Author name disambiguation in MEDLINE

Background: We recently described “Author-ity,” a model for estimating the probability that two articles in MEDLINE, sharing the same author name, were written by the same individual. Features include shared title words, journal name, coauthors, medical subject headings, language, affiliations, and author name features (middle initial, suffix, and prevalence in MEDLINE). Here we test the hypothesis that the Author-ity model will suffice to disambiguate author names for the vast majority of articles in MEDLINE. Methods: Enhancements include: (a) incorporating first names and their variants, email addresses, and correlations between specific last names and affiliation words; (b) new methods of generating large unbiased training sets; (c) new methods for estimating the prior probability; (d) a weighted least squares algorithm for correcting transitivity violations; and (e) a maximum likelihood based agglomerative algorithm for computing clusters of articles that represent inferred author-individuals. Results: Pairwise comparisons were computed for all author names on all 15.3 million articles in MEDLINE (2006 baseline), that share last name and first initial, to create Author-ity 2006, a database that has each name on each article assigned to one of 6.7 million inferred author-individual clusters. Recall is estimated at ∼98.8%. Lumping (putting two different individuals into the same cluster) affects ∼0.5% of clusters, whereas splitting (assigning articles written by the same individual to >1 cluster) affects ∼2% of articles. Impact: The Author-ity model can be applied generally to other bibliographic databases. Author name disambiguation allows information retrieval and data integration to become person-centered, not just document-centered, setting the stage for new data mining and social network tools that will facilitate the analysis of scholarly publishing and collaboration behavior. Availability: The Author-ity 2006 database is available for nonprofit academic research, and can be freely queried via http://arrowsmith.psych.uic.edu.

[1]  Douglas H. Fisher,et al.  Knowledge Acquisition Via Incremental Conceptual Clustering , 1987, Machine Learning.

[2]  Jane Qiu,et al.  Scientific publishing: Identity crisis , 2008, Nature.

[3]  James C. French,et al.  Using clustering strategies for creating authority files , 2000 .

[4]  David Yarowsky,et al.  Unsupervised Personal Name Disambiguation , 2003, CoNLL.

[5]  Philip S. Yu,et al.  Object Distinction: Distinguishing Objects with Identical Names , 2007, 2007 IEEE 23rd International Conference on Data Engineering.

[6]  María D. González-Lima,et al.  A primal-dual interior-point algorithm for quadratic programming , 2006, Numerical Algorithms.

[7]  Lise Getoor,et al.  A Latent Dirichlet Model for Unsupervised Entity Resolution , 2005, SDM.

[8]  Christopher Joseph Pal,et al.  Improving Author Coreference by Resource-Bounded Information Gathering from the Web , 2007, IJCAI.

[9]  Yang Song,et al.  Efficient topic-based unsupervised name disambiguation , 2007, JCDL '07.

[10]  Bernd Walter,et al.  Survey on test collections and techniques for personal name matching , 2006, Int. J. Metadata Semant. Ontologies.

[11]  Dongwon Lee,et al.  Search engine driven author disambiguation , 2006, Proceedings of the 6th ACM/IEEE-CS Joint Conference on Digital Libraries (JCDL '06).

[12]  Shlomo Argamon,et al.  Author Identification on the Large Scale , 2005 .

[13]  Elmer V. Bernstam,et al.  A day in the life of PubMed: analysis of a typical day's query log. , 2007, Journal of the American Medical Informatics Association : JAMIA.

[14]  Divesh Srivastava,et al.  Record linkage: similarity measures and algorithms , 2006, SIGMOD Conference.

[15]  Dmitri V. Kalashnikov,et al.  Domain-independent data cleaning via analysis of entity-relationship graph , 2006, TODS.

[16]  Wei Zhou,et al.  Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results , 2008, Journal of biomedical discovery and collaboration.

[17]  Caryn L Scoville,et al.  When A. Rose Is Not A. Rose , 2003, Medical reference services quarterly.

[18]  Neil R. Smalheiser,et al.  Arrowsmith two-node search interface: A tutorial on finding meaningful links between two disparate sets of articles in MEDLINE , 2009, Comput. Methods Programs Biomed..

[19]  Andrew McCallum,et al.  Tractable Learning and Inference with High-Order Representations , 2006 .

[20]  Lise Getoor,et al.  Collective entity resolution in relational data , 2007, TKDD.

[21]  Neil R. Smalheiser,et al.  A Quantitative Model for Linking Two Disparate Sets of Articles in Medline , 2022 .

[22]  EUGENE GARFIELD.  British Quest for Uniqueness versus American Egocentrism , 1969, Nature.

[23]  Neil R. Smalheiser,et al.  Author name disambiguation , 2009, Annu. Rev. Inf. Sci. Technol..

[24]  Y Yang,et al.  An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts , 1996, Comput. Biol. Medicine.

[25]  Matthew A. Jaro,et al.  Probabilistic linkage of large public health data files. , 1995, Statistics in medicine.

[26]  José M. Soler.  Separating the articles of authors with the same name , 2007, Scientometrics.

[27]  Roxanna Paez,et al.  Stephen Crane and the New-York Tribune: A Case Study in Traditional and Non-Traditional Authorship Attribution , 2001, Comput. Humanit..

[28]  James C. French,et al.  Using clustering strategies for creating authority files , 2000, J. Am. Soc. Inf. Sci..

[29]  Félix de Moya Anegón,et al.  Approximate personal name-matching through finite-state graphs , 2007, J. Assoc. Inf. Sci. Technol..

[30]  C. Lee Giles,et al.  Two supervised learning approaches for name disambiguation in author citations , 2004, Proceedings of the 2004 Joint ACM/IEEE Conference on Digital Libraries, 2004..

[31]  Neil R. Smalheiser,et al.  A probabilistic similarity metric for Medline records: A model for author name disambiguation: Research Articles , 2005 .

[32]  Raymond J. Mooney,et al.  Adaptive Blocking: Learning to Scale Up Record Linkage , 2006, Sixth International Conference on Data Mining (ICDM'06).

[33]  Byung-Won On,et al.  Comparative study of name disambiguation problem using a scalable blocking-based framework , 2005, Proceedings of the 5th ACM/IEEE-CS Joint Conference on Digital Libraries (JCDL '05).

[34]  C. Lee Giles,et al.  Efficient Name Disambiguation for Large-Scale Databases , 2006, PKDD.

[35]  Hui Han,et al.  Name disambiguation in author citations using a K-way spectral clustering method , 2005, Proceedings of the 5th ACM/IEEE-CS Joint Conference on Digital Libraries (JCDL '05).

[36]  Félix Moya-Anegón,et al.  Approximate personal name-matching through finite-state graphs , 2007 .

[37]  Neil R. Smalheiser,et al.  A probabilistic similarity metric for Medline records: A model for author name disambiguation , 2005, J. Assoc. Inf. Sci. Technol..

[38]  Andrew McCallum,et al.  Author Disambiguation using Error-driven Machine Learning with a Ranking Loss Function , 2007 .