We propose a method to improve the performance of the nonlinear Fourier transform (NFT)-based optical transmission system by applying the neural network post-processing of the nonlinear spectrum at the receiver. We demonstrate through numerical modeling about one order of magnitude bit error rate improvement and compare this method with machine learning processing based on the classification of the received symbols. The proposed approach also offers a way to improve numerical accuracy of the inverse NFT; therefore, it can find a range of applications beyond optical communications.