FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling

• Published in: Journal of biomolecular NMR 2021-05, Vol.75 (4-5), p.179-191
• Main Authors: Karunanithy, Gogulan, Hansen, D. Flemming
• Format: Article
• Language: English
• Subjects: Algorithms; Artificial neural networks; Biochemistry; Biological and Medical Physics; Biophysics; Computational Biology - methods; Computer architecture; Couplings; Decoupling; Deep Learning; Glycine; Histone Deacetylases - chemistry; Magnetic Resonance Imaging - methods; Muramidase - chemistry; Neural networks; Neural Networks, Computer; NMR; Nuclear magnetic resonance; Nuclear Magnetic Resonance, Biomolecular - methods; Physics; Physics and Astronomy; Reconstruction; Schedules; Spectra; Spectroscopy/Spectrometry; src Homology Domains - physiology; Time domain analysis
• ISSN: 0925-2738; 1573-5001
• DOI: 10.1007/s10858-021-00366-w

In recent years, the transformative potential of deep neural networks (DNNs) for analysing and interpreting NMR data has clearly been recognised. However, most applications of DNNs in NMR to date either struggle to outperform existing methodologies or are limited in scope to a narrow range of data that closely resemble the data that the network was trained on. These limitations have prevented a widescale uptake of DNNs in NMR. Addressing this, we introduce FID-Net, a deep neural network architecture inspired by WaveNet, for performing analyses on time domain NMR data. We first demonstrate the effectiveness of this architecture in reconstructing non-uniformly sampled (NUS) biomolecular NMR spectra. It is shown that a single network is able to reconstruct a diverse range of 2D NUS spectra that have been obtained with arbitrary sampling schedules, with a range of sweep widths, and a variety of other acquisition parameters. The performance of the trained FID-Net in this case exceeds or matches existing methods currently used for the reconstruction of NUS NMR spectra. Secondly, we present a network based on the FID-Net architecture that can efficiently virtually decouple 13 C α - 13 C β couplings in HNCA protein NMR spectra in a single shot analysis, while at the same time leaving glycine residues unmodulated. The ability for these DNNs to work effectively in a wide range of scenarios, without retraining, paves the way for their widespread usage in analysing NMR data.