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Jun'ichi Tsujii – One of the best experts on this subject based on the ideXlab platform.

  • building a high quality sense inventory for improved abbreviation disambiguation
    Bioinformatics, 2010
    Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi Tsujii
    Abstract:

    Motivation: The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. Results: A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. Availability: The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/ Contact: okazaki@chokkan.org

  • Building a high-quality sense inventory for improved abbreviation disambiguation
    Bioinformatics (Oxford England), 2010
    Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi Tsujii
    Abstract:

    The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/.

N Okazaki – One of the best experts on this subject based on the ideXlab platform.

  • building a high quality sense inventory for improved abbreviation disambiguation
    Bioinformatics, 2010
    Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi Tsujii
    Abstract:

    Motivation: The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. Results: A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. Availability: The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/ Contact: okazaki@chokkan.org

  • Building a high-quality sense inventory for improved abbreviation disambiguation
    Bioinformatics (Oxford England), 2010
    Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi Tsujii
    Abstract:

    The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/.

Sophia Ananiadou – One of the best experts on this subject based on the ideXlab platform.

  • building a high quality sense inventory for improved abbreviation disambiguation
    Bioinformatics, 2010
    Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi Tsujii
    Abstract:

    Motivation: The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. Results: A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. Availability: The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/ Contact: okazaki@chokkan.org

  • Building a high-quality sense inventory for improved abbreviation disambiguation
    Bioinformatics (Oxford England), 2010
    Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi Tsujii
    Abstract:

    The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/.

  • building an abbreviation dictionary using a term recognition approach
    Bioinformatics, 2006
    Co-Authors: Naoaki Okazaki, Sophia Ananiadou
    Abstract:

    Motivation: Acronyms result from a highly productive type of term variation and trigger the need for an acronym dictionary to establish associations between acronyms and their expanded forms. Results: We propose a novel method for recognizing acronym definitions in a text collection. Assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form, our method identifies acronym definitions in a similar manner to the statistical term recognition task. Applied to the whole MEDLINE (7 811 582 abstracts), the implemented system extracted 886 755 acronym candidates and recognized 300 954 expanded forms in reasonable time. Our method outperformed base-line systems, achieving 99% precision and 82–95% recall on our evaluation corpus that roughly emulates the whole MEDLINE. Availability and Supplementary information: The implementations and supplementary information are available at our web site: http://www.chokkan.org/research/acromine/ Contact: okazaki@mi.ci.i.u-tokyo.ac.jp