{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:05:10Z","timestamp":1792785910575,"version":"4.5.0"},"reference-count":114,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T00:00:00Z","timestamp":1756425600000},"content-version":"vor","delay-in-days":240,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Canadian Safety and Security Program","award":["CSSP-2022-CP-2538"],"award-info":[{"award-number":["CSSP-2022-CP-2538"]}]},{"name":"Canadian Safety and Security Program","award":["CSSP-2023-CP-2620"],"award-info":[{"award-number":["CSSP-2023-CP-2620"]}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010318","name":"University of Manitoba","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010318","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Canada Biomedical Research Fund","award":["CBRF2-2023-00008"],"award-info":[{"award-number":["CBRF2-2023-00008"]}]},{"name":"Biomedical Research Infrastructure Fund"},{"name":"Ontario Research Fund"},{"DOI":"10.13039\/501100000023","name":"Government of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000023","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007631","name":"Canadian Institute for Advanced Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007631","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Influenza A virus (IAV) poses a significant threat to animal health globally, with its ability to overcome species barriers and cause pandemics. Rapid and accurate IAV subtypes and host source prediction is crucial for effective surveillance and pandemic preparedness. Deep learning has emerged as a powerful tool for analyzing viral genomic sequences, offering new ways to uncover hidden patterns associated with viral characteristics and host adaptation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Findings<\/jats:title>\n                    <jats:p>We introduce WaveSeekerNet, a novel deep learning model for accurate and rapid prediction of IAV subtypes and host source. The model leverages attention-based mechanisms and efficient token mixing schemes, including the Fourier Transform and the Wavelet Transform, to capture intricate patterns within viral RNA and protein sequences. Extensive experiments on diverse datasets demonstrate WaveSeekerNet\u2019s superior performance to existing models that use the traditional self-attention mechanism. Notably, WaveSeekerNet rivals VADR (Viral Annotation DefineR) in subtype prediction using the high-quality RNA sequences, achieving the maximum score of 1.0 on metrics, including the Balanced Accuracy, F1-score (Macro Average), and Matthews Correlation Coefficient. Our approach to subtype and host source prediction also exceeds the pretrained ESM-2 (Evolutionary Scale Modeling) models with respect to generalization performance and computational cost. Furthermore, WaveSeekerNet exhibits remarkable accuracy in distinguishing between human, avian, and other mammalian hosts. The ability of WaveSeekerNet to flag potential cross-species transmission events underscores its significant value for real-time surveillance and proactive pandemic preparedness efforts.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>WaveSeekerNet\u2019s superior performance, efficiency, and ability to flag potential cross-species transmission events highlight its potential for real-time surveillance and pandemic preparedness. This model represents a significant advancement in applying deep learning for IAV classification and holds promise for future epidemiological, veterinary studies, and public health interventions.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/gigascience\/giaf089","type":"journal-article","created":{"date-parts":[[2025,8,4]],"date-time":"2025-08-04T11:23:20Z","timestamp":1754306600000},"source":"Crossref","is-referenced-by-count":2,"title":["WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning"],"prefix":"10.1093","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5858-9466","authenticated-orcid":false,"given":"Hoang-Hai","family":"Nguyen","sequence":"first","affiliation":[{"name":"Canadian Food Inspection Agency National Centre for Foreign Animal Disease, , Winnipeg, Manitoba R3E 3M4 ,","place":["Canada"]},{"name":"University of Manitoba Department of Computer Science, , Winnipeg, Manitoba R3T 2N2 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0484-8028","authenticated-orcid":false,"given":"Josip","family":"Rudar","sequence":"additional","affiliation":[{"name":"Canadian Food Inspection Agency National Centre