Abstract
We are concerned with the problem of inferring genetic regulatory networks from a collection of temporal observations. This is often done via estimating a Dynamic Bayesian Network (DBN) from time series of gene expression data. However, when applying this algorithm to the limited quantities of experimental data that nowadays technologies can provide, its estimation is not robust. We introduce a weak learners’ methodology for this inference problem, study few methods to produce Weak Dynamic Bayesian Networks (WDBNs), and demonstrate its advantages on simulated gene expression data.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Pearl, J.: Probabilistic Reasoning in Intelligent Systems. Morgan Kaufmann, San Francisco (1988)
Murphy, K., Mian, S.: Modelling Gene Expression Data using Dynamic Bayesian Networks. Technical Report, MIT Artificial Intelligence Laboratory (1999)
Friedman, N., et al.: Using Bayesian Networks to Analyze Expression Data. Journal of Computational Biology (2000)
Hartemink, A.J., et al.: Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. In: Pacific Symp. Biocomput., pp. 422–433 (2001)
Hartemink, A., et al.: Combining location and expression data for principled discovery of genetic regulatory network models. In: Pac. Symp. Biocomput., vol. 7, pp. 437–449 (2002)
Husmeier, D.: Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics 19, 2271–2282 (2003)
Smith, V.A., Jarvis, E.D., Hartemink, A.J.: Influence of Network Topology and Data Collection on Network Infernece. In: Pacific Symp. Biocomput., vol. 8, pp. 164–175 (2003)
Smith, V.A., Jarvis, E.D., Hartemink, A.J.: Evaluating functional network inference using simulations. Bioinformatics 18, S216–S224 (2002)
Yu, J., et al.: Using Bayesian Network Inference Algorithms to Recover Molecular Genetic Regulatory Networks. In: 3rd International Conference on System Biology, Karolinska Institute, Stockholm, Sweden (2002)
Jacobs, R.A., et al.: Adaptive Mixtures of Local Experts. Neural Computation 3, 79–87 (1991)
Hansen, L.K., Salamon, P.: Neural network ensembles. IEEE Transactions on Pattern Analysis and Machine Intelligence 12, 993–1001 (1990)
Tumer, K., Ghosh, J.: Error Correlation and Error Reduction in Ensemble Classifiers. Connection Science 8, 385–404 (1996)
Sharkey, A.J.C.: On Combining Artificial Neural Nets. Connection Science 8 (1996)
Raviv, Y., Intrator, N.: Bootstrapping with Noise: An Effective Regularization Technique. Connection Science 8, 355–372 (1996)
Pe’er, D., et al.: Inferring subnetworks from perturbed expression profiles. Bioinformatics 17(Suppl. 1), S215–S224 (2001)
Hartemink, A.J., et al.: Combining location and expression data for principled discovery of genetic regulatory network models. In: Pacific Symp. Biocomput., vol. 7, pp. 437–449 (2002)
Friedman, N., Koller, D.: Being Bayesian about Network Structure. A Bayesian Approach to Structure Discovery in Bayesian Networks. Machine Learning 50(1), 95–125 (2003)
Yu, J., et al.: Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatic 20(18), 3594–3603 (2004)
Basso, K., et al.: Reverse engineering of regulatory networks in human B cells. Nat Genet (2005)
Hartemink, A.J.: Reverse engineering gene regulatory networks. Nat. Biotechnol. 23(5), 554–555 (2005)
Hartemink, A.J.: BANJO (2005)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Berkman, O., Intrator, N. (2007). Robust Inference in Bayesian Networks with Application to Gene Expression Temporal Data. In: Haindl, M., Kittler, J., Roli, F. (eds) Multiple Classifier Systems. MCS 2007. Lecture Notes in Computer Science, vol 4472. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72523-7_48
Download citation
DOI: https://doi.org/10.1007/978-3-540-72523-7_48
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-72481-0
Online ISBN: 978-3-540-72523-7
eBook Packages: Computer ScienceComputer Science (R0)