Standards, technology, machine learning, and modeling

Section edited by Andreas Holzinger

This section considers manuscripts that investigate data analysis, data mining and machine learning in healthcare systems, disease prediction, forecasting and modeling, as well as studies in advanced information and data management systems, and knowledge bases.

  1. Technical advance

    Dynamic-ETL: a hybrid approach for health data extraction, transformation and loading

    Electronic health records (EHRs) contain detailed clinical data stored in proprietary formats with non-standard codes and structures. Participating in multi-site clinical research networks requires EHR data to...

    Toan C. Ong, Michael G. Kahn, Bethany M. Kwan, Traci Yamashita, Elias Brandt, Patrick Hosokawa, Chris Uhrich and Lisa M. Schilling

    BMC Medical Informatics and Decision Making 2017 17:134

    Published on: 13 September 2017

  2. Research article

    Enhancement of hepatitis virus immunoassay outcome predictions in imbalanced routine pathology data by data balancing and feature selection before the application of support vector machines

    Data mining techniques such as support vector machines (SVMs) have been successfully used to predict outcomes for complex problems, including for human health. Much health data is imbalanced, with many more co...

    Alice M. Richardson and Brett A. Lidbury

    BMC Medical Informatics and Decision Making 2017 17:121

    Published on: 14 August 2017

  3. Research article

    Predicting progression of mild cognitive impairment to dementia using neuropsychological data: a supervised learning approach using time windows

    Predicting progression from a stage of Mild Cognitive Impairment to dementia is a major pursuit in current research. It is broadly accepted that cognition declines with a continuum between MCI and dementia. As...

    Telma Pereira, Luís Lemos, Sandra Cardoso, Dina Silva, Ana Rodrigues, Isabel Santana, Alexandre de Mendonça, Manuela Guerreiro and Sara C. Madeira

    BMC Medical Informatics and Decision Making 2017 17:110

    Published on: 19 July 2017

  4. Research Article

    Utility-preserving anonymization for health data publishing

    Publishing raw electronic health records (EHRs) may be considered as a breach of the privacy of individuals because they usually contain sensitive information. A common practice for the privacy-preserving data...

    Hyukki Lee, Soohyung Kim, Jong Wook Kim and Yon Dohn Chung

    BMC Medical Informatics and Decision Making 2017 17:104

    Published on: 11 July 2017

  5. Research article

    Medical diagnosis as a linguistic game

    We present a formalized medical knowledge system using a linguistic approach combined with a semantic net.

    Peter Fritz, Andreas Kleinhans, Florian Kuisle, Patricius Albu, Christine Fritz-Kuisle and Mark Dominik Alscher

    BMC Medical Informatics and Decision Making 2017 17:103

    Published on: 10 July 2017

  6. Research article

    Evaluation of rational nonsteroidal anti-inflammatory drugs and gastro-protective agents use; association rule data mining using outpatient prescription patterns

    Nonsteroidal anti-inflammatory drugs (NSAIDs) and gastro-protective agents should be co-prescribed following a standard clinical practice guideline; however, adherence to this guideline in routine practice is ...

    Oraluck Pattanaprateep, Mark McEvoy, John Attia and Ammarin Thakkinstian

    BMC Medical Informatics and Decision Making 2017 17:96

    Published on: 4 July 2017

  7. Research article

    Clinical use of computational modeling for surgical planning of arteriovenous fistula for hemodialysis

    Autogenous arteriovenous fistula (AVF) is the best vascular access (VA) for hemodialysis, but its creation is still a critical procedure. Physical examination, vascular mapping and doppler ultrasound (DUS) eva...

    Michela Bozzetto, Stefano Rota, Valentina Vigo, Francesco Casucci, Carlo Lomonte, Walter Morale, Massimo Senatore, Luigi Tazza, Massimo Lodi, Giuseppe Remuzzi and Andrea Remuzzi

    BMC Medical Informatics and Decision Making 2017 17:26

    Published on: 14 March 2017

  8. Technical advance

    Applying openEHR’s Guideline Definition Language to the SITS international stroke treatment registry: a European retrospective observational study

    Interoperability standards intend to standardise health information, clinical practice guidelines intend to standardise care procedures, and patient data registries are vital for monitoring quality of care and...

    Nadim Anani, Michael V. Mazya, Rong Chen, Tiago Prazeres Moreira, Olivier Bill, Niaz Ahmed, Nils Wahlgren and Sabine Koch

    BMC Medical Informatics and Decision Making 2017 17:7

    Published on: 10 January 2017

  9. Research article

    Development of an algorithm for determining smoking status and behaviour over the life course from UK electronic primary care records

    Patients’ smoking status is routinely collected by General Practitioners (GP) in UK primary health care. There is an abundance of Read codes pertaining to smoking, including those relating to smoking cessation...

