AliClu - Temporal sequence alignment for clustering longitudinal clinical data.

Abstract:

BACKGROUND:Patient stratification is a critical task in clinical decision making since it can allow physicians to choose treatments in a personalized way. Given the increasing availability of electronic medical records (EMRs) with longitudinal data, one crucial problem is how to efficiently cluster the patients based on the temporal information from medical appointments. In this work, we propose applying the Temporal Needleman-Wunsch (TNW) algorithm to align discrete sequences with the transition time information between symbols. These symbols may correspond to a patient's current therapy, their overall health status, or any other discrete state. The transition time information represents the duration of each of those states. The obtained TNW pairwise scores are then used to perform hierarchical clustering. To find the best number of clusters and assess their stability, a resampling technique is applied. RESULTS:We propose the AliClu, a novel tool for clustering temporal clinical data based on the TNW algorithm coupled with clustering validity assessments through bootstrapping. The AliClu was applied for the analysis of the rheumatoid arthritis EMRs obtained from the Portuguese database of rheumatologic patient visits (Reuma.pt). In particular, the AliClu was used for the analysis of therapy switches, which were coded as letters corresponding to biologic drugs and included their durations before each change occurred. The obtained optimized clusters allow one to stratify the patients based on their temporal therapy profiles and to support the identification of common features for those groups. CONCLUSIONS:The AliClu is a promising computational strategy to analyse longitudinal patient data by providing validated clusters and by unravelling the patterns that exist in clinical outcomes. Patient stratification is performed in an automatic or semi-automatic way, allowing one to tune the alignment, clustering, and validation parameters. The AliClu is freely available at https://github.com/sysbiomed/AliClu.

authors

Rama K,Canhão H,Carvalho AM,Vinga S

doi

10.1186/s12911-019-1013-7

subject

Has Abstract

pub_date

2019-12-30 00:00:00

pages

289

issue

1

issn

1472-6947

pii

10.1186/s12911-019-1013-7

journal_volume

19

pub_type

杂志文章
  • Multiple constraints compromise decision-making about implantable medical devices for individual patients: qualitative interviews with physicians.

    abstract:BACKGROUND:Little research has examined how physicians choose medical devices for treating individual patients to reveal if interventions are needed to support decision-making and reduce device-associated morbidity and mortality. This study explored factors that influence choice of implantable device from among availab...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-017-0577-3

    authors: Gagliardi AR,Ducey A,Lehoux P,Turgeon T,Kolbunik J,Ross S,Trbovich P,Easty A,Bell C,Urbach DR

    更新日期:2017-12-22 00:00:00

  • Recommended practices for computerized clinical decision support and knowledge management in community settings: a qualitative study.

    abstract:BACKGROUND:The purpose of this study was to identify recommended practices for computerized clinical decision support (CDS) development and implementation and for knowledge management (KM) processes in ambulatory clinics and community hospitals using commercial or locally developed systems in the U.S. METHODS:Guided b...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-12-6

    authors: Ash JS,Sittig DF,Guappone KP,Dykstra RH,Richardson J,Wright A,Carpenter J,McMullen C,Shapiro M,Bunce A,Middleton B

    更新日期:2012-02-14 00:00:00

  • Dynamic prediction of hospital admission with medical claim data.

    abstract:BACKGROUND:Congestive heart failure is one of the most common reasons those aged 65 and over are hospitalized in the United States, which has caused a considerable economic burden. The precise prediction of hospitalization caused by congestive heart failure in the near future could prevent possible hospitalization, opt...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-019-0734-y

    authors: Yang T,Yang Y,Jia Y,Li X

    更新日期:2019-01-31 00:00:00

  • Recursive neural networks in hospital bed occupancy forecasting.

    abstract:BACKGROUND:Efficient planning of hospital bed usage is a necessary condition to minimize the hospital costs. In the presented work we deal with the problem of occupancy forecasting in the scale of several months, with a focus on personnel's holiday planning. METHODS:We construct a model based on a set of recursive neu...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-019-0776-1

    authors: Kutafina E,Bechtold I,Kabino K,Jonas SM

    更新日期:2019-03-07 00:00:00

  • The International Conference on Intelligent Biology and Medicine 2018: Medical Informatics Thematic Track (MedicalInfo2018).

    abstract::In this editorial, we first summarize the 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) that was held on June 10-12, 2018 in Los Angeles, California, USA, and then briefly introduce the six research articles included in this supplement issue. At ICIBM 2018, a special theme of Medical I...

