People: Principal Investigator
Trajectory analysis for postoperative pain using electronic health records: A nonparametric method with robust linear regression and K-medians cluster analysis.
Health informatics journal
Postoperative pain scores are widely monitored and collected in the electronic health record, yet current methods fail to fully leverage the data with fast implementation. A robust linear regression was fitted to describe the association between the log-scaled pain score and time from discharge after total knee replacement. The estimated trajectories were used for a subsequent K-medians cluster analysis to categorize the longitudinal pain score patterns into distinct clusters. For each cluster, a mixture regression model estimated the association between pain score and time to discharge adjusting for confounding. The fitted regression model generated the pain trajectory pattern for given cluster. Finally, regression analyses examined the association between pain trajectories and patient outcomes. A total of 3442 surgeries were identified with a median of 22 pain scores at an academic hospital during 2009-2016. Four pain trajectory patterns were identified and one was associated with higher rates of outcomes. In conclusion, we described a novel approach with fast implementation to model patients' pain experience using electronic health records. In the era of big data science, clinical research should be learning from all available data regarding a patient's episode of care instead of focusing on the "average" patient outcomes.
View details for DOI 10.1177/1460458219881339
View details for PubMedID 31621460
Real world evidence in cardiovascular medicine: assuring data validity in electronic health record-based studies.
Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: With growing availability of digital health data and technology, health-related studies are increasingly augmented or implemented using real world data (RWD). Recent federal initiatives promote the use of RWD to make clinical assertions that influence regulatory decision-making. Our objective was to determine whether traditional real world evidence (RWE) techniques in cardiovascular medicine achieve accuracy sufficient for credible clinical assertions, also known as "regulatory-grade" RWE.DESIGN: Retrospective observational study using electronic health records (EHR), 2010-2016.METHODS: A predefined set of clinical concepts was extracted from EHR structured (EHR-S) and unstructured (EHR-U) data using traditional query techniques and artificial intelligence (AI) technologies, respectively. Performance was evaluated against manually annotated cohorts using standard metrics. Accuracy was compared to pre-defined criteria for regulatory-grade. Differences in accuracy were compared using Chi-square test.RESULTS: The dataset included 10840 clinical notes. Individual concept occurrence ranged from 194 for coronary artery bypass graft to 4502 for diabetes mellitus. In EHR-S, average recall and precision were 51.7% and 98.3%, respectively and 95.5% and 95.3% in EHR-U, respectively. For each clinical concept, EHR-S accuracy was below regulatory-grade, while EHR-U met or exceeded criteria, with the exception of medications.CONCLUSIONS: Identifying an appropriate RWE approach is dependent on cohorts studied and accuracy required. In this study, recall varied greatly between EHR-S and EHR-U. Overall, EHR-S did not meet regulatory grade criteria, while EHR-U did. These results suggest that recall should be routinely measured in EHR-based studes intended for regulatory use. Furthermore, advanced data and technologies may be required to achieve regulatory grade results.
View details for DOI 10.1093/jamia/ocz119
View details for PubMedID 31414700
Comparison of Orthogonal NLP Methods for Clinical Phenotyping and Assessment of Bone Scan Utilization among Prostate Cancer Patients.
Journal of biomedical informatics
Clinical care guidelines recommend that newly diagnosed prostate cancer patients at high risk for metastatic spread receive a bone scan prior to treatment and that low risk patients not receive it. The objective was to develop an automated pipeline to interrogate heterogeneous data to evaluate the use of bone scans using a two different Natural Language Processing (NLP) approaches.Our cohort was divided into risk groups based on Electronic Health Records (EHR). Information on bone scan utilization was identified in both structured data and free text from clinical notes. Our pipeline annotated sentences with a combination of a rule-based method using the ConText algorithm (a generalization of NegEx) and a Convolutional Neural Network (CNN) method using word2vec to produce word embeddings.A total of 5,500 patients and 369,764 notes were included in the study. A total of 39% of patients were high-risk and 73% of these received a bone scan; of the 18% low risk patients, 10% received one. The accuracy of CNN model outperformed the rule-based model one (F-measure = 0.918 and 0.897 respectively). We demonstrate a combination of both models could maximize precision or recall, based on the study question.Using structured data, we accurately classified patients' cancer risk group, identified bone scan documentation with two NLP methods, and evaluated guideline adherence. Our pipeline can be used to provide concrete feedback to clinicians and guide treatment decisions.
View details for PubMedID 31014980
Predicting inadequate postoperative pain management in depressed patients: A machine learning approach.
2019; 14 (2): e0210575
Widely-prescribed prodrug opioids (e.g., hydrocodone) require conversion by liver enzyme CYP-2D6 to exert their analgesic effects. The most commonly prescribed antidepressant, selective serotonin reuptake inhibitors (SSRIs), inhibits CYP-2D6 activity and therefore may reduce the effectiveness of prodrug opioids. We used a machine learning approach to identify patients prescribed a combination of SSRIs and prodrug opioids postoperatively and to examine the effect of this combination on postoperative pain control. Using EHR data from an academic medical center, we identified patients receiving surgery over a 9-year period. We developed and validated natural language processing (NLP) algorithms to extract depression-related information (diagnosis, SSRI use, symptoms) from structured and unstructured data elements. The primary outcome was the difference between preoperative pain score and postoperative pain at discharge, 3-week and 8-week time points. We developed computational models to predict the increase or decrease in the postoperative pain across the 3 time points by using the patient's EHR data (e.g. medications, vitals, demographics) captured before surgery. We evaluate the generalizability of the model using 10-fold cross-validation method where the holdout test method is repeated 10 times and mean area-under-the-curve (AUC) is considered as evaluation metrics for the prediction performance. We identified 4,306 surgical patients with symptoms of depression. A total of 14.1% were prescribed both an SSRI and a prodrug opioid, 29.4% were prescribed an SSRI and a non-prodrug opioid, 18.6% were prescribed a prodrug opioid but were not on SSRIs, and 37.5% were prescribed a non-prodrug opioid but were not on SSRIs. Our NLP algorithm identified depression with a F1 score of 0.95 against manual annotation of 300 randomly sampled clinical notes. On average, patients receiving prodrug opioids had lower average pain scores (p<0.05), with the exception of the SSRI+ group at 3-weeks postoperative follow-up. However, SSRI+/Prodrug+ had significantly worse pain control at discharge, 3 and 8-week follow-up (p < .01) compared to SSRI+/Prodrug- patients, whereas there was no difference in pain control among the SSRI- patients by prodrug opioid (p>0.05). The machine learning algorithm accurately predicted the increase or decrease of the discharge, 3-week and 8-week follow-up pain scores when compared to the pre-operative pain score using 10-fold cross validation (mean area under the receiver operating characteristic curve 0.87, 0.81, and 0.69, respectively). Preoperative pain, surgery type, and opioid tolerance were the strongest predictors of postoperative pain control. We provide the first direct clinical evidence that the known ability of SSRIs to inhibit prodrug opioid effectiveness is associated with worse pain control among depressed patients. Current prescribing patterns indicate that prescribers may not account for this interaction when choosing an opioid. The study results imply that prescribers might instead choose direct acting opioids (e.g. oxycodone or morphine) in depressed patients on SSRIs.
View details for PubMedID 30726237
M.S., Stanford University, Health Services Research (2013)
Ph.D., University Claude Bernard, Lyon 1, Computational Biology (1999)
M.P.H., Yale University, Epidemiology (1993)
B.A., University California, Irvine, Psychology (1991)
B.S., University of California, Irvine, Biology (1991)