    Mark D. Atkinson, Jonathan I. Kennedy, Ann John, Keir E. Lewis, Ronan A. Lyons and Sinead T. Brophy

    BMC Medical Informatics and Decision Making 2017 17:2

    Published on: 5 January 2017

  10. Technical advance

    Secure and scalable deduplication of horizontally partitioned health data for privacy-preserving distributed statistical computation

    Techniques have been developed to compute statistics on distributed datasets without revealing private information except the statistical results. However, duplicate records in a distributed dataset may lead t...

    Kassaye Yitbarek Yigzaw, Antonis Michalas and Johan Gustav Bellika

    BMC Medical Informatics and Decision Making 2017 17:1

    Published on: 3 January 2017

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  1. Research article

    Predicting influenza with dynamical methods

    Prediction of influenza weeks in advance can be a useful tool in the management of cases and in the early recognition of pandemic influenza seasons.

    Linda Moniz, Anna L. Buczak, Ben Baugher, Erhan Guven and Jean-Paul Chretien

    BMC Medical Informatics and Decision Making 2016 16:134

    Published on: 19 October 2016

  2. Research article

    An information model for computable cancer phenotypes

    Standards, methods, and tools supporting the integration of clinical data and genomic information are an area of significant need and rapid growth in biomedical informatics. Integration of cancer clinical data...

    Harry Hochheiser, Melissa Castine, David Harris, Guergana Savova and Rebecca S. Jacobson

    BMC Medical Informatics and Decision Making 2016 16:121

    Published on: 15 September 2016

  3. Research article

    Legal assessment tool (LAT): an interactive tool to address privacy and data protection issues for data sharing

    In an unprecedented rate data in the life sciences is generated and stored in many different databases. An ever increasing part of this data is human health data and therefore falls under data protected by leg...

    Wolfgang Kuchinke, Christian Krauth, René Bergmann, Töresin Karakoyun, Astrid Woollard, Irene Schluender, Benjamin Braasch, Martin Eckert and Christian Ohmann

    BMC Medical Informatics and Decision Making 2016 16:81

    Published on: 7 July 2016

  4. Research article

    Temporal bone radiology report classification using open source machine learning and natural langue processing libraries

    Radiology reports are a rich resource for biomedical research. Prior to utilization, trained experts must manually review reports to identify discrete outcomes. The Audiological and Genetic Database (AudGenDB)...

    Aaron J. Masino, Robert W. Grundmeier, Jeffrey W. Pennington, John A. Germiller and E. Bryan Crenshaw III

    BMC Medical Informatics and Decision Making 2016 16:65

    Published on: 6 June 2016

  5. Technical advance

    Multiscale Poincaré plots for visualizing the structure of heartbeat time series

    Poincaré delay maps are widely used in the analysis of cardiac interbeat interval (RR) dynamics. To facilitate visualization of the structure of these time series, we introduce multiscale Poincaré (MSP) plots.

    Teresa S. Henriques, Sara Mariani, Anton Burykin, Filipa Rodrigues, Tiago F. Silva and Ary L. Goldberger

    BMC Medical Informatics and Decision Making 2016 16:17

    Published on: 9 February 2016

  6. Research article

    Semantic representation of reported measurements in radiology

    In radiology, a vast amount of diverse data is generated, and unstructured reporting is standard. Hence, much useful information is trapped in free-text form, and often lost in translation and transmission. On...

    Heiner Oberkampf, Sonja Zillner, James A. Overton, Bernhard Bauer, Alexander Cavallaro, Michael Uder and Matthias Hammon

    BMC Medical Informatics and Decision Making 2016 16:5

    Published on: 22 January 2016

  7. Research article

    Logic regression-derived algorithms for syndromic management of vaginal infections

    Syndromic management of vaginal infections is known to have poor diagnostic accuracy. Logic regression is a machine-learning procedure which allows for the identification of combinations of variables to predic...

    Sujit D. Rathod, Tan Li, Jeffrey D. Klausner, Alan Hubbard, Arthur L. Reingold and Purnima Madhivanan

    BMC Medical Informatics and Decision Making 2015 15:106

    Published on: 16 December 2015

  8. Research article

    A numerical similarity approach for using retired Current Procedural Terminology (CPT) codes for electronic phenotyping in the Scalable Collaborative Infrastructure for a Learning Health System (SCILHS)

    Interoperable phenotyping algorithms, needed to identify patient cohorts meeting eligibility criteria for observational studies or clinical trials, require medical data in a consistent structured, coded format...

