http://www.mdpi.com/journal/algorithms Latest open access articles published in Algorithms at http://www.mdpi.com/journal/algorithms/ http://www.mdpi.com/1999-4893/3/1/92/ 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 http://www.mdpi.com/1999-4893/2/1/247/ This paper presents a method for self-organization of the distributed systems operating in a dynamic context. We propose the use of a simple biologically (cognitive neuroscience) inspired method for system configuration that allows allocating most of the computational load to off-line in order to improve the scalability property of the system. The method proposed has less computational burden at runtime than traditional system adaptation approaches. http://www.mdpi.com/1999-4893/2/1/247/ Tue, 17 Feb 2009 00:00:00 CET Algorithms 2009-02-17 2 1 Article 247 258 1999-4893 Self-organization of Dynamic Distributed Computational Systems Applying Principles of Integrative Activity of Brain Neuronal Assemblies 2009-02-17 doi: 10.3390/a2010247 Eugene Burmakin Alexander A. Fingelkurts Andrew A. Fingelkurts http://www.mdpi.com/1999-4893/2/1/227/ In this paper a hybrid semi-analytical Finite Element formulation is proposed to efficiently calculate the time dependent response due to stress waves propagating in a slender solid with uniform cross-section when excited by impulsive forces. The formulation takes advantage of the direct and inverse Fourier transform to formulate and solve the governing wave equation. The framework is applied to an octagonal viscoelastic isotropic steel bar. http://www.mdpi.com/1999-4893/2/1/227/ Tue, 17 Feb 2009 00:00:00 CET Algorithms 2009-02-17 2 1 Article 227 246 1999-4893 High Frequency Waves Propagating in Octagonal Bars: a Low Cost Computation Algorithm 2009-02-17 doi: 10.3390/a2010227 Alessandro Marzani Ivan Bartoli http://www.mdpi.com/1999-4893/2/1/215/ The proportional integral controller, commonly used in engineering applications for process control, has been implemented for the tuning of the stepsizes in Metropolis Monte Carlo simulations. Similarly to the recent application for tuning the chemical potential parameter in grand-canonical ensemble simulation, the process-control approach was found to work well for the problem of selecting the stepsize for each torsion angle that results in a targeted acceptance rate during the simulation of an octapeptide in aqueous environment. http://www.mdpi.com/1999-4893/2/1/215/ Tue, 10 Feb 2009 00:00:00 CET Algorithms 2009-02-10 2 1 Article 215 226 1999-4893 Automatic Determination of Stepsize Parameters in Monte Carlo Simulation Tested on a Bromodomain-Binding Octapeptide 2009-02-10 doi: 10.3390/a2010215 Jason R. Banfelder Joshua A. Speidel Mihaly Mezei http://www.mdpi.com/1999-4893/2/1/200/ Unlike protein folding, the process by which a large RNA molecule adopts a functionally active conformation remains poorly understood. Chemical mapping techniques, such as Hydroxyl Radical (·OH) footprinting report on local structural changes in an RNA as it folds with single nucleotide resolution. The analysis and interpretation of this kinetic data requires the identification and subsequent optimization of a kinetic model and its parameters. We detail our approach to this problem, specifically focusing on a novel strategy to overcome a factorial explosion in the number of possible models that need to be tested to identify the best fitting model. Previously, smaller systems (less than three intermediates) were computationally tractable using a distributed computing approach. However, for larger systems with three or more intermediates, the problem became computationally intractable. With our new enumeration strategy, we are able to significantly reduce the number of models that need to be tested using non-linear least squares optimization, allowing us to study systems with up to five intermediates. Furthermore, two intermediate systems can now be analyzed on a desktop computer, which eliminates the need for a distributed computing solution for most mediumsized data sets. Our new approach also allows us to study potential degeneracy in kinetic model selection, elucidating the limits of the method when working with large systems. This work establishes clear criteria for determining if experimental ·OH data is sufficient to determine the underlying kinetic model, or if other experimental modalities are required to resolve any degeneracy. http://www.mdpi.com/1999-4893/2/1/200/ Tue, 10 Feb 2009 00:00:00 CET