Mixture-based Multiple Imputation Models for Clinical Data with a Temporal Dimension

The problem of missing values in multivariable time series is a key challenge in many applications such as clinical data mining. Although many imputation methods show their effectiveness in many applications, few of them are designed to accommodate clinical multivariable time series. In this work, we propose multiple imputation models that capture both cross-sectional information and temporal correlations. We integrate Gaussian processes with mixture models and introduce individualized mixing weights to handle the variance of predictive confidence of Gaussian process models. The proposed models are compared with several state-of-the-art imputation algorithms on both real-world and synthetic datasets. Experiments show that our best model can provide more accurate imputation than the benchmarks on all of our datasets.

Identification of Predictive Sub-Phenotypes of Acute Kidney Injury using Structured and Unstructured Electronic Health Record Data with Memory Networks

Acute Kidney Injury (AKI) is a common clinical syndrome characterized by the rapid loss of kidney excretory function, which aggravates the clinical severity of other diseases in a large number of hospitalized patients. Accurate early prediction of AKI can enable in-time interventions and treatments. However, AKI is highly heterogeneous, thus identification of AKI sub-phenotypes can lead to an improved understanding of the disease pathophysiology and development of more targeted clinical interventions. This study used a memory network-based deep learning approach to discover predictive AKI sub-phenotypes using structured and unstructured electronic health record (EHR) data of patients before AKI diagnosis. We leveraged a real world critical care EHR corpus including 37,486 ICU stays. Our approach identified three distinct sub-phenotypes: sub-phenotype I is with an average age of 63.03$ \pm 17.25 $ years, and is characterized by mild loss of kidney excretory function (Serum Creatinne (SCr) $1.55\pm 0.34$ mg/dL, estimated Glomerular Filtration Rate Test (eGFR) $107.65\pm 54.98$ mL/min/1.73$m^2$). These patients are more likely to develop stage I AKI. Sub-phenotype II is with average age 66.81$ \pm 10.43 $ years, and was characterized by severe loss of kidney excretory function (SCr $1.96\pm 0.49$ mg/dL, eGFR $82.19\pm 55.92$ mL/min/1.73$m^2$). These patients are more likely to develop stage III AKI. Sub-phenotype III is with average age 65.07$ \pm 11.32 $ years, and was characterized moderate loss of kidney excretory function and thus more likely to develop stage II AKI (SCr $1.69\pm 0.32$ mg/dL, eGFR $93.97\pm 56.53$ mL/min/1.73$m^2$). Both SCr and eGFR are significantly different across the three sub-phenotypes with statistical testing plus postdoc analysis, and the conclusion still holds after age adjustment.

Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study

While natural language processing (NLP) of unstructured clinical narratives holds the potential for patient care and clinical research, portability of NLP approaches across multiple sites remains a major challenge. This study investigated the portability of an NLP system developed initially at the Department of Veterans Affairs (VA) to extract 27 key cardiac concepts from free-text or semi-structured echocardiograms from three academic medical centers: Weill Cornell Medicine, Mayo Clinic and Northwestern Medicine. While the NLP system showed high precision and recall measurements for four target concepts (aortic valve regurgitation, left atrium size at end systole, mitral valve regurgitation, tricuspid valve regurgitation) across all sites, we found moderate or poor results for the remaining concepts and the NLP system performance varied between individual sites.

MedGCN: Graph Convolutional Networks for Multiple Medical Tasks

Laboratory testing and medication prescription are two of the most important routines in daily clinical practice. Developing an artificial intelligence system that can automatically make lab test imputations and medication recommendations can save cost on potentially redundant lab tests and inform physicians in more effective prescription. We present an intelligent model that can automatically recommend the patients' medications based on their incomplete lab tests, and can even accurately estimate the lab values that have not been taken. We model the complex relations between multiple types of medical entities with their inherent features in a heterogeneous graph. Then we learn a distributed representation for each entity in the graph based on graph convolutional networks to make the representations integrate information from multiple types of entities. Since the entity representations incorporate multiple types of medical information, they can be used for multiple medical tasks. In our experiments, we construct a graph to associate patients, encounters, lab tests and medications, and conduct the two tasks: medication recommendation and lab test imputation. The experimental results demonstrate that our model can outperform the state-of-the-art models in both tasks.

