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


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.


J Biomed Inform


Yu LC,Chan CL,Lin CC,Lin IC




Has Abstract


2011-08-01 00:00:00














  • Annotating risk factors for heart disease in clinical narratives for diabetic patients.

    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


    authors: Stubbs A,Uzuner Ö

    更新日期:2015-12-01 00:00:00

  • Genome-wide analysis of multi-view data of miRNA-seq to identify miRNA biomarkers for stomach cancer.

    abstract::Stomach cancer is one of the leading causes of cancer-related deaths worldwide. More than 80% diagnosis of this cancer occur at later stages leading to low 5-year survival rate. This emphasizes the need to have better prognostic techniques for stomach cancer. In this regard, the Next-Generation Sequencing of whole gen...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Pant N,Rakshit S,Paul S,Saha I

    更新日期:2019-09-01 00:00:00

  • Clinical coverage of an archetype repository over SNOMED-CT.

    abstract::Clinical archetypes provide a means for health professionals to design what should be communicated as part of an Electronic Health Record (EHR). An ever-growing number of archetype definitions follow this health information modelling approach, and this international archetype resource will eventually cover a large num...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Yu S,Berry D,Bisbal J

    更新日期:2012-06-01 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


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

    更新日期:2020-02-01 00:00:00

  • Personal health information in research: Perceived risk, trustworthiness and opinions from patients attending a tertiary healthcare facility.

    abstract:BACKGROUND:Personal health information is a valuable resource to the advancement of research. In order to achieve a comprehensive reform of data infrastructure in Australia, both public engagement and building social trust is vital. In light of this, we conducted a study to explore the opinions, perceived risks and tru...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Krahe M,Milligan E,Reilly S

    更新日期:2019-07-01 00:00:00

  • RedMed: Extending drug lexicons for social media applications.

    abstract::Social media has been identified as a promising potential source of information for pharmacovigilance. The adoption of social media data has been hindered by the massive and noisy nature of the data. Initial attempts to use social media data have relied on exact text matches to drugs of interest, and therefore suffer ...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Lavertu A,Altman RB

    更新日期:2019-11-01 00:00:00

  • Evaluation of relational and NoSQL database architectures to manage genomic annotations.

    abstract::While the adoption of next generation sequencing has rapidly expanded, the informatics infrastructure used to manage the data generated by this technology has not kept pace. Historically, relational databases have provided much of the framework for data storage and retrieval. Newer technologies based on NoSQL architec...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Schulz WL,Nelson BG,Felker DK,Durant TJS,Torres R

    更新日期:2016-12-01 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


    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

  • 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


    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

  • Characterizing and optimizing human anticancer drug targets based on topological properties in the context of biological pathways.

    abstract::One of the challenging problems in drug discovery is to identify the novel targets for drugs. Most of the traditional methods for drug targets optimization focused on identifying the particular families of "druggable targets", but ignored their topological properties based on the biological pathways. In this study, we...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Zhang J,Wang Y,Shang D,Yu F,Liu W,Zhang Y,Feng C,Wang Q,Xu Y,Liu Y,Bai X,Li X,Li C

    更新日期:2015-04-01 00:00:00

  • Exploiting the contextual cues for bio-entity name recognition in biomedical literature.

    abstract::To extract biomedical information about bio-entities from the huge amount of biomedical literature, the first key step is recognizing their names in these literatures, which remains a challenging task due to the irregularities and ambiguities in bio-entities nomenclature. The recognition performances of the current po...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Yang Z,Lin H,Li Y

    更新日期:2008-08-01 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


    authors: Tourassi G,Yoon HJ,Xu S

    更新日期:2016-06-01 00:00:00

  • Wisdom of artificial crowds feature selection in untargeted metabolomics: An application to the development of a blood-based diagnostic test for thrombotic myocardial infarction.

    abstract:INTRODUCTION:Heart disease remains a leading cause of global mortality. While acute myocardial infarction (colloquially: heart attack), has multiple proximate causes, proximate etiology cannot be determined by a blood-based diagnostic test. We enrolled a suitable patient cohort and conducted a non-targeted quantificati...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章,多中心研究


    authors: Trainor PJ,Yampolskiy RV,DeFilippis AP

    更新日期:2018-05-01 00:00:00

  • Multi-step ahead meningitis case forecasting based on decomposition and multi-objective optimization methods.

    abstract::Epidemiological time series forecasting plays an important role in health public systems, due to its ability to allow managers to develop strategic planning to avoid possible epidemics. In this paper, a hybrid learning framework is developed to forecast multi-step-ahead (one, two, and three-month-ahead) meningitis cas...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Ribeiro MHDM,Mariani VC,Coelho LDS

    更新日期:2020-11-01 00:00:00

  • A comprehensive review of feature based methods for drug target interaction prediction.

    abstract::Drug target interaction is a prominent research area in the field of drug discovery. It refers to the recognition of interactions between chemical compounds and the protein targets in the human body. Wet lab experiments to identify these interactions are expensive as well as time consuming. The computational methods o...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章,评审


    authors: Sachdev K,Gupta MK

    更新日期:2019-05-01 00:00:00

  • Classification of forensic autopsy reports through conceptual graph-based document representation model.

