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Journal Description

JMIR Medical Informatics (JMI, ISSN 2291-9694; Impact Factor: 3.188) (Editor-in-chief: Christian Lovis MD MPH FACMI) is a Pubmed/SCIE-indexed, top-rated, tier A journal which focuses on clinical informatics, big data in health and health care, decision support for health professionals, electronic health records, ehealth infrastructures and implementation. It has a focus on applied, translational research, with a broad readership including clinicians, CIOs, engineers, industry and health informatics professionals.

Published by JMIR Publications, publisher of the Journal of Medical Internet Research (JMIR), JMIR Med Inform has a slightly different scope (putting more emphasis on applications for clinicians and health professionals rather than consumers/citizens), publishes even faster, and also allows papers which are more technical or more formative than what would be published in JMIR.

JMIR Med Inform is indexed in PubMed Central/PubMed and has also been accepted for SCIE. JMIR Med Inform received an inaugural Journal Impact Factor for 2018 (released June 2019) of 3.188.

JMIR Medical Informatics adheres to the same quality standards as JMIR and all articles published here are also cross-listed in the Table of Contents of JMIR (http://www.jmir.org/issue/current).

 

Recent Articles:

  • Source: Image created by the Authors; Copyright: The Authors; URL: http://medinform.jmir.org/2020/1/e16912/; License: Licensed by JMIR.
    Decision Support for Health...

    Jan 20, 2020

    Accuracy and Effects of Clinical Decision Support Systems Integrated With BMJ Best Practice–Aided Diagnosis: Interrupted Time Series Study

    Authors List:

    Abstract:

    Background: Clinical decision support systems (CDSS) are an integral component of health information technologies and can assist disease interpretation, diagnosis, treatment, and prognosis. However, the utility of CDSS in the clinic remains controversial. Objective: The aim is to assess the effects of CDSS integrated with British Medical Journal (BMJ) Best Practice–aided diagnosis in real-world research. Methods: This was a retrospective, longitudinal observational study using routinely collected clinical diagnosis data from electronic medical records. A total of 34,113 hospitalized patient records were successively selected from December 2016 to February 2019 in six clinical departments. The diagnostic accuracy of the CDSS was verified before its implementation. A self-controlled comparison was then applied to detect the effects of CDSS implementation. Multivariable logistic regression and single-group interrupted time series analysis were used to explore the effects of CDSS. The sensitivity analysis was conducted using the subgroup data from January 2018 to February 2019. Results: The total accuracy rates of the recommended diagnosis from CDSS were 75.46% in the first-rank diagnosis, 83.94% in the top-2 diagnosis, and 87.53% in the top-3 diagnosis in the data before CDSS implementation. Higher consistency was observed between admission and discharge diagnoses, shorter confirmed diagnosis times, and shorter hospitalization days after the CDSS implementation (all P<.001). Multivariable logistic regression analysis showed that the consistency rates after CDSS implementation (OR 1.078, 95% CI 1.015-1.144) and the proportion of hospitalization time 7 days or less (OR 1.688, 95% CI 1.592-1.789) both increased. The interrupted time series analysis showed that the consistency rates significantly increased by 6.722% (95% CI 2.433%-11.012%, P=.002) after CDSS implementation. The proportion of hospitalization time 7 days or less significantly increased by 7.837% (95% CI 1.798%-13.876%, P=.01). Similar results were obtained in the subgroup analysis. Conclusions: The CDSS integrated with BMJ Best Practice improved the accuracy of clinicians’ diagnoses. Shorter confirmed diagnosis times and hospitalization days were also found to be associated with CDSS implementation in retrospective real-world studies. These findings highlight the utility of artificial intelligence-based CDSS to improve diagnosis efficiency, but these results require confirmation in future randomized controlled trials.