ImageGCN: Multi-Relational Image Graph Convolutional Networks for Disease Identification with Chest X-rays

Image representation is a fundamental task in computer vision. However, most of the existing approaches for image representation ignore the relations between images and consider each input image independently. Intuitively, relations between images can help to understand the images and maintain model consistency over related images. In this paper, we consider modeling the image-level relations to generate more informative image representations, and propose ImageGCN, an end-to-end graph convolutional network framework for multi-relational image modeling. We also apply ImageGCN to chest X-ray (CXR) images where rich relational information is available for disease identification. Unlike previous image representation models, ImageGCN learns the representation of an image using both its original pixel features and the features of related images. Besides learning informative representations for images, ImageGCN can also be used for object detection in a weakly supervised manner. The Experimental results on ChestX-ray14 dataset demonstrate that ImageGCN can outperform respective baselines in both disease identification and localization tasks and can achieve comparable and often better results than the state-of-the-art methods.

Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms

The automatic development of phenotype algorithms from Electronic Health Record data with machine learning (ML) techniques is of great interest given the current practice is very time-consuming and resource intensive. The extraction of design patterns from phenotype algorithms is essential to understand their rationale and standard, with great potential to automate the development process. In this pilot study, we perform network visualization on the design patterns and their associations with phenotypes and sites. We classify design patterns using the fragments from previously annotated phenotype algorithms as the ground truth. The classification performance is used as a proxy for coherence at the attribution level. The bag-of-words representation with knowledge-based features generated a good performance in the classification task (0.79 macro-f1 scores). Good classification accuracy with simple features demonstrated the attribution coherence and the feasibility of automatic identification of design patterns. Our results point to both the feasibility and challenges of automatic identification of phenotyping design patterns, which would power the automatic development of phenotype algorithms.

Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.

Early Prediction of Acute Kidney Injury in Critical Care Setting Using Clinical Notes

Acute kidney injury (AKI) in critically ill patients is associated with significant morbidity and mortality. Development of novel methods to identify patients with AKI earlier will allow for testing of novel strategies to prevent or reduce the complications of AKI. We developed data-driven prediction models to estimate the risk of new AKI onset. We generated models from clinical notes within the first 24 hours following intensive care unit (ICU) admission extracted from Medical Information Mart for Intensive Care III (MIMIC-III). From the clinical notes, we generated clinically meaningful word and concept representations and embeddings, respectively. Five supervised learning classifiers and knowledge-guided deep learning architecture were used to construct prediction models. The best configuration yielded a competitive AUC of 0.779. Our work suggests that natural language processing of clinical notes can be applied to assist clinicians in identifying the risk of incident AKI onset in critically ill patients upon admission to the ICU.

Graph Convolutional Networks for Text Classification

Text Classification is an important and classical problem in natural language processing. There have been a number of studies that applied convolutional neural networks (convolution on regular grid, e.g., sequence) to classification. However, only a limited number of studies have explored the more flexible graph convolutional neural networks (convolution on non-grid, e.g., arbitrary graph) for the task. In this work, we propose to use graph convolutional networks for text classification. We build a single text graph for a corpus based on word co-occurrence and document word relations, then learn a Text Graph Convolutional Network (Text GCN) for the corpus. Our Text GCN is initialized with one-hot representation for word and document, it then jointly learns the embeddings for both words and documents, as supervised by the known class labels for documents. Our experimental results on multiple benchmark datasets demonstrate that a vanilla Text GCN without any external word embeddings or knowledge outperforms state-of-the-art methods for text classification. On the other hand, Text GCN also learns predictive word and document embeddings. In addition, experimental results show that the improvement of Text GCN over state-of-the-art comparison methods become more prominent as we lower the percentage of training data, suggesting the robustness of Text GCN to less training data in text classification.

Supervised Nonnegative Matrix Factorization to Predict ICU Mortality Risk

ICU mortality risk prediction is a tough yet important task. On one hand, due to the complex temporal data collected, it is difficult to identify the effective features and interpret them easily; on the other hand, good prediction can help clinicians take timely actions to prevent the mortality. These correspond to the interpretability and accuracy problems. Most existing methods lack of the interpretability, but recently Subgraph Augmented Nonnegative Matrix Factorization (SANMF) has been successfully applied to time series data to provide a path to interpret the features well. Therefore, we adopted this approach as the backbone to analyze the patient data. One limitation of the raw SANMF method is its poor prediction ability due to its unsupervised nature. To deal with this problem, we proposed a supervised SANMF algorithm by integrating the logistic regression loss function into the NMF framework and solved it with an alternating optimization procedure. We used the simulation data to verify the effectiveness of this method, and then we applied it to ICU mortality risk prediction and demonstrated its superiority over other conventional supervised NMF methods.