for Foreign Animal Disease, , Winnipeg, Manitoba R3E 3M4 ,","place":["Canada"]},{"name":"University of Guelph Department of Integrative Biology & Centre for Biodiversity Genomics, , Guelph, Ontario N1G 2W1 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathaniel","family":"Lesperance","sequence":"additional","affiliation":[{"name":"University of Guelph Department of Integrative Biology & Centre for Biodiversity Genomics, , Guelph, Ontario N1G 2W1 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6444-3888","authenticated-orcid":false,"given":"Oksana","family":"Vernygora","sequence":"additional","affiliation":[{"name":"Canadian Food Inspection Agency National Centre for Foreign Animal Disease, , Winnipeg, Manitoba R3E 3M4 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5867-3652","authenticated-orcid":false,"given":"Graham W","family":"Taylor","sequence":"additional","affiliation":[{"name":"University of Guelph School of Engineering, , Guelph, Ontario N1G 2W1 ,","place":["Canada"]},{"name":"Vector Institute , Toronto, Ontario M5G 0C6 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1162-257X","authenticated-orcid":false,"given":"Chad","family":"Laing","sequence":"additional","affiliation":[{"name":"Canadian Food Inspection Agency National Centre for Animal Diseases, , Lethbridge, Alberta T1J 5R7 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3363-6964","authenticated-orcid":false,"given":"David","family":"Lapen","sequence":"additional","affiliation":[{"name":"Agriculture and Agri-Food Canada Science and Technology Branch, , Ottawa, Ontario K1A OC6 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7541-9127","authenticated-orcid":false,"given":"Carson K","family":"Leung","sequence":"additional","affiliation":[{"name":"University of Manitoba Department of Computer Science, , Winnipeg, Manitoba R3T 2N2 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0494-1620","authenticated-orcid":false,"given":"Oliver","family":"Lung","sequence":"additional","affiliation":[{"name":"Canadian Food Inspection Agency National Centre for Foreign Animal Disease, , Winnipeg, Manitoba R3E 3M4 ,","place":["Canada"]},{"name":"University of Manitoba Department of Biological Sciences, , Winnipeg, Manitoba R3T 2N2 ,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,8,29]]},"reference":[{"key":"2025082910100154200_bib1","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1128\/mr.56.1.152-179.1992","article-title":"Evolution and ecology of influenza A viruses","volume":"56","author":"Webster","year":"1992","journal-title":"Microbiol Rev"},{"key":"2025082910100154200_bib2","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1126\/science.1122818","article-title":"Host species barriers to influenza virus infections","volume":"312","author":"Kuiken","year":"2006","journal-title":"Science"},{"key":"2025082910100154200_bib3","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1016\/j.coviro.2012.03.003","article-title":"The role of receptor binding specificity in interspecies transmission of influenza viruses","volume":"2","author":"Imai","year":"2012","journal-title":"Curr Opin Virol"},{"key":"2025082910100154200_bib4","doi-asserted-by":"publisher","first-page":"D49","DOI":"10.1016\/j.vaccine.2008.07.039","article-title":"The biology of influenza viruses","volume":"26","author":"Bouvier","year":"2008","journal-title":"Vaccine"},{"key":"2025082910100154200_bib5","doi-asserted-by":"publisher","first-page":"2225645","DOI":"10.1080\/22221751.2023.2225645","article-title":"Genetic characterization of a new candidate hemagglutinin subtype of influenza A viruses","volume":"12","author":"Fereidouni","year":"2023","journal-title":"Emerg Microbes Infect"},{"key":"2025082910100154200_bib6","doi-asserted-by":"publisher","first-page":"9","DOI":"10.3201\/eid1201.051254","article-title":"Influenza pandemics of the 20th century","volume":"12","author":"Kilbourne","year":"2006","journal-title":"Emerg Infect Dis"},{"key":"2025082910100154200_bib7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4103\/0256-4947.59365","article-title":"The first influenza pandemic of the 21st century","volume":"30","author":"Al Hajjar","year":"2010","journal-title":"Ann Saudi Med"},{"key":"2025082910100154200_bib8","doi-asserted-by":"publisher","first-page":"16936","DOI":"10.1073\/pnas.0608157103","article-title":"Emergence and predominance of an H5N1 influenza variant in