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COSTA-SÁ, Clebiano. Traditional and time validation methods applied to the evaluation of coding and non-coding RNA classifiers. 2018. 101 p. Dissertation (Master in Bioinformatics) – Institute of Mathematics and Statistics, University of São Paulo, São Paulo, 2018. Ribonucleic acids (RNAs) can be classified into two main classes: coding and non-coding of protein. The coding, represented by messenger RNAs (mRNAs), has the necessary information for protein synthesis. Non-coding RNAs (ncRNAs) are not translated into proteins but are involved in several distinct cellular activities associated with various diseases such as heart disease, cancer and psychiatric disorders. The discovery of new ncRNAs and their molecular roles favors advances in the knowledge of molecular biology and may also boost the development of new therapies against diseases. The identification of ncRNAs is an active area of research and one of the current methods is the classification of transcribed sequences using pattern recognition systems based on their characteristics. Many classifiers have been developed for this purpose, especially in the last three years. An example is the Coding Potential Calculator (CPC), based on Supporting Vector Machines (SVM). However, other robust algorithms are also recognized for their potential in classification tasks, such as Random Forest (RF). The most commonly used method for evaluating these tools has been cross-validation k-fold. An issue not considered in this form of validation is the assumption that frequency distributions within the database, in terms of sequence classes and other variables, do not change over time. If this assumption is not true, traditional methods such as cross-validation and hold-out may underestimate classification errors. The need for a validation method that takes into account the constant evolution of databases over time is therefore needed to provide a more realistic performance analysis of these classifiers. In this work we compare two methods of evaluation of classifiers: time hold-out and traditional hold-out (without considering the time). In addition, we tested new classification models from the combination of different induction algorithms with state-ofthe-art classifier characteristics and a new set of characteristics. From the hypothesis tests, we observe that both the traditional hold-out validation and the time hold-out validation tend to underestimate the classification errors, that the time validation evaluation is more reliable, than classifiers trained from parameters calibrated by time validation did not improve classification and that our Random Forest-based classification model trained with state-of-the-art classifier characteristics and a new set of characteristics provided a significant improvement in the discrimination of the coding and non-coding RNAs. Finally, we highlight the potential of the Random Forest algorithm and the characteristics used, in view of this classification problem, and we suggest the use of the time hold-out validation method to obtain more reliable estimates of the protein coding and non-coding RNA classifiers.

Métodos de validação tradicional e temporal aplicados à avaliação de classificadores de RNAs codificantes e não codificantes