Computation

527 KiB

Open AccessArticle

Artificial Immune Classifier Based on ELLipsoidal Regions (AICELL) ^†

by Aris Lanaridis, Giorgos Siolas and Andreas Stafylopatis

Computation 2017, 5(2), 31; https://doi.org/10.3390/computation5020031 - 17 Jun 2017

Cited by 1 | Viewed by 3679

Pattern classification is a central problem in machine learning, with a wide array of applications, and rule-based classifiers are one of the most prominent approaches. Among these classifiers, Incremental Rule Learning algorithms combine the advantages of classic Pittsburg and Michigan approaches, while, on [...] Read more.

Pattern classification is a central problem in machine learning, with a wide array of applications, and rule-based classifiers are one of the most prominent approaches. Among these classifiers, Incremental Rule Learning algorithms combine the advantages of classic Pittsburg and Michigan approaches, while, on the other hand, classifiers using fuzzy membership functions often result in systems with fewer rules and better generalization ability. To discover an optimal set of rules, learning classifier systems have always relied on bio-inspired models, mainly genetic algorithms. In this paper we propose a classification algorithm based on an efficient bio-inspired approach, Artificial Immune Networks. The proposed algorithm encodes the patterns as antigens, and evolves a set of antibodies, representing fuzzy classification rules of ellipsoidal surface, to cover the problem space. The innate immune mechanisms of affinity maturation and diversity preservation are modified and adapted to the classification context, resulting in a classifier that combines the advantages of both incremental rule learning and fuzzy classifier systems. The algorithm is compared to a number of state-of-the-art rule-based classifiers, as well as Support Vector Machines (SVM), producing very satisfying results, particularly in problems with large number of attributes and classes. Full article

(This article belongs to the Special Issue Computational Aspects Related to Unconventional, Bio-Inspired and Quantum Methods)

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Figure 1
Comparison between the random and health-proportional initialization. The figure displays the decrease of average antigen health <math display="inline"> <semantics> <mover accent="true"> <mi>h</mi> <mo>¯</mo> </mover> </semantics> </math> with the number of training generations t. As evident from the figure, the proposed method results in faster convergence and smaller deviation between runs. Full article ">Figure 2
Removing rules of lower quality. The two rules in the center of (a) are inferior to the rest, one of them because it covers many patterns of the wrong class and the other because of its small coverage. Although the value of their evaluation metric, shown in (b), is indeed lower, they cannot be easily detected based on that value. However, by breaking the metric down to its coverage and precision components, the differences become much clearer, and the two rules can be rejected as outliers. Full article ">Figure 3
Performance of all classifiers on all problems, ordered clockwise in increasing number of features. As obvious, the performances of GASSIST and UCS significantly decrease as the number of features increases. For RIPPER and SLAVE the differences are significantly smaller, however their overall performance is inferior to that of AICELL.Radar plots Full article ">Figure 4
Boxplot of the precision of the algorithms tested on the problems mentioned. GASSIST and UCS fall behind in terms of both mean and median value. RIPPER has comparable distribution to SLAVE, despite not having the best performance in any problem. AICELL has the best overall performance, coming very close to SVM. Full article ">

2243 KiB

Open AccessArticle

Theoretical Prediction of Electronic Structures and Phonon Dispersion of Ce₂XN₂ (X = S, Se, and Te) Ternary

by Mohammed Benali Kanoun and Souraya Goumri-Said

Computation 2017, 5(2), 29; https://doi.org/10.3390/computation5020029 - 13 Jun 2017

Cited by 2 | Viewed by 3593

Abstract

A systematic study of structural, electronic, vibrational properties of new ternary dicerium selenide dinitride, Ce₂SeN₂ and predicted compounds—Ce₂SN₂ and Ce₂TeN₂—is performed using first-principles calculations within Perdew–Burke–Ernzerhof functional with Hubbard correction. Our calculated results [...] Read more.

