Search results for: Protein homology detection; support vectormachine; string kernel.
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 3745

Search results for: Protein homology detection; support vectormachine; string kernel.

3685 Selection of Pichia kudriavzevii Strain for the Production of Single-Cell Protein from Cassava Processing Waste

Authors: Phakamas Rachamontree, Theerawut Phusantisampan, Natthakorn Woravutthikul, Peerapong Pornwongthong, Malinee Sriariyanun

Abstract:

A total of 115 yeast strains isolated from local cassava processing wastes were measured for crude protein content. Among these strains, the strain MSY-2 possessed the highest protein concentration (>3.5 mg protein/mL). By using molecular identification tools, it was identified to be a strain of Pichia kudriavzevii based on similarity of D1/D2 domain of 26S rDNA region. In this study, to optimize the protein production by MSY-2 strain, Response Surface Methodology (RSM) was applied. The tested parameters were the carbon content, nitrogen content, and incubation time. Here, the value of regression coefficient (R2) = 0.7194 could be explained by the model which is high to support the significance of the model. Under the optimal condition, the protein content was produced up to 3.77 g per L of the culture and MSY-2 strain contains 66.8 g protein per 100 g of cell dry weight. These results revealed the plausibility of applying the novel strain of yeast in single-cell protein production.

Keywords: Single cell protein, response surface methodology, yeast, cassava processing waste.

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3684 Multiclass Support Vector Machines with Simultaneous Multi-Factors Optimization for Corporate Credit Ratings

Authors: Hyunchul Ahn, William X. S. Wong

Abstract:

Corporate credit rating prediction is one of the most important topics, which has been studied by researchers in the last decade. Over the last decade, researchers are pushing the limit to enhance the exactness of the corporate credit rating prediction model by applying several data-driven tools including statistical and artificial intelligence methods. Among them, multiclass support vector machine (MSVM) has been widely applied due to its good predictability. However, heuristics, for example, parameters of a kernel function, appropriate feature and instance subset, has become the main reason for the critics on MSVM, as they have dictate the MSVM architectural variables. This study presents a hybrid MSVM model that is intended to optimize all the parameter such as feature selection, instance selection, and kernel parameter. Our model adopts genetic algorithm (GA) to simultaneously optimize multiple heterogeneous design factors of MSVM.

Keywords: Corporate credit rating prediction, feature selection, genetic algorithms, instance selection, multiclass support vector machines.

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3683 Kernel Matching versus Inverse Probability Weighting: A Comparative Study

Authors: Andy Handouyahia, Tony Haddad, Frank Eaton

Abstract:

Recent quasi-experimental evaluation of the Canadian Active Labour Market Policies (ALMP) by Human Resources and Skills Development Canada (HRSDC) has provided an opportunity to examine alternative methods to estimating the incremental effects of Employment Benefits and Support Measures (EBSMs) on program participants. The focus of this paper is to assess the efficiency and robustness of inverse probability weighting (IPW) relative to kernel matching (KM) in the estimation of program effects. To accomplish this objective, the authors compare pairs of 1,080 estimates, along with their associated standard errors, to assess which type of estimate is generally more efficient and robust. In the interest of practicality, the authorsalso document the computationaltime it took to produce the IPW and KM estimates, respectively.

Keywords: Treatment effect, causal inference, observational studies, Propensity score based matching, Kernel Matching, Inverse Probability Weighting, Estimation methods for incremental effect.

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3682 State of the Art: A Study on Fall Detection

Authors: Goh Yongli, Ooi Shih Yin, Pang Ying Han

Abstract:

Unintentional falls are rife throughout the ages and have been the common factor of serious or critical injuries especially for the elderly society. Fortunately, owing to the recent rapid advancement in technology, fall detection system is made possible, enabling detection of falling events for the elderly, monitoring the patient and consequently provides emergency support in the event of falling. This paper presents a review of 3 main categories of fall detection techniques, ranging from year 2005 to year 2010. This paper will be focusing on discussing the techniques alongside with summary and conclusion for them.

Keywords: State of the art, fall detection, wearable devices, ambient analyser, motion detection.

