scholarly journals Predicting Apoptosis Protein Subcellular Locations based on the Protein Overlapping Property Matrix and Tri-Gram Encoding

2019 ◽  
Vol 20 (9) ◽  
pp. 2344
Author(s):  
Yang Yang ◽  
Huiwen Zheng ◽  
Chunhua Wang ◽  
Wanyue Xiao ◽  
Taigang Liu
Keyword(s):  
Support Vector Machine ◽  
Subcellular Location ◽  
Recursive Feature Elimination ◽  
Support Vector ◽  
Svm Classifier ◽  
Protein Subcellular Location ◽  
Promising Tool ◽  
Apoptosis Protein ◽  
Benchmark Datasets ◽  
Apoptosis Proteins

To reveal the working pattern of programmed cell death, knowledge of the subcellular location of apoptosis proteins is essential. Besides the costly and time-consuming method of experimental determination, research into computational locating schemes, focusing mainly on the innovation of representation techniques on protein sequences and the selection of classification algorithms, has become popular in recent decades. In this study, a novel tri-gram encoding model is proposed, which is based on using the protein overlapping property matrix (POPM) for predicting apoptosis protein subcellular location. Next, a 1000-dimensional feature vector is built to represent a protein. Finally, with the help of support vector machine-recursive feature elimination (SVM-RFE), we select the optimal features and put them into a support vector machine (SVM) classifier for predictions. The results of jackknife tests on two benchmark datasets demonstrate that our proposed method can achieve satisfactory prediction performance level with less computing capacity required and could work as a promising tool to predict the subcellular locations of apoptosis proteins.

Prediction of Apoptosis Proteins Subcellular Location Using Evolutionary Profiles and Motifs Information

2013 ◽  
Vol 647 ◽  
pp. 600-606 ◽  
Author(s):  
Tao Li ◽  
Qian Zhong Li
Keyword(s):  
Cell Proliferation ◽  
Support Vector Machine ◽  
Protein Sequences ◽  
Subcellular Location ◽  
Support Vector ◽  
Data Sets ◽  
Success Rates ◽  
Jackknife Test ◽  
Apoptosis Protein ◽  
Apoptosis Proteins

Apoptosis proteins are very important for regulating the balance between cell proliferation and death. Because the function of apoptosis protein is closely related to its subcellular location, it is desirable to explore their function by predicting the subcellular location of apoptosis protein. In this paper, based on evolutionary profiles and motifs information of protein sequences, an approach for predicting apoptosis proteins subcellular location is presented by using support vector machine (SVM). When the method is applied to three data sets (98 apoptosis proteins dataset, 225 apoptosis proteins dataset and 317 apoptosis proteins dataset), the overall accuracies of our method on the three data sets reach 95.9%, 86.7% and 91.8% in the jackknife test, respectively. The higher predictive success rates indicate that the proposed method is very useful for apoptosis proteins subcellular localization.

Integrating Second-order Moving Average and Over-sampling Algorithm to Predict Apoptosis Protein Subcellular Localization

2020 ◽  
Vol 15 (6) ◽  
pp. 517-527
Author(s):  
Yunyun Liang ◽  
Shengli Zhang
Keyword(s):  
Subcellular Localization ◽  
Moving Average ◽  
Subcellular Location ◽  
Second Order ◽  
Test Method ◽  
Support Vector ◽  
Protein Subcellular Localization ◽  
Protein Subcellular Location ◽  
Apoptosis Protein ◽  
Leibler Divergence

Background: Apoptosis proteins have a key role in the development and the homeostasis of the organism, and are very important to understand the mechanism of cell proliferation and death. The function of apoptosis protein is closely related to its subcellular location. Objective: Prediction of apoptosis protein subcellular localization is a meaningful task. Methods: In this study, we predict the apoptosis protein subcellular location by using the PSSMbased second-order moving average descriptor, nonnegative matrix factorization based on Kullback-Leibler divergence and over-sampling algorithms. This model is named by SOMAPKLNMF- OS and constructed on the ZD98, ZW225 and CL317 benchmark datasets. Then, the support vector machine is adopted as the classifier, and the bias-free jackknife test method is used to evaluate the accuracy. Results: Our prediction system achieves the favorable and promising performance of the overall accuracy on the three datasets and also outperforms the other listed models. Conclusion: The results show that our model offers a high throughput tool for the identification of apoptosis protein subcellular localization.

