Dataset Information

Extraction of Information Related to Drug Safety Surveillance From Electronic Health Record Notes: Joint Modeling of Entities and Relations Using Knowledge-Aware Neural Attentive Models.

ABSTRACT: BACKGROUND:An adverse drug event (ADE) is commonly defined as "an injury resulting from medical intervention related to a drug." Providing information related to ADEs and alerting caregivers at the point of care can reduce the risk of prescription and diagnostic errors and improve health outcomes. ADEs captured in structured data in electronic health records (EHRs) as either coded problems or allergies are often incomplete, leading to underreporting. Therefore, it is important to develop capabilities to process unstructured EHR data in the form of clinical notes, which contain a richer documentation of a patient's ADE. Several natural language processing (NLP) systems have been proposed to automatically extract information related to ADEs. However, the results from these systems showed that significant improvement is still required for the automatic extraction of ADEs from clinical notes. OBJECTIVE:This study aims to improve the automatic extraction of ADEs and related information such as drugs, their attributes, and reason for administration from the clinical notes of patients. METHODS:This research was conducted using discharge summaries from the Medical Information Mart for Intensive Care III (MIMIC-III) database obtained through the 2018 National NLP Clinical Challenges (n2c2) annotated with drugs, drug attributes (ie, strength, form, frequency, route, dosage, duration), ADEs, reasons, and relations between drugs and other entities. We developed a deep learning-based system for extracting these drug-centric concepts and relations simultaneously using a joint method enhanced with contextualized embeddings, a position-attention mechanism, and knowledge representations. The joint method generated different sentence representations for each drug, which were then used to extract related concepts and relations simultaneously. Contextualized representations trained on the MIMIC-III database were used to capture context-sensitive meanings of words. The position-attention mechanism amplified the benefits of the joint method by generating sentence representations that capture long-distance relations. Knowledge representations were obtained from graph embeddings created using the US Food and Drug Administration Adverse Event Reporting System database to improve relation extraction, especially when contextual clues were insufficient. RESULTS:Our system achieved new state-of-the-art results on the n2c2 data set, with significant improvements in recognizing crucial drug-reason (F1=0.650 versus F1=0.579) and drug-ADE (F1=0.490 versus F1=0.476) relations. CONCLUSIONS:This study presents a system for extracting drug-centric concepts and relations that outperformed current state-of-the-art results and shows that contextualized embeddings, position-attention mechanisms, and knowledge graph embeddings effectively improve deep learning-based concepts and relation extraction. This study demonstrates the potential for deep learning-based methods to help extract real-world evidence from unstructured patient data for drug safety surveillance.

SUBMITTER: Dandala B

PROVIDER: S-EPMC7382020 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Extraction of Information Related to Drug Safety Surveillance From Electronic Health Record Notes: Joint Modeling of Entities and Relations Using Knowledge-Aware Neural Attentive Models.

Dandala Bharath B Joopudi Venkata V Tsou Ching-Huei CH Liang Jennifer J JJ Suryanarayanan Parthasarathy P

JMIR medical informatics 20200710 7

<h4>Background</h4>An adverse drug event (ADE) is commonly defined as "an injury resulting from medical intervention related to a drug." Providing information related to ADEs and alerting caregivers at the point of care can reduce the risk of prescription and diagnostic errors and improve health outcomes. ADEs captured in structured data in electronic health records (EHRs) as either coded problems or allergies are often incomplete, leading to underreporting. Therefore, it is important to develop ...[more]

PMID: 32459650

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Project description:BackgroundPharmacovigilance and drug-safety surveillance are crucial for monitoring adverse drug events (ADEs), but the main ADE-reporting systems such as Food and Drug Administration Adverse Event Reporting System face challenges such as underreporting. Therefore, as complementary surveillance, data on ADEs are extracted from electronic health record (EHR) notes via natural language processing (NLP). As NLP develops, many up-to-date machine-learning techniques are introduced in this field, such as deep learning and multi-task learning (MTL). However, only a few studies have focused on employing such techniques to extract ADEs.ObjectiveWe aimed to design a deep learning model for extracting ADEs and related information such as medications and indications. Since extraction of ADE-related information includes two steps-named entity recognition and relation extraction-our second objective was to improve the deep learning model using multi-task learning between the two steps.MethodsWe employed the dataset from the Medication, Indication and Adverse Drug Events (MADE) 1.0 challenge to train and test our models. This dataset consists of 1089 EHR notes of cancer patients and includes 9 entity types such as Medication, Indication, and ADE and 7 types of relations between these entities. To extract information from the dataset, we proposed a deep-learning model that uses a bidirectional long short-term memory (BiLSTM) conditional random field network to recognize entities and a BiLSTM-Attention network to extract relations. To further improve the deep-learning model, we employed three typical MTL methods, namely, hard parameter sharing, parameter regularization, and task relation learning, to build three MTL models, called HardMTL, RegMTL, and LearnMTL, respectively.ResultsSince extraction of ADE-related information is a two-step task, the result of the second step (ie, relation extraction) was used to compare all models. We used microaveraged precision, recall, and F1 as evaluation metrics. Our deep learning model achieved state-of-the-art results (F1=65.9%), which is significantly higher than that (F1=61.7%) of the best system in the MADE1.0 challenge. HardMTL further improved the F1 by 0.8%, boosting the F1 to 66.7%, whereas RegMTL and LearnMTL failed to boost the performance.ConclusionsDeep learning models can significantly improve the performance of ADE-related information extraction. MTL may be effective for named entity recognition and relation extraction, but it depends on the methods, data, and other factors. Our results can facilitate research on ADE detection, NLP, and machine learning.

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.

Dataset Information

Extraction of Information Related to Drug Safety Surveillance From Electronic Health Record Notes: Joint Modeling of Entities and Relations Using Knowledge-Aware Neural Attentive Models.

Publications

Extraction of Information Related to Drug Safety Surveillance From Electronic Health Record Notes: Joint Modeling of Entities and Relations Using Knowledge-Aware Neural Attentive Models.

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