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Results: 1 to 10 of 64

Publication Record


Identifying lupus patients in electronic health records: Development and validation of machine learning algorithms and application of rule-based algorithms.
Jorge A, Castro VM, Barnado A, Gainer V, Hong C, Cai T, Cai T, Carroll R, Denny JC, Crofford L, Costenbader KH, Liao KP, Karlson EW, Feldman CH
(2019) Semin Arthritis Rheum 49: 84-90
MeSH Terms: Adult, Aged, Algorithms, Databases, Factual, Electronic Health Records, Female, Humans, Lupus Erythematosus, Systemic, Machine Learning, Male, Middle Aged, Natural Language Processing, Sensitivity and Specificity
Show Abstract · Added March 25, 2020
OBJECTIVE - To utilize electronic health records (EHRs) to study SLE, algorithms are needed to accurately identify these patients. We used machine learning to generate data-driven SLE EHR algorithms and assessed performance of existing rule-based algorithms.
METHODS - We randomly selected subjects with ≥ 1 SLE ICD-9/10 codes from our EHR and identified gold standard definite and probable SLE cases by chart review, based on 1997 ACR or 2012 SLICC Classification Criteria. From a training set, we extracted coded and narrative concepts using natural language processing and generated algorithms using penalized logistic regression to classify definite or definite/probable SLE. We assessed predictive characteristics in internal and external cohort validations. We also tested performance characteristics of published rule-based algorithms with pre-specified permutations of ICD-9 codes, laboratory tests and medications in our EHR.
RESULTS - At a specificity of 97%, our machine learning coded algorithm for definite SLE had 90% positive predictive value (PPV) and 64% sensitivity and for definite/probable SLE, 92% PPV and 47% sensitivity. In the external validation, at 97% specificity, the definite/probable algorithm had 94% PPV and 60% sensitivity. Adding NLP concepts did not improve performance metrics. The PPVs of published rule-based algorithms ranged from 45-79% in our EHR.
CONCLUSION - Our machine learning SLE algorithms performed well in internal and external validation. Rule-based SLE algorithms did not transport as well to our EHR. Unique EHR characteristics, clinical practices and research goals regarding the desired sensitivity and specificity of the case definition must be considered when applying algorithms to identify SLE patients.
Copyright © 2019 Elsevier Inc. All rights reserved.
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1 Members
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13 MeSH Terms
Evaluation of a Novel System to Enhance Clinicians' Recognition of Preadmission Adverse Drug Reactions.
Smith JC, Chen Q, Denny JC, Roden DM, Johnson KB, Miller RA
(2018) Appl Clin Inform 9: 313-325
MeSH Terms: Drug-Related Side Effects and Adverse Reactions, Health Personnel, Humans, Medical Informatics, Natural Language Processing, Patient Admission, Patient Discharge, Surveys and Questionnaires
Show Abstract · Added March 24, 2020
BACKGROUND - Often unrecognized by providers, adverse drug reactions (ADRs) diminish patients' quality of life, cause preventable admissions and emergency department visits, and increase health care costs.
OBJECTIVE - This article evaluates whether an automated system, the Adverse Drug Effect Recognizer (ADER), could assist clinicians in detecting and addressing inpatients' ongoing preadmission ADRs.
METHODS - ADER uses natural language processing to extract patients' medications, findings, and past diagnoses from admission notes. It compares excerpted information to a database of known medication adverse effects and promptly warns clinicians about potential ongoing ADRs and potential confounders via alerts placed in patients' electronic health records (EHRs). A 3-month intervention trial evaluated ADER's impact on antihypertensive medication ordering behaviors. At the time of patient admission, ADER warned providers on the Internal Medicine wards of Vanderbilt University Hospital about potential ongoing preadmission antihypertensive medication ADRs. A retrospective control group, comprised similar physicians from a period prior to the intervention, received no alerts. The evaluation compared ordering behaviors for each group to determine if preadmission medications changed during hospitalization or at discharge. The study also analyzed intervention group participants' survey responses and user comments.
RESULTS - ADER identified potential preadmission ADRs for 30% of both groups. Compared with controls, intervention providers more often withheld or discontinued suspected ADR-causing medications during the inpatient stay ( < 0.001). Intervention providers who responded to alert-related surveys held or discontinued suspected ADR-causing medications more often at discharge ( < 0.001).
CONCLUSION - Results indicate that ADER helped physicians recognize ADRs and reduced ordering of suspected ADR-causing medications. In hospitals using EHRs, ADER-like systems could improve clinicians' recognition and elimination of ongoing ADRs.
