This paper is concerned with the inverse problem of recovering the unknown signal components, along with extraction of their instantaneous frequencies (IFs), governed by the adaptive harmonic model (AHM), from discrete (and possibly non-uniform) samples of the blind-source composite signal. None of the existing decomposition methods and algorithms, including the most popular empirical mode decomposition (EMD) computational scheme and its current modifications, is capable of solving this inverse problem. In order to meet the AHM formulation and to extract the IFs of the decomposed components, called intrinsic mode functions (IMFs), each IMF of EMD is extended to an analytic function in the upper half of the complex plane via the Hilbert transform, followed by taking the real part of the polar form of the analytic extension. Unfortunately, this approach most often fails to resolve the inverse problem satisfactorily. More recently, to resolve the inverse problem, the notion of synchrosqueezed wavelet transform (SST) was proposed by Daubechies and Maes, and further developed in many other papers, while a more direct method, called signal separation operation (SSO), was proposed and developed in our previous work published in the journal, Applied and Computational Harmonic Analysis, vol. 30(2):243-261, 2016. In the present paper, we propose a synthesis of SSO using a deep neural network, based directly on a discrete sample set, that may be non-uniformly sampled, of the blind-source signal. Our method is localized, as illustrated by a number of numerical examples, including components with different signal arrival and departure times. It also yields short-term prediction of the signal components, along with their IFs. Our neural networks are inspired by theory, designed so that they do not require any training in the traditional sense.