Selecting Test Cases from the Electronic Health Record for Software Testing of Knowledge-Based Clinical Decision Support Systems.
Authors: Usman OA, Oshiro C, Chambers JG, Tu SW, Martins S, Robinson A, Goldstein MK Abstract Software testing of knowledge-based clinical decision support systems is challenging, labor intensive, and expensive; yet, testing is necessary since clinical applications have heightened consequences. Thoughtful test case selection improves testing coverage while minimizing testing burden. ATHENA-CDS is a knowledge-based system that provides guideline-based recommendations for chronic medical conditions. Using the ATHENA-CDS diabetes knowledgebase, we demonstrate a generalizable approach for selecting test cases using rul...
Source: AMIA Annual Symposium Proceedings - April 26, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Electronic Surveillance For Catheter-Associated Urinary Tract Infection Using Natural Language Processing.
Authors: Sanger PC, Granich M, Olsen-Scribner R, Jain R, Lober WB, Stapleton A, Pottinger PS Abstract Catheter-associated urinary tract infection (CAUTI) is a common and costly healthcare-associated infection, yet measuring it accurately is challenging and resource-intensive. Electronic surveillance promises to make this task more objective and efficient in an era of new financial and regulatory imperatives, but previous surveillance approaches have used a simplified version of the definition. We applied a complete definition, including subjective elements identified through natural language processing of clinical ...
Source: AMIA Annual Symposium Proceedings - April 23, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

The Problems of Realism-Based Ontology Design: a Case Study in Creating Definitions for an Application Ontology for Diabetes Camps.
Authors: Schuler JC, Ceusters WM Abstract A requirement of realism-based ontology design is that classes denote exclusively entities that exist objectively in reality and that their definitions adhere to strict criteria to ensure that the classes are re-usable in other ontologies while preserving their ontological commitment. Building realism-based ontologies is therefore quite challenging and time-consuming, demanding considerable training. Although the top-level in the form of the Basic Formal Ontology (BFO) is worked out very well, and also the upper levels of certain domains, there is still a disconnect with th...
Source: AMIA Annual Symposium Proceedings - April 23, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Reconciliation of multiple guidelines for decision support: a case study on the multidisciplinary management of breast cancer within the DESIREE project.
We describe the guideline-based decision support system (GL-DSS) of the project. Various breast cancer clinical practice guidelines (CPGs) have been selected to be concurrently applied to provide state-of-the-art patient-specific recommendations. The aim is to reconcile CPG recommendations with the objective of complementarity to enlarge the number of clinical situations covered by the GL-DSS. Input and output data exchange with the GL-DSS is performed using FHIR. We used a knowledge model of the domain as an ontology on which relies the reasoning process performed by rules that encode the selected CPGs. Semantic web tools...
Source: AMIA Annual Symposium Proceedings - April 23, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Harnessing Biomedical Natural Language Processing Tools to Identify Medicinal Plant Knowledge from Historical Texts.
This study explored the feasibility of using biomedical terminologies and natural language processing approaches for extracting relevant plant-associated therapeutic use information from historical biodiversity literature collection available from the Biodiversity Heritage Library. The results from this preliminary study suggest that there is potential utility of informatics methods to identify medicinal plant knowledge from digitized resources as well as highlight opportunities for improvement. PMID: 29854223 [PubMed - indexed for MEDLINE] (Source: AMIA Annual Symposium Proceedings)
Source: AMIA Annual Symposium Proceedings - April 23, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

The Effect of Neighborhood Disadvantage on Diabetes Prevalence.
This study evaluated the neighborhood-level Area Deprivation Index (ADI), a measure of neighborhood socioeconomic disadvantage, as a factor in diabetes mellitus prevalence. Electronic health records at an academic hospital system identified 4,770 Medicare beneficiaries. Logistic regression of diabetes diagnosis (ICD9=250.x) against ADI quintile, age, gender, and race/ethnicity found all these patient characteristics to be significantly associated. Diabetes prevalence was lowest in the least disadvantaged quintile of neighborhoods after adjusting for age, gender, and race/ethnicity. The positive non-linear association of di...
