A novel ACO–GA hybrid algorithm for feature selection in protein function prediction

Protein function prediction is an important problem in functional genomics. Typically, protein sequences are represented by feature vectors. A major problem of protein datasets that increase the complexity of classification models is their large number of features. Feature selection (FS) techniques are used to deal with this high dimensional space of features. In this paper, we propose a novel feature selection algorithm that combines genetic algorithms (GA) and ant colony optimization (ACO) for faster and better search capability. The hybrid algorithm makes use of advantages of both ACO and GA methods. Proposed algorithm is easily implemented and because of use of a simple classifier in that, its computational complexity is very low. The performance of proposed algorithm is compared to the performance of two prominent population-based algorithms, ACO and genetic algorithms. Experimentation is carried out using two challenging biological datasets, involving the hierarchical functional classification of GPCRs and enzymes. The criteria used for comparison are maximizing predictive accuracy, and finding the smallest subset of features. The results of experiments indicate the superiority of proposed algorithm.     

Building extraction from high-resolution satellite images in urban areas: recent methods and strategies against significant challenges

Building extraction from high-resolution satellite images (HRSI) in urban areas is an intricate problem. Recent studies proposed different methods during 2005–2015. However, in HRSI, they have not investigated the effects of challenges altogether. This paper studies the effects of non-building features which are the main drawbacks in building extraction. To overcome each challenge, it reviews recent strategies between 2005 and 2015. The pros and cons of each strategy are discussed, and proper strategies are combined to generate hybrid methods. Lower cost and fewer strategies are efficient attributes to recognize the best hybrid methods. Hybrid methods can be useful for different case studies in the future.     

Slippage control in soft finger grasping and manipulation

Handling objects with robotic soft fingers without considering the odds of slippage are not realistic. Grasping and manipulation algorithms have to be tested under such conditions for evaluating their robustness. In this paper, a dynamic analysis of rigid object manipulation with slippage control is studied using a two-link finger with soft hemispherical tip. Dependency on contact forces applied by a soft finger while grasping a rigid object is examined experimentally. A power-law model combined with a linear viscous damper is used to model the elastic behavior and damping effect of the soft tip, respectively. In order to obtain precise dynamic equations governing the system, two second-order differential equations with variable coefficients have been designed to describe the different possible states of the contact forces accordingly. A controller is designed based on the rigid fingertip model using the concept of feedback linearization for each phase of the system dynamics. Numerical simulations are used to evaluate the performance of the controller. The results reveal that the designed controller shows acceptable performance for both soft and rigid finger manipulation in reducing and canceling slippage. Furthermore, simulations indicate that the applied force in the soft finger manipulation is considerably less than the rigid “one.”.     

Commitments and interaction norms in organisations

In an organisational setting such as an online marketplace, an entity called the ‘organisation’ or ‘institution’ defines interaction protocols, monitors agent interaction, and intervenes to enforce the interaction protocols. The organisation might be a software system that thus regulates the marketplace, for example. In this article we abstract over application-specific protocols and consider commitment lifecycles as generic interaction protocols. We model interaction protocols by explicitly-represented norms, such that we can operationalise the enforcement of protocols by means of norm enforcement, and we can analyse the protocols by a logical analysis of the norms. We adopt insights and methods from commitment-based approaches to agent interaction as well as from norm-based approaches to agent behaviour governance. First, we show how to use explicitly-represented norms to model commitment dynamics (lifecycles). Second, we introduce an operational semantics to operationalise norm enforcement. Third, we show how to logically analyse interaction protocols by means of commitment dynamics and norm enforcement. The model, semantics, and analysis are illustrated by a running example from a vehicle insurance domain.     

A high-order non-oscillatory central scheme with non-staggered grids for hyperbolic conservation laws

In this work, we present a scheme which is based on non-staggered grids. This scheme is a new family of non-staggered central schemes for hyperbolic conservation laws. Motivation of this work is a staggered central scheme recently introduced by A.A.I. Peer et al. [A new fourth-order non-oscillatory central scheme for hyperbolic conservation laws, Appl. Numer. Math. 58 (2008) 674–688]. The most important properties of the technique developed in the current paper are simplicity, high-resolution and avoiding the use of staggered grids and hence is simpler to implement in frameworks which involve complex geometries and boundary conditions. Numerical implementation of the new scheme is carried out on the scalar conservation laws with linear, non-linear flux and systems of hyperbolic conservation laws. The numerical results confirm the expected accuracy and high-resolution properties of the scheme.     

QoS-based cooperative algorithm for integral multi-commodity flow problem

This paper treats with integral multi-commodity flow through a network. To enhance the Quality of Service (QoS) for channels, it is necessary to minimize delay and congestion. Decreasing the end-to-end delay and consumption of bandwidth across channels are dependent and may be considered in very complex mathematical equations. To capture with this problem, a multi-commodity flow model is introduced whose targets are minimizing delay and congestion in one model. The flow through the network such as packets, also needs to get integral values. A model covering these concepts, is NP-hard while it is very important to find transmission strategies in real-time. For this aim, we extend a cooperative algorithm including traditional mathematical programming such as path enumeration and a meta-heuristic algorithm such as genetic algorithm. To find integral solution satisfying demands of nodes, we generalize a hybrid genetic algorithm to assign the integral commodities where they are needed. In this hybrid algorithm, we use feasible encoding and try to keep feasibility of chromosomes over iterations. By considering some random networks, we show that the proposed algorithm yields reasonable results in a few number of iterations. Also, because this algorithm can be applied in a wide range of objective functions in terms of delay and congestion, it is possible to find some routs for each commodity with high QoS. Due to these outcomes, the presented model and algorithm can be utilized in a variety of application in computer networks and transportation systems to decrease the congestion and increase the usage of channels.     

