Abstract
We present an approach to revising qualitative causal models of gene regulation with DNA microarray data. The method combines search through a space of variable orderings with search through a space of parameters on causal links, with weight decay driving the model toward integer values. We illustrate the technique on a model of photosynthesis regulation and associated microarray data. Experiments with synthetic data that varied distance from the target model, noise, and number of training cases suggest the method is robust with respect to these factors. In closing, we suggest directions for future research and discuss related work on inducing causal regulatory models.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Friedman, N., Linial, M., Nachman, I., & Peer, D. (2000). Using Bayesian Networks to Analyze Expression Data. Journal of Computational Biology, 7, 601–620.
Grossman, A. R., Bhaya, D., & He, Q. (2001). Tracking the Light Environment by Cyanobacteria and the Dynamic Nature of Light Harvesting. The Journal of Biological Chemistry, 276, 11449–11452.
Hartemink, A. J., Gifford, D. K., Jaakkola, T. S., & Young, R. A. (2002). Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models. Pacific Symposium on Biocomputing, 7, 437–449.
Imoto, S., Goto, T., & Miyano, S. (2002). Estimation of Genetic Networks and Functional Structures Between Genes by using Bayesian Networks and Nonparametric Regression. Pacific Symposium on Biocomputing, 7, 175–186.
Koza, J. R., Mydlowec, W., Lanza, G., Yu, J., & Keane, M. A. (2001). Reverse engineering and automatic synthesis of metabolic pathways from observed data using genetic programming. Pacific Symposium on Biocomputing, 6, 434–445.
Langley, P., Shrager, J., & Saito, K. (in press). Computational discovery of communicable scientific knowledge. In L. Magnani, N. J. Nersessian, & C. Pizzi (Eds), Logical and computational aspects of model-based reasoning. Dordrecht: Kluwer Academic.
Mahidadia, A., & Compton, P. (2001). Assisting model-discovery in neuroendocrinology. Proceedings of the Fourth International Conference on Discovery Science (pp.214–227). Washington, D.C.: Springer.
Ong, I. M., Glasner, J., & Page, D. (2002). Modeling Regulatory Pathways in E.Coli from Time Series Expression Profiles. Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology.
Rissanen, J. (1989). Stochastic complexity in statistical inquiry. World Scientific, Singapore.
Saavedra, R., Spirtes, P., Scheines, R., Ramsey, J., & Glymour, C. (2001). Issues in Learning Gene Regulation from Microarray Databases. (Tech. Report No. IHMCTR-030101-01). Institute for Human and Machine Cognition, University of West Florida.
Saito, K., Langley, P., Grenager, T., Potter, C., Torregrosa, A., & Klooster, S. A. (2001). Computational revision of quantitative scientific models. Proceedings of the Fourth International Conference on Discovery Science (pp. 336–349). Washington, D.C.: Springer.
Saito, K., & Nakano, R. (1997). MDL regularizer: a new regularizer based on MDL principle. Proceedings of the 1997 International Conference on Neural Networks (pp. 1833–1838). Houston, Texas.
Shaffer, J. P. (1995). Multiple Hypothesis Testing. Annual Review Psychology, 46, 561–584.
Wiklund, R., Salih, G. F., Maenpaa, P., & Jansson, C. (2001) Engineering of the protein environment around the redox-active TyrZ in photosystem II. Journal of European Biochemistry, 268, 5356–5364.
Zupan, B., Bratko, I., Demsar, J., Beck, J. R., Kuspa, A., Shaulsky, G. (2001). Abductive inference of genetic networks. Proceedings of the Eighth European Conference on Artificial Intelligence in Medicine. Cascais, Portugal.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Saito, K., Bay, S., Langley, P. (2002). Revising Qualitative Models of Gene Regulation. In: Lange, S., Satoh, K., Smith, C.H. (eds) Discovery Science. DS 2002. Lecture Notes in Computer Science, vol 2534. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36182-0_8
Download citation
DOI: https://doi.org/10.1007/3-540-36182-0_8
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-00188-1
Online ISBN: 978-3-540-36182-4
eBook Packages: Springer Book Archive