    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


    authors: Mujtaba G,Shuib L,Raj RG,Rajandram R,Shaikh K,Al-Garadi MA

    更新日期:2018-06-01 00:00:00

  • Comparison between passive vision-based system and a wearable inertial-based system for estimating temporal gait parameters related to the GAITRite electronic walkway.

    abstract::Quantitative gait analysis allows clinicians to assess the inherent gait variability over time which is a functional marker to aid in the diagnosis of disabilities or diseases such as frailty, the onset of cognitive decline and neurodegenerative diseases, among others. However, despite the accuracy achieved by the cur...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: González I,López-Nava IH,Fontecha J,Muñoz-Meléndez A,Pérez-SanPablo AI,Quiñones-Urióstegui I

    更新日期:2016-08-01 00:00:00

  • Finding disease similarity based on implicit semantic similarity.

    abstract::Genomics has contributed to a growing collection of gene-function and gene-disease annotations that can be exploited by informatics to study similarity between diseases. This can yield insight into disease etiology, reveal common pathophysiology and/or suggest treatment that can be appropriated from one disease to ano...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Mathur S,Dinakarpandian D

    更新日期:2012-04-01 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


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

    更新日期:2015-08-01 00:00:00

  • Information extraction from biomedical text.

    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


    authors: Hobbs JR

    更新日期:2002-08-01 00:00:00

  • The European cross-border health data exchange roadmap: Case study in the Italian setting.

    abstract::Health data exchange is a major challenge due to the sensitive information and the privacy issues entailed. Considering the European context, in which health data must be exchanged between different European Union (EU) Member States, each having a different national regulatory framework as well as different national h...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Nalin M,Baroni I,Faiella G,Romano M,Matrisciano F,Gelenbe E,Martinez DM,Dumortier J,Natsiavas P,Votis K,Koutkias V,Tzovaras D,Clemente F

    更新日期:2019-06-01 00:00:00

  • The impact of SNOMED CT revisions on a mapped interface terminology: terminology development and implementation issues.

    abstract::Large-scale mapping efforts have been done in attempts to migrate systems that use proprietary concepts to ones that use terminological standards such as SNOMED CT. As efforts move towards implementation, the target maps should retain a predictable structure including those targets requiring post-coordination of SNOME...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Wade G,Rosenbloom ST

    更新日期:2009-06-01 00:00:00

  • A cascaded approach for Chinese clinical text de-identification with less annotation effort.

    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


    authors: Jian Z,Guo X,Liu S,Ma H,Zhang S,Zhang R,Lei J

    更新日期:2017-09-01 00:00:00

  • Phenotypic similarity for rare disease: Ciliopathy diagnoses and subtyping.

    abstract::Rare diseases are often hard and long to be diagnosed precisely, and most of them lack approved treatment. For some complex rare diseases, precision medicine approach is further required to stratify patients into homogeneous subgroups based on the clinical, biological or molecular features. In such situation, deep phe...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Chen X,Garcelon N,Neuraz A,Billot K,Lelarge M,Bonald T,Garcia H,Martin Y,Benoit V,Vincent M,Faour H,Douillet M,Lyonnet S,Saunier S,Burgun A

    更新日期:2019-12-01 00:00:00

  • Serum cancer biomarker discovery through analysis of gene expression data sets across multiple tumor and normal tissues.

    abstract::The development of convenient serum bioassays for cancer screening, diagnosis, prognosis, and monitoring of treatment is one of top priorities in cancer research community. Although numerous biomarker candidates have been generated by applying high-throughput technologies such as transcriptomics, proteomics, and metab...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Jin H,Lee HC,Park SS,Jeong YS,Kim SY

    更新日期:2011-12-01 00:00:00

  • A framework for modeling health behavior protocols and their linkage to behavioral theory.

    abstract::With the rise in chronic, behavior-related disease, computerized behavioral protocols (CBPs) that help individuals improve behaviors have the potential to play an increasing role in the future health of society. To be effective and widely used CBPs should be based on accepted behavioral theory. However, designing CBPs...

    journal_title:Journal of biomedical informatics

    pub_type: 临床试验,杂志文章


    authors: Lenert L,Norman GJ,Mailhot M,Patrick K

    更新日期:2005-08-01 00:00:00

  • A hybrid knowledge-based and data-driven approach to identifying semantically similar concepts.

    abstract::An open research question when leveraging ontological knowledge is when to treat different concepts separately from each other and when to aggregate them. For instance, concepts for the terms "paroxysmal cough" and "nocturnal cough" might be aggregated in a kidney disease study, but should be left separate in a pneumo...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Pivovarov R,Elhadad N

    更新日期:2012-06-01 00:00:00

  • Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: the SHARPn project.

    abstract::The Strategic Health IT Advanced Research Projects (SHARP) Program, established by the Office of the National Coordinator for Health Information Technology in 2010 supports research findings that remove barriers for increased adoption of health IT. The improvements envisioned by the SHARP Area 4 Consortium (SHARPn) wi...

    journal_title:Journal of biomedical informatics

    pub_type: 杂志文章


    authors: Rea S,Pathak J,Savova G,Oniki TA,Westberg L,Beebe CE,Tao C,Parker CG,Haug PJ,Huff SM,Chute CG

    更新日期:2012-08-01 00:00:00

  • Chester: towards a personal medication advisor.

    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


    authors: Allen J,Ferguson G,Blaylock N,Byron D,Chambers N,Dzikovska M,Galescu L,Swift M

    更新日期:2006-10-01 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


    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