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Journal of Biomedical Informatics

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https://www.readbyqxmd.com/read/28526460/semi-supervised-medical-entity-recognition-a-study-on-spanish-and-swedish-clinical-corpora
#1
Alicia Pérez, Rebecka Weegar, Arantza Casillas, Koldo Gojenola, Maite Oronoz, Hercules Dalianis
OBJECTIVE: The goal of this study is to investigate entity recognition within Electronic Health Records (EHRs) focusing on Spanish and Swedish. Of particular importance is a robust representation of the entities. In our case, we utilized unsupervised methods to generate such representations. METHODS: The significance of this work stands on its experimental layout. The experiments were carried out under the same conditions for both languages. Several classification approaches were explored: maximum probability, CRF, Perceptron and SVM...
May 16, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28506904/ordinal-convolutional-neural-networks-for-predicting-rdoc-positive-valence-psychiatric-symptom-severity-scores
#2
Anthony Rios, Ramakanth Kavuluru
BACKGROUND: The CEGS N-GRID 2016 Shared Task in Clinical Natural Language Processing (NLP) provided a set of 1000 neuropsychiatric notes to participants as part of a competition to predict psychiatric symptom severity scores. This paper summarizes our methods, results, and experiences based on our participation in the second track of the shared task. OBJECTIVE: Classical methods of text classification usually fall into one of three problem types: binary, multi-class, and multi-label classification...
May 12, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28502910/balancing-volume-and-duration-of-information-consumption-by-physicians-the-case-of-health-information-exchange-in-critical-care
#3
Liran Politi, Shlomi Codish, Iftach Sagy, Lior Fink
BACKGROUND: The realization of the potential benefits of health information exchange systems (HIEs) for emergency departments (EDs) depends on the way these systems are actually used. The attributes of volume of information and duration of information processing are important for the study of HIE use patterns in the ED, as cognitive load and time constraints may result in a trade-off between these attributes. Experts and non-experts often use different problem-solving strategies, which may be consequential for their system use patterns...
May 11, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28502909/character-level-neural-network-for-biomedical-named-entity-recognition
#4
Mourad Gridach
Biomedical named entity recognition (BNER), which extracts important named entities such as genes and proteins, is a challenging task in automated systems that mine knowledge in biomedical texts. The previous state-of-the-art systems required large amounts of task-specific knowledge in the form of feature engineering, lexicons and data pre-processing to achieve high performance. In this paper, we introduce a novel neural network architecture that benefits from both word- and character-level representations automatically, by using a combination of bidirectional long short-term memory (LSTM) and conditional random field (CRF) eliminating the need for most feature engineering tasks...
May 11, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28501646/developing-a-framework-for-digital-objects-in-the-big-data-to-knowledge-bd2k-commons-report-from-the-commons-framework-pilots-workshop
#5
Kathleen M Jagodnik, Simon Koplev, Sherry Jenkins, Lucila Ohno-Machado, Benedict Paten, Stephan C Schurer, Michel Dumontier, Ruben Verborgh, Alex Bui, Peipei Ping, Neil J McKenna, Ravi Madduri, Ajay Pillai, Avi Ma'ayan
The volume and diversity of data in biomedical research has been rapidly increasing in recent years. While such data hold significant promise for accelerating discovery, their use entails many challenges including: the need for adequate computational infrastructure, secure processes for data sharing and access, tools that allow researchers to find and integrate diverse datasets, and standardized methods of analysis. These are just some elements of a complex ecosystem that needs to be built to support the rapid accumulation of these data...
May 10, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28499953/analysis-and-modeling-of-septic-shock-microarray-data-using-singular-value-decomposition
#6
Srinivas Allanki, Madhulika Dixit, Paul Thangaraj, Nandan Kumar Sinha
Being a high throughput technique, enormous amounts of microarray data has been generated and there arises a need for more efficient techniques of analysis, in terms of speed and accuracy. Finding the differentially expressed genes based on just fold change and p-value might not extract all the vital biological signals that occur at a lower gene expression level. Besides this, numerous mathematical models have been generated to predict the clinical outcome from microarray data, while very few, if not none, aim at predicting the vital genes that are important in a disease progression...
May 9, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28499952/data-management-plans-the-missing-perspective
#7
Mary Williams, Jacqueline Bagwell, Meredith Nahm Zozus
The National Institutes of Health requires data sharing plans for projects with over five hundred thousand dollars in direct costs in a single year and has recently released a new guidance on rigor and reproducibility in grant applications. The National Science Foundation outright requires Data Management Plans (DMPs) as part of applications for funding. However, there is no general and definitive list of topics that should be covered in a DMP for a research project. We identified and reviewed DMP requirements from research funders...
