Abstract：
:This paper presents a natural language processing (NLP) system that was designed to participate in the 2014 i2b2 de-identification challenge. The challenge task aims to identify and classify seven main Protected Health Information (PHI) categories and 25 associated sub-categories. A hybrid model was proposed which combines machine learning techniques with keyword-based and rule-based approaches to deal with the complexity inherent in PHI categories. Our proposed approaches exploit a rich set of linguistic features, both syntactic and word surface-oriented, which are further enriched by task-specific features and regular expression template patterns to characterize the semantics of various PHI categories. Our system achieved promising accuracy on the challenge test data with an overall micro-averaged F-measure of 93.6%, which was the winner of this de-identification challenge.
journal_name
J Biomed Informjournal_title
Journal of biomedical informaticsauthors
Yang H,Garibaldi JMdoi
10.1016/j.jbi.2015.06.015subject
Has Abstractpub_date
2015-12-01 00:00:00pages
S30-8eissn
1532-0464issn
1532-0480pii
S1532-0464(15)00125-2journal_volume
58 Supplpub_type
杂志文章abstract：:Electronic health records (EHR) are a major source of information in biomedical informatics. Yet, missing values are prominent characteristics of EHR. Prediction on dataset with missing values results in inaccurate inferences. Nearest neighbour imputation based on lazy learning approach is a proven technique for missi...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103190
更新日期：2019-06-01 00:00:00
abstract：:Semantic-based sublanguage grammars have been shown to be an efficient method for medical language processing. However, given the complexity of the medical domain, parsers using such grammars inevitably encounter ambiguous sentences, which could be interpreted by different groups of production rules and consequently r...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.08.009
更新日期：2011-12-01 00:00:00
abstract：:The physical spaces within which the work of health occurs - the home, the intensive care unit, the emergency room, even the bedroom - influence the manner in which behaviors unfold, and may contribute to efficacy and effectiveness of health interventions. Yet the study of such complex workspaces is difficult. Health ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.07.007
更新日期：2015-10-01 00:00:00
abstract：BACKGROUND:The determination of risk factors and their temporal relations in natural language patient records is a complex task which has been addressed in the i2b2/UTHealth 2014 shared task. In this context, in most systems it was broadly decomposed into two sub-tasks implemented by two components: entity detection, a...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.06.014
更新日期：2015-12-01 00:00:00
abstract：BACKGROUND:Identifying key variables such as disorders within the clinical narratives in electronic health records has wide-ranging applications within clinical practice and biomedical research. Previous research has demonstrated reduced performance of disorder named entity recognition (NER) and normalization (or groun...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.07.010
更新日期：2015-10-01 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：:Human musculoskeletal system resources of the human body are valuable for the learning and medical purposes. Internet-based information from conventional search engines such as Google or Yahoo cannot response to the need of useful, accurate, reliable and good-quality human musculoskeletal resources related to medical ...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2012.11.001
更新日期：2013-02-01 00:00:00
abstract：:Information extraction is the process of scanning text for information relevant to some interest, including extracting entities, relations, and events. It requires deeper analysis than key word searches, but its aims fall short of the very hard and long-term problem of full text understanding. Information extraction r...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/s1532-0464(03)00015-7
更新日期：2002-08-01 00:00:00
abstract：OBJECTIVE:To classify and characterize the variables commonly used to measure the impact of Information Technology (IT) adoption in health care, as well as settings and IT interventions tested, and to guide future research. MATERIALS AND METHODS:We conducted a descriptive study screening a sample of 236 studies from a...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2016.07.018
更新日期：2016-10-01 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：:The Breast Imaging Reporting and Data System (BI-RADS) was developed to reduce variation in the descriptions of findings. Manual analysis of breast radiology report data is challenging but is necessary for clinical and healthcare quality assurance activities. The objective of this study is to develop a natural languag...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.04.011
更新日期：2017-05-01 00:00:00
abstract：:Dialogue systems for health communication hold out the promise of providing intelligent assistance to patients through natural interfaces that require no training to use. But in order to make the development of such systems cost effective, we must be able to use generic techniques and components which are then special...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2006.02.004
更新日期：2006-10-01 00:00:00
abstract：:The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function....
