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Table 2 Classification quality for the classification of 23 archaeal genomes into methanogens and non-methanogens using the 5 most relevant pathways

From: Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes

Classifier

ReliefF

SVM

Wrapper

All pathways

Random

J48

0.88

0.88

0.59

0.83

0.17

IB1

0.94

1.00

1.00

0.29

0.31

Naïve Bayes

0.94

1.00

0.83

0.83

0.38

SMO

1.00

1.00

1.00

1.00

0.01

  1. The 23 archaeal genomes were classified into methanogens and non-methanogens using only the five most relevant pathways from Table 1. We applied four different classifiers (J48, IB1, naïve Bayes, and SMO) with tenfold cross-validation. In addition, the genomes were classified based on all pathways (290) in the pathway profile as well as on five randomly chosen pathways. To estimate the quality of classification, we calculated the product of classification selectivity and sensitivity, which is shown in this table. In the case of randomly chosen pathways, the value was derived by averaging the classification quality of 25 sets of 5 randomly chosen pathways.