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.

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.

The World as a Graph: Improving El Niño Forecasts with Graph Neural Networks

Deep learning-based models have recently outperformed state-of-the-art seasonal forecasting models, such as for predicting El Ni\~no-Southern Oscillation (ENSO). However, current deep learning models are based on convolutional neural networks which are difficult to interpret and can fail to model large-scale atmospheric patterns. In comparison, graph neural networks (GNNs) are capable of modeling large-scale spatial dependencies and are more interpretable due to the explicit modeling of information flow through edge connections. We propose the first application of graph neural networks to seasonal forecasting. We design a novel graph connectivity learning module that enables our GNN model to learn large-scale spatial interactions jointly with the actual ENSO forecasting task. Our model, \graphino, outperforms state-of-the-art deep learning-based models for forecasts up to six months ahead. Additionally, we show that our model is more interpretable as it learns sensible connectivity structures that correlate with the ENSO anomaly pattern.

Graph Neural Networks for Improved El Niño Forecasting

Deep learning-based models have recently outperformed state-of-the-art seasonal forecasting models, such as for predicting El Ni\~no-Southern Oscillation (ENSO). However, current deep learning models are based on convolutional neural networks which are difficult to interpret and can fail to model large-scale atmospheric patterns called teleconnections. Hence, we propose the application of spatiotemporal Graph Neural Networks (GNN) to forecast ENSO at long lead times, finer granularity and improved predictive skill than current state-of-the-art methods. The explicit modeling of information flow via edges may also allow for more interpretable forecasts. Preliminary results are promising and outperform state-of-the art systems for projections 1 and 3 months ahead.