A Computational Method for the Identification of Endolysins and Autolysins

2020 ◽  
Vol 27 (4) ◽  
pp. 329-336 ◽  
Author(s):  
Lei Xu ◽  
Guangmin Liang ◽  
Baowen Chen ◽  
Xu Tan ◽  
Huaikun Xiang ◽  
...  
Keyword(s):  
Support Vector Machine ◽  
Cell Wall ◽  
Experimental Results ◽  
Computational Method ◽  
Lytic Enzyme ◽  
Support Vector ◽  
Lytic Enzymes ◽  
Data Set ◽  
Optimal Feature ◽  
Better Than

Background: Cell lytic enzyme is a kind of highly evolved protein, which can destroy the cell structure and kill the bacteria. Compared with antibiotics, cell lytic enzyme will not cause serious problem of drug resistance of pathogenic bacteria. Thus, the study of cell wall lytic enzymes aims at finding an efficient way for curing bacteria infectious. Compared with using antibiotics, the problem of drug resistance becomes more serious. Therefore, it is a good choice for curing bacterial infections by using cell lytic enzymes. Cell lytic enzyme includes endolysin and autolysin and the difference between them is the purpose of the break of cell wall. The identification of the type of cell lytic enzymes is meaningful for the study of cell wall enzymes. Objective: In this article, our motivation is to predict the type of cell lytic enzyme. Cell lytic enzyme is helpful for killing bacteria, so it is meaningful for study the type of cell lytic enzyme. However, it is time consuming to detect the type of cell lytic enzyme by experimental methods. Thus, an efficient computational method for the type of cell lytic enzyme prediction is proposed in our work. Method: We propose a computational method for the prediction of endolysin and autolysin. First, a data set containing 27 endolysins and 41 autolysins is built. Then the protein is represented by tripeptides composition. The features are selected with larger confidence degree. At last, the classifier is trained by the labeled vectors based on support vector machine. The learned classifier is used to predict the type of cell lytic enzyme. Results: Following the proposed method, the experimental results show that the overall accuracy can attain 97.06%, when 44 features are selected. Compared with Ding's method, our method improves the overall accuracy by nearly 4.5% ((97.06-92.9)/92.9%). The performance of our proposed method is stable, when the selected feature number is from 40 to 70. The overall accuracy of tripeptides optimal feature set is 94.12%, and the overall accuracy of Chou's amphiphilic PseAAC method is 76.2%. The experimental results also demonstrate that the overall accuracy is improved by nearly 18% when using the tripeptides optimal feature set. Conclusion: The paper proposed an efficient method for identifying endolysin and autolysin. In this paper, support vector machine is used to predict the type of cell lytic enzyme. The experimental results show that the overall accuracy of the proposed method is 94.12%, which is better than some existing methods. In conclusion, the selected 44 features can improve the overall accuracy for identification of the type of cell lytic enzyme. Support vector machine performs better than other classifiers when using the selected feature set on the benchmark data set.

scholarly journals Using the Relevance Vector Machine Model Combined with Local Phase Quantization to Predict Protein-Protein Interactions from Protein Sequences

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Ji-Yong An ◽  
Fan-Rong Meng ◽  
Zhu-Hong You ◽  
Yu-Hong Fang ◽  
Yu-Jun Zhao ◽  
...  
Keyword(s):  
Protein Sequences ◽  
Relevance Vector Machine ◽  
Experimental Results ◽  
Computational Method ◽  
Support Vector ◽  
Svm Classifier ◽  
Local Phase ◽  
Local Phase Quantization ◽  
Phase Quantization ◽  
Better Than

We propose a novel computational method known as RVM-LPQ that combines the Relevance Vector Machine (RVM) model and Local Phase Quantization (LPQ) to predict PPIs from protein sequences. The main improvements are the results of representing protein sequences using the LPQ feature representation on a Position Specific Scoring Matrix (PSSM), reducing the influence of noise using a Principal Component Analysis (PCA), and using a Relevance Vector Machine (RVM) based classifier. We perform 5-fold cross-validation experiments onYeastandHumandatasets, and we achieve very high accuracies of 92.65% and 97.62%, respectively, which is significantly better than previous works. To further evaluate the proposed method, we compare it with the state-of-the-art support vector machine (SVM) classifier on theYeastdataset. The experimental results demonstrate that our RVM-LPQ method is obviously better than the SVM-based method. The promising experimental results show the efficiency and simplicity of the proposed method, which can be an automatic decision support tool for future proteomics research.

