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.

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 Gender Classification Based on Multiscale Facial Fusion Feature

2018 ◽  
Vol 2018 ◽  
pp. 1-6 ◽  
Author(s):  
Chunyu Zhang ◽  
Hui Ding ◽  
Yuanyuan Shang ◽  
Zhuhong Shao ◽  
Xiaoyan Fu
Keyword(s):  
Local Binary Pattern ◽  
State Of The Art ◽  
Support Vector ◽  
Gender Classification ◽  
Local Phase ◽  
New Approach ◽  
Local Phase Quantization ◽  
Face Images ◽  
Phase Quantization ◽  
Fusion Feature

For gender classification, we present a new approach based on Multiscale facial fusion feature (MS3F) to classify gender from face images. Fusion feature is extracted by the combination of Local Binary Pattern (LBP) and Local Phase Quantization (LPQ) descriptors, and a multiscale feature is generated through Multiblock (MB) and Multilevel (ML) methods. Support Vector Machine (SVM) is employed as the classifier to conduct gender classification. All the experiments are performed based on the Images of Groups (IoG) dataset. The results demonstrate that the application of Multiscale fusion feature greatly improves the performance of gender classification, and our approach outperforms the state-of-the-art techniques.

A NEW TECHNIQUE FOR SELECTING FEATURES FROM PROTEIN SEQUENCES

2006 ◽  
Vol 20 (02) ◽  
pp. 271-283 ◽  
Author(s):  
XING-MING ZHAO ◽  
JI-XIANG DU ◽  
HONG-QIANG WANG ◽  
YUNPING ZHU ◽  
YIXUE LI
Keyword(s):  
Support Vector Machine ◽  
Relative Entropy ◽  
Protein Sequences ◽  
Entropy Method ◽  
Experimental Results ◽  
New Method ◽  
Support Vector ◽  
Svm Classifier ◽  
A New Technique ◽  
Relative Entropy Method

A new method for selecting features from protein sequences is proposed in this paper. First, the protein sequences are converted into fixed-dimensional feature vectors. Then, a subset of features is selected using relative entropy method and used as the inputs for Support Vector Machine (SVM). Finally, the trained SVM classifier is utilized to classify protein sequences into certain known protein families. Experimental results over proteins obtained from PIR database and GPCRs have shown that our proposed approach is really effective and efficient in selecting features from protein sequences.

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.

scholarly journals A Comprehensive Evaluation of Approaches for Built-Up Area Extraction from Landsat OLI Images Using Massive Samples

2018 ◽  
Vol 11 (1) ◽  
pp. 2 ◽  
Author(s):  
Tao Zhang ◽  
Hong Tang
Keyword(s):  
Learning Strategies ◽  
Classification Accuracy ◽  
Feature Learning ◽  
Automatic Generation ◽  
Experimental Results ◽  
Support Vector ◽  
Feature Engineering ◽  
Classification Algorithms ◽  
Sample Points ◽  
Better Than

Detailed information about built-up areas is valuable for mapping complex urban environments. Although a large number of classification algorithms for such areas have been developed, they are rarely tested from the perspective of feature engineering and feature learning. Therefore, we launched a unique investigation to provide a full test of the Operational Land Imager (OLI) imagery for 15-m resolution built-up area classification in 2015, in Beijing, China. Training a classifier requires many sample points, and we proposed a method based on the European Space Agency’s (ESA) 38-m global built-up area data of 2014, OpenStreetMap, and MOD13Q1-NDVI to achieve the rapid and automatic generation of a large number of sample points. Our aim was to examine the influence of a single pixel and image patch under traditional feature engineering and modern feature learning strategies. In feature engineering, we consider spectra, shape, and texture as the input features, and support vector machine (SVM), random forest (RF), and AdaBoost as the classification algorithms. In feature learning, the convolutional neural network (CNN) is used as the classification algorithm. In total, 26 built-up land cover maps were produced. The experimental results show the following: (1) The approaches based on feature learning are generally better than those based on feature engineering in terms of classification accuracy, and the performance of ensemble classifiers (e.g., RF) are comparable to that of CNN. Two-dimensional CNN and the 7-neighborhood RF have the highest classification accuracies at nearly 91%; (2) Overall, the classification effect and accuracy based on image patches are better than those based on single pixels. The features that can highlight the information of the target category (e.g., PanTex (texture-derived built-up presence index) and enhanced morphological building index (EMBI)) can help improve classification accuracy. The code and experimental results are available at https://github.com/zhangtao151820/CompareMethod.

Colored spun fabric texture representation and application by combining spatial features with frequency features

2020 ◽  
pp. 004051752096140
Author(s):  
Li Yuan ◽  
Xue Gong ◽  
Junping Liu ◽  
Yali Yang ◽  
Muli Liu
Keyword(s):  
Classification Accuracy ◽  
Local Binary Pattern ◽  
Learning Algorithm ◽  
Woven Fabric ◽  
Local Phase ◽  
Texture Representation ◽  
Local Phase Quantization ◽  
Fuzzy Transformation ◽  
Representation Model ◽  
Phase Quantization

Colored spun fabrics are difficult to accurately characterize with a local binary pattern due to texture anisotropy caused by the uneven distribution of dyed fibers. In this paper, we present a texture representation model based on spatial and frequency characteristics. The proposed model takes advantage of the local binary pattern and local phase quantization to extract the texture of woven fabric. Then, the two features are connected in series, and the features of dimension reduction by principal component analysis are used to represent the texture of the fabric image. Finally, the hierarchical hybrid classifier is applied to classify the fabric structure. The experimental results show that the local phase quantization feature is robust to the fuzzy transformation and the texture representation model has a stronger ability of texture description than the single local binary pattern feature, with the average classification accuracy of 97.59% on 336 samples. In addition, compared with the deep learning algorithm, the texture representation algorithm can ensure a high classification accuracy.

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