Antioxidant Proteins’ Identification Based on Support Vector Machine

Background: Evidence have increasingly indicated that for human disease, cell metabolism are deeply associated with proteins. Structural mutations and dysregulations of these proteins contribute to the development of the complex disease. Free radicals are unstable molecules that seek for electrons from the surrounding atoms for stability. Once a free radical binds to an atom in the body, a chain reaction occurs, which causes damage to cells and DNA. An antioxidant protein is a substance that protects cells from free radical damage. Accurate identification of antioxidant proteins is important for understanding their role in delaying aging and preventing and treating related diseases. Therefore, computational methods to identify antioxidant proteins have become an effective prior-pinpointing approach to experimental verification. Methods: In this study, support vector machines was used to identify antioxidant proteins, using amino acid compositions and 9-gap dipeptide compositions as feature extraction, and feature reduction by Principal Component Analysis. Results: The prediction accuracy Acc of this experiment reached 98.38%, the recall rate Sn of the positive sample was found to be 99.27%, the recall rate Sp of the negative sample reached 97.54%, and the MCC value was 0.9678. To evaluate our proposed method, the predictive performance of 20 antioxidant proteins from the National Center for Biotechnology Information(NCBI) was studied. As a result, 20 antioxidant proteins were correctly predicted by our method. Experimental results demonstrate that the performance of our method is better than the state-of-the-art methods for identification of antioxidant proteins. Conclusion: We collected experimental protein data from Uniport, including 253 antioxidant proteins and 1552 non-antioxidant proteins. The optimal feature extraction used in this paper is composed of amino acid composition and 9-gap dipeptide. The protein is identified by support vector machine, and the model evaluation index is obtained based on 5-fold cross-validation. Compared with the existing classification model, it is further explained that the SVM recognition model constructed in this paper is helpful for the recognition of antioxidized proteins.

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Deep Learning Feature Extraction Approach for Hematopoietic Cancer Subtype Classification

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18042197 ◽

2021 ◽

Vol 18 (4) ◽

pp. 2197

Author(s):

Kwang Ho Park ◽

Erdenebileg Batbaatar ◽

Yongjun Piao ◽

Nipon Theera-Umpon ◽

Keun Ho Ryu

Keyword(s):

Support Vector Machine ◽

Feature Extraction ◽

Feature Selection ◽

Classification Model ◽

Support Vector ◽

Classification Algorithms ◽

K Nearest Neighbor ◽

Subtype Classification ◽

Cancer Subtype ◽

Hematopoietic Cancer

Hematopoietic cancer is a malignant transformation in immune system cells. Hematopoietic cancer is characterized by the cells that are expressed, so it is usually difficult to distinguish its heterogeneities in the hematopoiesis process. Traditional approaches for cancer subtyping use statistical techniques. Furthermore, due to the overfitting problem of small samples, in case of a minor cancer, it does not have enough sample material for building a classification model. Therefore, we propose not only to build a classification model for five major subtypes using two kinds of losses, namely reconstruction loss and classification loss, but also to extract suitable features using a deep autoencoder. Furthermore, for considering the data imbalance problem, we apply an oversampling algorithm, the synthetic minority oversampling technique (SMOTE). For validation of our proposed autoencoder-based feature extraction approach for hematopoietic cancer subtype classification, we compared other traditional feature selection algorithms (principal component analysis, non-negative matrix factorization) and classification algorithms with the SMOTE oversampling approach. Additionally, we used the Shapley Additive exPlanations (SHAP) interpretation technique in our model to explain the important gene/protein for hematopoietic cancer subtype classification. Furthermore, we compared five widely used classification algorithms, including logistic regression, random forest, k-nearest neighbor, artificial neural network and support vector machine. The results of autoencoder-based feature extraction approaches showed good performance, and the best result was the SMOTE oversampling-applied support vector machine algorithm consider both focal loss and reconstruction loss as the loss function for autoencoder (AE) feature selection approach, which produced 97.01% accuracy, 92.60% recall, 99.52% specificity, 93.54% F1-measure, 97.87% G-mean and 95.46% index of balanced accuracy as subtype classification performance measures.