Algorithms 2009-02-10 2 1 Article 200 214 1999-4893 Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding 2009-02-10 doi: 10.3390/a2010200 Joshua S. Martin Katrina Simmons Alain Laederach http://www.mdpi.com/1999-4893/2/1/183/ The proposed Autonomous Stress Indicator (ASI) is a device that monitors the contents of the protection relays on a suspect weak power system bus and generates a performance level related to the degree of system performance degradation or instability. This gives the system operators some time (minutes) to take corrective action. In a given operating area there would not likely be a need for an ASI on every bus. Note that the ASI does not trip any breakers; it is an INFORMATION ONLY device. An important feature is that the system operator can subsequently interrogate the ASI to determine the factor(s) that led to the performance level that has been initially annunciated, thereby leading to a course of action. This paper traces the development of the ASI which is an ongoing project. The ASI could be also described as a stress-alert device whose function is to alert the System Operator of a stressful condition at its location. The characteristics (or essential qualities) of this device are autonomy, selectivity, accuracy and intelligence. These will fulfill the requirements of the recommendation of the Canada –US Task Force in the August 2003 system collapse. Preliminary tests on the IEEE 39-bus model indicate that the concept has merit and development work is in progress. While the ASI can be applied to all power system operating conditions, its principal application is to the degraded state of the system where the System Operator must act to restore the system to the secure state before it migrates to a stage of collapse. The work of ASI actually begins with the Areas of Vulnerability and ends with the Predictive Module as described in detail in this paper. An application example of a degraded system using the IEEE 39-bus system is included. http://www.mdpi.com/1999-4893/2/1/183/ Tue, 10 Feb 2009 00:00:00 CET Algorithms 2009-02-10 2 1 Article 183 199 1999-4893 The Autonomous Stress Indicator for Remotely Monitoring Power System State and Watching for Potential Instability 2009-02-10 doi: 10.3390/a2010183 Donald McGillis Reginald Brearley Khalil El Arroudi Geza Joos http://www.mdpi.com/1999-4893/2/1/158/ Wireless sensor networks (WSN) have attracted much attention in recent years for its unique characteristics and wide use in many different applications. Routing protocol is one of key technologies in WSN. In this paper, the position-based routing protocols are surveyed and classified into four categories: flooding-based, curve-based, grid-based and ant algorithm-based intelligent. To each category, the main contribution of related routing protocols is shown including the relationship among the routing protocols. The different routing algorithms in the same category and the different categories are compared based on popular metrics. Moreover, some open research directions in WSN are also discussed. http://www.mdpi.com/1999-4893/2/1/158/ Mon, 09 Feb 2009 00:00:00 CET Algorithms 2009-02-09 2 1 Review 158 182 1999-4893 A Survey on Position-Based Routing Algorithms in Wireless Sensor Networks 2009-02-09 doi: 10.3390/a2010158 Zhang Jin Yu Jian-Ping Zhou Si-Wang Lin Ya-Ping Li Guang http://www.mdpi.com/1999-4893/2/1/121/ In this work we focus on the energy efficiency challenge in wireless sensor networks, from both an on-line perspective (related to routing), as well as a network design perspective (related to tracking). We investigate a few representative, important aspects of energy efficiency: a) the robust and fast data propagation b) the problem of balancing the energy dissipation among all sensors in the network and c) the problem of efficiently tracking moving entities in sensor networks. Our work here is a methodological survey of selected results that have already appeared in the related literature. In particular, we investigate important issues of energy optimization, like minimizing the total energy dissipation, minimizing the number of transmissions as well as balancing the energy load to prolong the system’s lifetime. We review characteristic protocols and techniques in the recent literature, including probabilistic forwarding and local optimization methods. We study the problem of localizing and tracking multiple moving targets from a network design perspective i.e. towards estimating the