Abramson, B., Brown, J., Edwards, W., Murphy, A., & Winkler, R. L. (1996). Hailfinder: A Bayesian system for forecasting severe weather.

*International Journal of Forecasting*,

*12*, 57–71.

CrossRefGoogle ScholarAcid, S., de Campos, L., Fernandez-Luna, J., Rodriguez, S., Rodriguez, J., & Salcedo, J. (2004). A comparison of learning algorithms for Bayesian networks: A case study based on data from an emergency medical service.

*Artificial Intelligence in Medicine, 30*, 215–232.

Google ScholarAcid, S., & de Cam-pos, L. M. (2003). Searching for Bayesian network structures in the space of restricted acyclic partially directed graphs. *Journal of Artificial Intelligence Research*, 445–490.

Acid, S., & de Cam-pos, L. (2001). A hybrid methodology for learning belief networks: BENEDICT. *International Journal of Approximate Reasoning*, 235–262.

Akaike, H. (1974). A new look at the statistical model identification.

*IEEE Transactions on Automatic Control*,

*19*, 716–723.

MATHMathSciNetCrossRefGoogle ScholarAliferis, C. F., Tsamardinos, I., Statnikov, A., & Brown, L. E. (2003a). Causal explorer: A causal probabilistic network learning toolkit for biomedical discovery. In *International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS ’03)* (pp. 371–376).

Aliferis, C. F., Tsamardinos, I., & Statnikov, A. (2003b). HITON, A novel markov blanket algorithm for optimal variable selection. In *American Medical Informatics Association (AMIA)* (pp. 21–25).

Andreassen, S., Jensen, F. V., Andersen, S. K., Falck, B., Kharulff, U., & Woldbye, M. (1989). MUNIN—An expert EMG assistant. In J. E. Desmedt (Eds.), *Computer-aided electromyography and expert systems*.

Baeze-Yates, R., & Ribiero-Neto, B. (1999). *Modern information retrieval*. Addison-Wesley Pub Co.

Beal, M. J. & Ghahramani, Z. (2003). The variational Bayesian EM algorithm for incomplete data: With application to scoring graphical model structures. In J. M. Bernardo, M. J. Bayarri, J. O. Berger, A. P. Dawid, D. Heckerman, A. F. M. Smith, & M. West (Eds.), *Bayesian statistics 7*. Oxford University Press.

Beinlich, I. A., Suermondt, H., Chavez, R., Cooper, G., et al. (1989). The ALARM monitoring system: A case study with two probabilistic inference techniques for belief networks. In *Second European Conference in Artificial Intelligence in Medicine*.

Binder, J., Koller, D., Russell, S., & Kanazawa, K. (1997). Adaptive probabilistic networks with hidden variables. *Machine Learning, 29*.

Bouckaert, R. (1995). Bayesian belief networks from construction to inference. Ph.D. thesis, University of Utrecht.

Brown, L., Tsamardinos, I., & Aliferis, C. (2004). A novel algorithm for scalable and accurate bayesian network learning. In *11th World Congress on Medical Informatics (MEDINFO)*. San Francisco, California.

Brown, L. E., Tsamardinos, I., & Aliferis, C. F. (2005). A comparison of novel and state-of-the-art polynomial Bayesian network learning algorithms. In *Proceedings of the Twentieth National Conference on Artificial Intelligence (AAAI)*.

Chapman, W. W., Fizman, M., Chapman, B. E. & Haug, P. J. (2001). A comparison of classification algorithms to automatically identify chest X-ray reports that support pneumonia.

*Journal of Biomedical Informatics, 34*, 4–14.

Google ScholarCheng, J., Bell, D., & Liu, W. (1998). Learning Bayesian networks from data: An efficient approach based on information theory. Technical report, University of Alberta, Canada.

Cheng, J., Greiner, R., Kelly, J., Bell, D. A. & Liu, W. (2002). Learning Bayesian networks from data: An information-theory based approach.

*Artificial Intelligence, 137*, 43–90.