China","volume":"103","author":"Smith","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025082910100154200_bib9"},{"key":"2025082910100154200_bib10","doi-asserted-by":"publisher","first-page":"11729","DOI":"10.1038\/s41598-022-13447-z","article-title":"Transatlantic spread of highly pathogenic avian influenza H5N1 by wild birds from Europe to North America in 2021","volume":"12","author":"Caliendo","year":"2022","journal-title":"Sci Rep"},{"key":"2025082910100154200_bib11","article-title":"Status of ongoing avian influenza response by province 2023","author":"CFIA"},{"key":"2025082910100154200_bib12","article-title":"USDA Reported H5N1 Bird Flu Detections in Poultry","volume-title":"Avian Influenza Bird Flu 2025","author":"CDC"},{"key":"2025082910100154200_bib13","article-title":"Egg shortage: as prices climb 15%, stores nationwide begin to ration egg purchases","author":"Bohannon","journal-title":"Forbes"},{"key":"2025082910100154200_bib14","doi-asserted-by":"publisher","first-page":"114479","DOI":"10.1016\/j.celrep.2024.114479","article-title":"Multiple transatlantic incursions of highly pathogenic avian influenza clade 2.3.4.4b A(H5N5) virus into North America and spillover to mammals","volume":"43","author":"Erdelyan","year":"2024","journal-title":"Cell Rep"},{"key":"2025082910100154200_bib15","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1038\/s41586-024-07849-4","article-title":"Spillover of highly pathogenic avian influenza H5N1 virus to dairy cattle","volume":"634","author":"Caserta","year":"2024","journal-title":"Nature"},{"key":"2025082910100154200_bib16","doi-asserted-by":"publisher","first-page":"3055","DOI":"10.1128\/JCM.01388-09","article-title":"Influenza A virus subtyping: paradigm shift in influenza diagnosis","volume":"47","author":"Vinikoor","year":"2009","journal-title":"J Clin Microbiol"},{"key":"2025082910100154200_bib17","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.coviro.2021.03.001","article-title":"Entry of influenza A virus into host cells\u2014recent progress and remaining challenges","volume":"48","author":"Sempere Borau","year":"2021","journal-title":"Curr Opin Virol"},{"key":"2025082910100154200_bib18","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.ajic.2009.12.007","article-title":"Research findings from nonpharmaceutical intervention studies for pandemic influenza and current gaps in the research","volume":"38","author":"Aiello","year":"2010","journal-title":"Am J Infect Control"},{"key":"2025082910100154200_bib19","doi-asserted-by":"publisher","first-page":"e03584","DOI":"10.1128\/spectrum.03584-23","article-title":"Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source","volume":"12","author":"Rudar","year":"2024","journal-title":"Microbiol Spectr"},{"key":"2025082910100154200_bib20","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/1755-8794-7-S3-S1","article-title":"Predicting host tropism of influenza A virus proteins using random forest","volume":"7","author":"Eng","year":"2014","journal-title":"BMC Med Genomics"},{"key":"2025082910100154200_bib21","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.3390\/ijms18061135","article-title":"Predicting zoonotic risk of influenza A viruses from host tropism protein signature using random forest","volume":"18","author":"Eng","year":"2017","journal-title":"Int J Mol Sci"},{"key":"2025082910100154200_bib22","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/s12920-019-0656-7","article-title":"HopPER: an adaptive model for probability estimation of influenza reassortment through host prediction","volume":"13","author":"Yin","year":"2020","journal-title":"BMC Med Genomics"},{"key":"2025082910100154200_bib23","doi-asserted-by":"publisher","first-page":"106351","DOI":"10.1016\/j.prevetmed.2024.106351","article-title":"Utilizing machine learning and hemagglutinin sequences to identify likely hosts of influenza H3Nx viruses","volume":"233","author":"Alberts","year":"2024","journal-title":"Prev Vet Med"},{"key":"2025082910100154200_bib24","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1007\/s42979-023-01839-5","article-title":"MC-NN: an end-to-end multi-channel neural network approach for predicting influenza A virus hosts and antigenic types","volume":"4","author":"Xu","year":"2023","journal-title":"SN Comput Sci"},{"key":"2025082910100154200_bib25","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1093\/bioinformatics\/btaa705","article-title":"VIDHOP, viral host prediction with deep learning","volume":"37","author":"Mock","year":"2021","journal-title":"Bioinformatics"},{"key":"2025082910100154200_bib26","doi-asserted-by":"publisher","first-page":"924","DOI":"10.1007\/s42979-024-03252-y","article-title":"Ensemble