Hybrid adapted fast correlation FCBF-support vector machine recursive feature elimination for feature selection

2020 ◽  
Vol 14 (3) ◽  
pp. 269-279
Author(s):  
Hayet Djellali ◽  
Nacira Ghoualmi-Zine ◽  
Souad Guessoum
Keyword(s):  
Support Vector Machine ◽  
Feature Selection ◽  
Recursive Feature Elimination ◽  
Support Vector ◽  
Svm Classifier ◽  
Hybrid Architecture ◽  
Features Selection ◽  
K Nearest Neighbors ◽  
Correlation Based Feature Selection ◽  
Embedded Method

This paper investigates feature selection methods based on hybrid architecture using feature selection algorithm called Adapted Fast Correlation Based Feature selection and Support Vector Machine Recursive Feature Elimination (AFCBF-SVMRFE). The AFCBF-SVMRFE has three stages and composed of SVMRFE embedded method with Correlation based Features Selection. The first stage is the relevance analysis, the second one is a redundancy analysis, and the third stage is a performance evaluation and features restoration stage. Experiments show that the proposed method tested on different classifiers: Support Vector Machine SVM and K nearest neighbors KNN provide a best accuracy on various dataset. The SVM classifier outperforms KNN classifier on these data. The AFCBF-SVMRFE outperforms FCBF multivariate filter, SVMRFE, Particle swarm optimization PSO and Artificial bees colony ABC.

Predicting subcellular location of apoptosis proteins based on wavelet transform and support vector machine

Amino Acids ◽  
2009 ◽  
Vol 38 (4) ◽  
pp. 1201-1208 ◽  
Author(s):  
Jian-Ding Qiu ◽  
San-Hua Luo ◽  
Jian-Hua Huang ◽  
Xing-Yu Sun ◽  
Ru-Ping Liang
Keyword(s):  
Support Vector Machine ◽  
Wavelet Transform ◽  
Subcellular Location ◽  
Support Vector ◽  
Apoptosis Proteins

scholarly journals WR-SVM Model Based on the Margin Radius Approach for Solving the Minimum Enclosing Ball Problem in Support Vector Machine Classification

2021 ◽  
Vol 11 (10) ◽  
pp. 4657
Author(s):  
Atif Rizwan ◽  
Naeem Iqbal ◽  
Rashid Ahmad ◽  
Do-Hyeun Kim
Keyword(s):  
Support Vector Machine ◽  
Computational Cost ◽  
Experimental Results ◽  
Support Vector ◽  
Svm Classifier ◽  
Limited Area ◽  
Robust Solution ◽  
Two Factors ◽  
Benchmark Datasets ◽  
Minimum Enclosing Ball

The generalization error of conventional support vector machine (SVM) depends on the ratio of two factors; radius and margin. The traditional SVM aims to maximize margin but ignore minimization of radius, which decreases the overall performance of the SVM classifier. However, different approaches are developed to achieve a trade-off between the margin and radius. Still, the computational cost of all these approaches is high due to the requirements of matrix transformation. Furthermore, a conventional SVM tries to set the best hyperplane between classes, and due to some robust kernel tricks, an SVM is used in many non-linear and complex problems. The configuration of the best hyperplane between classes is not effective; therefore, it is required to bind a class within its limited area to enhance the performance of the SVM classifier. The area enclosed by a class is called its Minimum Enclosing Ball (MEB), and it is one of the emerging problems of SVM. Therefore, a robust solution is needed to improve the performance of the conventional SVM to overcome the highlighted issues. In this research study, a novel weighted radius SVM (WR-SVM) is proposed to determine the tighter bounds of MEB. The proposed solution uses a weighted mean to find tighter bounds of radius, due to which the size of MEB decreases. Experiments are conducted on nine different benchmark datasets and one synthetic dataset to demonstrate the effectiveness of our proposed model. The experimental results reveal that the proposed WR-SVM significantly performed well compared to the conventional SVM classifier. Furthermore, experimental results are compared with F-SVM and traditional SVM in terms of classification accuracy to demonstrate the significance of the proposed WR-SVM.

scholarly journals Analog Circuit Fault Diagnosis Based on Support Vector Machine Classifier and Fuzzy Feature Selection

Electronics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1496
Author(s):  
Hao Liang ◽  
Yiman Zhu ◽  
Dongyang Zhang ◽  
Le Chang ◽  
Yuming Lu ◽  
...  
Keyword(s):  
Support Vector Machine ◽  
Fault Diagnosis ◽  
Mutual Information ◽  
Analog Circuit ◽  
Fault Classification ◽  
Support Vector ◽  
Svm Classifier ◽  
Fault Parameters ◽  
Diagnosis Method ◽  
Circuit Fault Diagnosis