Processing Optimal Sequenced Route Queries Using Voronoi Diagrams

The Optimal Sequenced Route (OSR) query strives to find a route of minimum length starting from a given source location and passing through a number of typed locations in a specific sequence imposed on the types of the locations. In this paper, we propose a pre-computation approach to OSR query in both vector and metric spaces. We exploit the geometric properties of the solution space and theoretically prove its relation to additively weighted Voronoi diagrams. Our approach recursively accesses these diagrams to incrementally build the OSR. Introducing the analogous diagrams for the space of road networks, we show that our approach is also efficiently applicable to this metric space. Our experimental results verify that our pre-computation approach outperforms the previous index-based approaches in terms of query response time. This research has been funded in part by NSF grants EEC-9529152 (IMSC ERC), IIS-0238560 (PECASE), IIS-0324955 (ITR), IIS-0534761, and unrestricted cash gifts from Google and Microsoft. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.

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A Wavelet-ANFIS Hybrid Model for Groundwater Level Forecasting for Different Prediction Periods

Artificial neural network (ANN) and Adaptive Neuro-Fuzzy Inference System (ANFIS) have an extensive range of applications in water resources management. Wavelet transformation as a preprocessing approach can improve the ability of a forecasting model by capturing useful information on various resolution levels. The objective of this research is to compare several data-driven models for forecasting groundwater level for different prediction periods. In this study, a number of model structures for Artificial Neural Network (ANN), Adaptive Neuro-Fuzzy Inference System (ANFIS), Wavelet-ANN and Wavelet-ANFIS models have been compared to evaluate their performances to forecast groundwater level with 1, 2, 3 and 4 months ahead under two case studies in two sub-basins. It was demonstrated that wavelet transform can improve accuracy of groundwater level forecasting. It has been also shown that the forecasts made by Wavelet-ANFIS models are more accurate than those by ANN, ANFIS and Wavelet-ANN models. This study confirms that the optimum number of neurons in the hidden layer cannot be always determined by using a specific formula but trial-and-error method. The decomposition level in wavelet transform should be determined according to the periodicity and seasonality of data series. The prediction of these models is more accurate for 1 and 2 months ahead (for example RMSE?=?0.12, E?=?0.93 and R ²?=?0.99 for wavelet-ANFIS model for 1 month ahead) than for 3 and 4 months ahead (for example RMSE?=?2.07, E?=?0.63 and R ²?=?0.91 for wavelet-ANFIS model for 4 months ahead).     

Efficient biodegradation of naphthalene by a newly characterized indigenous Achromobacter sp. FBHYA2 isolated from Tehran Oil Refinery Complex

A bacterial strain, FBHYA2, capable of degrading naphthalene, was isolated from the American Petroleum Institute (API) separator of the Tehran Oil Refinery Complex (TORC). Strain FBHYA2 was identified as Achromobacter sp. based on physiological and biochemical characteristics and also phylogenetic similarity of 16S rRNA gene sequence. The optimal growth conditions for strain FBHYA2 were pH 6.0, 30 °C and 1.0% NaCl. Strain FBHYA2 can utilize naphthalene as the sole source of carbon and energy and was able to degrade naphthalene aerobically very fast, 48 h for 96% removal at 500 mg/L concentration. The physiological response of Achromobacter sp., FBHYA2 to several hydrophobic chemicals (aliphatic and aromatic hydrocarbons) was also investigated. No biosurfactant was detected during bacterial growth on any aliphatic/aromatic hydrocarbons. The results of hydrophobicity measurements showed no significant difference between naphthalene- and LB-grown cells. The capability of the strain FBHYA2 to degrade naphthalene completely and rapidly without the need to secrete biosurfactant may make it an ideal candidate to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated sites.     

Stores clustering using a data mining approach for distributing automotive spare-parts to reduce transportation costs

Clustering of retail stores in a distribution network with specific geographical limits plays an important and effective role in distribution and transportation costs reduction. In this paper, the relevant data and information for an established automotive spare-parts distribution and after-sales services company (ISACO) for a 3-year period have been analyzed. With respect to the diversity and lot size of the available information such as stores location, order, goods, transportation vehicles and road and traffic information, three effecting factors with specific weights have been defined for the similarity function: 1. Euclidean distance, 2. Lot size 3. Order concurrency. Based on these three factors, the similarity function has been examined through 5 steps using the Association Rules principles, where the clustering of the stores is performed using k-means algorithm and similar stores are allocated to the clusters. These steps include: 1. Similarity function based on the Euclidean distances, 2. Similarity function based on the order concurrency, 3. Similarity function based on the combination of the order concurrency and lot size, 4. Similarity function based on the combination of these three factors and 5. Improved similarity function. The above mentioned clustering operation for each 5 cases addressed in data mining have been carried out using R software and the improved combinational function has been chosen as the optimal clustering function. Then, trend of each retail store have been analyzed using the improved combinational function and along with determining the priority of the depot center establishment for every cluster, the appropriate distribution policies have been formulated for every cluster. The obtained results of this study indicate a significant cost reduction (32%) in automotive spare-parts distribution and transportation costs.