18,839 research outputs found
Predicting diabetes-related hospitalizations based on electronic health records
OBJECTIVE: To derive a predictive model to identify patients likely to be hospitalized during the following year due to complications attributed to Type II diabetes. METHODS: A variety of supervised machine learning classification methods were tested and a new method that discovers hidden patient clusters in the positive class (hospitalized) was developed while, at the same time, sparse linear support vector machine classifiers were derived to separate positive samples from the negative ones (non-hospitalized). The convergence of the new method was established and theoretical guarantees were proved on how the classifiers it produces generalize to a test set not seen during training. RESULTS: The methods were tested on a large set of patients from the Boston Medical Center - the largest safety net hospital in New England. It is found that our new joint clustering/classification method achieves an accuracy of 89% (measured in terms of area under the ROC Curve) and yields informative clusters which can help interpret the classification results, thus increasing the trust of physicians to the algorithmic output and providing some guidance towards preventive measures. While it is possible to increase accuracy to 92% with other methods, this comes with increased computational cost and lack of interpretability. The analysis shows that even a modest probability of preventive actions being effective (more than 19%) suffices to generate significant hospital care savings. CONCLUSIONS: Predictive models are proposed that can help avert hospitalizations, improve health outcomes and drastically reduce hospital expenditures. The scope for savings is significant as it has been estimated that in the USA alone, about $5.8 billion are spent each year on diabetes-related hospitalizations that could be prevented.Accepted manuscrip
Deepr: A Convolutional Net for Medical Records
Feature engineering remains a major bottleneck when creating predictive
systems from electronic medical records. At present, an important missing
element is detecting predictive regular clinical motifs from irregular episodic
records. We present Deepr (short for Deep record), a new end-to-end deep
learning system that learns to extract features from medical records and
predicts future risk automatically. Deepr transforms a record into a sequence
of discrete elements separated by coded time gaps and hospital transfers. On
top of the sequence is a convolutional neural net that detects and combines
predictive local clinical motifs to stratify the risk. Deepr permits
transparent inspection and visualization of its inner working. We validate
Deepr on hospital data to predict unplanned readmission after discharge. Deepr
achieves superior accuracy compared to traditional techniques, detects
meaningful clinical motifs, and uncovers the underlying structure of the
disease and intervention space
Processing of Electronic Health Records using Deep Learning: A review
Availability of large amount of clinical data is opening up new research
avenues in a number of fields. An exciting field in this respect is healthcare,
where secondary use of healthcare data is beginning to revolutionize
healthcare. Except for availability of Big Data, both medical data from
healthcare institutions (such as EMR data) and data generated from health and
wellbeing devices (such as personal trackers), a significant contribution to
this trend is also being made by recent advances on machine learning,
specifically deep learning algorithms
Profiling risk factors for chronic uveitis in juvenile idiopathic arthritis: a new model for EHR-based research.
BackgroundJuvenile idiopathic arthritis is the most common rheumatic disease in children. Chronic uveitis is a common and serious comorbid condition of juvenile idiopathic arthritis, with insidious presentation and potential to cause blindness. Knowledge of clinical associations will improve risk stratification. Based on clinical observation, we hypothesized that allergic conditions are associated with chronic uveitis in juvenile idiopathic arthritis patients.MethodsThis study is a retrospective cohort study using Stanford's clinical data warehouse containing data from Lucile Packard Children's Hospital from 2000-2011 to analyze patient characteristics associated with chronic uveitis in a large juvenile idiopathic arthritis cohort. Clinical notes in patients under 16 years of age were processed via a validated text analytics pipeline. Bivariate-associated variables were used in a multivariate logistic regression adjusted for age, gender, and race. Previously reported associations were evaluated to validate our methods. The main outcome measure was presence of terms indicating allergy or allergy medications use overrepresented in juvenile idiopathic arthritis patients with chronic uveitis. Residual text features were then used in unsupervised hierarchical clustering to compare clinical text similarity between patients with and without uveitis.ResultsPreviously reported associations with uveitis in juvenile idiopathic arthritis patients (earlier age at arthritis diagnosis, oligoarticular-onset disease, antinuclear antibody status, history of psoriasis) were reproduced in our study. Use of allergy medications and terms describing allergic conditions were independently associated with chronic uveitis. The association with allergy drugs when adjusted for known associations remained significant (OR 2.54, 95% CI 1.22-5.4).ConclusionsThis study shows the potential of using a validated text analytics pipeline on clinical data warehouses to examine practice-based evidence for evaluating hypotheses formed during patient care. Our study reproduces four known associations with uveitis development in juvenile idiopathic arthritis patients, and reports a new association between allergic conditions and chronic uveitis in juvenile idiopathic arthritis patients
Using Machine Learning and Natural Language Processing to Review and Classify the Medical Literature on Cancer Susceptibility Genes
PURPOSE: The medical literature relevant to germline genetics is growing
exponentially. Clinicians need tools monitoring and prioritizing the literature
to understand the clinical implications of the pathogenic genetic variants. We
developed and evaluated two machine learning models to classify abstracts as
relevant to the penetrance (risk of cancer for germline mutation carriers) or
prevalence of germline genetic mutations. METHODS: We conducted literature
searches in PubMed and retrieved paper titles and abstracts to create an
annotated dataset for training and evaluating the two machine learning
classification models. Our first model is a support vector machine (SVM) which
learns a linear decision rule based on the bag-of-ngrams representation of each
title and abstract. Our second model is a convolutional neural network (CNN)
which learns a complex nonlinear decision rule based on the raw title and
abstract. We evaluated the performance of the two models on the classification
of papers as relevant to penetrance or prevalence. RESULTS: For penetrance
classification, we annotated 3740 paper titles and abstracts and used 60% for
training the model, 20% for tuning the model, and 20% for evaluating the model.
The SVM model achieves 89.53% accuracy (percentage of papers that were
correctly classified) while the CNN model achieves 88.95 % accuracy. For
prevalence classification, we annotated 3753 paper titles and abstracts. The
SVM model achieves 89.14% accuracy while the CNN model achieves 89.13 %
accuracy. CONCLUSION: Our models achieve high accuracy in classifying abstracts
as relevant to penetrance or prevalence. By facilitating literature review,
this tool could help clinicians and researchers keep abreast of the burgeoning
knowledge of gene-cancer associations and keep the knowledge bases for clinical
decision support tools up to date
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Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia.
The identification of novel disease associations using big-data for patient care has had limited success. In this study, we created a longitudinal disease network of traced readmissions (disease trajectories), merging data from over 10.4 million inpatients through the Healthcare Cost and Utilization Project, which allowed the representation of disease progression mapping over 300 diseases. From these disease trajectories, we discovered an interesting association between schizophrenia and rhabdomyolysis, a rare muscle disease (incidence < 1E-04) (relative risk, 2.21 [1.80-2.71, confidence interval = 0.95], P-value 9.54E-15). We validated this association by using independent electronic medical records from over 830,000 patients at the University of California, San Francisco (UCSF) medical center. A case review of 29 rhabdomyolysis incidents in schizophrenia patients at UCSF demonstrated that 62% are idiopathic, without the use of any drug known to lead to this adverse event, suggesting a warning to physicians to watch for this unexpected risk of schizophrenia. Large-scale analysis of disease trajectories can help physicians understand potential sequential events in their patients
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