Lost in the Forest

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dc.citation.volumePreprint
dc.contributor.authorSmith HL
dc.contributor.authorBiggs PJ
dc.contributor.authorFrench NP
dc.contributor.authorSmith ANH
dc.contributor.authorMarshall JC
dc.date.accessioned2023-11-17T01:55:57Z
dc.date.accessioned2023-11-20T01:37:38Z
dc.date.available2022-09-19
dc.date.available2023-11-17T01:55:57Z
dc.date.available2023-11-20T01:37:38Z
dc.date.issued2022
dc.description.abstractTo date, there remains no satisfactory solution for absent levels in random forest models. Absent levels are levels of a predictor variable encountered during prediction for which no explicit rule exists. Imposing an order on nominal predictors allows absent levels to be integrated and used for prediction. The ordering of predictors has traditionally been via class probabilities with absent levels designated the lowest order. Using a combination of simulated data and pathogen source-attribution models using whole-genome sequencing data, we examine how the method of ordering predictors with absent levels can (i) systematically bias a model, and (ii) affect the out-of-bag error rate. We show that the traditional approach is systematically biased and underestimates out-of-bag error rates, and that this bias is resolved by ordering absent levels according to the a priori hypothesis of equal class probability. We present a novel method of ordering predictors via principal coordinates analysis (PCO) which capitalizes on the similarity between pairs of predictor levels. Absent levels are designated an order according to their similarity to each of the other levels in the training data. We show that the PCO method performs at least as well as the traditional approach of ordering and is not biased.
dc.description.confidentialfalse
dc.identifier.citationSmith H, Biggs P, French N, Smith A, Marshall J. (2022). Lost in the Forest. BioRxiv. Preprint.
dc.identifier.doi10.1101/2022.09.12.507676
dc.identifier.elements-typejournal-article
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/69115
dc.languageEnglish
dc.publisherCold Spring Harbor Laboratory
dc.publisher.urihttps://www.biorxiv.org/content/10.1101/2022.09.12.507676v2
dc.relation.isPartOfBioRxiv
dc.rightsCC BY-NC-ND 4.0
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectAbsent levels
dc.subjectCampylobacter
dc.subjectcategorical predictors
dc.subjectclassification
dc.subjectdecision trees
dc.subjectout-of-bag error
dc.subjectprincipal co-ordinates analysis
dc.subjectrandom forest
dc.subjectsource attribution
dc.subjectwhole genome sequencing data
dc.titleLost in the Forest
dc.typeJournal article
pubs.elements-id457987
pubs.organisational-groupOther
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