Combining Block DCV and Support Vector Machine for Ear Recognition

2016 ◽  
Vol 8 (2) ◽  
pp. 36-44 ◽  
Author(s):  
Zhao Hailong ◽  
Yi Junyan
Keyword(s):  
Support Vector Machine ◽  
Feature Extraction ◽  
Image Retrieval ◽  
Construction Method ◽  
Experimental Results ◽  
Support Vector ◽  
Recognition Method ◽  
Ear Recognition ◽  
Human Ear ◽  
Better Than

In recent years, automatic ear recognition has become a popular research. Effective feature extraction is one of the most important steps in Content-based ear image retrieval applications. In this paper, the authors proposed a new vectors construction method for ear retrieval based on Block Discriminative Common Vector. According to this method, the ear image is divided into 16 blocks firstly and the features are extracted by applying DCV to the sub-images. Furthermore, Support Vector Machine is used as classifier to make decision. The experimental results show that the proposed method performs better than classical PCA+LDA, so it is an effective human ear recognition method.

An Improvement Of Least Square - Twin Support Vector Machine

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Thanh Vi Nguyen ◽  
Thế Cường Nguyễn
Keyword(s):  
Support Vector Machine ◽  
Binary Classification ◽  
Least Square ◽  
Experimental Results ◽  
Twin Support Vector Machine ◽  
Support Vector ◽  
Classification Problems ◽  
Training Time ◽  
Data Points ◽  
Better Than

n binary classification problems, two classes of data seem tobe different from each other. It is expected to be more complicated dueto the number of data points of clusters in each class also be different.Traditional algorithms as Support Vector Machine (SVM), Twin Support Vector Machine (TSVM), or Least Square Twin Support VectorMachine (LSTSVM) cannot sufficiently exploit information about thenumber of data points in each cluster of the data. Which may be effectto the accuracy of classification problems. In this paper, we proposes anew Improved Least Square - Support Vector Machine (called ILS-SVM)for binary classification problems with a class-vs-clusters strategy. Experimental results show that the ILS-SVM training time is faster thanthat of TSVM, and the ILS-SVM accuracy is better than LSTSVM andTSVM in most cases.

Combining Block DCV and Support Vector Machine for Ear Recognition

2018 ◽  
pp. 774-783
Author(s):  
Zhao Hailong ◽  
Yi Junyan
Keyword(s):  
Support Vector Machine ◽  
Feature Extraction ◽  
Image Retrieval ◽  
Construction Method ◽  
Experimental Results ◽  
Support Vector ◽  
Recognition Method ◽  
Ear Recognition ◽  
Human Ear ◽  
Better Than

In recent years, automatic ear recognition has become a popular research. Effective feature extraction is one of the most important steps in Content-based ear image retrieval applications. In this paper, the authors proposed a new vectors construction method for ear retrieval based on Block Discriminative Common Vector. According to this method, the ear image is divided into 16 blocks firstly and the features are extracted by applying DCV to the sub-images. Furthermore, Support Vector Machine is used as classifier to make decision. The experimental results show that the proposed method performs better than classical PCA+LDA, so it is an effective human ear recognition method.

Detection and Recognition of RF Devices Using Support Vector Machine

2013 ◽  
Vol 5 (4) ◽  
pp. 13-20
Author(s):  
Shikhar P. Acharya ◽  
Ivan G. Guardiola
Keyword(s):  
Support Vector Machine ◽  
Radio Frequency ◽  
Experimental Results ◽  
Support Vector ◽  
Noise Band ◽  
Detection And Identification ◽  
Electromagnetic Emissions ◽  
Rf Devices ◽  
Unintended Electromagnetic Emissions ◽  
Detection And Recognition

Radio Frequency (RF) devices produce some amount of Unintended Electromagnetic Emissions (UEEs). UEEs are generally unique to a device and can be used as a signature for the purpose of detection and identification. The problem with UEEs is that they are very low in power and are often buried deep inside the noise band. The research herein provides the application of Support Vector Machine (SVM) for detection and identification of RF devices using their UEEs. Experimental Results shows that SVM can detect RF devices within the noise band, and can also identify RF devices using their UEEs.