    journal_title:BMC medical informatics and decision making

    pub_type:

    doi:10.1186/s12911-019-0732-0

    authors: Zhang Y,Tao C,Gong Y,Wang K,Zhao Z

    更新日期:2019-01-31 00:00:00

  • A survey of factors affecting clinician acceptance of clinical decision support.

    abstract:BACKGROUND:Real-time clinical decision support (CDS) integrated into clinicians' workflow has the potential to profoundly affect the cost, quality, and safety of health care delivery. Recent reports have identified a surprisingly low acceptance rate for different types of CDS. We hypothesized that factors affecting CDS...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-6-6

    authors: Sittig DF,Krall MA,Dykstra RH,Russell A,Chin HL

    更新日期:2006-02-01 00:00:00

  • Design and evaluation of a mobile application to assist the self-monitoring of the chronic kidney disease in developing countries.

    abstract:BACKGROUND:The chronic kidney disease (CKD) is a worldwide critical problem, especially in developing countries. CKD patients usually begin their treatment in advanced stages, which requires dialysis and kidney transplantation, and consequently, affects mortality rates. This issue is faced by a mobile health (mHealth) ...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-018-0587-9

    authors: Sobrinho A,da Silva LD,Perkusich A,Pinheiro ME,Cunha P

    更新日期:2018-01-12 00:00:00

  • Assessing measures of comorbidity and functional status for risk adjustment to compare hospital performance for colorectal cancer surgery: a retrospective data-linkage study.

    abstract:BACKGROUND:Comparing outcomes between hospitals requires consideration of patient factors that could account for any observed differences. Adjusting for comorbid conditions is common when studying outcomes following cancer surgery, and a commonly used measure is the Charlson comorbidity index. Other measures of patient...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-015-0175-1

    authors: Dobbins TA,Badgery-Parker T,Currow DC,Young JM

    更新日期:2015-07-15 00:00:00

  • Caregivers' role in using a personal electronic health record: a qualitative study of cancer patients and caregivers in Germany.

    abstract:BACKGROUND:Particularly in the context of severe diseases like cancer, many patients wish to include caregivers in the planning of treatment and care. Many caregivers like to be involved but feel insufficiently enabled. This study aimed at providing insight into patients' and caregivers' perspectives on caregivers' rol...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-020-01172-4

    authors: Weis A,Pohlmann S,Poss-Doering R,Strauss B,Ullrich C,Hofmann H,Ose D,Winkler EC,Szecsenyi J,Wensing M

    更新日期:2020-07-13 00:00:00

  • The validity of synthetic clinical data: a validation study of a leading synthetic data generator (Synthea) using clinical quality measures.

    abstract:BACKGROUND:Clinical data synthesis aims at generating realistic data for healthcare research, system implementation and training. It protects patient confidentiality, deepens our understanding of the complexity in healthcare, and is a promising tool for situations where real world data is difficult to obtain or unneces...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-019-0793-0

    authors: Chen J,Chun D,Patel M,Chiang E,James J

    更新日期:2019-03-14 00:00:00

  • Automated extraction of Biomarker information from pathology reports.

    abstract:BACKGROUND:Pathology reports are written in free-text form, which precludes efficient data gathering. We aimed to overcome this limitation and design an automated system for extracting biomarker profiles from accumulated pathology reports. METHODS:We designed a new data model for representing biomarker knowledge. The ...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-018-0609-7

    authors: Lee J,Song HJ,Yoon E,Park SB,Park SH,Seo JW,Park P,Choi J

    更新日期:2018-05-21 00:00:00

  • Evaluating predictive modeling algorithms to assess patient eligibility for clinical trials from routine data.

    abstract:BACKGROUND:The necessity to translate eligibility criteria from free text into decision rules that are compatible with data from the electronic health record (EHR) constitutes the main challenge when developing and deploying clinical trial recruitment support systems. Recruitment decisions based on case-based reasoning...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-13-134

    authors: Köpcke F,Lubgan D,Fietkau R,Scholler A,Nau C,Stürzl M,Croner R,Prokosch HU,Toddenroth D

    更新日期:2013-12-09 00:00:00

  • Evidence in clinical reasoning: a computational linguistics analysis of 789,712 medical case summaries 1983-2012.

    abstract:BACKGROUND:Better understanding of clinical reasoning could reduce diagnostic error linked to 8% of adverse medical events and 30% of malpractice cases. To a greater extent than the evidence-based movement, the clinical reasoning literature asserts the importance of practitioner intuition—unconscious elements of diagno...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章,meta分析

    doi:10.1186/s12911-015-0136-8

    authors: Seidel BM,Campbell S,Bell E

    更新日期:2015-03-21 00:00:00

  • Implementation of automated reporting of estimated glomerular filtration rate among Veterans Affairs laboratories: a retrospective study.