least possible number of sensors, their positions and operation characteristics needed to efficiently perform the tracking task. To avoid an expensive massive deployment, we try to take advantage of possible coverage overlaps over space and time, by introducing a novel combinatorial model that captures such overlaps. Under this model, we abstract the tracking network design problem by a covering combinatorial problem and then design and analyze an efficient approximate method for sensor placement and operation. http://www.mdpi.com/1999-4893/2/1/121/ Tue, 03 Feb 2009 00:00:00 CET Algorithms 2009-02-03 2 1 Review 121 157 1999-4893 Probabilistic Distributed Algorithms for Energy Efficient Routing and Tracking in Wireless Sensor Networks 2009-02-03 doi: 10.3390/a2010121 Sotiris Nikoletseas Paul G. Spirakis http://www.mdpi.com/1999-4893/2/1/108/ The algorithm here described concerns generation, visualization, and modification of molecular nanostructures of single-walled nanotubes (NTs) of particular configurations (armchair, zipper, multiple zipper, zigzag, or chiral) by means of a Graphical User Interface (GUI). NTs are made from a carbon graphene sheet created according to certain parameters defining required nanostructures. Generated NTs can easily be modified by replacing carbon atoms for nitrogen or boron, visualized and exported into a standard format useful as input to be analyzed and submitted to other applications in order to get optimized geometries and to carry out further calculations of molecular and electronic properties. http://www.mdpi.com/1999-4893/2/1/108/ Mon, 02 Feb 2009 00:00:00 CET Algorithms 2009-02-02 2 1 Article 108 120 1999-4893 Algorithm for Nanotubes Computer Generation with Different Configurations 2009-02-02 doi: 10.3390/a2010108 M. Leonor Contreras Eliseo Benítez José Alvarez Roberto Rozas http://www.mdpi.com/1999-4893/2/1/93/ The author surveys algorithms used in star identification, commonly used in star trackers to determine the attitude of a spacecraft. Star trackers are a staple of attitude determination systems for most types of satellites. The paper covers: (a) lost-in-space algorithms (when no a priori attitude information is available), (b) recursive algorithms (when some a priori attitude information is available), and (c) non-dimensional algorithms (when the star tracker calibration is not well-known). The performance of selected algorithms and supporting algorithms are compared. http://www.mdpi.com/1999-4893/2/1/93/ Thu, 29 Jan 2009 00:00:00 CET Algorithms 2009-01-29 2 1 Review 93 107 1999-4893 A Survey on Star Identification Algorithms 2009-01-29 doi: 10.3390/a2010093 Benjamin B. Spratling Daniele Mortari http://www.mdpi.com/1999-4893/2/1/76/ The problem of protein structure prediction is one of the long-standing goals of Computational Biology. Although we are still not able to provide first principle solutions, several shortcuts have been discovered to compute the protein three-dimensional structure when similar protein sequences are available (by means of comparative modeling and remote homology detection). Nonetheless, these approaches can assign structures only to a fraction of proteins in genomes and ab-initio methods are still needed. One relevant step of ab-initio prediction methods is the reconstruction of the protein structures starting from inter-protein residue contacts. In this paper we review the methods developed so far to accomplish the reconstruction task in order to highlight their differences and similarities. The different approaches are fully described and their reported performances, together with their computational complexity, are also discussed. http://www.mdpi.com/1999-4893/2/1/76/ Thu, 22 Jan 2009 00:00:00 CET Algorithms 2009-01-22 2 1 Review 76 92 1999-4893 On the Reconstruction of Three-dimensional Protein Structures from Contact Maps 2009-01-22 doi: 10.3390/a2010076 Pietro Di Lena Marco Vassura Luciano Margara Piero Fariselli Rita Casadio http://www.mdpi.com/1999-4893/2/1/46/ In this paper, a block-based watermarking scheme based on the Singular Value Decomposition (SVD) is proposed. Our watermark, a pseudo-random Gaussian sequence, is embedded by modifying the angles formed by the right singular vectors of each block of the original image. The orthogonality property of the right singular vector matrix is preserved during the embedding process. Several experiments have been carried out to test the performance of the proposed scheme against different