A systematic study of structural, electronic, vibrational properties of new ternary dicerium selenide dinitride, Ce₂SeN₂ and predicted compounds—Ce₂SN₂ and Ce₂TeN₂—is performed using first-principles calculations within Perdew–Burke–Ernzerhof functional with Hubbard correction. Our calculated results for structural parameters nicely agree to the experimental measurements. We predict that all ternary dicerium chalcogenide nitrides are thermodynamically stable. The predicted elastic constants and related mechanical properties demonstrate its profound mechanical stability as well. Moreover, our results show that Ce₂XN₂ are insulator materials. Trends of the structural parameters, electronic structures, and phonon dispersion are discussed in terms of the characteristics of the Ce (4f) states. Full article

(This article belongs to the Special Issue Advances in Electronic Structure Theory: Method Development and Application)

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283 KiB

Open AccessArticle

Levy-Lieb-Based Monte Carlo Study of the Dimensionality Behaviour of the Electronic Kinetic Functional

by Seshaditya A., Luca M. Ghiringhelli and Luigi Delle Site

Computation 2017, 5(2), 30; https://doi.org/10.3390/computation5020030 - 10 Jun 2017

Cited by 1 | Viewed by 4508

Abstract

We consider a gas of interacting electrons in the limit of nearly uniform density and treat the one dimensional (1D), two dimensional (2D) and three dimensional (3D) cases. We focus on the determination of the correlation part of the kinetic functional by employing [...] Read more.

We consider a gas of interacting electrons in the limit of nearly uniform density and treat the one dimensional (1D), two dimensional (2D) and three dimensional (3D) cases. We focus on the determination of the correlation part of the kinetic functional by employing a Monte Carlo sampling technique of electrons in space based on an analytic derivation via the Levy-Lieb constrained search principle. Of particular interest is the question of the behaviour of the functional as one passes from 1D to 3D; according to the basic principles of Density Functional Theory (DFT) the form of the universal functional should be independent of the dimensionality. However, in practice the straightforward use of current approximate functionals in different dimensions is problematic. Here, we show that going from the 3D to the 2D case the functional form is consistent (concave function) but in 1D becomes convex; such a drastic difference is peculiar of 1D electron systems as it is for other quantities. Given the interesting behaviour of the functional, this study represents a basic first-principle approach to the problem and suggests further investigations using highly accurate (though expensive) many-electron computational techniques, such as Quantum Monte Carlo. Full article

(This article belongs to the Special Issue Advances in Electronic Structure Theory: Method Development and Application)

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318 KiB

Open AccessArticle

Geometric Derivation of the Stress Tensor of the Homogeneous Electron Gas

by Jianmin Tao, Giovanni Vignale and Jian-Xin Zhu

Computation 2017, 5(2), 28; https://doi.org/10.3390/computation5020028 - 8 Jun 2017

Cited by 2 | Viewed by 3724

Abstract

The foundation of many approximations in time-dependent density functional theory (TDDFT) lies in the theory of the homogeneous electron gas. However, unlike the ground-state DFT, in which the exchange-correlation potential of the homogeneous electron gas is known exactly via the quantum Monte Carlo [...] Read more.

The foundation of many approximations in time-dependent density functional theory (TDDFT) lies in the theory of the homogeneous electron gas. However, unlike the ground-state DFT, in which the exchange-correlation potential of the homogeneous electron gas is known exactly via the quantum Monte Carlo calculation, the time-dependent or frequency-dependent dynamical potential of the homogeneous electron gas has not been known exactly, due to the absence of a similar variational principle for excited states. In this work, we present a simple geometric derivation of the time-dependent dynamical exchange-correlation potential for the homogeneous system. With this derivation, the dynamical potential can be expressed in terms of the stress tensor, offering an alternative to calculate the bulk and shear moduli, two key input quantities in TDDFT. Full article

(This article belongs to the Special Issue Advances in Electronic Structure Theory: Method Development and Application)