  • Source: FreeDigitalPhotos.net; Copyright: andongob; URL: http://www.freedigitalphotos.net/images/laptop-computer-and-retro-medical-instruments-photo-p474046; License: Public Domain (CC0).
    Natural Language Processing

    Jan 15, 2020

    Generating Medical Assessments Using a Neural Network Model: Algorithm Development and Validation

    Authors List:

    Abstract:

    Background: Since its inception, artificial intelligence has aimed to use computers to help make clinical diagnoses. Evidence-based medical reasoning is important for patient care. Inferring clinical diagnoses is a crucial step during the patient encounter. Previous works mainly used expert systems or machine learning–based methods to predict the International Classification of Diseases - Clinical Modification codes based on electronic health records. We report an alternative approach: inference of clinical diagnoses from patients’ reported symptoms and physicians’ clinical observations. Objective: We aimed to report a natural language processing system for generating medical assessments based on patient information described in the electronic health record (EHR) notes. Methods: We processed EHR notes into the Subjective, Objective, Assessment, and Plan sections. We trained a neural network model for medical assessment generation (N2MAG). Our N2MAG is an innovative deep neural model that uses the Subjective and Objective sections of an EHR note to automatically generate an “expert-like” assessment of the patient. N2MAG can be trained in an end-to-end fashion and does not require feature engineering and external knowledge resources. Results: We evaluated N2MAG and the baseline models both quantitatively and qualitatively. Evaluated by both the Recall-Oriented Understudy for Gisting Evaluation metrics and domain experts, our results show that N2MAG outperformed the existing state-of-the-art baseline models. Conclusions: N2MAG could generate a medical assessment from the Subject and Objective section descriptions in EHR notes. Future work will assess its potential for providing clinical decision support.

  • Source: Freepik; Copyright: Freepik; URL: https://www.freepik.com/free-photo/serious-young-doctor-browsing-laptop_3004290.htm#page=1&query=search%20hospital&position=2; License: Licensed by JMIR.
    Big Data

    Dec 20, 2019

    Building a Semantic Health Data Warehouse in the Context of Clinical Trials: Development and Usability Study

    Authors List:

    Abstract:

    Background: The huge amount of clinical, administrative, and demographic data recorded and maintained by hospitals can be consistently aggregated into health data warehouses with a uniform data model. In 2017, Rouen University Hospital (RUH) initiated the design of a semantic health data warehouse enabling both semantic description and retrieval of health information. Objective: This study aimed to present a proof of concept of this semantic health data warehouse, based on the data of 250,000 patients from RUH, and to assess its ability to assist health professionals in prescreening eligible patients in a clinical trials context. Methods: The semantic health data warehouse relies on 3 distinct semantic layers: (1) a terminology and ontology portal, (2) a semantic annotator, and (3) a semantic search engine and NoSQL (not only structured query language) layer to enhance data access performances. The system adopts an entity-centered vision that provides generic search capabilities able to express data requirements in terms of the whole set of interconnected conceptual entities that compose health information. Results: We assessed the ability of the system to assist the search for 95 inclusion and exclusion criteria originating from 5 randomly chosen clinical trials from RUH. The system succeeded in fully automating 39% (29/74) of the criteria and was efficiently used as a prescreening tool for 73% (54/74) of them. Furthermore, the targeted sources of information and the search engine–related or data-related limitations that could explain the results for each criterion were also observed. Conclusions: The entity-centered vision contrasts with the usual patient-centered vision adopted by existing systems. It enables more genericity in the information retrieval process. It also allows to fully exploit the semantic description of health information. Despite their semantic annotation, searching within clinical narratives remained the major challenge of the system. A finer annotation of the clinical texts and the addition of specific functionalities would significantly improve the results. The semantic aspect of the system combined with its generic entity-centered vision enables the processing of a large range of clinical questions. However, an important part of health information remains in clinical narratives, and we are currently investigating novel approaches (deep learning) to enhance the semantic annotation of those unstructured data.

  • Source: Unsplash.com; Copyright: Glenn Carstens-Peters; URL: https://unsplash.com/photos/npxXWgQ33ZQ; License: Licensed by JMIR.
    Natural Language Processing

    Dec 17, 2019

    Efficient Reuse of Natural Language Processing Models for Phenotype-Mention Identification in Free-text Electronic Medical Records: A Phenotype Embedding...

