IMPROVING CLASSIFICATION OF CANCER AND MINING BIOMARKERS FROM GENE EXPRESSION PROFILES USING HYBRID OPTIMIZATION ALGORITHMS AND FUZZY SUPPORT VECTOR MACHINE

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YOUSEFI MOTEGHAED NILOOFAR; MAGHOOLI KEIVAN; GARSHASBI MASOUD

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Journal: JOURNAL OF MEDICAL SIGNALS AND SENSORS (JMSS) Year:2018 | Volume:8 | Issue:1 Page(s): 1-11

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Title

IMPROVING CLASSIFICATION OF CANCER AND MINING BIOMARKERS FROM GENE EXPRESSION PROFILES USING HYBRID OPTIMIZATION ALGORITHMS AND FUZZY SUPPORT VECTOR MACHINE

Author(s)

YOUSEFI MOTEGHAED NILOOFAR | MAGHOOLI KEIVAN | GARSHASBI MASOUD | Issue Writer Certificate

Keywords

CANCER CLASSIFICATION

FUZZY SUPPORT VECTOR MACHINE

GENE EXPRESSION

GENETIC ALGORITHM

PARTICLE SWARM OPTIMIZATION ALGORITHM

Abstract

Background: GENE EXPRESSION data are characteristically high dimensional with a small sample size in contrast to the feature size and variability inherent in biological processes that contribute to difficulties in analysis. Selection of highly discriminative features decreases the computational cost and complexity of the classifier and improves its reliability for prediction of a new class of samples. Methods: The present study used hybrid particle swarm optimization and GENETIC ALGORITHMs for gene selection and a FUZZY SUPPORT VECTOR MACHINE (SVM) as the classifier. Fuzzy logic is used to infer the importance of each sample in the training phase and decrease the outlier sensitivity of the system to increase the ability to generalize the classifier. A decision-tree algorithm was applied to the most frequent genes to develop a set of rules for each type of cancer. This improved the abilities of the algorithm by finding the best parameters for the classifier during the training phase without the need for trial-and-error by the user. The proposed approach was tested on four benchmark GENE EXPRESSION profiles. Results: Good results have been demonstrated for the proposed algorithm. The classification accuracy for leukemia data is 100%, for colon cancer is 96.67% and for breast cancer is 98%. The results show that the best kernel used in training the SVM classifier is the radial basis function.Conclusions: The experimental results show that the proposed algorithm can decrease the dimensionality of the dataset, determine the most informative gene subset, and improve classification accuracy using the optimal parameters of the classifier with no user interface.

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APA: Copy

YOUSEFI MOTEGHAED, NILOOFAR, MAGHOOLI, KEIVAN, & GARSHASBI, MASOUD. (2018). IMPROVING CLASSIFICATION OF CANCER AND MINING BIOMARKERS FROM GENE EXPRESSION PROFILES USING HYBRID OPTIMIZATION ALGORITHMS AND FUZZY SUPPORT VECTOR MACHINE. JOURNAL OF MEDICAL SIGNALS AND SENSORS (JMSS), 8(1), 1-11. SID. https://sid.ir/paper/333748/en

Vancouver: Copy

YOUSEFI MOTEGHAED NILOOFAR, MAGHOOLI KEIVAN, GARSHASBI MASOUD. IMPROVING CLASSIFICATION OF CANCER AND MINING BIOMARKERS FROM GENE EXPRESSION PROFILES USING HYBRID OPTIMIZATION ALGORITHMS AND FUZZY SUPPORT VECTOR MACHINE. JOURNAL OF MEDICAL SIGNALS AND SENSORS (JMSS)[Internet]. 2018;8(1):1-11. Available from: https://sid.ir/paper/333748/en

IEEE: Copy

NILOOFAR YOUSEFI MOTEGHAED, KEIVAN MAGHOOLI, and MASOUD GARSHASBI, “IMPROVING CLASSIFICATION OF CANCER AND MINING BIOMARKERS FROM GENE EXPRESSION PROFILES USING HYBRID OPTIMIZATION ALGORITHMS AND FUZZY SUPPORT VECTOR MACHINE,” JOURNAL OF MEDICAL SIGNALS AND SENSORS (JMSS), vol. 8, no. 1, pp. 1–11, 2018, [Online]. Available: https://sid.ir/paper/333748/en

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