Schattauer GmbH Stuttgart.
0 Communities
1 Members
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MeSH Terms
Development of an automated phenotyping algorithm for hepatorenal syndrome.
Koola JD, Davis SE, Al-Nimri O, Parr SK, Fabbri D, Malin BA, Ho SB, Matheny ME
(2018) J Biomed Inform 80: 87-95
MeSH Terms: Acute Kidney Injury, Aged, Algorithms, Diagnosis, Computer-Assisted, Electronic Health Records, Female, Hepatorenal Syndrome, Humans, Liver Cirrhosis, Male, Middle Aged, Natural Language Processing, Odds Ratio, Phenotype, ROC Curve, Retrospective Studies, Support Vector Machine
Show Abstract · Added April 10, 2018
OBJECTIVE - Hepatorenal Syndrome (HRS) is a devastating form of acute kidney injury (AKI) in advanced liver disease patients with high morbidity and mortality, but phenotyping algorithms have not yet been developed using large electronic health record (EHR) databases. We evaluated and compared multiple phenotyping methods to achieve an accurate algorithm for HRS identification.
MATERIALS AND METHODS - A national retrospective cohort of patients with cirrhosis and AKI admitted to 124 Veterans Affairs hospitals was assembled from electronic health record data collected from 2005 to 2013. AKI was defined by the Kidney Disease: Improving Global Outcomes criteria. Five hundred and four hospitalizations were selected for manual chart review and served as the gold standard. Electronic Health Record based predictors were identified using structured and free text clinical data, subjected through NLP from the clinical Text Analysis Knowledge Extraction System. We explored several dimension reduction techniques for the NLP data, including newer high-throughput phenotyping and word embedding methods, and ascertained their effectiveness in identifying the phenotype without structured predictor variables. With the combined structured and NLP variables, we analyzed five phenotyping algorithms: penalized logistic regression, naïve Bayes, support vector machines, random forest, and gradient boosting. Calibration and discrimination metrics were calculated using 100 bootstrap iterations. In the final model, we report odds ratios and 95% confidence intervals.
RESULTS - The area under the receiver operating characteristic curve (AUC) for the different models ranged from 0.73 to 0.93; with penalized logistic regression having the best discriminatory performance. Calibration for logistic regression was modest, but gradient boosting and support vector machines were superior. NLP identified 6985 variables; a priori variable selection performed similarly to dimensionality reduction using high-throughput phenotyping and semantic similarity informed clustering (AUC of 0.81 - 0.82).
CONCLUSION - This study demonstrated improved phenotyping of a challenging AKI etiology, HRS, over ICD-9 coding. We also compared performance among multiple approaches to EHR-derived phenotyping, and found similar results between methods. Lastly, we showed that automated NLP dimension reduction is viable for acute illness.
Copyright © 2018 Elsevier Inc. All rights reserved.
0 Communities
1 Members
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17 MeSH Terms
A comparison of rule-based and machine learning approaches for classifying patient portal messages.
Cronin RM, Fabbri D, Denny JC, Rosenbloom ST, Jackson GP
(2017) Int J Med Inform 105: 110-120
MeSH Terms: Bayes Theorem, Communication, Electronic Health Records, Health Personnel, Health Services Needs and Demand, Humans, Machine Learning, Natural Language Processing, Patient Portals
Show Abstract · Added March 14, 2018
OBJECTIVE - Secure messaging through patient portals is an increasingly popular way that consumers interact with healthcare providers. The increasing burden of secure messaging can affect clinic staffing and workflows. Manual management of portal messages is costly and time consuming. Automated classification of portal messages could potentially expedite message triage and delivery of care.
MATERIALS AND METHODS - We developed automated patient portal message classifiers with rule-based and machine learning techniques using bag of words and natural language processing (NLP) approaches. To evaluate classifier performance, we used a gold standard of 3253 portal messages manually categorized using a taxonomy of communication types (i.e., main categories of informational, medical, logistical, social, and other communications, and subcategories including prescriptions, appointments, problems, tests, follow-up, contact information, and acknowledgement). We evaluated our classifiers' accuracies in identifying individual communication types within portal messages with area under the receiver-operator curve (AUC). Portal messages often contain more than one type of communication. To predict all communication types within single messages, we used the Jaccard Index. We extracted the variables of importance for the random forest classifiers.