    Authors List:

    Abstract:

    Background: Much effort has been put into the use of automated approaches, such as natural language processing (NLP), to mine or extract data from free-text medical records in order to construct comprehensive patient profiles for delivering better health care. Reusing NLP models in new settings, however, remains cumbersome, as it requires validation and retraining on new data iteratively to achieve convergent results. Objective: The aim of this work is to minimize the effort involved in reusing NLP models on free-text medical records. Methods: We formally define and analyze the model adaptation problem in phenotype-mention identification tasks. We identify “duplicate waste” and “imbalance waste,” which collectively impede efficient model reuse. We propose a phenotype embedding–based approach to minimize these sources of waste without the need for labelled data from new settings. Results: We conduct experiments on data from a large mental health registry to reuse NLP models in four phenotype-mention identification tasks. The proposed approach can choose the best model for a new task, identifying up to 76% waste (duplicate waste), that is, phenotype mentions without the need for validation and model retraining and with very good performance (93%-97% accuracy). It can also provide guidance for validating and retraining the selected model for novel language patterns in new tasks, saving around 80% waste (imbalance waste), that is, the effort required in “blind” model-adaptation approaches. Conclusions: Adapting pretrained NLP models for new tasks can be more efficient and effective if the language pattern landscapes of old settings and new settings can be made explicit and comparable. Our experiments show that the phenotype-mention embedding approach is an effective way to model language patterns for phenotype-mention identification tasks and that its use can guide efficient NLP model reuse.

  • Tablet with submission form for www.zorgkaart.nl. Source: Image created by the authors; Copyright: Roy Hendrikx; URL: http://medinform.jmir.org/2019/4/e13053/; License: Creative Commons Attribution (CC-BY).
    Quality Improvement

    Dec 16, 2019

    Measuring Regional Quality of Health Care Using Unsolicited Online Data: Text Analysis Study

    Authors List:

    Abstract:

    Background: Regional population management (PM) health initiatives require insight into experienced quality of care at the regional level. Unsolicited online provider ratings have shown potential for this use. This study explored the addition of comments accompanying unsolicited online ratings to regional analyses. Objective: The goal was to create additional insight for each PM initiative as well as overall comparisons between these initiatives by attempting to determine the reasoning and rationale behind a rating. Methods: The Dutch Zorgkaart database provided the unsolicited ratings from 2008 to 2017 for the analyses. All ratings included both quantitative ratings as well as qualitative text comments. Nine PM regions were used to aggregate ratings geographically. Sentiment analyses were performed by categorizing ratings into negative, neutral, and positive ratings. Per category, as well as per PM initiative, word frequencies (ie, unigrams and bigrams) were explored. Machine learning—naïve Bayes and random forest models—was applied to identify the most important predictors for rating overall sentiment and for identifying PM initiatives. Results: A total of 449,263 unsolicited ratings were available in the Zorgkaart database: 303,930 positive ratings, 97,739 neutral ratings, and 47,592 negative ratings. Bigrams illustrated that feeling like not being “taken seriously” was the dominant bigram in negative ratings, while bigrams in positive ratings were mostly related to listening, explaining, and perceived knowledge. Comparing bigrams between PM initiatives showed a lot of overlap but several differences were identified. Machine learning was able to predict sentiments of comments but was unable to distinguish between specific PM initiatives. Conclusions: Adding information from text comments that accompany online ratings to regional evaluations provides insight for PM initiatives into the underlying reasons for ratings. Text comments provide useful overarching information for health care policy makers but due to a lot of overlap, they add little region-specific information. Specific outliers for some PM initiatives are insightful.

  • TOC Image. Source: freepik / Icons made by freepik from www.flaticon.com; Copyright: pressfoto; URL: https://www.freepik.com/free-photo/asian-doctor-using-medical-app-his-digital-device_5698718.htm#page=4&query=doctor+computer&position=45; License: Licensed by JMIR.
    Natural Language Processing

    Dec 9, 2019

    Impact of Automatic Query Generation and Quality Recognition Using Deep Learning to Curate Evidence From Biomedical Literature: Empirical Study

    Authors List:

    Abstract:

    Background: The quality of health care is continuously improving and is expected to improve further because of the advancement of machine learning and knowledge-based techniques along with innovation and availability of wearable sensors. With these advancements, health care professionals are now becoming more interested and involved in seeking scientific research evidence from external sources for decision making relevant to medical diagnosis, treatments, and prognosis. Not much work has been done to develop methods for unobtrusive and seamless curation of data from the biomedical literature. Objective: This study aimed to design a framework that can enable bringing quality publications intelligently to the users’ desk to assist medical practitioners in answering clinical questions and fulfilling their informational needs. Methods: The proposed framework consists of methods for efficient biomedical literature curation, including the automatic construction of a well-built question, the recognition of evidence quality by proposing extended quality recognition model (E-QRM), and the ranking and summarization of the extracted evidence. Results: Unlike previous works, the proposed framework systematically integrates the echelons of biomedical literature curation by including methods for searching queries, content quality assessments, and ranking and summarization. Using an ensemble approach, our high-impact classifier E-QRM obtained significantly improved accuracy than the existing quality recognition model (1723/1894, 90.97% vs 1462/1894, 77.21%). Conclusions: Our proposed methods and evaluation demonstrate the validity and rigorousness of the results, which can be used in different applications, including evidence-based medicine, precision medicine, and medical education.