learning methods: an empirical study","volume":"5","author":"Sarmah","year":"2024","journal-title":"SN Comput Sci"},{"key":"2025082910100154200_bib27","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/s12859-022-04631-z","article-title":"LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data","volume":"23","author":"Rudar","year":"2022","journal-title":"BMC Bioinf"},{"key":"2025082910100154200_bib28","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random forests","volume":"45","author":"Breiman","year":"2001","journal-title":"Mach Learn"},{"key":"2025082910100154200_bib29","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1016\/S0893-6080(05)80023-1","article-title":"Stacked generalization","volume":"5","author":"Wolpert","year":"1992","journal-title":"Neural Netw"},{"key":"2025082910100154200_bib30","first-page":"6405","article-title":"Simple and scalable predictive uncertainty estimation using deep ensembles","volume-title":"Proceedings of the 31st International Conference on Neural Information Processing Systems","author":"Lakshminarayanan","year":"2017"},{"key":"2025082910100154200_bib31","first-page":"33646","article-title":"Deep ensembles work, but are they necessary?","volume-title":"Proceedings of the 36th International Conference on Neural Information Processing Systems","author":"Abe","year":"2022"},{"key":"2025082910100154200_bib32","first-page":"1929","article-title":"Dropout: a simple way to prevent neural networks from overfitting","volume":"15","author":"Srivastava","year":"2014","journal-title":"J Mach Learn Res"},{"key":"2025082910100154200_bib33","first-page":"6000","article-title":"Attention is all you need","volume-title":"Proceedings of the 31st International Conference on Neural Information Processing Systems","author":"Vaswani","year":"2017"},{"key":"2025082910100154200_bib34","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1701.06538","article-title":"Outrageously large neural networks: the sparsely-gated mixture-of-experts layer","author":"Shazeer","year":"2017","journal-title":"In: Proc. ICLR (Poster)"},{"key":"2025082910100154200_bib35","doi-asserted-by":"publisher","first-page":"30494","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","article-title":"GISAID: global initiative on sharing all influenza data\u2014from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Eurosurveillance"},{"key":"2025082910100154200_bib36","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1186\/s12859-020-3537-3","article-title":"VADR: validation and annotation of virus sequence submissions to GenBank","volume":"21","author":"Sch\u00e4ffer","year":"2020","journal-title":"BMC Bioinf"},{"key":"2025082910100154200_bib37","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1145\/3386052.3386053","article-title":"Rapid detection and prediction of influenza A subtype using deep convolutional neural network based Ensemble learning","volume-title":"In: Proceedings of the 10th International Conference on Bioscience, Biochemistry and Bioinformatics","author":"Wang","year":"2020"},{"key":"2025082910100154200_bib38","doi-asserted-by":"crossref","unstructured":"Avila Cartes J, Anand S, Ciccolella S, et al. \u00a0Accurate and fast clade assignment via deep learning and frequency chaos game representation. Gigascience. 2023;12:giac119. 10.1093\/gigascience\/giac119.","DOI":"10.1093\/gigascience\/giac119"},{"key":"2025082910100154200_bib39","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1093\/bioinformatics\/btz493","article-title":"Deep learning on chaos game representation for proteins","volume":"36","author":"L\u00f6chel","year":"2020","journal-title":"Bioinformatics"},{"key":"2025082910100154200_bib40","doi-asserted-by":"publisher","first-page":"3294","DOI":"10.1093\/bioinformatics\/btz094","article-title":"Biological sequence modeling with convolutional kernel networks","volume":"35","author":"Chen","year":"2019","journal-title":"Bioinformatics"},{"key":"2025082910100154200_bib41","doi-asserted-by":"publisher","first-page":"2163","DOI":"10.1093\/nar\/18.8.2163","article-title":"Chaos game representation of gene structure","volume":"18","author":"Jeffrey","year":"1990","journal-title":"Nucleic Acids Res"},{"key":"2025082910100154200_bib42","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1093\/bioinformatics\/17.5.429","article-title":"Analysis of genomic sequences by Chaos Game