attack scenarios. We conclude that the proposed scheme is resistant against common signal processing operations and attacks, while it preserves the quality of the original image. http://www.mdpi.com/1999-4893/2/1/46/ Thu, 22 Jan 2009 00:00:00 CET Algorithms 2009-01-22 2 1 Article 46 75 1999-4893 A Novel Block-based Watermarking Scheme Using the SVD Transform 2009-01-22 doi: 10.3390/a2010046 Alessandro Basso Francesco Bergadano Davide Cavagnino Victor Pomponiu Annamaria Vernone http://www.mdpi.com/1999-4893/2/1/31/ In this study different approaches based on multilayer perceptron neural networks are proposed and evaluated with the aim to retrieve tropospheric profiles by using GPS radio occultation data. We employed a data set of 445 occultations covering the land surface within the Tropics, split into desert and vegetation zone. The neural networks were trained with refractivity profiles as input computed from geometrical occultation parameters provided by the FORMOSAT-3/COSMIC satellites, while the targets were the dry and wet refractivity profiles and the dry pressure profiles obtained from the contemporary European Centre for Medium-Range Weather Forecast data. Such a new retrieval algorithm was chosen to solve the atmospheric profiling problem without the constraint of an independent knowledge of one atmospheric parameter at each GPS occultation. http://www.mdpi.com/1999-4893/2/1/31/ Tue, 20 Jan 2009 00:00:00 CET Algorithms 2009-01-20 2 1 Article 31 45 1999-4893 Comparison of Different Neural Network Approaches for the Tropospheric Profiling over the Inter-tropical lands Using GPS Radio Occultation Data 2009-01-20 doi: 10.3390/a2010031 Stefania Bonafoni Fabrizio Pelliccia Roberta Anniballe http://www.mdpi.com/1999-4893/2/1/19/ The aim of the present study is to obtain a highly objective automatic fetal heart rate (FHR) diagnosis. The neural network software was composed of three layers with the back propagation, to which 8 FHR data, including sinusoidal FHR, were input and the system was educated by the data of 20 cases with a known outcome. The output was the probability of a normal, intermediate, or pathologic outcome. The neural index studied prolonged monitoring. The neonatal states and the FHR score strongly correlated with the outcome probability. The neural index diagnosis was correct. The completed software was transferred to other computers, where the system function was correct. http://www.mdpi.com/1999-4893/2/1/19/ Fri, 16 Jan 2009 00:00:00 CET Algorithms 2009-01-16 2 1 Review 19 30 1999-4893 Neural Network Analysis and Evaluation of the Fetal Heart Rate 2009-01-16 doi: 10.3390/a2010019 Yasuaki Noguchi Fujihiko Matsumoto Kazuo Maeda Takashi Nagasawa http://www.mdpi.com/1999-4893/2/1/1/ When moving discontinuities in solids need to be simulated, standard finite element (FE) procedures usually attain low accuracy because of spurious oscillations appearing behind the discontinuity fronts. To assure an accurate tracking of traveling stress waves in heterogeneous media, we propose here a flux-corrected transport (FCT) technique for structured as well as unstructured space discretizations. The FCT technique consists of post-processing the FE velocity field via diffusive/antidiffusive fluxes, which rely upon an algorithmic length-scale parameter. To study the behavior of heterogeneous bodies featuring compliant interphases of any shape, a general scheme for computing diffusive/antidiffusive fluxes close to phase boundaries is proposed too. The performance of the new FE-FCT method is assessed through one-dimensional and two-dimensional simulations of dilatational stress waves propagating along homogeneous and composite rods. http://www.mdpi.com/1999-4893/2/1/1/ Tue, 13 Jan 2009 00:00:00 CET Algorithms 2009-01-13 2 1 Article 1 18 1999-4893 A Finite Element Flux-Corrected Transport Method for Wave Propagation in Heterogeneous Solids 2009-01-13 doi: 10.3390/a2010001 Stefano Mariani Roberto Martini Aldo Ghisi http://www.mdpi.com/1999-4893/1/2/183/ A new algorithm for divisive hierarchical clustering of chemical compounds based on 2D structural fragments is suggested. The algorithm is deterministic, and given a random ordering of the input, will always give the same clustering and can process a database up to 2 million records on a standard PC. The algorithm was used for classification of 1,183 antibiotics mixed with 999,994 random chemical structures. Similarity threshold, at which best separation of active and non active compounds took place, was estimated as 0.6. 