Classification with imbalanced data is a common and challenging problem in many practical machine learning problems. Ensemble learning is a popular solution where the results from multiple base classifiers are synthesized to reduce the effect of a possibly skewed distribution of the training set. In this paper, binary classifiers based on Gaussian processes are chosen as bases for inferring the predictive distributions of test latent variables. We apply a Gaussian process latent variable model where the outputs of the Gaussian processes are used for making the final decision. The tests of the new method in both synthetic and real data sets show improved performance over standard approaches.