Estimating a form of equation that explains data is very useful to understand various physical, chemical, social, and biological phenomena. One effective approach for finding the form of an equation is to solve the symbolic regression problem using genetic programming (GP). However, this approach requires a long computation time because of the explosion of the number of combinations of candidate functions that are used as elements to construct equations. In the present paper, a novel method to effectively eliminate unnecessary functions from an initial set of functions using a deep neural network was proposed to reduce the number of computations of GP. Moreover, a method was proposed to improve the accuracy of the classification using eigenvalues when classifying whether functions are required for symbolic regression. Experiment results showed that the proposed method can successfully classify functions with over 90% of the data created in the present study.