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Hybrid Tile based Feature Extraction and Support Vector Machine Base Content-Based Image Retrieval System for Medical Application

International Journal of Recent Technology and Engineering - 2 ◽

10.35940/ijrte.c5433.098319 ◽

2019 ◽

Vol 8 (3) ◽

pp. 3305-3310

Keyword(s):

Support Vector Machine ◽

Feature Extraction ◽

Image Retrieval ◽

Color Image ◽

Medical Application ◽

Recall Rate ◽

Image Features ◽

Support Vector ◽

Svm Classifier ◽

Feature Extraction Method

Through the landing of therapeutic endoscopes, earth perception satellites and individual telephones, content-based picture recovery (CBIR) has concerned critical consideration, activated by its broad applications, e.g., medicinal picture investigation, removed detecting, and individual re-distinguishing proof. Be that as it may, developing successful component extraction is as yet reported as an invigorating issue.In this paper, to overcome the feature extraction problems a hybrid Tile Based Feature Extraction (TBFE) is introduced. The TBFE algorithm is hybrid with the local binary pattern (LBP) and Local derivative pattern (LDP). These hybrid TBFE feature extraction method helps to extract the color image features in automatic manner. Support vector machine (SVM) is used as a classifier in this image retrieval approach to retrieve the images from the database. The hybrid TBFE along with the SVM classifier image retrieval is named as IR-TBFE-SVM. Experiments show that IR-TBFE-SVMdelivers a higher correctness and recall rate than single feature employed retrieval systems, and ownsdecentweight balancing and query efficiency performance.

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An Efficient Coding Network Based Feature Extraction with Support Vector Machine Based Classification Model for CT Lung Images

Journal of Medical Imaging and Health Informatics ◽

10.1166/jmihi.2020.3263 ◽

2020 ◽

Vol 10 (11) ◽

pp. 2628-2633 ◽

Cited By ~ 4

Author(s):

A. Sheryl Oliver ◽

M. Anuradha ◽

J. Jean Justus ◽

Kiranmai Bellam ◽

T. Jayasankar

Keyword(s):

Lung Cancer ◽

Support Vector Machine ◽

Feature Extraction ◽

Feature Fusion ◽

Classification Model ◽

Support Vector ◽

Efficient Coding ◽

Svm Model ◽

High Level ◽

Lung Ct

Lung cancer is a serious illness affects people all over the globe. To increase the survival rate of patients affected by lung cancer, in advance recognition of lung cancer with effective treatments is important. This study introduces a new deep learning (DL) based feature extraction and classification technique for CT lung images. A DL model using Coding Network (CN) is presented for the extraction of high-level features and classical features. Initially, the convolution neural network is trained as a coding network and the actual pixels are coded into feature vectors for representing the high-level concepts for classification. Next, an extraction of chosen classical features takes place depending upon background knowledge of lung CT images. In addition, an automatic feature fusion takes place to avoid annoying parameter choice. Besides, support vector machine (SVM) model is employed for classify CT lung images in an effective way. For experimentation, a benchmark dataset is utilized to appraise the outcome of the presented CN-SVM model and is validated under several dimensions.

