Abstract:
:Medical error is a leading cause of patient death in the United States. Among the different types of medical errors, harm to patients caused by doctors missing early signs of deterioration is especially challenging to address due to the heterogeneity of patients' physiological patterns. In this study, we implemented risk prediction models using the gradient boosted tree method to derive risk estimates for acute onset diseases in the near future. The prediction model uses physiological variables as input signals and the time of the administration of outcome-related interventions and discharge diagnoses as labels. We examine four categories of acute onset illness: acute heart failure (AHF), acute lung injury (ALI), acute kidney injury (AKI), and acute liver failure (ALF). To develop and test the model, we consider data from two sources: 23,578 admissions to the Intensive Care Unit (ICU) from the MIMIC-3 dataset (Beth-Israel Hospital) and 16,612 ICU admissions on hospitals affiliated with our institution (University of Washington Medical Center and Harborview Medical Center, the UW-CDR dataset). We systematically identify outcome-related interventions for each acute organ failure, then use them, along with discharge diagnoses, to label proxy events to train gradient boosted trees. The trained models achieve the highest F1 score with a value of 0.6018 when predicting the need for life-saving interventions for ALI within the next 24 h in the MIMIC-3 dataset while showing a median F1 score of 0.3850 from all acute organ failures in both datasets. The approach also achieves the highest F1 score of 0.6301 when classifying a patient's ALI status at the time of discharge from the MIMIC-3 dataset, with a median F1 score of 0.4307 in both datasets. This study shows the potential for using the time of outcome-related intervention administrations and discharge diagnoses as labels to train supervised machine learning models that predict the risk of acute onset illnesses.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Lee DH,Yetisgen M,Vanderwende L,Horvitz Edoi
10.1016/j.jbi.2020.103425subject
Has Abstractpub_date
2020-07-01 00:00:00pages
103425eissn
1532-0464issn
1532-0480pii
S1532-0464(20)30053-8journal_volume
107pub_type
杂志文章abstract::Medication errors are common and cause serious health issues during care transitions, particularly for older adults with multiple chronic conditions. In this paper, we discuss the design and evaluation of the Colorado Care Tablet, a Personal Health Application (PHA) that helps older adults and their lay caregivers man...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2010.05.007
更新日期:2010-10-01 00:00:00
abstract::Balancing workload among nurses on a hospital unit is important for the satisfaction and safety of nurses and patients. To balance nurse workloads, direct patient care activities, indirect patient care activities, and non-patient care activities that occur throughout a shift must be considered. The layout of a hospita...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2016.10.006
更新日期:2016-12-01 00:00:00
abstract:OBJECTIVE:Structured data on mammographic findings are difficult to obtain without manual review. We developed and evaluated a rule-based natural language processing (NLP) system to extract mammographic findings from free-text mammography reports. MATERIALS AND METHODS:The NLP system extracted four mammographic findin...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2015.01.010
更新日期:2015-04-01 00:00:00
abstract::Linkage analysis uses information from family pedigrees to map genes and locate disease genes on particular chromosomes. A recombination fraction denoted as theta is estimated as a measure of crossing over between two loci. Genetic linkage calculations are very time-consuming particularly for large family pedigrees, a...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1006/jbin.2002.1031
更新日期:2001-12-01 00:00:00
abstract:OBJECTIVE:This paper introduces a model that predicts future changes in systolic blood pressure (SBP) based on structured and unstructured (text-based) information from longitudinal clinical records. METHOD:For each patient, the clinical records are sorted in chronological order and SBP measurements are extracted from...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2015.06.024
更新日期:2015-12-01 00:00:00
abstract::Phylogeography is a field that focuses on the geographical lineages of species such as vertebrates or viruses. Here, geographical data, such as location of a species or viral host is as important as the sequence information extracted from the species. Together, this information can help illustrate the migration of the...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2011.06.005
更新日期:2011-12-01 00:00:00
abstract::This research aims to depict the methodological steps and tools about the combined operation of case-based reasoning (CBR) and multi-agent system (MAS) to expose the ontological application in the field of clinical decision support. The multi-agent architecture works for the consideration of the whole cycle of clinica...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2015.06.012
更新日期:2015-08-01 00:00:00
abstract::Text categorization has been used extensively in recent years to classify plain-text clinical reports. This study employs text categorization techniques for the classification of open narrative forensic autopsy reports. One of the key steps in text classification is document representation. In document representation,...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2018.04.013
更新日期:2018-06-01 00:00:00
abstract::Identification of co-referent entity mentions inside text has significant importance for other natural language processing (NLP) tasks (e.g. event linking). However, this task, known as co-reference resolution, remains a complex problem, partly because of the confusion over different evaluation metrics and partly beca...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.03.007
更新日期:2013-06-01 00:00:00
abstract::Community pharmacists are critically placed in the patient care chain being an extended frontline within primary healthcare networks across Europe. They are trained to ensure safe and effective medication use, a crucial and responsible role, extending beyond the common misconception limited to just providing timely ac...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2019.103336
更新日期:2019-12-01 00:00:00
abstract:BACKGROUND:The difficulty of managing patient recruitment and documentation for clinical trials prompts a demand for instruments for closely monitoring these critical but unpredictable processes. Increasingly adopted Electronic Data Capture (EDC) applications provide novel opportunities to reutilize stored information ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2016.10.010
更新日期:2016-12-01 00:00:00
abstract::SNPs (Single Nucleotide Polymorphisms) include millions of changes in human genome, and therefore, are promising tools for disease-gene association studies. However, this kind of studies is constrained by the high expense of genotyping millions of SNPs. For this reason, it is required to obtain a suitable subset of SN...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2012.12.002
更新日期:2013-04-01 00:00:00
