Improving DNA Barcode-based Fish Identification System on Imbalanced Data using SMOTE

Wisnu Ananta Kusuma, Nurdevi Noviana, Lailan Sahrina Hasibuan, Mala Nurilmala

Abstract


Problem in imbalanced data is very common in classification or identification. The problem is raised when the number of instances of one class far exceeds the other. In the previous research, our DNA barcode-based Identification System of Tuna and Mackerel was developed in imbalanced dataset. The number of samples of Tuna and Mackerel were much more than those of other fish samples. Therefore, the accuracy of the classification model was probably still in bias. This research aimed at employing Synthetic Minority Oversampling Technique (SMOTE) to yield balanced dataset. We used k-mers frequencies from DNA barcode sequences as features and Support Vector Machine (SVM) as classification method. In this research we used trinucleotide (3-mers) and tetranucleotide (4-mers). The training dataset was taken from Barcode of Life Database (BOLD). For evaluating the model, we compared the accuracy of model using SMOTE and without SMOTE in order to classify DNA barcode sequences which is taken from Department of Aquatic Product Technology, Bogor Agricultural University. The results showed that the accuracy of the model in the species level using SMOTE was 7% and 13% higher than those of non-SMOTE for trinucleotide (3-mers) and tetranucleotide (4-mers), respectively. It is expected that the use of SMOTE, as one of data balancing technique, could increase the accuracy of DNA barcode based fish classification system, particularly in the species level which is difficult to be identified.

Keywords


DNA Barcode; imbalanced dataset; mislabeled fish; smote; support vector machine;

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DOI: http://dx.doi.org/10.12928/telkomnika.v15i3.5011

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