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Register a new userNeural Topic Models with Survival Supervision: Jointly Predicting Time-to-Event Outcomes and Learning How Clinical Features Relate
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In time-to-event prediction problems, a standard approach to estimating an interpretable model is to use Cox proportional hazards, where features are selected based on lasso regularization or stepwise regression. However, these Cox-based models do not learn how different features relate. As an alternative, we present an interpretable neural network approach to jointly learn a survival model to predict time-to-event outcomes while simultaneously learning how features relate in terms of a topic model. In particular, we model each subject as a distribution over topics, which are learned from clinical features as to help predict a time-to-event outcome. From a technical standpoint, we extend existing neural topic modeling approaches to also minimize a survival analysis loss function. We study the effectiveness of this approach on seven healthcare datasets on predicting time until death as well as hospital ICU length of stay, where we find that neural survival-supervised topic models achieves competitive accuracy with existing approaches while yielding interpretable clinical topics that explain feature relationships.
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Scoring systems are highly interpretable and widely used to evaluate time-to-event outcomes in healthcare research. However, existing time-to-event scores are predominantly created ad-hoc using a few manually selected variables based on clinicians knowledge, suggesting an unmet need for a robust and efficient generic score-generating method. AutoScore was previously developed as an interpretable machine learning score generator, integrated both machine learning and point-based scores in the strong discriminability and accessibility. We have further extended it to time-to-event data and developed AutoScore-Survival, for automatically generating time-to-event scores with right-censored survival data. Random survival forest provides an efficient solution for selecting variables, and Cox regression was used for score weighting. We illustrated our method in a real-life study of 90-day mortality of patients in intensive care units and compared its performance with survival models (i.e., Cox) and the random survival forest. The AutoScore-Survival-derived scoring model was more parsimonious than survival models built using traditional variable selection methods (e.g., penalized likelihood approach and stepwise variable selection), and its performance was comparable to survival models using the same set of variables. Although AutoScore-Survival achieved a comparable integrated area under the curve of 0.782 (95% CI: 0.767-0.794), the integer-valued time-to-event scores generated are favorable in clinical applications because they are easier to compute and interpret. Our proposed AutoScore-Survival provides an automated, robust and easy-to-use machine learning-based clinical score generator to studies of time-to-event outcomes. It provides a systematic guideline to facilitate the future development of time-to-event scores for clinical applications.
Survival analysis is a technique to predict the times of specific outcomes, and is widely used in predicting the outcomes for intensive care unit (ICU) trauma patients. Recently, deep learning models have drawn increasing attention in healthcare. However, there is a lack of deep learning methods that can model the relationship between measurements, clinical notes and mortality outcomes. In this paper we introduce BERTSurv, a deep learning survival framework which applies Bidirectional Encoder Representations from Transformers (BERT) as a language representation model on unstructured clinical notes, for mortality prediction and survival analysis. We also incorporate clinical measurements in BERTSurv. With binary cross-entropy (BCE) loss, BERTSurv can predict mortality as a binary outcome (mortality prediction). With partial log-likelihood (PLL) loss, BERTSurv predicts the probability of mortality as a time-to-event outcome (survival analysis). We apply BERTSurv on Medical Information Mart for Intensive Care III (MIMIC III) trauma patient data. For mortality prediction, BERTSurv obtained an area under the curve of receiver operating characteristic curve (AUC-ROC) of 0.86, which is an improvement of 3.6% over baseline of multilayer perceptron (MLP) without notes. For survival analysis, BERTSurv achieved a concordance index (C-index) of 0.7. In addition, visualizations of BERTs attention heads help to extract patterns in clinical notes and improve model interpretability by showing how the model assigns weights to different inputs.
Training deep neural models in the presence of corrupted supervision is challenging as the corrupted data points may significantly impact the generalization performance. To alleviate this problem, we present an efficient robust algorithm that achieves strong guarantees without any assumption on the type of corruption and provides a unified framework for both classification and regression problems. Unlike many existing approaches that quantify the quality of the data points (e.g., based on their individual loss values), and filter them accordingly, the proposed algorithm focuses on controlling the collective impact of data points on the average gradient. Even when a corrupted data point failed to be excluded by our algorithm, the data point will have a very limited impact on the overall loss, as compared with state-of-the-art filtering methods based on loss values. Extensive experiments on multiple benchmark datasets have demonstrated the robustness of our algorithm under different types of corruption.
Recurrent neural network based solutions are increasingly being used in the analysis of longitudinal Electronic Health Record data. However, most works focus on prediction accuracy and neglect prediction uncertainty. We propose Deep Kernel Accelerated Failure Time models for the time-to-event prediction task, enabling uncertainty-awareness of the prediction by a pipeline of a recurrent neural network and a sparse Gaussian Process. Furthermore, a deep metric learning based pre-training step is adapted to enhance the proposed model. Our model shows better point estimate performance than recurrent neural network based baselines in experiments on two real-world datasets. More importantly, the predictive variance from our model can be used to quantify the uncertainty estimates of the time-to-event prediction: Our model delivers better performance when it is more confident in its prediction. Compared to related methods, such as Monte Carlo Dropout, our model offers better uncertainty estimates by leveraging an analytical solution and is more computationally efficient.
In this paper, we make an experimental comparison of semi-parametric (Cox proportional hazards model, Aalens additive regression model), parametric (Weibull AFT model), and machine learning models (Random Survival Forest, Gradient Boosting with Cox Proportional Hazards Loss, DeepSurv) through the concordance index on two different datasets (PBC and GBCSG2). We present two comparisons: one with the default hyper-parameters of these models and one with the best hyper-parameters found by randomized search.
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