An improved Binary Particle Swarm Optimization (iBPSO) for Gene Selection and Cancer Classification using DNA Microarrays

2018 ◽  
Author(s):  
Indu Jain ◽  
Vinod Kumar Jain ◽  
Renu Jain
Keyword(s):  
Particle Swarm Optimization ◽  
Dna Microarrays ◽  
Gene Selection ◽  
Particle Swarm ◽  
Cancer Classification ◽  
Binary Particle Swarm Optimization ◽  
Swarm Optimization

scholarly journals A Novel Weighted Support Vector Machine Based on Particle Swarm Optimization for Gene Selection and Tumor Classification

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Mohammad Javad Abdi ◽  
Seyed Mohammad Hosseini ◽  
Mansoor Rezghi
Keyword(s):  
Particle Swarm Optimization ◽  
Dna Microarrays ◽  
Gene Selection ◽  
Particle Swarm ◽  
Tumor Classification ◽  
Support Vector ◽  
Classification Problems ◽  
Target Class ◽  
Swarm Optimization ◽  
Kernel Parameters

We develop a detection model based on support vector machines (SVMs) and particle swarm optimization (PSO) for gene selection and tumor classification problems. The proposed model consists of two stages: first, the well-known minimum redundancy-maximum relevance (mRMR) method is applied to preselect genes that have the highest relevance with the target class and are maximally dissimilar to each other. Then, PSO is proposed to form a novel weighted SVM (WSVM) to classify samples. In this WSVM, PSO not only discards redundant genes, but also especially takes into account the degree of importance of each gene and assigns diverse weights to the different genes. We also use PSO to find appropriate kernel parameters since the choice of gene weights influences the optimal kernel parameters and vice versa. Experimental results show that the proposed mRMR-PSO-WSVM model achieves highest classification accuracy on two popular leukemia and colon gene expression datasets obtained from DNA microarrays. Therefore, we can conclude that our proposed method is very promising compared to the previously reported results.

Selection of Pathway Markers for Cancer Using Collaborative Binary Multi-Swarm Optimization

2018 ◽  
pp. 337-363
Author(s):  
Prativa Agarwalla ◽  
Sumitra Mukhopadhyay
Keyword(s):  
Particle Swarm Optimization ◽  
Artificial Bee Colony ◽  
Gene Selection ◽  
Heuristic Algorithms ◽  
Particle Swarm ◽  
High Accuracy ◽  
Marker Genes ◽  
Binary Particle Swarm Optimization ◽  
Swarm Optimization ◽  
Bee Colony

Pathway information for cancer detection helps to find co-regulated gene groups whose collective expression is strongly associated with cancer development. In this paper, a collaborative multi-swarm binary particle swarm optimization (MS-BPSO) based gene selection technique is proposed that outperforms to identify the pathway marker genes. We have compared our proposed method with various statistical and pathway based gene selection techniques for different popular cancer datasets as well as a detailed comparative study is illustrated using different meta-heuristic algorithms like binary coded particle swarm optimization (BPSO), binary coded differential evolution (BDE), binary coded artificial bee colony (BABC) and genetic algorithm (GA). Experimental results show that the proposed MS-BPSO based method performs significantly better and the improved multi swarm concept generates a good subset of pathway markers which provides more effective insight to the gene-disease association with high accuracy and reliability.

scholarly journals An enhancement of binary particle swarm optimization for gene selection in classifying cancer classes

2013 ◽  
Vol 8 (1) ◽  
Author(s):  
Mohd Saberi Mohamad ◽  
Sigeru Omatu ◽  
Safaai Deris ◽  
Michifumi Yoshioka ◽  
Afnizanfaizal Abdullah ◽  
...  
Keyword(s):  
Particle Swarm Optimization ◽  
Gene Selection ◽  
Particle Swarm ◽  
Binary Particle Swarm Optimization ◽  
Swarm Optimization

scholarly journals Cancer Feature Selection and Classification Using a Binary Quantum-Behaved Particle Swarm Optimization and Support Vector Machine

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Maolong Xi ◽  
Jun Sun ◽  
Li Liu ◽  
Fangyun Fan ◽  
Xiaojun Wu
Keyword(s):  
Support Vector Machine ◽  
Particle Swarm Optimization ◽  
Gene Selection ◽  
Optimization Problems ◽  
Particle Swarm ◽  
Cancer Classification ◽  
Support Vector ◽  
Swarm Optimization ◽  
Binary Pso ◽  
Leave One Out

This paper focuses on the feature gene selection for cancer classification, which employs an optimization algorithm to select a subset of the genes. We propose a binary quantum-behaved particle swarm optimization (BQPSO) for cancer feature gene selection, coupling support vector machine (SVM) for cancer classification. First, the proposed BQPSO algorithm is described, which is a discretized version of original QPSO for binary 0-1 optimization problems. Then, we present the principle and procedure for cancer feature gene selection and cancer classification based on BQPSO and SVM with leave-one-out cross validation (LOOCV). Finally, the BQPSO coupling SVM (BQPSO/SVM), binary PSO coupling SVM (BPSO/SVM), and genetic algorithm coupling SVM (GA/SVM) are tested for feature gene selection and cancer classification on five microarray data sets, namely, Leukemia, Prostate, Colon, Lung, and Lymphoma. The experimental results show that BQPSO/SVM has significant advantages in accuracy, robustness, and the number of feature genes selected compared with the other two algorithms.

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