Representation","volume":"17","author":"Almeida","year":"2001","journal-title":"Bioinformatics"},{"key":"2025082910100154200_bib43","doi-asserted-by":"publisher","first-page":"1391","DOI":"10.1093\/oxfordjournals.molbev.a026048","article-title":"Genomic signature: characterization and classification of species assessed by chaos game representation of sequences","volume":"16","author":"Deschavanne","year":"1999","journal-title":"Mol Biol Evol"},{"key":"2025082910100154200_bib44","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.gene.2004.10.021","article-title":"The spectrum of genomic signatures: from dinucleotides to chaos game representation","volume":"346","author":"Wang","year":"2005","journal-title":"Gene"},{"key":"2025082910100154200_bib45","volume-title":"complexCGR","author":"Cartes","year":"2025"},{"key":"2025082910100154200_bib46","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1186\/s40246-025-00812-y","article-title":"Flu-CNN: identifying host specificity of Influenza A virus using convolutional networks","volume-title":"Hum Genomics","author":"Hu","year":"2025"},{"key":"2025082910100154200_bib47","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2010.11929","article-title":"An image is worth 16\u00d716 words: transformers for image recognition at scale","volume-title":"In: Proc. ICLR","author":"Dosovitskiy","year":"2021"},{"key":"2025082910100154200_bib48","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1706.10295","article-title":"Noisy networks for exploration","volume-title":"In: Proc. ICLR 2018","author":"Fortunato"},{"key":"2025082910100154200_bib49","doi-asserted-by":"publisher","first-page":"453","DOI":"10.18653\/v1\/2022.findings-aacl.42","article-title":"A simple yet effective learnable positional encoding method for improving document transformer model","volume-title":"Findings of the Association for Computational Linguistics, AACL-IJCNLP.","author":"Wang","year":"2022:"},{"key":"2025082910100154200_bib50","doi-asserted-by":"publisher","first-page":"1405","DOI":"10.1093\/bioinformatics\/btz768","article-title":"Expectation pooling: an effective and interpretable pooling method for predicting DNA\u2013protein binding","volume":"36","author":"Luo","year":"2020","journal-title":"Bioinformatics"},{"key":"2025082910100154200_bib51","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2404.19756","article-title":"KAN: Kolmogorov-Arnold networks","volume-title":"In: Proc. ICLR","author":"Liu","year":"2025"},{"key":"2025082910100154200_bib52","doi-asserted-by":"publisher","first-page":"9204","DOI":"10.48550\/arXiv.2105.08050","article-title":"Pay attention to MLPs","volume-title":"Adv Neural Inf Process Syst","author":"Liu"},{"key":"2025082910100154200_bib53","doi-asserted-by":"publisher","first-page":"5694","DOI":"10.48550\/arXiv.2403.19967","volume-title":"Rewrite the stars. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition","author":"Ma","year":"2024"},{"key":"2025082910100154200_bib54","doi-asserted-by":"publisher","first-page":"24261","DOI":"10.48550\/arXiv.2105.01601","article-title":"MLP-mixer: an all-MLP architecture for vision","volume-title":"Proceedings of the 35th International Conference on Neural Information Processing Systems","author":"Tolstikhin","year":"2024"},{"key":"2025082910100154200_bib55","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2404.15045","volume-title":"Multi-head mixture-of-experts","author":"Wu","year":"2024"},{"key":"2025082910100154200_bib56","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2202.08906","volume-title":"ST-MoE: designing stable and transferable sparse expert models","author":"Zoph","year":"2022"},{"key":"2025082910100154200_bib57","doi-asserted-by":"publisher","DOI":"10.18653\/v1\/2022.naacl-main.319","article-title":"FNet: mixing tokens with Fourier transforms","author":"Lee-Thorp","journal-title":"Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies"},{"key":"2025082910100154200_bib58","doi-asserted-by":"publisher","first-page":"3530","DOI":"10.1109\/WACV48630.2021.00357","article-title":"Efficient attention: attention with linear complexities","volume-title":"In: 2021 IEEE Winter Conference on Applications of Computer Vision (WACV)","author":"Zhuoran","year":"2021"},{"key":"2025082910100154200_bib59","doi-asserted-by":"publisher","first-page":"12381","DOI":"10.48550\/arXiv.1910.07467","article-title":"Root mean square layer normalization","volume-title":"In: Proceedings of the 33rd International Conference on Neural Information Processing Systems","author":"Zhang","year":"2019"},{"key":"2025082910100154200_bib60","doi-asserted-by":"publisher","author":"Guibas","year":"2022","DOI":"10.48550\/arXiv.2111.13587"},{"key":"2025082910100154200_bib61","volume-title":"Fundamentals of molecular evolution. 