Source: AMIA Annual Symposium Proceedings - April 23, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis.
In this study, we proposed a collaborative filtering system enriched with natural language processing and semantic techniques to assist rare disease diagnosis based on phenotypic characterization. Specifically, we leveraged four similarity measurements with two neighborhood algorithms on 2010-2015 Mayo Clinic unstructured large patient cohort and evaluated different approaches. Preliminary results demonstrated that the use of collaborative filtering with phenotypic information is able to stratify patients with relatively similar rare diseases. PMID: 29854225 [PubMed - indexed for MEDLINE] (Source: AMIA Annual Symposium Proceedings)
Source: AMIA Annual Symposium Proceedings - April 23, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Utilizing Smartphone-Based Machine Learning in Medical Monitor Data Collection: Seven Segment Digit Recognition.
Authors: Shenoy VN, Aalami OO Abstract Biometric measurements captured from medical devices, such as blood pressure gauges, glucose monitors, and weighing scales, are essential to tracking a patient's health. Trends in these measurements can accurately track diabetes, cardiovascular issues, and assist medication management for patients. Currently, patients record their results and date of measurement in a physical notebook. It may be weeks before a doctor sees a patient's records and can assess the health of the patient. With a predicted 6.8 billion smartphones in the world by 20221, health monitoring platforms, su...
Source: AMIA Annual Symposium Proceedings - April 23, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Leveraging Clinical Time-Series Data for Prediction: A Cautionary Tale.
Authors: Sherman E, Gurm H, Balis U, Owens S, Wiens J Abstract In healthcare, patient risk stratification models are often learned using time-series data extracted from electronic health records. When extracting data for a clinical prediction task, several formulations exist, depending on how one chooses the time of prediction and the prediction horizon. In this paper, we show how the formulation can greatly impact both model performance and clinical utility. Leveraging a publicly available ICU dataset, we consider two clinical prediction tasks: in-hospital mortality, and hypokalemia. Through these case studies, we...
Source: AMIA Annual Symposium Proceedings - April 23, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Secondary Use of Patients' Electronic Records (SUPER): An Approach for Meeting Specific Data Needs of Clinical and Translational Researchers.
Authors: Sholle ET, Kabariti J, Johnson SB, Leonard JP, Pathak J, Varughese VI, Cole CL, Campion TR Abstract Academic medical centers commonly approach secondary use of electronic health record (EHR) data by implementing centralized clinical data warehouses (CDWs). However, CDWs require extensive resources to model data dimensions and harmonize clinical terminology, which can hinder effective support of the specific and varied data needs of investigators. We hypothesized that an approach that aggregates raw data from source systems, ignores initial modeling typical of CDWs, and transforms raw data for specific rese...
Source: AMIA Annual Symposium Proceedings - April 23, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Disease-Specific Integration of Omics Data to Guide Functional Validation of Genetic Associations.
Authors: Shumyatcher M, Hong R, Levin J, Himes BE Abstract Unbiased genetic association studies, including genome-wide association and whole-genome sequencing studies, have uncovered many novel disease-associated variants. Relatively few of these associated regions, however, have led to insights that are biologically mechanistic or clinically actionable due in part to the difficulty in designing appropriate functional validation studies to understand how variants contribute to disease. Asthma is a complex inflammatory lung disease for which many genetic associations have been identified. Using asthma as a disease m...
Source: AMIA Annual Symposium Proceedings - April 23, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Architecting the Data Loading Process for an i2b2 Research Data Warehouse: Full Reload versus Incremental Updating.
Authors: Post AR, Ai M, Kalsanka Pai A, Overcash M, Stephens DS Abstract Research data warehouses integrate research and patient data from one or more sources into a single data model that is designed for research. Typically, institutions update their warehouse by fully reloading it periodically. The alternative is to update the warehouse incrementally with new, changed and/or deleted data. Full reloads avoid having to correct and add to a live system, but they can render the data outdated for clinical trial accrual. They place a substantial burden on source systems, involve intermittent work that is challenging to...
