{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T18:29:11Z","timestamp":1784917751819,"version":"3.55.0"},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2019,2,4]],"date-time":"2019-02-04T00:00:00Z","timestamp":1549238400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100011118","name":"Office of the Vice Chancellor for Research, University of Illinois at Chicago","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011118","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","award":["R01HL138628"],"award-info":[{"award-number":["R01HL138628"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["U01AI132898"],"award-info":[{"award-number":["U01AI132898"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"UIC CCTS","award":["UL1TR002003"],"award-info":[{"award-number":["UL1TR002003"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006693","type":"journal-article","created":{"date-parts":[[2019,2,4]],"date-time":"2019-02-04T18:26:23Z","timestamp":1549304783000},"page":"e1006693","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":62,"title":["Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0155-7412","authenticated-orcid":true,"given":"Ahmed A.","family":"Metwally","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3491-5968","authenticated-orcid":true,"given":"Philip S.","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7955-3980","authenticated-orcid":true,"given":"Derek","family":"Reiman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Dai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia W.","family":"Finn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David L.","family":"Perkins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2019,2,4]]},"reference":[{"issue":"1","key":"ref1","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1542\/peds.2011-0204","article-title":"The prevalence, severity, and distribution of childhood food allergy in the United States","volume":"128","author":"RS Gupta","year":"2011","journal-title":"Pediatrics"},{"issue":"36","key":"ref2","doi-asserted-by":"crossref","first-page":"13145","DOI":"10.1073\/pnas.1412008111","article-title":"Commensal bacteria protect against food allergen sensitization","volume":"111","author":"AT Stefka","year":"2014","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1","key":"ref3","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.jaci.2012.10.026","article-title":"A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis","volume":"131","author":"M Noval Rivas","year":"2013","journal-title":"Journal of Allergy and Clinical Immunology"},{"issue":"1","key":"ref4","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1111\/all.13232","article-title":"A prospective microbiome-wide association study of food sensitization and food allergy in early childhood","volume":"73","author":"JH Savage","year":"2018","journal-title":"Allergy"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/j.ebiom.2015.11.038","article-title":"Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project","volume":"3","author":"X Hua","year":"2016","journal-title":"EBioMedicine"},{"issue":"8","key":"ref6","doi-asserted-by":"crossref","first-page":"2546","DOI":"10.1128\/AEM.00003-14","article-title":"Altered fecal microbiota composition associated with food allergy in infants","volume":"80","author":"Z Ling","year":"2014","journal-title":"Applied and environmental microbiology"},{"key":"ref7","first-page":"35","article-title":"Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases","author":"ON Aktas","year":"2018"},{"issue":"4","key":"ref8","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1016\/j.jaci.2016.03.041","article-title":"Early-life gut microbiome composition and milk allergy resolution","volume":"138","author":"S Bunyavanich","year":"2016","journal-title":"Journal of Allergy and Clinical Immunology"},{"issue":"12","key":"ref9","doi-asserted-by":"crossref","first-page":"2809","DOI":"10.1016\/j.celrep.2016.05.047","article-title":"Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways","volume":"15","author":"J Tan","year":"2016","journal-title":"Cell Reports"},{"issue":"3","key":"ref10","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1038\/ismej.2015.151","article-title":"Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants","volume":"10","author":"R Berni Canani","year":"2016","journal-title":"The ISME Journal"},{"issue":"2","key":"ref11","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.chom.2015.01.001","article-title":"The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes","volume":"17","author":"AD Kostic","year":"2015","journal-title":"Cell host & microbe"},{"issue":"4","key":"ref12","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1016\/j.cell.2016.04.007","article-title":"Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans","volume":"165","author":"T