RESULTS - The best performing approaches to classification for the major communication types were: logistic regression for medical communications (AUC: 0.899); basic (rule-based) for informational communications (AUC: 0.842); and random forests for social communications and logistical communications (AUCs: 0.875 and 0.925, respectively). The best performing classification approach of classifiers for individual communication subtypes was random forests for Logistical-Contact Information (AUC: 0.963). The Jaccard Indices by approach were: basic classifier, Jaccard Index: 0.674; Naïve Bayes, Jaccard Index: 0.799; random forests, Jaccard Index: 0.859; and logistic regression, Jaccard Index: 0.861. For medical communications, the most predictive variables were NLP concepts (e.g., Temporal_Concept, which maps to 'morning', 'evening' and Idea_or_Concept which maps to 'appointment' and 'refill'). For logistical communications, the most predictive variables contained similar numbers of NLP variables and words (e.g., Telephone mapping to 'phone', 'insurance'). For social and informational communications, the most predictive variables were words (e.g., social: 'thanks', 'much', informational: 'question', 'mean').
CONCLUSIONS - This study applies automated classification methods to the content of patient portal messages and evaluates the application of NLP techniques on consumer communications in patient portal messages. We demonstrated that random forest and logistic regression approaches accurately classified the content of portal messages, although the best approach to classification varied by communication type. Words were the most predictive variables for classification of most communication types, although NLP variables were most predictive for medical communication types. As adoption of patient portals increases, automated techniques could assist in understanding and managing growing volumes of messages. Further work is needed to improve classification performance to potentially support message triage and answering.
Copyright © 2017 Elsevier B.V. All rights reserved.
0 Communities
1 Members
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9 MeSH Terms
An active learning-enabled annotation system for clinical named entity recognition.
Chen Y, Lask TA, Mei Q, Chen Q, Moon S, Wang J, Nguyen K, Dawodu T, Cohen T, Denny JC, Xu H
(2017) BMC Med Inform Decis Mak 17: 82
MeSH Terms: Computer Simulation, Humans, Medical Informatics, Natural Language Processing, Problem-Based Learning
Show Abstract · Added March 14, 2018
BACKGROUND - Active learning (AL) has shown the promising potential to minimize the annotation cost while maximizing the performance in building statistical natural language processing (NLP) models. However, very few studies have investigated AL in a real-life setting in medical domain.
METHODS - In this study, we developed the first AL-enabled annotation system for clinical named entity recognition (NER) with a novel AL algorithm. Besides the simulation study to evaluate the novel AL algorithm, we further conducted user studies with two nurses using this system to assess the performance of AL in real world annotation processes for building clinical NER models.
RESULTS - The simulation results show that the novel AL algorithm outperformed traditional AL algorithm and random sampling. However, the user study tells a different story that AL methods did not always perform better than random sampling for different users.
CONCLUSIONS - We found that the increased information content of actively selected sentences is strongly offset by the increased time required to annotate them. Moreover, the annotation time was not considered in the querying algorithms. Our future work includes developing better AL algorithms with the estimation of annotation time and evaluating the system with larger number of users.
0 Communities
1 Members
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5 MeSH Terms
A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD).
Wu Y, Denny JC, Trent Rosenbloom S, Miller RA, Giuse DA, Wang L, Blanquicett C, Soysal E, Xu J, Xu H
(2017) J Am Med Inform Assoc 24: e79-e86
MeSH Terms: Abbreviations as Topic, Electronic Health Records, Humans, Machine Learning, Natural Language Processing, Patient Discharge
Show Abstract · Added March 14, 2018
Objective - The goal of this study was to develop a practical framework for recognizing and disambiguating clinical abbreviations, thereby improving current clinical natural language processing (NLP) systems' capability to handle abbreviations in clinical narratives.
Methods - We developed an open-source framework for clinical abbreviation recognition and disambiguation (CARD) that leverages our previously developed methods, including: (1) machine learning based approaches to recognize abbreviations from a clinical corpus, (2) clustering-based semiautomated methods to generate possible senses of abbreviations, and (3) profile-based word sense disambiguation methods for clinical abbreviations. We applied CARD to clinical corpora from Vanderbilt University Medical Center (VUMC) and generated 2 comprehensive sense inventories for abbreviations in discharge summaries and clinic visit notes. Furthermore, we developed a wrapper that integrates CARD with MetaMap, a widely used general clinical NLP system.
