Designing optimal treatment plans for patients with comorbidities requires accurate cause-specific mortality prognosis. Motivated by the recent availability of linked electronic health records, we develop a nonparametric Bayesian model for survival analysis with competing risks, which can be used for jointly assessing a patient's risk of multiple (competing) adverse outcomes. The model views a patient's survival times with respect to the competing risks as the outputs of a deep multi-task Gaussian process (DMGP), the inputs to which are the patients' covariates. Unlike parametric survival analysis methods based on Cox and Weibull models, our model uses DMGPs to capture complex non-linear interactions between the patients' covariates and cause-specific survival times, thereby learning flexible patient-specific and cause-specific survival curves, all in a data-driven fashion without explicit parametric assumptions on the hazard rates. We propose a variational inference algorithm that is capable of learning the model parameters from time-to-event data while handling right censoring. Experiments on synthetic and real data show that our model outperforms the state-of-the-art survival models.

Medical researchers are coming to appreciate that many diseases are in fact complex, heterogeneous syndromes composed of subpopulations that express different variants of a related complication. Longitudinal data extracted from individual electronic health records (EHR) offer an exciting new way to study subtle differences in the way these diseases progress over time. In this paper, we focus on answering two questions that can be asked using these databases of longitudinal EHR data. First, we want to understand whether there are individuals with similar disease trajectories and whether there are a small number of degrees of freedom that account for differences in trajectories across the population. Second, we want to understand how important clinical outcomes are associated with disease trajectories. To answer these questions, we propose the Disease Trajectory Map (DTM), a novel probabilistic model that learns low-dimensional representations of sparse and irregularly sampled longitudinal data. We propose a stochastic variational inference algorithm for learning the DTM that allows the model to scale to large modern medical datasets. To demonstrate the DTM, we analyze data collected on patients with the complex autoimmune disease, scleroderma. We find that DTM learns meaningful representations of disease trajectories and that the representations are significantly associated with important clinical outcomes.

Accuracy and interpretability are two dominant features of successful predictive models. Typically, a choice must be made in favor of complex black box models such as recurrent neural networks (RNN) for accuracy versus less accurate but more interpretable traditional models such as logistic regression. This tradeoff poses challenges in medicine where both accuracy and interpretability are important. We addressed this challenge by developing the REverse Time AttentIoN model (RETAIN) for application to Electronic Health Records (EHR) data. RETAIN achieves high accuracy while remaining clinically interpretable and is based on a two-level neural attention model that detects influential past visits and significant clinical variables within those visits (e.g.

Deep learning models exhibit state-of-the-art performance for many predictive healthcare tasks using electronic health records (EHR) data, but these models typically require training data volume that exceeds the capacity of most healthcare systems. External resources such as medical ontologies are used to bridge the data volume constraint, but this approach is often not directly applicable or useful because of inconsistencies with terminology. To solve the data insufficiency challenge, we leverage the inherent multilevel structure of EHR data and, in particular, the encoded relationships among medical codes. We propose Multilevel Medical Embedding (MiME) which learns the multilevel embedding of EHR data while jointly performing auxiliary prediction tasks that rely on this inherent EHR structure without the need for external labels. We conducted two prediction tasks, heart failure prediction and sequential disease prediction, where MiME outperformed baseline methods in diverse evaluation settings. In particular, MiME consistently outperformed all baselines when predicting heart failure on datasets of different volumes, especially demonstrating the greatest performance improvement (15% relative gain in PR-AUC over the best baseline) on the smallest dataset, demonstrating its ability to effectively model the multilevel structure of EHR data.

We present a new approach to the problems of evaluating and learning personalized decision policies from observational data of past contexts, decisions, and outcomes. Only the outcome of the enacted decision is available and the historical policy is unknown. These problems arise in personalized medicine using electronic health records and in internet advertising. Existing approaches use inverse propensity weighting (or, doubly robust versions) to make historical outcome (or, residual) data look like it were generated by a new policy being evaluated or learned. But this relies on a plug-in approach that rejects data points with a decision that disagrees with the new policy, leading to high variance estimates and ineffective learning. We propose a new, balance-based approach that too makes the data look like the new policy but does so directly by finding weights that optimize for balance between the weighted data and the target policy in the given, finite sample, which is equivalent to minimizing worst-case or posterior conditional mean square error.

Electronic health records provide a rich source of data for machine learning methods to learn dynamic treatment responses over time. However, any direct estimation is hampered by the presence of time-dependent confounding, where actions taken are dependent on time-varying variables related to the outcome of interest. Drawing inspiration from marginal structural models, a class of methods in epidemiology which use propensity weighting to adjust for time-dependent confounders, we introduce the Recurrent Marginal Structural Network - a sequence-to-sequence architecture for forecasting a patient's expected response to a series of planned treatments.

Despite their impressive performance, Deep Neural Networks (DNNs) typically underperform Gradient Boosting Trees (GBTs) on many tabular-dataset learning tasks. We propose that applying a different regularization coefficient to each weight might boost the performance of DNNs by allowing them to make more use of the more relevant inputs. However, this will lead to an intractable number of hyperparameters. Here, we introduce Regularization Learning Networks (RLNs), which overcome this challenge by introducing an efficient hyperparameter tuning scheme which minimizes a new Counterfactual Loss. Our results show that RLNs significantly improve DNNs on tabular datasets, and achieve comparable results to GBTs, with the best performance achieved with an ensemble that combines GBTs and RLNs. RLNs produce extremely sparse networks, eliminating up to 99.8% of the network edges and 82% of the input features, thus providing more interpretable models and reveal the importance that the network assigns to different inputs. RLNs could efficiently learn a single network in datasets that comprise both tabular and unstructured data, such as in the setting of medical imaging accompanied by electronic health records.

Attention mechanism is effective in both focusing the deep learning models on relevant features and interpreting them. However, attentions may be unreliable since the networks that generate them are often trained in a weakly-supervised manner. To overcome this limitation, we introduce the notion of input-dependent uncertainty to the attention mechanism, such that it generates attention for each feature with varying degrees of noise based on the given input, to learn larger variance on instances it is uncertain about. We learn this Uncertainty-aware Attention (UA) mechanism using variational inference, and validate it on various risk prediction tasks from electronic health records on which our model significantly outperforms existing attention models. The analysis of the learned attentions shows that our model generates attentions that comply with clinicians' interpretation, and provide richer interpretation via learned variance. Further evaluation of both the accuracy of the uncertainty calibration and the prediction performance with I don't know'' decision show that UA yields networks with high reliability as well.

Microsoft's Copilot Health can use AI to turn your fitness data and medical records'into a coherent story' The aim is to help users have the right context and questions to take to their doctor. Microsoft has unveiled Copilot Health, an AI-powered tool it claims can help make sense of your medical records, health history and fitness data from wearables, should you grant it access to that information. The company said it will be in a separate, secure space in the Copilot app and that the idea is to help provide you with more context and insights so you can ask your doctor the right questions when you see them. Copilot Health is designed to help you better understand your medical information as a whole, Microsoft says. It is not intended to diagnose, treat or prevent diseases or other conditions and is not a substitute for professional medical advice, the company pointed out in a blog post.