Mining association language patterns using a distributional semantic model for negative life event classification.

Abstract:

PURPOSE:Negative life events, such as the death of a family member, an argument with a spouse or the loss of a job, play an important role in triggering depressive episodes. Therefore, it is worthwhile to develop psychiatric services that can automatically identify such events. This study describes the use of association language patterns, i.e., meaningful combinations of words (e.g., ), as features to classify sentences with negative life events into predefined categories (e.g., Family, Love, Work). METHODS:This study proposes a framework that combines a supervised data mining algorithm and an unsupervised distributional semantic model to discover association language patterns. The data mining algorithm, called association rule mining, was used to generate a set of seed patterns by incrementally associating frequently co-occurring words from a small corpus of sentences labeled with negative life events. The distributional semantic model was then used to discover more patterns similar to the seed patterns from a large, unlabeled web corpus. RESULTS:The experimental results showed that association language patterns were significant features for negative life event classification. Additionally, the unsupervised distributional semantic model was not only able to improve the level of performance but also to reduce the reliance of the classification process on the availability of a large, labeled corpus.

journal_name

J Biomed Inform

authors

Yu LC,Chan CL,Lin CC,Lin IC

doi

10.1016/j.jbi.2011.01.006

subject

Has Abstract

pub_date

2011-08-01 00:00:00

pages

509-18

issue

4

eissn

1532-0464

issn

1532-0480

pii

S1532-0464(11)00008-6

journal_volume

44

pub_type

杂志文章
  • Personal discovery in diabetes self-management: Discovering cause and effect using self-monitoring data.

    abstract:OBJECTIVE:To outline new design directions for informatics solutions that facilitate personal discovery with self-monitoring data. We investigate this question in the context of chronic disease self-management with the focus on type 2 diabetes. MATERIALS AND METHODS:We conducted an observational qualitative study of d...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2017.09.013

    authors: Mamykina L,Heitkemper EM,Smaldone AM,Kukafka R,Cole-Lewis HJ,Davidson PG,Mynatt ED,Cassells A,Tobin JN,Hripcsak G

    更新日期:2017-12-01 00:00:00

  • DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx.

    abstract::In Electronic Health Records (EHRs), much of valuable information regarding patients' conditions is embedded in free text format. Natural language processing (NLP) techniques have been developed to extract clinical information from free text. One challenge faced in clinical NLP is that the meaning of clinical entities...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.02.010

    authors: Mehrabi S,Krishnan A,Sohn S,Roch AM,Schmidt H,Kesterson J,Beesley C,Dexter P,Max Schmidt C,Liu H,Palakal M

    更新日期:2015-04-01 00:00:00

  • Combining automatic table classification and relationship extraction in extracting anticancer drug-side effect pairs from full-text articles.

    abstract::Anticancer drug-associated side effect knowledge often exists in multiple heterogeneous and complementary data sources. A comprehensive anticancer drug-side effect (drug-SE) relationship knowledge base is important for computation-based drug target discovery, drug toxicity predication and drug repositioning. In this s...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2014.10.002

    authors: Xu R,Wang Q

    更新日期:2015-02-01 00:00:00

  • Comparing image search behaviour in the ARRS GoldMiner search engine and a clinical PACS/RIS.

    abstract::Information search has changed the way we manage knowledge and the ubiquity of information access has made search a frequent activity, whether via Internet search engines or increasingly via mobile devices. Medical information search is in this respect no different and much research has been devoted to analyzing the w...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2015.04.013

    authors: De-Arteaga M,Eggel I,Do B,Rubin D,Kahn CE Jr,Müller H

    更新日期:2015-08-01 00:00:00

  • Consensus and Meta-analysis regulatory networks for combining multiple microarray gene expression datasets.

    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

    authors: Steele E,Tucker A

    更新日期:2008-12-01 00:00:00

  • Comparison of reversible-jump Markov-chain-Monte-Carlo learning approach with other methods for missing enzyme identification.

    abstract::Computational identification of missing enzymes plays a significant role in accurate and complete reconstruction of metabolic network for both newly sequenced and well-studied organisms. For a metabolic reaction, given a set of candidate enzymes identified according to certain biological evidences, a powerful mathemat...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2007.09.002

    authors: Geng B,Zhou X,Zhu J,Hung YS,Wong ST

    更新日期:2008-04-01 00:00:00

  • Game-based interventions for neuropsychological assessment, training and rehabilitation: Which game-elements to use? A systematic review.

    abstract::Game-based interventions (GBI) have been used to promote health-related outcomes, including cognitive functions. Criteria for game-elements (GE) selection are insufficiently characterized in terms of their adequacy to patients' clinical conditions or targeted cognitive outcomes. This study aimed to identify GE applied...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2019.103287

    authors: Ferreira-Brito F,Fialho M,Virgolino A,Neves I,Miranda AC,Sousa-Santos N,Caneiras C,Carriço L,Verdelho A,Santos O

    更新日期:2019-10-01 00:00:00

  • Predictive modeling of bacterial infections and antibiotic therapy needs in critically ill adults.