Vatanen","year":"2016","journal-title":"Cell"},{"issue":"5","key":"ref13","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2011-12-5-r50","article-title":"Moving pictures of the human microbiome","volume":"12","author":"JG Caporaso","year":"2011","journal-title":"Genome biology"},{"issue":"7228","key":"ref14","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature07540","article-title":"A core gut microbiome in obese and lean twins","volume":"457","author":"PJ Turnbaugh","year":"2009","journal-title":"Nature"},{"issue":"Suppl 1","key":"ref15","doi-asserted-by":"crossref","first-page":"4578","DOI":"10.1073\/pnas.1000081107","article-title":"Succession of microbial consortia in the developing infant gut microbiome","volume":"108","author":"JE Koenig","year":"2011","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"1","key":"ref16","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/s40168-016-0183-0","article-title":"Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection","volume":"4","author":"A Morris","year":"2016","journal-title":"Microbiome"},{"issue":"4","key":"ref17","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1016\/j.bbrc.2015.12.083","article-title":"Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing","volume":"469","author":"R Ranjan","year":"2015","journal-title":"Biochemical and Biophysical Research Communications"},{"issue":"9","key":"ref18","doi-asserted-by":"crossref","first-page":"e0163527","DOI":"10.1371\/journal.pone.0163527","article-title":"WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences","volume":"11","author":"AA Metwally","year":"2016","journal-title":"PLOS ONE"},{"key":"ref19","article-title":"QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science","author":"E Bolyen","year":"2018","journal-title":"PeerJ"},{"issue":"11","key":"ref20","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1038\/s41592-018-0176-y","article-title":"Species-level functional profiling of metagenomes and metatranscriptomes","volume":"15","author":"EA Franzosa","year":"2018","journal-title":"Nature Methods"},{"issue":"1","key":"ref21","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/s40168-018-0402-y","article-title":"MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies","volume":"6","author":"AA Metwally","year":"2018","journal-title":"Microbiome"},{"issue":"1","key":"ref22","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1109\/MASSP.1986.1165342","article-title":"An introduction to hidden Markov models","volume":"3","author":"L Rabiner","year":"1986","journal-title":"IEEE ASSP Magazine"},{"issue":"1","key":"ref23","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/BF02532251","article-title":"Fitting autoregressive models for prediction","volume":"21","author":"H Akaike","year":"1969","journal-title":"Annals of the institute of Statistical Mathematics"},{"key":"ref24","article-title":"Deep Learning","author":"I Goodfellow","year":"2016"},{"key":"ref25","unstructured":"Pascanu R, Mikolov T, Bengio Y. On the difficulty of training recurrent neural networks; 2013. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/dl.acm.org\/citation.cfm?id=3043083\" xlink:type=\"simple\">https:\/\/dl.acm.org\/citation.cfm?id=3043083<\/ext-link>."},{"issue":"6","key":"ref26","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1109\/TNB.2015.2461219","article-title":"Multi-Layer and Recursive Neural Networks for Metagenomic Classification","volume":"14","author":"G Ditzler","year":"2015","journal-title":"IEEE transactions on nanobioscience"},{"key":"ref27","doi-asserted-by":"crossref","unstructured":"Reiman D, Metwally A, Dai Y. Using Convolutional Neural Networks to Explore the Microbiome. In: 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). Jeju Island, South Korea: IEEE; 2017. p. 4269\u20134272.","DOI":"10.1109\/EMBC.2017.8037799"},{"key":"ref28","first-page":"257931","article-title":"PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolution Neural Networks for Metagenomic Data","author":"D Reiman","year":"2018","journal-title":"bioRxiv"},{"issue":"S2","key":"ref29","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/s12859-018-2033-5","article-title":"Phylogenetic convolutional neural networks in metagenomics","volume":"19","author":"D Fioravanti","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"ref30","article-title":"Semantically Conditioned LSTM-based Natural Language Generation for Spoken Dialogue Systems","author":"TH Wen","year":"2015","journal-title":"arXiv"},{"key":"ref31","article-title":"Speech Recognition with Deep Recurrent Neural Networks","author":"A Graves","year":"2013","journal-title":"arXiv"},{"issue":"8","key":"ref32","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1162\/neco.1997.9.8.1735","article-title":"Long