1641 KiB

Open AccessArticle

Energetic Study of Clusters and Reaction Barrier Heights from Efficient Semilocal Density Functionals

by Guocai Tian, Yuxiang Mo and Jianmin Tao

Computation 2017, 5(2), 27; https://doi.org/10.3390/computation5020027 - 3 Jun 2017

Cited by 7 | Viewed by 4361

Abstract

The accurate first-principles prediction of the energetic properties of molecules and clusters from efficient semilocal density functionals is of broad interest. Here we study the performance of a non-empirical Tao-Mo (TM) density functional on binding energies and excitation energies of titanium dioxide and [...] Read more.

The accurate first-principles prediction of the energetic properties of molecules and clusters from efficient semilocal density functionals is of broad interest. Here we study the performance of a non-empirical Tao-Mo (TM) density functional on binding energies and excitation energies of titanium dioxide and water clusters, as well as reaction barrier heights. To make a comparison, a combination of the TM exchange part with the TPSS (Tao–Perdew–Staroverov–Scuseria) correlation functional—called TMTPSS—is also included in this study. Our calculations show that the best binding energies of titanium dioxide are predicted by PBE0 (Perdew–Burke–Ernzerhof hybrid functional), TM, and TMTPSS with nearly the same accuracy, while B3LYP (Beck’s three-parameter exchange part with Lee-Yang-Parr correlation), TPSS, and PBE (Perdew–Burke–Ernzerhof) yield larger mean absolute errors. For excitation energies of titanium and water clusters, PBE0 and B3LYP are the most accurate functionals, outperforming the performance of semilocal functionals due to the nonlocality problem suffered by the latter. Nevertheless, TMTPSS and TM functionals are still good accurate semilocal methods, improving upon the commonly-used TPSS and PBE functionals. We also find that the best reaction barrier heights are predicted by PBE0 and B3LYP, thanks to the nonlocality incorporated into these two hybrid functionals, but TMTPSS and TM are obviously more accurate than SCAN (Strongly Constrained and Appropriately Normed), TPSS, and PBE, suggesting the good performance of TM and TMTPSS for physically different systems and properties. Full article

(This article belongs to the Special Issue Advances in Electronic Structure Theory: Method Development and Application)

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Equilibrium structure of <math display="inline"> <semantics> <msub> <mrow> <mo>(</mo> <msub> <mi>TiO</mi> <mn>2</mn> </msub> <mo>)</mo> </mrow> <mi>n</mi> </msub> </semantics> </math> and <math display="inline"> <semantics> <msub> <mrow> <mo>(</mo> <msub> <mi mathvariant="normal">H</mi> <mn>2</mn> </msub> <mi mathvariant="normal">O</mi> <mo>)</mo> </mrow> <mi>n</mi> </msub> </semantics> </math> clusters. Full article ">Figure 2
Lowest singlet excitation energies (eV) of <math display="inline"> <semantics> <msub> <mrow> <mo>(</mo> <msub> <mi>TiO</mi> <mn>2</mn> </msub> <mo>)</mo> </mrow> <mi>n</mi> </msub> </semantics> </math> (n = 1–4) calculated with different methods at 6-311++G(3df,3pd) basis set. Full article ">Figure 3
The lowest excitation energy (eV) of <math display="inline"> <semantics> <mo>(</mo> <msub> <mi mathvariant="normal">H</mi> <mn>2</mn> </msub> <mi mathvariant="normal">O</mi> <mo>)</mo> <mi>n</mi> </semantics> </math> (n = 2–5) calculated with different methods at 6-311++G(3df,3pd) basis set. Full article ">

5164 KiB

Open AccessArticle

Deep Visual Attributes vs. Hand-Crafted Audio Features on Multidomain Speech Emotion Recognition

by Michalis Papakostas, Evaggelos Spyrou, Theodoros Giannakopoulos, Giorgos Siantikos, Dimitrios Sgouropoulos, Phivos Mylonas and Fillia Makedon

Computation 2017, 5(2), 26; https://doi.org/10.3390/computation5020026 - 1 Jun 2017

Cited by 45 | Viewed by 7327

Abstract

Emotion recognition from speech may play a crucial role in many applications related to human–computer interaction or understanding the affective state of users in certain tasks, where other modalities such as video or physiological parameters are unavailable. In general, a human’s emotions may [...] Read more.