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3681 Hardware Error Analysis and Severity Characterization in Linux-Based Server Systems

Authors: N. Georgoulopoulos, A. Hatzopoulos, K. Karamitsios, K. Kotrotsios, A. I. Metsai

Abstract:

Current server systems are responsible for critical applications that run in different infrastructures, such as the cloud, physical machines, and virtual machines. A common challenge that these systems face are the various hardware faults that may occur due to the high load, among other reasons, which translates to errors resulting in malfunctions or even server downtime. The most important hardware parts, that are causing most of the errors, are the CPU, RAM, and the hard drive - HDD. In this work, we investigate selected CPU, RAM, and HDD errors, observed or simulated in kernel ring buffer log files from GNU/Linux servers. Moreover, a severity characterization is given for each error type. Understanding these errors is crucial for the efficient analysis of kernel logs that are usually utilized for monitoring servers and diagnosing faults. In addition, to support the previous analysis, we present possible ways of simulating hardware errors in RAM and HDD, aiming to facilitate the testing of methods for detecting and tackling the above issues in a server running on GNU/Linux.

Keywords: hardware errors, Kernel logs, GNU/Linux servers, RAM, HDD, CPU

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3680 An Iterative Algorithm for KLDA Classifier

Authors: D.N. Zheng, J.X. Wang, Y.N. Zhao, Z.H. Yang

Abstract:

The Linear discriminant analysis (LDA) can be generalized into a nonlinear form - kernel LDA (KLDA) expediently by using the kernel functions. But KLDA is often referred to a general eigenvalue problem in singular case. To avoid this complication, this paper proposes an iterative algorithm for the two-class KLDA. The proposed KLDA is used as a nonlinear discriminant classifier, and the experiments show that it has a comparable performance with SVM.

Keywords: Linear discriminant analysis (LDA), kernel LDA (KLDA), conjugate gradient algorithm, nonlinear discriminant classifier.

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3679 Boosting Method for Automated Feature Space Discovery in Supervised Quantum Machine Learning Models

Authors: Vladimir Rastunkov, Jae-Eun Park, Abhijit Mitra, Brian Quanz, Steve Wood, Christopher Codella, Heather Higgins, Joseph Broz

Abstract:

Quantum Support Vector Machines (QSVM) have become an important tool in research and applications of quantum kernel methods. In this work we propose a boosting approach for building ensembles of QSVM models and assess performance improvement across multiple datasets. This approach is derived from the best ensemble building practices that worked well in traditional machine learning and thus should push the limits of quantum model performance even further. We find that in some cases, a single QSVM model with tuned hyperparameters is sufficient to simulate the data, while in others - an ensemble of QSVMs that are forced to do exploration of the feature space via proposed method is beneficial.

Keywords: QSVM, Quantum Support Vector Machines, quantum kernel, boosting, ensemble.

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3678 The Performance of the Character-Access on the Checking Phase in String Searching Algorithms

Authors: Mahmoud M. Mhashi

Abstract:

A new algorithm called Character-Comparison to Character-Access (CCCA) is developed to test the effect of both: 1) converting character-comparison and number-comparison into character-access and 2) the starting point of checking on the performance of the checking operation in string searching. An experiment is performed; the results are compared with five algorithms, namely, Naive, BM, Inf_Suf_Pref, Raita, and Circle. With the CCCA algorithm, the results suggest that the evaluation criteria of the average number of comparisons are improved up to 74.0%. Furthermore, the results suggest that the clock time required by the other algorithms is improved in range from 28% to 68% by the new CCCA algorithm

Keywords: Pattern matching, string searching, charactercomparison, character-access, and checking.

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3677 Using ε Value in Describe Regular Languages by Using Finite Automata, Operation on Languages and the Changing Algorithm Implementation

Authors: Abdulmajid Mukhtar Afat

Abstract:

This paper aims at introducing nondeterministic finite automata with ε value which is used to perform some operations on languages. a program is created to implement the algorithm that converts nondeterministic finite automata with ε value (ε-NFA) to deterministic finite automata (DFA).The program is written in c++ programming language. The program inputs are FA 5-tuples from text file and then classifies it into either DFA/NFA or ε -NFA. For DFA, the program will get the string w and decide whether it is accepted or rejected. The tracking path for an accepted string is saved by the program. In case of NFA or ε-NFA automation, the program changes the automation to DFA to enable tracking and to decide if the string w exists in the regular language or not.