  • Bone age assessment via an MRI of the knee (montage). Source: The Authors / Placeit; Copyright: JMIR Publications; URL: https://medinform.jmir.org/2019/4/e16291; License: Creative Commons Attribution (CC-BY).
    Machine Learning

    Dec 5, 2019

    Age Assessment of Youth and Young Adults Using Magnetic Resonance Imaging of the Knee: A Deep Learning Approach

    Authors List:

    Abstract:

    Background: Bone age assessment (BAA) is an important tool for diagnosis and in determining the time of treatment in a number of pediatric clinical scenarios, as well as in legal settings where it is used to estimate the chronological age of an individual where valid documents are lacking. Traditional methods for BAA suffer from drawbacks, such as exposing juveniles to radiation, intra- and interrater variability, and the time spent on the assessment. The employment of automated methods such as deep learning and the use of magnetic resonance imaging (MRI) can address these drawbacks and improve the assessment of age. Objective: The aim of this paper is to propose an automated approach for age assessment of youth and young adults in the age range when the length growth ceases and growth zones are closed (14-21 years of age) by employing deep learning using MRI of the knee. Methods: This study carried out MRI examinations of the knee of 402 volunteer subjects—221 males (55.0%) and 181 (45.0%) females—aged 14-21 years. The method comprised two convolutional neural network (CNN) models: the first one selected the most informative images of an MRI sequence, concerning age-assessment purposes; these were then used in the second module, which was responsible for the age estimation. Different CNN architectures were tested, both training from scratch and employing transfer learning. Results: The CNN architecture that provided the best results was GoogLeNet pretrained on the ImageNet database. The proposed method was able to assess the age of male subjects in the range of 14-20.5 years, with a mean absolute error (MAE) of 0.793 years, and of female subjects in the range of 14-19.5 years, with an MAE of 0.988 years. Regarding the classification of minors—with the threshold of 18 years of age—an accuracy of 98.1% for male subjects and 95.0% for female subjects was achieved. Conclusions: The proposed method was able to assess the age of youth and young adults from 14 to 20.5 years of age for male subjects and 14 to 19.5 years of age for female subjects in a fully automated manner, without the use of ionizing radiation, addressing the drawbacks of traditional methods.

  • Source: Freepik; Copyright: pressfoto; URL: https://www.freepik.com/free-photo/asian-doctor-with-stethoscope-around-neck-sitting-office-working-computer_5839246.htm#page=3&query=doctor+computer&position=2; License: Licensed by JMIR.
    Reviews

    Dec 3, 2019

    Electronic Consultation in Primary Care Between Providers and Patients: Systematic Review

    Authors List:

    Abstract:

    Background: Governments and health care providers are keen to find innovative ways to deliver care more efficiently. Interest in electronic consultation (e-consultation) has grown, but the evidence of benefit is uncertain. Objective: This study aimed to assess the evidence of delivering e-consultation using secure email and messaging or video links in primary care. Methods: A systematic review was conducted on the use and application of e-consultations in primary care. We searched 7 international databases (MEDLINE, EMBASE, CINAHL, Cochrane Library, PsycINFO, EconLit, and Web of Science; 1999-2017), identifying 52 relevant studies. Papers were screened against a detailed inclusion and exclusion criteria. Independent dual data extraction was conducted and assessed for quality. The resulting evidence was synthesized using thematic analysis. Results: This review included 57 studies from a range of countries, mainly the United States (n=30) and the United Kingdom (n=13). There were disparities in uptake and utilization toward more use by younger, employed adults. Patient responses to e-consultation were mixed. Patients reported satisfaction with services and improved self-care, communication, and engagement with clinicians. Evidence for the acceptability and ease of use was strong, especially for those with long-term conditions and patients located in remote regions. However, patients were concerned about the privacy and security of their data. For primary health care staff, e-consultation delivers challenges around time management, having the correct technological infrastructure, whether it offers a comparable standard of clinical quality, and whether it improves health outcomes. Conclusions: E-consultations may improve aspects of care delivery, but the small scale of many of the studies and low adoption rates leave unanswered questions about usage, quality, cost, and sustainability. We need to improve e-consultation implementation, demonstrate how e-consultations will not increase disparities in access, provide better reassurance to patients about privacy, and incorporate e-consultation as part of a manageable clinical workflow.