May 9, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28487263/a-pragmatic-method-for-transforming-clinical-research-data-from-the-research-electronic-data-capture-redcap-to-clinical-data-interchange-standards-consortium-cdisc-study-data-tabulation-model-sdtm-development-and-evaluation-of-redcap2sdtm
#8
Keiichi Yamamoto, Keiko Ota, Ippei Akiya, Ayumi Shintani
The Clinical Data Interchange Standards Consortium (CDISC) Study Data Tabulation Model (SDTM) can be used for new drug application studies as well as secondarily for creating a clinical research data warehouse to leverage clinical research study data across studies conducted within the same disease area. However, currently not all clinical research uses Clinical Data Acquisition Standards Harmonization (CDASH) beginning in the set-up phase of the study. Once already initiated, clinical studies that have not utilized CDASH are difficult to map in the SDTM format...
May 6, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28478268/the-uab-informatics-institute-and-2016-cegs-n-grid-de-identification-shared-task-challenge
#9
Duy Duc An Bui, Mathew Wyatt, James J Cimino
Clinical narratives (the text notes found in patients' medical records) are important information sources for secondary use in research. However, in order to protect patient privacy, they must be de-identified prior to use. Manual de-identification is considered to be the gold standard approach but is tedious, expensive, slow, and impractical for use with large-scale clinical data. Automated or semi-automated de-identification using computer algorithms is a potentially promising alternative. The Informatics Institute of the University of Alabama at Birmingham is applying de-identification to clinical data drawn from the UAB hospital's electronic medical records system before releasing them for research...
May 3, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28478267/the-effect-of-american-and-british-spelling-differences-on-information-retrieval-by-pubmed
#10
LETTER
Esmaeil Akbari
No abstract text is available yet for this article.
May 3, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28465082/computational-prediction-of-drug-drug-interactions-based-on-drugs-functional-similarities
#11
Reza Ferdousi, Reza Safdari, Yadollah Omidi
Therapeutic activities of drugs are often influenced by co-administration of drugs that may cause inevitable drug-drug interactions (DDIs) and side effects. Prediction and identification of DDIs are extremely vital for patient safety and success of treatment modalities. A number of computational methods have been employed for the prediction of DDIs based on drugs structures and/or functions. Here, we report on a computational method for DDIs prediction based on functional similarity of drugs. The model was set based on biological elements including carriers, transporters, enzymes and targets (CTET)...
April 29, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28455151/symptom-severity-prediction-from-neuropsychiatric-clinical-records-overview-of-2016-cegs-n-grid-shared-tasks-track-2
#12
Michele Filannino, Amber Stubbs, Özlem Uzuner
The second track of the CEGS N-GRID 2016 natural language processing shared tasks focused on predicting symptom severity from neuropsychiatric clinical records. For the first time, initial psychiatric evaluation records have been collected, de-identified, annotated and shared with the scientific community. One-hundred-ten researchers organized in twenty-four teams participated in this track and submitted sixty-five system runs for evaluation. The top ten teams each achieved an inverse normalized macro-averaged mean absolute error score over 0...
April 25, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28455150/evaluation-of-a-rule-based-method-for-epidemiological-document-classification-towards-the-automation-of-systematic-reviews
#13
George Karystianis, Kristina Thayer, Mary Wolfe, Guy Tsafnat
INTRODUCTION: Most data extraction efforts in epidemiology are focused on obtaining targeted information from clinical trials. In contrast, limited research has been conducted on the identification of information from observational studies, a major source for human evidence in many fields, including environmental health. The recognition of key epidemiological information (e.g., exposures) through text mining techniques can assist in the automation of systematic reviews and other evidence summaries...
April 25, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28442434/clinical-code-set-engineering-for-reusing-ehr-data-for-research-a-review
#14
REVIEW
Richard Williams, Evangelos Kontopantelis, Iain Buchan, Niels Peek
INTRODUCTION: The construction of reliable, reusable clinical code sets is essential when re-using Electronic Health Record (EHR) data for research. Yet code set definitions are rarely transparent and their sharing is almost non-existent. There is a lack of methodological standards for the management (construction, sharing, revision and reuse) of clinical code sets which needs to be addressed to ensure the reliability and credibility of studies which use code sets. OBJECTIVE: To review methodological literature on the management of sets of clinical codes used in research on clinical databases and to provide a list of best practice recommendations for future studies and software tools...