Keywords: Finite automata, DFA, NFA, ε-NFA, Eclose, operations on languages.

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3676 Approximation Algorithm for the Shortest Approximate Common Superstring Problem

Authors: A.S. Rebaï, M. Elloumi

Abstract:

The Shortest Approximate Common Superstring (SACS) problem is : Given a set of strings f={w1, w2, ... , wn}, where no wi is an approximate substring of wj, i ≠ j, find a shortest string Sa, such that, every string of f is an approximate substring of Sa. When the number of the strings n>2, the SACS problem becomes NP-complete. In this paper, we present a greedy approximation SACS algorithm. Our algorithm is a 1/2-approximation for the SACS problem. It is of complexity O(n2*(l2+log(n))) in computing time, where n is the number of the strings and l is the length of a string. Our SACS algorithm is based on computation of the Length of the Approximate Longest Overlap (LALO).

Keywords: Shortest approximate common superstring, approximation algorithms, strings overlaps, complexities.

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3675 Evaluating some Feature Selection Methods for an Improved SVM Classifier

Authors: Daniel Morariu, Lucian N. Vintan, Volker Tresp

Abstract:

Text categorization is the problem of classifying text documents into a set of predefined classes. After a preprocessing step the documents are typically represented as large sparse vectors. When training classifiers on large collections of documents, both the time and memory restrictions can be quite prohibitive. This justifies the application of features selection methods to reduce the dimensionality of the document-representation vector. Four feature selection methods are evaluated: Random Selection, Information Gain (IG), Support Vector Machine (called SVM_FS) and Genetic Algorithm with SVM (GA_FS). We showed that the best results were obtained with SVM_FS and GA_FS methods for a relatively small dimension of the features vector comparative with the IG method that involves longer vectors, for quite similar classification accuracies. Also we present a novel method to better correlate SVM kernel-s parameters (Polynomial or Gaussian kernel).

Keywords: Features selection, learning with kernels, support vector machine, genetic algorithms and classification.

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3674 Empirical Process Monitoring Via Chemometric Analysis of Partially Unbalanced Data

Authors: Hyun-Woo Cho

Abstract:

Real-time or in-line process monitoring frameworks are designed to give early warnings for a fault along with meaningful identification of its assignable causes. In artificial intelligence and machine learning fields of pattern recognition various promising approaches have been proposed such as kernel-based nonlinear machine learning techniques. This work presents a kernel-based empirical monitoring scheme for batch type production processes with small sample size problem of partially unbalanced data. Measurement data of normal operations are easy to collect whilst special events or faults data are difficult to collect. In such situations, noise filtering techniques can be helpful in enhancing process monitoring performance. Furthermore, preprocessing of raw process data is used to get rid of unwanted variation of data. The performance of the monitoring scheme was demonstrated using three-dimensional batch data. The results showed that the monitoring performance was improved significantly in terms of detection success rate of process fault.

Keywords: Process Monitoring, kernel methods, multivariate filtering, data-driven techniques, quality improvement.

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3673 Genetic-based Anomaly Detection in Logs of Process Aware Systems

Authors: Hanieh Jalali, Ahmad Baraani

Abstract:

Nowaday-s, many organizations use systems that support business process as a whole or partially. However, in some application domains, like software development and health care processes, a normative Process Aware System (PAS) is not suitable, because a flexible support is needed to respond rapidly to new process models. On the other hand, a flexible Process Aware System may be vulnerable to undesirable and fraudulent executions, which imposes a tradeoff between flexibility and security. In order to make this tradeoff available, a genetic-based anomaly detection model for logs of Process Aware Systems is presented in this paper. The detection of an anomalous trace is based on discovering an appropriate process model by using genetic process mining and detecting traces that do not fit the appropriate model as anomalous trace; therefore, when used in PAS, this model is an automated solution that can support coexistence of flexibility and security.

Keywords: Anomaly Detection, Genetic Algorithm, ProcessAware Systems, Process Mining.