Source: AMIA Annual Symposium Proceedings - April 16, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Stage-Specific Survivability Prediction Models across Different Cancer Types.
Authors: Hossein Pour ES, Kate RJ Abstract For all cancer types, survivability rates vary widely across different stages of cancer. But survivability prediction models built in past were trained using examples of all stages together and were also evaluated on all stages together. In this work, for ten cancer types and using three machine learning methods, we built survivability prediction models trained on each stage separately and compared their performance with the traditional models trained on all stages together. For both kinds of models, the evaluation was done on each stage separately as well as on all stages...
Source: AMIA Annual Symposium Proceedings - April 16, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

An Open Source Tool for Game Theoretic Health Data De-Identification.
Authors: Prasser F, Gaupp J, Wan Z, Xia W, Vorobeychik Y, Kantarcioglu M, Kuhn K, Malin B Abstract Biomedical data continues to grow in quantity and quality, creating new opportunities for research and data-driven applications. To realize these activities at scale, data must be shared beyond its initial point of collection. To maintain privacy, healthcare organizations often de-identify data, but they assume worst-case adversaries, inducing high levels of data corruption. Recently, game theory has been proposed to account for the incentives of data publishers and recipients (who attempt to re-identify patients), bu...
Source: AMIA Annual Symposium Proceedings - April 16, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Leveraging Health Information Exchange to Construct a Registry for Traumatic Brain Injury, Spinal Cord Injury and Stroke in Indiana.
Authors: Rahurkar S, McFarlane TD, Wang J, Hoover S, Hammond F, Kean J, Dixon BE Abstract Traumatic brain injury (TBI), spinal cord injury (SCI) and stroke are conditions of interest to public health as they can result in long-term outcomes and disabilities. Specialized registries can facilitate public health surveillance, however only 4% of hospitals in the United States actively engage in electronic reporting to these registries. We leveraged electronic claims and clinical data from a health information exchange to create a statewide TBI/SCI/Stroke registry to facilitate the study of long-term outcomes and health...
Source: AMIA Annual Symposium Proceedings - April 16, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Stakeholder Use and Feedback on Vaccination History and Clinical Decision Support for Immunizations Offered by Public Health.
The objective of this study was to collect stakeholder feedback on access and utilization of CDSi from the Minnesota Immunization Information Connection (MIIC), Minnesota's IIS. Input was solicited using a semi-structured questionnaire developed by experts, and from a sample of 17 key informants from February 2015 through May 2016. Analysis highlighted the appreciation of MIIC services, comprehensive vaccination history across providers and CDSi functionality, with public health users relying on MIIC. It also identified issues such as data entry due to read-only view, data quality and communications for improvement. These ...
Source: AMIA Annual Symposium Proceedings - April 16, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Formative Evaluation of Care Nexus: a Tool for the Visualization and Management of Care Teams of Complex Pediatric Patients.
In this study, we iteratively design and develop two alternative user interfaces (graphical and tabular) of a prototype of a tool for visualizing and managing care teams and conduct a formative assessment of the usability, usefulness, and efficiency of the tool. The median time to task completion for the 21 study participants was less than 7 seconds for 19 out of the 22 usability tasks. While both the prototype formats were well-liked in terms of usability and usefulness, the tabular format was rated higher for usefulness (p=0.02). Inclusion of CareNexus-like tools in electronic and personal health records has the potentia...
Source: AMIA Annual Symposium Proceedings - April 16, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Understanding Patient Questions about their Medical Records in an Online Health Forum: Opportunity for Patient Portal Design.
