In this study, we introduce ExBEHRT, an extended version of BEHRT (BERT applied to electronic health records), and apply different algorithms to interpret its results. While BEHRT considers only diagnoses and patient age, we extend the feature space to several multimodal records, namely demographics, clinical characteristics, vital signs, smoking status, diagnoses, procedures, medications, and laboratory tests, by applying a novel method to unify the frequencies and temporal dimensions of the different features. We show that additional features significantly improve model performance for various downstream tasks in different diseases. To ensure robustness, we interpret model predictions using an adaptation of expected gradients, which has not been previously applied to transformers with EHR data and provides more granular interpretations than previous approaches such as feature and token importances. Furthermore, by clustering the model representations of oncology patients, we show that the model has an implicit understanding of the disease and is able to classify patients with the same cancer type into different risk groups. Given the additional features and interpretability, ExBEHRT can help make informed decisions about disease trajectories, diagnoses, and risk factors of various diseases.

Electronic Health Records (EHRs) exhibit a high amount of missing data due to variations of patient conditions and treatment needs. Imputation of missing values has been considered an effective approach to deal with this challenge. Existing work separates imputation method and prediction model as two independent parts of an EHR-based machine learning system. We propose an integrated end-to-end approach by utilizing a Compound Density Network (CDNet) that allows the imputation method and prediction model to be tuned together within a single framework. CDNet consists of a Gated recurrent unit (GRU), a Mixture Density Network (MDN), and a Regularized Attention Network (RAN). The GRU is used as a latent variable model to model EHR data. The MDN is designed to sample latent variables generated by GRU. The RAN serves as a regularizer for less reliable imputed values. The architecture of CDNet enables GRU and MDN to iteratively leverage the output of each other to impute missing values, leading to a more accurate and robust prediction. We validate CDNet on the mortality prediction task on the MIMIC-III dataset. Our model outperforms state-of-the-art models by significant margins. We also empirically show that regularizing imputed values is a key factor for superior prediction performance. Analysis of prediction uncertainty shows that our model can capture both aleatoric and epistemic uncertainties, which offers model users a better understanding of the model results.

Building models for health prediction based on Electronic Health Records (EHR) has become an active research area. EHR patient journey data consists of patient time-ordered clinical events/visits from patients. Most existing studies focus on modeling long-term dependencies between visits, without explicitly taking short-term correlations between consecutive visits into account, where irregular time intervals, incorporated as auxiliary information, are fed into health prediction models to capture latent progressive patterns of patient journeys. We present a novel deep neural network with four modules to take into account the contributions of various variables for health prediction: i) the Stacked Attention module strengthens the deep semantics in clinical events within each patient journey and generates visit embeddings, ii) the Short-Term Temporal Attention module models short-term correlations between consecutive visit embeddings while capturing the impact of time intervals within those visit embeddings, iii) the Long-Term Temporal Attention module models long-term dependencies between visit embeddings while capturing the impact of time intervals within those visit embeddings, iv) and finally, the Coupled Attention module adaptively aggregates the outputs of Short-Term Temporal Attention and Long-Term Temporal Attention modules to make health predictions. Experimental results on MIMIC-III demonstrate superior predictive accuracy of our model compared to existing state-of-the-art methods, as well as the interpretability and robustness of this approach. Furthermore, we found that modeling short-term correlations contributes to local priors generation, leading to improved predictive modeling of patient journeys.

Sequential diagnosis prediction on the Electronic Health Record (EHR) has been proven crucial for predictive analytics in the medical domain. EHR data, sequential records of a patient's interactions with healthcare systems, has numerous inherent characteristics of temporality, irregularity and data insufficiency. Some recent works train healthcare predictive models by making use of sequential information in EHR data, but they are vulnerable to irregular, temporal EHR data with the states of admission/discharge from hospital, and insufficient data. To mitigate this, we propose an end-to-end robust transformer-based model called SETOR, which exploits neural ordinary differential equation to handle both irregular intervals between a patient's visits with admitted timestamps and length of stay in each visit, to alleviate the limitation of insufficient data by integrating medical ontology, and to capture the dependencies between the patient's visits by employing multi-layer transformer blocks. Experiments conducted on two real-world healthcare datasets show that, our sequential diagnoses prediction model SETOR not only achieves better predictive results than previous state-of-the-art approaches, irrespective of sufficient or insufficient training data, but also derives more interpretable embeddings of medical codes. The experimental codes are available at the GitHub repository (https://github.com/Xueping/SETOR).

