One of the main issues in hadron spectroscopy is to identify the origin of threshold or near-threshold enhancement. Prior to our study, there is no straightforward way of distinguishing even the lowest channel threshold-enhancement of the nucleon-nucleon system using only the cross-sections. The difficulty lies in the proximity of either a bound or virtual state pole to the threshold which creates an almost identical structure in the scattering region. Identifying the nature of the pole causing the enhancement falls under the general classification problem and supervised machine learning using a feed-forward neural network is known to excel in this task. In this study, we discuss the basic idea behind deep neural network and how it can be used to identify the nature of the pole causing the enhancement. The applicability of the trained network can be explored by using an exact separable potential model to generate a validation dataset. We find that within some acceptable range of the cut-off parameter, the neural network gives high accuracy of inference. The result also reveals the important role played by the background singularities in the training dataset. Finally, we apply the method to nucleon-nucleon scattering data and show that the network was able to give the correct nature of pole, i.e. virtual pole for ${}^1S_0$ partial cross-section and bound state pole for ${}^3S_0$.