Machine learning pedagogy to support the research community

Abstract

Machine learning methods are increasingly leveraged in disparate domains of research. Herein, we describe our curriculum design to introduce undergraduate students to applied research through a series of course assignments and a competition among peers to inspire other educators. We describe the overall course structure and detail how the assignments were tailored to a selected open research question while developing student understanding of machine learning. We outline the lessons learned from this new undergraduate curriculum design and describe how it may be adapted to similar courses. For the selected COVID19-related course-long problem of predicting which drugs might interact with specific proteins, we leveraged state-of-the-art tools for representing drug and protein sequences. We challenged students to develop unique solutions competitive with a current state-of-the-art model using reproducible Notebooks and cloud-based computing resources with the expectation that top-ranking solutions would be used to predict novel druggable targets within the SARS-CoV-2 proteome to possibly treat COVID19 patients. We motivate this curriculum design based on related competition frameworks that have led to notable research advancements and contributed to machine learning pedagogy. From our experience, the top student solutions were ultimately combined using a stacked classifier to create a publishable solution representing an actual research contribution. We highly recommend introducing undergraduate students to open research applications early in their program to encourage them to consider pursuing a career in research.