    abstract::Unnecessary antibiotic regimens in the intensive care unit (ICU) are associated with adverse patient outcomes and antimicrobial resistance. Bacterial infections (BI) are both common and deadly in ICUs, and as a result, patients with a suspected BI are routinely started on broad-spectrum antibiotics prior to having con...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103540

    authors: Eickelberg G,Sanchez-Pinto LN,Luo Y

    更新日期:2020-09-01 00:00:00

  • Comparison with manual registration reveals satisfactory completeness and efficiency of a computerized cancer registration system.

    abstract::Automated software for cancer registration, called Open Registry and developed by ourselves was adopted by the Varese (population-based) Cancer Registry starting from 1997. Since the use of automated cancer registration is increasing, it is important to assess the quality and completeness of the automated data being p...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2007.03.003

    authors: Contiero P,Tittarelli A,Maghini A,Fabiano S,Frassoldi E,Costa E,Gada D,Codazzi T,Crosignani P,Tessandori R,Tagliabue G

    更新日期:2008-02-01 00:00:00

  • Enhancing phylogeography by improving geographical information from GenBank.

    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

    authors: Scotch M,Sarkar IN,Mei C,Leaman R,Cheung KH,Ortiz P,Singraur A,Gonzalez G

    更新日期:2011-12-01 00:00:00

  • A comparison of two methods for retrieving ICD-9-CM data: the effect of using an ontology-based method for handling terminology changes.

    abstract:OBJECTIVE:Most existing controlled terminologies can be characterized as collections of terms, wherein the terms are arranged in a simple list or organized in a hierarchy. These kinds of terminologies are considered useful for standardizing terms and encoding data and are currently used in many existing information sys...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2011.01.005

    authors: Yu AC,Cimino JJ

    更新日期:2011-04-01 00:00:00

  • Modelling and analysing the dynamics of disease progression from cross-sectional studies.

    abstract::Clinical trials are typically conducted over a population within a defined time period in order to illuminate certain characteristics of a health issue or disease process. These cross-sectional studies give us a 'snapshot' of this disease process over a large number of people but do not allow us to model the temporal ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2012.11.003

    authors: Li Y,Swift S,Tucker A

    更新日期:2013-04-01 00:00:00

  • Task definition, annotated dataset, and supervised natural language processing models for symptom extraction from unstructured clinical notes.

    abstract:INTRODUCTION:Machine learning (ML) and natural language processing have great potential to improve information extraction (IE) within electronic medical records (EMRs) for a wide variety of clinical search and summarization tools. Despite ML advancements, clinical adoption of real time IE tools for patient care remains...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2019.103354

    authors: Steinkamp JM,Bala W,Sharma A,Kantrowitz JJ

    更新日期:2020-02-01 00:00:00

  • DiseaSE: A biomedical text analytics system for disease symptom extraction and characterization.

    abstract::Due to increasing volume and unstructured nature of the scientific literatures in biomedical domain, most of the information embedded within them remain untapped. This paper presents a biomedical text analytics system, DiseaSE (Disease Symptom Extraction), to identify and extract disease symptoms and their association...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2019.103324

    authors: Abulaish M,Parwez MA,Jahiruddin

    更新日期:2019-12-01 00:00:00

  • Specifying computer-based counseling systems in health care: a new approach to user-interface and interaction design.

    abstract::Computer-based counseling systems in health care play an important role in the toolset available for medical doctors to inform, motivate and challenge their patients according to a well-defined therapeutic goal. The design, development and implementation of such systems require close collaboration between users, i.e. ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2008.10.005

    authors: Herzberg D,Marsden N,Kübler P,Leonhardt C,Thomanek S,Jung H,Becker A

    更新日期:2009-04-01 00:00:00

  • An image score inference system for RNAi genome-wide screening based on fuzzy mixture regression modeling.

    abstract::With recent advances in fluorescence microscopy imaging techniques and methods of gene knock down by RNA interference (RNAi), genome-scale high-content screening (HCS) has emerged as a powerful approach to systematically identify all parts of complex biological processes. However, a critical barrier preventing fulfill...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2008.04.007

    authors: Wang J,Zhou X,Li F,Bradley PL,Chang SF,Perrimon N,Wong ST

    更新日期:2009-02-01 00:00:00

  • On the reproducibility of results of pathway analysis in genome-wide expression studies of colorectal cancers.

    abstract::One of the major problems in genomics and medicine is the identification of gene networks and pathways deregulated in complex and polygenic diseases, like cancer. In this paper, we address the problem of assessing the variability of results of pathways analysis identified in different and independent genome wide expre...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2009.09.005

    authors: Maglietta R,Distaso A,Piepoli A,Palumbo O,Carella M,D'Addabbo A,Mukherjee S,Ancona N

    更新日期:2010-06-01 00:00:00

  • A controlled greedy supervised approach for co-reference resolution on clinical text.

