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arXiv · 2010.14026

Sequential knockoffs for continuous and categorical predictors: with application to a large Psoriatic Arthritis clinical trial pool

Matthias Kormaksson·Luke J. Kelly·Xuan Zhu·Sibylle Haemmerle·Luminita Pricop·David Ohlssen
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Abstract

Knockoffs provide a general framework for controlling the false discovery rate when performing variable selection. Much of the Knockoffs literature focuses on theoretical challenges and we recognize a need for bringing some of the current ideas into practice. In this paper we propose a sequential algorithm for generating knockoffs when underlying data consists of both continuous and categorical (factor) variables. Further, we present a heuristic multiple knockoffs approach that offers a practical assessment of how robust the knockoff selection process is for a given data set. We conduct extensive simulations to validate performance of the proposed methodology. Finally, we demonstrate the utility of the methods on a large clinical data pool of more than $2,000$ patients with psoriatic arthritis evaluated in 4 clinical trials with an IL-17A inhibitor, secukinumab (Cosentyx), where we determine prognostic factors of a well established clinical outcome. The analyses presented in this paper could provide a wide range of applications to commonly encountered data sets in medical practice and other fields where variable selection is of particular interest.

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Matthias Kormaksson, Luke J. Kelly, Xuan Zhu, Sibylle Haemmerle, Luminita Pricop, David Ohlssen. 2020-10-27. Sequential knockoffs for continuous and categorical predictors: with application to a large Psoriatic Arthritis clinical trial pool. https://arxiv.org/abs/2010.14026

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