2nd edition","author":"Graur","year":"2000."},{"key":"2025082910100154200_bib62","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1145\/3524086.3524094","article-title":"An introduction to wavelet analysis with applications to image and JPEG 2000","volume-title":"In: 2022 4th International Conference on Intelligent Medicine and Image Processing","author":"Chen","year":"2022"},{"key":"2025082910100154200_bib63","volume-title":"Insight into wavelets from theory to practice. 2nd ed","author":"Soman","year":"2005"},{"key":"2025082910100154200_bib64","doi-asserted-by":"publisher","author":"Cotter","year":"2020.","DOI":"10.17863\/CAM.53748"},{"key":"2025082910100154200_bib65","doi-asserted-by":"publisher","first-page":"104740","DOI":"10.1016\/j.biosystems.2022.104740","article-title":"Dive into machine learning algorithms for influenza virus host prediction with hemagglutinin sequences","volume":"220","author":"Xu","year":"2022","journal-title":"Biosystems"},{"key":"2025082910100154200_bib66","doi-asserted-by":"publisher","first-page":"e2016239118","DOI":"10.1073\/pnas.2016239118","article-title":"Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences","volume":"118","author":"Rives","year":"2021","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025082910100154200_bib67","author":"Sunde","year":"2025"},{"key":"2025082910100154200_bib68","doi-asserted-by":"publisher","first-page":"1","DOI":"10.48550\/arXiv.1606.04316","article-title":"Time for a change: a tutorial for comparing multiple classifiers through Bayesian analysis","volume":"18","author":"Benavoli","year":"2017","journal-title":"J Mach Learn Res"},{"key":"2025082910100154200_bib69","author":"Dem\u0161ar","year":"2025"},{"key":"2025082910100154200_bib70","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1007\/978-3-030-58452-8_37","article-title":"Gradient centralization: a new optimization technique for deep neural networks","volume-title":"In: Computer Vision\u2014ECCV 2020 16th European Conference, Glasgow, UK, August 23\u201328 2020: Proceedings Part I","author":"Yong","year":"2020"},{"key":"2025082910100154200_bib71","doi-asserted-by":"publisher","first-page":"9597","DOI":"10.48550\/arXiv.1907.08610","article-title":"Lookahead optimizer: k steps forward, 1 step back","volume-title":"In: 33rd International Conference on Neural Information Processing Systems","author":"Zhang","year":"2019"},{"key":"2025082910100154200_bib72","author":"Misra","year":"2020"},{"key":"2025082910100154200_bib73","doi-asserted-by":"publisher","author":"Hendrycks","year":"2023","DOI":"10.48550\/arXiv.1606.08415"},{"key":"2025082910100154200_bib74","doi-asserted-by":"publisher","author":"Agarap","year":"2019","DOI":"10.48550\/arXiv.1803.08375"},{"key":"2025082910100154200_bib75","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinf"},{"key":"2025082910100154200_bib76","doi-asserted-by":"publisher","first-page":"baae091","DOI":"10.1093\/database\/baae091","article-title":"Influenza sequence validation and annotation using VADR","volume":"2024","author":"Calhoun","year":"2024","journal-title":"Database"},{"key":"2025082910100154200_bib77","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2025082910100154200_bib78","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2025082910100154200_bib79","doi-asserted-by":"publisher","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol"},{"key":"2025082910100154200_bib80","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1093\/molbev\/msi103","article-title":"Bayesian coalescent inference of past population dynamics from molecular sequences","volume":"22","author":"Drummond","year":"2005","journal-title":"Mol Biol Evol"},{"key":"2025082910100154200_bib81","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1093\/genetics\/161.3.1307","article-title":"Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data","volume":"161","author":"Drummond","year":"2002","journal-title":"Genetics"},{"key":"2025082910100154200_bib82","doi-asserted-by":"publisher","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","article-title":"Relaxed phylogenetics and dating with confidence","volume":"4","author":"Drummond","year":"2006","journal-title":"PLoS Biol"},{"key":"2025082910100154200_bib83","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in bayesian phylogenetics using tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst Biol"},{"key":"2025082910100154200_bib84","author":"FigTree"},{"key":"2025082910100154200_bib85","author":"Developers"},{"key":"2025082910100154200_bib86","unstructured":"Rudar J, Lung O. TrinomialTest. 