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Register a new userUncertainty-Aware Variational-Recurrent Imputation Network for Clinical Time Series
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Electronic health records (EHR) consist of longitudinal clinical observations portrayed with sparsity, irregularity, and high-dimensionality, which become major obstacles in drawing reliable downstream clinical outcomes. Although there exist great numbers of imputation methods to tackle these issues, most of them ignore correlated features, temporal dynamics and entirely set aside the uncertainty. Since the missing value estimates involve the risk of being inaccurate, it is appropriate for the method to handle the less certain information differently than the reliable data. In that regard, we can use the uncertainties in estimating the missing values as the fidelity score to be further utilized to alleviate the risk of biased missing value estimates. In this work, we propose a novel variational-recurrent imputation network, which unifies an imputation and a prediction network by taking into account the correlated features, temporal dynamics, as well as the uncertainty. Specifically, we leverage the deep generative model in the imputation, which is based on the distribution among variables, and a recurrent imputation network to exploit the temporal relations, in conjunction with utilization of the uncertainty. We validated the effectiveness of our proposed model on two publicly available real-world EHR datasets: PhysioNet Challenge 2012 and MIMIC-III, and compared the results with other competing state-of-the-art methods in the literature.
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Real-world clinical time series data sets exhibit a high prevalence of missing values. Hence, there is an increasing interest in missing data imputation. Traditional statistical approaches impose constraints on the data-generating process and decouple imputation from prediction. Recent works propose recurrent neural network based approaches for missing data imputation and prediction with time series data. However, they generate deterministic outputs and neglect the inherent uncertainty. In this work, we introduce a unified Bayesian recurrent framework for simultaneous imputation and prediction on time series data sets. We evaluate our approach on two real-world mortality prediction tasks using the MIMIC-III and PhysioNet benchmark datasets. We demonstrate strong performance gains over state-of-the-art (SOTA) methods, and provide strategies to use the resulting probability distributions to better assess reliability of the imputations and predictions.
Time series imputation is a fundamental task for understanding time series with missing data. Existing methods either do not directly handle irregularly-sampled data or degrade severely with sparsely observed data. In this work, we reformulate time series as permutation-equivariant sets and propose a novel imputation model NRTSI that does not impose any recurrent structures. Taking advantage of the permutation equivariant formulation, we design a principled and efficient hierarchical imputation procedure. In addition, NRTSI can directly handle irregularly-sampled time series, perform multiple-mode stochastic imputation, and handle data with partially observed dimensions. Empirically, we show that NRTSI achieves state-of-the-art performance across a wide range of time series imputation benchmarks.
Deep learning-based support systems have demonstrated encouraging results in numerous clinical applications involving the processing of time series data. While such systems often are very accurate, they have no inherent mechanism for explaining what influenced the predictions, which is critical for clinical tasks. However, existing explainability techniques lack an important component for trustworthy and reliable decision support, namely a notion of uncertainty. In this paper, we address this lack of uncertainty by proposing a deep ensemble approach where a collection of DNNs are trained independently. A measure of uncertainty in the relevance scores is computed by taking the standard deviation across the relevance scores produced by each model in the ensemble, which in turn is used to make the explanations more reliable. The class activation mapping method is used to assign a relevance score for each time step in the time series. Results demonstrate that the proposed ensemble is more accurate in locating relevant time steps and is more consistent across random initializations, thus making the model more trustworthy. The proposed methodology paves the way for constructing trustworthy and dependable support systems for processing clinical time series for healthcare related tasks.
Time series models with recurrent neural networks (RNNs) can have high accuracy but are unfortunately difficult to interpret as a result of feature-interactions, temporal-interactions, and non-linear transformations. Interpretability is important in domains like healthcare where constructing models that provide insight into the relationships they have learned are required to validate and trust model predictions. We want accurate time series models where users can understand the contribution of individual input features. We present the Interpretable-RNN (I-RNN) that balances model complexity and accuracy by forcing the relationship between variables in the model to be additive. Interactions are restricted between hidden states of the RNN and additively combined at the final step. I-RNN specifically captures the unique characteristics of clinical time series, which are unevenly sampled in time, asynchronously acquired, and have missing data. Importantly, the hidden state activations represent feature coefficients that correlate with the prediction target and can be visualized as risk curves that capture the global relationship between individual input features and the outcome. We evaluate the I-RNN model on the Physionet 2012 Challenge dataset to predict in-hospital mortality, and on a real-world clinical decision support task: predicting hemodynamic interventions in the intensive care unit. I-RNN provides explanations in the form of global and local feature importances comparable to highly intelligible models like decision trees trained on hand-engineered features while significantly outperforming them. I-RNN remains intelligible while providing accuracy comparable to state-of-the-art decay-based and interpolation-based recurrent time series models. The experimental results on real-world clinical datasets refute the myth that there is a tradeoff between accuracy and interpretability.
The Nonlinear autoregressive exogenous (NARX) model, which predicts the current value of a time series based upon its previous values as well as the current and past values of multiple driving (exogenous) series, has been studied for decades. Despite the fact that various NARX models have been developed, few of them can capture the long-term temporal dependencies appropriately and select the relevant driving series to make predictions. In this paper, we propose a dual-stage attention-based recurrent neural network (DA-RNN) to address these two issues. In the first stage, we introduce an input attention mechanism to adaptively extract relevant driving series (a.k.a., input features) at each time step by referring to the previous encoder hidden state. In the second stage, we use a temporal attention mechanism to select relevant encoder hidden states across all time steps. With this dual-stage attention scheme, our model can not only make predictions effectively, but can also be easily interpreted. Thorough empirical studies based upon the SML 2010 dataset and the NASDAQ 100 Stock dataset demonstrate that the DA-RNN can outperform state-of-the-art methods for time series prediction.
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