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Learning Qualitative Models of Physical and Biological Systems

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Computational Discovery of Scientific Knowledge

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 4660))

Abstract

We present a qualitative model-learning system, Qoph, developed for application to scientific discovery problems. Qoph learns the structural relations between a set of observed variables. It has been shown capable of learning models with intermediate (unmeasured) variables, and intermediate relations, under different levels of noise, and from qualitative or quantitative data. A biological application of Qoph is explored. An additional significant outcome of this work is the discovery and identification of kernel subsets of key states that must be present for model-learning to succeed.

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References

  • Bakshi, B.R., Stephanopoulos, G.: Representation of process trends – Part 3: multiscale extraction of trends from process data. Computers and Chemical Engineering 18, 267–302 (1994)

    Article  Google Scholar 

  • Bhaskhar, R., Nigam, A.: Qualitative physics using dimensional analysis. Artificial Intelligence 45, 73–111 (1990)

    Article  Google Scholar 

  • Blackman, R.B., Tukey, J.W.: The measurement of power spectra. John Wiley and Sons, New York (1958)

    Google Scholar 

  • Bratko, I., Muggleton, S., Varšek, A.: Learning qualitative models of dynamic systems. In: Muggleton, S. (ed.) Inductive logic programming, pp. 437–452. Academic Press, San Diego, CA (1992)

    Google Scholar 

  • Cellier, F.E.: Continuous system modelling. Springer, Berlin (1991)

    Google Scholar 

  • Cheung, J.T.-Y., Stephanopoulos, G.: Representation of process trends – Part 1: a formal representation framework. Computers and Chemical Engineering 14, 495–510 (1990)

    Article  Google Scholar 

  • Cheung, J.T.-Y., Stephanopoulos, G.: Representation of process trends – Part 2: the problem of scale and qualitative scaling. Computers and Chemical Engineering 14, 511–539 (1990b)

    Article  Google Scholar 

  • Cleland, W.W.: The kinetics of enzyme-catalysed reactions with two or more substrates and products: 1. nomenclature and rate equations. Biochimica et Biophysica Acta 67, 104–137 (1963)

    Article  Google Scholar 

  • Coiera, E.W.: Generating qualitative models from example behaviours (Technical Report 8901). University of New South Wales, Deptartment of Computer Science (1989a)

    Google Scholar 

  • Coiera, E.W.: Learning qualitative models from example behaviours. In: Proceedings of the Third Workshop on Qualitative Physics, Stanford, CA, pp. 45–51 (1989)

    Google Scholar 

  • DeCoste, D.: Dynamic across-time measurement interpretation. Artificial Intelligence 51, 273–341 (1991)

    Article  Google Scholar 

  • Džeroski, S.: Learning qualitative models with inductive logic programming. Informatica 16, 30–41 (1992)

    Google Scholar 

  • Džeroski, S., Todorovski, L.: Discovering dynamics: from inductive logic programming to machine discovery. Journal of Intelligenty Information Systems 4, 89–108 (1995)

    Article  Google Scholar 

  • Flach, P.A., Kakas, A.C.: Abduction and induction: Essays on their relation and integration. Kluwer Academic Publishers, Amsterdam, The Netherlands (2000)

    MATH  Google Scholar 

  • Forbus, K.D.: Qualitative process theory. Artificial Intelligence 24, 169–204 (1984)

    Article  Google Scholar 

  • Fürnkranz, J.: Separate-and-conquor rule learning. Artificial Intelligence Review 13, 3–54 (1999)

    Article  MATH  Google Scholar 

  • Garrett, S.M., Coghill, G.M., King, R.D., Srinivasan, A.: On learning qualitative models of qualitative and real-valued data (Technical Report UWA-DCS-01-037). University of Wales, Aberystwyth (2001)

    Google Scholar 

  • Gawthrop, P.J., Smith, L.P.S.: Metamodelling: Bond graphs and dynamic systems. Prentice Hall, Hemel Hempstead, Herts, England (1996)

    Google Scholar 

  • Gold, E.M.: Language identification in the limit. Information and Control 10, 447–474 (1967)

    Article  MATH  Google Scholar 

  • Hau, D.T., Coiera, E.W.: Learning qualitative models of dynamic systems. Machine Learning 26, 177–211 (1993)

    Article  Google Scholar 

  • Iwasaki, Y., Simon, H.A.: Causality in device behavior. Artificial Intelligence (See also de Kleer and Brown’s rebuttal and Iwasaki and Simon’s reply to their rebuttal in the same volume of this journal) 29, 3–32 (1986)

    Article  Google Scholar 

  • Kakas, A.C., Kowalski, R.A., Toni, F.: Abductive logic programming. Journal of Logic and Computation 2, 719–770 (1992)

    Article  MATH  MathSciNet  Google Scholar 

  • King, R.D., Muggleton, S., Lewis, R.A., Sternberg, M.J.E.: Drug design by machine learning — the use of inductive logic programming to model the structure-activity-relationships of trimethoprim analogs binding to dihydrofolate-reductase. In: Proceedings of the National Academy of Sciences of the USA, vol. 89, pp. 11322–11326 (1992)