2025. 10.5281\/zenodo.15353378. Accessed 08 May 2025."},{"key":"2025082910100154200_bib87","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.1016\/j.matcom.2010.11.002","article-title":"A trinomial test for paired data when there are many ties","volume":"81","author":"Bian","year":"2011","journal-title":"Math Comput Simul"},{"key":"2025082910100154200_bib88","doi-asserted-by":"publisher","first-page":"2300107","DOI":"10.2807\/1560-7917.ES.2023.28.8.2300107","article-title":"Influenza A(H5N1) detection in two asymptomatic poultry farm workers in Spain, September to October 2022: suspected environmental contamination","volume":"28","author":"Aznar","year":"2023","journal-title":"Eurosurveillance"},{"key":"2025082910100154200_bib89","doi-asserted-by":"publisher","first-page":"6817","DOI":"10.1038\/s41467-022-34601-1","article-title":"Human infection with a reassortment avian influenza A H3N8 virus: an epidemiological investigation study","volume":"13","author":"Bao","year":"2022","journal-title":"Nat Commun"},{"key":"2025082910100154200_bib90","author":"Avian Influenza A(H5N1)\u2014Viet Nam"},{"key":"2025082910100154200_bib91","doi-asserted-by":"publisher","first-page":"e8930","DOI":"10.2903\/j.efsa.2024.8930","article-title":"Avian influenza overview March\u2013June 2024","volume":"22","author":"European Food Safety Authority","year":"2024","journal-title":"EFSmA J"},{"key":"2025082910100154200_bib92","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s44298-024-00042-4","article-title":"Reverse zoonosis of the 2022\u20132023 human seasonal H3N2 detected in swine","volume":"2","author":"Zeller","year":"2024","journal-title":"NPJ Viruses"},{"key":"2025082910100154200_bib93","doi-asserted-by":"publisher","first-page":"e2301926120","DOI":"10.1073\/pnas.2301926120","article-title":"The genomic landscape of swine influenza A viruses in Southeast Asia","volume":"120","author":"Zeller","year":"2023","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025082910100154200_bib94","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1038\/s41586-024-08166-6","article-title":"Dairy cows inoculated with highly pathogenic avian influenza virus H5N1","volume":"637","author":"Baker","year":"2025","journal-title":"Nature"},{"key":"2025082910100154200_bib95","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1071\/WR14229","article-title":"Human\u2013wildlife interactions in urban areas: a review of conflicts, benefits and opportunities","volume":"42","author":"Soulsbury","year":"2015","journal-title":"Wildl Res"},{"key":"2025082910100154200_bib96","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1111\/mam.12182","article-title":"A systematic review of adaptive wildlife management for the control of invasive, non-native mammals, and other human\u2013wildlife conflicts","volume":"50","author":"Richardson","year":"2020","journal-title":"Mammal Rev"},{"key":"2025082910100154200_bib97","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1126\/science.1176225","article-title":"Antigenic and genetic characteristics of Swine-origin 2009 A(H1N1) influenza viruses circulating in humans","volume":"325","author":"Garten","year":"2009","journal-title":"Science"},{"key":"2025082910100154200_bib98","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1016\/S0140-6736(20)30251-8","article-title":"Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding","volume":"395","author":"Lu","year":"2020","journal-title":"Lancet"},{"key":"2025082910100154200_bib99","doi-asserted-by":"publisher","first-page":"1847","DOI":"10.3390\/ijms23031847","article-title":"Fractal analysis of DNA sequences using frequency chaos game representation and small-angle scattering","volume":"23","author":"Anitas","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2025082910100154200_bib100","doi-asserted-by":"publisher","first-page":"312","DOI":"10.3390\/fractalfract8060312","article-title":"Multifractal properties of human chromosome sequences","volume":"8","author":"Correia","year":"2024","journal-title":"Fractal Fract"},{"key":"2025082910100154200_bib101","doi-asserted-by":"publisher","first-page":"3082","DOI":"10.1038\/s41467-023-38415-7","article-title":"Rapid evolution of