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We present a new method of classification of imbalanced classes. The crucial point of the method lies in applying Atanassov’s intuitionistic fuzzy sets (which are a generalization of fuzzy sets) while representing the classes during the first training phase. The Atanassov’s intuitionistic fuzzy sets are generated according to an automatic and mathematically justified procedure from the relative frequency distributions representing the data. Next, we use the information about so-called hesitation margins (which besides membership and non-membership values characterize Atanassov’s intuitionistic fuzzy sets) making it possible to improve the results of data classification. The results obtained in the testing phase were examined not only in the sense of general error/accuracy but also by using confusion matrices, that is, exploring a detailed behavior of the intuitionistic fuzzy classifiers. Detailed analysis of the errors for the examined examples has shown that applying Atanassov’s intuitionistic fuzzy sets gives better results than the counterpart approach via fuzzy sets. Better performance of the intuitionistic fuzzy classifier concerns mainly the recognition power of a smaller class. The method was tested using a benchmark problem from UCI machine learning repository.

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