Emotion recognition from speech may play a crucial role in many applications related to human–computer interaction or understanding the affective state of users in certain tasks, where other modalities such as video or physiological parameters are unavailable. In general, a human’s emotions may be recognized using several modalities such as analyzing facial expressions, speech, physiological parameters (e.g., electroencephalograms, electrocardiograms) etc. However, measuring of these modalities may be difficult, obtrusive or require expensive hardware. In that context, speech may be the best alternative modality in many practical applications. In this work we present an approach that uses a Convolutional Neural Network (CNN) functioning as a visual feature extractor and trained using raw speech information. In contrast to traditional machine learning approaches, CNNs are responsible for identifying the important features of the input thus, making the need of hand-crafted feature engineering optional in many tasks. In this paper no extra features are required other than the spectrogram representations and hand-crafted features were only extracted for validation purposes of our method. Moreover, it does not require any linguistic model and is not specific to any particular language. We compare the proposed approach using cross-language datasets and demonstrate that it is able to provide superior results vs. traditional ones that use hand-crafted features. Full article

(This article belongs to the Special Issue Computational Aspects Related to Unconventional, Bio-Inspired and Quantum Methods)

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3835 KiB

Open AccessArticle

Numerical Simulation of the Laminar Forced Convective Heat Transfer between Two Concentric Cylinders

by Ioan Sarbu and Anton Iosif

Computation 2017, 5(2), 25; https://doi.org/10.3390/computation5020025 - 13 May 2017

Cited by 2 | Viewed by 5182

Abstract

The dual reciprocity method (DRM) is a highly efficient numerical method of transforming domain integrals arising from the non-homogeneous term of the Poisson equation into equivalent boundary integrals. In this paper, the velocity and temperature fields of laminar forced heat convection in a [...] Read more.

The dual reciprocity method (DRM) is a highly efficient numerical method of transforming domain integrals arising from the non-homogeneous term of the Poisson equation into equivalent boundary integrals. In this paper, the velocity and temperature fields of laminar forced heat convection in a concentric annular tube, with constant heat flux boundary conditions, have been studied using numerical simulations. The DRM has been used to solve the governing equation, which is expressed in the form of a Poisson equation. A test problem is employed to verify the DRM solutions with different boundary element discretizations and numbers of internal points. The results of the numerical simulations are discussed and compared with exact analytical solutions. Good agreement between the numerical results and exact solutions is evident, as the maximum relative errors are less than 5% to 6%, and the R²-values are greater than 0.999 in all cases. These results confirm the effectiveness and accuracy of the proposed numerical model, which is based on the DRM. Full article

(This article belongs to the Section Computational Engineering)

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6929 KiB

Open AccessFeature PaperArticle

Analyzing the Effect and Performance of Lossy Compression on Aeroacoustic Simulation of Gas Injector

by Seyyed Mahdi Najmabadi, Philipp Offenhäuser, Moritz Hamann, Guhathakurta Jajnabalkya, Fabian Hempert, Colin W. Glass and Sven Simon

Computation 2017, 5(2), 24; https://doi.org/10.3390/computation5020024 - 12 May 2017

Cited by 5 | Viewed by 4874

Abstract

Computational fluid dynamic simulations involve large state data, leading to performance degradation due to data transfer times, while requiring large disk space. To alleviate the situation, an adaptive lossy compression algorithm has been developed, which is based on regions of interest. This algorithm [...] Read more.