abstract::Recently, online health expert question-answering (HQA) services (systems) have attracted more and more health consumers to ask health-related questions everywhere at any time due to the convenience and effectiveness. However, the quality of answers in existing HQA systems varies in different situations. It is signifi...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2017.06.012
更新日期:2017-07-01 00:00:00
abstract::Generation of entity coreference chains provides a means to extract linked narrative events from clinical notes, but despite being a well-researched topic in natural language processing, general-purpose coreference tools perform poorly on clinical texts. This paper presents a knowledge-centric and pattern-based approa...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2012.02.012
更新日期:2012-10-01 00:00:00
abstract::This paper proposes a new framework for the selection of tag SNPs based on haplotypes instead of on a single SNP. The tag SNPs found by this framework form a set of haplotypes completely predictive of the alleles of all untyped SNPs. We refer to this problem as MTMH, which is defined as follows: given a set of SNPs, f...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2008.04.003
更新日期:2008-12-01 00:00:00
abstract::The class of continuous time Bayesian network classifiers is defined; it solves the problem of supervised classification on multivariate trajectories evolving in continuous time. The trajectory consists of the values of discrete attributes that are measured in continuous time, while the predicted class is expected to ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2012.07.002
更新日期:2012-12-01 00:00:00
abstract: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,...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2017.05.007
更新日期:2017-07-01 00:00:00
abstract::Protein name recognition aims to detect each and every protein names appearing in a PubMed abstract. The task is not simple, as the graphic word boundary (space separator) assumed in conventional preprocessing does not necessarily coincide with the protein name boundary. Such boundary disagreement caused by tokenizati...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2004.08.001
更新日期:2004-12-01 00:00:00
abstract::With rapid adoption of Electronic Health Records (EHR) in China, an increasing amount of clinical data has been available to support clinical research. Clinical data secondary use usually requires de-identification of personal information to protect patient privacy. Since manually de-identification of free clinical te...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2017.07.017
更新日期:2017-09-01 00:00:00
abstract::The 2014 i2b2/UTHealth natural language processing shared task featured a track focused on identifying risk factors for heart disease (specifically, Cardiac Artery Disease) in clinical narratives. For this track, we used a "light" annotation paradigm to annotate a set of 1304 longitudinal medical records describing 29...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2015.05.009
更新日期:2015-12-01 00:00:00
abstract::Computerized survival prediction in healthcare identifying the risk of disease mortality, helps healthcare providers to effectively manage their patients by providing appropriate treatment options. In this study, we propose to apply a classification algorithm, Contrast Pattern Aided Logistic Regression (CPXR(Log)) wit...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2016.01.009
更新日期:2016-04-01 00:00:00
abstract:OBJECTIVE:Targeted drugs dramatically improve the treatment outcomes in cancer patients; however, these innovative drugs are often associated with unexpectedly high cardiovascular toxicity. Currently, cardiovascular safety represents both a challenging issue for drug developers, regulators, researchers, and clinicians ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.10.008
更新日期:2014-02-01 00:00:00
abstract:BACKGROUND:One of the significant problems in the field of healthcare is the low survival rate of people who have experienced sudden cardiac arrest. Early prediction of cardiac arrest can provide the time required for intervening and preventing its onset in order to reduce mortality. Traditional statistical methods hav...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2018.10.008
更新日期:2018-12-01 00:00:00
abstract::In many respects, the critical care workplace resembles a paradigmatic complex system: on account of the dynamic and interactive nature of collaborative clinical work, these settings are characterized by non-linear, inter-dependent and emergent activities. Developing a comprehensive understanding of the work activitie...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2011.02.007
更新日期:2011-06-01 00:00:00
abstract::Microarray data is a key source of experimental data for modelling gene regulatory interactions from expression levels. With the rapid increase of publicly available microarray data comes the opportunity to produce regulatory network models based on multiple datasets. Such models are potentially more robust with great...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章,meta分析
doi:10.1016/j.jbi.2008.01.011
更新日期:2008-12-01 00:00:00
abstract::We have been investigating registration methods for improving digital subtraction angiography (DSA) images to extract blood vessels by reducing artifacts due to body motion, such as rotation, contraction, and dilation. In this paper, we propose a new and simple DSA registration algorithm with local distortion vectors ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1006/jbin.2001.1018
更新日期:2001-06-01 00:00:00
abstract::Computers allow describing the progress of a disease using computerized models. These models allow aggregating expert and clinical information to allow researchers and decision makers to forecast disease progression. To make this forecast reliable, good models and therefore good modeling tools are required. This paper...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2010.06.003
更新日期:2010-10-01 00:00:00
abstract:BACKGROUND:One of the major concerns of the biomedical community is the increasing prevalence of antimicrobial resistant microorganisms. Recent findings show that the diversification of colony morphology may be indicative of the expression of virulence factors and increased resistance to antibiotic therapeutics. To tra...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2015.03.007
更新日期:2015-06-01 00:00:00
abstract::In this paper we propose a novel approach to the design and implementation of knowledge-based decision support systems for translational research, specifically tailored to the analysis and interpretation of data from high-throughput experiments. Our approach is based on a general epistemological model of the scientifi...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2009.11.005
更新日期:2010-06-01 00:00:00
abstract::Sensitive biomedical data is often collected from distributed sources, involving different information systems and different organizational units. Local autonomy and legal reasons lead to the need of privacy preserving integration concepts. In this article, we focus on anonymization, which plays an important role for ...
journal_title:Journal of biomedical informatics
pub_type: 杂志文章
doi:10.1016/j.jbi.2013.12.002
更新日期:2014-08-01 00:00:00