FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling
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 t...
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Veröffentlicht in: | Journal of biomolecular NMR 2021-05, Vol.75 (4-5), p.179-191 |
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creator | Karunanithy, Gogulan Hansen, D. Flemming |
description | 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
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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. |
doi_str_mv | 10.1007/s10858-021-00366-w |
format | Article |
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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.</description><identifier>ISSN: 0925-2738</identifier><identifier>EISSN: 1573-5001</identifier><identifier>DOI: 10.1007/s10858-021-00366-w</identifier><identifier>PMID: 33870472</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>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</subject><ispartof>Journal of biomolecular NMR, 2021-05, Vol.75 (4-5), p.179-191</ispartof><rights>Crown 2021</rights><rights>Crown 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c474t-f1c694b5f437e8849cc54c1c2258c43383ff35d52525289d5f8ba8ac6c18d7903</citedby><cites>FETCH-LOGICAL-c474t-f1c694b5f437e8849cc54c1c2258c43383ff35d52525289d5f8ba8ac6c18d7903</cites><orcidid>0000-0003-0891-220X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10858-021-00366-w$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10858-021-00366-w$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33870472$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Karunanithy, Gogulan</creatorcontrib><creatorcontrib>Hansen, D. Flemming</creatorcontrib><title>FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling</title><title>Journal of biomolecular NMR</title><addtitle>J Biomol NMR</addtitle><addtitle>J Biomol NMR</addtitle><description>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
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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.</description><subject>Algorithms</subject><subject>Artificial neural networks</subject><subject>Biochemistry</subject><subject>Biological and Medical Physics</subject><subject>Biophysics</subject><subject>Computational Biology - methods</subject><subject>Computer architecture</subject><subject>Couplings</subject><subject>Decoupling</subject><subject>Deep Learning</subject><subject>Glycine</subject><subject>Histone Deacetylases - chemistry</subject><subject>Magnetic Resonance Imaging - methods</subject><subject>Muramidase - chemistry</subject><subject>Neural networks</subject><subject>Neural Networks, Computer</subject><subject>NMR</subject><subject>Nuclear magnetic resonance</subject><subject>Nuclear Magnetic Resonance, Biomolecular - methods</subject><subject>Physics</subject><subject>Physics and Astronomy</subject><subject>Reconstruction</subject><subject>Schedules</subject><subject>Spectra</subject><subject>Spectroscopy/Spectrometry</subject><subject>src Homology Domains - physiology</subject><subject>Time domain analysis</subject><issn>0925-2738</issn><issn>1573-5001</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp9kU1rFTEYhYMo9lr9Ay4k4MZNNJ-TjAuhVKuFWkF0HXIzmdvUuck0H_fivzfjrfVjIVm8kPPk5LwcAJ4S_JJgLF9lgpVQCFOCMGZdh_b3wIoIyZDAmNwHK9xTgahk6gg8yvkaY9wr2j0ER4wpibmkKzCdnb9Fl668hidw51I2xU8ODs7NMLiazNRG2cf0DZpkr3xxttTk4BgTvPz4Gea5XSxUcjaGXFK1xccATRjgzqdSmzQ0qc6TD5vH4MFopuye3M5j8PXs3ZfTD-ji0_vz05MLZLnkBY3Edj1fi5Ez6ZTivbWCW2IpFcrylp2NIxODoMtR_SBGtTbK2M4SNcges2Pw5uA71_XWDdaFJaOek9-a9F1H4_XfSvBXehN3WhFGGOfN4MWtQYo31eWitz5bN00muFizpoIILInsF_T5P-h1rCm09fSSrmOC97RR9EDZFHNObrwLQ7BeytSHMnUrU_8sU-_bo2d_rnH35Fd7DWAHIDcpbFz6_fd_bH8AS5GsKg</recordid><startdate>20210501</startdate><enddate>20210501</enddate><creator>Karunanithy, Gogulan</creator><creator>Hansen, D. Flemming</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7QO</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-0891-220X</orcidid></search><sort><creationdate>20210501</creationdate><title>FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling</title><author>Karunanithy, Gogulan ; Hansen, D. Flemming</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c474t-f1c694b5f437e8849cc54c1c2258c43383ff35d52525289d5f8ba8ac6c18d7903</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Algorithms</topic><topic>Artificial neural networks</topic><topic>Biochemistry</topic><topic>Biological and Medical Physics</topic><topic>Biophysics</topic><topic>Computational Biology - methods</topic><topic>Computer architecture</topic><topic>Couplings</topic><topic>Decoupling</topic><topic>Deep Learning</topic><topic>Glycine</topic><topic>Histone Deacetylases - chemistry</topic><topic>Magnetic Resonance Imaging - methods</topic><topic>Muramidase - chemistry</topic><topic>Neural networks</topic><topic>Neural Networks, Computer</topic><topic>NMR</topic><topic>Nuclear magnetic resonance</topic><topic>Nuclear Magnetic Resonance, Biomolecular - methods</topic><topic>Physics</topic><topic>Physics and Astronomy</topic><topic>Reconstruction</topic><topic>Schedules</topic><topic>Spectra</topic><topic>Spectroscopy/Spectrometry</topic><topic>src Homology Domains - physiology</topic><topic>Time domain analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Karunanithy, Gogulan</creatorcontrib><creatorcontrib>Hansen, D. 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Flemming</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling</atitle><jtitle>Journal of biomolecular NMR</jtitle><stitle>J Biomol NMR</stitle><addtitle>J Biomol NMR</addtitle><date>2021-05-01</date><risdate>2021</risdate><volume>75</volume><issue>4-5</issue><spage>179</spage><epage>191</epage><pages>179-191</pages><issn>0925-2738</issn><eissn>1573-5001</eissn><abstract>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
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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.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>33870472</pmid><doi>10.1007/s10858-021-00366-w</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0003-0891-220X</orcidid><oa>free_for_read</oa></addata></record> |
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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 |
title | FID-Net: A versatile deep neural network architecture for NMR spectral reconstruction and virtual decoupling |
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