Results and Conclusion - CARD detected 27 317 and 107 303 distinct abbreviations from discharge summaries and clinic visit notes, respectively. Two sense inventories were constructed for the 1000 most frequent abbreviations in these 2 corpora. Using the sense inventories created from discharge summaries, CARD achieved an F1 score of 0.755 for identifying and disambiguating all abbreviations in a corpus from the VUMC discharge summaries, which is superior to MetaMap and Apache's clinical Text Analysis Knowledge Extraction System (cTAKES). Using additional external corpora, we also demonstrated that the MetaMap-CARD wrapper improved MetaMap's performance in recognizing disorder entities in clinical notes. The CARD framework, 2 sense inventories, and the wrapper for MetaMap are publicly available at https://sbmi.uth.edu/ccb/resources/abbreviation.htm . We believe the CARD framework can be a valuable resource for improving abbreviation identification in clinical NLP systems.
© The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com
0 Communities
1 Members
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6 MeSH Terms
Evaluating electronic health record data sources and algorithmic approaches to identify hypertensive individuals.
Teixeira PL, Wei WQ, Cronin RM, Mo H, VanHouten JP, Carroll RJ, LaRose E, Bastarache LA, Rosenbloom ST, Edwards TL, Roden DM, Lasko TA, Dart RA, Nikolai AM, Peissig PL, Denny JC
(2017) J Am Med Inform Assoc 24: 162-171
MeSH Terms: Aged, Algorithms, Blood Pressure Determination, Clinical Coding, Electronic Health Records, Female, Humans, Hypertension, Information Storage and Retrieval, Machine Learning, Male, Middle Aged, Natural Language Processing, Phenotype, ROC Curve
Show Abstract · Added April 7, 2017
OBJECTIVE - Phenotyping algorithms applied to electronic health record (EHR) data enable investigators to identify large cohorts for clinical and genomic research. Algorithm development is often iterative, depends on fallible investigator intuition, and is time- and labor-intensive. We developed and evaluated 4 types of phenotyping algorithms and categories of EHR information to identify hypertensive individuals and controls and provide a portable module for implementation at other sites.
MATERIALS AND METHODS - We reviewed the EHRs of 631 individuals followed at Vanderbilt for hypertension status. We developed features and phenotyping algorithms of increasing complexity. Input categories included International Classification of Diseases, Ninth Revision (ICD9) codes, medications, vital signs, narrative-text search results, and Unified Medical Language System (UMLS) concepts extracted using natural language processing (NLP). We developed a module and tested portability by replicating 10 of the best-performing algorithms at the Marshfield Clinic.
RESULTS - Random forests using billing codes, medications, vitals, and concepts had the best performance with a median area under the receiver operator characteristic curve (AUC) of 0.976. Normalized sums of all 4 categories also performed well (0.959 AUC). The best non-NLP algorithm combined normalized ICD9 codes, medications, and blood pressure readings with a median AUC of 0.948. Blood pressure cutoffs or ICD9 code counts alone had AUCs of 0.854 and 0.908, respectively. Marshfield Clinic results were similar.
CONCLUSION - This work shows that billing codes or blood pressure readings alone yield good hypertension classification performance. However, even simple combinations of input categories improve performance. The most complex algorithms classified hypertension with excellent recall and precision.
© The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
0 Communities
4 Members
0 Resources
15 MeSH Terms
PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability.
Kirby JC, Speltz P, Rasmussen LV, Basford M, Gottesman O, Peissig PL, Pacheco JA, Tromp G, Pathak J, Carrell DS, Ellis SB, Lingren T, Thompson WK, Savova G, Haines J, Roden DM, Harris PA, Denny JC
(2016) J Am Med Inform Assoc 23: 1046-1052
MeSH Terms: Algorithms, Data Mining, Electronic Health Records, Genomics, Humans, International Classification of Diseases, Knowledge Bases, Natural Language Processing, Phenotype
Show Abstract · Added March 14, 2018
OBJECTIVE - Health care generated data have become an important source for clinical and genomic research. Often, investigators create and iteratively refine phenotype algorithms to achieve high positive predictive values (PPVs) or sensitivity, thereby identifying valid cases and controls. These algorithms achieve the greatest utility when validated and shared by multiple health care systems.Materials and Methods We report the current status and impact of the Phenotype KnowledgeBase (PheKB, http://phekb.org), an online environment supporting the workflow of building, sharing, and validating electronic phenotype algorithms. We analyze the most frequent components used in algorithms and their performance at authoring institutions and secondary implementation sites.
RESULTS - As of June 2015, PheKB contained 30 finalized phenotype algorithms and 62 algorithms in development spanning a range of traits and diseases. Phenotypes have had over 3500 unique views in a 6-month period and have been reused by other institutions. International Classification of Disease codes were the most frequently used component, followed by medications and natural language processing. Among algorithms with published performance data, the median PPV was nearly identical when evaluated at the authoring institutions (n = 44; case 96.0%, control 100%) compared to implementation sites (n = 40; case 97.5%, control 100%).
