Dataset Information

Unsupervised ensemble ranking of terms in electronic health record notes based on their importance to patients.

ABSTRACT: Allowing patients to access their own electronic health record (EHR) notes through online patient portals has the potential to improve patient-centered care. However, EHR notes contain abundant medical jargon that can be difficult for patients to comprehend. One way to help patients is to reduce information overload and help them focus on medical terms that matter most to them. Targeted education can then be developed to improve patient EHR comprehension and the quality of care.The aim of this work was to develop FIT (Finding Important Terms for patients), an unsupervised natural language processing (NLP) system that ranks medical terms in EHR notes based on their importance to patients.We built FIT on a new unsupervised ensemble ranking model derived from the biased random walk algorithm to combine heterogeneous information resources for ranking candidate terms from each EHR note. Specifically, FIT integrates four single views (rankers) for term importance: patient use of medical concepts, document-level term salience, word co-occurrence based term relatedness, and topic coherence. It also incorporates partial information of term importance as conveyed by terms' unfamiliarity levels and semantic types. We evaluated FIT on 90 expert-annotated EHR notes and used the four single-view rankers as baselines. In addition, we implemented three benchmark unsupervised ensemble ranking methods as strong baselines.FIT achieved 0.885 AUC-ROC for ranking candidate terms from EHR notes to identify important terms. When including term identification, the performance of FIT for identifying important terms from EHR notes was 0.813 AUC-ROC. Both performance scores significantly exceeded the corresponding scores from the four single rankers (P<0.001). FIT also outperformed the three ensemble rankers for most metrics. Its performance is relatively insensitive to its parameter.FIT can automatically identify EHR terms important to patients. It may help develop future interventions to improve quality of care. By using unsupervised learning as well as a robust and flexible framework for information fusion, FIT can be readily applied to other domains and applications.

SUBMITTER: Chen J

PROVIDER: S-EPMC5505865 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Unsupervised ensemble ranking of terms in electronic health record notes based on their importance to patients.

Chen Jinying J Yu Hong H

Journal of biomedical informatics 20170304

<h4>Background</h4>Allowing patients to access their own electronic health record (EHR) notes through online patient portals has the potential to improve patient-centered care. However, EHR notes contain abundant medical jargon that can be difficult for patients to comprehend. One way to help patients is to reduce information overload and help them focus on medical terms that matter most to them. Targeted education can then be developed to improve patient EHR comprehension and the quality of car ...[more]

PMID: 28267590

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Project description:BackgroundMedical terms are a major obstacle for patients to comprehend their electronic health record (EHR) notes. Clinical natural language processing (NLP) systems that link EHR terms to lay terms or definitions allow patients to easily access helpful information when reading through their EHR notes, and have shown to improve patient EHR comprehension. However, high-quality lay language resources for EHR terms are very limited in the public domain. Because expanding and curating such a resource is a costly process, it is beneficial and even necessary to identify terms important for patient EHR comprehension first.ObjectiveWe aimed to develop an NLP system, called adapted distant supervision (ADS), to rank candidate terms mined from EHR corpora. We will give EHR terms ranked as high by ADS a higher priority for lay language annotation-that is, creating lay definitions for these terms.MethodsAdapted distant supervision uses distant supervision from consumer health vocabulary and transfer learning to adapt itself to solve the problem of ranking EHR terms in the target domain. We investigated 2 state-of-the-art transfer learning algorithms (ie, feature space augmentation and supervised distant supervision) and designed 5 types of learning features, including distributed word representations learned from large EHR data for ADS. For evaluating ADS, we asked domain experts to annotate 6038 candidate terms as important or nonimportant for EHR comprehension. We then randomly divided these data into the target-domain training data (1000 examples) and the evaluation data (5038 examples). We compared ADS with 2 strong baselines, including standard supervised learning, on the evaluation data.ResultsThe ADS system using feature space augmentation achieved the best average precision, 0.850, on the evaluation set when using 1000 target-domain training examples. The ADS system using supervised distant supervision achieved the best average precision, 0.819, on the evaluation set when using only 100 target-domain training examples. The 2 ADS systems both performed significantly better than the baseline systems (P<.001 for all measures and all conditions). Using a rich set of learning features contributed to ADS's performance substantially.ConclusionsADS can effectively rank terms mined from EHRs. Transfer learning improved ADS's performance even with a small number of target-domain training examples. EHR terms prioritized by ADS were used to expand a lay language resource that supports patient EHR comprehension. The top 10,000 EHR terms ranked by ADS are available upon request.

