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This paper highlights the current literatures in usability studies, performance metrics and machine learning algorithm. A literature review is done in these three areas of studies to find a research gap that can be explored further. The paper will then propose a research methodology to attend to the issues of machine learning and usability. An experiment is proposed to compare the efficiency results in between data consistency, correlation between performance metrics and self-reported metrics of a Mobile Augmented Reality learning application. The methodology proposes hierarchical agglomerative clustering technique as a solution in differentiating usability issues according to priority in order to help with usability re-engineering decisions. This paper proposes two objectives through the proposed framework and present evidence on how to achieve them. Lastly, this paper will discuss the results, conclusion and future works of the proposed study.