-19 3 1 Article 10.3390/a3010044 44 62 1999-4893 2010-01-19 doi: 10.3390/a3010044 Yufeng Zheng http://www.mdpi.com/1999-4893/3/1/21 We present a complete, end-to-end computer-aided detection (CAD) system for identifying lesions in the colon, imaged with computed tomography (CT). This system includes facilities for colon segmentation, candidate generation, feature analysis, and classification. The algorithms have been designed to offer robust performance to variation in image data and patient preparation. By utilizing efficient 2D and 3D processing, software optimizations, multi-threading, feature selection, and an optimized cascade classifier, the CAD system quickly determines a set of detection marks. The colon CAD system has been validated on the largest set of data to date, and demonstrates excellent performance, in terms of its high sensitivity, low false positive rate, and computational efficiency. Algorithms 2010-01-05 3 1 Article 10.3390/a3010021 21 43 1999-4893 2010-01-05 doi: 10.3390/a3010021 Greg Slabaugh Xiaoyun Yang Xujiong Ye Richard Boyes Gareth Beddoe http://www.mdpi.com/1999-4893/3/1/1 We present in this paper a novel dynamic learning method for classifying polyp candidate detections in Computed Tomographic Colonography (CTC) using an adaptation of the Least Square Support Vector Machine (LS-SVM). The proposed technique, called Weighted Proximal Support Vector Machines (WP-SVM), extends the offline capabilities of the SVM scheme to address practical CTC applications. Incremental data are incorporated in the WP-SVM as a weighted vector space, and the only storage requirements are the hyperplane parameters. WP-SVM performance evaluation based on 169 clinical CTC cases using a 3D computer-aided diagnosis (CAD) scheme for feature reduction comparable favorably with previously published CTC CAD studies that have however involved only binary and offline classification schemes. The experimental results obtained from iteratively applying WP-SVM to improve detection sensitivity demonstrate its viability for incremental learning, thereby motivating further follow on research to address a wider range of true positive subclasses such as pedunculated, sessile, and flat polyps, and over a wider range of false positive subclasses such as folds, stool, and tagged materials. Algorithms 2010-01-04 3 1 Article 10.3390/a3010001 1 20 1999-4893 2010-01-04 doi: 10.3390/a3010001 Mariette Awad Yuichi Motai Janne Näppi Hiroyuki Yoshida http://www.mdpi.com/1999-4893/2/4/1503 Techniques in image similarity can be used to improve the classification of breast cancer images. Breast cancer images in the mammogram modality have an abundance of non-cancerous structures that are similar to cancer, which make classification of images as containing cancer especially difficult to work with. Only the cancerous part of the image is relevant, so the techniques must learn to recognize cancer in noisy mammograms and extract features from that cancer to appropriately classify images. There are also many types or classes of cancer with different characteristics over which the system must work. Mammograms come in sets of four, two images of each breast, which enables comparison of the left and right breast images to help determine relevant features and remove irrelevant features. In this work, image feature clustering is done to reduce the noise and the feature space, and the results are used in a distance function that uses a learned threshold in order to produce a classification. The threshold parameter of the distance function is learned simultaneously with the underlying clustering and then integrated to produce an agglomeration that is relevant to the images. This technique can diagnose breast cancer more accurately than commercial systems and other published results. Algorithms 2009-12-01 2 4 Article 10.3390/a2041503 1503 1525 1999-4893 2009-12-01 doi: 10.3390/a2041503 Dave Tahmoush http://www.mdpi.com/1999-4893/2/4/1473 This paper uses an ensemble of classifiers and active learning strategies to predict radiologists’ assessment of the nodules of the Lung Image Database Consortium (LIDC). In particular, the paper presents machine learning classifiers that model agreement among ratings in seven semantic characteristics: spiculation, lobulation, texture, sphericity, margin, subtlety, and malignancy. The ensemble of classifiers (which can be considered as a computer panel of experts) uses 64 image features of the nodules across four categories (shape, intensity, texture, and size) to predict semantic characteristics. The active learning begins the training phase with nodules on which radiologists’ semantic ratings agree, and incrementally learns how to classify nodules on which the radiologists do not agree. Using our proposed approach, the classification accuracy of the ensemble of classifiers is higher than the accuracy of a single classifier. In the long run, our proposed approach can be used to increase consistency among radiological interpretations by providing physicians a “second read”. Algorithms 2009-11-30 2 4 Article 10.3390/a2041473 1473 1502 1999-4893 2009-11-30 doi: 10.3390/a2041473 Dmitriy Zinovev Daniela Raicu Jacob Furst Samuel G. Armato III http://www.mdpi.com/1999-4893/2/4/1449 Non-preemptive schedulers, despite their many discussed drawbacks, remain a very popular choice for practitioners of real-time and embedded systems. The