MATHMathSciNetCrossRefGoogle ScholarChickering, D. (1995). A transformational characterization of equivalent Bayesian network structures. In *Proceedings of the 11th Annual Conference on Uncertainty in Artificial Intelligence (UAI-95)*. San Francisco, CA (pp. 87–98). Morgan Kaufmann Publishers.

Chickering, D. (1996). Learning Bayesian networks is NP-complete. In D. Fisher and H. Lenz (Eds.), *Learning from data: Artificial intelligence and statistics V* (pp. 121–130) Springer-Verlag.

Chickering, D. (2002b). Learning equivalence classes of Bayesian-network structures. *Journal of Machine Learning Research*, 445–498.

Chickering, D., Geiger, D. & Heckerman, D. (1995). Learning Bayesian networks: Search methods and experimental results. In *Fifth International Workshop on Artificial Intelligence and Statistics* (pp. 112–128).

Chickering, D., Meek, C. & Heckerman D. (2004). Large-sample learning of Bayesian networks is NP-hard.

*Journal of Machine Learning Research, 5*, 1287–1330.

Google ScholarChickering, D. M. (2002a). Optimal structure identification with greedy search. *Journal of Machine Learning Research*, 507–554.

Cooper, G. F., & Herskovits, E. (1992). A Bayesian method for the induction of probabilistic networks from data.

*Machine Learning, 9 (4)*, 309–347.

MATHGoogle ScholarCowell, R. G., Dawid, A. P., Lauritzen, S. L., & Spiegelhalter, D. J. (1999). *Probabilistic networks and expert systems*. Springer.

Dash, D. (2005). Restructuring dynamic causal systems in equilibrium. In *Proceedings of the Tenth International Workshop on Artificial Intelligence and Statistics (AIStats 2005)*.

Dash, D. & Druzdzel, M. (1999). A hybrid anytime algorithm for the construction of causal models from sparse data. In *Fifteenth Conference on Uncertainty in Artificial Intelligence (UAI-99)*.

Dash, D., & Druzdzel, M. (2003). Robust independence testing for constraint-based learning of causal structure. In *Proceedings of the Nineteenth Annual Conference on Uncertainty in Artificial Intelligence (UAI-03)* (pp. 167–174), Morgan Kaufmann.

Dor, D., & Tarsi, M. (1992). A simple algorithm to construct a consistent extension of a partially oriented graph. Technicial Report R-185, Cognitive Systems Laboratory, UCLA.

Friedman, N. (1998). The Bayesian structural EM algorithm. In *Proceedings of the 14th Annual Conference on Uncertainty in Artificial Intelligence (UAI-98)*. (pp. 129–138), San Francisco, CA, Morgan Kaufmann Publishers.

Friedman, N., Linial, M., Nachman, I., & Pe’er, D. (2000). Using Bayesian networks to analyze expression data.

*Computational Biology, 7*, 601–620.

CrossRefGoogle ScholarFriedman, N., Nachman, I., & Pe’er, D., (1999). Learning Bayesian network structure from massive datasets: The “sparse candidate” algorithm. In *Fifteenth Conference on Uncertainty in Artificial Intelligence (UAI-99)*.

Ghahramani, Z., & Beal, M. (2001). Graphical models and variational methods. In M. Opper, & D. Saad (Eds.), *Advanced mean field methods—Theory and practice*. MIT Press.

Glymour, C., & Cooper, G. F. (eds.) (1999). *Computation, causation, and discovery*. AAAI Press/The MIT Press.

Glymour, C. N. (2001). *The mind’s arrows: Bayes nets & graphical causal models in psychology*. MIT Press.

Goldenberg, A., & Moore, A. (2004). Tractable learning of large Bayes net structures from sparse data. In *Proceedings of 21st International Conference on Machine Learning*.

Heckerman, D. E., Geiger, D., & Chickering, D. M. (1995). Learning Bayesian networks: The combination of knowledge and statistical data.

*Machine Learning, 20*, 197–243.

