Accepted Papers

A permutation approach to assess confounding in machine learning applications for digital health

Elias Chaibub Neto (Sage Bionetworks);Abhishek Pratap (Sage Bionetworks);Thanneer Perumal (Sage Bionetworks);Meghasyam Tummalacherla (Sage Bionetworks);Brian Bot (Sage Bionetworks);Lara Mangravite (Sage Bionetworks);Larsson Omberg (Sage Bionetworks);


Machine learning applications are often plagued with confounders that can impact the generalizability of the learners. In clinical settings, demographic characteristics often play the role of confounders. Confounding is especially problematic in remote digital health studies where the participants self-select to enter the study, thereby making it difficult to balance the demographic characteristics of participants. One effective approach to combat confounding is to match samples with respect to the confounding variables in order to improve the balance of the data. This procedure, however, leads to smaller datasets and hence negatively impact the inferences drawn from the learners. Alternatively, confounding adjustment methods that make more efficient use of the data (such as inverse probability weighting) usually rely on modeling assumptions, and it is unclear how robust these methods are to violations of these assumptions. Here, instead of proposing a new method to control for confounding, we develop novel permutation based statistical tools to detect and quantify the influence of observed confounders, and estimate the unconfounded performance of the learner. Our tools can be used to evaluate the effectiveness of existing confounding adjustment methods. We evaluate the statistical properties of our methods in a simulation study, and illustrate their application using real-life data from a Parkinson’s disease mobile health study collected in an uncontrolled environment.

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