A(H5N1) influenza viruses after intercontinental spread to North America","volume":"14","author":"Kandeil","year":"2023","journal-title":"Nat Commun"},{"key":"2025082910100154200_bib102","doi-asserted-by":"publisher","first-page":"11563","DOI":"10.1038\/s41598-024-62585-z","article-title":"Applying oversampling before cross-validation will lead to high bias in radiomics","volume":"14","author":"Demircio\u011flu","year":"2024","journal-title":"Sci Rep"},{"key":"2025082910100154200_bib103","doi-asserted-by":"publisher","first-page":"4171","DOI":"10.18653\/v1\/N19-1423","article-title":"BERT: pre-training of deep bidirectional transformers for language understanding","volume-title":"Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers)","author":"Devlin","year":"2019"},{"key":"2025082910100154200_bib104","doi-asserted-by":"publisher","first-page":"2112","DOI":"10.1093\/bioinformatics\/btab083","article-title":"DNABERT: pre-trained bidirectional encoder representations from transformers model for DNA-language in genome","volume":"37","author":"Ji","year":"2021","journal-title":"Bioinformatics"},{"key":"2025082910100154200_bib105","doi-asserted-by":"publisher","first-page":"9733","DOI":"10.1128\/jvi.00694-10","article-title":"Viral mutation rates","volume":"84","author":"Sanju\u00e1n","year":"2010","journal-title":"J Virol"},{"key":"2025082910100154200_bib106","doi-asserted-by":"publisher","first-page":"13269","DOI":"10.1128\/jvi.01636-14","article-title":"Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom","volume":"88","author":"Elderfield","year":"2014","journal-title":"J Virol"},{"key":"2025082910100154200_bib107","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1016\/j.chom.2010.05.009","article-title":"Influenza virus evolution, host adaptation, and pandemic formation","volume":"7","author":"Taubenberger","year":"2010","journal-title":"Cell Host Microbe"},{"key":"2025082910100154200_bib108","doi-asserted-by":"publisher","first-page":"4768","DOI":"10.48550\/arXiv.1705.07874","article-title":"A unified approach to interpreting model predictions","volume-title":"Adv Neural Inf Process Syst","author":"Lundberg","year":"2017"},{"key":"2025082910100154200_bib109","unstructured":"Kruczkiewicz P, Nguyen HH, Meknas A, et al. \u00a0CFIA-NCFAD\/nf-flu: 3.7.0. 2025. 10.5281\/zenodo.14728750. Accessed 19 February 2025."},{"key":"2025082910100154200_bib110","doi-asserted-by":"publisher","first-page":"603","DOI":"10.3390\/cancers12030603","article-title":"The application of deep learning in cancer prognosis prediction","volume":"12","author":"Zhu","year":"2020","journal-title":"Cancers"},{"key":"2025082910100154200_bib111","doi-asserted-by":"publisher","first-page":"1199087","DOI":"10.3389\/fgene.2023.1199087","article-title":"A review of multi-omics data integration through deep learning approaches for disease diagnosis, prognosis, and treatment","volume":"14","author":"Wekesa","year":"2023","journal-title":"Front Genet"},{"key":"2025082910100154200_bib112","doi-asserted-by":"crossref","unstructured":"Nguyen H, Rudar J, Lesperance N, et al. \u00a0Supporting data for \u201cWaveSeekerNet: Accurate Prediction of Influenza A Virus Subtypes and Host Source Using Attention-Based Deep Learning.\u201d \u00a0GigaScience Database. 2025. 10.5524\/102732.","DOI":"10.1101\/2025.02.25.639900"},{"key":"2025082910100154200_bib113","doi-asserted-by":"crossref","DOI":"10.1101\/2025.02.25.639900","article-title":"WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning","author":"Nguyen","year":"2025"},{"key":"2025082910100154200_bib114","article-title":"WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning [Computer software]","author":"Nguyen","year":"2025.","journal-title":"Software Heritage"}],"container-title":["GigaScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/doi\/10.1093\/gigascience\/giaf089\/64161817\/giaf089.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/doi\/10.1093\/gigascience\/giaf089\/64161817\/giaf089.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T14:10:13Z","timestamp":1756476613000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gigascience\/article\/doi\/10.1093\/gigascience\/giaf089\/8244095"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":114,"URL":"https:\/\/doi.org\/10.1093\/gigascience\/giaf089","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.02.25.639900","asserted-by":"object"}]},"ISSN":["2047-217X"],"issn-type":[{"value":"2047-217X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"giaf089"}}