DeepECMP: Predicting Extracellular Matrix Proteins using Deep Learning

Abstract

Introduction: The extracellular matrix (ECM) is a networkof proteins and carbohydrates that has a structural and bio-chemical function. The ECM plays an important role in dif-ferentiation, migration and signaling. Several studies havepredicted ECM proteins using machine learning algorithmssuch as Random Forests, K-nearest neighbours and supportvector machines but is yet to be explored using deep learn-ing. Method: DeepECMP was developed using several previ-ously used ECM datasets, asymmetric undersampling andan ensemble of 11 feed-forward neural networks. Results: The performance of DeepECMP was 83.6% bal-anced accuracy which outperformed several algorithms. Inaddition, the pipeline of DeepECMP has been shown to behighly efficient. Conclusion: This paper is the first to focus on utilizingdeep learning for ECM prediction. Several limitations areovercome by DeepECMP such as computational expense,availability to the public and usability outside of the humanspecies