We examined patient question posts that contain laboratory results to gain insights into the nature of these questions and of the answers. Our analyses revealed a typology of confusion (i.e., topics of their questions) and potential gaps in traditional healthcare supports (i.e., patients' requests and situational factors), as well as the supports patients may gain through the forum (i.e., what the community provides). These results offer preliminary evidence of opportunities to redesign patient portals, and will inform our future work. PMID: 29854216 [PubMed - indexed for MEDLINE] (Source: AMIA Annual Symposium Proceedings)
Source: AMIA Annual Symposium Proceedings - April 16, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

A Semantic Parsing Method for Mapping Clinical Questions to Logical Forms.
Authors: Roberts K, Patra BG Abstract This paper presents a method for converting natural language questions about structured data in the electronic health record (EHR) into logical forms. The logical forms can then subsequently be converted to EHR-dependent structured queries. The natural language processing task, known as semantic parsing, has the potential to convert questions to logical forms with extremely high precision, resulting in a system that is usable and trusted by clinicians for real-time use in clinical settings. We propose a hybrid semantic parsing method, combining rule-based methods with a machine...
Source: AMIA Annual Symposium Proceedings - April 16, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Is the Application of SNOMED CT Concept Model sufficiently Quality Assured?
Authors: Rodrigues JM, Schulz S, Mizen B, Rector A, Serir S Abstract The terminological content of SNOMED CT, the world's largest clinical terminology is linked to description logics expressions, which give support to consider SNOMED CT a formal ontology. The Terminology Quality Assurance (TQA) of such a terminology resource is hampered by errors in modeling, which act as a barrier for the successful use of electronic health records to ensure semantic interoperability. One application case is the new version of ICD, now in its pre-final form, the content of which is based on a subset of SNOMED CT. The ongoing align...
Source: AMIA Annual Symposium Proceedings - April 16, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Mining the literature for genes associated with placenta-mediated maternal diseases.
Authors: Rodriguez LM, Morrison SM, Greenberg K, Fushman DD Abstract Automated literature analysis could significantly speed up understanding of the role of the placenta and the impact of its development and functions on the health of the mother and the child. To facilitate automatic extraction of information about placenta-mediated disorders from the literature, we manually annotated genes and proteins, the associated diseases, and the functions and processes involved in the development and function of placenta in a collection of PubMed/MEDLINE abstracts. We developed three baseline approaches to finding sentences...
Source: AMIA Annual Symposium Proceedings - April 16, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Supervised Learning Methods for Predicting Healthcare Costs: Systematic Literature Review and Empirical Evaluation.
Authors: Morid MA, Kawamoto K, Ault T, Dorius J, Abdelrahman S Abstract An important informatics tool for controlling healthcare costs is accurately predicting the likely future healthcare costs of individuals. To address this important need, we conducted a systematic literature review and identified five methods for predicting healthcare costs. To enable a direct comparison of these different approaches, we empirically evaluated the predictive performance of each reported approach, as well as other state-of-the-art supervised learning methods, using data from University of Utah Health Plans for October 2013 throug...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

The Role of Surface, Semantic and Grammatical Features on Simplification of Spanish Medical Texts: A User Study.
Authors: Mukherjee P, Leroy G, Kauchak D, Navarrete BA, Diaz DY, Colina S Abstract Simplifying medical texts facilitates readability and comprehension. While most simplification work focuses on English, we investigate whether features important for simplifying English text are similarly helpful for simplifying Spanish text. We conducted a user study on 15 Spanish medical texts using Amazon Mechanical Turk and measured perceived and actual difficulty. Using the median of the difficulty scores, we split the texts into easy and difficult groups and extracted 10 surface, 2 semantic and 4 grammatical features. Using t-t...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Identification of Clinically Meaningful Plasma Transfusion Subgroups Using Unsupervised Random Forest Clustering.