Computational fluid dynamic simulations involve large state data, leading to performance degradation due to data transfer times, while requiring large disk space. To alleviate the situation, an adaptive lossy compression algorithm has been developed, which is based on regions of interest. This algorithm uses prediction-based compression and exploits the temporal coherence between subsequent simulation frames. The difference between the actual value and the predicted value is adaptively quantized and encoded. The adaptation is in line with user requirements, that consist of the acceptable inaccuracy, the regions of interest and the required compression throughput. The data compression algorithm was evaluated with simulation data obtained by the discontinuous Galerkin spectral element method. We analyzed the performance, compression ratio and inaccuracy introduced by the lossy compression algorithm. The post processing analysis shows high compression ratios, with reasonable quantization errors. Full article

(This article belongs to the Section Computational Engineering)

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5825 KiB

Open AccessArticle

Implicit Large Eddy Simulation of Flow in a Micro-Orifice with the Cumulant Lattice Boltzmann Method

by Ehsan Kian Far, Martin Geier, Konstantin Kutscher and Manfred Krafczyk

Computation 2017, 5(2), 23; https://doi.org/10.3390/computation5020023 - 5 May 2017

Cited by 15 | Viewed by 6748

Abstract

A detailed numerical study of turbulent flow through a micro-orifice is presented in this work. The flow becomes turbulent due to the orifice at the considered Reynolds numbers (∼

10^{4}

). The obtained flow rates are in good agreement with the experimental [...] Read more.

A detailed numerical study of turbulent flow through a micro-orifice is presented in this work. The flow becomes turbulent due to the orifice at the considered Reynolds numbers (∼

10^{4}

). The obtained flow rates are in good agreement with the experimental measurements. The discharge coefficient and the pressure loss are presented for two input pressures. The laminar stress and the generated turbulent stresses are investigated in detail, and the location of the vena contracta is quantitatively reproduced. Full article

(This article belongs to the Special Issue CFD: Recent Advances in Lattice Boltzmann Methods)

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1603 KiB

Open AccessArticle

Scatter Search Applied to the Inference of a Development Gene Network

by Amir Masoud Abdol, Damjan Cicin-Sain, Jaap A. Kaandorp and Anton Crombach

Computation 2017, 5(2), 22; https://doi.org/10.3390/computation5020022 - 4 May 2017

Cited by 4 | Viewed by 5885

Abstract

Efficient network inference is one of the challenges of current-day biology. Its application to the study of development has seen noteworthy success, yet a multicellular context, tissue growth, and cellular rearrangements impose additional computational costs and prohibit a wide application of current methods. [...] Read more.

Efficient network inference is one of the challenges of current-day biology. Its application to the study of development has seen noteworthy success, yet a multicellular context, tissue growth, and cellular rearrangements impose additional computational costs and prohibit a wide application of current methods. Therefore, reducing computational cost and providing quick feedback at intermediate stages are desirable features for network inference. Here we propose a hybrid approach composed of two stages: exploration with scatter search and exploitation of intermediate solutions with low temperature simulated annealing. We test the approach on the well-understood process of early body plan development in flies, focusing on the gap gene network. We compare the hybrid approach to simulated annealing, a method of network inference with a proven track record. We find that scatter search performs well at exploring parameter space and that low temperature simulated annealing refines the intermediate results into excellent model fits. From this we conclude that for poorly-studied developmental systems, scatter search is a valuable tool for exploration and accelerates the elucidation of gene regulatory networks. Full article

(This article belongs to the Special Issue Multiscale and Hybrid Modeling of the Living Systems)