DISCUSSION - These results demonstrate that a broad range of algorithms to mine electronic health record data from different health systems can be developed with high PPV, and algorithms developed at one site are generally transportable to others.
CONCLUSION - By providing a central repository, PheKB enables improved development, transportability, and validity of algorithms for research-grade phenotypes using health care generated data.
© The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
0 Communities
2 Members
0 Resources
9 MeSH Terms
Optimizing annotation resources for natural language de-identification via a game theoretic framework.
Li M, Carrell D, Aberdeen J, Hirschman L, Kirby J, Li B, Vorobeychik Y, Malin BA
(2016) J Biomed Inform 61: 97-109
MeSH Terms: Confidentiality, Electronic Health Records, Humans, Language, Natural Language Processing, Risk
Show Abstract · Added April 10, 2018
OBJECTIVE - Electronic medical records (EMRs) are increasingly repurposed for activities beyond clinical care, such as to support translational research and public policy analysis. To mitigate privacy risks, healthcare organizations (HCOs) aim to remove potentially identifying patient information. A substantial quantity of EMR data is in natural language form and there are concerns that automated tools for detecting identifiers are imperfect and leak information that can be exploited by ill-intentioned data recipients. Thus, HCOs have been encouraged to invest as much effort as possible to find and detect potential identifiers, but such a strategy assumes the recipients are sufficiently incentivized and capable of exploiting leaked identifiers. In practice, such an assumption may not hold true and HCOs may overinvest in de-identification technology. The goal of this study is to design a natural language de-identification framework, rooted in game theory, which enables an HCO to optimize their investments given the expected capabilities of an adversarial recipient.
METHODS - We introduce a Stackelberg game to balance risk and utility in natural language de-identification. This game represents a cost-benefit model that enables an HCO with a fixed budget to minimize their investment in the de-identification process. We evaluate this model by assessing the overall payoff to the HCO and the adversary using 2100 clinical notes from Vanderbilt University Medical Center. We simulate several policy alternatives using a range of parameters, including the cost of training a de-identification model and the loss in data utility due to the removal of terms that are not identifiers. In addition, we compare policy options where, when an attacker is fined for misuse, a monetary penalty is paid to the publishing HCO as opposed to a third party (e.g., a federal regulator).
RESULTS - Our results show that when an HCO is forced to exhaust a limited budget (set to $2000 in the study), the precision and recall of the de-identification of the HCO are 0.86 and 0.8, respectively. A game-based approach enables a more refined cost-benefit tradeoff, improving both privacy and utility for the HCO. For example, our investigation shows that it is possible for an HCO to release the data without spending all their budget on de-identification and still deter the attacker, with a precision of 0.77 and a recall of 0.61 for the de-identification. There also exist scenarios in which the model indicates an HCO should not release any data because the risk is too great. In addition, we find that the practice of paying fines back to a HCO (an artifact of suing for breach of contract), as opposed to a third party such as a federal regulator, can induce an elevated level of data sharing risk, where the HCO is incentivized to bait the attacker to elicit compensation.
CONCLUSIONS - A game theoretic framework can be applied in leading HCO's to optimized decision making in natural language de-identification investments before sharing EMR data.
Copyright © 2016 Elsevier Inc. All rights reserved.
0 Communities
1 Members
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MeSH Terms
Automated Classification of Consumer Health Information Needs in Patient Portal Messages.
Cronin RM, Fabbri D, Denny JC, Jackson GP
(2015) AMIA Annu Symp Proc 2015: 1861-70
MeSH Terms: Consumer Health Information, Electronic Health Records, Health Resources, Health Services Needs and Demand, Humans, Natural Language Processing, Patient Portals
Show Abstract · Added March 14, 2018
Patients have diverse health information needs, and secure messaging through patient portals is an emerging means by which such needs are expressed and met. As patient portal adoption increases, growing volumes of secure messages may burden healthcare providers. Automated classification could expedite portal message triage and answering. We created four automated classifiers based on word content and natural language processing techniques to identify health information needs in 1000 patient-generated portal messages. Logistic regression and random forest classifiers detected single information needs well, with area under the curves of 0.804-0.914. A logistic regression classifier accurately found the set of needs within a message, with a Jaccard index of 0.859 (95% Confidence Interval: (0.847, 0.871)). Automated classification of consumer health information needs expressed in patient portal messages is feasible and may allow direct linking to relevant resources or creation of institutional resources for commonly expressed needs.
0 Communities
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7 MeSH Terms