Instability in clinical risk stratification models using deep learning

While it has been well known in the ML community that deep learning models suffer from instability, the consequences for healthcare deployments are under characterised. We study the stability of different model architectures trained on electronic health records, using a set of outpatient prediction tasks as a case study. We show that repeated training runs of the same deep learning model on the same training data can result in significantly different outcomes at a patient level even though global performance metrics remain stable. We propose two stability metrics for measuring the effect of randomness of model training, as well as mitigation strategies for improving model stability.

Boosting the interpretability of clinical risk scores with intervention predictions

Machine learning systems show significant promise for forecasting patient adverse events via risk scores. However, these risk scores implicitly encode assumptions about future interventions that the patient is likely to receive, based on the intervention policy present in the training data. Without this important context, predictions from such systems are less interpretable for clinicians. We propose a joint model of intervention policy and adverse event risk as a means to explicitly communicate the model's assumptions about future interventions. We develop such an intervention policy model on MIMIC-III, a real world de-identified ICU dataset, and discuss some use cases that highlight the utility of this approach. We show how combining typical risk scores, such as the likelihood of mortality, with future intervention probability scores leads to more interpretable clinical predictions.

Improved Patient Classification with Language Model Pretraining Over Clinical Notes

Clinical notes in electronic health records contain highly heterogeneous writing styles, including non-standard terminology or abbreviations. Using these notes in predictive modeling has traditionally required preprocessing (e.g. taking frequent terms or topic modeling) that removes much of the richness of the source data. We propose a pretrained hierarchical recurrent neural network model that parses minimally processed clinical notes in an intuitive fashion, and show that it improves performance for multiple classification tasks on the Medical Information Mart for Intensive Care III (MIMIC-III) dataset, improving top-5 recall to 89.7% (increase of 4.8%) for primary diagnosis classification and AUPRC to 35.2% (increase of 2.1%) for multilabel diagnosis classification compared to models that treat the notes as an unordered collection of terms, using no pretraining. We also apply an attribution technique to several examples to identify the words and the nearby context that the model uses to make its prediction, and show the importance of the words' context.

Learning an Adaptive Learning Rate Schedule

The learning rate is one of the most important hyper-parameters for model training and generalization. However, current hand-designed parametric learning rate schedules offer limited flexibility and the predefined schedule may not match the training dynamics of high dimensional and non-convex optimization problems. In this paper, we propose a reinforcement learning based framework that can automatically learn an adaptive learning rate schedule by leveraging the information from past training histories. The learning rate dynamically changes based on the current training dynamics. To validate this framework, we conduct experiments with different neural network architectures on the Fashion MINIST and CIFAR10 datasets. Experimental results show that the auto-learned learning rate controller can achieve better test results. In addition, the trained controller network is generalizable -- able to be trained on one data set and transferred to new problems.

Analyzing the Role of Model Uncertainty for Electronic Health Records

In medicine, both ethical and monetary costs of incorrect predictions can be significant, and the complexity of the problems often necessitates increasingly complex models. Recent work has shown that changing just the random seed is enough for otherwise well-tuned deep neural networks to vary in their individual predicted probabilities. In light of this, we investigate the role of model uncertainty methods in the medical domain. Using RNN ensembles and various Bayesian RNNs, we show that population-level metrics, such as AUC-PR, AUC-ROC, log-likelihood, and calibration error, do not capture model uncertainty. Meanwhile, the presence of significant variability in patient-specific predictions and optimal decisions motivates the need for capturing model uncertainty. Understanding the uncertainty for individual patients is an area with clear clinical impact, such as determining when a model decision is likely to be brittle. We further show that RNNs with only Bayesian embeddings can be a more efficient way to capture model uncertainty compared to ensembles, and we analyze how model uncertainty is impacted across individual input features and patient subgroups.