We describe our experience in the development of a probabilistic network for the diagnosis of acute cardiopulmonary diseases. A panel of expert physicians collaborated to specify the qualitative part, that is a directed acyclic graph defining a factorization of the joint probability distribution of domain variables. The quantitative part, that is the set of all conditional probability distributions defined by each factor, was estimated in the Bayesian paradigm: we applied a special formal representation, characterized by a low number of parameters and a parameterization intelligible for physicians, elicited the joint prior distribution of parameters from medical experts, and updated it by conditioning on a dataset of hospital patient records using Markov Chain Monte Carlo simulation. Refinement was cyclically performed until the probabilistic network provided satisfactory Concordance Index values for a selection of acute diseases and reasonable inference on six fictitious patient cases. The probabilistic network can be employed to perform medical diagnosis on a total of 63 diseases (38 acute and 25 chronic) on the basis of up to 167 patient findings.
Identifying a patient's key problems over time is a common task for providers at the point care, yet a complex and time-consuming activity given current electric health records. To enable a problem-oriented summarizer to identify a patient's comprehensive list of problems and their salience, we propose an unsupervised phenotyping approach that jointly learns a large number of phenotypes/problems across structured and unstructured data. To identify the appropriate granularity of the learned phenotypes, the model is trained on a target patient population of the same clinic. To enable the content organization of a problem-oriented summarizer, the model identifies phenotype relatedness as well. The model leverages a correlated-mixed membership approach with variational inference applied to heterogenous clinical data. In this paper, we focus our experiments on assessing the learned phenotypes and their relatedness as learned from a specific patient population. We ground our experiments in phenotyping patients from an HIV clinic in a large urban care institution (n=7,523), where patients have voluminous, longitudinal documentation, and where providers would benefit from summaries of these patient's medical histories, whether about their HIV or any comorbidities. We find that the learned phenotypes and their relatedness are clinically valid when assessed qualitatively by clinical experts, and that the model surpasses baseline in inferring phenotype-relatedness when comparing to existing expert-curated condition groupings.
The opioid epidemic in the United States claims over 40,000 lives per year, and it is estimated that well over two million Americans have an opioid use disorder. Over-prescription and misuse of prescription opioids play an important role in the epidemic. Individuals who are prescribed opioids, and who are diagnosed with opioid use disorder, have diverse underlying health states. Policy interventions targeting prescription opioid use, opioid use disorder, and overdose often fail to account for this variation. To identify latent health states, or phenotypes, pertinent to opioid use and opioid use disorders, we use probabilistic topic modeling with medical diagnosis histories from a statewide population of individuals who were prescribed opioids. We demonstrate that our learned phenotypes are predictive of future opioid use-related outcomes. In addition, we show how the learned phenotypes can provide important context for variability in opioid prescriptions. Understanding the heterogeneity in individual health states and in prescription opioid use can help identify policy interventions to address this public health crisis.
With a neural sequence generation model, this study aims to develop a method of writing the patient clinical text s given a brief medical history. As a proof - of - a - concept, we have demonstrated that it can be workable t o use medical concept embedding in clinical text generation . Our model was based on the Sequence - to - Sequence architecture and trained with a large set of de - identified clinical text data . T he quantitative result shows that our concept embedding method decr eased the perplexity of the baseline architecture . Also, we discuss the analyzed r esults from a human evaluation performed by medical doctors .
Objective: We investigate whether deep learning techniques for natural language processing (NLP) can be used efficiently for patient phenotyping. Patient phenotyping is a classification task for determining whether a patient has a medical condition, and is a crucial part of secondary analysis of healthcare data. We assess the performance of deep learning algorithms and compare them with classical NLP approaches. Materials and Methods: We compare convolutional neural networks (CNNs), n-gram models, and approaches based on cTAKES that extract pre-defined medical concepts from clinical notes and use them to predict patient phenotypes. The performance is tested on 10 different phenotyping tasks using 1,610 discharge summaries extracted from the MIMIC-III database. Results: CNNs outperform other phenotyping algorithms in all 10 tasks. The average F1-score of our model is 76 (PPV of 83, and sensitivity of 71) with our model having an F1-score up to 37 points higher than alternative approaches. We additionally assess the interpretability of our model by presenting a method that extracts the most salient phrases for a particular prediction. Conclusion: We show that NLP methods based on deep learning improve the performance of patient phenotyping. Our CNN-based algorithm automatically learns the phrases associated with each patient phenotype. As such, it reduces the annotation complexity for clinical domain experts, who are normally required to develop task-specific annotation rules and identify relevant phrases. Our method performs well in terms of both performance and interpretability, which indicates that deep learning is an effective approach to patient phenotyping based on clinicians' notes.