    Google Scholar 

  • King, R.D., Srinivasan, A.: The discovery of indicator variables for QSAR using inductive logic programming. Journal of Computer-Aided Molecular Design 11, 571–580 (1997)

    Article  Google Scholar 

  • Koza, J.R.: Genetic programming. MIT Press, Cambridge (1992)

    MATH  Google Scholar 

  • Kraan, I.C., Richards, B.L., Kuipers, B.J.: Automatic abduction of qualitative models. In: Proceedings of the Fifth International Workshop on Qualitative Reasoning about Physical Systems, Austin, TX, pp. 295–301 (1991)

    Google Scholar 

  • Kuipers, B.: Qualitative simulation. Artificial Intelligence 29, 289–338 (1986)

    Article  MATH  MathSciNet  Google Scholar 

  • Kuipers, B.: Qualitative reasoning. MIT Press, Cambridge (1994)

    Google Scholar 

  • Laird, J.E., Rosenbloom, P.S., Newell, A.: Chunking in SOAR: The anatomy of a general learning mechanism. Machine Learning 1, 11–46 (1986)

    Google Scholar 

  • Lavrač, N., Džeroski, S.: Inductive logic programming: Techniques and applications. Ellis-Horwood, New York (1994)

    MATH  Google Scholar 

  • Ljung, L.: System identification: Theory for the user, 2nd edn. PRT Prentice Hall, Upper Saddle River, NJ (1999)

    Google Scholar 

  • Mitchell, T.M.: Version spaces: An approach to concept learning. Doctoral dissertation, Stanford University (1979)

    Google Scholar 

  • Muggleton, S.: Inductive logic programming. Academic Press, London (1992)

    MATH  Google Scholar 

  • Muggleton, S.: Inverse entailment and progol. New Generation Computing 13, 245–286 (1995)

    Google Scholar 

  • Muggleton, S.: Learning from positive data. In: Proceedings of the Sixth International Workshop on Inductive Logic Programming, Stockholm, Sweden, pp. 358–376 (1996)

    Google Scholar 

  • Muggleton, S., Feng, C.: Efficient induction of logic programs. In: Proceedings of the First Conference on Algorithmic Learning Theory, Tokyo, Japan, pp. 368–381 (1990)

    Google Scholar 

  • Plotkin, G.: Automatic methods of inductive inference. Doctoral dissertation, Edinburgh University (1971)

    Google Scholar 

  • Ramachandran, S., Mooney, R.J., Kuipers, B.J.: Learning qualitative models for systems with multiple operating regions. In: Working Papers of the Eighth International Workshop on Qualitative Reasoning about Physical Systems, Nara, Japan, pp. 212–223 (1994)

    Google Scholar 

  • Richards, B.L., Kraan, I., Kuipers, B.J.: Automatic abduction of qualitative models. In: Proceedings of the Tenth National Conference on Artificial Intelligence, San Jose, CA, pp. 723–728 (1992)

    Google Scholar 

  • Richards, B.L., Mooney, R.J.: Automated refinement of first-order horn-clause domain theories. Machine Learning 19, 95–131 (1995)

    Google Scholar 

  • Say, A.C.C., Kuru, S.: Qualitative system indentification: deriving structure from behavior. Artificial Intelligence 83, 75–141 (1996)

    Article  Google Scholar 

  • Shoup, T.E.: A practical guide to computer methods for engineers. Prentice-Hall, Englewood Cliffs (1979)

    Google Scholar 

  • Srinivasan, A.: Aleph web site (2000), http://web.comlab.ox.ac.uk/oucl/research/areas/mach-learn/Aleph/aleph_toc.html

  • Srinivasan, A., King, R.D.: Feature construction with inductive logic programming: A study of quantitative predictions of biological activity aided by structural attributes. Data Mining and Knowledge Discovery 3, 37–57 (1999)

    Article  Google Scholar 

  • Srinivasan, A., Muggleton, S.H., Sternberg, M.J.E., King, R.D.: Theories for mutagenicity: A study in first-order and feature-based induction. Artificial Intelligence 85, 277–299 (1996)

    Article  Google Scholar 

  • Sternberg, M.J.E., King, R.D., Lewis, R.A., Muggleton, S.: Application of machine learning to structural molecular biology. Philosophical Transactions of the Royal Society of London Series B - Biological Sciences 344, 365–371 (1994)

    Article  Google Scholar 

  • Todorovski, L., Džeroski, S.: Declarative bias in equation discovery. In: Proceedings of the Fourteenth International Conference on Machine Learning, Nashville, TN, pp. 376–384 (1997)

    Google Scholar 

  • Yamamoto, A.: Revising the logical foundations of inductive logic programming systems with ground reduced programs. New Generation Computing 17, 119–127 (1999)

    Article  Google Scholar 

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Sašo Džeroski Ljupčo Todorovski

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Garrett, S.M., Coghill, G.M., Srinivasan, A., King, R.D. (2007). Learning Qualitative Models of Physical and Biological Systems. In: Džeroski, S., Todorovski, L. (eds) Computational Discovery of Scientific Knowledge. Lecture Notes in Computer Science(), vol 4660. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73920-3_12

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  • DOI: https://doi.org/10.1007/978-3-540-73920-3_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-73919-7

  • Online ISBN: 978-3-540-73920-3

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