In analog circuit, the component parameters have tolerances and the fault component parameters present a wide distribution, which brings obstacle to classification diagnosis. To tackle this problem, this article proposes a soft fault diagnosis method combining the improved barnacles mating optimizer(BMO) algorithm with the support vector machine (SVM) classifier, which can achieve the minimum redundancy and maximum relevance for feature dimension reduction with fuzzy mutual information. To be concrete, first, the improved barnacles mating optimizer algorithm is used to optimize the parameters for learning and classification. We adopt six test functions that are on three data sets from the University of California, Irvine (UCI) machine learning repository to test the performance of SVM classifier with five different optimization algorithms. The results show that the SVM classifier combined with the improved barnacles mating optimizer algorithm is characterized with high accuracy in classification. Second, fuzzy mutual information, enhanced minimum redundancy, and maximum relevance principle are applied to reduce the dimension of the feature vector. Finally, a circuit experiment is carried out to verify that the proposed method can achieve fault classification effectively when the fault parameters are both fixed and distributed. The accuracy of the proposed fault diagnosis method is 92.9% when the fault parameters are distributed, which is 1.8% higher than other classifiers on average. When the fault parameters are fixed, the accuracy rate is 99.07%, which is 0.7% higher than other classifiers on average.

scholarly journals Intuitionistic Fuzzy Laplacian Twin Support Vector Machine for Semi-supervised Classification

2021 ◽  
Author(s):  
Jia-Bin Zhou ◽  
Yan-Qin Bai ◽  
Yan-Ru Guo ◽  
Hai-Xiang Lin
Keyword(s):  
Support Vector Machine ◽  
Negative Impact ◽  
Twin Support Vector Machine ◽  
Fuzzy Membership ◽  
Support Vector ◽  
Membership Functions ◽  
Fuzzy Membership Functions ◽  
Intuitionistic Fuzzy ◽  
Benchmark Datasets ◽  
The Impact

AbstractIn general, data contain noises which come from faulty instruments, flawed measurements or faulty communication. Learning with data in the context of classification or regression is inevitably affected by noises in the data. In order to remove or greatly reduce the impact of noises, we introduce the ideas of fuzzy membership functions and the Laplacian twin support vector machine (Lap-TSVM). A formulation of the linear intuitionistic fuzzy Laplacian twin support vector machine (IFLap-TSVM) is presented. Moreover, we extend the linear IFLap-TSVM to the nonlinear case by kernel function. The proposed IFLap-TSVM resolves the negative impact of noises and outliers by using fuzzy membership functions and is a more accurate reasonable classifier by using the geometric distribution information of labeled data and unlabeled data based on manifold regularization. Experiments with constructed artificial datasets, several UCI benchmark datasets and MNIST dataset show that the IFLap-TSVM has better classification accuracy than other state-of-the-art twin support vector machine (TSVM), intuitionistic fuzzy twin support vector machine (IFTSVM) and Lap-TSVM.

scholarly journals A Roller Bearing Fault Diagnosis Method Based on LCD Energy Entropy and ACROA-SVM

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
HungLinh Ao ◽  
Junsheng Cheng ◽  
Kenli Li ◽  
Tung Khac Truong
Keyword(s):  
Support Vector Machine ◽  
Fault Diagnosis ◽  
Roller Bearing ◽  
Local Characteristic ◽  
Support Vector ◽  
Svm Classifier ◽  
Outer Race ◽  
Bearing Fault ◽  
Bearing Fault Diagnosis ◽  
Energy Entropy

This study investigates a novel method for roller bearing fault diagnosis based on local characteristic-scale decomposition (LCD) energy entropy, together with a support vector machine designed using an Artificial Chemical Reaction Optimisation Algorithm, referred to as an ACROA-SVM. First, the original acceleration vibration signals are decomposed into intrinsic scale components (ISCs). Second, the concept of LCD energy entropy is introduced. Third, the energy features extracted from a number of ISCs that contain the most dominant fault information serve as input vectors for the support vector machine classifier. Finally, the ACROA-SVM classifier is proposed to recognize the faulty roller bearing pattern. The analysis of roller bearing signals with inner-race and outer-race faults shows that the diagnostic approach based on the ACROA-SVM and using LCD to extract the energy levels of the various frequency bands as features can identify roller bearing fault patterns accurately and effectively. The proposed method is superior to approaches based on Empirical Mode Decomposition method and requires less time.

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