http://www.mdpi.com/journal/algorithms Latest open access articles published in Algorithms at http://www.mdpi.com/journal/algorithms/ http://www.mdpi.com/1999-4893/5/1/18/ 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. http://www.mdpi.com/1999-4893/5/1/18/ Fri, 13 Jan 2012 00:00:00 CET Algorithms 2012-01-13 5 1 Article 18 29 1999-4893 How to Solve the Torus Puzzle 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. http://www.mdpi.com/1999-4893/5/1/1/ Tue, 10 Jan 2012 00:00:00 CET Algorithms 2012-01-10 5 1 Article 1 17 1999-4893 Compression-Based Tools for Navigation with an Image Database 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. http://www.mdpi.com/1999-4893/4/4/307/ Tue, 01 Nov 2011 00:00:00 CET Algorithms 2011-11-01 4 4 Article 307 333 1999-4893 A Catalog of Self-Affine Hierarchical Entropy Functions 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. http://www.mdpi.com/1999-4893/4/4/285/ Mon, 31 Oct 2011 00:00:00 CET Algorithms 2011-10-31 4 4 Article 285 306 1999-4893 An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms 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. http://www.mdpi.com/1999-4893/4/4/262/ Wed, 26 Oct 2011 00:00:00 CEST Algorithms 2011-10-26 4 4 Article 262 284 1999-4893 The Smallest Grammar Problem as Constituents Choice and Minimal Grammar Parsing 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. http://www.mdpi.com/1999-4893/4/4/239/ Tue, 25 Oct 2011 00:00:00 CEST Algorithms 2011-10-25 4 4 Article 239 261 1999-4893 Radio Frequency Interference Detection and Mitigation Algorithms Based on Spectrogram Analysis 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. http://www.mdpi.com/1999-4893/4/4/223/ Fri, 21 Oct 2011 00:00:00 CEST Algorithms 2011-10-21 4 4 Article 223 238 1999-4893 Applying Length-Dependent Stochastic Context-Free Grammars to RNA Secondary Structure Prediction 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. http://www.mdpi.com/1999-4893/4/3/200/ Thu, 22 Sep 2011 00:00:00 CEST Algorithms 2011-09-22 4 3 Article 200 222 1999-4893 Approximating Frequent Items in Asynchronous Data Stream over a Sliding Window 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. http://www.mdpi.com/1999-4893/4/3/183/ Wed, 14 Sep 2011 00:00:00 CEST Algorithms 2011-09-14 4 3 Article 183 199 1999-4893 Lempel–Ziv Data Compression on Parallel and Distributed Systems 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. http://www.mdpi.com/1999-4893/4/3/155/ Tue, 30 Aug 2011 00:00:00 CEST Algorithms 2011-08-30 4 3 Article 155 182 1999-4893 Radio-Frequency Interference Detection and Mitigation Algorithms for Synthetic Aperture Radiometers 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. http://www.mdpi.com/1999-4893/4/2/131/ Wed, 20 Jul 2011 00:00:00 CEST Algorithms 2011-07-20 4 2 Article 131 154 1999-4893 Requirements for Semantic Educational Recommender Systems in Formal E-Learning Scenarios 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. http://www.mdpi.com/1999-4893/4/2/115/ Thu, 23 Jun 2011 00:00:00 CEST Algorithms 2011-06-23 4 2 Article 115 130 1999-4893 Alternatives to the Least Squares Solution to Peelle’s Pertinent Puzzle 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. http://www.mdpi.com/1999-4893/4/2/87/ Tue, 26 Apr 2011 00:00:00 CEST Algorithms 2011-04-26 4 2 Article 87 114 1999-4893 Goodness-of-Fit Tests For Elliptical and Independent Copulas through Projection Pursuit 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. http://www.mdpi.com/1999-4893/4/2/75/ Wed, 20 Apr 2011 00:00:00 CEST Algorithms 2011-04-20 4 2 Article 75 86 1999-4893 Approximating the Minimum Tour Cover of a Digraph 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. http://www.mdpi.com/1999-4893/4/1/61/ Tue, 22 Mar 2011 00:00:00 CET Algorithms 2011-03-22 4 1 Article 61 74 1999-4893 Compressed Matching in Dictionaries 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. http://www.mdpi.com/1999-4893/4/1/40/ Mon, 07 Mar 2011 00:00:00 CET Algorithms 2011-03-07 4 1 Article 40 60 1999-4893 Edit Distance with Block Deletions 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. http://www.mdpi.com/1999-4893/4/1/28/ Tue, 15 Feb 2011 00:00:00 CET Algorithms 2011-02-15 4 1 Article 28 39 1999-4893 Defense of the Least Squares Solution to Peelle’s Pertinent Puzzle 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. http://www.mdpi.com/1999-4893/4/1/16/ Tue, 15 Feb 2011 00:00:00 CET Algorithms 2011-02-15 4 1 Article 16 27 1999-4893 Quantification of the Variability of Continuous Glucose Monitoring Data 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. http://www.mdpi.com/1999-4893/4/1/1/ Fri, 28 Jan 2011 00:00:00 CET Algorithms 2011-01-28 4 1 Article 1 15 1999-4893 Recognizing the Repeatable Configurations of Time-Reversible Generalized Langton’s Ant Is PSPACE-Hard 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. http://www.mdpi.com/1999-4893/3/4/329/ Wed, 29 Sep 2010 00:00:00 CEST Algorithms 2010-09-29 3 4 Article 329 350 1999-4893 A Complete Theory of Everything (Will Be Subjective) 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. http://www.mdpi.com/1999-4893/3/3/311/ Fri, 20 Aug 2010 00:00:00 CEST Algorithms 2010-08-20 3 3 Article 311 328 1999-4893 Univariate Cubic L1 Interpolating Splines: Spline Functional, Window Size and Analysis-based Algorithm 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. http://www.mdpi.com/1999-4893/3/3/294/ Mon, 09 Aug 2010 00:00:00 CEST Algorithms 2010-08-09 3 3 Article 294 310 1999-4893 Fluidsim: A Car Traffic Simulation Prototype Based on FluidDynamic 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. http://www.mdpi.com/1999-4893/3/3/276/ Fri, 30 Jul 2010 00:00:00 CEST Algorithms 2010-07-30 3 3 Article 276 293 1999-4893 Univariate Cubic L1 Interpolating Splines: Analytical Results for Linearity, Convexity and Oscillation on 5-PointWindows 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. http://www.mdpi.com/1999-4893/3/3/265/ Mon, 26 Jul 2010 00:00:00 CEST Algorithms 2010-07-26 3 3 Article 265 275 1999-4893 Computation of the Metric Average of 2D Sets with Piecewise Linear Boundaries 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. [...] http://www.mdpi.com/1999-4893/3/3/260/ Tue, 20 Jul 2010 00:00:00 CEST Algorithms 2010-07-20 3 3 Obituary 260 264 1999-4893 Ray Solomonoff, Founding Father of Algorithmic Information Theory 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. [...] http://www.mdpi.com/1999-4893/3/3/255/ Tue, 20 Jul 2010 00:00:00 CEST Algorithms 2010-07-20 3 3 Obituary 255 259 1999-4893 Ray Solomonoff (1926-2009) 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. http://www.mdpi.com/1999-4893/3/3/244/ Thu, 15 Jul 2010 00:00:00 CEST Algorithms 2010-07-15 3 3 Article 244 254 1999-4893 An O(n)-Round Strategy for the Magnus-Derek Game 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. http://www.mdpi.com/1999-4893/3/3/224/ Mon, 12 Jul 2010 00:00:00 CEST Algorithms 2010-07-12 3 3 Article 224 243 1999-4893 Segment LLL Reduction of Lattice Bases Using Modular Arithmetic 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. http://www.mdpi.com/1999-4893/3/3/216/ Thu, 01 Jul 2010 00:00:00 CEST Algorithms 2010-07-01 3 3 Article 216 223 1999-4893 Algorithmic Solution of Stochastic Differential Equations 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. http://www.mdpi.com/1999-4893/3/2/197/ Fri, 14 May 2010 00:00:00 CEST Algorithms 2010-05-14 3 2 Review 197 215 1999-4893 An Introduction to Clique Minimal Separator Decomposition 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. http://www.mdpi.com/1999-4893/3/2/183/ Tue, 20 Apr 2010 00:00:00 CEST Algorithms 2010-04-20 3 2 Article 183 196 1999-4893 Integrating New Technologies and Existing Tools to Promote Programming Learning 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. http://www.mdpi.com/1999-4893/3/2/168/ Thu, 15 Apr 2010 00:00:00 CEST Algorithms 2010-04-15 3 2 Article 168 182 1999-4893 A Family of Tools for Supporting the Learning of Programming 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. http://www.mdpi.com/1999-4893/3/2/145/ Thu, 01 Apr 2010 00:00:00 CEST Algorithms 2010-04-01 3 2 Article 145 167 1999-4893 Suffix-Sorting via Shannon-Fano-Elias Codes 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. http://www.mdpi.com/1999-4893/3/2/125/ Wed, 31 Mar 2010 00:00:00 CEST Algorithms 2010-03-31 3 2 Article 125 144 1999-4893 Recognition of Pulmonary Nodules in Thoracic CT Scans Using 3-D Deformable Object Models of Different Classes 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. http://www.mdpi.com/1999-4893/3/2/100/ Wed, 24 Mar 2010 00:00:00 CET Algorithms 2010-03-24 3 2 Article 100 124 1999-4893 Graph Extremities Defined by Search Algorithms 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. http://www.mdpi.com/1999-4893/3/1/92/ Tue, 23 Feb 2010 00:00:00 CET Algorithms 2010-02-23 3 1 Article 92 99 1999-4893 Base Oils Biodegradability Prediction with Data Mining Techniques 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. http://www.mdpi.com/1999-4893/3/1/76/ Wed, 10 Feb 2010 00:00:00 CET Algorithms 2010-02-10 3 1 Article 76 91 1999-4893 InfoVis Interaction Techniques in Animation of Recursive Programs 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. http://www.mdpi.com/1999-4893/3/1/63/ Fri, 29 Jan 2010 00:00:00 CET Algorithms 2010-01-29 3 1 Article 63 75 1999-4893 Interactive Compression of Digital Data 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. http://www.mdpi.com/1999-4893/3/1/44/ Tue, 19 Jan 2010 00:00:00 CET Algorithms 2010-01-19 3 1 Article 44 62 1999-4893 Breast Cancer Detection with Gabor Features from Digital Mammograms 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. http://www.mdpi.com/1999-4893/3/1/21/ Tue, 05 Jan 2010 00:00:00 CET Algorithms 2010-01-05 3 1 Article 21 43 1999-4893 A Robust and Fast System for CTC Computer-Aided Detection of Colorectal Lesions 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. http://www.mdpi.com/1999-4893/3/1/1/ Mon, 04 Jan 2010 00:00:00 CET Algorithms 2010-01-04 3 1 Article 1 20 1999-4893 A Clinical Decision Support Framework for Incremental Polyps Classification in Virtual Colonoscopy 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. http://www.mdpi.com/1999-4893/2/4/1503/ Tue, 01 Dec 2009 00:00:00 CET Algorithms 2009-12-01 2 4 Article 1503 1525 1999-4893 Image Similarity to Improve the Classification of Breast Cancer Images 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”. http://www.mdpi.com/1999-4893/2/4/1473/ Mon, 30 Nov 2009 00:00:00 CET Algorithms 2009-11-30 2 4 Article 1473 1502 1999-4893 Predicting Radiological Panel Opinions Using a Panel of Machine Learning Classifiers 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. http://www.mdpi.com/1999-4893/2/4/1449/ Thu, 26 Nov 2009 00:00:00 CET Algorithms 2009-11-26 2 4 Article 1449 1472 1999-4893 Exact and Heuristic Algorithms for Thrift Cyclic Scheduling 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. http://www.mdpi.com/1999-4893/2/4/1429/ Wed, 25 Nov 2009 00:00:00 CET Algorithms 2009-11-25 2 4 Article 1429 1448 1999-4893 Linear-Time Text Compression by Longest-First Substitution 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. http://www.mdpi.com/1999-4893/2/4/1410/ Wed, 18 Nov 2009 00:00:00 CET Algorithms 2009-11-18 2 4 Article 1410 1428 1999-4893 A Framework for Bioacoustic Vocalization Analysis Using Hidden Markov Models 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. http://www.mdpi.com/1999-4893/2/4/1368/ Wed, 18 Nov 2009 00:00:00 CET Algorithms 2009-11-18 2 4 Article 1368 1409 1999-4893 Methodology, Algorithms, and Emerging Tool for Automated Design of Intelligent Integrated Multi-Sensor Systems 2009-11-18 doi: 10.3390/a2041368 Kuncup Iswandy Andreas König http://www.mdpi.com/1999-4893/2/4/1350/ The goal of this study was to develop a computer-aided therapeutic response (CADrx) system for early prediction of drug treatment response for glioblastoma multiforme (GBM) brain tumors with diffusion weighted (DW) MR images. In conventional Macdonald assessment, tumor response is assessed nine weeks or more post-treatment. However, we will investigate the ability of DW-MRI to assess response earlier, at five weeks post treatment. The apparent diffusion coefficient (ADC) map, calculated from DW images, has been shown to reveal changes in the tumor’s microenvironment preceding morphologic tumor changes. ADC values in treated brain tumors could theoretically both increase due to the cell kill (and thus reduced cell density) and decrease due to inhibition of edema. In this study, we investigated the effectiveness of features that quantify changes from pre- and post-treatment tumor ADC histograms to detect treatment response. There are three parts to this study: first, tumor regions were segmented on T1w contrast enhanced images by Otsu’s thresholding method, and mapped from T1w images onto ADC images by a 3D region of interest (ROI) mapping tool using DICOM header information; second, ADC histograms of the tumor region were extracted from both pre- and five weeks post-treatment scans, and fitted by a two-component Gaussian mixture model (GMM). The GMM features as well as standard histogram-based features were extracted. Finally, supervised machine learning techniques were applied for classification of responders or non-responders. The approach was evaluated with a dataset of 85 patients with GBM under chemotherapy, in which 39 responded and 46 did not, based on tumor volume reduction. We compared adaBoost, random forest and support vector machine classification algorithms, using ten-fold cross validation, resulting in the best accuracy of 69.41% and the corresponding area under the curve (Az) of 0.70. http://www.mdpi.com/1999-4893/2/4/1350/ Mon, 16 Nov 2009 00:00:00 CET Algorithms 2009-11-16 2 4 Article 1350 1367 1999-4893 CADrx for GBM Brain Tumors: Predicting Treatment Response from Changes in Diffusion-Weighted MRI 2009-11-16 doi: 10.3390/a2041350 Jing Huo Kazunori Okada Hyun J. Kim Whitney B. Pope Jonathan G. Goldin Jeffrey R. Alger Matthew S. Brown http://www.mdpi.com/1999-4893/2/4/1327/ Recently a Delaunay refinement algorithm has been proposed that can mesh piecewise smooth complexes which include polyhedra, smooth and piecewise smooth surfaces, and non-manifolds. However, this algorithm employs domain dependent numerical predicates, some of which could be computationally expensive and hard to implement. In this paper we develop a refinement strategy that eliminates these complicated domain dependent predicates. As a result we obtain a meshing algorithm that is practical and implementation-friendly. http://www.mdpi.com/1999-4893/2/4/1327/ Wed, 11 Nov 2009 00:00:00 CET Algorithms 2009-11-11 2 4 Article 1327 1349 1999-4893 Delaunay Meshing of Piecewise Smooth Complexes without Expensive Predicates 2009-11-11 doi: 10.3390/a2041327 Tamal K. Dey Joshua A. Levine http://www.mdpi.com/1999-4893/2/4/1303/ We consider the problem of all-to-one selfish routing in the absence of a payment scheme in wireless sensor networks, where a natural model for cost is the power required to forward, referring to the resulting game as a Locally Minimum Cost Forwarding (LMCF). Our objective is to characterize equilibria and their global costs in terms of stretch and diameter, in particular finding incentive compatible algorithms that are also close to globally optimal. We find that although social costs for equilibria of LMCF exhibit arbitrarily bad worst-case bounds and computational infeasibility of reaching optimal equilibria, there exist greedy and local incentive compatible heuristics achieving near-optimal global costs. http://www.mdpi.com/1999-4893/2/4/1303/ Wed, 14 Oct 2009 00:00:00 CEST Algorithms 2009-10-14 2 4 Article 1303 1326 1999-4893 Incentive Compatible and Globally Efficient Position Based Routing for Selfish Reverse Multicast in Wireless Sensor Networks 2009-10-14 doi: 10.3390/a2041303 Stephan Eidenbenz Gunes Ercal-Ozkaya Adam Meyerson Allon Percus Sarvesh Varatharajan http://www.mdpi.com/1999-4893/2/4/1301/ The Encyclopedia of Algorithms provides a comprehensive set of solutions to important algorithmic problems for students and researchers, including high-impact solutions from the most recent decade. [...] http://www.mdpi.com/1999-4893/2/4/1301/ Mon, 12 Oct 2009 00:00:00 CEST Algorithms 2009-10-12 2 4 Books Received 1301 1302 1999-4893 Encyclopedia of Algorithms. Edited by Kao, Ming-Yang, Springer-Verlag GmbH, 2008; 1220 pages, 183 figures, 38 tables; Hard Cover. Price: € 309.- / CHF 479.50.- ISBN 978-0-387-30770-1 2009-10-12 doi: 10.3390/a2041301 Shu-Kun Lin http://www.mdpi.com/1999-4893/2/4/1281/ An adaptive mesh refinement strategy is proposed for local damage models that often arise from internal state variable based continuum damage models. The proposed algorithm employs both the finite element method and the finite difference method to integrate the equations of motion of a linear elastic material with simple isotropic microcracking. The challenges of this problem include the time integration of coupled partial differential equations with time-dependent coefficients, and the proper choice of solution spaces to yield a stable finite element formulation. Discontinuous elements are used for the representation of the damage field, as it is believed that this reduction in regularity is more consistent with the physical nature of evolving microcracking. The adaptive mesh refinement algorithm relies on custom refinement indicators, two of which are presented and compared. The two refinement indicators we explore are based on the time rate of change of the damage field and on the energy release rate, respectively, where the energy release rate measures the energy per unit volume available for damage to evolve. We observe the performance of the proposed algorithm and refinement indicators by comparing the predicted damage morphology on different meshes, hence judging the capability of the proposed technique to address, but not eliminate, the mesh dependency present in the solutions of the damage field. http://www.mdpi.com/1999-4893/2/4/1281/ Tue, 06 Oct 2009 00:00:00 CEST Algorithms 2009-10-06 2 4 Article 1281 1300 1999-4893 An Adaptive h-Refinement Algorithm for Local Damage Models 2009-10-06 doi: 10.3390/a2041281 Jonathan S. Pitt Francesco Costanzo http://www.mdpi.com/1999-4893/2/4/1263/ In geometric models with high-valence vertices, current subdivision wavelets may not deal with the special cases well for good visual effect of multiresolution surfaces. In this paper, we present the novel biorthogonal polar subdivision wavelets, which can efficiently perform wavelet analysis to the control nets with polar structures. The polar subdivision can generate more natural subdivision surfaces around the high-valence vertices and avoid the ripples and saddle points where Catmull-Clark subdivision may produce. Based on polar subdivision, our wavelet scheme supports special operations on the polar structures, especially suitable to models with many facets joining. For seamless fusing with Catmull-Clark subdivision wavelet, we construct the wavelets in circular and radial layers of polar structures, so can combine the subdivision wavelets smoothly for composite models formed by quadrilaterals and polar structures. The computations of wavelet analysis and synthesis are highly efficient and fully in-place. The experimental results have confirmed the stability of our proposed approach. http://www.mdpi.com/1999-4893/2/4/1263/ Mon, 28 Sep 2009 00:00:00 CEST Algorithms 2009-09-28 2 4 Article 1263 1280 1999-4893 Compound Biorthogonal Wavelets on Quadrilaterals and Polar Structures 2009-09-28 doi: 10.3390/a2041263 Chong Zhao Hanqiu Sun Huawei Wang Kaihuai Qin http://www.mdpi.com/1999-4893/2/3/1248/ The performance of microwave radiometers can be seriously degraded by the presence of radio-frequency interference (RFI). Spurious signals and harmonics from lower frequency bands, spread-spectrum signals overlapping the “protected” band of operation, or out-of-band emissions not properly rejected by the pre-detection filters due to the finite rejection modify the detected power and the estimated antenna temperature from which the geophysical parameters will be retrieved. In recent years, techniques to detect the presence of RFI have been developed. They include time- and/or frequency domain analyses, or statistical analysis of the received signal which, in the absence of RFI, must be a zero-mean Gaussian process. Current mitigation techniques are mostly based on blanking in the time and/or frequency domains where RFI has been detected. However, in some geographical areas, RFI is so persistent in time that is not possible to acquire RFI-free radiometric data. In other applications such as sea surface salinity retrieval, where the sensitivity of the brightness temperature to salinity is weak, small amounts of RFI are also very difficult to detect and mitigate. In this work a wavelet-based technique is proposed to mitigate RFI (cancel RFI as much as possible). The interfering signal is estimated by using the powerful denoising capabilities of the wavelet transform. The estimated RFI signal is then subtracted from the received signal and a “cleaned” noise signal is obtained, from which the power is estimated later. The algorithm performance as a function of the threshold type, and the threshold selection method, the decomposition level, the wavelet type and the interferenceto-noise ratio is presented. Computational requirements are evaluated in terms of quantization levels, number of operations, memory requirements (sequence length). Even though they are high for today’s technology, the algorithms presented can be applied to recorded data. The results show that even RFI much larger than the noise signal can be very effectively mitigated, well below the noise level. http://www.mdpi.com/1999-4893/2/3/1248/ Wed, 23 Sep 2009 00:00:00 CEST Algorithms 2009-09-23 2 3 Article 1248 1262 1999-4893 RFI Mitigation in Microwave Radiometry Using Wavelets 2009-09-23 doi: 10.3390/a2031248 Adriano Camps José Miguel Tarongí http://www.mdpi.com/1999-4893/2/3/1232/ With the aim of classifying sperm whales, this report compares two methods that can use Gaussian functions, a radial basis function network, and support vector machines which were trained with two different approaches known as C-SVM and ν-SVM. The methods were tested on data recordings from seven different male sperm whales, six containing single click trains and the seventh containing a complete dive. Both types of classifiers could distinguish between the clicks of the seven different whales, but the SVM seemed to have better generalisation towards unknown data, at the cost of needing more information and slower performance. http://www.mdpi.com/1999-4893/2/3/1232/ Tue, 22 Sep 2009 00:00:00 CEST Algorithms 2009-09-22 2 3 Article 1232 1247 1999-4893 Classification of Sperm Whale Clicks (Physeter Macrocephalus) with Gaussian-Kernel-Based Networks 2009-09-22 doi: 10.3390/a2031232 Mike Van der Schaar Eric Delory Michel André http://www.mdpi.com/1999-4893/2/3/1221/ The symmetric-convolution multiplication (SCM) property of discrete trigonometric transforms (DTTs) based on unitary transform matrices is developed. Then as the reciprocity of this property, the novel multiplication symmetric-convolution (MSC) property of discrete trigonometric transforms, is developed. http://www.mdpi.com/1999-4893/2/3/1221/ Tue, 22 Sep 2009 00:00:00 CEST Algorithms 2009-09-22 2 3 Article 1221 1231 1999-4893 Multiplication Symmetric Convolution Property for Discrete Trigonometric Transforms 2009-09-22 doi: 10.3390/a2031221 Do Nyeon Kim K. R. Rao http://www.mdpi.com/1999-4893/2/3/1177/ A general review of the extended finite element method and its application to the simulation of first-order phase transitions is provided. Detailed numerical investigations are then performed by focusing on the one-dimensional case and studying: (i) spatial and temporal discretisations, (ii) different numerical techniques for the interface-condition enforcement, and (iii) different treatments for the blending elements. An embeddeddiscontinuity finite element approach is also developed and compared with the extended finite element method, so that a clearer insight of the latter can be given. Numerical examples for melting/solidification in planar, cylindrical, and spherical symmetry are presented and the results are compared with analytical solutions. http://www.mdpi.com/1999-4893/2/3/1177/ Mon, 21 Sep 2009 00:00:00 CEST Algorithms 2009-09-21 2 3 Article 1177 1220 1999-4893 Stefan Problem through Extended Finite Elements: Review and Further Investigations 2009-09-21 doi: 10.3390/a2031177 Luca Salvatori Niccolò Tosi http://www.mdpi.com/1999-4893/2/3/1155/ The fluorescence properties of tryptophan residues are sensitive to the microenvironment of fluorophores in proteins. Therefore, fluorescence characteristics are widely used to study structural transitions in proteins. However, the decoding of the structural information from spectroscopic data is challenging. Here we present a review of approaches developed for the decomposition of multi-component protein tryptophan fluorescence spectra and correlation of these spectral parameters with protein structural properties. http://www.mdpi.com/1999-4893/2/3/1155/ Wed, 16 Sep 2009 00:00:00 CEST Algorithms 2009-09-16 2 3 Review 1155 1176 1999-4893 Algorithm for the Analysis of Tryptophan Fluorescence Spectra and Their Correlation with Protein Structural Parameters 2009-09-16 doi: 10.3390/a2031155 John Hixon Yana K. Reshetnyak http://www.mdpi.com/1999-4893/2/3/1137/ Wireless sensor networks are a relatively new area where technology is developing fast and are used to solve a great diversity of problems that range from museums’ security to wildlife protection. The geometric optimisation problem solved in this paper is aimed at minimising the sensors’ range so that every point on a polygonal region R is within the range of at least two sensors. Moreover, it is also shown how to minimise the sensors’ range to assure the existence of a path within R that stays as close to two sensors as possible. http://www.mdpi.com/1999-4893/2/3/1137/ Mon, 14 Sep 2009 00:00:00 CEST Algorithms 2009-09-14 2 3 Article 1137 1154 1999-4893 Optimal 2-Coverage of a Polygonal Region in a Sensor Network 2009-09-14 doi: 10.3390/a2031137 Manuel Abellanas Antonio L. Bajuelos Inês Matos http://www.mdpi.com/1999-4893/2/3/1105/ A compressed full-text self-index for a text T is a data structure requiring reduced space and able to search for patterns P in T. It can also reproduce any substring of T, thus actually replacing T. Despite the recent explosion of interest on compressed indexes, there has not been much progress on functionalities beyond the basic exact search. In this paper we focus on indexed approximate string matching (ASM), which is of great interest, say, in bioinformatics. We study ASM algorithms for Lempel-Ziv compressed indexes and for compressed suffix trees/arrays. Most compressed self-indexes belong to one of these classes. We start by adapting the classical method of partitioning into exact search to self-indexes, and optimize it over a representative of either class of self-index. Then, we show that a Lempel- Ziv index can be seen as an extension of the classical q-samples index. We give new insights on this type of index, which can be of independent interest, and then apply them to a Lempel- Ziv index. Finally, we improve hierarchical verification, a successful technique for sequential searching, so as to extend the matches of pattern pieces to the left or right. Most compressed suffix trees/arrays support the required bidirectionality, thus enabling the implementation of the improved technique. In turn, the improved verification largely reduces the accesses to the text, which are expensive in self-indexes. We show experimentally that our algorithms are competitive and provide useful space-time tradeoffs compared to classical indexes. http://www.mdpi.com/1999-4893/2/3/1105/ Thu, 10 Sep 2009 00:00:00 CEST Algorithms 2009-09-10 2 3 Article 1105 1136 1999-4893 Approximate String Matching with Compressed Indexes 2009-09-10 doi: 10.3390/a2031105 Luís M. S. Russo Gonzalo Navarro Arlindo L. Oliveira Pedro Morales http://www.mdpi.com/1999-4893/2/3/1087/ Spatial registration of multidate or multisensorial images is required for many applications in remote sensing. Automatic image registration, which has been extensively studied in other areas of image processing, is still a complex problem in the framework of remote sensing. In this work we explore an alternative strategy for a fully automatic and operational registration system capable of registering multitemporal and multisensorial remote sensing satellite images with high accuracy and avoiding the use of ground control points, exploiting the maximum reliable information in both images (coastlines not occluded by clouds), which have been coarsely geometrically corrected only using an orbital prediction model. The automatic feature-based approach is summarized as follows: i) Reference image coastline extraction; ii) Sensed image gradient energy map estimation and iii) Contour matching, mapping function estimation and transformation of the sensed images. Several experimental results for single sensor imagery (AVHRR/3) and multisensorial imagery (AVHRR/3-SeaWiFS-MODIS-ATSR) from different viewpoints and dates have verified the robustness and accuracy of the proposed automatic registration algorithm, demonstrating its capability of registering satellite images of coastal areas within one pixel. http://www.mdpi.com/1999-4893/2/3/1087/ Tue, 08 Sep 2009 00:00:00 CEST Algorithms 2009-09-08 2 3 Article 1087 1104 1999-4893 Featured-Based Algorithm for the Automated Registration of Multisensorial / Multitemporal Oceanographic Satellite Imagery 2009-09-08 doi: 10.3390/a2031087 Francisco Eugenio Javier Marcello http://www.mdpi.com/1999-4893/2/3/1069/ We consider a pursuit-evasion problem where some lions have the task to clear a grid graph whose nodes are initially contaminated. The contamination spreads one step per time unit in each direction not blocked by a lion. A vertex is cleared from its contamination whenever a lion moves to it. Brass et al. [5] showed that n/2 lions are not enough to clear the n x n-grid. In this paper, we consider the same problem in dimension d > 2 and prove that Θ(nd-1/√d) lions are necessary and sufficient to clear the nd-grid. Furthermore, we analyze a problem variant where the lions are also allowed to jump from grid vertices to non-adjacent grid vertices. http://www.mdpi.com/1999-4893/2/3/1069/ Mon, 07 Sep 2009 00:00:00 CEST Algorithms 2009-09-07 2 3 Article 1069 1086 1999-4893 How Many Lions Are Needed to Clear a Grid? 2009-09-07 doi: 10.3390/a2031069 Florian Berger Alexander Gilbers Ansgar Grüne Rolf Klein http://www.mdpi.com/1999-4893/2/3/1045/ A cascade correlation learning architecture has been devised for the first time for radial basis function processing units. The proposed algorithm was evaluated with two synthetic data sets and two chemical data sets by comparison with six other standard classifiers. The ability to detect a novel class and an imbalanced class were demonstrated with synthetic data. In the chemical data sets, the growth regions of Italian olive oils were identified by their fatty acid profiles; mass spectra of polychlorobiphenyl compounds were classified by chlorine number. The prediction results by bootstrap Latin partition indicate that the proposed neural network is useful for pattern recognition. http://www.mdpi.com/1999-4893/2/3/1045/ Thu, 27 Aug 2009 00:00:00 CEST Algorithms 2009-08-27 2 3 Article 1045 1068 1999-4893 Radial Basis Function Cascade Correlation Networks 2009-08-27 doi: 10.3390/a2031045 Weiying Lu Peter de B. Harrington http://www.mdpi.com/1999-4893/2/3/1031/ The Web Graph is a large-scale graph that does not fit in main memory, so that lossless compression methods have been proposed for it. This paper introduces a compression scheme that combines efficient storage with fast retrieval for the information in a node. The scheme exploits the properties of the Web Graph without assuming an ordering of the URLs, so that it may be applied to more general graphs. Tests on some datasets of use achieve space savings of about 10% over existing methods. http://www.mdpi.com/1999-4893/2/3/1031/ Tue, 25 Aug 2009 00:00:00 CEST Algorithms 2009-08-25 2 3 Article 1031 1044 1999-4893 Graph Compression by BFS 2009-08-25 doi: 10.3390/a2031031 Alberto Apostolico Guido Drovandi http://www.mdpi.com/1999-4893/2/3/1008/ The automated approximation of solutions to differential equations which involve discontinuities across evolving surfaces is addressed. Finite element technology has developed to the point where it is now possible to model evolving discontinuities independently of the underlying mesh, which is particularly useful in simulating failure of solids. However, the approach remains tedious to program, particularly in the case of coupled problems where a variety of finite element bases are employed and where a mixture of continuous and discontinuous fields may be used. We tackle this point by exploring the scope for employing automated code generation techniques for modelling discontinuities. Function spaces and variational forms are defined in a language that resembles mathematical notation, and computer code for modelling discontinuities is automatically generated. Principles underlying the approach are elucidated and a number of two- and three-dimensional examples for different equations are presented. http://www.mdpi.com/1999-4893/2/3/1008/ Tue, 18 Aug 2009 00:00:00 CEST Algorithms 2009-08-18 2 3 Article 1008 1030 1999-4893 Automated Modelling of Evolving Discontinuities 2009-08-18 doi: 10.3390/a2031008 Mehdi Nikbakht Garth N. Wells http://www.mdpi.com/1999-4893/2/3/973/ Artificial neural networks as a major soft-computing technology have been extensively studied and applied during the last three decades. Research on backpropagation training algorithms for multilayer perceptron networks has spurred development of other neural network training algorithms for other networks such as radial basis function, recurrent network, feedback network, and unsupervised Kohonen self-organizing network. These networks, especially the multilayer perceptron network with a backpropagation training algorithm, have gained recognition in research and applications in various scientific and engineering areas. In order to accelerate the training process and overcome data over-fitting, research has been conducted to improve the backpropagation algorithm. Further, artificial neural networks have been integrated with other advanced methods such as fuzzy logic and wavelet analysis, to enhance the ability of data interpretation and modeling and to avoid subjectivity in the operation of the training algorithm. In recent years, support vector machines have emerged as a set of high-performance supervised generalized linear classifiers in parallel with artificial neural networks. A review on development history of artificial neural networks is presented and the standard architectures and algorithms of artificial neural networks are described. Furthermore, advanced artificial neural networks will be introduced with support vector machines, and limitations of ANNs will be identified. The future of artificial neural network development in tandem with support vector machines will be discussed in conjunction with further applications to food science and engineering, soil and water relationship for crop management, and decision support for precision agriculture. Along with the network structures and training algorithms, the applications of artificial neural networks will be reviewed as well, especially in the fields of agricultural and biological engineering. http://www.mdpi.com/1999-4893/2/3/973/ Mon, 03 Aug 2009 00:00:00 CEST Algorithms 2009-08-03 2 3 Review 973 1007 1999-4893 Advances in Artificial Neural Networks – Methodological Development and Application 2009-08-03 doi: 10.3390/algor2030973 Yanbo Huang http://www.mdpi.com/1999-4893/2/3/953/ Online OVSF code assignment has an important application to wireless communications. Recently, this problem was formally modeled as an online problem, and performances of online algorithms have been analyzed by the competitive analysis. The previous best upper and lower bounds on the competitive ratio were 10 and 5/3, respectively. In this paper, we improve them to 7 and 2, respectively. We also show that our analysis for the upper bound is tight by giving an input sequence for which the competitive ratio of our algorithm is 7 ― ε for an arbitrary constant ε > 0. http://www.mdpi.com/1999-4893/2/3/953/ Fri, 17 Jul 2009 00:00:00 CEST Algorithms 2009-07-17 2 3 Article 953 972 1999-4893 Improving the Competitive Ratio of the Online OVSF Code Assignment Problem 2009-07-17 doi: 10.3390/a2030953 Shuichi Miyazaki Kazuya Okamoto http://www.mdpi.com/1999-4893/2/3/925/ This paper reviews the basics and recent researches of computer-aided diagnosis (CAD) systems for assisting neuroradiologists in detection of brain diseases, e.g., asymptomatic unruptured aneurysms, Alzheimer\'s disease, vascular dementia, and multiple sclerosis (MS), in magnetic resonance (MR) images. The CAD systems consist of image feature extraction based on image processing techniques and machine learning classifiers such as linear discriminant analysis, artificial neural networks, and support vector machines. We introduce useful examples of the CAD systems in the neuroradiology, and conclude with possibilities in the future of the CAD systems for brain diseases in MR images. http://www.mdpi.com/1999-4893/2/3/925/ Fri, 10 Jul 2009 00:00:00 CEST Algorithms 2009-07-10 2 3 Review 925 952 1999-4893 Computer-Aided Diagnosis Systems for Brain Diseases in Magnetic Resonance Images 2009-07-10 doi: 10.3390/a2030925 Hidetaka Arimura Taiki Magome Yasuo Yamashita Daisuke Yamamoto http://www.mdpi.com/1999-4893/2/3/907/ Calls from 14 species of bat were classified to genus and species using discriminant function analysis (DFA), support vector machines (SVM) and ensembles of neural networks (ENN). Both SVMs and ENNs outperformed DFA for every species while ENNs (mean identification rate – 97%) consistently outperformed SVMs (mean identification rate – 87%). Correct classification rates produced by the ENNs varied from 91% to 100%; calls from six species were correctly identified with 100% accuracy. Calls from the five species of Myotis, a genus whose species are considered difficult to distinguish acoustically, had correct identification rates that varied from 91 – 100%. Five parameters were most important for classifying calls correctly while seven others contributed little to classification performance. http://www.mdpi.com/1999-4893/2/3/907/ Thu, 09 Jul 2009 00:00:00 CEST Algorithms 2009-07-09 2 3 Article 907 924 1999-4893 Classification of Echolocation Calls from 14 Species of Bat by Support Vector Machines and Ensembles of Neural Networks 2009-07-09 doi: 10.3390/a2030907 Robert D. Redgwell Joseph M. Szewczak Gareth Jones Stuart Parsons http://www.mdpi.com/1999-4893/2/3/879/ Specialized intelligent systems can be found everywhere: finger print, handwriting, speech, and face recognition, spam filtering, chess and other game programs, robots, et al. This decade the first presumably complete mathematical theory of artificial intelligence based on universal induction-prediction-decision-action has been proposed. This informationtheoretic approach solidifies the foundations of inductive inference and artificial intelligence. Getting the foundations right usually marks a significant progress and maturing of a field. The theory provides a gold standard and guidance for researchers working on intelligent algorithms. The roots of universal induction have been laid exactly half-a-century ago and the roots of universal intelligence exactly one decade ago. So it is timely to take stock of what has been achieved and what remains to be done. Since there are already good recent surveys, I describe the state-of-the-art only in passing and refer the reader to the literature. This article concentrates on the open problems in universal induction and its extension to universal intelligence. http://www.mdpi.com/1999-4893/2/3/879/ Thu, 02 Jul 2009 00:00:00 CEST Algorithms 2009-07-02 2 3 Article 879 906 1999-4893 Open Problems in Universal Induction & Intelligence 2009-07-02 doi: 10.3390/a2030879 Marcus Hutter http://www.mdpi.com/1999-4893/2/2/850/ Basics of Bayesian statistics in inverse problems using the maximum entropy principle are summarized in connection with the restoration of positive, additive images from various types of data like X-ray digital mammograms. An efficient iterative algorithm for image