Project description:BACKGROUND:Many health care systems now allow patients to access their electronic health record (EHR) notes online through patient portals. Medical jargon in EHR notes can confuse patients, which may interfere with potential benefits of patient access to EHR notes. OBJECTIVE:The aim of this study was to develop and evaluate the usability and content quality of NoteAid, a Web-based natural language processing system that links medical terms in EHR notes to lay definitions, that is, definitions easily understood by lay people. METHODS:NoteAid incorporates two core components: CoDeMed, a lexical resource of lay definitions for medical terms, and MedLink, a computational unit that links medical terms to lay definitions. We developed innovative computational methods, including an adapted distant supervision algorithm to prioritize medical terms important for EHR comprehension to facilitate the effort of building CoDeMed. Ten physician domain experts evaluated the user interface and content quality of NoteAid. The evaluation protocol included a cognitive walkthrough session and a postsession questionnaire. Physician feedback sessions were audio-recorded. We used standard content analysis methods to analyze qualitative data from these sessions. RESULTS:Physician feedback was mixed. Positive feedback on NoteAid included (1) Easy to use, (2) Good visual display, (3) Satisfactory system speed, and (4) Adequate lay definitions. Opportunities for improvement arising from evaluation sessions and feedback included (1) improving the display of definitions for partially matched terms, (2) including more medical terms in CoDeMed, (3) improving the handling of terms whose definitions vary depending on different contexts, and (4) standardizing the scope of definitions for medicines. On the basis of these results, we have improved NoteAid's user interface and a number of definitions, and added 4502 more definitions in CoDeMed. CONCLUSIONS:Physician evaluation yielded useful feedback for content validation and refinement of this innovative tool that has the potential to improve patient EHR comprehension and experience using patient portals. Future ongoing work will develop algorithms to handle ambiguous medical terms and test and evaluate NoteAid with patients.

Project description:ImportanceAs health information transparency increases, patients more often seek their health data. More than 44 million patients in the US can now readily access their ambulatory visit notes online, and the practice is increasing abroad. Few studies have assessed documentation errors that patients identify in their notes and how these may inform patient engagement and safety strategies.ObjectiveTo assess the frequency and types of errors identified by patients who read open ambulatory visit notes.Design, setting, and participantsIn this survey study, a total of 136?815 patients at 3 US health care organizations with open notes, including 79 academic and community ambulatory care practices, received invitations to an online survey from June 5 to October 20, 2017. Patients who had at least 1 ambulatory note and had logged onto the portal at least once in the past 12 months were included. Data analysis was performed from July 3, 2018, to April 27, 2020.ExposuresAccess to ambulatory care open notes through patient portals for up to 7 years (2010-2017).Main outcomes and measuresProportion of patients reporting a mistake and how serious they perceived the mistake to be, factors associated with finding errors characterized by patients as serious, and categories of patient-reported errors.ResultsOf 136?815 patients who received survey invitations, 29?656 (21.7%) responded and 22?889 patients (mean [SD] age, 55.16 [15.96] years; 14 447 [63.1%] female; 18 301 [80.0%] white) read 1 or more notes in the past 12 months and completed error questions. Of these patients, 4830 (21.1%) reported a perceived mistake and 2043 (42.3%) reported that the mistake was serious (somewhat serious: 1563 [32.4%]; very serious: 480 [9.9%]). In multivariable analysis, female patients (relative risk [RR], 1.79; 95% CI, 1.72-1.85), more educated patients (RR, 1.38; 95% CI, 1.29-1.48), sicker patients (RR, 1.89; 95% CI, 1.84-1.94), those aged 45 to 64 years (RR, 2.23; 95% CI, 2.06-2.42), those 65 years or older (RR, 2.00; 95% CI, 1.73-2.32), and those who read more than 1 note (2-3 notes: RR, 1.82; 95% CI, 1.34-2.47; ?4 notes: RR, 3.09; 95% CI, 2.02-4.73) were more likely to report a mistake that they found to be serious compared with their reference groups. After categorization of patient-reported very serious mistakes, those specifically mentioning the word diagnosis or describing a specific error in current or past diagnoses were most common (98 of 356 [27.5%]), followed by inaccurate medical history (85 of 356 [23.9%]), medications or allergies (50 of 356 [14.0%]), and tests, procedures, or results (30 of 356 [8.4%]). A total of 23 (6.5%) reflected notes reportedly written on the wrong patient. Of 433 very serious errors, 255 (58.9%) included at least 1 perceived error potentially associated with the diagnostic process (eg, history, physical examination, tests, referrals, and communication).Conclusions and relevanceIn this study, patients who read ambulatory notes online perceived mistakes, a substantial proportion of which they found to be serious. Older and sicker patients were twice as likely to report a serious error compared with younger and healthier patients, indicating important safety and quality implications. Sharing notes with patients may help engage them to improve record accuracy and health care safety together with practitioners.

