A hybrid Stacking-SMOTE model for optimizing the prediction of autistic genes

Abstract

Purpose: Autism spectrum disorder(ASD) is a disease associated with the neurodevelopment of the brain. The autism spectrum can be observed in early childhood, where the symptoms of the disease usually appear in children within the first year of their life. Currently, ASD can only be diagnosed based on the apparent symptoms due to the lack of information on genes related to the disease. Therefore, in this paper, we need to predict the largest number of disease-causing genes for a better diagnosis.

Methods: A hybrid stacking ensemble model with Synthetic Minority Oversampling TEchnique (Stack-SMOTE) is proposed to predict the genes associated with ASD. The proposed model uses the gene ontology database to measure the similarities between the genes using a hybrid gene similarity function(HGS). HGS is effective in measuring the similarity as it combines the features of information gain-based methods and graph-based methods. The proposed model solves the imbalanced ASD dataset problem using the Synthetic Minority Oversampling Technique (SMOTE), which generates synthetic data rather than duplicates the data to reduce the overfitting. Sequentially, a gradient boosting-based random forest classifier (GBBRF) is introduced as a new combination technique to enhance the prediction of ASD genes. Moreover, the GBBRF classifier combined with random forest(RF), k-nearest neighbor, support vector machine(SVM), and logistic regression(LR) to form the proposed Stacking-SMOTE model to optimize the prediction of ASD genes.

Results: The proposed Stacking-SMOTE model is evaluated using the Simons Foundation Autism Research Initiative (SFARI) gene database and a set of candidates ASD genes.The results of the proposed model-based SMOTE outperform other reported undersampling and oversampling techniques. Sequentially, the results of GBBRF achieve higher accuracy than using the basic classifiers. Moreover, the experimental results show that the proposed Stacking-SMOTE model outperforms the existing ASD prediction models with approximately 95.5% accuracy.

Conclusion: The proposed Stacking-SMOTE model demonstrates that SMOTE is effective in handling the autism imbalanced data. Sequentially, the integration between the gradient boosting and random forest classifier (GBBRF) support to build a robust stacking ensemble model(Stacking-SMOTE).

Keywords: Boosting techniques; Ensemble learning; Gene ontology; Gene prediction; Gene similarity function; Stacking.