Skip to main content

Searching for Meaningful Feature Interactions with Backward-Chaining Rule Induction

  • Conference paper

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 3646))

Abstract

Exploring the vast number of possible feature interactions in domains such as gene expression microarray data is an onerous task. We propose Backward-Chaining Rule Induction (BCRI) as a semi-supervised mechanism for biasing the search for plausible feature interactions. BCRI adds to a relatively limited tool-chest of hypothesis generation software, and it can be viewed as an alternative to purely unsupervised association rule learning. We illustrate BCRI by using it to search for gene-to-gene causal mechanisms. Mapping hypothesized gene interactions against a domain theory of prior knowledge offers support and explanations for hypothesized interactions, and suggests gaps in the current domain theory, which induction might help fill.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Guffanti, A.: Modeling molecular networks: a systems biology approach to gene function. Genome Biol 3: reports4031 (2002)

    Google Scholar 

  2. Weston, A., Hood, L.: Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res 3, 179–196 (2004)

    Article  Google Scholar 

  3. Provart, N., McCourt, P.: Systems approaches to understanding cell signaling and gene regulation. Curr Opin Plant Biol 7, 605–609 (2004)

    Article  Google Scholar 

  4. Huels, C., Muellner, S., Meyer, H., et al.: The impact of protein biochips and microarrays on the drug development process. Drug Discov Today 7(18 suppl.), S119–S124 (2002)

    Article  Google Scholar 

  5. Evans, B., Fisher, D.: Overcoming process delays with decision tree induction. IEEE Expert 9, 60–66 (1994)

    Article  Google Scholar 

  6. Evans, B., Fisher, D.: Decision tree induction to minimize process delays. In: Klosgen, W., Zytkow, J. (eds.) Handbook of Data Mining and Knowledge Discovery, pp. 874–881. Oxford University Press, Oxford (2002)

    Google Scholar 

  7. Waitman, L.R., Fisher, D., King, P.: Bootstrapping rule induction. In: Proceedings of the IEEE International Conference on Data Mining, pp. 677–680. IEEE Computer Society Publications Office, Los Alamitos (2003)

    Google Scholar 

  8. Waitman, L.R., Fisher, D., King, P.: Bootstrapping rule induction to achieve and increase rule stability. Journal of Intelligent Information Systems (in press)

    Google Scholar 

  9. Mannila, H.: Association rules. In: Klosgen, W., Zytkow, J. (eds.) Handbook of Data Mining and Knowledge Discovery, pp. 344–348. Oxford University Press, Oxford (2002)

    Google Scholar 

  10. Beer, D., Kardia, S., Huang, C., et al.: Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nature Medicine 8, 816–824 (2002)

    Google Scholar 

  11. Quinlan, J.R.: C4.5: Programs for Machine Learning. Morgan Kaufmann, San Francisco (1993), http://quinlan.com

    Google Scholar 

  12. Shortliffe, E., Davis, R., Axline, S., et al.: Computer –based consultations in clinical therapeutics: explanation and rule acquisition capabilities of the MYCIN system. Comput. Biomed. Res. 8, 303–320 (1975)

    Article  Google Scholar 

  13. Nikitin, A., Egorov, S., Daraselia, N., Mazo, I.: Pathway studio – the analysis and navigation of molecular networks. Bioinformatics 19, 2155–2157 (2003)

    Article  Google Scholar 

  14. PubMED Central, a free archive of life sciences journals, http://www.pubmedcentral.nih.gov/

  15. Pruitt, K., Katz, K., Sicotte, H., et al.: Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet 16(1), 44–47 (2000)

    Article  Google Scholar 

  16. http://www.ncbi.nlm.nih.gov/projects/LocusLink/

  17. Pruitt, K., Maglott, D.: RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res 29(1), 137–140 (2001)

    Article  Google Scholar 

  18. Rebhan, M., Chalifa-Caspi, V., Prilusky, J., et al.: GeneCards: encyclopedia for genes, proteins and diseases. In: Weizmann Institute of Science, Bioinformatics Unit and Genome Center, Rehovot, Israel (1997). http://bioinformatics.weizmann.ac.il/cards

  19. Higashiyama, M., Doi, O., Kodama, K., et al.: An evaluation of the prognostic significance of alpha-1-antitrypsin expression in adenocarcinomas of the lung: an immunohistochemical analysis. Br J Cancer 65, 300–302 (1992)

    Article  Google Scholar 

  20. Yamashita, J., Tashiro, K., Yoneda, S., et al.: Local increase in polymorphonuclear leukocute elastase is associated with tumor invasiveness in non-small cell lung cancer. Chest 109, 1328–1334 (1996)

    Article  Google Scholar 

  21. Yamashita, J., Ogawa, M., Abe, M., et al.: Tumor neutrophil elastase is closely associated with the direct extension of non-small cell lung cancer into the aorta. Chest 111, 885–890 (1997)

    Article  Google Scholar 

  22. Massion, P., Carbone, D.: The molecular basis of lung cancer: molecular abnormalities and therapeutic implications. Respiratory Research 4, 12 (2003)

    Article  Google Scholar 

  23. Langley, P., Shrager, J., Saito, K.: Computational discovery of communicable scientific knowledge. In: Magnani, L., Nersessian, N.J., Pizzi, C. (eds.) Logical and Computational Aspects of Model-Based Reasoning. Kluwer, Dordrecht (2002)

    Google Scholar 

  24. Mooney, R.: Induction over the unexplained: Using overly-general theories to aid concept learning. Machine Learning 10, 79–110 (1993)

    Google Scholar 

  25. Ortega, J., Fisher, D.: Flexibly exploiting prior knowledge in empirical learning. In: Proceedings of the International Joint Conference on Artificial Intelligence, pp. 1041–1047. Morgan Kaufmann, San Francisco (1995)

    Google Scholar 

  26. Frey, L., Edgerton, M., Fisher, D., Tang, L., Chen, Z.: Discovery of molecular markers of poor prognosis from rule induction methods. In: Poster presented at the American Association for Cancer Research (AACR) Conference on Molecular Pathogenesis of Lung Cancer: Opportunities for Translation to the Clinic, San Diego, CA (2005)

    Google Scholar 

  27. Frey, L., Edgerton, M., Fisher, D., Tang, L., Chen, Z.:(under review). Using prior knowledge and rule induction methods to discover molecular markers of prognosis in lung cancer. In: American Medical Informatics Association Symposium 2005, Washington DC (2005)

    Google Scholar 

  28. Riddle, P., Segal, R., Etzioni, O.: Representation Design and Brute-force induction in the Boeing Manufacturing Domain. Applied Artificial Intelligence 8, 125–147 (1994)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Fisher, D., Edgerton, M., Tang, L., Frey, L., Chen, Z. (2005). Searching for Meaningful Feature Interactions with Backward-Chaining Rule Induction. In: Famili, A.F., Kok, J.N., Peña, J.M., Siebes, A., Feelders, A. (eds) Advances in Intelligent Data Analysis VI. IDA 2005. Lecture Notes in Computer Science, vol 3646. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11552253_9

Download citation

  • DOI: https://doi.org/10.1007/11552253_9

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28795-7

  • Online ISBN: 978-3-540-31926-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics