Our microPred classifier yielded higher and, especially, much more reliable classification results in terms of both sensitivity (90.02%) and specificity (97.28%) than the exiting pre-miRNA classification methods. When validated with 6095 non-human animal pre-miRNAs and 139 virus pre-miRNAs from miRBase, microPred resulted in 92.71% (5651/6095) and 94.24% (131/139) recognition rates, respectively.

Support vector machines (SVMs) is a popular machine learning technique, which works effectively with balanced datasets. However, when it comes to imbalanced datasets, SVMs produce suboptimal classification models. On the other hand, the SVM algorithm is sensitive to outliers and noise present in the datasets. Therefore, although the existing class imbalance learning (CIL) methods can make SVMs less sensitive to class imbalance, they can still suffer from the problem of outliers and noise. Fuzzy SVMs (FSVMs) is a variant of the SVM algorithm, which has been proposed to handle the problem of outliers and noise. In FSVMs, training examples are assigned different fuzzy-membership values based on their importance, and these membership values are incorporated into the SVM learning algorithm to make it less sensitive to outliers and noise. However, like the normal SVM algorithm, FSVMs can also suffer from the problem of class imbalance. In this paper, we present a method to improve FSVMs for CIL (called FSVM-CIL), which can be used to handle the class imbalance problem in the presence of outliers and noise. We thoroughly evaluated the proposed FSVM-CIL method on ten real-world imbalanced datasets and compared its performance with five existing CIL methods, which are available for normal SVM training. Based on the overall results, we can conclude that the proposed FSVM-CIL method is a very effective method for CIL, especially in the presence of outliers and noise in datasets.

Random undersampling and oversampling are simple but well-known resampling methods applied to solve the problem of class imbalance. In this paper we show that the random oversampling method can produce better classification results than the random undersampling method, since the oversampling can increase the minority class recognition rate by sacrificing less amount of majority class recognition rate than the undersampling method. However, the random oversampling method would increase the computational cost associated with the SVM training largely due to the addition of new training examples. In this paper we present an investigation carried out to develop efficient resampling methods that can produce comparable classification results to the random oversampling results, but with the use of less amount of data. The main idea of the proposed methods is to first select the most informative data examples located closer to the class boundary region by using the separating hyperplane found by training an SVM model on the original imbalanced dataset, and then use only those examples in resampling. We demonstrate that it would be possible to obtain comparable classification results to the random oversampling results through two sets of efficient resampling methods which use 50% less amount of data and 75% less amount of data, respectively, compared to the sizes of the datasets generated by the random oversampling method.

One common and challenging problem faced by many bioinformatics applications, such as promoter recognition, splice site prediction, RNA gene prediction, drug discovery and protein classification, is the imbalance of the available datasets. In most of these applications, the positive data examples are largely outnumbered by the negative data examples, which often leads to the development of sub-optimal prediction models having high negative recognition rate (Specificity = SP) and low positive recognition rate (Sensitivity = SE). When class imbalance learning methods are applied, usually, the SE is increased at the expense of reducing some amount of the SP. In this paper, we point out that in these data-imbalanced bioinformatics applications, the goal of applying class imbalance learning methods would be to increase the SE as high as possible by keeping the reduction of SP as low as possible. We explain that the existing performance measures used in class imbalance learning can still produce sub-optimal models with respect to this classification goal. In order to overcome these problems, we introduce a new performance measure called Adjusted Geometric-mean (AGm). The experimental results obtained on ten real-world imbalanced bioinformatics datasets demonstrates that the AGm metric can achieve a lower rate of reduction of SP than the existing performance metrics, when increasing the SE through class imbalance learning methods. This characteristic of AGm metric makes it more suitable for achieving the proposed classification goal in imbalanced bioinformatics datasets learning.