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Figure 1
Body plan patterning in D. melanogaster. In both panels, the trunk gap genes are hunchback (hb), Krüppel (Kr), giant (gt), and knirps (kni)). External inputs to these four genes are the maternal factors Bicoid (Bcd), Caudal (Cad), and the terminal gap proteins Tailless (Tll), and Huckebein (Hkb). (a) Schematic depiction of a Drosophila embryo with the anterior (head) oriented to the left and its dorsal side to the top. Gap gene expression domains are shown as vertical bands along the trunk region. Expression in the head and terminal area is omitted; (b) The gap gene network mapped onto the expression domains of the trunk region. Background gradients of Bcd (purple) and Cad (cyan) activate the gap genes. Each rectangle is an expression domain. Circular arrows indicate self-activation, interactions with T-bars represent inhibition. Dashed interactions signal a net effect. Full article ">Figure 2
Scatter search algorithm design as presented in [<a href="#B21-computation-05-00022" class="html-bibr">21</a>]. See main text for details. Full article ">Figure 3
Gap gene network representations. (a) Diagram of the gap gene network as shown in <a href="#computation-05-00022-f001" class="html-fig">Figure 1</a>, with interactions between the expression domains along the A–P axis. Each number refers to an interaction in panel b; (b) Matrix representation. Column names are regulators (proteins), row names are gap genes (gene names) receiving the regulation. Gap-gap and terminal-gap interactions are numbered 1–19, and maternal gradients are coloured to match the background gradients in panel a. The gap-gap interactions with a dashed border are depicted as a net regulatory effect from one gap gene to an other in panel a (as in [<a href="#B14-computation-05-00022" class="html-bibr">14</a>]). The regulatory effect of Tll on hb and Kr (white boxes) are ignored in panel a. Full article ">Figure 4
Performance of (sequential) scatter search method (SSm) and parallel Lam simulated annealing (pLSA). All panels plot function evaluations against cost (see Equation (<a href="#FD3-computation-05-00022" class="html-disp-formula">3</a>)). A function evaluation is defined as computing gene expression levels of a gene circuit from time <math display="inline"> <semantics> <mrow> <mi>t</mi> <mo>=</mo> <mn>0</mn> <mo>.</mo> <mn>0</mn> </mrow> </semantics> </math> to <math display="inline"> <semantics> <mrow> <mn>71</mn> <mo>.</mo> <mn>1</mn> </mrow> </semantics> </math> min. It is a performance measure independent of compiler settings and hardware. The cost indicates how well a gene circuit reproduces gap gene expression data (lower is better). (a) The main body of results is based on gene circuits derived from mRNA expression data, using scatter search with the Nelder-Mead algorithm as a local search method. Gene circuits from SSm are grey blue, the 200 selected circuits are blue, of which the 50 best in dark blue. Gene circuits from pLSA are red; (b–d) Gene circuit performance using mRNA and protein data expression data, and switching between Nelder-Mead and stochastic hill climbing. Circuits from scatter search are grey-blue, those from pLSA are red. Full article ">Figure 5
Exploring genetic interactions of the 50 best scatter search circuits. (a) Genetic interaction matrix summarizing the type of regulation found amongst the circuits (see also <a href="#computation-05-00022-f003" class="html-fig">Figure 3</a>). Number triplets define the number of solutions with repressive/no/activating interactions. Columns are regulators, rows target genes. The colour code indicates green for activation and red for repression. Saturated colours indicate full consensus amongst gene circuits, light colours a two-third fraction of circuits for one type of regulation; (b) Histogram of parameter values for hb self-regulation. Inset shows the same parameter values split by Hb activating (purple) and inhibiting (orange) gt. See also panel d; (c) Histogram of parameter values for Hb regulating gt. The distribution splits into an inhibitory and activating set of gene circuits (see inset); (d) Self-regulation of gt split along Hb–gt regulation. Activation (→) is purple, inhibition (⊣) is orange. The peak of the purple distribution extends to 17 gene circuits; (e) Regulation of hb by Kr split along Hb–gt regulation, similar to panel d. Full article ">Figure 6
Performance of simulated annealing (pLSA) and the two-stage approach. (a) Total number of function evaluations per optimization scenario. The two-stage approaches shares the first explorative stage by scatter search (blue bars), after which different starting temperatures were used for low temperature SA; (b) Number of function evaluations per excellent gene circuit, defined as a circuit with an RMS <math display="inline"> <semantics> <mrow> <mo><</mo> <mn>22</mn> <mo>.</mo> <mn>0</mn> </mrow> </semantics> </math>. In both panels, we replace <math display="inline"> <semantics> <msup> <mn>10</mn> <mn>3</mn> </msup> </semantics> </math> by the letter ‘k’ in scenario names. The two last columns (‘50 k’ and ‘100 k’) are labelled as “fixed” to signal a constrained search space was used. Full article ">Figure 7
Comparison of the best gene circuits resulting from low temperature Simulated Annealing (SA) and parallel Lam Simulated Annealing (pLSA). Panels (a,c) show scenario T = 50 k, and (b,d) show pLSA. (a,b) Genetic interaction matrices. See <a href="#computation-05-00022-f005" class="html-fig">Figure 5</a> and main text for details; (c,d) Gene expression profiles at four time points. Gene circuit expression is given by solid lines, data by dashed lines. The embryo’s trunk region is shown, spanning 35–87% A–P position. Time points are mitotic cycle C13 and time classes of cycle C14A, T2/5/8. Full article ">

