Next Issue
Volume 2, June
Previous Issue
Volume 1, December
 
 

Algorithms, Volume 2, Issue 1 (March 2009) – 32 articles , Pages 1-622

  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Reader to open them.
Order results
Result details
Section
Select all
Export citation of selected articles as:
417 KiB  
Article
Mixed Variational Formulations for Micro-cracked Continua in the Multifield Framework
by Matteo Bruggi and Paolo Venini
Algorithms 2009, 2(1), 606-622; https://doi.org/10.3390/a2010606 - 27 Mar 2009
Cited by 50 | Viewed by 7497
Abstract
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 [...] Read more.
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). Full article
(This article belongs to the Special Issue Numerical Simulation of Discontinuities in Mechanics)
Show Figures

Figure 1

241 KiB  
Review
Recent Advances in the Computational Discovery of Transcription Factor Binding Sites
by Tung T. Nguyen and Ioannis P. Androulakis
Algorithms 2009, 2(1), 582-605; https://doi.org/10.3390/a2010582 - 24 Mar 2009
Cited by 19 | Viewed by 11094
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Show Figures

Figure 1

365 KiB  
Review
Mathematical Programming Techniques for Sensor Networks
by Alexey Sorokin, Nikita Boyko, Vladimir Boginski, Stan Uryasev and Panos M. Pardalos
Algorithms 2009, 2(1), 565-581; https://doi.org/10.3390/a2010565 - 17 Mar 2009
Cited by 17 | Viewed by 8460
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Show Figures

Figure 1

1207 KiB  
Article
Multi-Band Spectral Subtraction Method for Electrolarynx Speech Enhancement
by Sheng Li, MingXi Wan and SuPin Wang
Algorithms 2009, 2(1), 550-564; https://doi.org/10.3390/a2010550 - 13 Mar 2009
Cited by 39 | Viewed by 9634
Abstract
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 [...] Read more.
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. Full article
Show Figures

Figure 1

370 KiB  
Article
An Image Pattern Tracking Algorithm for Time-resolved Measurement of Mini- and Micro-scale Motion of Complex Object
by Lichuan Gui and John M. Seiner
Algorithms 2009, 2(1), 533-549; https://doi.org/10.3390/a2010533 - 12 Mar 2009
Cited by 39 | Viewed by 7570
Abstract
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 [...] Read more.
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. Full article
Show Figures

Figure 1

204 KiB  
Review
A Review of Closed-Loop Algorithms for Glycemic Control in the Treatment of Type 1 Diabetes
by Joseph El Youssef, Jessica Castle and W. Kenneth Ward
Algorithms 2009, 2(1), 518-532; https://doi.org/10.3390/a2010518 - 12 Mar 2009
Cited by 50 | Viewed by 14022
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Show Figures

Figure 1

1685 KiB  
Article
A Novel Algorithm for Macromolecular Epitope Matching
by Stanislav Jakuschev and Daniel Hoffmann
Algorithms 2009, 2(1), 498-517; https://doi.org/10.3390/a2010498 - 11 Mar 2009
Cited by 17 | Viewed by 9056
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Show Figures

Figure 1

809 KiB  
Article
Semi-empirical Algorithm for the Retrieval of Ecology-Relevant Water Constituents in Various Aquatic Environments
by Anton A. Korosov, Dmitry V. Pozdnyakov, Are Folkestad, Lasse H. Pettersson, Kai Sørensen and Robert Shuchman
Algorithms 2009, 2(1), 470-497; https://doi.org/10.3390/a2010470 - 10 Mar 2009
Cited by 60 | Viewed by 10037
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Show Figures

Figure 1

1258 KiB  
Article
Structural Fingerprints of Transcription Factor Binding Site Regions
by Eleanor J. J. Gardiner, Christopher A. Hunter and Peter Willett
Algorithms 2009, 2(1), 448-469; https://doi.org/10.3390/a2010448 - 10 Mar 2009
Cited by 60 | Viewed by 8287
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Show Figures