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3672 Optimal Feature Extraction Dimension in Finger Vein Recognition Using Kernel Principal Component Analysis

Authors: Amir Hajian, Sepehr Damavandinejadmonfared

Abstract:

In this paper the issue of dimensionality reduction is investigated in finger vein recognition systems using kernel Principal Component Analysis (KPCA). One aspect of KPCA is to find the most appropriate kernel function on finger vein recognition as there are several kernel functions which can be used within PCA-based algorithms. In this paper, however, another side of PCA-based algorithms -particularly KPCA- is investigated. The aspect of dimension of feature vector in PCA-based algorithms is of importance especially when it comes to the real-world applications and usage of such algorithms. It means that a fixed dimension of feature vector has to be set to reduce the dimension of the input and output data and extract the features from them. Then a classifier is performed to classify the data and make the final decision. We analyze KPCA (Polynomial, Gaussian, and Laplacian) in details in this paper and investigate the optimal feature extraction dimension in finger vein recognition using KPCA.

Keywords: Biometrics, finger vein recognition, Principal Component Analysis (PCA), Kernel Principal Component Analysis (KPCA).

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3671 An ensemble of Weighted Support Vector Machines for Ordinal Regression

Authors: Willem Waegeman, Luc Boullart

Abstract:

Instead of traditional (nominal) classification we investigate the subject of ordinal classification or ranking. An enhanced method based on an ensemble of Support Vector Machines (SVM-s) is proposed. Each binary classifier is trained with specific weights for each object in the training data set. Experiments on benchmark datasets and synthetic data indicate that the performance of our approach is comparable to state of the art kernel methods for ordinal regression. The ensemble method, which is straightforward to implement, provides a very good sensitivity-specificity trade-off for the highest and lowest rank.

Keywords: Ordinal regression, support vector machines, ensemblelearning.

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3670 Predicting Protein-Protein Interactions from Protein Sequences Using Phylogenetic Profiles

Authors: Omer Nebil Yaveroglu, Tolga Can

Abstract:

In this study, a high accuracy protein-protein interaction prediction method is developed. The importance of the proposed method is that it only uses sequence information of proteins while predicting interaction. The method extracts phylogenetic profiles of proteins by using their sequence information. Combining the phylogenetic profiles of two proteins by checking existence of homologs in different species and fitting this combined profile into a statistical model, it is possible to make predictions about the interaction status of two proteins. For this purpose, we apply a collection of pattern recognition techniques on the dataset of combined phylogenetic profiles of protein pairs. Support Vector Machines, Feature Extraction using ReliefF, Naive Bayes Classification, K-Nearest Neighborhood Classification, Decision Trees, and Random Forest Classification are the methods we applied for finding the classification method that best predicts the interaction status of protein pairs. Random Forest Classification outperformed all other methods with a prediction accuracy of 76.93%

Keywords: Protein Interaction Prediction, Phylogenetic Profile, SVM , ReliefF, Decision Trees, Random Forest Classification

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3669 Flame Kernel Growth and Related Effects of Spark Plug Electrodes: Fluid Motion Interaction in an Optically Accessible DISI Engine

Authors: A. Schirru, A. Irimescu, S. Merola, A. d’Adamo, S. Fontanesi

Abstract:

One of the aspects that are usually neglected during the design phase of an engine is the effect of the spark plug on the flow field inside the combustion chamber. Because of the difficulties in the experimental investigation of the mutual interaction between flow alteration and early flame kernel convection effect inside the engine combustion chamber, CFD-3D simulation is usually exploited in such cases. Experimentally speaking, a particular type of engine has to be used in order to directly observe the flame propagation process. In this study, a double electrode spark plug was fitted into an optically accessible engine and a high-speed camera was used to capture the initial stages of the combustion process. Both the arc and the kernel phases were observed. Then, a morphologic analysis was carried out and the position of the center of mass of the flame, relative to the spark plug position, was calculated. The crossflow orientation was chosen for the spark plug and the kernel growth process was observed for different air-fuel ratios. It was observed that during a normal cycle the flow field between the electrodes tends to transport the arc deforming it. Because of that, the kernel growth phase takes place away from the electrodes and the flame propagates with a preferential direction dictated by the flow field.