April 22, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28442433/electronic-health-record-as-a-research-tool-frequency-of-exposure-to-targeted-clinical-problems-and-health-care-providers-clinical-proficiency
#15
Tim Wysocki, Maria Carmen G Diaz, James H Crutchfield, James P Franciosi, Lloyd N Werk
OBJECTIVES: The Electronic Health Record (EHR) could provide insight into possible decay in health care providers' (HCP) clinical knowledge and cognitive performance. Analyses of the contributions of variables such as frequency of exposure to targeted clinical problems could inform the development and testing of appropriate individualized interventions to mitigate these threats to quality and safety of care. MATERIALS/METHODS: Nine targeted clinical problems (TCP) were selected for further study, and de-identified, aggregated study data were obtained for one calendar year...
April 22, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28438706/towards-generalizable-entity-centric-clinical-coreference-resolution
#16
Timothy Miller, Dmitriy Dligach, Steven Bethard, Chen Lin, Guergana Savova
OBJECTIVE: This work investigates the problem of clinical coreference resolution in a model that explicitly tracks entities, and aims to measure the performance of that model in both traditional in-domain train/test splits and cross-domain experiments that measure the generalizability of learned models. METHODS: The two methods we compare are a baseline mention-pair coreference system that operates over pairs of mentions with best-first conflict resolution and a mention-synchronous system that incrementally builds coreference chains...
April 21, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28435015/using-classification-models-for-the-generation-of-disease-specific-medications-from-biomedical-literature-and-clinical-data-repository
#17
Liqin Wang, Peter J Haug, Guilherme Del Fiol
OBJECTIVE: Mining disease-specific associations from existing knowledge resources can be useful for building disease-specific ontologies and supporting knowledge-based applications. Many association mining techniques have been exploited. However, the challenge remains when those extracted associations contained much noise. It is unreliable to determine the relevance of the association by simply setting up arbitrary cut-off points on multiple scores of relevance; and it would be expensive to ask human experts to manually review a large number of associations...
April 20, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28433826/data-summarization-method-for-chronic-disease-tracking
#18
Dejan Aleksić, Petar Rajković, Dušan Vučković, Dragan Janković, Aleksandar Milenković
OBJECTIVES: Bearing in mind the rising prevalence of chronic medical conditions, the chronic disease management is one of the key features required by medical information systems used in primary healthcare. Our research group paid a particular attention to this specific area by offering a set of custom data collection forms and reports in order to improve medical professionals' daily routine. The main idea was to provide an overview of history for chronic diseases, which, as it seems, had not been properly supported in previous administrative workflows...
April 19, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28433825/a-distributed-framework-for-health-information-exchange-using-smartphone-technologies
#19
Mohamed Abdulnabi, Ahmed Al-Haiqi, Mlm Kiah, A A Zaidan, B B Zaidan, Muzammil Hussein
Nationwide health information exchange (NHIE) continues to be a persistent concern for government agencies, despite the many efforts and the conceived benefits of sharing patient data among healthcare providers. Difficulties in ensuring global connectivity, interoperability, and concerns on security have always hampered the government from successfully deploying NHIE. By looking at NHIE from a fresh perspective and bearing in mind the pervasiveness and power of modern mobile platforms, this paper proposes a new approach to NHIE that builds on the notion of consumer-mediated HIE, albeit without the focus on central health record banks...
April 19, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28410983/toward-better-public-health-reporting-using-existing-off-the-shelf-approaches-the-value-of-medical-dictionaries-in-automated-cancer-detection-using-plaintext-medical-data
#20
Suranga N Kasthurirathne, Brian E Dixon, Judy Gichoya, Huiping Xu, Yuni Xia, Burke Mamlin, Shaun J Grannis
OBJECTIVES: Existing approaches to derive decision models from plaintext clinical data frequently depend on medical dictionaries as the sources of potential features. Prior research suggests that decision models developed using non-dictionary based feature sourcing approaches and "off the shelf" tools could predict cancer with performance metrics between 80%-90%. We sought to compare non-dictionary based models to models built using features derived from medical dictionaries. MATERIALS AND METHODS: We evaluated the detection of cancer cases from free text pathology reports using decision models built with combinations of dictionary or non-dictionary based feature sourcing approaches, 4 feature subset sizes, and 5 classification algorithms...
April 11, 2017: Journal of Biomedical Informatics
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