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The relationship between Precision-Recall and ROC curves. In: Proceedings of the 23rd international conference on Machine learning. New York, NY, USA: ACM; 2006. p. 233\u2013240.","DOI":"10.1145\/1143844.1143874"},{"issue":"3","key":"ref38","doi-asserted-by":"crossref","first-page":"e92209","DOI":"10.1371\/journal.pone.0092209","article-title":"Area under precision-recall curves for weighted and unweighted data","volume":"9","author":"J Keilwagen","year":"2014","journal-title":"PLOS ONE"},{"issue":"367","key":"ref39","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1080\/01621459.1979.10481670","article-title":"Using weighted rankings in the analysis of complete blocks with additive block effects","volume":"74","author":"D Quade","year":"1979","journal-title":"J Am Stat Assoc"},{"key":"ref40","unstructured":"R Core Team. R: A language and environment for statistical computing; 2018. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.R-project.org\" xlink:type=\"simple\">https:\/\/www.R-project.org<\/ext-link>."},{"key":"ref41","doi-asserted-by":"crossref","unstructured":"Pohlert T. PMCMRplus: calculate pairwise multiple comparisons of mean rank sums Extended; 2018. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/CRAN.R-project.org\/package=PMCMRplus\" xlink:type=\"simple\">https:\/\/CRAN.R-project.org\/package=PMCMRplus<\/ext-link>.","DOI":"10.32614\/CRAN.package.PMCMRplus"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nbt.3535","article-title":"Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity","volume":"34","author":"JV Bredeson","year":"2016","journal-title":"Nat Biotech"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/nbt.2906","article-title":"Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication","volume":"32","author":"GA Wu","year":"2014","journal-title":"Nat Biotech"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1038\/nature11798","article-title":"Repeated polyploidization of <italic>Gossypium<\/italic> genomes and the evolution of spinnable cotton fibres","volume":"492","author":"AH Paterson","year":"2012","journal-title":"Nature"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/nature11119","article-title":"The tomato genome sequence provides insights into fleshy fruit evolution","volume":"485","year":"2012","journal-title":"Nature"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/ng.2877","article-title":"Genome sequence of the hot pepper provides insights into the evolution of pungency in <italic>Capsicum<\/italic> species","volume":"46","author":"S Kim","year":"2014","journal-title":"Nat Genet"},{"issue":"5850","key":"ref47","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1126\/science.1144956","article-title":"A bacterial effector acts 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