  • Source: freepik.com; Copyright: Nensuria; URL: https://www.freepik.com/free-photo/employees-closeup-young-nurse-service_1108592.htm#page=1&query=doctor&position=19; License: Licensed by JMIR.
    Quality Improvement

    Dec 2, 2019

    How Online Reviews and Services Affect Physician Outpatient Visits: Content Analysis of Evidence From Two Online Health Care Communities

    Authors List:

    Abstract:

    Background: Online healthcare communities are changing the ways of physician-patient communication and how patients choose outpatient care physicians. Although a majority of empirical work has examined the role of online reviews in consumer decisions, less research has been done in health care, and endogeneity of online reviews has not been fully considered. Moreover, the important factor of physician online services has been neglected in patient decisions. Objective: In this paper, we addressed the endogeneity of online reviews and examined the impact of online reviews and services on outpatient visits based on theories of reviews and channel effects. Methods: We used a difference-in-difference approach to account for physician- and website-specific effects by collecting information from 474 physician homepages on two online health care communities. Results: We found that the number of reviews was more effective in influencing patient decisions compared with the overall review rating. An improvement in reviews leads to a relative increase in physician outpatient visits on that website. There are channel effects in health care: online services complement offline services (outpatient care appointments). Results further indicate that online services moderate the relationship between online reviews and physician outpatient visits. Conclusions: This study investigated the effect of reviews and channel effects in health care by conducting a difference-in-difference analysis on two online health care communities. Our findings provide basic research on online health care communities.

  • Source: Image created by the Authors; Copyright: The Authors; URL: http://medinform.jmir.org/2019/4/e14325/; License: Licensed by JMIR.
    Ontologies, Classifications, and Coding

    Nov 29, 2019

    Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation

    Authors List:

    Abstract:

    Background: The phecode system was built upon the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) for phenome-wide association studies (PheWAS) using the electronic health record (EHR). Objective: The goal of this paper was to develop and perform an initial evaluation of maps from the International Classification of Diseases, 10th Revision (ICD-10) and the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) codes to phecodes. Methods: We mapped ICD-10 and ICD-10-CM codes to phecodes using a number of methods and resources, such as concept relationships and explicit mappings from the Centers for Medicare & Medicaid Services, the Unified Medical Language System, Observational Health Data Sciences and Informatics, Systematized Nomenclature of Medicine-Clinical Terms, and the National Library of Medicine. We assessed the coverage of the maps in two databases: Vanderbilt University Medical Center (VUMC) using ICD-10-CM and the UK Biobank (UKBB) using ICD-10. We assessed the fidelity of the ICD-10-CM map in comparison to the gold-standard ICD-9-CM phecode map by investigating phenotype reproducibility and conducting a PheWAS. Results: We mapped >75% of ICD-10 and ICD-10-CM codes to phecodes. Of the unique codes observed in the UKBB (ICD-10) and VUMC (ICD-10-CM) cohorts, >90% were mapped to phecodes. We observed 70-75% reproducibility for chronic diseases and <10% for an acute disease for phenotypes sourced from the ICD-10-CM phecode map. Using the ICD-9-CM and ICD-10-CM maps, we conducted a PheWAS with a Lipoprotein(a) genetic variant, rs10455872, which replicated two known genotype-phenotype associations with similar effect sizes: coronary atherosclerosis (ICD-9-CM: P<.001; odds ratio (OR) 1.60 [95% CI 1.43-1.80] vs ICD-10-CM: P<.001; OR 1.60 [95% CI 1.43-1.80]) and chronic ischemic heart disease (ICD-9-CM: P<.001; OR 1.56 [95% CI 1.35-1.79] vs ICD-10-CM: P<.001; OR 1.47 [95% CI 1.22-1.77]). Conclusions: This study introduces the beta versions of ICD-10 and ICD-10-CM to phecode maps that enable researchers to leverage accumulated ICD-10 and ICD-10-CM data for PheWAS in the EHR.