Short-Term Memory","volume":"9","author":"S Hochreiter","year":"1997","journal-title":"Neural Computation"},{"issue":"8","key":"ref33","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1109\/TPAMI.2005.159","article-title":"Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy","volume":"27","author":"Hanchuan Peng","year":"2005","journal-title":"IEEE Transactions on Pattern Analysis and Machine Intelligence"},{"issue":"6789","key":"ref34","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1038\/35016072","article-title":"Erratum: Digital selection and analogue amplification coexist in a cortex-inspired silicon circuit","volume":"405","author":"RHR Hahnloser","year":"2000","journal-title":"Nature"},{"issue":"1","key":"ref35","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1214\/aoms\/1177729694","article-title":"On Information and Sufficiency","volume":"22","author":"S Kullback","year":"1951","journal-title":"The Annals of Mathematical Statistics"},{"key":"ref36","unstructured":"Ng A. Sparse autoencoder; 2011. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/web.stanford.edu\/class\/cs294a\/sparseAutoencoder_2011new.pdf\" xlink:type=\"simple\">https:\/\/web.stanford.edu\/class\/cs294a\/sparseAutoencoder_2011new.pdf<\/ext-link>."},{"issue":"10","key":"ref37","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1038\/nmeth.3589","article-title":"MetaPhlAn2 for enhanced metagenomic taxonomic profiling","volume":"12","author":"DT Truong","year":"2015","journal-title":"Nature Methods"},{"key":"ref38","article-title":"Neural networks: a comprehensive foundation","author":"SS Simon Haykin","year":"1994"},{"issue":"3","key":"ref39","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/BF00994018","article-title":"Support-vector networks","volume":"20","author":"C Cortes","year":"1995","journal-title":"Machine Learning"},{"key":"ref40","unstructured":"Tin Kam Ho. Random decision forests. In: Proceedings of 3rd International Conference on Document Analysis and Recognition. vol. 1. IEEE Comput. Soc. Press;. p. 278\u2013282. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/ieeexplore.ieee.org\/document\/598994\/\" xlink:type=\"simple\">http:\/\/ieeexplore.ieee.org\/document\/598994\/<\/ext-link>."},{"issue":"1","key":"ref41","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","article-title":"Regression Shrinkage and Selection via the Lasso","volume":"58","author":"R Tibshirani","year":"1996","journal-title":"Journal of the Royal Statistical Society"},{"key":"ref42","unstructured":"Abadi M, Agarwal A, Barham P, Brevdo E, Chen Z, Citro C, et al. TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems. In: OSDI\u201916 Proceedings of the 12th USENIX conference on Operating Systems Design and Implementation; 2016. p. 265\u2013283. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/arxiv.org\/abs\/1603.04467\" xlink:type=\"simple\">http:\/\/arxiv.org\/abs\/1603.04467<\/ext-link>."},{"key":"ref43","unstructured":"Kingma DP, Ba J. Adam: A Method for Stochastic Optimization. In: International Conference on Learning Representations (ICLR); 2015.Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/arxiv.org\/abs\/1412.6980\" xlink:type=\"simple\">http:\/\/arxiv.org\/abs\/1412.6980<\/ext-link>."},{"key":"ref44","first-page":"1929","article-title":"Dropout: A Simple Way to Prevent Neural Networks from Overfitting","volume":"15","author":"N Srivastava","year":"2014","journal-title":"Journal of Machine Learning Research"},{"issue":"1-2","key":"ref45","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1159\/000484897","article-title":"Fecal Microbiome and Food Allergy in Pediatric Atopic Dermatitis: A Cross-Sectional Pilot Study","volume":"175","author":"KB Fieten","year":"2018","journal-title":"International archives of allergy and immunology"},{"issue":"3","key":"ref46","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1016\/j.jaci.2015.08.021","article-title":"Faecalibacterium prausnitzii subspecies\u2013level dysbiosis in the human gut microbiome underlying atopic dermatitis","volume":"137","author":"H Song","year":"2016","journal-title":"Journal of Allergy and Clinical Immunology"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006693","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,14]],"date-time":"2024-07-14T14:48:21Z","timestamp":1720968501000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006693"}},"subtitle":[],"editor":[{"given":"Yana","family":"Bromberg","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,2,4]]},"references-count":46,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2019,2,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006693","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,2,4]]}}}