Authors: Ngufor C, Warner MA, Murphree DH, Liu H, Carter R, Storlie CB, Kor DJ Abstract Statistical techniques such as propensity score matching and instrumental variable are commonly employed to "simulate" randomization and adjust for measured confounders in comparative effectiveness research. Despite such adjustments, the results of these methods apply essentially to an "average" patient. However, as patients show significant heterogeneity in their responses to treatments, this average effect is of limited value. It does not account for individual level variabilities, which can deviate substan...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Value of Genetics-informed Drug Dosing Guidance in Pregnant Women: A Needs Assessment with Obstetric Healthcare Providers at Johns Hopkins.
This study motivates future research to help obstetric healthcare providers tailor drug dose to individual patients based upon models integrating multiple patient characteristics, including genetics. PMID: 29854203 [PubMed - indexed for MEDLINE] (Source: AMIA Annual Symposium Proceedings)
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Evaluation of Semantic Web Technologies for Storing Computable Definitions of Electronic Health Records Phenotyping Algorithms.
Authors: Pape┼ż V, Denaxas S, Hemingway H Abstract Electronic Health Records are electronic data generated during or as a byproduct of routine patient care. Structured, semi-structured and unstructured EHR offer researchers unprecedented phenotypic breadth and depth and have the potential to accelerate the development of precision medicine approaches at scale. A main EHR use-case is defining phenotyping algorithms that identify disease status, onset and severity. Phenotyping algorithms utilize diagnoses, prescriptions, laboratory tests, symptoms and other elements in order to identify patients with or without a spe...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Tracking Health Related Discussions on Reddit for Public Health Applications.
Discussions on Reddit for Public Health Applications. AMIA Annu Symp Proc. 2017;2017:1362-1371 Authors: Park A, Conway M Abstract We use Reddit to demonstrate social media's potential for public health applications. First, we employ a lexicon-based approach to track the prevalence of keywords indicating public interest in Ebola, electronic cigarette, influenza, and marijuana. Second, to better understand the public reactions, we use the Latent Dirichlet Allocation algorithm, to identify either the general themes or motivations for extreme changes in the volume of discussion over time. We observe that d...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Mining Hierarchies and Similarity Clusters from Value Set Repositories.
In this study, we describe methods to extract implicit relationships between value sets, and utilize these relationships to overlay organizational structure onto value set repositories. We successfully extract two different structurings, hierarchy and clustering, and show how tooling can leverage these structures to enable more effective value set discovery. PMID: 29854206 [PubMed - indexed for MEDLINE] (Source: AMIA Annual Symposium Proceedings)
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

A Conceptual Measurement Model for eHealth Readiness: a Team Based Perspective.
Authors: Phillips J, Poon SK, Yu D, Lam M, Hines M, Brunner M, Power E, Keep M, Shaw T, Togher L Abstract Despite the shift towards collaborative healthcare and the increase in the use of eHealth technologies, there does not currently exist a model for the measurement of eHealth readiness in interdisciplinary healthcare teams. This research aims to address this gap in the literature through the development of a three phase methodology incorporating qualitative and quantitative methods. We propose a conceptual measurement model consisting of operationalized themes affecting readiness across four factors: (i) Organiz...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Challenges with Collecting Smoking Status in Electronic Health Records.
In this study, we assessed the quality of smoking status captured in an electronic health record from a large academic medical center. We analyzed data from structured notes, finding that smoking status was documented in 98% of 64,451 hospital encounters in 2016. 32% hospital encounters had discrepant documentation, and 54.5% of patients had implausible changes (e.g., changes from "current smoker" to "never smoker"). Overall, only 2.9% of patients were documented as active smokers, but 36.4% were documented as "unknown" or had discrepancies in their smoking status. These results suggest that p...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Design and evaluation of a web-based decision support tool for district-level disease surveillance in a low-resource setting.
Authors: Pore M, Sengeh DM, Mugambi P, Purswani NV, Sesay T, Arnold AL, Tran AA, Myers R Abstract During the 2014 West African Ebola Virus outbreak it became apparent that the initial response to the outbreak was hampered by limitations in the collection, aggregation, analysis and use of data for intervention planning. As part of the post-Ebola recovery phase, IBM Research Africa partnered with the Port Loko District Health Management Team (DHMT) in Sierra Leone and GOAL Global, to design, implement and deploy a web-based decision support tool for district-level disease surveillance. This paper discusses the design...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Data Visualization of Home Care Admission Nurses' Decision-Making.
