Ashley Beecy

Hyun Gi Lee, Evan Sholle, Ashley Beecy et al.

Utilizing clinical texts in survival analysis is difficult because they are largely unstructured. Current automatic extraction models fail to capture textual information comprehensively since their labels are limited in scope. Furthermore, they typically require a large amount of data and high-quality expert annotations for training. In this work, we present a novel method of using BERT-based hidden layer representations of clinical texts as covariates for proportional hazards models to predict patient survival outcomes. We show that hidden layers yield notably more accurate predictions than predefined features, outperforming the previous baseline model by 5.7% on average across C-index and time-dependent AUC. We make our work publicly available at https://github.com/bionlplab/heart_failure_mortality.

Erica Chiang, Divya Shanmugam, Ashley N. Beecy et al.

Disease progression models are widely used to inform the diagnosis and treatment of many progressive diseases. However, a significant limitation of existing models is that they do not account for health disparities that can bias the observed data. To address this, we develop an interpretable Bayesian disease progression model that captures three key health disparities: certain patient populations may (1) start receiving care only when their disease is more severe, (2) experience faster disease progression even while receiving care, or (3) receive follow-up care less frequently conditional on disease severity. We show theoretically and empirically that failing to account for any of these disparities can result in biased estimates of severity (e.g., underestimating severity for disadvantaged groups). On a dataset of heart failure patients, we show that our model can identify groups that face each type of health disparity, and that accounting for these disparities while inferring disease severity meaningfully shifts which patients are considered high-risk.