Keywords: Combustion, Kernel growth, optically accessible engine, spark-ignition engine, spark plug orientation.

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3668 An Integrative Bayesian Approach to Supporting the Prediction of Protein-Protein Interactions: A Case Study in Human Heart Failure

Authors: Fiona Browne, Huiru Zheng, Haiying Wang, Francisco Azuaje

Abstract:

Recent years have seen a growing trend towards the integration of multiple information sources to support large-scale prediction of protein-protein interaction (PPI) networks in model organisms. Despite advances in computational approaches, the combination of multiple “omic" datasets representing the same type of data, e.g. different gene expression datasets, has not been rigorously studied. Furthermore, there is a need to further investigate the inference capability of powerful approaches, such as fullyconnected Bayesian networks, in the context of the prediction of PPI networks. This paper addresses these limitations by proposing a Bayesian approach to integrate multiple datasets, some of which encode the same type of “omic" data to support the identification of PPI networks. The case study reported involved the combination of three gene expression datasets relevant to human heart failure (HF). In comparison with two traditional methods, Naive Bayesian and maximum likelihood ratio approaches, the proposed technique can accurately identify known PPI and can be applied to infer potentially novel interactions.

Keywords: Bayesian network, Classification, Data integration, Protein interaction networks.

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3667 An Algebra for Protein Structure Data

Authors: Yanchao Wang, Rajshekhar Sunderraman

Abstract:

This paper presents an algebraic approach to optimize queries in domain-specific database management system for protein structure data. The approach involves the introduction of several protein structure specific algebraic operators to query the complex data stored in an object-oriented database system. The Protein Algebra provides an extensible set of high-level Genomic Data Types and Protein Data Types along with a comprehensive collection of appropriate genomic and protein functions. The paper also presents a query translator that converts high-level query specifications in algebra into low-level query specifications in Protein-QL, a query language designed to query protein structure data. The query transformation process uses a Protein Ontology that serves the purpose of a dictionary.

Keywords: Domain-Specific Data Management, Protein Algebra, Protein Ontology, Protein Structure Data.

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3666 Feature Selection Methods for an Improved SVM Classifier

Authors: Daniel Morariu, Lucian N. Vintan, Volker Tresp

Abstract:

Text categorization is the problem of classifying text documents into a set of predefined classes. After a preprocessing step, the documents are typically represented as large sparse vectors. When training classifiers on large collections of documents, both the time and memory restrictions can be quite prohibitive. This justifies the application of feature selection methods to reduce the dimensionality of the document-representation vector. In this paper, three feature selection methods are evaluated: Random Selection, Information Gain (IG) and Support Vector Machine feature selection (called SVM_FS). We show that the best results were obtained with SVM_FS method for a relatively small dimension of the feature vector. Also we present a novel method to better correlate SVM kernel-s parameters (Polynomial or Gaussian kernel).

Keywords: Feature Selection, Learning with Kernels, SupportVector Machine, and Classification.

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3665 The Finite Difference Scheme for the Suspended String Equation with the Nonlinear Damping Term

Authors: Jaipong Kasemsuwan

Abstract:

A numerical solution of the initial boundary value problem of the suspended string vibrating equation with the particular nonlinear damping term based on the finite difference scheme is presented in this paper. The investigation of how the second and third power terms of the nonlinear term affect the vibration characteristic. We compare the vibration amplitude as a result of the third power nonlinear damping with the second power obtained from previous report provided that the same initial shape and initial velocities are assumed. The comparison results show that the vibration amplitude is inversely proportional to the coefficient of the damping term for the third power nonlinear damping case, while the vibration amplitude is proportional to the coefficient of the damping term in the second power nonlinear damping case.

Keywords: Finite-difference method, the nonlinear damped equation, the numerical simulation, the suspended string equation

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3664 Semi-Automatic Trend Detection in Scholarly Repository Using Semantic Approach

Authors: Fereshteh Mahdavi, Maizatul Akmar Ismail, Noorhidawati Abdullah

Abstract:

Currently WWW is the first solution for scholars in finding information. But, analyzing and interpreting this volume of information will lead to researchers overload in pursuing their research. Trend detection in scientific publication retrieval systems helps scholars to find relevant, new and popular special areas by visualizing the trend of input topic. However, there are few researches on trend detection in scientific corpora while their proposed models do not appear to be suitable. Previous works lack of an appropriate representation scheme for research topics. This paper describes a method that combines Semantic Web and ontology to support advance search functions such as trend detection in the context of scholarly Semantic Web system (SSWeb).