85.7% of the antibiotics were successfully classified at this threshold with 0.4% of inaccurate compounds. A .sdf file was created with the probe molecules for clustering of external databases. http://www.mdpi.com/1999-4893/1/2/183/ Thu, 18 Dec 2008 00:00:00 CET Algorithms 2008-12-18 1 2 Article 183 200 1999-4893 Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels 2008-12-18 doi: 10.3390/a1020183 Sergei V. Trepalin Alexander V. Yarkov http://www.mdpi.com/1999-4893/1/2/153/ This paper surveys the developments of last 10 years in the area of vision based target tracking for autonomous vehicles navigation. First, the motivations and applications of using vision based target tracking for autonomous vehicles navigation are presented in the introduction section. It can be concluded that it is very necessary to develop robust visual target tracking based navigation algorithms for the broad applications of autonomous vehicles. Then this paper reviews the recent techniques in three different categories: vision based target tracking for the applications of land, underwater and aerial vehicles navigation. Next, the increasing trends of using data fusion for visual target tracking based autonomous vehicles navigation are discussed. Through data fusion the tracking performance is improved and becomes more robust. Based on the review, the remaining research challenges are summarized and future research directions are investigated. http://www.mdpi.com/1999-4893/1/2/153/ Mon, 15 Dec 2008 00:00:00 CET Algorithms 2008-12-15 1 2 Review 153 182 1999-4893 Autonomous Vehicles Navigation with Visual Target Tracking: Technical Approaches 2008-12-15 doi: 10.3390/a1020153 Zhen Jia Arjuna Balasuriya Subhash Challa http://www.mdpi.com/1999-4893/1/2/130/ Sensors have been widely used for disease diagnosis, environmental quality monitoring, food quality control, industrial process analysis and control, and other related fields. As a key tool for sensor data analysis, machine learning is becoming a core part of novel sensor design. Dividing a complete machine learning process into three steps: data pre-treatment, feature extraction and dimension reduction, and system modeling, this paper provides a review of the methods that are widely used for each step. For each method, the principles and the key issues that affect modeling results are discussed. After reviewing the potential problems in machine learning processes, this paper gives a summary of current algorithms in this field and provides some feasible directions for future studies. http://www.mdpi.com/1999-4893/1/2/130/ Wed, 03 Dec 2008 00:00:00 CET Algorithms 2008-12-03 1 2 Review 130 152 1999-4893 Machine Learning: A Crucial Tool for Sensor Design 2008-12-03 doi: 10.3390/a1020130 Weixiang Zhao Abhinav Bhushan Anthony D. Santamaria Melinda G. Simon Cristina E. Davis http://www.mdpi.com/1999-4893/1/2/100/ The field of computational biology has experienced a tremendous growth in the past 15 years. In this bibliography, we survey some of the most significant contributions that were made to the field and which employ mathematical programming techniques, while giving a broad overview of application areas of modern computational molecular biology. The areas include sequence analysis, microarrays, protein structure and function, haplotyping and evolutionary distances. http://www.mdpi.com/1999-4893/1/2/100/ Mon, 24 Nov 2008 00:00:00 CET Algorithms 2008-11-24 1 2 Review 100 129 1999-4893 Mathematical Programming in Computational Biology: an Annotated Bibliography 2008-11-24 doi: 10.3390/a1020100 Giuseppe Lancia http://www.mdpi.com/1999-4893/1/2/69/ Traditional local active noise control systems minimise the measured acoustic pressure to generate a zone of quiet at the physical error sensor location. The resulting zone of quiet is generally limited in size and this requires the physical error sensor be placed at the desired location of attenuation, which is often inconvenient. To overcome this, a number of virtual sensing algorithms have been developed for active noise control. Using the physical error signal, the control signal and knowledge of the system, these virtual sensing algorithms estimate the error signal at a location that is remote from the physical error sensor, referred to as the virtual location. Instead of minimising the physical error signal, the estimated error signal is minimised with the active noise control system to generate