Figure 1

198 KiB  
Article
Resonance in Interacting Induced-Dipole Polarizing Force Fields: Application to Force-Field Derivatives
by Francisco Torrens and Gloria Castellano
Algorithms 2009, 2(1), 437-447; https://doi.org/10.3390/a2010437 - 10 Mar 2009
Cited by 60 | Viewed by 8122
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Show Figures

Figure 1

122 KiB  
Article
Protein-Protein Interaction Analysis by Docking
by Florian Fink, Stephan Ederer and Wolfram Gronwald
Algorithms 2009, 2(1), 429-436; https://doi.org/10.3390/a2010429 - 10 Mar 2009
Cited by 60 | Viewed by 7979
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Show Figures

Figure 1

597 KiB  
Review
Genetic Algorithms in Application to the Geometry Optimization of Nanoparticles
by Nazım Dugan and Şakir Erkoç
Algorithms 2009, 2(1), 410-428; https://doi.org/10.3390/a2010410 - 04 Mar 2009
Cited by 35 | Viewed by 11800
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Show Figures

Figure 1

2618 KiB  
Article
A Sensor-Based Learning Algorithm for the Self-Organization of Robot Behavior
by Frank Hesse, Georg Martius, Ralf Der and J. Michael Herrmann
Algorithms 2009, 2(1), 398-409; https://doi.org/10.3390/a2010398 - 04 Mar 2009
Cited by 35 | Viewed by 10371
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Neural Networks and Sensors)
Show Figures

Figure 1

903 KiB  
Article
Algorithm for Active Suppression of Radiation and Acoustical Scattering Fields by Some Physical Bodies in Liquids
by Vladimir V. Arabadzhi
Algorithms 2009, 2(1), 361-397; https://doi.org/10.3390/a2010361 - 04 Mar 2009
Cited by 23 | Viewed by 7512
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Show Figures

Figure 1

424 KiB  
Review
Radio-Isotope Identification Algorithms for NaI γ Spectra
by Tom Burr and Michael Hamada
Algorithms 2009, 2(1), 339-360; https://doi.org/10.3390/a2010339 - 03 Mar 2009
Cited by 70 | Viewed by 10858
Abstract
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, [...] Read more.
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. Full article
Show Figures

Figure 1

304 KiB  
Review
Actual Pathogen Detection: Sensors and Algorithms - a Review
by Federico Hahn
Algorithms 2009, 2(1), 301-338; https://doi.org/10.3390/a2010301 - 03 Mar 2009
Cited by 45 | Viewed by 12007
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Neural Networks and Sensors)
422 KiB  
Article
Recognizing Human Activities from Sensors Using Hidden Markov Models Constructed by Feature Selection Techniques
by Rodrigo Cilla, Miguel A. Patricio, Jesús García, Antonio Berlanga and Jose M. Molina
Algorithms 2009, 2(1), 282-300; https://doi.org/10.3390/a2010282 - 21 Feb 2009
Cited by 23 | Viewed by 9915
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Show Figures

Figure 1

244 KiB  
Article
Design of Sensor Networks for Chemical Plants Based on Meta-Heuristics
by Mercedes Carnero, José L. Hernández and Mabel C. Sánchez
Algorithms 2009, 2(1), 259-281; https://doi.org/10.3390/a2010259 - 20 Feb 2009
Cited by 6 | Viewed by 7963
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Sensor Algorithms)
336 KiB  
Article
Self-organization of Dynamic Distributed Computational Systems Applying Principles of Integrative Activity of Brain Neuronal Assemblies
by Eugene Burmakin, Alexander A. Fingelkurts and Andrew A. Fingelkurts
Algorithms 2009, 2(1), 247-258; https://doi.org/10.3390/a2010247 - 17 Feb 2009
Cited by 10 | Viewed by 7232
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Neural Networks and Sensors)
Show Figures

Figure 1

462 KiB  
Article
High Frequency Waves Propagating in Octagonal Bars: a Low Cost Computation Algorithm
by Alessandro Marzani and Ivan Bartoli
Algorithms 2009, 2(1), 227-246; https://doi.org/10.3390/a2010227 - 17 Feb 2009
Cited by 242 | Viewed by 9094
Abstract
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 [...] Read more.
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. Full article
Show Figures