Keywords: Trend, Semi-Automatic Trend Detection, Ontology, Semantic Trend Detection.

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3663 Anomaly Detection with ANN and SVM for Telemedicine Networks

Authors: Edward Guillén, Jeisson Sánchez, Carlos Omar Ramos

Abstract:

In recent years, a wide variety of applications are developed with Support Vector Machines -SVM- methods and Artificial Neural Networks -ANN-. In general, these methods depend on intrusion knowledge databases such as KDD99, ISCX, and CAIDA among others. New classes of detectors are generated by machine learning techniques, trained and tested over network databases. Thereafter, detectors are employed to detect anomalies in network communication scenarios according to user’s connections behavior. The first detector based on training dataset is deployed in different real-world networks with mobile and non-mobile devices to analyze the performance and accuracy over static detection. The vulnerabilities are based on previous work in telemedicine apps that were developed on the research group. This paper presents the differences on detections results between some network scenarios by applying traditional detectors deployed with artificial neural networks and support vector machines.

Keywords: Anomaly detection, back-propagation neural networks, network intrusion detection systems, support vector machines.

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3662 Composite Kernels for Public Emotion Recognition from Twitter

Authors: Chien-Hung Chen, Yan-Chun Hsing, Yung-Chun Chang

Abstract:

The Internet has grown into a powerful medium for information dispersion and social interaction that leads to a rapid growth of social media which allows users to easily post their emotions and perspectives regarding certain topics online. Our research aims at using natural language processing and text mining techniques to explore the public emotions expressed on Twitter by analyzing the sentiment behind tweets. In this paper, we propose a composite kernel method that integrates tree kernel with the linear kernel to simultaneously exploit both the tree representation and the distributed emotion keyword representation to analyze the syntactic and content information in tweets. The experiment results demonstrate that our method can effectively detect public emotion of tweets while outperforming the other compared methods.

Keywords: Public emotion recognition, natural language processing, composite kernel, sentiment analysis, text mining.

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3661 Hybrid Anomaly Detection Using Decision Tree and Support Vector Machine

Authors: Elham Serkani, Hossein Gharaee Garakani, Naser Mohammadzadeh, Elaheh Vaezpour

Abstract:

Intrusion detection systems (IDS) are the main components of network security. These systems analyze the network events for intrusion detection. The design of an IDS is through the training of normal traffic data or attack. The methods of machine learning are the best ways to design IDSs. In the method presented in this article, the pruning algorithm of C5.0 decision tree is being used to reduce the features of traffic data used and training IDS by the least square vector algorithm (LS-SVM). Then, the remaining features are arranged according to the predictor importance criterion. The least important features are eliminated in the order. The remaining features of this stage, which have created the highest level of accuracy in LS-SVM, are selected as the final features. The features obtained, compared to other similar articles which have examined the selected features in the least squared support vector machine model, are better in the accuracy, true positive rate, and false positive. The results are tested by the UNSW-NB15 dataset.

Keywords: Intrusion detection system, decision tree, support vector machine, feature selection.

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3660 On Discretization of Second-order Derivatives in Smoothed Particle Hydrodynamics

Authors: R. Fatehi, M.A. Fayazbakhsh, M.T. Manzari

Abstract:

Discretization of spatial derivatives is an important issue in meshfree methods especially when the derivative terms contain non-linear coefficients. In this paper, various methods used for discretization of second-order spatial derivatives are investigated in the context of Smoothed Particle Hydrodynamics. Three popular forms (i.e. "double summation", "second-order kernel derivation", and "difference scheme") are studied using one-dimensional unsteady heat conduction equation. To assess these schemes, transient response to a step function initial condition is considered. Due to parabolic nature of the heat equation, one can expect smooth and monotone solutions. It is shown, however in this paper, that regardless of the type of kernel function used and the size of smoothing radius, the double summation discretization form leads to non-physical oscillations which persist in the solution. Also, results show that when a second-order kernel derivative is used, a high-order kernel function shall be employed in such a way that the distance of inflection point from origin in the kernel function be less than the nearest particle distance. Otherwise, solutions may exhibit oscillations near discontinuities unlike the "difference scheme" which unconditionally produces monotone results.

