alexa LVQ-SMOTE - Learning Vector Quantization based Synthetic Minority Over-sampling Technique for biomedical data.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Computer Science & Systems Biology

Author(s): Nakamura M, Kajiwara Y, Otsuka A, Kimura H

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Abstract BACKGROUND: Over-sampling methods based on Synthetic Minority Over-sampling Technique (SMOTE) have been proposed for classification problems of imbalanced biomedical data. However, the existing over-sampling methods achieve slightly better or sometimes worse result than the simplest SMOTE. In order to improve the effectiveness of SMOTE, this paper presents a novel over-sampling method using codebooks obtained by the learning vector quantization. In general, even when an existing SMOTE applied to a biomedical dataset, its empty feature space is still so huge that most classification algorithms would not perform well on estimating borderlines between classes. To tackle this problem, our over-sampling method generates synthetic samples which occupy more feature space than the other SMOTE algorithms. Briefly saying, our over-sampling method enables to generate useful synthetic samples by referring to actual samples taken from real-world datasets. RESULTS: Experiments on eight real-world imbalanced datasets demonstrate that our proposed over-sampling method performs better than the simplest SMOTE on four of five standard classification algorithms. Moreover, it is seen that the performance of our method increases if the latest SMOTE called MWMOTE is used in our algorithm. Experiments on datasets for β-turn types prediction show some important patterns that have not been seen in previous analyses. CONCLUSIONS: The proposed over-sampling method generates useful synthetic samples for the classification of imbalanced biomedical data. Besides, the proposed over-sampling method is basically compatible with basic classification algorithms and the existing over-sampling methods.
This article was published in BioData Min and referenced in Journal of Computer Science & Systems Biology

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