MATHGoogle ScholarJensen, A., & Jensen, F. (1996). Midas—An influence diagram for management of mildew in winter wheat. In *Proceedings of the 12th Annual Conference on Uncertainty in Artificial Intelligence (UAI-96)* (pp. 349–356). Morgan Kaufmann Publishers.

Jensen, C. S. (1997). Blocking Gibbs sampling for inference in large and complex Bayesian networks with applications in genetics. Ph.D. thesis, Aalborg University, Denmark.

Jensen, C. S., & Kong, A. (1996). Blocking Gibbs sampling for linkage analysis in large pedigrees with many loops. Research Report R-96-2048, Department of Computer Science, Aalborg University, Denmark.

Jordan, M. I., Ghahramani, Z., T.S., J., & L.K., S. (1999). An introduction to variational methods for graphical models.

*Machine Learning, 37*, 183–233.

MATHCrossRefGoogle ScholarKocka, T., Bouckaert, R., & Studeny, M. (2001). On the inclusion problem. Technical report, Academy of Sciences of the Czech Republic.

Kovisto, M., & Sood, K. (2004). Exact Bayesian structure discovery in Bayesian networks.

*Journal of Machine Learning Research, 5*, 549–573.

Google ScholarKoller, D., & Sahami, M. (1996). Toward optimal feature selection. In *Thirteen International Conference in Machine Learning*.

Komarek, P., & Moore, A. (2000). A dynamic adaptation of AD-trees for efficient machine learning on large data sets. In *Proc. 17th International Conf. on Machine Learning* (pp. 495–502). San Francisco, CA: Morgan Kaufmann.

Kristensen, K., & Rasmussen, I. A. (2002). The use of a Bayesian network in the design of a decision support system for growing malting barley without use of pesticides.

*Computers and Electronics in Agriculture, 33*, 197–217.

CrossRefGoogle ScholarKullback, S., & Leibler, R. (1951). On information and sufficiency.

*Annals of Mathematical Statistics, 22*, 79–86.

MATHMathSciNetGoogle ScholarMargaritis, D., & Thrun, S. (1999). Bayesian network induction via local neighborhoods. In *Advances in Neural Information Processing Systems 12 (NIPS)*.

Margaritis, D., & Thrun, S. (2001). A Bayesian multiresolution independence test for continuous variables. In *17th Conference on Uncertainty in Artificial Intelligence (UAI)*.

Meek, C. (1995). Strong completeness and faithfulnes in Bayesian networks. In *Conference on Uncertainty in Artificial Intelligence* 411–418.

Meek, C. (1997). Graphical models: Selecting causal and statistical models. Ph.D. thesis, Carnegie Mellon University.

Moore, A., & Lee, M. (1998). Cached sufficient statistics for efficient machine learning with large datasets.

*Journal of Artificial Intelligence Research, 8*, 67–91.

MATHMathSciNetGoogle ScholarMoore, A., & Schneider, J. (2002). Real-valued all-dimensions search: Low-overhead rapid searching over subsets of attributes. In *Proceedings of the Conference on Uncertainty in Artificial Intelligence (UAI-2002)* (pp. 360–369).

Moore, A., & Wong, W. (2003). Optimal reinsertion: A new search operator for accelerated and more accurate Bayesian network structure learning. In *Twentieth International Conference on Machine Learning (ICML-2003)*.

Neapolitan, R. (2003). *Learning Bayesian networks*. Prentice Hall.

Nielson, J., Kocka, T., & Pena, J. (2003). On local optima in learning bayesian networks. In *Proceedings of the Nineteenth Conference on Uncertainty in Artificial Intelligence*, 435–442.

Pearl, J. (1988).

*Probabilistic reasoning in intelligent systems*. San Mateo, CA: Morgan Kaufmann.

MATHGoogle ScholarPearl, J. (2000). *Causality, models, reasoning, and inference*. Cambridge University Press.

Pearl, J., & Verma, T. (1991). A theory of inferred causation. In J. F. Allen, R. Fikes, & E. Sandewall (Eds.), *KR’91: Principles of knowledge representation and reasoning* (pp. 441–452). San Mateo, California: Morgan Kaufmann.

