One important challenge of applying deep learning to electronic health records (EHR) is the complexity of their multimodal structure. EHR usually contains a mixture of structured (codes) and unstructured (free-text) data with sparse and irregular longitudinal features -- all of which doctors utilize when making decisions. In the deep learning regime, determining how different modality representations should be fused together is a difficult problem, which is often addressed by handcrafted modeling and intuition. In this work, we extend state-of-the-art neural architecture search (NAS) methods and propose MUltimodal Fusion Architecture SeArch (MUFASA) to simultaneously search across multimodal fusion strategies and modality-specific architectures for the first time. We demonstrate empirically that our MUFASA method outperforms established unimodal NAS on public EHR data with comparable computation costs. In addition, MUFASA produces architectures that outperform Transformer and Evolved Transformer. Compared with these baselines on CCS diagnosis code prediction, our discovered models improve top-5 recall from 0.88 to 0.91 and demonstrate the ability to generalize to other EHR tasks. Studying our top architecture in depth, we provide empirical evidence that MUFASA's improvements are derived from its ability to both customize modeling for each modality and find effective fusion strategies.

Effective modeling of electronic health records (EHR) is rapidly becoming an important topic in both academia and industry. A recent study showed that using the graphical structure underlying EHR data (e.g. relationship between diagnoses and treatments) improves the performance of prediction tasks such as heart failure prediction. However, EHR data do not always contain complete structure information. Moreover, when it comes to claims data, structure information is completely unavailable to begin with. Under such circumstances, can we still do better than just treating EHR data as a flat-structured bag-of-features? In this paper, we study the possibility of jointly learning the hidden structure of EHR while performing supervised prediction tasks on EHR data. Specifically, we discuss that Transformer is a suitable basis model to learn the hidden EHR structure, and propose Graph Convolutional Transformer, which uses data statistics to guide the structure learning process. The proposed model consistently outperformed previous approaches empirically, on both synthetic data and publicly available EHR data, for various prediction tasks such as graph reconstruction and readmission prediction, indicating that it can serve as an effective general-purpose representation learning algorithm for EHR data.

This paper studies a training method to jointly estimate an energy-based model and a flow-based model, in which the two models are iteratively updated based on a shared adversarial value function. This joint training method has the following traits. (1) The update of the energy-based model is based on noise contrastive estimation, with the flow model serving as a strong noise distribution. (2) The update of the flow model approximately minimizes the Jensen-Shannon divergence between the flow model and the data distribution. (3) Unlike generative adversarial networks (GAN) which estimates an implicit probability distribution defined by a generator model, our method estimates two explicit probabilistic distributions on the data. Using the proposed method we demonstrate a significant improvement on the synthesis quality of the flow model, and show the effectiveness of unsupervised feature learning by the learned energy-based model. Furthermore, the proposed training method can be easily adapted to semi-supervised learning. We achieve competitive results to the state-of-the-art semi-supervised learning methods.

Capturing the inter-dependencies among multiple types of clinically-critical events is critical not only to accurate future event prediction, but also to better treatment planning. In this work, we propose a deep latent state-space generative model to capture the interactions among different types of correlated clinical events (e.g., kidney failure, mortality) by explicitly modeling the temporal dynamics of patients' latent states. Based on these learned patient states, we further develop a new general discrete-time formulation of the hazard rate function to estimate the survival distribution of patients with significantly improved accuracy. Extensive evaluations over real EMR data show that our proposed model compares favorably to various state-of-the-art baselines. Furthermore, our method also uncovers meaningful insights about the latent correlations among mortality and different types of organ failures.