Healthcare representation learning on the Electronic Health Record (EHR) is seen as crucial for predictive analytics in the medical field. Many natural language processing techniques, such as word2vec, RNN and self-attention, have been adapted for use in hierarchical and time stamped EHR data, but fail when they lack either general or task-specific data. Hence, some recent works train healthcare representations by incorporating medical ontology (a.k.a. knowledge graph), by self-supervised tasks like diagnosis prediction, but (1) the small-scale, monotonous ontology is insufficient for robust learning, and (2) critical contexts or dependencies underlying patient journeys are never exploited to enhance ontology learning. To address this, we propose an end-to-end robust Transformer-based solution, Mutual Integration of patient journey and Medical Ontology (MIMO) for healthcare representation learning and predictive analytics. Specifically, it consists of task-specific representation learning and graph-embedding modules to learn both patient journey and medical ontology interactively. Consequently, this creates a mutual integration to benefit both healthcare representation learning and medical ontology embedding. Moreover, such integration is achieved by a joint training of both task-specific predictive and ontology-based disease typing tasks based on fused embeddings of the two modules. Experiments conducted on two real-world diagnosis prediction datasets show that, our healthcare representation model MIMO not only achieves better predictive results than previous state-of-the-art approaches regardless of sufficient or insufficient training data, but also derives more interpretable embeddings of diagnoses.

Electronic health records (EHRs) are longitudinal records of a patient's interactions with healthcare systems. A patient's EHR data is organized as a three-level hierarchy from top to bottom: patient journey - all the experiences of diagnoses and treatments over a period of time; individual visit - a set of medical codes in a particular visit; and medical code - a specific record in the form of medical codes. As EHRs begin to amass in millions, the potential benefits, which these data might hold for medical research and medical outcome prediction, are staggering - including, for example, predicting future admissions to hospitals, diagnosing illnesses or determining the efficacy of medical treatments. Each of these analytics tasks requires a domain knowledge extraction method to transform the hierarchical patient journey into a vector representation for further prediction procedure. The representations should embed a sequence of visits and a set of medical codes with a specific timestamp, which are crucial to any downstream prediction tasks. Hence, expressively powerful representations are appealing to boost learning performance. To this end, we propose a novel self-attention mechanism that captures the contextual dependency and temporal relationships within a patient's healthcare journey. An end-to-end bidirectional temporal encoder network (BiteNet) then learns representations of the patient's journeys, based solely on the proposed attention mechanism. We have evaluated the effectiveness of our methods on two supervised prediction and two unsupervised clustering tasks with a real-world EHR dataset. The empirical results demonstrate the proposed BiteNet model produces higher-quality representations than state-of-the-art baseline methods.

Understanding patients' journeys in healthcare system is a fundamental prepositive task for a broad range of AI-based healthcare applications. This task aims to learn an informative representation that can comprehensively encode hidden dependencies among medical events and its inner entities, and then the use of encoding outputs can greatly benefit the downstream application-driven tasks. A patient journey is a sequence of electronic health records (EHRs) over time that is organized at multiple levels: patient, visits and medical codes. The key challenge of patient journey understanding is to design an effective encoding mechanism which can properly tackle the aforementioned multi-level structured patient journey data with temporal sequential visits and a set of medical codes. This paper proposes a novel self-attention mechanism that can simultaneously capture the contextual and temporal relationships hidden in patient journeys. A multi-level self-attention network (MusaNet) is specifically designed to learn the representations of patient journeys that is used to be a long sequence of activities. The MusaNet is trained in end-to-end manner using the training data derived from EHRs. We evaluated the efficacy of our method on two medical application tasks with real-world benchmark datasets. The results have demonstrated the proposed MusaNet produces higher-quality representations than state-of-the-art baseline methods. The source code is available in https://github.com/xueping/MusaNet.

Healthcare professionals have long envisioned using the enormous processing powers of computers to discover new facts and medical knowledge locked inside electronic health records. These vast medical archives contain time-resolved information about medical visits, tests and procedures, as well as outcomes, which together form individual patient journeys. By assessing the similarities among these journeys, it is possible to uncover clusters of common disease trajectories with shared health outcomes. The assignment of patient journeys to specific clusters may in turn serve as the basis for personalized outcome prediction and treatment selection. This procedure is a non-trivial computational problem, as it requires the comparison of patient data with multi-dimensional and multi-modal features that are captured at different times and resolutions. In this review, we provide a comprehensive overview of the tools and methods that are used in patient similarity analysis with longitudinal data and discuss its potential for improving clinical decision making.

Improving the customer experience is no longer an idea that's relegated to the retail or hospitality industries. Now, the idea has gained traction across many industries, including healthcare. For health plans, improving the customer experience and providing member-centric care helps drive member acquisition and retention and improve reimbursement (via a better STARS rating). With so many benefits at their fingertips, why haven't the majority of health plans become member-centric yet? Health plans need to engage both members and providers to deliver on an approach to member-centric care.

Automatic representation learning of key entities in electronic health record (EHR) data is a critical step for healthcare informatics that turns heterogeneous medical records into structured and actionable information. Here we propose ME2Vec, an algorithmic framework for learning low-dimensional vectors of the most common entities in EHR: medical services, doctors, and patients. ME2Vec leverages diverse graph embedding techniques to cater for the unique characteristic of each medical entity. Using real-world clinical data, we demonstrate the efficacy of ME2Vec over competitive baselines on disease diagnosis prediction.