Keywords: Heat conduction, Meshfree methods, Smoothed ParticleHydrodynamics (SPH), Second-order derivatives.

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3659 Weighted k-Nearest-Neighbor Techniques for High Throughput Screening Data

Authors: Kozak K, M. Kozak, K. Stapor

Abstract:

The k-nearest neighbors (knn) is a simple but effective method of classification. In this paper we present an extended version of this technique for chemical compounds used in High Throughput Screening, where the distances of the nearest neighbors can be taken into account. Our algorithm uses kernel weight functions as guidance for the process of defining activity in screening data. Proposed kernel weight function aims to combine properties of graphical structure and molecule descriptors of screening compounds. We apply the modified knn method on several experimental data from biological screens. The experimental results confirm the effectiveness of the proposed method.

Keywords: biological screening, kernel methods, KNN, QSAR

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3658 Cloning of a β-Glucosidase Gene (BGL1) from Traditional Starter Yeast Saccharomycopsis fibuligera BMQ 908 and Expression in Pichia pastoris

Authors: Le Thuy Mai, Vu Nguyen Thanh

Abstract:

β-Glucosidase is an important enzyme for production of ethanol from lignocellulose. With hydrolytic activity on cellooligosaccharides, especially cellobiose, β-glucosidase removes product inhibitory effect on cellulases and forms fermentable sugars. In this study, β-glucosidase encoding gene (BGL1) from traditional starter yeast Saccharomycosis fibuligera BMQ908 was cloned and expressed in Pichia pastoris. BGL1 of S. fibuligera BMQ 908 shared 98% nucleotide homology with the closest GenBank sequence (M22475) but identity in amino-acid sequences of catalytic domains. Recombinant plasmid pPICZαA/BGL1 containing the sequence encoding BGL1 mature protein and α-factor secretion signal was constructed and transformed into methylotrophic yeast P. pastoris by electroporation. The recombinant strain produced single extracellular protein with molecular weight of 120 kDa and cellobiase activity of 60 IU/ml. The optimum pH of the recombinant β-glucosidase was 5.0 and the optimum temperature was 50°C.

Keywords: β-Glucosidase, Pichia pastoris, Saccharomycopsisfibuligera, recombinant enzyme.

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3657 Community Detection-based Analysis of the Human Interactome Network

Authors: Razvan Bocu, Sabin Tabirca

Abstract:

The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents a new technique that allows for an accurate analysis of the human interactome network. It is basically a two-step analysis process that involves, at first, the detection of each protein-s absolute importance through the betweenness centrality computation. Then, the second step determines the functionallyrelated communities of proteins. For this purpose, we use a community detection technique that is based on the edge betweenness calculation. The new technique was thoroughly tested on real biological data and the results prove some interesting properties of those proteins that are involved in the carcinogenesis process. Apart from its experimental usefulness, the novel technique is also computationally effective in terms of execution times. Based on the analysis- results, some topological features of cancer mutated proteins are presented and a possible optimization solution for cancer drugs design is suggested.

Keywords: Betweenness centrality, interactome networks, proteinprotein interactions, protein communities, cancer.

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3656 Annual Power Load Forecasting Using Support Vector Regression Machines: A Study on Guangdong Province of China 1985-2008

Authors: Zhiyong Li, Zhigang Chen, Chao Fu, Shipeng Zhang

Abstract:

Load forecasting has always been the essential part of an efficient power system operation and planning. A novel approach based on support vector machines is proposed in this paper for annual power load forecasting. Different kernel functions are selected to construct a combinatorial algorithm. The performance of the new model is evaluated with a real-world dataset, and compared with two neural networks and some traditional forecasting techniques. The results show that the proposed method exhibits superior performance.

Keywords: combinatorial algorithm, data mining, load forecasting, support vector machines

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