Authors: Sockolow PS, Yang Y, Bass EJ, Bowles KH, Holmberg A, Sheryl P Abstract The hospital to home care admission process is when nurses make important decisions about the post-transition episode, including medication reconciliation, plan of care, future visit patterns, and the inclusion of other disciplines. It is not clear how nurses get and use information to support decision-making. We conducted a focus group case study with six admitting home health nurses at a rural agency in Pennsylvania. We analyzed the data using thematic analysis and using our enhanced custom high level node-link diagram that highlights...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Current State of Electronic Consent Processes in Behavioral Health: Outcomes from an Observational Study.
Conclusions include need to streamline and standardize consent technologies and improve consenter engagement. This study supports the development of an electronic consent tool, My Data Choices (MDC), funded by the National Institute of Mental Health, that offers individuals with behavioral health conditions more control over their medical records. PMID: 29854231 [PubMed - indexed for MEDLINE] (Source: AMIA Annual Symposium Proceedings)
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Modeling Contextual Knowledge for Clinical Decision Support.
Authors: Sordo M, Tokachichu P, Vitale CJ, Maviglia SM, Rocha RA Abstract In theory, the logic of decision rules should be atomic. In practice, this is not always possible; initially simple logic statements tend to be overloaded with additional conditions restricting the scope of such rules. By doing so, the original logic soon becomes encumbered with contextual knowledge. Contextual knowledge is re-usable on its own and could be modeled separately from the logic of a rule without losing the intended functionality. We model constraints to explicitly define the context where knowledge of decision rules is actionable...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Reducing the Toxicity Risk in Antibiotic Prescriptions by Combining Ontologies with a Multiple Criteria Decision Model.
Authors: Souissi SB, Abed M, Elhiki L, Fortemps P, Pirlot M Abstract We consider the risk of adverse drug events caused by antibiotic prescriptions. Antibiotics are the second most common cause of drug related adverse events and one of the most common classes of drugs associated with medical malpractice claims. To cope with this serious issue, physicians rely on guidelines, especially in the context of hospital prescriptions. Unfortunately such guidelines do not offer sufficient support to solve the problem of adverse events. To cope with these issues our work proposes a clinical decision support system based on ex...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

A Data-Driven Method for Generating Robust Symptom Onset Indicators in Huntington's Disease Registry Data.
Authors: Sun Z, Li Y, Ghosh S, Cheng Y, Mohan A, Sampaio C, Hu J PMID: 29854234 [PubMed - indexed for MEDLINE] (Source: AMIA Annual Symposium Proceedings)
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Designing Decision-Support Technologies for Patient-Generated Data in Type 1 Diabetes.
Authors: Sun S, Costello KL Abstract People living with type 1 diabetes generate data as a byproduct of diabetes management. The development of decision support technologies can be enabled by harnessing these patient-generated data, but a major challenge is for these technologies to provide meaningful and highly personalized guidance to support individual patients' decision-making processes. In this paper, results from a year-long qualitative study were reported. Twenty-six people with type 1 diabetes were interviewed regarding the types of self-generated data they use for decision-making, their decision-making pro...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Causal Phenotyping for Susceptibility to Cardiotoxicity from Antineoplastic Breast Cancer Medications.
Authors: Sun D, Simon GJ, Skube S, Blaes AH, Melton GB, Zhang R Abstract Cardiotoxicity is a relatively common and particularly important adverse event caused by chemotherapy for breast cancer patients. Typical associative phenotypes, such as risk factors associated with diabetes, can often be detected solely based on the data elements existing in electronic health records; however, causal phenotypes, such as risk factors causing cardiotoxicity, require establishing causation between chemotherapy and determining new heart disease, and cannot be directly observedfrom EHR. We propose three phenotyping algorithms to a...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

A Multi-Task Framework for Monitoring Health Conditions via Attention-based Recurrent Neural Networks.
