scholarly journals A Robust Hybrid Approach Based on Estimation of Distribution Algorithm and Support Vector Machine for Hunting Candidate Disease Genes

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Li Li ◽  
Hongmei Chen ◽  
Chang Liu ◽  
Fang Wang ◽  
Fangfang Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Support Vector Machine ◽  
High Dimension ◽  
Microarray Data ◽  
Hybrid Method ◽  
Estimation Of Distribution Algorithm ◽  
Support Vector ◽  
Disease Genes ◽  
Profile Data ◽  
Estimation Of Distribution

Microarray data are high dimension with high noise ratio and relatively small sample size, which makes it a challenge to use microarray data to identify candidate disease genes. Here, we have presented a hybrid method that combines estimation of distribution algorithm with support vector machine for selection of key feature genes. We have benchmarked the method using the microarray data of both diffuse B cell lymphoma and colon cancer to demonstrate its performance for identifying key features from the profile data of high-dimension gene expression. The method was compared with a probabilistic model based on genetic algorithm and another hybrid method based on both genetics algorithm and support vector machine. The results showed that the proposed method provides new computational strategy for hunting candidate disease genes from the profile data of disease gene expression. The selected candidate disease genes may help to improve the diagnosis and treatment for diseases.

ITERATIVE FEATURE PERTURBATION AS A GENE SELECTOR FOR MICROARRAY DATA

2012 ◽  
Vol 26 (05) ◽  
pp. 1260003 ◽  
Author(s):  
JUANA CANUL-REICH ◽  
LAWRENCE O. HALL ◽  
DMITRY B. GOLDGOF ◽  
JOHN N. KORECKI ◽  
STEVEN ESCHRICH
Keyword(s):  
Gene Expression ◽  
Colon Cancer ◽  
Support Vector Machine ◽  
Performance Improvement ◽  
Microarray Data ◽  
T Test ◽  
Recursive Feature Elimination ◽  
Support Vector ◽  
Gene Sets ◽  
Microarray Datasets

Gene-expression microarray datasets often consist of a limited number of samples with a large number of gene-expression measurements, usually on the order of thousands. Therefore, dimensionality reduction is critical prior to any classification task. In this work, the iterative feature perturbation method (IFP), an embedded gene selector, is introduced and applied to four microarray cancer datasets: colon cancer, leukemia, Moffitt colon cancer, and lung cancer. We compare results obtained by IFP to those of support vector machine-recursive feature elimination (SVM-RFE) and the t-test as a feature filter using a linear support vector machine as the base classifier. Analysis of the intersection of gene sets selected by the three methods across the four datasets was done. Additional experiments included an initial pre-selection of the top 200 genes based on their p values. IFP and SVM-RFE were then applied on the reduced feature sets. These results showed up to 3.32% average performance improvement for IFP across the four datasets. A statistical analysis (using the Friedman/Holm test) for both scenarios showed the highest accuracies came from the t-test as a filter on experiments without gene pre-selection. IFP and SVM-RFE had greater classification accuracy after gene pre-selection. Analysis showed the t-test is a good gene selector for microarray data. IFP and SVM-RFE showed performance improvement on a reduced by t-test dataset. The IFP approach resulted in comparable or superior average class accuracy when compared to SVM-RFE on three of the four datasets. The same or similar accuracies can be obtained with different sets of genes.

A visual terrain classification method for mobile robots’ navigation based on convolutional neural network and support vector machine

2021 ◽  
pp. 014233122098791
Author(s):  
Wanli Wang ◽  
Botao Zhang ◽  
Kaiqi Wu ◽  
Sergey A Chepinskiy ◽  
Anton A Zhilenkov ◽  
...  
Keyword(s):  
Neural Network ◽  
Support Vector Machine ◽  
Mobile Robots ◽  
Convolutional Neural Network ◽  
Hybrid Method ◽  
Classification Accuracy ◽  
Support Vector ◽  
High Classification Accuracy ◽  
Enhance Efficiency ◽  
Multi Class Classification

In this paper, a hybrid method based on deep learning is proposed to visually classify terrains encountered by mobile robots. Considering the limited computing resource on mobile robots and the requirement for high classification accuracy, the proposed hybrid method combines a convolutional neural network with a support vector machine to keep a high classification accuracy while improve work efficiency. The key idea is that the convolutional neural network is used to finish a multi-class classification and simultaneously the support vector machine is used to make a two-class classification. The two-class classification performed by the support vector machine is aimed at one kind of terrain that users are mostly concerned with. Results of the two classifications will be consolidated to get the final classification result. The convolutional neural network used in this method is modified for the on-board usage of mobile robots. In order to enhance efficiency, the convolutional neural network has a simple architecture. The convolutional neural network and the support vector machine are trained and tested by using RGB images of six kinds of common terrains. Experimental results demonstrate that this method can help robots classify terrains accurately and efficiently. Therefore, the proposed method has a significant potential for being applied to the on-board usage of mobile robots.

Logic Learning Machine and standard supervised methods for Hodgkin’s lymphoma prognosis using gene expression data and clinical variables

2016 ◽  
Vol 24 (1) ◽  
pp. 54-65 ◽  
Author(s):  
Stefano Parodi ◽  
Chiara Manneschi ◽  
Damiano Verda ◽  
Enrico Ferrari ◽  
Marco Muselli
Keyword(s):  
Gene Expression ◽  
Machine Learning ◽  
Support Vector Machine ◽  
Decision Tree ◽  
Hodgkin’S Lymphoma ◽  
Hodgkin's Lymphoma ◽  
Support Vector ◽  
Expression Data ◽  
Clinical Variables ◽  
Learning Machine

This study evaluates the performance of a set of machine learning techniques in predicting the prognosis of Hodgkin’s lymphoma using clinical factors and gene expression data. Analysed samples from 130 Hodgkin’s lymphoma patients included a small set of clinical variables and more than 54,000 gene features. Machine learning classifiers included three black-box algorithms ( k-nearest neighbour, Artificial Neural Network, and Support Vector Machine) and two methods based on intelligible rules (Decision Tree and the innovative Logic Learning Machine method). Support Vector Machine clearly outperformed any of the other methods. Among the two rule-based algorithms, Logic Learning Machine performed better and identified a set of simple intelligible rules based on a combination of clinical variables and gene expressions. Decision Tree identified a non-coding gene ( XIST) involved in the early phases of X chromosome inactivation that was overexpressed in females and in non-relapsed patients. XIST expression might be responsible for the better prognosis of female Hodgkin’s lymphoma patients.

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