Quantification of kidney function in Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) requires careful segmentation of the renal region of interest (ROI). Traditionally, human experts are required to manually delineate the kidney ROI across multiple images in the dynamic sequence. This approach is costly, time-consuming and labour intensive, and therefore acts to limit patient throughout and acts as one of the factors limiting the wider adoption of DCR-MRI in clinical practice. Therefore, to address this issue, we present the first use of Dynamic Mode Decomposition (DMD) as a basis for automatic segmentation of a dynamic sequence, in this case, kidney ROIs in DCE-MRI. Using DMD coupled combined with thresholding and connected component analysis is first validated on synthetically generated data with known ground-truth, and then applied to ten healthy volunteers' DCE-MRI datasets. We find that the segmentation result obtained from our proposed DMD framework is comparable to that of expert observers and very significantly better than that of an a-priori bounding box segmentation. Our result gives a mean Jaccard coefficient of 0.87, compared to mean scores of 0.85, 0.88 and 0.87 produced from three independent manual annotations. This represents the first use of DMD as a robust automatic data-driven segmentation approach without requiring any human intervention. This is a viable, efficient alternative approach to current manual methods of isolation of kidney function in DCE-MRI.
Acute Kidney Injury (AKI), a sudden decline in kidney function, is associated with increased mortality, morbidity, length of stay, and hospital cost. Since AKI is sometimes preventable, there is great interest in prediction. Most existing studies consider all patients and therefore restrict to features available in the first hours of hospitalization. Here, the focus is instead on rehospitalized patients, a cohort in which rich longitudinal features from prior hospitalizations can be analyzed. Our objective is to provide a risk score directly at hospital re-entry. Gradient boosting, penalized logistic regression (with and without stability selection), and a recurrent neural network are trained on two years of adult inpatient EHR data (3,387 attributes for 34,505 patients who generated 90,013 training samples with 5,618 cases and 84,395 controls). Predictions are internally evaluated with 50 iterations of 5-fold grouped cross-validation with special emphasis on calibration, an analysis of which is performed at the patient as well as hospitalization level. Error is assessed with respect to diagnosis, race, age, gender, AKI identification method, and hospital utilization. In an additional experiment, the regularization penalty is severely increased to induce parsimony and interpretability. Predictors identified for rehospitalized patients are also reported with a special analysis of medications that might be modifiable risk factors. Insights from this study might be used to construct a predictive tool for AKI in rehospitalized patients. An accurate estimate of AKI risk at hospital entry might serve as a prior for an admitting provider or another predictive algorithm.
A patient's estimated glomerular filtration rate (eGFR) can provide important information about disease progression and kidney function. Traditionally, an eGFR time series is interpreted by a human expert labelling it as stable or unstable. While this approach works for individual patients, the time consuming nature of it precludes the quick evaluation of risk in large numbers of patients. However, automating this process poses significant challenges as eGFR measurements are usually recorded at irregular intervals and the series of measurements differs in length between patients. Here we present a two-tier system to automatically classify an eGFR trend. First, we model the time series using Gaussian process regression (GPR) to fill in `gaps' by resampling a fixed size vector of fifty time-dependent observations. Second, we classify the resampled eGFR time series using a K-NN/SVM classifier, and evaluate its performance via 5-fold cross validation. Using this approach we achieved an F-score of 0.90, compared to 0.96 for 5 human experts when scored amongst themselves.
We study the problem of estimating the continuous response over time to interventions using observational time series---a retrospective dataset where the policy by which the data are generated is unknown to the learner. We are motivated by applications where response varies by individuals and therefore, estimating responses at the individual-level is valuable for personalizing decision-making. We refer to this as the problem of estimating individualized treatment response (ITR) curves. In statistics, G-computation formula (Robins, 1986) has been commonly used for estimating treatment responses from observational data containing sequential treatment assignments. However, past studies have focused predominantly on obtaining point-in-time estimates at the population level. We leverage the G-computation formula and develop a novel Bayesian nonparametric (BNP) method that can flexibly model functional data and provide posterior inference over the treatment response curves at both the individual and population level. On a challenging dataset containing time series from patients admitted to a hospital, we estimate responses to treatments used in managing kidney function and show that the resulting fits are more accurate than alternative approaches. Accurate methods for obtaining ITRs from observational data can dramatically accelerate the pace at which personalized treatment plans become possible.
A Convolutional Neural Network was used to predict kidney function in patients with chronic kidney disease from high-resolution digital pathology scans of their kidney biopsies. Kidney biopsies were taken from participants of the NEPTUNE study, a longitudinal cohort study whose goal is to set up infrastructure for observing the evolution of 3 forms of idiopathic nephrotic syndrome, including developing predictors for progression of kidney disease. The knowledge of future kidney function is desirable as it can identify high-risk patients and influence treatment decisions, reducing the likelihood of irreversible kidney decline.
Congestive Heart Failure, or CHF, is a serious medical condition that can result in fluid buildup in the body as a result of a weak heart. When the heart can't pump enough blood to efficiently deliver nutrients and oxygen to the body, kidney function may be impaired, resulting in fluid retention. CHF patients require a broad drug regimen to maintain the delicate system balance, particularly between their heart and kidneys. These drugs include ACE inhibitors and Beta Blockers to control blood pressure, anticoagulants to prevent blood clots, and diuretics to reduce fluid overload. Many of these drugs may interact, and potential effects of these interactions must be weighed against their benefits. For this project, we consider a set of 44 drugs identified as specifically relevant for treating CHF by pediatric cardiologists at Lucile Packard Children's Hospital. This list was generated as part of our current work at the LPCH Heart Center. The goal of this project is to identify and evaluate potentially harmful drug-drug interactions (DDIs) within pediatric patients with Congestive Heart Failure. This identification will be done autonomously, so that it may continuously update by evaluating newly published literature.
This letter presente a comment on the paper Prediction of Kidney Function from Biopsy Images using Convolutional Neural Networks by Ledbetter et al. (2017)
Acute Kidney Injury (AKI), the abrupt decline in kidney function due to temporary or permanent injury, is associated with increased mortality, morbidity, length of stay, and hospital cost. Sometimes, simple interventions such as medication review or hydration can prevent AKI. There is therefore interest in estimating risk of AKI at hospitalization. To gain insight into this task, we employ multilayer perceptron (MLP) and recurrent neural networks (RNNs) using serum creatinine (sCr) as a lone feature. We explore different feature input structures, including variable-length look-backs and a nested formulation for rehospitalized patients with previous sCr measurements. Experimental results show that the simplest model, MLP processing the sum of sCr, had best performance: AUROC 0.92 and AUPRC 0.70. Such a simple model could be easily integrated into an EHR. Preliminary results also suggest that inpatient data streams with missing outpatient measurements---common in the medical setting---might be best modeled with a tailored architecture.
Kidney function evaluation using dynamic contrast-enhanced MRI (DCE-MRI) images could help in diagnosis and treatment of kidney diseases of children. Automatic segmentation of renal parenchyma is an important step in this process. In this paper, we propose a time and memory efficient fully automated segmentation method which achieves high segmentation accuracy with running time in the order of seconds in both normal kidneys and kidneys with hydronephrosis. The proposed method is based on a cascaded application of two 3D convolutional neural networks that employs spatial and temporal information at the same time in order to learn the tasks of localization and segmentation of kidneys, respectively. Segmentation performance is evaluated on both normal and abnormal kidneys with varying levels of hydronephrosis. We achieved a mean dice coefficient of 91.4 and 83.6 for normal and abnormal kidneys of pediatric patients, respectively.