Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites

2019 ◽  
Vol 22 (7) ◽  
pp. 455-469
Author(s):  
Yi-Heng Zhu ◽  
Jun Hu ◽  
Yong Qi ◽  
Xiao-Ning Song ◽  
Dong-Jun Yu
Keyword(s):  
Machine Learning ◽  
Support Vector Machines ◽  
Ligand Binding ◽  
Binding Sites ◽  
Negative Impact ◽  
Class Imbalance ◽  
Nucleotide Binding ◽  
Support Vector ◽  
Vector Machines ◽  
Ligand Binding Sites

Aim and Objective: The accurate identification of protein-ligand binding sites helps elucidate protein function and facilitate the design of new drugs. Machine-learning-based methods have been widely used for the prediction of protein-ligand binding sites. Nevertheless, the severe class imbalance phenomenon, where the number of nonbinding (majority) residues is far greater than that of binding (minority) residues, has a negative impact on the performance of such machine-learning-based predictors. Materials and Methods: In this study, we aim to relieve the negative impact of class imbalance by Boosting Multiple Granular Support Vector Machines (BGSVM). In BGSVM, each base SVM is trained on a granular training subset consisting of all minority samples and some reasonably selected majority samples. The efficacy of BGSVM for dealing with class imbalance was validated by benchmarking it with several typical imbalance learning algorithms. We further implemented a protein-nucleotide binding site predictor, called BGSVM-NUC, with the BGSVM algorithm. Results: Rigorous cross-validation and independent validation tests for five types of proteinnucleotide interactions demonstrated that the proposed BGSVM-NUC achieves promising prediction performance and outperforms several popular sequence-based protein-nucleotide binding site predictors. The BGSVM-NUC web server is freely available at http://csbio.njust.edu.cn/bioinf/BGSVM-NUC/ for academic use.

scholarly journals Predicting RNA-binding sites of proteins using support vector machines and evolutionary information

2008 ◽  
Vol 9 (Suppl 12) ◽  
pp. S6 ◽  
Author(s):  
Cheng-Wei Cheng ◽  
Emily Su ◽  
Jenn-Kang Hwang ◽  
Ting-Yi Sung ◽  
Wen-Lian Hsu
Keyword(s):  
Support Vector Machines ◽  
Binding Sites ◽  
Rna Binding ◽  
Evolutionary Information ◽  
Support Vector ◽  
Vector Machines ◽  
Rna Binding Sites

scholarly journals Research on Parallel Support Vector Machine Based on Spark Big Data Platform

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Yao Huimin
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Big Data ◽  
Support Vector Machines ◽  
Cross Validation ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Lambda Architecture ◽  
Vector Machines ◽  
Data Platform

With the development of cloud computing and distributed cluster technology, the concept of big data has been expanded and extended in terms of capacity and value, and machine learning technology has also received unprecedented attention in recent years. Traditional machine learning algorithms cannot solve the problem of effective parallelization, so a parallelization support vector machine based on Spark big data platform is proposed. Firstly, the big data platform is designed with Lambda architecture, which is divided into three layers: Batch Layer, Serving Layer, and Speed Layer. Secondly, in order to improve the training efficiency of support vector machines on large-scale data, when merging two support vector machines, the “special points” other than support vectors are considered, that is, the points where the nonsupport vectors in one subset violate the training results of the other subset, and a cross-validation merging algorithm is proposed. Then, a parallelized support vector machine based on cross-validation is proposed, and the parallelization process of the support vector machine is realized on the Spark platform. Finally, experiments on different datasets verify the effectiveness and stability of the proposed method. Experimental results show that the proposed parallelized support vector machine has outstanding performance in speed-up ratio, training time, and prediction accuracy.

scholarly journals Impacts of multicollinearity on CAPT modalities: An heterogeneous machine learning framework for computer-assisted French phoneme pronunciation training

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0257901
Author(s):  
Yanjing Bi ◽  
Chao Li ◽  
Yannick Benezeth ◽  
Fan Yang
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Support Vector Machines ◽  
Partial Least Square ◽  
Least Square ◽  
Support Vector ◽  
Computer Assisted ◽  
Long Distance ◽  
Relationship Analysis ◽  
Vector Machines

Phoneme pronunciations are usually considered as basic skills for learning a foreign language. Practicing the pronunciations in a computer-assisted way is helpful in a self-directed or long-distance learning environment. Recent researches indicate that machine learning is a promising method to build high-performance computer-assisted pronunciation training modalities. Many data-driven classifying models, such as support vector machines, back-propagation networks, deep neural networks and convolutional neural networks, are increasingly widely used for it. Yet, the acoustic waveforms of phoneme are essentially modulated from the base vibrations of vocal cords, and this fact somehow makes the predictors collinear, distorting the classifying models. A commonly-used solution to address this issue is to suppressing the collinearity of predictors via partial least square regressing algorithm. It allows to obtain high-quality predictor weighting results via predictor relationship analysis. However, as a linear regressor, the classifiers of this type possess very simple topology structures, constraining the universality of the regressors. For this issue, this paper presents an heterogeneous phoneme recognition framework which can further benefit the phoneme pronunciation diagnostic tasks by combining the partial least square with support vector machines. A French phoneme data set containing 4830 samples is established for the evaluation experiments. The experiments of this paper demonstrates that the new method improves the accuracy performance of the phoneme classifiers by 0.21 − 8.47% comparing to state-of-the-arts with different data training data density.

Combination with Machine Learning Algorithms for the Classification in E-Bussiness

2011 ◽  
Vol 230-232 ◽  
pp. 625-628
Author(s):  
Lei Shi ◽  
Xin Ming Ma ◽  
Xiao Hong Hu
Keyword(s):  
Machine Learning ◽  
Support Vector Machines ◽  
Set Theory ◽  
Rough Set ◽  
Rough Set Theory ◽  
Machine Learning Algorithms ◽  
Classification Model ◽  
Support Vector ◽  
Mathematical Tool ◽  
Vector Machines

E-bussiness has grown rapidly in the last decade and massive amount of data on customer purchases, browsing pattern and preferences has been generated. Classification of electronic data plays a pivotal role to mine the valuable information and thus has become one of the most important applications of E-bussiness. Support Vector Machines are popular and powerful machine learning techniques, and they offer state-of-the-art performance. Rough set theory is a formal mathematical tool to deal with incomplete or imprecise information and one of its important applications is feature selection. In this paper, rough set theory and support vector machines are combined to construct a classification model to classify the data of E-bussiness effectively.

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