  • Toward the advance use of electronic medical records. Source: Flickr; Copyright: ILO / Thierry Falise; URL: https://www.flickr.com/photos/iloasiapacific/8055934815/; License: Creative Commons Attribution + Noncommercial + NoDerivatives (CC-BY-NC-ND).
    Electronic Health Records

    Nov 29, 2019

    Primary Care Physicians’ Experience Using Advanced Electronic Medical Record Features to Support Chronic Disease Prevention and Management: Qualitative Study

    Authors List:

    Abstract:

    Background: Chronic diseases are the leading cause of death worldwide. In Canada, more than half of all health care spending is used for managing chronic diseases. Although studies have shown that the use of advanced features of electronic medical record (EMR) systems improves the quality of chronic disease prevention and management (CDPM), a 2012 international survey found that Canadian physicians were the least likely to use 2 or more EMR system functions. Some studies show that maturity vis-à-vis clinicians’ EMR use is an important factor when evaluating the use of advanced features of health information systems. The Clinical Adoption Framework (CAF), a common evaluation framework used to assess the success of EMR adoption, does not incorporate the process of maturing. Nevertheless, the CAF and studies that discuss the barriers to and facilitators of the adoption of EMR systems can be the basis for exploring the use of advanced EMR features. Objective: This study aimed to explore the factors that primary care physicians in Ontario identified as influencing their use of advanced EMR features to support CDPM and to extend the CAF to include primary care physicians’ perceptions of how their use of EMRs for performing clinical tasks has matured. Methods: Guided by the CAF, directed content analysis was used to explore the barriers and facilitating factors encountered by primary care physicians when using EMR features. Participants were primary care physicians in Ontario, Canada, who use EMRs. Data were coded using categories from the CAF. Results: A total of 9 face-to-face interviews were conducted from January 2017 to July 2017. Dimensions from the CAF emerged from the data, and one new dimension was derived: physicians’ perception of their maturity of EMR use. Primary care physicians identified the following key factors that impacted their use of advanced EMR features: performance of EMR features, information quality of EMR features, training and technical support, user satisfaction, provider’s productivity, personal characteristics and roles, cost benefits of EMR features, EMR systems infrastructure, funding, and government leadership. Conclusions: The CAF was extended to include physicians’ perceptions of how their use of EMR systems had matured. Most participants agreed that their use of EMR systems for performing clinical tasks had evolved since their adoption of the system and that certain system features facilitated their care for patients with chronic diseases. However, several barriers were identified and should be addressed to further enhance primary care physicians’ use of advanced EMR features to support CDPM.

  • Source: https://www.istockphoto.com; Copyright: Po-Ting Lai; URL: https://www.istockphoto.com/photo/presentation-about-machine-learning-technology-scientist-touching-screen-artificial-gm844535726-138201361; License: Licensed by the authors.
    Natural Language Processing

    Nov 26, 2019

    Using a Large Margin Context-Aware Convolutional Neural Network to Automatically Extract Disease-Disease Association from Literature: Comparative Analytic Study

    Authors List:

    Abstract:

    Background: Research on disease-disease association (DDA), like comorbidity and complication, provides important insights into disease treatment and drug discovery, and a large body of the literature has been published in the field. However, using current search tools, it is not easy for researchers to retrieve information on the latest DDA findings. First, comorbidity and complication keywords pull up large numbers of PubMed studies. Second, disease is not highlighted in search results. Finally, DDA is not identified, as currently no disease-disease association extraction (DDAE) dataset or tools are available. Objective: As there are no available DDAE datasets or tools, this study aimed to develop (1) a DDAE dataset and (2) a neural network model for extracting DDA from the literature. Methods: In this study, we formulated DDAE as a supervised machine learning classification problem. To develop the system, we first built a DDAE dataset. We then employed two machine learning models, support vector machine and convolutional neural network, to extract DDA. Furthermore, we evaluated the effect of using the output layer as features of the support vector machine-based model. Finally, we implemented large margin context-aware convolutional neural network architecture to integrate context features and convolutional neural networks through the large margin function. Results: Our DDAE dataset consisted of 521 PubMed abstracts. Experiment results showed that the support vector machine-based approach achieved an F1 measure of 80.32%, which is higher than the convolutional neural network-based approach (73.32%). Using the output layer of convolutional neural network as a feature for the support vector machine does not further improve the performance of support vector machine. However, our large margin context-aware-convolutional neural network achieved the highest F1 measure of 84.18% and demonstrated that combining the hinge loss function of support vector machine with a convolutional neural network into a single neural network architecture outperforms other approaches. Conclusions: To facilitate the development of text-mining research for DDAE, we developed the first publicly available DDAE dataset consisting of disease mentions, Medical Subject Heading IDs, and relation annotations. We developed different conventional machine learning models and neural network architectures and evaluated their effects on our DDAE dataset. To further improve DDAE performance, we propose an large margin context-aware-convolutional neural network model for DDAE that outperforms other approaches.