    abstract:BACKGROUND:Automated reporting of estimated glomerular filtration rate (eGFR) is a recent advance in laboratory information technology (IT) that generates a measure of kidney function with chemistry laboratory results to aid early detection of chronic kidney disease (CKD). Because accurate diagnosis of CKD is critical ...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-12-69

    authors: Hall RK,Wang V,Jackson GL,Hammill BG,Maciejewski ML,Yano EM,Svetkey LP,Patel UD

    更新日期:2012-07-12 00:00:00

  • A predictive analytics model for differentiating between transient ischemic attacks (TIA) and its mimics.

    abstract:BACKGROUND:Transient ischemic attack (TIA) is a brief episode of neurological dysfunction resulting from cerebral ischemia not associated with permanent cerebral infarction. TIA is associated with high diagnostic errors because of the subjective nature of findings and the lack of clinical and imaging biomarkers. The go...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-020-01154-6

    authors: Stanciu A,Banciu M,Sadighi A,Marshall KA,Holland NR,Abedi V,Zand R

    更新日期:2020-06-18 00:00:00

  • Quality of human-computer interaction--results of a national usability survey of hospital-IT in Germany.

    abstract:BACKGROUND:Due to the increasing functionality of medical information systems, it is hard to imagine day to day work in hospitals without IT support. Therefore, the design of dialogues between humans and information systems is one of the most important issues to be addressed in health care. This survey presents an anal...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-11-69

    authors: Bundschuh BB,Majeed RW,Bürkle T,Kuhn K,Sax U,Seggewies C,Vosseler C,Röhrig R

    更新日期:2011-11-09 00:00:00

  • A simulation study comparing aberration detection algorithms for syndromic surveillance.

    abstract:BACKGROUND:The usefulness of syndromic surveillance for early outbreak detection depends in part on effective statistical aberration detection. However, few published studies have compared different detection algorithms on identical data. In the largest simulation study conducted to date, we compared the performance of...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-7-6

    authors: Jackson ML,Baer A,Painter I,Duchin J

    更新日期:2007-03-01 00:00:00

  • EURISWEB--Web-based epidemiological surveillance of antibiotic-resistant pneumococci in day care centers.

    abstract:BACKGROUND:EURIS (European Resistance Intervention Study) was launched as a multinational study in September of 2000 to identify the multitude of complex risk factors that contribute to the high carriage rate of drug resistant Streptococcus pneumoniae strains in children attending Day Care Centers in several European c...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-3-9

    authors: Silva S,Gouveia-Oliveira R,Maretzek A,Carriço J,Gudnason T,Kristinsson KG,Ekdahl K,Brito-Avô A,Tomasz A,Sanches IS,de Lencastre H,Almeida J

    更新日期:2003-07-08 00:00:00

  • Use of online knowledge base in primary health care and correlation to health care quality: an observational study.

    abstract:BACKGROUND:Evidence-based information available at the point of care improves patient care outcomes. Online knowledge bases can increase the application of evidence-based medicine and influence patient outcome data which may be captured in quality registries. The aim of this study was to explore the effect of use of an...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-020-01313-9

    authors: Gerdesköld C,Toth-Pal E,Wårdh I,Nilsson GH,Nager A

    更新日期:2020-11-16 00:00:00

  • Locating previously unknown patterns in data-mining results: a dual data- and knowledge-mining method.

    abstract:BACKGROUND:Data mining can be utilized to automate analysis of substantial amounts of data produced in many organizations. However, data mining produces large numbers of rules and patterns, many of which are not useful. Existing methods for pruning uninteresting patterns have only begun to automate the knowledge acquis...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-6-13

    authors: Siadaty MS,Knaus WA

    更新日期:2006-03-07 00:00:00

  • Evaluating performance of health care facilities at meeting HIV-indicator reporting requirements in Kenya: an application of K-means clustering algorithm.

    abstract:BACKGROUND:The ability to report complete, accurate and timely data by HIV care providers and other entities is a key aspect in monitoring trends in HIV prevention, treatment and care, hence contributing to its eradication. In many low-middle-income-countries (LMICs), aggregate HIV data reporting is done through the Di...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-020-01367-9

    authors: Gesicho MB,Were MC,Babic A

    更新日期:2021-01-06 00:00:00

  • Designing a multifaceted survivorship care plan to meet the information and communication needs of breast cancer patients and their family physicians: results of a qualitative pilot study.