Authors: Suo Q, Ma F, Canino G, Gao J, Zhang A, Veltri P, Agostino G Abstract Monitoring the future health status of patients from the historical Electronic Health Record (EHR) is a core research topic in predictive healthcare. The most important challenges are to model the temporality of sequential EHR data and to interpret the prediction results. In order to reduce the future risk of diseases, we propose a multi-task framework that can monitor the multiple status ofdiagnoses. Patients' historical records are directly fed into a Recurrent Neural Network (RNN) which memorizes all the past visit information, and the...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Physician Information Needs in Managing Delirium.
Authors: Taft T, Nelsen SD, Slager S, Weir C Abstract Delirium has the highest occurrence rate of any complication in hospitalized adults over the age of 65. The study objective was to determine physician information needs for use in the development of electronic clinical decision support for physicians managing the care of patients with delirium. Critical incident interviews were conducted with 8 experienced internal medicine physicians and 1 cardiologist. Thematic analysis revealed the following 6 themes: 1) Clinician's experience an impoverished information field for mental status, 2) Uncertainty is pervasive, 3...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Facilitating Cohort Discovery by Enhancing Ontology Exploration, Query Management and Query Sharing for Large Clinical Data Repositories.
Authors: Tao S, Cui L, Wu X, Zhang GQ Abstract To help researchers better access clinical data, we developed a prototype query engine called DataSphere for exploring large-scale integrated clinical data repositories. DataSphere expedites data importing using a NoSQL data management system and dynamically renders its user interface for concept-based querying tasks. DataSphere provides an interactive query-building interface together with query translation and optimization strategies, which enable users to build and execute queries effectively and efficiently. We successfully loaded a dataset of one million patients ...
Source: AMIA Annual Symposium Proceedings - April 13, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Detection of Adverse Drug Reactions using Medical Named Entities on Twitter.
Authors: MacKinlay A, Aamer H, Yepes AJ Abstract Adverse Drug Reactions (ADRs) are unintentional reactions caused by a drug or combination of drugs taken by a patient. The current ADR reporting systems inevitably have delays in reporting such events. The broad scope of social media conversations on sites such as Twitter means that inevitably health-related topics will be covered. This means that these sites could then be used to detect potentially novel ADRs with less latency for subsequent further investigation. In this work, we investigate ADR surveillance using a large corpus of Twitter data, containing around 5...
Source: AMIA Annual Symposium Proceedings - April 5, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Usability and Learnability of RxUniverse, an Enterprise-Wide App Prescribing Platform Used in an Academic Tertiary Care Hospital.
The objective of this study was to assess the usability of RxUniverse, a novel platform that enables health care providers to directly disseminate proven, evidence-based mobile health apps to patients. Among five pilot clinical sites, 40 physicians and front-line providers were trained on the RxUniverse platform. They were educated on the platform's functionality and instructed how to prescribe apps to their patients. The well-validated System Usability Score (SUS) was used to assess the usability of the platform. The adoption goal was set as 100 prescriptions of relevant apps within an 8-week pilot period. Within the pilo...
Source: AMIA Annual Symposium Proceedings - April 5, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Deep Learning Meets Biomedical Ontologies: Knowledge Embeddings for Epilepsy.
Authors: Maldonado R, Goodwin TR, Skinner MA, Harabagiu SM Abstract While biomedical ontologies have traditionally been used to guide the identification of concepts or relations in biomedical data, recent advances in deep learning are able to capture high-quality knowledge from textual data and represent it in graphical structures. As opposed to the top-down methodology used in the generation of ontologies, which starts with the principled design of the upper ontology, the bottom-up methodology enabled by deep learning encodes the likelihood that concepts share certain relations, as evidenced by data. In this paper...
