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Previously we developed Lilikoi, a personalized pathway-based method to classify diseases using metabolomics data. Given the new trends of computation in the metabolomics field, here we report the next version of Lilikoi as a significant upgrade. The new Lilikoi v2.0 R package has implemented a deep-learning method for classification, in addition to popular machine learning methods. It also has several new modules, including the most significant addition of prognosis prediction, implemented bydoi:10.1101/2020.07.09.195677 fatcat:op2s5dl6bzcypiwng2x4licy4i