Figure 1

170 KiB  
Article
Automatic Determination of Stepsize Parameters in Monte Carlo Simulation Tested on a Bromodomain-Binding Octapeptide
by Jason R. Banfelder, Joshua A. Speidel and Mihaly Mezei
Algorithms 2009, 2(1), 215-226; https://doi.org/10.3390/a2010215 - 10 Feb 2009
Cited by 61 | Viewed by 7252
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
1395 KiB  
Article
Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding
by Joshua S. Martin, Katrina Simmons and Alain Laederach
Algorithms 2009, 2(1), 200-214; https://doi.org/10.3390/a2010200 - 10 Feb 2009
Cited by 36 | Viewed by 9808
Abstract
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. [...] Read more.
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. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Show Figures

Figure 1

722 KiB  
Article
The Autonomous Stress Indicator for Remotely Monitoring Power System State and Watching for Potential Instability
by Donald McGillis, Reginald Brearley, Khalil El Arroudi and Geza Joos
Algorithms 2009, 2(1), 183-199; https://doi.org/10.3390/a2010183 - 10 Feb 2009
Cited by 15 | Viewed by 7360
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Neural Networks and Sensors)
Show Figures

Figure 1

568 KiB  
Review
A Survey on Position-Based Routing Algorithms in Wireless Sensor Networks
by Zhang Jin, Yu Jian-Ping, Zhou Si-Wang, Lin Ya-Ping and Li Guang
Algorithms 2009, 2(1), 158-182; https://doi.org/10.3390/a2010158 - 09 Feb 2009
Cited by 37 | Viewed by 11605
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Show Figures

Figure 1

413 KiB  
Review
Probabilistic Distributed Algorithms for Energy Efficient Routing and Tracking in Wireless Sensor Networks
by Sotiris Nikoletseas and Paul G. Spirakis
Algorithms 2009, 2(1), 121-157; https://doi.org/10.3390/a2010121 - 03 Feb 2009
Cited by 240 | Viewed by 8222
Abstract
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) [...] Read more.
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. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Show Figures

Figure 1

1056 KiB  
Article
Algorithm for Nanotubes Computer Generation with Different Configurations
by M. Leonor Contreras, Eliseo Benítez, José Alvarez and Roberto Rozas
Algorithms 2009, 2(1), 108-120; https://doi.org/10.3390/a2010108 - 02 Feb 2009
Cited by 15 | Viewed by 11099
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Show Figures

Graphical abstract

370 KiB  
Review
A Survey on Star Identification Algorithms
by Benjamin B. Spratling IV and Daniele Mortari
Algorithms 2009, 2(1), 93-107; https://doi.org/10.3390/a2010093 - 29 Jan 2009
Cited by 157 | Viewed by 15236
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Show Figures

Figure 1

240 KiB  
Review
On the Reconstruction of Three-dimensional Protein Structures from Contact Maps
by Pietro Di Lena, Marco Vassura, Luciano Margara, Piero Fariselli and Rita Casadio
Algorithms 2009, 2(1), 76-92; https://doi.org/10.3390/a2010076 - 22 Jan 2009
Cited by 60 | Viewed by 9509
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
763 KiB  
Article
A Novel Block-based Watermarking Scheme Using the SVD Transform
by Alessandro Basso, Francesco Bergadano, Davide Cavagnino, Victor Pomponiu and Annamaria Vernone
Algorithms 2009, 2(1), 46-75; https://doi.org/10.3390/a2010046 - 22 Jan 2009
Cited by 60 | Viewed by 9787
Abstract
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 [...] Read more.
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. Full article
Show Figures

Figure 1

980 KiB  
Article
Comparison of Different Neural Network Approaches for the Tropospheric Profiling over the Inter-tropical lands Using GPS Radio Occultation Data
by Stefania Bonafoni, Fabrizio Pelliccia and Roberta Anniballe
Algorithms 2009, 2(1), 31-45; https://doi.org/10.3390/a2010031 - 20 Jan 2009
Cited by 19 | Viewed by 6786
Abstract
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, [...] Read more.
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. Full article
Show Figures

Figure 1

Previous Issue
Next Issue
Back to TopTop