auton-survival: an Open-Source Package for Regression, Counterfactual Estimation, Evaluation and Phenotyping with Censored Time-to-Event Data

Applications of machine learning in healthcare often require working with time-to-event prediction tasks including prognostication of an adverse event, re-hospitalization or death. Such outcomes are typically subject to censoring due to loss of follow up. Standard machine learning methods cannot be applied in a straightforward manner to datasets with censored outcomes. In this paper, we present auton-survival, an open-source repository of tools to streamline working with censored time-to-event or survival data. auton-survival includes tools for survival regression, adjustment in the presence of domain shift, counterfactual estimation, phenotyping for risk stratification, evaluation, as well as estimation of treatment effects. Through real world case studies employing a large subset of the SEER oncology incidence data, we demonstrate the ability of auton-survival to rapidly support data scientists in answering complex health and epidemiological questions

Forecasting Response to Treatment with Deep Learning and Pharmacokinetic Priors

Forecasting healthcare time series is crucial for early detection of adverse outcomes and for patient monitoring. Forecasting, however, can be difficult in practice due to noisy and intermittent data. The challenges are often exacerbated by change points induced via extrinsic factors, such as the administration of medication. We propose a novel encoder that informs deep learning models of the pharmacokinetic effects of drugs to allow for accurate forecasting of time series affected by treatment. We showcase the effectiveness of our approach in a task to forecast blood glucose using both realistically simulated and real-world data. Our pharmacokinetic encoder helps deep learning models surpass baselines by approximately 11% on simulated data and 8% on real-world data. The proposed approach can have multiple beneficial applications in clinical practice, such as issuing early warnings about unexpected treatment responses, or helping to characterize patient-specific treatment effects in terms of drug absorption and elimination characteristics

Robust Rule Learning for Reliable and Interpretable Insight into Expertise Transfer Opportunities

Intensive care in hospitals is distributed to different units that care for patient populations reflecting specific comorbidities, treatments, and outcomes. Unit expertise can be shared to potentially improve the quality of methods and outcomes for patients across units. We propose an algorithmic rule pruning approach for use in building short lists of human-interpretable rules that reliably identify patient beneficiaries of expertise transfers in the form of machine learning risk models. Our experimental results, obtained with two intensive care monitoring datasets, demonstrate the potential utility of the proposed method in practice