Civil Aeroengine Fault Diagnosis Based on Fuzzy Least Square Support Vector Machine

2011 ◽  
Vol 130-134 ◽  
pp. 2047-2050 ◽  
Author(s):  
Hong Chun Qu ◽  
Xie Bin Ding
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Support Vector Machine ◽  
Fault Diagnosis ◽  
Coefficient Matrix ◽  
Least Square ◽  
Support Vector ◽  
Influence Coefficient ◽  
Structural Risk ◽  
Better Than

SVM(Support Vector Machine) is a new artificial intelligence methodolgy, basing on structural risk mininization principle, which has better generalization than the traditional machine learning and SVM shows powerfulability in learning with limited samples. To solve the problem of lack of engine fault samples, FLS-SVM theory, an improved SVM, which is a method is applied. 10 common engine faults are trained and recognized in the paper.The simulated datas are generated from PW4000-94 engine influence coefficient matrix at cruise, and the results show that the diagnostic accuracy of FLS-SVM is better than LS-SVM.

Analog Circuits Fault Diagnosis Using Multifractal Analysis

2013 ◽  
Vol 721 ◽  
pp. 367-371
Author(s):  
Yong Kui Sun ◽  
Zhi Bin Yu
Keyword(s):  
Support Vector Machine ◽  
Fault Diagnosis ◽  
Analog Circuits ◽  
Multifractal Analysis ◽  
Multifractal Spectrum ◽  
Experimental Results ◽  
Support Vector ◽  
Diagnosis Accuracy ◽  
Circuit Under Test

Analog circuits fault diagnosis using multifractal analysis is presented in this paper. The faulty response of circuit under test is analyzed by multifratal formalism, and the fault feature consists of multifractal spectrum parameters. Support vector machine is used to identify the faults. Experimental results prove the proposed method is effective and the diagnosis accuracy reaches 98%.

scholarly journals Multi-phase classification by a least-squares support vector machine approach in tomography images of geological samples

Solid Earth ◽  
2016 ◽  
Vol 7 (2) ◽  
pp. 481-492 ◽  
Author(s):  
Faisal Khan ◽  
Frieder Enzmann ◽  
Michael Kersten
Keyword(s):  
Support Vector Machine ◽  
Least Squares ◽  
Image Data ◽  
Main Beam ◽  
Support Vector ◽  
Geological Samples ◽  
Data Set ◽  
Corrected Image ◽  
Phase Classification ◽  
Multi Phase

Abstract. Image processing of X-ray-computed polychromatic cone-beam micro-tomography (μXCT) data of geological samples mainly involves artefact reduction and phase segmentation. For the former, the main beam-hardening (BH) artefact is removed by applying a best-fit quadratic surface algorithm to a given image data set (reconstructed slice), which minimizes the BH offsets of the attenuation data points from that surface. A Matlab code for this approach is provided in the Appendix. The final BH-corrected image is extracted from the residual data or from the difference between the surface elevation values and the original grey-scale values. For the segmentation, we propose a novel least-squares support vector machine (LS-SVM, an algorithm for pixel-based multi-phase classification) approach. A receiver operating characteristic (ROC) analysis was performed on BH-corrected and uncorrected samples to show that BH correction is in fact an important prerequisite for accurate multi-phase classification. The combination of the two approaches was thus used to classify successfully three different more or less complex multi-phase rock core samples.

Recognition of 3D Objects from 2D Views Features

2015 ◽  
Vol 13 (2) ◽  
pp. 50-58
Author(s):  
R. Khadim ◽  
R. El Ayachi ◽  
Mohamed Fakir
Keyword(s):  
Neural Network ◽  
Support Vector Machine ◽  
Nearest Neighbor ◽  
Color Image ◽  
Recognition Rate ◽  
Experimental Results ◽  
Support Vector ◽  
K Nearest Neighbor ◽  
3D Objects ◽  
Color Descriptor

This paper focuses on the recognition of 3D objects using 2D attributes. In order to increase the recognition rate, the present an hybridization of three approaches to calculate the attributes of color image, this hybridization based on the combination of Zernike moments, Gist descriptors and color descriptor (statistical moments). In the classification phase, three methods are adopted: Neural Network (NN), Support Vector Machine (SVM), and k-nearest neighbor (KNN). The database COIL-100 is used in the experimental results.

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