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. 2008 Jun 6:9:270.
doi: 10.1186/1471-2105-9-270.

PageRank without hyperlinks: reranking with PubMed related article networks for biomedical text retrieval

Jimmy Lin  1
Affiliations

PageRank without hyperlinks: reranking with PubMed related article networks for biomedical text retrieval

Jimmy Lin. BMC Bioinformatics. .

Abstract

Background: Graph analysis algorithms such as PageRank and HITS have been successful in Web environments because they are able to extract important inter-document relationships from manually-created hyperlinks. We consider the application of these techniques to biomedical text retrieval. In the current PubMed(R) search interface, a MEDLINE(R) citation is connected to a number of related citations, which are in turn connected to other citations. Thus, a MEDLINE record represents a node in a vast content-similarity network. This article explores the hypothesis that these networks can be exploited for text retrieval, in the same manner as hyperlink graphs on the Web.

Results: We conducted a number of reranking experiments using the TREC 2005 genomics track test collection in which scores extracted from PageRank and HITS analysis were combined with scores returned by an off-the-shelf retrieval engine. Experiments demonstrate that incorporating PageRank scores yields significant improvements in terms of standard ranked-retrieval metrics.

Conclusion: The link structure of content-similarity networks can be exploited to improve the effectiveness of information retrieval systems. These results generalize the applicability of graph analysis algorithms to text retrieval in the biomedical domain.

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Figures

Figure 1
Figure 1
Screenshot of PubMed showing a MEDLINE abstract. The "Related Articles" panel on the right is populated with titles of articles that may be of interest.
Figure 2
Figure 2
Effectiveness of interpolating Terrier retrieval scores with PageRank scores (MAP20).
Figure 3
Figure 3
Effectiveness of interpolating Terrier retrieval scores with PageRank scores (MAP40).
Figure 4
Figure 4
Effectiveness of interpolating Terrier retrieval scores with PageRank scores (P20).
Figure 5
Figure 5
Effectiveness of interpolating Terrier retrieval scores with HITS authority scores (MAP20).
Figure 6
Figure 6
Effectiveness of interpolating Terrier retrieval scores with HITS authority scores (MAP40).
Figure 7
Figure 7
Effectiveness of interpolating Terrier retrieval scores with HITS authority scores (P20).
Figure 8
Figure 8
Effectiveness of interpolating Terrier retrieval scores with HITS hub scores (MAP20).
Figure 9
Figure 9
Effectiveness of interpolating Terrier retrieval scores with HITS hub scores (MAP40).
Figure 10
Figure 10
Effectiveness of interpolating Terrier retrieval scores with HITS hub scores (P20).
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References

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