Epistasis Blog

From the Computational Genetics Laboratory at the University of Pennsylvania (www.epistasis.org)

Wednesday, September 09, 2020

Evaluating recommender systems for AI-driven biomedical informatics

La Cava W, Williams H, Fu W, Vitale S, Srivatsan D, Moore JH. Evaluating recommender systems for AI-driven biomedical informatics. Bioinformatics. 2020 Aug 7:btaa698. doi: 10.1093/bioinformatics/btaa698. Epub ahead of print. PMID: 32766825. [PubMed] [Bioinformatics]

Abstract

Motivation: Many researchers with domain expertise are unable to easily apply machine learning to their bioinformatics data due to a lack of machine learning and/or coding expertise. Methods that have been proposed thus far to automate machine learning mostly require programming experience as well as expert knowledge to tune and apply the algorithms correctly. Here, we study a method of automating biomedical data science using a web-based platform that uses AI to recommend model choices and conduct experiments. We have two goals in mind: first, to make it easy to construct sophisticated models of biomedical processes; and second, to provide a fully automated AI agent that can choose and conduct promising experiments for the user, based on the user's experiments as well as prior knowledge. To validate this framework, we experiment with hundreds of classification problems, comparing to state-of-the-art, automated approaches. Finally, we use this tool to develop predictive models of septic shock in critical care patients.

Results: We find that matrix factorization-based recommendation systems outperform meta-learning methods for automating machine learning. This result mirrors the results of earlier recommender systems research in other domains. The proposed AI is competitive with state-of-the-art automated machine learning methods in terms of choosing optimal algorithm configurations for datasets. In our application to prediction of septic shock, the AI-driven analysis produces a competent machine learning model (AUROC 0.85 +/- 0.02) that performs on par with state-of-the-art deep learning results for this task, with much less computational effort.

Availability: PennAI is available free of charge and open-source. It is distributed under the GNU public license (GPL) version 3.

Supplementary information: Software and experiments are available from epistasislab.github.io/pennai.

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