    abstract:BACKGROUND:Following the completion of treatment and as they enter the follow-up phase, breast cancer patients (BCPs) often recount feeling 'lost in transition', and are left with many questions concerning how their ongoing care and monitoring for recurrence will be managed. Family physicians (FPs) also frequently repo...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-13-76

    authors: Haq R,Heus L,Baker NA,Dastur D,Leung FH,Leung E,Li B,Vu K,Parsons JA

    更新日期:2013-07-25 00:00:00

  • Assessing data availability and quality within an electronic health record system through external validation against an external clinical data source.

    abstract:BACKGROUND:Approximately 20% of deaths in the US each year are attributable to smoking, yet current practices in the recording of this health risk in electronic health records (EHRs) have not led to discernable changes in health outcomes. Several groups have developed algorithms for extracting smoking behaviors from cl...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-019-0864-2

    authors: Palmer EL,Higgins J,Hassanpour S,Sargent J,Robinson CM,Doherty JA,Onega T

    更新日期:2019-07-25 00:00:00

  • Non-redundant association rules between diseases and medications: an automated method for knowledge base construction.

    abstract:BACKGROUND:The widespread use of electronic health records (EHRs) has generated massive clinical data storage. Association rules mining is a feasible technique to convert this large amount of data into usable knowledge for clinical decision making, research or billing. We present a data driven method to create a knowle...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-015-0151-9

    authors: Séverac F,Sauleau EA,Meyer N,Lefèvre H,Nisand G,Jay N

    更新日期:2015-04-15 00:00:00

  • Medicine in words and numbers: a cross-sectional survey comparing probability assessment scales.

    abstract:BACKGROUND:In the complex domain of medical decision making, reasoning under uncertainty can benefit from supporting tools. Automated decision support tools often build upon mathematical models, such as Bayesian networks. These networks require probabilities which often have to be assessed by experts in the domain of a...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-7-13

    authors: Witteman CL,Renooij S,Koele P

    更新日期:2007-06-11 00:00:00

  • Fine-grained information extraction from German transthoracic echocardiography reports.

    abstract:BACKGROUND: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 methods typically rely on standardized terminologies that guide this process. Many languages and cli...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-015-0215-x

    authors: Toepfer M,Corovic H,Fette G,Klügl P,Störk S,Puppe F

    更新日期:2015-11-12 00:00:00

  • Stratification of coronary artery disease patients for revascularization procedure based on estimating adverse effects.

    abstract:BACKGROUND:Percutaneous coronary intervention (PCI) is the most commonly performed treatment for coronary atherosclerosis. It is associated with a higher incidence of repeat revascularization procedures compared to coronary artery bypass grafting surgery. Recent results indicate that PCI is only cost-effective for a su...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/s12911-015-0131-0

    authors: Pölsterl S,Singh M,Katouzian A,Navab N,Kastrati A,Ladic L,Kamen A

    更新日期:2015-02-14 00:00:00

  • Dual processing model of medical decision-making.

    abstract:BACKGROUND:Dual processing theory of human cognition postulates that reasoning and decision-making can be described as a function of both an intuitive, experiential, affective system (system I) and/or an analytical, deliberative (system II) processing system. To date no formal descriptive model of medical decision-maki...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-12-94

    authors: Djulbegovic B,Hozo I,Beckstead J,Tsalatsanis A,Pauker SG

    更新日期:2012-09-03 00:00:00

  • Concordance between decision analysis and matching systematic review of randomized controlled trials in assessment of treatment comparisons: a systematic review.

    abstract:BACKGROUND:Systematic review (SR) of randomized controlled trials (RCT) is the gold standard for informing treatment choice. Decision analyses (DA) also play an important role in informing health care decisions. It is unknown how often the results of DA and matching SR of RCTs are in concordance. We assessed whether th...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章,评审

    doi:10.1186/1472-6947-14-57

    authors: Mhaskar RS,Wao H,Mahony H,Kumar A,Djulbegovic B

    更新日期:2014-07-15 00:00:00

  • Use of and attitudes to a hospital information system by medical secretaries, nurses and physicians deprived of the paper-based medical record: a case report.

    abstract:BACKGROUND:Most hospitals keep and update their paper-based medical records after introducing an electronic medical record or a hospital information system (HIS). This case report describes a HIS in a hospital where the paper-based medical records are scanned and eliminated. To evaluate the HIS comprehensively, the per...

    journal_title:BMC medical informatics and decision making

    pub_type: 杂志文章

    doi:10.1186/1472-6947-4-18

    authors: Laerum H,Karlsen TH,Faxvaag A

    更新日期:2004-10-16 00:00:00