1807 KiB

Open AccessArticle

An Information Technology Framework for the Development of an Embedded Computer System for the Remote and Non-Destructive Study of Sensitive Archaeology Sites

by Iliya Georgiev and Ivo Georgiev

Computation 2017, 5(2), 21; https://doi.org/10.3390/computation5020021 - 5 Apr 2017

Cited by 2 | Viewed by 4944

Abstract

The paper proposes an information technology framework for the development of an embedded remote system for non-destructive observation and study of sensitive archaeological sites. The overall concept and motivation are described. The general hardware layout and software configuration are presented. The paper concentrates [...] Read more.

The paper proposes an information technology framework for the development of an embedded remote system for non-destructive observation and study of sensitive archaeological sites. The overall concept and motivation are described. The general hardware layout and software configuration are presented. The paper concentrates on the implementation of the following informational technology components: (a) a geographically unique identification scheme supporting a global key space for a key-value store; (b) a common method for octree modeling for spatial geometrical models of the archaeological artifacts, and abstract object representation in the global key space; (c) a broadcast of the archaeological information as an Extensible Markup Language (XML) stream over the Web for worldwide availability; and (d) a set of testing methods increasing the fault tolerance of the system. This framework can serve as a foundation for the development of a complete system for remote archaeological exploration of enclosed archaeological sites like buried churches, tombs, and caves. An archaeological site is opened once upon discovery, the embedded computer system is installed inside upon a robotic platform, equipped with sensors, cameras, and actuators, and the intact site is sealed again. Archaeological research is conducted on a multimedia data stream which is sent remotely from the system and conforms to necessary standards for digital archaeology. Full article

(This article belongs to the Special Issue Selected Papers from the 7th International Conference from Scientific Computing to Computational Engineering (IC-SCCE 2016))

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498 KiB

Open AccessArticle

Detecting Perturbed Subpathways towards Mouse Lung Regeneration Following H1N1 Influenza Infection

by Aristidis G. Vrahatis, Konstantina Dimitrakopoulou, Andreas Kanavos, Spyros Sioutas and Athanasios Tsakalidis

Computation 2017, 5(2), 20; https://doi.org/10.3390/computation5020020 - 3 Apr 2017

Cited by 3 | Viewed by 5416

Abstract

It has already been established by the systems-level approaches that the future of predictive disease biomarkers will not be sketched by plain lists of genes or proteins or other biological entities but rather integrated entities that consider all underlying component relationships. Towards this [...] Read more.