non-preemptive ‘thrift’ cyclic scheduler—variations of which can be found in other application areas—has recently received considerable attention for the implementation of such embedded systems. A thrift scheduler provides a flexible and compact implementation model for periodic task sets with comparatively small overheads; additionally, it can overcome several of the problems associated with traditional ‘cyclic executives’. However, severe computational difficulties can still arise when designing schedules for non-trivial task sets. This paper is concerned with an optimization version of the offset-assignment problem, in which the objective is to assign task offsets such that the required CPU clock speed is minimized whilst ensuring that task overruns do not occur; it is known that the decision version of this problem is complete for Σ2p. The paper first considers the problemof candidate solution verification—itself strongly coNP-Complete—and a fast, exact algorithm for this problem is proposed; it is shown that for any fixed number of tasks, its execution time is polynomial. The paper then proposes two heuristic algorithms of pseudopolynomial complexity for solving the offset-assignment problem, and considers how redundant choices of offset combinations can be eliminated to help speed up the search. The performance of these algorithms is then experimentally evaluated, before conclusions are drawn. Algorithms 2009-11-26 2 4 Article 10.3390/a2041449 1449 1472 1999-4893 2009-11-26 doi: 10.3390/a2041449 Michael J. Short http://www.mdpi.com/1999-4893/2/4/1429 We consider grammar-based text compression with longest first substitution (LFS), where non-overlapping occurrences of a longest repeating factor of the input text are replaced by a new non-terminal symbol. We present the first linear-time algorithm for LFS. Our algorithm employs a new data structure called sparse lazy suffix trees. We also deal with a more sophisticated version of LFS, called LFS2, that allows better compression. The first linear-time algorithm for LFS2 is also presented. Algorithms 2009-11-25 2 4 Article 10.3390/a2041429 1429 1448 1999-4893 2009-11-25 doi: 10.3390/a2041429 Ryosuke Nakamura Shunsuke Inenaga Hideo Bannai Takashi Funamoto Masayuki Takeda Ayumi Shinohara http://www.mdpi.com/1999-4893/2/4/1410 Using Hidden Markov Models (HMMs) as a recognition framework for automatic classification of animal vocalizations has a number of benefits, including the ability to handle duration variability through nonlinear time alignment, the ability to incorporate complex language or recognition constraints, and easy extendibility to continuous recognition and detection domains. In this work, we apply HMMs to several different species and bioacoustic tasks using generalized spectral features that can be easily adjusted across species and HMM network topologies suited to each task. This experimental work includes a simple call type classification task using one HMM per vocalization for repertoire analysis of Asian elephants, a language-constrained song recognition task using syllable models as base units for ortolan bunting vocalizations, and a stress stimulus differentiation task in poultry vocalizations using a non-sequential model via a one-state HMM with Gaussian mixtures. Results show strong performance across all tasks and illustrate the flexibility of the HMM framework for a variety of species, vocalization types, and analysis tasks. Algorithms 2009-11-18 2 4 Article 10.3390/a2041410 1410 1428 1999-4893 2009-11-18 doi: 10.3390/a2041410 Yao Ren Michael T. Johnson Patrick J. Clemins Michael Darre Sharon Stuart Glaeser Tomasz S. Osiejuk Ebenezer Out-Nyarko http://www.mdpi.com/1999-4893/2/4/1368 The emergence of novel sensing elements, computing nodes, wireless communication and integration technology provides unprecedented possibilities for the design and application of intelligent systems. Each new application system must be designed from scratch, employing sophisticated methods ranging from conventional signal processing to computational intelligence. Currently, a significant part of this overall algorithmic chain of the computational system model still has to be assembled manually by experienced designers in a time and labor consuming process. In this research work, this challenge is picked up and a methodology and algorithms for automated design of intelligent integrated and resource-aware multi-sensor systems employing multi-objective evolutionary computation are introduced. The proposed methodology tackles the challenge of rapid-prototyping of such systems under realization constraints and, additionally, includes features of system instance specific self-correction for sustained operation of a large volume and in a dynamically changing environment. The extension of these concepts to the reconfigurable hardware platform renders so called self-x sensor systems, which stands, e.g., for self-monitoring, -calibrating, -trimming, and -repairing/-healing systems. Selected experimental results prove the applicability and effectiveness of our proposed methodology and emerging tool. By our approach, competitive results were achieved with regard to classification accuracy, flexibility, and design speed under additional design constraints. Algorithms 2009-11-18 2 4 Article 10.3390/a2041368 1368 1409 1999-4893 2009-11-18 doi: 10.3390/a2041368 Kuncup Iswandy Andreas König