    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

    authors: Chowdhury MF,Zweigenbaum P

    更新日期:2013-06-01 00:00:00

  • Neural network-based approaches for biomedical relation classification: A review.

    abstract::The explosive growth of biomedical literature has created a rich source of knowledge, such as that on protein-protein interactions (PPIs) and drug-drug interactions (DDIs), locked in unstructured free text. Biomedical relation classification aims to automatically detect and classify biomedical relations, which has gre...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章,评审

    doi:10.1016/j.jbi.2019.103294

    authors: Zhang Y,Lin H,Yang Z,Wang J,Sun Y,Xu B,Zhao Z

    更新日期:2019-11-01 00:00:00

  • Molecular property diagnostic suite for diabetes mellitus (MPDSDM): An integrated web portal for drug discovery and drug repurposing.

    abstract::Molecular Property Diagnostic Suite - Diabetes Mellitus (MPDSDM) is a Galaxy-based, open source disease-specific web portal for diabetes. It consists of three modules namely (i) data library (ii) data processing and (iii) data analysis tools. The data library (target library and literature) module provide extensive an...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2018.08.003

    authors: Gaur AS,Nagamani S,Tanneeru K,Druzhilovskiy D,Rudik A,Poroikov V,Narahari Sastry G

    更新日期:2018-09-01 00:00:00

  • Emerging medical informatics with case-based reasoning for aiding clinical decision in multi-agent system.

    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

    authors: Shen Y,Colloc J,Jacquet-Andrieu A,Lei K

    更新日期:2015-08-01 00:00:00

  • The REDCap consortium: Building an international community of software platform partners.

    abstract::The Research Electronic Data Capture (REDCap) data management platform was developed in 2004 to address an institutional need at Vanderbilt University, then shared with a limited number of adopting sites beginning in 2006. Given bi-directional benefit in early sharing experiments, we created a broader consortium shari...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2019.103208

    authors: Harris PA,Taylor R,Minor BL,Elliott V,Fernandez M,O'Neal L,McLeod L,Delacqua G,Delacqua F,Kirby J,Duda SN,REDCap Consortium.

    更新日期:2019-07-01 00:00:00

  • Systematic comparison of the protein-protein interaction databases from a user's perspective.

    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

    authors: Bajpai AK,Davuluri S,Tiwary K,Narayanan S,Oguru S,Basavaraju K,Dayalan D,Thirumurugan K,Acharya KK

    更新日期:2020-03-01 00:00:00

  • TRAK ontology: defining standard care for the rehabilitation of knee conditions.

    abstract::In this paper we discuss the design and development of TRAK (Taxonomy for RehAbilitation of Knee conditions), an ontology that formally models information relevant for the rehabilitation of knee conditions. TRAK provides the framework that can be used to collect coded data in sufficient detail to support epidemiologic...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2013.04.009

    authors: Button K,van Deursen RW,Soldatova L,Spasić I

    更新日期:2013-08-01 00:00:00

  • A novel web informatics approach for automated surveillance of cancer mortality trends.

    abstract::Cancer surveillance data are collected every year in the United States via the National Program of Cancer Registries (NPCR) and the Surveillance, Epidemiology and End Results (SEER) Program of the National Cancer Institute (NCI). General trends are closely monitored to measure the nation's progress against cancer. The...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.03.027

    authors: Tourassi G,Yoon HJ,Xu S

    更新日期:2016-06-01 00:00:00

  • Modified Needleman-Wunsch algorithm for clinical pathway clustering.

    abstract::Clinical pathways are used to guide clinicians to provide a standardised delivery of care. Because of their standardisation, the aim of clinical pathways is to reduce variation in both care process and patient outcomes. When learning clinical pathways from data through data mining, it is common practice to represent e...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2020.103668

    authors: Aspland E,Harper PR,Gartner D,Webb P,Barrett-Lee P

    更新日期:2021-01-27 00:00:00

  • High-performance implementation and analysis of the Linkmap program.

    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

    authors: Kothari K,Lopez-Benitez N,Poduslo SE

    更新日期:2001-12-01 00:00:00

  • Hierarchical data security in a Query-By-Example interface for a shared database.

    abstract::Whenever a shared database resource, containing critical patient data, is created, protecting the contents of the database is a high priority goal. This goal can be achieved by developing a Query-By-Example (QBE) interface, designed to access a shared database, and embedding within the QBE a hierarchical security modu...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/s1532-0464(02)00524-5

    authors: Taylor M

    更新日期:2002-06-01 00:00:00

  • MorphoCol: An ontology-based knowledgebase for the characterisation of clinically significant bacterial colony morphologies.

    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

    authors: Sousa AM,Pereira MO,Lourenço A

    更新日期:2015-06-01 00:00:00

  • A Health Surveillance Software Framework to deliver information on preventive healthcare strategies.

    abstract::A software framework can reduce costs related to the development of an application because it allows developers to reuse both design and code. Recently, companies and research groups have announced that they have been employing health software frameworks. This paper presents the design, proof-of-concept implementation...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章

    doi:10.1016/j.jbi.2016.06.002

    authors: Macedo AA,Pollettini JT,Baranauskas JA,Chaves JC

    更新日期:2016-08-01 00:00:00