Project description:BackgroundSuicide is an important public health concern in the United States and around the world. There has been significant work examining machine learning approaches to identify and predict intentional self-harm and suicide using existing data sets. With recent advances in computing, deep learning applications in health care are gaining momentum.ObjectiveThis study aimed to leverage the information in clinical notes using deep neural networks (DNNs) to (1) improve the identification of patients treated for intentional self-harm and (2) predict future self-harm events.MethodsWe extracted clinical text notes from electronic health records (EHRs) of 835 patients with International Classification of Diseases (ICD) codes for intentional self-harm and 1670 matched controls who never had any intentional self-harm ICD codes. The data were divided into training and holdout test sets. We tested a number of algorithms on clinical notes associated with the intentional self-harm codes using the training set, including several traditional bag-of-words-based models and 2 DNN models: a convolutional neural network (CNN) and a long short-term memory model. We also evaluated the predictive performance of the DNNs on a subset of patients who had clinical notes 1 to 6 months before the first intentional self-harm event. Finally, we evaluated the impact of a pretrained model using Word2vec (W2V) on performance.ResultsThe area under the receiver operating characteristic curve (AUC) for the CNN on the phenotyping task, that is, the detection of intentional self-harm in clinical notes concurrent with the events was 0.999, with an F1 score of 0.985. In the predictive task, the CNN achieved the highest performance with an AUC of 0.882 and an F1 score of 0.769. Although pretraining with W2V shortened the DNN training time, it did not improve performance.ConclusionsThe strong performance on the first task, namely, phenotyping based on clinical notes, suggests that such models could be used effectively for surveillance of intentional self-harm in clinical text in an EHR. The modest performance on the predictive task notwithstanding, the results using DNN models on clinical text alone are competitive with other reports in the literature using risk factors from structured EHR data.

Project description:BACKGROUND:The bidirectional encoder representations from transformers (BERT) model has achieved great success in many natural language processing (NLP) tasks, such as named entity recognition and question answering. However, little prior work has explored this model to be used for an important task in the biomedical and clinical domains, namely entity normalization. OBJECTIVE:We aim to investigate the effectiveness of BERT-based models for biomedical or clinical entity normalization. In addition, our second objective is to investigate whether the domains of training data influence the performances of BERT-based models as well as the degree of influence. METHODS:Our data was comprised of 1.5 million unlabeled electronic health record (EHR) notes. We first fine-tuned BioBERT on this large collection of unlabeled EHR notes. This generated our BERT-based model trained using 1.5 million electronic health record notes (EhrBERT). We then further fine-tuned EhrBERT, BioBERT, and BERT on three annotated corpora for biomedical and clinical entity normalization: the Medication, Indication, and Adverse Drug Events (MADE) 1.0 corpus, the National Center for Biotechnology Information (NCBI) disease corpus, and the Chemical-Disease Relations (CDR) corpus. We compared our models with two state-of-the-art normalization systems, namely MetaMap and disease name normalization (DNorm). RESULTS:EhrBERT achieved 40.95% F1 in the MADE 1.0 corpus for mapping named entities to the Medical Dictionary for Regulatory Activities and the Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT), which have about 380,000 terms. In this corpus, EhrBERT outperformed MetaMap by 2.36% in F1. For the NCBI disease corpus and CDR corpus, EhrBERT also outperformed DNorm by improving the F1 scores from 88.37% and 89.92% to 90.35% and 93.82%, respectively. Compared with BioBERT and BERT, EhrBERT outperformed them on the MADE 1.0 corpus and the CDR corpus. CONCLUSIONS:Our work shows that BERT-based models have achieved state-of-the-art performance for biomedical and clinical entity normalization. BERT-based models can be readily fine-tuned to normalize any kind of named entities.

Dataset Information

Unsupervised ensemble ranking of terms in electronic health record notes based on their importance to patients.

Publications

Unsupervised ensemble ranking of terms in electronic health record notes based on their importance to patients.

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