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Analysis of Feature Reduction Techniques for Online News Popularity Prediction

SMART MOVES JOURNAL IJOSCIENCE ◽

10.24113/ijo-science.v4i10.165 ◽

2018 ◽

Vol 4 (10) ◽

pp. 6

Author(s):

Shivangi Bhargava ◽

Dr. Shivnath Ghosh

Keyword(s):

Neural Network ◽

Support Vector Machine ◽

Particle Swarm Optimization ◽

Naive Bayes ◽

Particle Swarm ◽

Naïve Bayes ◽

Online News ◽

Feature Reduction ◽

Support Vector ◽

Swarm Optimization

News popularity is the maximum growth of attention given for particular news article. The popularity of online news depends on various factors such as the number of social media, the number of visitor comments, the number of Likes, etc. It is therefore necessary to build an automatic decision support system to predict the popularity of the news as it will help in business intelligence too. The work presented in this study aims to find the best model to predict the popularity of online news using machine learning methods. In this work, the result analysis is performed by applying Co-relation algorithm, particle swarm optimization and principal component analysis. For performance evaluation support vector machine, naïve bayes, k-nearest neighbor and neural network classifiers are used to classify the popular and unpopular data. From the experimental results, it is observed that support vector machine and naïve bayes outperforms better with co-relation algorithm as well as k-NN and neural network outperforms better with particle swarm optimization.

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OFFLINE YORÙBÁ HANDWRITTEN WORD RECOGNITION USING GEOMETRIC FEATURE EXTRACTION AND SUPPORT VECTOR MACHINE CLASSIFIER

MALAYSIAN JOURNAL OF COMPUTING ◽

10.24191/mjoc.v5i2.8947 ◽

2020 ◽

Vol 5 (2) ◽

pp. 504

Author(s):

Matthias Omotayo Oladele ◽

Temilola Morufat Adepoju ◽

Olaide ` Abiodun Olatoke ◽

Oluwaseun Adewale Ojo

Keyword(s):

Support Vector Machine ◽

Feature Extraction ◽

Word Recognition ◽

Support Vector Machine Classifier ◽

Recognition Accuracy ◽

Recognition System ◽

Support Vector ◽

Geometric Features ◽

Total Length ◽

Yoruba Language

Yorùbá language is one of the three main languages that is been spoken in Nigeria. It is a tonal language that carries an accent on the vowel alphabets. There are twenty-five (25) alphabets in Yorùbá language with one of the alphabets a digraph (GB). Due to the difficulty in typing handwritten Yorùbá documents, there is a need to develop a handwritten recognition system that can convert the handwritten texts to digital format. This study discusses the offline Yorùbá handwritten word recognition system (OYHWR) that recognizes Yorùbá uppercase alphabets. Handwritten characters and words were obtained from different writers using the paint application and M708 graphics tablets. The characters were used for training and the words were used for testing. Pre-processing was done on the images and the geometric features of the images were extracted using zoning and gradient-based feature extraction. Geometric features are the different line types that form a particular character such as the vertical, horizontal, and diagonal lines. The geometric features used are the number of horizontal lines, number of vertical lines, number of right diagonal lines, number of left diagonal lines, total length of all horizontal lines, total length of all vertical lines, total length of all right slanting lines, total length of all left-slanting lines and the area of the skeleton. The characters are divided into 9 zones and gradient feature extraction was used to extract the horizontal and vertical components and geometric features in each zone. The words were fed into the support vector machine classifier and the performance was evaluated based on recognition accuracy. Support vector machine is a two-class classifier, hence a multiclass SVM classifier least square support vector machine (LSSVM) was used for word recognition. The one vs one strategy and RBF kernel were used and the recognition accuracy obtained from the tested words ranges between 66.7%, 83.3%, 85.7%, 87.5%, and 100%. The low recognition rate for some of the words could be as a result of the similarity in the extracted features.

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ABC-Gly: identifying protein lysine glycation sites with artificial bee colony algorithm

Current Proteomics ◽

10.2174/1570164617666191227120136 ◽

2019 ◽

Vol 17 ◽

Author(s):

Yanqiu Yao ◽

Xiaosa Zhao ◽

Qiao Ning ◽

Junping Zhou

Keyword(s):

