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Designing Views in HypothesisCreator: System for Assisting in Discovery

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Discovery Science (DS 1999)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 1721))

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Abstract

We discuss the significance of designing views on data in a computational system assisting scientists in the process of discovery. A view on data is considered as a particular way to interpret the data. In the scientific literature, devising a new view capturing the essence of data is a key to discovery. A system HypothesisCreator, which we have been developing to assist scientists in the process of discovery, supports users’ designing views on data and have the function of searching for good views on the data. In this paper we report a series of computational experiments on scientific data with HypothesisCreator and analyses of the produced hypotheses, some of which select several views good for explaining given data, searched and selected from over ten millions of designed views. Through these experiments we have convinced that view is one of the important factors in discovery process, and that discovery systems should have an ability of designing and selecting views on data in a systematic way so that experts on the data can employ their knowledge and thoughts efficiently for their purposes.

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References

  1. T. Alber, W. Gilbert, D. Ponzi, and G. Petsko. The role of mobility in the substrate binding and catalytic machinery of enzymes. In Ciba Found. Symp., volume 93, pages 4–24, 1983.

    Google Scholar 

  2. A. Bloomer, J. Champness, G. Bricogne, R. Staden, and A. Klug. Protein disk of tobacco mosaic virus at 2.8 a resolution showing the interactions within and between subunits. Nature, 276, 1978.

    Google Scholar 

  3. A. Brazma, I. Jonassen, J. Vilo, and E. Ukkonen. Pattern discovery in biosequences. In Proc. 4th International Colloquium on Grammatical Inference (ICGI-98), Lecture Notes in Artificial Intelligence, pages 257–270, 1998.

    Google Scholar 

  4. P. Cheeseman, D. Freeman, J. Kelly, M. Self, J. Stutz, and W. Taylor. Autoclass: A bayesian classification system. In Proc. 5th International Conference on Machine Learning, pages 54–64, 1988.

    Google Scholar 

  5. R. Cho, M. Campbell, E. Winzeler, L. Steinmetz, A. Conway, L. Wodicka, T. Wolfsberg, A. Gabrielian, D. L. D. Lockhart, and R. Davis. A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell, 2:65–73, 1998.

    Article  Google Scholar 

  6. G. Daughdrill, M. Chadsey, J. Karlinsey, K. Hughes, and F. Dahlquist. The C-terminal half of the anti-sigma factor, FlgM, becomes structured when bound to its target, sigma 28. Nat. Struct. Biol., 4(4):285–291, 1997.

    Article  Google Scholar 

  7. J. DeRisi, V. Iyer, and P. Brown. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278:680–686, 1997.

    Article  Google Scholar 

  8. D. Duggan, M. Bittner, Y. Chen, P. Meltzer, and J. Trent. Expression profiling using cDNA microarrays. Nature Genetics, 21:10–14, 1999.

    Article  Google Scholar 

  9. M. Eisen, P. Spellman, P. Brown, and D. Botstein. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 95:14863–14868, 1998.

    Article  Google Scholar 

  10. Y. Kitamura, T. Nozaki, S. Tatsumi, and A. Tanigami. Supporting genome information processing by MetaCommander. In Genome Informatics 1997, pages 238–239. Universal Academy Press, Inc, 1997.

    Google Scholar 

  11. R. Kriwacki, L. Hengst, L. Tennant, S. Reed, and P. Wright. Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2 bound state: conformational disorder mediates binding diversity. Proc. Natl. Acad. Sci. USA, 93(21), 1996.

    Google Scholar 

  12. P. Langley. The computer-aided discovery of scientific knowledge. In The First International Conference on Discovery Science, volume 1532 of Lecture Notes in Artificial Intelligence, pages 25–39. Springer-Verlag, 1998.

    Google Scholar 

  13. Y. Lee, B. G. Buchanan, and J. M. Aronis. Knowledge-based learning in exploratory science: Learning rules to predict rodent carcinogenicity. Machine Learning, 30:217–240, 1998.

    Article  Google Scholar 

  14. N. Lowndes, A. Johnson, and L.H. Johnston. Coordination of expression of DNA synthesis genes in budding yeast by cell-cycle regulated trans factor. Nature, 350:247–250, 1991.

    Article  Google Scholar 

  15. O. Maruyama, T. Uchida, T. Shoudai, and S. Miyano. Toward genomic hypothesis creator: View designer for discovery. In The first international conference on Discovery Science, volume 1532 of Lecture Notes in Artificial Intelligence, pages 105–116. Springer-Verlag, 1998.

    Google Scholar 

  16. J. Quinlan. Induction of decision trees. Machine Learning, 1:81–106, 1986.

    Google Scholar 

  17. P. Romero, Z. Obradovic, C. Kissinger, J. Villafranca, and A. Dunker. Identifying disordered regions in proteins from amino acid sequences. In Proc. I.E.E.E. International Conference on Neural Networks, volume 1, pages 90–95, 1997.

    Google Scholar 

  18. S. Shimozono and S. Miyano. Complexity of finding alphabet indexing. IEICE TRANS. INF. & SYS., E78-D:13–18, 1995.

    Google Scholar 

  19. S. Shimozono, A. Shinohara, T. Shinohara, S. Miyano, S. Kuhara, and S. Arikawa. Knowledge acquisition from amino acid sequences by machine learning system BONSAI. Trans. Information Processing Society of Japan, 35:2009–2018, 1994.

    Google Scholar 

  20. R. Verma, A. Patapoutian, C. Gordon, and J. Campbell. Identification and purification of a factor that binds to the Mlu I cell cycle box of yeast DNA replication genes. Proc. Natl. Acad. Sci. USA, 88:7155–7159, 1991.

    Article  Google Scholar 

  21. S. Wu and U. Manber. Fast text searching with errors. Technical report, Department of computer science, the university of Arizona, 1991.

    Google Scholar 

  22. ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/S_cerevisiae.

    Google Scholar 

  23. http://cmgm.stanford.edu/pbrown.

    Google Scholar 

  24. http://pc21.phy.sci.yamaguchi-u.ac.jp/ichimura/perl/pdbid.html.

    Google Scholar 

  25. http://quest7.proteome.com/databases/YPD.

    Google Scholar 

  26. http://transfac.gbf-braunschweig.de/TRANSFAC.

    Google Scholar 

  27. http://www.a_ymax.com.

    Google Scholar 

  28. http://www.ddbj.nig.ac.jp/ft/full_index.html.

    Google Scholar 

  29. http://www.expasy.ch/prosite.

    Google Scholar 

  30. http://www.pdb.bnl.gov/pdb-bin/pdbmain.

    Google Scholar 

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© 1999 Springer-Verlag Berlin Heidelberg

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Maruyama, O., Uchida, T., Sim, K.L., Miyano, S. (1999). Designing Views in HypothesisCreator: System for Assisting in Discovery. In: Arikawa, S., Furukawa, K. (eds) Discovery Science. DS 1999. Lecture Notes in Computer Science(), vol 1721. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-46846-3_11

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  • DOI: https://doi.org/10.1007/3-540-46846-3_11

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  • Print ISBN: 978-3-540-66713-1

  • Online ISBN: 978-3-540-46846-2

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