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  • Use of Clinical Notes and Machine Learning to Predict Onset of Dementia

    Date Submitted: Jan 15, 2020

    Open Peer Review Period: Jan 14, 2020 - Mar 10, 2020

    Background: Clinical trials need efficient tools to assist in recruiting patients at risk of Alzheimer’s Disease and related dementia (ADRD). Early detection can also assist patients with financial...

    Background: Clinical trials need efficient tools to assist in recruiting patients at risk of Alzheimer’s Disease and related dementia (ADRD). Early detection can also assist patients with financial planning for long-term care. Clinical notes are an important under-utilized source of information in machine learning models due to the cost of collection and complexity of analysis. Objective: This study investigates using de-identified clinical notes from multiple hospital systems collected over 10 years to augment retrospective machine learning models of ADRD risk. Methods: The models use two years of data to predict a future outcome of ADRD onset. Notes data are provided in a de-identified format with specific terms and sentiments. Terms in notes are embedded into a 100-dimensional vector space to identify clusters of related terms and abbreviations that differ across hospital systems and individual clinicians. Results: When using notes, AUC improved from 85% to 94% and positive predictive value (PPV) increased from 45% to 68% in the model at disease onset. Models with notes improved in both AUC and PPV in years 3-6 when notes volume was largest, results are mixed in years 7 and 8 with smallest cohorts. Conclusions: While notes helped in the short term, the presence of ADRD symptomatic terms years earlier than onset adds evidence to other studies that clinicians under-code ADRD diagnoses. De-identified clinical notes increase the accuracy of risk models. Clinical notes collected across multiple hospital systems via natural language processing can be merged using post-processing techniques to aid model accuracy.

  • Factors influencing the adoption of health information standards: a “Best-fit” framework synthesis

    Date Submitted: Dec 7, 2019

    Open Peer Review Period: Dec 7, 2019 - Feb 1, 2020

    Background: The deployment of Health Information Technologies (HIT) has often been conducted in silos, at different organizational levels, in different regions and in various healthcare settings; this...

    Background: The deployment of Health Information Technologies (HIT) has often been conducted in silos, at different organizational levels, in different regions and in various healthcare settings; this has resulted in HIT infrastructures often being difficult to integrate or manage. Health information standards are expected to address these issues, yet their adoption remains frustratingly low. Objective: To synthesize a comprehensive framework of factors that affect the adoption and deployment of health information standards by healthcare organizations. Methods: We conducted a systematic review combined with a “Best-fit” framework synthesis approach to develop a comprehensive framework. Results: In total, 35 records were incorporated in our analysis, with the final synthesized framework including four dimensions, namely: Technology, Organization, Environment and Inter-organizational relationships. The technology dimension included: Relative advantage, Complexity, Compatibility, Trialability, Observability, Switching cost, Standards uncertainty and Shared business process attributes. The organization dimension included: Organizational scale, Organizational culture, Staff resistance to change, Staff training, Top management support and Organizational readiness. The environment dimension comprised: External pressure, External support, Network externality, Installed base/drag, and Information communication. The inter-organizational relationships dimension included: Partner trust, Partner dependence, Relationship commitment, and Partner power. Conclusions: The synthesized framework has addressed the gap in knowledge of the adoption of health information standards in healthcare organizations. It provides decision makers with more understanding of the factors that hinder or facilitate the adoption of health information standards to better judge and develop suitable strategies for adoption interventions, and supplies research direction and a basis for future follow-up research.

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