restoration from large data sets based on the conjugate gradient method and Lagrange multipliers in nonlinear optimization of a specific potential function was developed. The point spread function of the imaging system was determined by numerical simulations of inhomogeneous breast-like tissue with microcalcification inclusions of various opacities. The processed digital and digitized mammograms resulted superior in comparison with their raw counterparts in terms of contrast, resolution, noise, and visibility of details. http://www.mdpi.com/1999-4893/2/2/850/ Tue, 09 Jun 2009 00:00:00 CEST Algorithms 2009-06-09 2 2 Article 850 878 1999-4893 Bayesian Maximum Entropy Based Algorithm for Digital X-ray Mammogram Processing 2009-06-09 doi: 10.3390/a2020850 Radu Mutihac http://www.mdpi.com/1999-4893/2/2/808/ We present a coupled finite element, Kalman filter approach to foresee impactinduced delamination of layered composites when mechanical properties are partially unknown. Since direct numerical simulations, which require all the constitutive parameters to be assigned, cannot be run in such cases, an inverse problem is formulated to allow for modeling as well as constitutive uncertainties. Upon space discretization through finite elements and time integration through the explicit ®¡method, the resulting nonlinear stochastic state model, wherein nonlinearities are due to delamination growth, is attacked with sigma-point Kalman filtering. Comparison with experimental data available in the literature and concerning inter-laminar failure of layered composites subject to low-velocity impacts, shows that the proposed procedure leads to: an accurate description of the failure mode; converged estimates of inter-laminar strength and toughness in good agreement with experimental data. http://www.mdpi.com/1999-4893/2/2/808/ Thu, 04 Jun 2009 00:00:00 CEST Algorithms 2009-06-04 2 2 Article 808 827 1999-4893 Failure Assessment of Layered Composites Subject to Impact Loadings: a Finite Element, Sigma-Point Kalman Filter Approach 2009-06-04 doi: 10.3390/a2020808 Stefano Mariani http://www.mdpi.com/1999-4893/2/2/828/ As the rapid advance of digital imaging technologies, the content-based image retrieval (CBIR) has became one of the most vivid research areas in computer vision. In the last several years, developing computer-aided detection and/or diagnosis (CAD) schemes that use CBIR to search for the clinically relevant and visually similar medical images (or regions) depicting suspicious lesions has also been attracting research interest. CBIR-based CAD schemes have potential to provide radiologists with “visual aid” and increase their confidence in accepting CAD-cued results in the decision making. The CAD performance and reliability depends on a number of factors including the optimization of lesion segmentation, feature selection, reference database size, computational efficiency, and relationship between the clinical relevance and visual similarity of the CAD results. By presenting and comparing a number of approaches commonly used in previous studies, this article identifies and discusses the optimal approaches in developing CBIR-based CAD schemes and assessing their performance. Although preliminary studies have suggested that using CBIR-based CAD schemes might improve radiologists’ performance and/or increase their confidence in the decision making, this technology is still in the early development stage. Much research work is needed before the CBIR-based CAD schemes can be accepted in the clinical practice. http://www.mdpi.com/1999-4893/2/2/828/ Thu, 04 Jun 2009 00:00:00 CEST Algorithms 2009-06-04 2 2 Review 828 849 1999-4893 Computer-Aided Diagnosis in Mammography Using Content-Based Image Retrieval Approaches: Current Status and Future Perspectives 2009-06-04 doi: 10.3390/a2020828 Bin Zheng http://www.mdpi.com/1999-4893/2/2/790/ The theoretical Quantum Key-Distribution scheme of Bennett and Brassard (BB84) has been proven secure against very strong attacks including the collective attacks and the joint attacks. Though the latter are the most general attacks, collective attacks are much easier to analyze, yet, they are conjectured to be as informative to the eavesdropper. Thus, collective attacks are likely to be useful in the analysis of many theoretical and practical schemes that are still lacking a proof of security, including practical BB84 schemes. We show how powerful tools developed in previous works for proving security against the joint attack, are simplified when applied to the security of BB84 against collective attacks whilst providing the same bounds on leaked information and the same error threshold. http://www.mdpi.com/1999-4893/2/2/790/ Wed, 03 Jun 2009 00:00:00 CEST Algorithms 2009-06-03 2 2 Article 790 807 1999-4893 Security of the Bennett-Brassard Quantum Key Distribution Protocol against Collective Attacks 2009-06-03 doi: 10.3390/a2020790 Michel Boyer Ran Gelles Tal Mor http://www.mdpi.com/1999-4893/2/2/764/ Considerable importance in molecular biophysics is attached to influencing by mutagenesis the specific properties of a protein family. The working hypothesis is that mutating residues at few selected positions can affect specificity. Statistical analysis of homologue sequences can identify putative specificity determining positions (SDPs) and help to shed some light on the peculiarities underlying their functional role. In this work, we present an approach to identify such positions inspired by state of the art mutual information-based SDP prediction methods. The algorithm based on this approach provides a systematic procedure to point at the relevant physical characteristics of putative SPDs and can investigate the effects of correlated mutations. The method is tested on two standard benchmarks in the field and further validated in the context of a biologically interesting problem: the multimerization of the Intrinsically Fluorescent Proteins (IFP). http://www.mdpi.com/1999-4893/2/2/764/ Tue, 26 May 2009 00:00:00 CEST Algorithms 2009-05-26 2 2 Article 764 789 1999-4893 SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions 2009-05-26 doi: 10.3390/a2020764 Sara Bonella Walter Rocchia Pietro Amat Riccardo Nifosí Valentina Tozzini http://www.mdpi.com/1999-4893/2/2/750/ Complexity of failure is reflected from sensitivity of strength to small defects and wide scatter of macroscopic behaviors. In engineering practices, spatial information of materials at fine scales can only be partially measurable. Random field (RF) models are important to address the uncertainty in spatial distribution. To transform a RF of micro-cracks into failure probability at full structural-scale crossing a number of length scales, the operator representing physics laws need be implemented in a multiscale framework, and to be realized in a stochastic setting. Multiscale stochastic modeling of materials is emerging as a new methodology at this research frontier, which provides a new multiscale thinking by upscaling fine-scale RFs. In this study, a preliminary framework of probabilistic upscaling is presented for bottom-up hierarchical modeling of failure propagation across micro-meso-macro scales. In the micro-to-meso process, the strength of stochastic representative volume element (SRVE) is probabilistically assessed by using a lattice model. A mixed Weibull-Gaussian distribution is proposed to characterize the statistical strength of SRVE, which can be used as input for the subsequent meso-to-macro upscaling process using smeared crack finite element analysis. http://www.mdpi.com/1999-4893/2/2/750/ Thu, 30 Apr 2009 00:00:00 CEST Algorithms 2009-04-30 2 2 Article 750 763 1999-4893 Probabilistic Upscaling of Material Failure Using Random Field Models – A Preliminary Investigation 2009-04-30 doi: 10.3390/a2020750 Keqiang Hu X. Frank Xu http://www.mdpi.com/1999-4893/2/2/735/ An image tracking algorithm, which was originally used with the particle image velocimetry (PIV) to determine velocities of buoyant solid particles in water, is modified and applied in the presented work to detect motion of fire ant on a planar surface. A group of fire ant workers are put to the bottom of a tub and excited with vibration of selected frequency and intensity. The moving fire ants are captured with an image system that successively acquires image frames of high digital resolution. The background noise in the imaging recordings is extracted by averaging hundreds of frames and removed from each frame. The individual fire ant images are identified with a recursive digital filter, and then they are tracked between frames according to the size, brightness, shape, and orientation angle of the ant image. The speed of an individual ant is determined with the displacement of its images and the time interval between frames. The trail of the individual fire ant is determined with the image tracking results, and a statistical analysis is conducted for all the fire ants in the group. The purpose of the experiment is to investigate the response of fire ants to the substrate vibration. Test results indicate that the fire ants move faster after being excited, but the number of active ones are not increased even after a strong excitation. http://www.mdpi.com/1999-4893/2/2/735/ Thu, 30 Apr 2009 00:00:00 CEST Algorithms 2009-04-30 2 2 Article 735 749 1999-4893 Application of an Image Tracking Algorithm in Fire Ant Motion Experiment 2009-04-30 doi: 10.3390/a2020735 Lichuan Gui John M. Seiner http://www.mdpi.com/1999-4893/2/2/710/ This paper presents an adaptive PSO algorithm whose numerical parameters can be updated following a scheduled protocol respecting some known criteria of convergence in order to enhance the chances to reach the global optimum of a hard combinatorial optimization problem, such those encountered in global optimization problems of composite laminates. Some examples concerning hard design problems are provided, showing the effectiveness of the approach. http://www.mdpi.com/1999-4893/2/2/710/ Tue, 21 Apr 2009 00:00:00 CEST Algorithms 2009-04-21 2 2 Article 710 734 1999-4893 ALE-PSO: An Adaptive Swarm Algorithm to Solve Design Problems of Laminates 2009-04-21 doi: 10.3390/a2020710 Paolo Vannucci http://www.mdpi.com/1999-4893/2/2/692/ This work presents a generalized approach for the fast structural alignment of thousands of macromolecular structures. The method uses string representations of a macromolecular structure and a hash table that stores n-grams of a certain size for searching. To this end, macromolecular structure-to-string translators were implemented for protein and RNA structures. A query against the index is performed in two hierarchical steps to unite speed and precision. In the first step the query structure is translated into n-grams, and all target structures containing these n-grams are retrieved from the hash table. In the second step all corresponding n-grams of the query and each target structure are subsequently aligned, and after each alignment a score is calculated based on the matching n-grams of query and target. The extendable framework enables the user to query and structurally align thousands of protein and RNA structures on a commodity machine and is available as open source from http://lajolla.sf.net. http://www.mdpi.com/1999-4893/2/2/692/ Tue, 21 Apr 2009 00:00:00 CEST Algorithms 2009-04-21 2 2 Article 692 709 1999-4893 Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors 2009-04-21 doi: 10.3390/a2020692 Raphael André Bauer Kristian Rother Peter Moor Knut Reinert Thomas Steinke Janusz M. Bujnicki Robert Preissner http://www.mdpi.com/1999-4893/2/2/667/ Functional mapping of dynamic traits measured in a longitudinal study was originally derived within the maximum likelihood (ML) context and implemented with the EM algorithm. Although ML-based functional mapping possesses many favorable statistical properties in parameter estimation, it may be computationally intractable for analyzing longitudinal data with high dimensions and high measurement errors. In this article, we derive a general functional mapping framework for quantitative trait locus mapping of dynamic traits within the Bayesian paradigm. Markov chain Monte Carlo techniques were implemented for functional mapping to estimate biologically and statistically sensible parameters that model the structures of time-dependent genetic effects and covariance matrix. The Bayesian approach is useful to handle difficulties in constructing confidence intervals as well as the identifiability problem, enhancing the statistical inference of functional mapping. We have undertaken simulation studies to investigate the statistical behavior of Bayesian-based functional mapping and used a real example with F2 mice to validate the utilization and usefulness of the model. http://www.mdpi.com/1999-4893/2/2/667/ Tue, 21 Apr 2009 00:00:00 CEST Algorithms 2009-04-21 2 2 Article 667 691 1999-4893 A Bayesian Algorithm for Functional Mapping of Dynamic Complex Traits 2009-04-21 doi: 10.3390/a2020667 Tian Liu Rongling Wu http://www.mdpi.com/1999-4893/2/2/638/ A robust and complete workflow for metabolic profiling and data mining was described in detail. Three independent and complementary analytical techniques for metabolic profiling were applied: hydrophilic interaction chromatography (HILIC–LC–ESI–MS), reversed-phase liquid chromatography (RP–LC–ESI–MS), and gas chromatography (GC–TOF–MS) all coupled to mass spectrometry (MS). Unsupervised methods, such as principle component analysis (PCA) and clustering, and supervised methods, such as classification and PCA-DA (discriminatory analysis) were used for data mining. Genetic Algorithms (GA), a multivariate approach, was probed for selection of the smallest subsets of potentially discriminative predictors. From thousands of peaks found in total, small subsets selected by GA were considered as highly potential predictors allowing discrimination among groups. It was found that small groups of potential top predictors selected with PCA-DA and GA are different and unique. Annotated GC–TOF–MS data generated identified feature metabolites. Metabolites putatively detected with LC–ESI–MS profiling require further elemental composition assignment with accurate mass measurement by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and structure elucidation by nuclear magnetic resonance spectroscopy (NMR). GA was also used to generate correlated networks for pathway analysis. Several case studies, comprising groups of plant samples bearing different genotypes and groups of samples of human origin, namely patients and healthy volunteers’ urine samples, demonstrated that such a workflow combining comprehensive metabolic profiling and advanced data mining techniques provides a powerful approach for pattern recognition and biomarker discovery http://www.mdpi.com/1999-4893/2/2/638/ Fri, 03 Apr 2009 00:00:00 CEST Algorithms 2009-04-03 2 2 Article 638 666 1999-4893 Pattern Recognition and Pathway Analysis with Genetic Algorithms in Mass Spectrometry Based Metabolomics 2009-04-03 doi: 10.3390/a2020638 Wei Zou Vladimir V. Tolstikov http://www.mdpi.com/1999-4893/2/2/623/ Greenhouse-grown butter lettuce (Lactuca sativa L.) can potentially be stored for 21 days at constant 0°C. When storage temperature was increased to 5°C or 10°C, shelf life was shortened to 14 or 10 days, respectively, in our previous observations. Also, commercial shelf life of 7 to 10 days is common, due to postharvest temperature fluctuations. The objective of this study was to establish neural network (NN) models to predict the remaining shelf life (RSL) under fluctuating postharvest temperatures. A box of 12 - 24 lettuce heads constituted a sample unit. The end of the shelf life of each head was determined when it showed initial signs of decay or yellowing. Air temperatures inside a shipping box were recorded. Daily average temperatures in storage and averaged shelf life of each box were used as inputs, and the RSL was modeled as an output. An R2 of 0.57 could be observed when a simple NN structure was employed. Since the "future" (or remaining) storage temperatures were unavailable at the time of making a prediction, a second NN model was introduced to accommodate a range of future temperatures and associated shelf lives. Using such 2-stage NN models, an R2 of 0.61 could be achieved for predicting RSL. This study indicated that NN modeling has potential for cold chain quality control and shelf life prediction. http://www.mdpi.com/1999-4893/2/2/623/ Fri, 03 Apr 2009 00:00:00 CEST Algorithms 2009-04-03 2 2 Article 623 637 1999-4893 Neural Network Modeling to Predict Shelf Life of Greenhouse Lettuce 2009-04-03 doi: 10.3390/a2020623 Wei-Chin Lin Glen S. Block http://www.mdpi.com/1999-4893/2/1/606/ Within the framework of multifield continua, we move from the model of elastic microcracked body introduced in (Mariano, P.M. and Stazi, F.L., Strain localization in elastic microcracked bodies, Comp. Methods Appl. Mech. Engrg. 2001, 190, 5657–5677) and propose a few novel variational formulations of mixed type along with relevant mixed FEM discretizations. To this goal, suitably extended Hellinger-Reissner principles of primal and dual type are derived. A few numerical studies are presented that include an investigation on the interaction between a single cohesive macrocrack and diffuse microcracks (Mariano, P.M. and Stazi, F.L., Strain localization due to crack–microcrack interactions: X–FEM for a multifield approach, Comp. Methods Appl. Mech. Engrg. 2004, 193, 5035–5062). http://www.mdpi.com/1999-4893/2/1/606/ Fri, 27 Mar 2009 00:00:00 CET Algorithms 2009-03-27 2 1 Article 606 622 1999-4893 Mixed Variational Formulations for Micro-cracked Continua in the Multifield Framework 2009-03-27 doi: 10.3390/a2010606 Matteo Bruggi Paolo Venini http://www.mdpi.com/1999-4893/2/1/582/ The discovery of gene regulatory elements requires the synergism between computational and experimental techniques in order to reveal the underlying regulatory mechanisms that drive gene expression in response to external cues and signals. Utilizing the large amount of high-throughput experimental data, constantly growing in recent years, researchers have attempted to decipher the patterns which are hidden in the genomic sequences. These patterns, called motifs, are potential binding sites to transcription factors which are hypothesized to be the main regulators of the transcription process. Consequently, precise detection of these elements is required and thus a large number of computational approaches have been developed to support the de novo identification of TFBSs. Even though novel approaches are continuously proposed and almost all have reported some success in yeast and other lower organisms, in higher organisms the problem still remains a challenge. In this paper, we therefore review the recent developments in computational methods for transcription factor binding site prediction. We start with a brief review of the basic approaches for binding site representation and promoter identification, then discuss the techniques to locate physical TFBSs, identify functional binding sites using orthologous information, and infer functional TFBSs within some context defined by additional prior knowledge. Finally, we briefly explore the opportunities for expanding these approaches towards the computational identification of transcriptional regulatory networks. http://www.mdpi.com/1999-4893/2/1/582/ Tue, 24 Mar 2009 00:00:00 CET Algorithms 2009-03-24 2 1 Review 582 605 1999-4893 Recent Advances in the Computational Discovery of Transcription Factor Binding Sites 2009-03-24 doi: 10.3390/a2010582 Tung T. Nguyen Ioannis P. Androulakis http://www.mdpi.com/1999-4893/2/1/565/ This paper presents a survey describing recent developments in the area of mathematical programming techniques for various types of sensor network applications. We discuss mathematical programming formulations associated with these applications, as well as methods for solving the corresponding problems. We also address some of the challenges arising in this area, including both conceptual and computational aspects. http://www.mdpi.com/1999-4893/2/1/565/ Tue, 17 Mar 2009 00:00:00 CET Algorithms 2009-03-17 2 1 Review 565 581 1999-4893 Mathematical Programming Techniques for Sensor Networks 2009-03-17 doi: 10.3390/a2010565 Alexey Sorokin Nikita Boyko Vladimir Boginski Stan Uryasev Panos M. Pardalos http://www.mdpi.com/1999-4893/2/1/550/ Although the electrolarynx (EL) provides an important means of voice reconstruction for patients who lose their vocal cords by laryngectomies, the radiated noise and additive environment noise reduce the intelligibility of the resulting EL speech. This paper proposes an improved spectrum subtract algorithm by taking into account the non-uniform effect of colored noise on the spectrum of EL speech. Since the over-subtraction factor of each frequency band can be adjusted in the enhancement process, a better noise reduction effect was obtained and the perceptually annoying musical noise was efficiently reduced, as compared to other standard speech enhancement algorithms. http://www.mdpi.com/1999-4893/2/1/550/ Fri, 13 Mar 2009 00:00:00 CET Algorithms 2009-03-13 2 1 Article 550 564 1999-4893 Multi-Band Spectral Subtraction Method for Electrolarynx Speech Enhancement 2009-03-13 doi: 10.3390/a2010550 Sheng Li MingXi Wan SuPin Wang http://www.mdpi.com/1999-4893/2/1/533/ An image pattern tracking algorithm is described in this paper for time-resolved measurements of mini- and micro-scale movements of complex objects. This algorithm works with a high-speed digital imaging system, which records thousands of successive image frames in a short time period. The image pattern of the observed object is tracked among successively recorded image frames with a correlation-based algorithm, so that the time histories of the position and displacement of the investigated object in the camera focus plane are determined with high accuracy. The speed, acceleration and harmonic content of the investigated motion are obtained by post processing the position and displacement time histories. The described image pattern tracking algorithm is tested with synthetic image patterns and verified with tests on live insects. http://www.mdpi.com/1999-4893/2/1/533/ Thu, 12 Mar 2009 00:00:00 CET Algorithms 2009-03-12 2 1 Article 533 549 1999-4893 An Image Pattern Tracking Algorithm for Time-resolved Measurement of Mini- and Micro-scale Motion of Complex Object 2009-03-12 doi: 10.3390/a2010533 Lichuan Gui John M. Seiner http://www.mdpi.com/1999-4893/2/1/518/ With the discovery of insulin came a deeper understanding of therapeutic options for one of the most devastating chronic diseases of the modern era, diabetes mellitus. The use of insulin in the treatment of diabetes, especially in those with severe insulin deficiency (type 1 diabetes), with multiple injections or continuous subcutaneous infusion, has been largely successful, but the risk for short term and long term complications remains substantial. Insulin treatment decisions are based on the patient’s knowledge of meal size, exercise plans and the intermittent knowledge of blood glucose values. As such, these are open loop methods that require human input. The idea of closed loop control of diabetes treatment is quite different: automated control of a device that delivers insulin (and possibly glucagon or other medications) and is based on continuous or very frequent glucose measurements. Closed loop insulin control for type 1 diabetes is not new but is far from optimized. The goal of such a system is to avoid short-term complications (hypoglycemia) and long-term complications (diseases of the eyes, kidneys, nerves and cardiovascular system) by mimicking the normal insulin secretion pattern of the pancreatic beta cell. A control system for automated diabetes treatment consists of three major components, (1) a glucose sensing device that serves as the afferent limb of the system; (2) an automated control unit that uses algorithms which acquires sensor input and generates treatment outputs; and (3) a drug delivery device (primarily for delivery of insulin), which serves as the system’s efferent limb. There are several major issues that highlight the difficulty of interacting with the complex unknowns of the biological world. For example, development of accurate continuous glucose monitors is crucial; the state of the art in 2009 is that such devices sometimes experience drift and are intended only to supplement information received from standard intermittent blood glucose data. In addition, it is important to acknowledge that an “automated” closed loop pancreas cannot approach the complexity of the normal human endocrine pancreas, which takes continuous data from substrates, hormones, paracrine compounds and autonomic neural inputs, and in response, secretes four hormones. Another major issue is the substantial absorption/action delay of insulin given by the subcutaneous route. Because of this delay, some researchers have recently given a portion of the meal-related insulin in an open loop manner before the meal and found this hybrid approach to be superior to closed loop control. Proportional-Integral-Derivative (PID) systems adapted from the industrial sector utilize control algorithms that alter output based on proportional (difference between actual and target levels), derivative (rate of change) and integral (time-related summative) errors in glucose. These algorithms have proven to be very promising in limited clinical trials. Related algorithms include a “fading memory” system that combines the proportional-derivative components of a classic PID system with time-relating decay of input signals that allow greater emphasis on more recent glucose values, a characteristic noted in mammalian beta-cells. Model Predictive Control (MPC) systems are highly adaptive methods that utilize mathematical models based on observations of biological behavior patterns using system identification and are now undergoing testing in humans. The application of further mathematical models, such as fuzzy control and artificial neural networks, are also promising, but are largely clinically untested. In summary, the prospects for closed loop control of glycemia in persons with diabetes have improved considerably. Major limitations include the delayed absorption/action of subcutaneous insulin and the imperfect stability of currently-available continuous glucose sensors. The potential for improved glycemic control in persons with diabetes brings with it the potential for reduction in the frequency of acute and chronic complications of diabetes. http://www.mdpi.com/1999-4893/2/1/518/ Thu, 12 Mar 2009 00:00:00 CET Algorithms 2009-03-12 2 1 Review 518 532 1999-4893 A Review of Closed-Loop Algorithms for Glycemic Control in the Treatment of Type 1 Diabetes 2009-03-12 doi: 10.3390/a2010518 Joseph El Youssef Jessica Castle W. Kenneth Ward http://www.mdpi.com/1999-4893/2/1/498/ Many macromolecules, namely proteins, show functional substructures or epitopes defined by characteristic spatial arrangements of groups of specific atoms or residues. The identification of such substructures in a set of macromolecular 3D-structures solves an important problem in molecular biology as it allows the assignment of functions to molecular moieties and thus opens the possibility of a mechanistic understanding of molecular function. We have devised an algorithm that models a functional epitope formed by a group of atoms or residues as set of points in cartesian space with associated functional properties. The algorithm searches for similar epitopes in a database of structures by an efficient multistage comparison of distance sets in the epitope and in the structures from the database. The search results in a list of optimal matches and corresponding optimal superpositions of query epitope and matching epitopes from the database. The algorithm is discussed against the background of related approaches, and it is successfully tested in three application scenarios: global match of two homologous proteins, search for an epitope on a homologous protein, and finding matching epitopes in a protein database. http://www.mdpi.com/1999-4893/2/1/498/ Wed, 11 Mar 2009 00:00:00 CET Algorithms 2009-03-11 2 1 Article 498 517 1999-4893 A Novel Algorithm for Macromolecular Epitope Matching 2009-03-11 doi: 10.3390/a2010498 Stanislav Jakuschev Daniel Hoffmann http://www.mdpi.com/1999-4893/2/1/470/ An advanced operational semi-empirical algorithm for processing satellite remote sensing data in the visible region is described. Based on the Levenberg-Marquardt multivariate optimization procedure, the algorithm is developed for retrieving major water colour producing agents: chlorophyll-a, suspended minerals and dissolved organics. Two assurance units incorporated by the algorithm are intended to flag pixels with inaccurate atmospheric correction and specific hydro-optical properties not covered by the applied hydro-optical model. The hydro-optical model is a set of spectral cross-sections of absorption and backscattering of the colour producing agents. The combination of the optimization procedure and a replaceable hydro-optical model makes the developed algorithm not specific to a particular satellite sensor or a water body. The algorithm performance efficiency is amply illustrated for SeaWiFS, MODIS and MERIS images over a variety of water bodies. http://www.mdpi.com/1999-4893/2/1/470/ Tue, 10 Mar 2009 00:00:00 CET Algorithms 2009-03-10 2 1 Article 470 497 1999-4893 Semi-empirical Algorithm for the Retrieval of Ecology-Relevant Water Constituents in Various Aquatic Environments 2009-03-10 doi: 10.3390/a2010470 Anton A. Korosov Dmitry V. Pozdnyakov Are Folkestad Lasse H. Pettersson Kai Sørensen Robert Shuchman http://www.mdpi.com/1999-4893/2/1/448/ Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to the analysis of the structural properties of human chromosomes 21 and 22 and also to three sets of transcription factor binding sites within these chromosomes. We find that, for a given structural property, the structural property power spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their power spectra for both Sp1 and p53 transcription factor binding sites. We use the power spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data. http://www.mdpi.com/1999-4893/2/1/448/ Tue, 10 Mar 2009 00:00:00 CET Algorithms 2009-03-10 2 1 Article 448 469 1999-4893 Structural Fingerprints of Transcription Factor Binding Site Regions 2009-03-10 doi: 10.3390/a2010448 Eleanor J. J. Gardiner Christopher A. Hunter Peter Willett http://www.mdpi.com/1999-4893/2/1/437/ The Silberstein model of the molecular polarizability of diatomic molecules, generalized by Applequist et al. for polyatomic molecules, is analyzed. The atoms are regarded as isotropically polarizable points located at their nuclei, interacting via the fields of their induced dipoles. The use of additive values for atom polarizabilities gives poor results, in some cases leading to artificial predictions of absorption bands. The molecular polarizability of methane and its derivative are computed. The agreement with experimental mean molecular polarizabilities is within 1–5%. A hypothesis is indispensable for a suitable representation of polarizability derivative. http://www.mdpi.com/1999-4893/2/1/437/ Tue, 10 Mar 2009 00:00:00 CET Algorithms 2009-03-10 2 1 Article 437 447 1999-4893 Resonance in Interacting Induced-Dipole Polarizing Force Fields: Application to Force-Field Derivatives 2009-03-10 doi: 10.3390/a2010437 Francisco Torrens Gloria Castellano http://www.mdpi.com/1999-4893/2/1/429/ Based on a protein-protein docking approach we have developed a procedure to verify or falsify protein-protein interactions that were proposed by other methods such as yeast-2-hybrid assays. Our method currently utilizes intermolecular energies but can be expanded to incorporate additional terms such as amino acid based pair-potentials. We show some early results that demonstrate the general applicability of our approach. http://www.mdpi.com/1999-4893/2/1/429/ Tue, 10 Mar 2009 00:00:00 CET Algorithms 2009-03-10 2 1 Article 429 436 1999-4893 Protein-Protein Interaction Analysis by Docking 2009-03-10 doi: 10.3390/a2010429 Florian Fink Stephan Ederer Wolfram Gronwald http://www.mdpi.com/1999-4893/2/1/410/ Applications of genetic algorithms to the global geometry optimization problem of nanoparticles are reviewed. Genetic operations are investigated and importance of phenotype genetic operations, considering the geometry of nanoparticles, are mentioned. Other efficiency improving developments such as floating point representation and local relaxation are described broadly. Parallelization issues are also considered and a recent parallel working single parent Lamarckian genetic algorithm is reviewed with applications on carbon clusters and SiGe core-shell structures. http://www.mdpi.com/1999-4893/2/1/410/ Wed, 04 Mar 2009 00:00:00 CET Algorithms 2009-03-04 2 1 Review 410 428 1999-4893 Genetic Algorithms in Application to the Geometry Optimization of Nanoparticles 2009-03-04 doi: 10.3390/a2010410 Nazım Dugan Şakir Erkoç http://www.mdpi.com/1999-4893/2/1/398/ Ideally, sensory information forms the only source of information to a robot. We consider an algorithm for the self-organization of a controller. At short time scales the controller is merely reactive but the parameter dynamics and the acquisition of knowledge by an internal model lead to seemingly purposeful behavior on longer time scales. As a paradigmatic example, we study the simulation of an underactuated snake-like robot. By interacting with the real physical system formed by the robotic hardware and the environment, the controller achieves a sensitive and body-specific actuation of the robot. http://www.mdpi.com/1999-4893/2/1/398/ Wed, 04 Mar 2009 00:00:00 CET Algorithms 2009-03-04 2 1 Article 398 409 1999-4893 A Sensor-Based Learning Algorithm for the Self-Organization of Robot Behavior 2009-03-04 doi: 10.3390/a2010398 Frank Hesse Georg Martius Ralf Der J. Michael Herrmann http://www.mdpi.com/1999-4893/2/1/361/ An algorithm for the suppression of the radiation and scattering fields created by vibration of the smooth closed surface of a body of arbitrary shape placed in a liquid is designed and analytically explored. The frequency range of the suppression allows for both large and small wave sizes on the protected surface. An active control system is designed that consists of: (a) a subsystem for fast formation of a desired distribution of normal oscillatory velocities or displacements (on the basis of pulsed Huygens\' sources) and (b) a subsystem for catching and targeting of incident waves on the basis of a grid (one layer) of monopole microphones, surrounding the surface to be protected. The efficiency and stability of the control algorithm are considered. The algorithm forms the control signal during a time much smaller than the minimum time scale of the waves to be damped. The control algorithm includes logical and nonlinear operations, thus excluding interpretation of the control system as a traditional combination of linear electric circuits, where all parameters are constant (in time). This algorithm converts some physical body placed in a liquid into one that is transparent to a special class of incident waves. The active control system needs accurate information on its geometry, but does not need either prior or current information about the vibroacoustical characteristics of the protected surface, which in practical cases represents a vast amount of data. http://www.mdpi.com/1999-4893/2/1/361/ Wed, 04 Mar 2009 00:00:00 CET Algorithms 2009-03-04 2 1 Article 361 397 1999-4893 Algorithm for Active Suppression of Radiation and Acoustical Scattering Fields by Some Physical Bodies in Liquids 2009-03-04 doi: 10.3390/a2010361 Vladimir V. Arabadzhi http://www.mdpi.com/1999-4893/2/1/339/ The performance of Radio-Isotope Identification (RIID) algorithms using NaI-based γ spectroscopy is increasingly important. For example, sensors at locations that screen for illicit nuclear material rely on isotope identification using NaI detectors to distinguish innocent nuisance alarms, arising from naturally occurring radioactive material, from alarms arising from threat isotopes. Recent data collections for RIID testing consist of repeat measurements for each of several measurement scenarios to test RIID algorithms. It is anticipated that vendors can modify their algorithms on the basis of performance on chosen measurement scenarios and then test modified algorithms on data for other measurement scenarios. It is therefore timely to review the current status of RIID algorithms on NaI detectors. This review describes γ spectra from NaI detectors, measurement issues and challenges, current RIID algorithms, data preprocessing steps, the role and current quality of synthetic spectra, and opportunities for improvements. http://www.mdpi.com/1999-4893/2/1/339/ Tue, 03 Mar 2009 00:00:00 CET Algorithms 2009-03-03 2 1 Review 339 360 1999-4893 Radio-Isotope Identification Algorithms for NaI γ Spectra 2009-03-03 doi: 10.3390/a2010339 Tom Burr Michael Hamada http://www.mdpi.com/1999-4893/2/1/301/ Pathogens feed on fruits and vegetables causing great food losses or at least reduction of their shelf life. These pathogens can cause losses of the final product or in the farms were the products are grown, attacking leaves, stems and trees. This review analyses disease detection sensors and algorithms for both the farm and postharvest management of fruit and vegetable quality. Mango, avocado, apple, tomato, potato, citrus and grapes were selected as the fruits and vegetables for study due to their world-wide consumption. Disease warning systems for predicting pathogens and insects on farms during fruit and vegetable production are commonly used for all the crops and are available where meteorological stations are present. It can be seen that these disease risk systems are being slowly replaced by remote sensing monitoring in developed countries. Satellite images have reduced their temporal resolution, but are expensive and must become cheaper for their use world-wide. In the last 30 years, a lot of research has been carried out in non-destructive sensors for food quality. Actually, non-destructive technology has been applied for sorting high quality fruit which is desired by the consumer. The sensors require algorithms to work properly; the most used being discriminant analysis and training neural networks. New algorithms will be required due to the high quantity of data acquired and its processing, and for disease warning strategies for disease detection. http://www.mdpi.com/1999-4893/2/1/301/ Tue, 03 Mar 2009 00:00:00 CET Algorithms 2009-03-03 2 1 Review 301 338 1999-4893 Actual Pathogen Detection: Sensors and Algorithms - a Review 2009-03-03 doi: 10.3390/a2010301 Federico Hahn http://www.mdpi.com/1999-4893/2/1/282/ In this paper a method for selecting features for Human Activity Recognition from sensors is presented. Using a large feature set that contains features that may describe the activities to recognize, Best First Search and Genetic Algorithms are employed to select the feature subset that maximizes the accuracy of a Hidden Markov Model generated from the subset. A comparative of the proposed techniques is presented to demonstrate their performance building Hidden Markov Models to classify different human activities using video sensors. http://www.mdpi.com/1999-4893/2/1/282/ Sat, 21 Feb 2009 00:00:00 CET Algorithms 2009-02-21 2 1 Article 282 300 1999-4893 Recognizing Human Activities from Sensors Using Hidden Markov Models Constructed by Feature Selection Techniques 2009-02-21 doi: 10.3390/a2010282 Rodrigo Cilla Miguel A. Patricio Jesús García Antonio Berlanga Jose M. Molina http://www.mdpi.com/1999-4893/2/1/259/ In this work the optimal design of sensor networks for chemical plants is addressed using stochastic optimization strategies. The problem consists in selecting the type, number and location of new sensors that provide the required quantity and quality of process information. Ad-hoc strategies based on Tabu Search, Scatter Search and Population Based Incremental Learning Algorithms are proposed. Regarding Tabu Search, the intensification and diversification capabilities of the technique are enhanced using Path Relinking. The strategies are applied for solving minimum cost design problems subject to quality constraints on variable estimates, and their performances are compared. http://www.mdpi.com/1999-4893/2/1/259/ Fri, 20 Feb 2009 00:00:00 CET Algorithms 2009-02-20 2 1 Article 259 281 1999-4893 Design of Sensor Networks for Chemical Plants Based on Meta-Heuristics 2009-02-20 doi: 10.3390/a2010259 Mercedes Carnero José L. Hernández Mabel C. Sánchez