Optimization of Spaced K-mer Frequency Feature Extraction using Genetic Algorithms for Metagenome Fragment Classification

Arini Pekuwali, Wisnu Ananta Kusuma, Agus Buono

Abstract


K-mer frequencies are commonly used in extracting features from metagenome fragments. In spite of this, researchers have found that their use is still inefficient. In this research, a genetic algorithm was employed to find optimally spaced k-mers. These were obtained by generating the possible combinations of match positions and don’t care positions (written as *). This approach was adopted from the concept of spaced seeds in PatternHunter. The use of spaced k-mers could reduce the size of the k-mer frequency feature’s dimension. To measure the accuracy of the proposed method we used the naïve Bayesian classifier (NBC). The result showed that the chromosome 111111110001, representing spaced k-mer model [111 1111 10001], was the best chromosome, with a higher fitness (85.42) than that of the k-mer frequency feature. Moreover, the proposed approach also reduced the feature extraction time. 

Keywords


genetic algorithm; k-mers; metagenome; naïve Bayesian classifier; spaced k-mers

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DOI: http://dx.doi.org/10.5614%2Fitbj.ict.res.appl.2018.12.2.2

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