It has already been established by the systems-level approaches that the future of predictive disease biomarkers will not be sketched by plain lists of genes or proteins or other biological entities but rather integrated entities that consider all underlying component relationships. Towards this orientation, early pathway-based approaches coupled expression data with whole pathway interaction topologies but it was the recent approaches that zoomed into subpathways (local areas of the entire biological pathway) that provided more targeted and context-specific candidate disease biomarkers. Here, we explore the application potential of PerSubs, a graph-based algorithm which identifies differentially activated disease-specific subpathways. PerSubs is applicable both for microarray and RNA-Seq data and utilizes the Kyoto Encyclopedia of Genes and Genomes (KEGG) database as reference for biological pathways. PerSubs operates in two stages: first, identifies differentially expressed genes (or uses any list of disease-related genes) and in second stage, treating each gene of the list as start point, it scans the pathway topology around to build meaningful subpathway topologies. Here, we apply PerSubs to investigate which pathways are perturbed towards mouse lung regeneration following H1N1 influenza infection. Full article

(This article belongs to the Special Issue Computational Aspects Related to Unconventional, Bio-Inspired and Quantum Methods)

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7364 KiB

Open AccessArticle

Esoteric Twist: An Efficient in-Place Streaming Algorithmus for the Lattice Boltzmann Method on Massively Parallel Hardware

by Martin Geier and Martin Schönherr

Computation 2017, 5(2), 19; https://doi.org/10.3390/computation5020019 - 23 Mar 2017

Cited by 49 | Viewed by 7971

Abstract

We present and analyze the Esoteric Twist algorithm for the Lattice Boltzmann Method. Esoteric Twist is a thread safe in-place streaming method that combines streaming and collision and requires only a single data set. Compared to other in-place streaming techniques, Esoteric Twist minimizes [...] Read more.

We present and analyze the Esoteric Twist algorithm for the Lattice Boltzmann Method. Esoteric Twist is a thread safe in-place streaming method that combines streaming and collision and requires only a single data set. Compared to other in-place streaming techniques, Esoteric Twist minimizes the memory footprint and the memory traffic when indirect addressing is used. Esoteric Twist is particularly suitable for the implementation of the Lattice Boltzmann Method on Graphic Processing Units. Full article

(This article belongs to the Special Issue CFD: Recent Advances in Lattice Boltzmann Methods)

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Figure 1
AA-pattern in 2D. (left) Odd time step; (right) Even time step. Full article ">Figure 2
The EsoTwist algorithm in 2D. (left) Odd time step; (right) Even time step. Full article ">Figure 3
Ghost nodes in the AA-pattern and EsoTwist when indirect addressing is used. Since both methods store part of the distributions at neighboring nodes the memory for these ghost nodes (in gray) have to be allocated even though they are not part of the simulation domain. EsoTwist has an advantage over the AA-pattern in that it requires these neighbors only in positive directions. Thus, fewer ghost nodes are required for EsoTwist than for the AA-pattern. Full article ">Figure 4
Different orientations of the same test geometry to probe the isotropy of EsoTwist with indirect addressing. The performance in terms of Million Node Updates Per Second is seen to depend only weakly on the orientation. Picture reproduced from [<a href="#B37-computation-05-00019" class="html-bibr">37</a>]. Full article ">Figure 5
The random packing of 6864 spheres is discretized with a sparse matrix. Picture reproduced from [<a href="#B37-computation-05-00019" class="html-bibr">37</a>]. Full article ">Figure 6
The discretization of the random packing of spheres with a lattice spacing of 40 <math display="inline"> <semantics> <mi mathvariant="sans-serif">μ</mi> </semantics> </math>m. Picture reproduced from [<a href="#B37-computation-05-00019" class="html-bibr">37</a>]. Full article ">Figure 7
The discretization of the random packing of spheres with a lattice spacing of 20 <math display="inline"> <semantics> <mi mathvariant="sans-serif">μ</mi> </semantics> </math>m. Picture reproduced from [<a href="#B37-computation-05-00019" class="html-bibr">37</a>]. Full article ">

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Computation, Volume 5, Issue 2 (June 2017) – 13 articles

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