Support Vector Machine ◽

Amino Acid ◽

Artificial Bee Colony Algorithm ◽

Artificial Bee Colony ◽

Training Dataset ◽

Support Vector ◽

Supplementary File ◽

Feature Subset ◽

Lipid Molecule ◽

Bee Colony

Background: Glycation is a nonenzymatic post-translational modification process by attaching a sugar molecule to a protein or lipid molecule. It may impair the function and change the characteristic of the proteins which may lead to some metabolic diseases. In order to understand the underlying molecular mechanisms of glycation, computational prediction methods have been developed because of their convenience and high speed. However, a more effective computational tool is still a challenging task in computational biology. Methods: In this study, we showed an accurate identification tool named ABC-Gly for predicting lysine glycation sites. At first, we utilized three informative features, including position-specific amino acid propensity, secondary structure and the composition of k-spaced amino acid pairs to encode the peptides. Moreover, to sufficiently exploit discriminative features thus can improve the prediction and generalization ability of the model, we developed a two-step feature selection, which combined the Fisher score and an improved binary artificial bee colony algorithm based on support vector machine. Finally, based on the optimal feature subset, we constructed the effective model by using Support Vector Machine on the training dataset. Results: The performance of the proposed predictor ABC-Gly was measured with the sensitivity of 76.43%, the specificity of 91.10%, the balanced accuracy of 83.76%, the area under the receiver-operating characteristic curve (AUC) of 0.9313, a Matthew’s Correlation Coefficient (MCC) of 0.6861 by 10-fold cross-validation on training dataset, and a balanced accuracy of 59.05% on independent dataset. Compared to the state-of-the-art predictors on the training dataset, the proposed predictor achieved significant improvement in the AUC of 0.156 and MCC of 0.336. Conclusion: The detailed analysis results indicated that our predictor may serve as a powerful complementary tool to other existing methods for predicting protein lysine glycation. The source code and datasets of the ABC-Gly were provided in the Supplementary File 1.

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Predicting Hub Genes of Glioblastomas Based on Support Vector Machine Combined with CFS algorithms

Current Bioinformatics ◽

10.2174/1574893615999200819162140 ◽

2020 ◽

Vol 15 ◽

Author(s):

Chun Qiu ◽

Sai Li ◽

Shenghui Yang ◽

Lin Wang ◽

Aihui Zeng ◽

...

Keyword(s):

Support Vector Machine ◽

Expression Profiles ◽

Independent Set ◽

Classification Model ◽

Support Vector ◽

Feature Subset ◽

Hub Genes ◽

Effective Prevention ◽

Key Genes ◽

Control Samples

Aim: To search the genes related to the mechanisms of the occurrence of glioma and to try to build a prediction model for glioblastomas. Background: The morbidity and mortality of glioblastomas are very high, which seriously endangers human health. At present, the goals of many investigations on gliomas are mainly to understand the cause and mechanism of these tumors at the molecular level and to explore clinical diagnosis and treatment methods. However, there is no effective early diagnosis method for this disease, and there are no effective prevention, diagnosis or treatment measures. Methods: First, the gene expression profiles derived from GEO were downloaded. Then, differentially expressed genes (DEGs) in the disease samples and the control samples were identified. After that, GO and KEGG enrichment analyses of DEGs were performed by DAVID. Furthermore, the correlation-based feature subset (CFS) method was applied to the selection of key DEGs. In addition, the classification model between the glioblastoma samples and the controls was built by an Support Vector Machine (SVM) based on selected key genes. Results and Discussion: Thirty-six DEGs, including 17 upregulated and 19 downregulated genes, were selected as the feature genes to build the classification model between the glioma samples and the control samples by the CFS method. The accuracy of the classification model by using a 10-fold cross-validation test and independent set test was 76.25% and 70.3%, respectively. In addition, PPP2R2B and CYBB can also be found in the top 5 hub genes screened by the protein– protein interaction (PPI) network. Conclusions: This study indicated that the CFS method is a useful tool to identify key genes in glioblastomas. In addition, we also predicted that genes such as PPP2R2B and CYBB might be potential biomarkers for the diagnosis of glioblastomas.

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