Jessica Gronsbell

Jessica Gronsbell, Vidul Ayakulangara Panickan, Chris Lin et al.

Integrative analysis of multi-institutional Electronic Health Record (EHR) data enhances the reliability and generalizability of translational research by leveraging larger, more diverse patient cohorts and incorporating multiple data modalities. However, harmonizing EHR data across institutions poses major challenges due to data heterogeneity, semantic differences, and privacy concerns. To address these challenges, we introduce $\textit{PEHRT}$, a standardized pipeline for efficient EHR data harmonization consisting of two core modules: (1) data pre-processing and (2) representation learning. PEHRT maps EHR data to standard coding systems and uses advanced machine learning to generate research-ready datasets without requiring individual-level data sharing. Our pipeline is also data model agnostic and designed for streamlined execution across institutions based on our extensive real-world experience. We provide a complete suite of open source software, accompanied by a user-friendly tutorial, and demonstrate the utility of PEHRT in a variety of tasks using data from diverse healthcare systems.

Jessica Gronsbell, Jianhui Gao, Yaqi Shi et al.

From structural biology to epidemiology, predictions from machine learning (ML) models increasingly complement costly gold-standard data to enable faster, more affordable, and scalable scientific inquiry. In response, prediction-based (PB) inference has emerged to accommodate statistical analysis using a large volume of predictions together with a small amount of gold-standard data. The goals of PB inference are two-fold: (i) to mitigate bias from errors in predictions and (ii) to improve efficiency relative to classical inference using only the gold-standard data. While early PB inference methods focused on bias, their ability to enhance efficiency remains a focus of ongoing research. We revisit a foundational PB inference method and show that a simple modification can be applied to guarantee provable improvements in efficiency. In doing so, we establish new connections between augmented inverse probability weighted estimators (AIPW) and several recently proposed PB inference methods with a similar focus. The utility of our proposal, which leverages prediction-based outcomes to enhance efficiency, is demonstrated through extensive simulation studies and an application to real data from the UK Biobank. Further, we contextualize PB inference by drawing connections to historical literature from economics and statistics, highlighting how classic methods directly inform this contemporary problem.

Jianhui Gao, Benson Chou, Zachary R. McCaw et al.

Ensuring that machine learning (ML) models are safe, effective, and equitable across all patients is critical for clinical decision-making and for preventing the amplification of existing health disparities. In this work, we examine how fairness is conceptualized in ML for health, including why ML models may lead to unfair decisions and how fairness has been measured in diverse real-world applications. We review commonly used fairness notions within group, individual, and causal-based frameworks. We also discuss the outlook for future research and highlight opportunities and challenges in operationalizing fairness in health-focused applications.

Jessica Gronsbell, Molei Liu, Lu Tian et al.

In many contemporary applications, large amounts of unlabeled data are readily available while labeled examples are limited. There has been substantial interest in semi-supervised learning (SSL) which aims to leverage unlabeled data to improve estimation or prediction. However, current SSL literature focuses primarily on settings where labeled data is selected randomly from the population of interest. Non-random sampling, while posing additional analytical challenges, is highly applicable to many real world problems. Moreover, no SSL methods currently exist for estimating the prediction performance of a fitted model under non-random sampling. In this paper, we propose a two-step SSL procedure for evaluating a prediction rule derived from a working binary regression model based on the Brier score and overall misclassification rate under stratified sampling. In step I, we impute the missing labels via weighted regression with nonlinear basis functions to account for nonrandom sampling and to improve efficiency. In step II, we augment the initial imputations to ensure the consistency of the resulting estimators regardless of the specification of the prediction model or the imputation model. The final estimator is then obtained with the augmented imputations. We provide asymptotic theory and numerical studies illustrating that our proposals outperform their supervised counterparts in terms of efficiency gain. Our methods are motivated by electronic health records (EHR) research and validated with a real data analysis of an EHR-based study of diabetic neuropathy.