Peterson, W., TG, B., & Fox, W. (1954). The theory of signal detectability. *IRE Professional Group on Information Theory PGIT-4*, 171–212.

Rissanen, J. (1978). Modeling by shortest data description.

*Automatica, 14*, 465–671.

MATHCrossRefGoogle ScholarRissanen, J. (1987). Stochastic complexity.

*Journal of the Royal Statistical Soceity, Series B, 49*, 223–239.

MathSciNetGoogle ScholarSchwarz, G. (1978). Estimating the dimension of a model.

*The Annals of Statistics, 6*, 461–464.

MATHMathSciNetGoogle ScholarSilverstein, C., Brin, S., Motwani, R., & Ullman, J. (2000). Scalable techniques for mining causal structures.

*Data Mining and Knowledge Discovery, 4 (2/3)*, 163–192.

CrossRefGoogle ScholarSingh, M., & Valtorta, M. (1993). An algorithm for the construction of Bayesian network structures from data. In *9th Conference on Uncertainty in Artificial Intelligence*, pp. 259–265.

Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K.

*et al*. & Eisen, M. B. (1998). Comprehensive identification of cell cycle regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization.

*Molecular Biology of the Cell, 9*, 3273–3297.

Google ScholarSpirtes, P., Glymour, C., & Scheines, R. (1990). Causality from probability. In J. Tiles, G. McKee, & G. Dean (eds.): *Evolving knowledge in the natural and behavioral sciences* (pp. 181–199). London: Pittman.

Spirtes, P., Glymour, C. & Scheines, R. (1993). *Causation, prediction, and search*. Springer/Verlag, first edition.

Spirtes, P., Glymour, C., & Scheines, R. (2000). *Causation, prediction, and search*. The MIT Press, second edition.

Spirtes, P., & Meek, C. (1995). Learning Bayesian networks with discrete variables from data. In *Proceedings from First Annual Conference on Knowledge Discovery and Data Mining* (pp. 294–299). Morgan Kaufmann.

Statnikov, A., Tsamardinos, I., & Aliferis, C. F. (2003). An algorithm for the generation of large Bayesian networks. Technical Report DSL-03-01, Vanderbilt University.

Steck, H., & Jaakkola, T. (2002). On the dirichlet prior and Bayesian regularization. In *Advances in Neural Information Processing Systems, 15*.

Tsamardinos, I., & Aliferis, C. F. (2003). Towards principled feature selection: Relevancy, filters and wrappers. In *Ninth International Workshop on Artificial Intelligence and Statistics (AI & Stats 2003)*.

Tsamardinos, I., Aliferis, C. F., & Statnikov, A. (2003b). Algorithms for large scale markov blanket discovery. In *The 16th International FLAIRS Conference* (pp. 376–381).

Tsamardinos, I., Aliferis, C. F., & Statnikov, A. (2003c). Time and sample efficient discovery of Markov blankets and direct causal relations. In *The Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining* (pp. 673–678).

Tsamardinos, I., Aliferis, C. F., & Statnikov, A. (2003a). Time and sample efficient discovery of Markov Blankets and direct causal relations. Technical Report DSL-03-02, Vanderbilt University.

Tsamardinos, I., Aliferis, C. F., Statnikov, A., & Brown. L. E. (2003a). Scaling-Up Bayesian network learning to thousands of variables using local Learning Technique. Technical Report DSL TR-03-02, Dept. Biomedical Informatics, Vanderbilt University.

Tsamardinos, I., Statnikov, A., Brown, L. E., and Aliferis, C. F. (2006) Generating realistic large bayesian networks by tiling. In *The 19th International FLAIRS Conference* (to appear).

Verma, T., & Pearl, J. (1988). Causal networks: Semantics and expressiveness. In: *4th Workshop on Uncertainty in Artificial Intelligence*.

Verma, T., & Pearl, J. (1990). Equivalence and synthesis of causal models. In *Proceedins of 6th Annual Conference on Uncertainty in Artificial Intelligence* (pp. 255–268). Elsevier Science.