Graph and topological structure mining on scientific articles

Fan Wang, Ruoming Jin, Gagan Agrawal, Helen Piontkivska

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

In this paper, we investigate a new approach for literature mining. We use frequent subgraph mining, and its generalization topological structure mining, for finding interesting relationships between gene names and other key biological terms from the text of scientific articles. We show how we can find keywords of interest and represent them as nodes of the graphs. We also propose several methods for inserting edges between these nodes. Our study initially focused on comparing: 1) different methods for constructing edges, and 2) patterns found from sub-graph mining and topological structure mining. Subsequently, we analyzed several frequent topological minors reported by our experiments, and explained their scientific significance. Overall, our study shows the following. First, a simple method of constructing edges, which is based on sliding windows, seems to provide the best results. Second, we are able to find much larger number of well-known and meaningful topological patterns with high support values, as compared to sub-graphs. Overall, the frequent topological minors our algorithm found correspond well to known relationships between genes and biological terms. Thus, we believe that topological structure mining can be a very valuable tool for researchers who are not deeply familiar with the existing literature, and want to obtain a quick summary about known relationships among key scientific names or terms.

Original languageEnglish (US)
Title of host publicationProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Pages1318-1322
Number of pages5
DOIs
StatePublished - 2007
Externally publishedYes
Event7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE - Boston, MA, United States
Duration: Jan 14 2007Jan 17 2007

Publication series

NameProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Conference

Conference7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
CountryUnited States
CityBoston, MA
Period1/14/071/17/07

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Bioengineering

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