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23 research outcomes, page 1 of 3
  • publication . Article . 2019
    Open Access English
    Authors:
    Canlin Zhang; Daniel Biś; Xiuwen Liu; Zhe He;
    Persistent Identifiers
    Publisher: BioMed Central
    Project: NIH | Systematic Analysis of Cl... (1R21AG061431-01)

    <jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>In recent years, deep learning methods have been applied to many natural language processing tasks to achieve state-of-the-art performance. However, in the biomedical domain, they ha...

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  • publication . Article . Other literature type . 2019
    Open Access English
    Authors:
    Sharma, Vivekanand; Restrepo, Maria Isabel; Sarkar, Indra Neil;
    Persistent Identifiers
    Publisher: BioMed Central
    Project: NIH | In silico identification ... (1R01LM011963-01)

    Abstract Background The retrieval of plant-related information is a challenging task due to variations in species name mentions as well as spelling or typographical errors across data sources. Scalable solutions are needed for identifying plant name mentions from text a...

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  • publication . Article . Other literature type . 2019
    Open Access English
    Authors:
    Hong Yu; Solomiya Nysak; Noemi Garg; Edison Ong; Xianwei Ye; Xiangyan Zhang; Yongqun He;
    Persistent Identifiers
    Publisher: BioMed Central
    Project: NIH | Ontology-based Informatio... (5R01AI081062-02)

    Background Drug adverse events (AEs), or called adverse drug events (ADEs), are ranked one of the leading causes of mortality. The Ontology of Adverse Events (OAE) has been widely used for adverse event AE representation, standardization, and analysis. OAE-based ADE-spe...

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  • publication . Article . Other literature type . Preprint . 2019
    Open Access English
    Authors:
    Stanke, Mario; Bruhn, Willy; Becker, Felix; Hoff, Katharina J.;
    Publisher: BMC
    Project: NIH | Addressing Open Challenge... (1R01GM128145-01)

    <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>Vast amounts of next generation sequencing RNA data has been deposited in archives, accompanying very diverse original studies. The data is readily available also for other purposes...

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  • publication . Other literature type . Article . 2019
    Open Access
    Authors:
    Serra, Lucas M.; Duncan, William D.; Diehl, Alexander D.;
    Persistent Identifiers
    Publisher: Springer Science and Business Media LLC
    Project: NIH | ROSWELL PARK MEMORIAL INS... (5P30CA016056-17), NIH | Buffalo Clinical and Tran... (5UL1TR001412-03)

    Abstract Background Within the cancer domain, ontologies play an important role in the integration and annotation of data in order to support numerous biomedical tools and applications. This work seeks to leverage existing standards in immunophenotyping cell types found...

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  • publication . Article . Other literature type . 2019
    Open Access English
    Authors:
    Liu, Meng; Thomas, Paul D.;
    Persistent Identifiers
    Publisher: BMC
    Project: NIH | Gene Ontology Consortium (4U41HG002273-16)

    Background Biological knowledge, and therefore Gene Ontology annotation sets, for human genes is incomplete. Recent studies have reported that biases in available GO annotations result in biased estimates of functional similarities of genes, but it is still unclear what...

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  • publication . Article . Other literature type . 2018
    Open Access English
    Authors:
    Zeng, Zexian; Espino, Sasa; Roy, Ankita; Li, Xiaoyu; Khan, Seema A.; Clare, Susan E.; Jiang, Xia; Neapolitan, Richard; Luo, Yuan;
    Persistent Identifiers
    Publisher: BMC
    Project: NIH | Bayesian Generative Metho... (1R21LM012618-01), NIH | A New Generation Clinical... (1R01LM011663-01A1), NIH | Multidimensional Computer... (5R01LM011962-02)

    Background Identifying local recurrences in breast cancer from patient data sets is important for clinical research and practice. Developing a model using natural language processing and machine learning to identify local recurrences in breast cancer patients can reduce...

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  • publication . Other literature type . Article . 2018
    Open Access
    Authors:
    Badal, Varsha D.; Kundrotas, Petras J.; Vakser, Ilya A.;
    Persistent Identifiers
    Publisher: Springer Science and Business Media LLC
    Project: NIH | Integrated Resource for P... (2R01GM074255-05), NSF | ABI Innovation: Target - ... (1262621), NIH | MOLECULAR ANALYSIS OF THE... (1F32GM013039-01)

    Background Structural modeling of protein-protein interactions produces a large number of putative configurations of the protein complexes. Identification of the near-native models among them is a serious challenge. Publicly available results of biomedical research may ...

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  • publication . Other literature type . Article . 2016
    Open Access
    Authors:
    Tseytlin, Eugene; Mitchell, Kevin; Legowski, Elizabeth; Corrigan, Julia; Chavan, Girish; Jacobson, Rebecca S.;
    Persistent Identifiers
    Publisher: Springer Science and Business Media LLC
    Project: NIH | Continued Development and... (5R01CA132672-04), NIH | Advanced Development of T... (5U24CA180921-05)

    Background Natural language processing (NLP) applications are increasingly important in biomedical data analysis, knowledge engineering, and decision support. Concept recognition is an important component task for NLP pipelines, and can be either general-purpose or doma...

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  • publication . Article . Other literature type . 2016
    Open Access
    Authors:
    Jain, Suvir; R., Kashyap; Kuo, Tsung-Ting; Bhargava, Shitij; Lin, Gordon; Hsu, Chun-Nan;
    Persistent Identifiers
    Publisher: eScholarship, University of California
    Project: NIH | Accelerating Curation of ... (7U01HG006894-03)

    Background Numerous publicly available biomedical databases derive data by curating from literatures. The curated data can be useful as training examples for information extraction, but curated data usually lack the exact mentions and their locations in the text require...

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23 research outcomes, page 1 of 3