a zone of quiet at the virtual location. This paper will review a number of virtual sensing algorithms developed for active noise control. Additionally, the performance of these virtual sensing algorithms in numerical simulations and in experiments is discussed and compared. http://www.mdpi.com/1999-4893/1/2/69/ Mon, 03 Nov 2008 00:00:00 CET Algorithms 2008-11-03 1 2 Review 69 99 1999-4893 A Review of Virtual Sensing Algorithms for Active Noise Control 2008-11-03 doi: 10.3390/a1020069 Danielle Moreau Ben Cazzolato Anthony Zander Cornelis Petersen http://www.mdpi.com/1999-4893/1/2/52/ The main objective of this study is to present an improved modeling technique called Vegetation ET (VegET) that integrates commonly used water balance algorithms with remotely sensed Land Surface Phenology (LSP) parameter to conduct operational vegetation water balance modeling of rainfed systems at the LSP’s spatial scale using readily available global data sets. Evaluation of the VegET model was conducted using Flux Tower data and two-year simulation for the conterminous US. The VegET model is capable of estimating actual evapotranspiration (ETa) of rainfed crops and other vegetation types at the spatial resolution of the LSP on a daily basis, replacing the need to estimate crop- and region-specific crop coefficients. http://www.mdpi.com/1999-4893/1/2/52/ Thu, 30 Oct 2008 00:00:00 CET Algorithms 2008-10-30 1 2 Article 52 68 1999-4893 Modeling Landscape Evapotranspiration by Integrating Land Surface Phenology and a Water Balance Algorithm 2008-10-30 doi: 10.3390/a1020052 Gabriel B. Senay http://www.mdpi.com/1999-4893/1/2/43/ In this paper we consider a basic clustering problem that has uses in bioinformatics. A structural fragment is a sequence of l points in a 3D space, where l is a fixed natural number. Two structural fragments f1 and f2 are equivalent if and only if f1 = f2 x R + τ under some rotation R and translation τ . We consider the distance between two structural fragments to be the sum of the squared Euclidean distance between all corresponding points of the structural fragments. Given a set of n structural fragments, we consider the problem of finding k (or fewer) structural fragments g1, g2, ... , gk, so as to minimize the sum of the distances between each of f1, f2, ... , fn to its nearest structural fragment in g1, ... , gk. In this paper we show a polynomial-time approximation scheme (PTAS) for the problem through a simple sampling strategy. http://www.mdpi.com/1999-4893/1/2/43/ Thu, 09 Oct 2008 00:00:00 CEST Algorithms 2008-10-09 1 2 Article 43 51 1999-4893 A PTAS For The k-Consensus Structures Problem Under Squared Euclidean Distance 2008-10-09 doi: 10.3390/a1020043 Shuai Cheng Li Yen Kaow Ng Louxin Zhang http://www.mdpi.com/1999-4893/1/1/30/ We prove that there exists a randomized online algorithm for the 2-server 3-point problem whose expected competitive ratio is at most 1.5897. This is the first nontrivial upper bound for randomized k-server algorithms in a general metric space whose competitive ratio is well below the corresponding deterministic lower bound (= 2 in the 2-server case). http://www.mdpi.com/1999-4893/1/1/30/ Fri, 19 Sep 2008 00:00:00 CEST Algorithms 2008-09-19 1 1 Article 30 42 1999-4893 Randomized Competitive Analysis for Two Server Problems 2008-09-19 doi: 10.3390/a1010030 Wolfgang Bein Kazuo Iwama Jun Kawahara http://www.mdpi.com/1999-4893/1/1/2/ Due to their importance for studies oi wireless networks, recent years have seen a surge of activity on the design of local algorithms for the solution of a variety of network tasks. We study the behaviour of algorithms with very low localities. Despite of this restriction we propose local constant ratio approximation algorithms for solving minimum dominating and connected dominating set, maximum independent set and minimum vertex cover in location aware Unit Disk Graphs. We also prove the first ever lower bounds for local algorithms for these problems with a given locality in the location aware setting. http://www.mdpi.com/1999-4893/1/1/2/ Fri, 12 Sep 2008 00:00:00 CEST Algorithms 2008-09-12 1 1 Article 2 29 1999-4893 Impact of Locality on Location Aware Unit Disk Graphs 2008-09-12 doi: 10.3390/a1010002 Andreas Wiese Evangelos Kranakis http://www.mdpi.com/1999-4893/1/1/1/ n/a http://www.mdpi.com/1999-4893/1/1/1/ Thu, 04 Sep 2008 00:00:00 CEST Algorithms 2008-09-04 1 1 Editorial 1 1 1999-4893 Editor's Foreword 2008-09-04 doi: 10.3390/a1010001 Kazuo Iwama