Notes

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De-identification of electric health record narratives is a fundamental task applying natural language processing to better protect patient information privacy. We explore different types of ensemble learning methods to improve clinical text de-identification. We present two ensemble-based approaches for combining multiple predictive models. The first method selects an optimal subset of de-identification models by greedy exclusion. This ensemble pruning allows one to save computational time or physical resources while achieving similar or better performance than the ensemble of all members. The second method uses a sequence of words to train a sequential model. For this sequence labelling-based stacked ensemble, we employ search-based structured prediction and bidirectional long short-term memory algorithms. We create ensembles consisting of de-identification models trained on two clinical text corpora. Experimental results show that our ensemble systems can effectively integrate predictions from individual models and offer better generalization across two different corpora.Chief complaints are important textual data that can serve to enrich diagnosis and symptom data in electronic health record (EHR) systems. In this study, a method is presented to preprocess chief complaints and assign corresponding ICD-10-CM codes using the MetaMap natural language processing (NLP) system and Unified Medical Language System (UMLS) Metathesaurus. An exploratory analysis was conducted using a set of 7,942 unique chief complaints from the statewide health information exchange containing EHR data from hospitals across Rhode Island. An evaluation of the proposed method was then performed using a set of 123,086 chief complaints with corresponding ICD-10-CM encounter diagnoses. With 87.82% of MetaMap-extracted concepts correctly assigned, the preliminary findings support the potential use of the method explored in this study for improving upon existing NLP techniques for enabling use of data captured within chief complaints to support clinical care, research, and public health surveillance.Deep learning models are increasingly studied in the field of critical care. However, due to the lack of external validation and interpretability, it is difficult to generalize deep learning models in critical care senarios. Few works have validated the performance of the deep learning models with external datasets. To address this, we propose a clinically practical and interpretable deep model for intensive care unit (ICU) mortality prediction with external validation. We use the newly published dataset Philips eICU to train a recurrent neural network model with two-level attention mechanism, and use the MIMIC III dataset as the external validation set to verify the model performance. This model achieves a high accuracy (AUC = 0.855 on the external validation set) and have good interpretability. Based on this model, we develop a system to support clinical decision-making in ICUs.The efficacy of early fluid treatment in patients with sepsis is unclear and may contribute to serious adverse events due to fluid non-responsiveness. The current method of deciding if patients are responsive to fluid administration is often subjective and requires manual intervention. This study utilizes MIMIC III and associated matched waveform datasets across the entire ICU stay duration of each patient to develop prediction models for assessing fluid responsiveness in sepsis patients. We developed a pipeline to extract high frequency continuous waveform data and included waveform features in the prediction models. Comparing across five machine learning models, random forest performed the best when no waveform information is added (AUC = 0.84), with mean arterial blood pressure and age identified as key factors. After incorporation of features from physiologic waveforms, logistic regression with L1 penalty provided consistent performance and high interpretability, achieving an accuracy of 0.89 and F1 score of 0.90.The amount of time spent working in the Electronic Health Record (EHR) has become a burden for many providers. L-glutamate molecular weight We propose computational methods to learn EHR tasks of Pediatrics residents and attending physicians in the treatment of healthy newborns by analyzing EHR audit log data. We perform statistical analyses of the association between EHR events and provider role, leverage word embedding, k-means, and ProM process mining software on audit log data to learn EHR tasks and visualize them. Residents more commonly perform note preparation and result viewing relative to attendings. Attendings perform more communication and chart review. Task workflows analysis resulted in 2 tasks for attendings and 3 tasks for residents. The attending tasks focus on chart review patient report and history, and inbox service. Primary themes for residents are admit/discharge with order creation, note review, and result review.Predictive models can be useful in predicting patient outcomes under uncertainty. Many algorithms employ "population" methods, which optimize a single model to perform well on average over an entire population, but the model may perform poorly on some patients. Personalized methods optimize predictive performance for each patient by tailoring the model to the individual. We present a new personalized method based on decision trees the Personalized Decision Path using a Bayesian score (PDP-Bay). Performance on eight synthetic, genomic, and clinical datasets was compared to that of decision trees and a previously described personalized decision path method in terms of area under the ROC curve (AUC) and expected calibration error (ECE). Model complexity was measured by average path length. The PDP-Bay model outperformed the decision tree in terms of both AUC and ECE. The results support the conclusion that personalization may achieve better predictive performance and produce simpler models than population approaches.The application of deep learning algorithms in medical imaging analysis is a steadily growing research area. While deep learning methods are thriving in the medical domain, they seldom utilize the rich knowledge associated with connected radiology reports. The knowledge derived from these reports can be utilized to enhance the performance of deep learning models. In this work, we used a comprehensive chest X-ray findings vocabulary to automatically annotate an extensive collection of chest X-rays using associated radiology reports and a vocabulary-driven concept annotation algorithm. The annotated X-rays are used to train a deep neural network classifier for finding detection. Finally, we developed a knowledge-driven reasoning algorithm that leverages knowledge learned from X-ray reports to improve upon the deep learning module's performance on finding detection. Our results suggest that combining deep learning and knowledge from radiology reports in a hybrid framework can significantly enhance overall performance in the CXR finding detection.
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