    Jeffrey G. Klann, Lori C. Phillips, Alexander Turchin, Sarah Weiler, Kenneth D. Mandl and Shawn N. Murphy

    BMC Medical Informatics and Decision Making 2015 15:104

    Published on: 11 December 2015

  9. Research article

    Estimating the value of medical treatments to patients using probabilistic multi criteria decision analysis

    Estimating the value of medical treatments to patients is an essential part of healthcare decision making, but is mostly done implicitly and without consulting patients. Multi criteria decision analysis (MCDA)...

    Henk Broekhuizen, Catharina G. M. Groothuis-Oudshoorn, A. Brett Hauber, Jeroen P. Jansen and Maarten J. IJzerman

    BMC Medical Informatics and Decision Making 2015 15:102

    Published on: 2 December 2015

  10. Technical advance

    A generic solution for web-based management of pseudonymized data

    Collaborative collection and sharing of data have become a core element of biomedical research. Typical applications are multi-site registries which collect sensitive person-related data prospectively, often t...

    Ronald Lautenschläger, Florian Kohlmayer, Fabian Prasser and Klaus A. Kuhn

    BMC Medical Informatics and Decision Making 2015 15:100

    Published on: 30 November 2015

  11. Research Article

    Rough set theory based prognostic classification models for hospice referral

    This paper explores and evaluates the application of classical and dominance-based rough set theory (RST) for the development of data-driven prognostic classification models for hospice referral. In this work,...

    Eleazar Gil-Herrera, Garrick Aden-Buie, Ali Yalcin, Athanasios Tsalatsanis, Laura E. Barnes and Benjamin Djulbegovic

    BMC Medical Informatics and Decision Making 2015 15:98

    Published on: 25 November 2015

  12. Research article

    How to model temporal changes in comorbidity for cancer patients using prospective cohort data

    The presence of comorbid conditions is strongly related to survival and also affects treatment choices in cancer patients. This comorbidity is often quantified by the Charlson Comorbidity Index (CCI) using spe...

    Lars Lindhagen, Mieke Van Hemelrijck, David Robinson, Pär Stattin and Hans Garmo

    BMC Medical Informatics and Decision Making 2015 15:96

    Published on: 18 November 2015

  13. Research Article

    Surveillance of dengue vectors using spatio-temporal Bayesian modeling

    At present, dengue control focuses on reducing the density of the primary vector for the disease, Aedes aegypti, which is the only vulnerable link in the chain of transmission. The use of new approaches for dengu...

    Ana Carolina C. Costa, Cláudia T. Codeço, Nildimar A. Honório, Gláucio R. Pereira, Carmen Fátima N. Pinheiro and Aline A. Nobre

    BMC Medical Informatics and Decision Making 2015 15:93

    Published on: 13 November 2015

  14. Research Article

    Fine-grained information extraction from German transthoracic echocardiography reports

    Information extraction techniques that get structured representations out of unstructured data make a large amount of clinically relevant information about patients accessible for semantic applications. These ...

    Martin Toepfer, Hamo Corovic, Georg Fette, Peter Klügl, Stefan Störk and Frank Puppe

    BMC Medical Informatics and Decision Making 2015 15:91

    Published on: 12 November 2015

    The Erratum to this article has been published in BMC Medical Informatics and Decision Making 2015 15:103

  15. Research article

    Prediction of delayed graft function after kidney transplantation: comparison between logistic regression and machine learning methods

    Predictive models for delayed graft function (DGF) after kidney transplantation are usually developed using logistic regression. We want to evaluate the value of machine learning methods in the prediction of DGF.

    Alexander Decruyenaere, Philippe Decruyenaere, Patrick Peeters, Frank Vermassen, Tom Dhaene and Ivo Couckuyt

    BMC Medical Informatics and Decision Making 2015 15:83

    Published on: 14 October 2015

  16. Research article

    An end-to-end hybrid algorithm for automated medication discrepancy detection

    In this study we implemented and developed state-of-the-art machine learning (ML) and natural language processing (NLP) technologies and built a computerized algorithm for medication reconciliation. Our specif...

    Qi Li, Stephen Andrew Spooner, Megan Kaiser, Nataline Lingren, Jessica Robbins, Todd Lingren, Huaxiu Tang, Imre Solti and Yizhao Ni

    BMC Medical Informatics and Decision Making 2015 15:37

    Published on: 6 May 2015

  17. Research article

    From prescription drug purchases to drug use periods – a second generation method (PRE2DUP)

    Databases of prescription drug purchases are now widely used in pharmacoepidemiologic studies. Several methods have been used to generate drug use periods from drug purchases to investigate various aspects; e....

    Antti Tanskanen, Heidi Taipale, Marjaana Koponen, Anna-Maija Tolppanen, Sirpa Hartikainen, Riitta Ahonen and Jari Tiihonen

    BMC Medical Informatics and Decision Making 2015 15:21

    Published on: 25 March 2015

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