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.01.008
更新日期：2015-04-01 00:00:00
abstract：BACKGROUND:Correlation of data within electronic health records is necessary for implementation of various clinical decision support functions, including patient summarization. A key type of correlation is linking medications to clinical problems; while some databases of problem-medication links are available, they are...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.11.010
更新日期：2014-04-01 00:00:00
abstract：OBJECTIVE:Clinical care guidelines recommend that newly diagnosed prostate cancer patients at high risk for metastatic spread receive a bone scan prior to treatment and that low risk patients not receive it. The objective was to develop an automated pipeline to interrogate heterogeneous data to evaluate the use of bone...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2019.103184
更新日期：2019-06-01 00:00:00
abstract：:With a rapid progress in the field, a great many fMRI studies are published every year, to the extent that it is now becoming difficult for researchers to keep up with the literature, since reading papers is extremely time-consuming and labor-intensive. Thus, automatic information extraction has become an important is...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.04.003
更新日期：2009-10-01 00:00:00
abstract：:Big data technologies are critical to the medical field which requires new frameworks to leverage them. Such frameworks would benefit medical experts to test hypotheses by querying huge volumes of unstructured medical data to provide better patient care. The objective of this work is to implement and examine the feasi...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.12.005
更新日期：2016-02-01 00:00:00
abstract：:The ubiquity and commoditisation of wearable biosensors (fitness bands) has led to a deluge of personal healthcare data, but with limited analytics typically fed back to the user. The feasibility of feeding back more complex, seemingly unrelated measures to users was investigated, by assessing whether increased levels...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103610
更新日期：2020-12-01 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：:CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus of medical forum posts on patient-reported Adverse Drug Events (ADEs). The corpus is sourced from posts on social media, and contains text that is largely written in colloquial language and often deviates from formal English grammar and punctuation...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2015.03.010
更新日期：2015-06-01 00:00:00
abstract：MOTIVATION:PubMed is the most widely used database of biomedical literature. To the detriment of the user though, the ranking of the documents retrieved for a query is not content-based, and important semantic information in the form of assigned Medical Subject Headings (MeSH) terms is not readily presented or producti...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2011.05.009
更新日期：2011-12-01 00:00:00
abstract：:Evaluating automated indexing applications requires comparing automatically indexed terms against manual reference standard annotations. However, there are no standard guidelines for determining which words from a textual document to include in manual annotations, and the vague task can result in substantial variation...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2005.06.004
更新日期：2006-04-01 00:00:00
abstract：:We address the assignment of ICD-10 codes for causes of death by analyzing free-text descriptions in death certificates, together with the associated autopsy reports and clinical bulletins, from the Portuguese Ministry of Health. We leverage a deep neural network that combines word embeddings, recurrent units, and neu...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.02.011
更新日期：2018-04-01 00:00:00
abstract：BACKGROUND:The association of genotyping information with common traits is not satisfactorily solved. One of the most complex traits is pain and association studies have failed so far to provide reproducible predictions of pain phenotypes from genotypes in the general population despite a well-established genetic basis...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2013.07.010
更新日期：2013-10-01 00:00:00
abstract：:Agglomerating results from studies of individual biological components has shown the potential to produce biomedical discovery and the promise of therapeutic development. Such knowledge integration could be tremendously facilitated by automated text mining for relation extraction in the biomedical literature. Relation...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2009.02.001
更新日期：2009-10-01 00:00:00
abstract：OBJECTIVE:To report the results of a systematic literature review concerning the security and privacy of electronic health record (EHR) systems. DATA SOURCES:Original articles written in English found in MEDLINE, ACM Digital Library, Wiley InterScience, IEEE Digital Library, Science@Direct, MetaPress, ERIC, CINAHL and...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章,评审
doi：10.1016/j.jbi.2012.12.003
更新日期：2013-06-01 00:00:00
abstract：:In the past, algorithms exploiting varying semantics in interactions between biological objects such as genes and diseases have been used in bioinformatics to uncover latent relationships within biological datasets. In this paper, we consider the algorithm Medusa in parallel with binary classification in order to find...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2018.07.005
更新日期：2018-08-01 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：:Outbreaks of infectious diseases such as influenza are a significant threat to human health. Because there are different strains of influenza which can cause independent outbreaks, and influenza can affect demographic groups at different rates and times, there is a need to recognize and characterize multiple outbreaks...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2017.08.003
更新日期：2017-09-01 00:00:00
abstract：:In absence of periodic systematic comparisons, biologists/bioinformaticians may be forced to make a subjective selection among the many protein-protein interaction (PPI) databases and tools. We conducted a comprehensive compilation and comparison of such resources. We compiled 375 PPI resources, short-listed 125 impor...
journal_title：Journal of biomedical informatics
pub_type： 杂志文章
doi：10.1016/j.jbi.2020.103380
更新日期：2020-03-01 00:00:00