Source: AMIA Annual Symposium Proceedings - April 5, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Extracting Healthcare Quality Information from Unstructured Data.
Authors: Malmasi S, Hosomura N, Chang LS, Brown CJ, Skentzos S, Turchin A Abstract Healthcare quality research is a fundamental task that involves assessing treatment patterns and measuring the associated patient outcomes to identify potential areas for improving healthcare. While both qualitative and quantitative approaches are used, a major obstacle for the quantitative approach is that many useful healthcare quality indicators are buried within provider narrative notes, requiring expensive and laborious manual chart review to identify and measure them. Information extraction is a key Natural Language Processing ...
Source: AMIA Annual Symposium Proceedings - April 5, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

A novel application of point-of-sales grocery transaction data to enhance community nutrition monitoring.
Authors: Mamiya H, Moodie EEM, Buckeridge DL Abstract Unhealthy eating is the most important preventable cause of global death and disability. Effective development and evaluation of preventive initiatives and the identification of disparities in dietary patterns require surveillance of nutrition at a community level. However, nutrition monitoring currently relies on dietary surveys, which cannot efficiently assess food selection at high spatial resolution. However, marketing companies continuously collect and centralize digital grocery transaction data from a geographically representative sample of chain retail fo...
Source: AMIA Annual Symposium Proceedings - April 5, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Point of Care Research: Integrating patient-generated data into electronic health records for clinical trials.
Authors: Marceglia S, D'Antrassi P, Prenassi M, Rossi L, Barbieri S Abstract Integrating patient-generated data into clinical research would improve the reliability of results, especially when longitudinal, chronic, home-based monitoring is needed. To this end, we designed, implemented, and tested a system that allows integrating patient-generated data into electronic case report form (eCRF), using a standards based architecture that ensured the fulfillment of the major requirements for digital data in clinical studies. The system was tested in a clinical investigation for the optimization of deep brain stimulation...
Source: AMIA Annual Symposium Proceedings - April 5, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations.
Authors: Martínez-Romero M, O'Connor MJ, Shankar RD, Panahiazar M, Willrett D, Egyedi AL, Gevaert O, Graybeal J, Musen MA Abstract In biomedicine, high-quality metadata are crucial for finding experimental datasets, for understanding how experiments were performed, and for reproducing those experiments. Despite the recent focus on metadata, the quality of metadata available in public repositories continues to be extremely poor. A key difficulty is that the typical metadata acquisition process is time-consuming and error prone, with weak or nonexistent support for linking metadata to ontologies. There is a pr...
Source: AMIA Annual Symposium Proceedings - April 5, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Developing a concussion assessment mHealth app for certified Athletic Trainers.
Authors: McGrath SP, McGrath ML, Bastola D Abstract Annually, 1.6-3.8 million concussions occur from sports in the United States, which account for 5-9% of all sports injuries. The dangers of concussions include prolonged post-concussive symptoms, increased risk of subsequent concussions, seizures, mental health issues, and in cases of second-impact syndrome (SIS), possible death. Certified Athletic Trainers (ATC) continue to serve an important role in providing assessment and treatments for athletes with sports-related injuries. They provide a critical safety net due to limited knowledge and misconceptions of conc...
Source: AMIA Annual Symposium Proceedings - April 5, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research

Does a Community-Engaged Health Informatics Platform Facilitate Resource Connectivity? An Evaluation Framework.
We present a framework for evaluating the process and outcomes of a CEHI platform designed to improve connectivity among community health resources. The GetHealthyHeights.org CEHI platform was implemented in an urban low-income community. It was designed to facilitate connectivity among health-related community-based organizations (CBOs). To evaluate the process towards and the achievement of connectivity, a conceptual framework, methodology, and operational measures were defined. A system-level approach, such as social network analysis, is required to capture the community as one dynamic unit. The evaluation framework spe...
Source: AMIA Annual Symposium Proceedings - April 5, 2019 Category: Bioinformatics Tags: AMIA Annu Symp Proc Source Type: research