{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T13:24:27Z","timestamp":1769520267133,"version":"3.49.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,7,2]],"date-time":"2019-07-02T00:00:00Z","timestamp":1562025600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Natural Sciences and Engineering Research Council Discovery"},{"name":"Natural Sciences and Engineering Research Council Post Doctoral Fellowship"},{"DOI":"10.13039\/501100001804","name":"Canada Research Chair","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001804","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>HIV is difficult to treat because its virus mutates at a high rate and mutated viruses easily develop resistance to existing drugs. If the relationships between mutations and drug resistances can be determined from historical data, patients can be provided personalized treatment according to their own mutation information. The HIV Drug Resistance Database was built to investigate the relationships. Our goal is to build a model using data in this database, which simultaneously predicts the resistance of multiple drugs using mutation information from sequences of viruses for any new patient.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We propose two variations of a stacking algorithm which borrow information among multiple prediction tasks to improve multivariate prediction performance. The most attractive feature of our proposed methods is the flexibility with which complex multivariate prediction models can be constructed using any univariate prediction models. Using cross-validation studies, we show that our proposed methods outperform other popular multivariate prediction methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>An R package is being developed. In the meantime, R code can be requested by email.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz531","type":"journal-article","created":{"date-parts":[[2019,6,28]],"date-time":"2019-06-28T11:08:57Z","timestamp":1561720137000},"page":"65-72","source":"Crossref","is-referenced-by-count":26,"title":["Simultaneous prediction of multiple outcomes using revised stacking algorithms"],"prefix":"10.1093","volume":"36","author":[{"given":"Li","family":"Xing","sequence":"first","affiliation":[{"name":"Department of Mathematics and Statistics, University of Saskatchewan , Saskatoon, SK S7N 5E6, Canada"}]},{"given":"Mary L","family":"Lesperance","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Victoria , Victoria, BC V8W 2Y2, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4728-2343","authenticated-orcid":false,"given":"Xuekui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, University of Victoria , Victoria, BC V8W 2Y2, Canada"}]}],"member":"286","published-online":{"date-parts":[[2019,7,2]]},"reference":[{"key":"2023013109505886300_btz531-B1","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1613\/jair.731","article-title":"A model of inductive bias learning","volume":"12","author":"Baxter","year":"2000","journal-title":"J. Artif. Intell. Res"},{"key":"2023013109505886300_btz531-B2","volume-title":"Classification and Regression Trees","author":"Breiman","year":"1984"},{"key":"2023013109505886300_btz531-B14","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1023\/A:1007379606734","article-title":"Multitask learning","volume":"28","author":"Caruana","year":"1997","journal-title":"Mach. Learn"},{"key":"2023013109505886300_btz531-B3","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.meegid.2016.08.031","article-title":"HIV-1 drug resistance and resistance testing","volume":"46","author":"Clutter","year":"2016","journal-title":"Infect. Genet. Evol"},{"key":"2023013109505886300_btz531-B4","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1214\/009053604000000067","article-title":"Least angle regression","volume":"32","author":"Efron","year":"2004","journal-title":"Ann. Stat"},{"key":"2023013109505886300_btz531-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v033.i01","article-title":"Regularization paths for generalized linear models via coordinate descent","volume":"33","author":"Friedman","year":"2010","journal-title":"J. Stat. Software"},{"key":"2023013109505886300_btz531-B6","doi-asserted-by":"crossref","first-page":"1946","DOI":"10.1093\/bioinformatics\/btt331","article-title":"Multilabel classification for exploiting cross-resistance information in HIV-1 drug resistance prediction","volume":"29","author":"Heider","year":"2013","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023013109505886300_btz531-B9","doi-asserted-by":"crossref","first-page":"14.","DOI":"10.1186\/1756-0381-7-14","article-title":"A simple structure-based model for the prediction of HIV-1 co-receptor tropism","volume":"7","author":"Heider","year":"2014","journal-title":"BioData Min"},{"key":"2023013109505886300_btz531-B7","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nature14539","article-title":"Deep learning","volume":"521","author":"LeCun","year":"2015","journal-title":"Nature"},{"key":"2023013109505886300_btz531-B8","author":"Leisch","year":"2010"},{"key":"2023013109505886300_btz531-B10","first-page":"90","volume-title":"10th International Conference on Machine Learning and Applications and Workshops","author":"Pierce","year":"2011"},{"key":"2023013109505886300_btz531-B11","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/s10994-011-5256-5","article-title":"Classifier chains for multi-label classification","volume":"85","author":"Read","year":"2011","journal-title":"Mach. Learn"},{"key":"2023013109505886300_btz531-B12","doi-asserted-by":"crossref","first-page":"17355","DOI":"10.1073\/pnas.0607274103","article-title":"Genotypic predictors of human immunodeficiency virus type 1 drug resistance","volume":"103","author":"Rhee","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023013109505886300_btz531-B13","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511812651","volume-title":"Pattern Recognition and Neural Networks","author":"Ripley","year":"1996"},{"key":"2023013109505886300_btz531-B15","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1159\/000331998","article-title":"The HIVdb system for HIV-1 genotypic resistance interpretation","volume":"55","author":"Tang","year":"2012","journal-title":"Intervirology"},{"key":"2023013109505886300_btz531-B16","first-page":"640","article-title":"Is learning the n-th thing any easier than learning the first?","volume":"8","author":"Thrun","year":"1996","journal-title":"Adv. Neural Inf. Process. Syst"},{"key":"2023013109505886300_btz531-B17","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1111\/j.1467-9868.2011.01004.x","article-title":"Strong rules for discarding predictors in lasso-type problems","volume":"74","author":"Tibshirani","year":"2012","journal-title":"J. R. Stat. Soc. Ser. B. Stat. Method"},{"key":"2023013109505886300_btz531-B18","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/S0893-6080(05)80023-1","article-title":"Stacked generalization","volume":"5","author":"Wolpert","year":"1992","journal-title":"Neural Networks"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz531\/28982125\/btz531.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/1\/65\/48981723\/bioinformatics_36_1_65.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/1\/65\/48981723\/bioinformatics_36_1_65.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:33:39Z","timestamp":1675190019000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/1\/65\/5526872"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,7,2]]},"references-count":18,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz531","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,1,1]]},"published":{"date-parts":[[2019,7,2]]}}}