Published on October 29, 2007
Bayesian Network Tools in Java (BNJ) v2.0: Bayesian Network Tools in Java (BNJ) v2.0 William H. Hsu Other Contributors Roby Joehanes Prashanth Boddhireddy Haipeng Guo Siddharth Chandak Benjamin B. Perry Charles Thornton Julie A. Thornton http://bndev.sourceforge.net What is BNJ?: What is BNJ? Software toolkit for research and development using graphical models Open source (GNU General Public License) 100% Java (J2EE v1.4) Developed at KDD Lab, Kansas State University http://bndev.sourceforge.net Version 2 currently in alpha stage Intended Users: Intended Users Researchers / students Experiment with algorithms for learning, inference Standardized comparison Synthesis Create, edit, convert networks, data sets Developers New algorithms for graphical models using BNJ API Applications BNJ History: BNJ History BNC: initiated 1997, U. Illinois BNJ 1: developed 1999-2002, KS State Hard to maintain Redesigned from scratch BNJ 2: development started Dec 2002 Surpasses BNJ v1 in features, flexibility, performance More standardized API BNJ Highlights :Network Interchange: BNJ Highlights : Network Interchange 8 network formats supported Hugin .net (both 5.7 and 6.0) XML-Bif Legacy BIF Microsoft XBN Legacy DSC Genie DSL Ergo ENT LibB .net Opens, saves, converts BNJ Highlights :Data Formats Supported: BNJ Highlights : Data Formats Supported Microsoft Excel (.xls) WEKA (.arff) LibB data XML-data Legacy .dat format Flat files Space/tab delimited ASCII .txt Comma-separated BNJ Highlights :Exact Inference: BNJ Highlights : Exact Inference Junction Tree [Lauritzen & Spiegelhalter, 1988] Variable elimination [Shenoy; Dechter] with optimizations JavaBayes [Cozman, 2001] Kansas State KDD Lab [Joehanes & Hsu, 2003] Singly-connected network belief propagation [Pearl, 1983] Cutset Conditioning – under revision [Suermondt, Horvitz, & Cooper, 1990] BNJ Highlights :Approximate Inference: Sampling based: Logic Sampling Forward Sampling Likelihood Weighting Self-Importance Sampling Adaptive Importance Sampling (AIS) Bounded Cutset Conditioning (BCC) – under revision Hybrid: AIS-BCC bridge – under revision BNJ Highlights : Approximate Inference BNJ Highlights :Structure Learning: BNJ Highlights : Structure Learning Greedy (Bayesian Dirichlet) score-based: K2 [Cooper & Herskovits, 1992] Genetic wrapper cf. [Larranaga, 1998; Hsu, Guo, Perry, Stilson, 2002] GAWK (for K2) [Joehanes, 2003] Direct structure learning [Perry, 2003] Iterative Improvement Straightforward hill-climbing Simulated annealing (SA) SA with adversarial reweighting Other algorithms BNJ Highlights :Analysis and Experimentation: BNJ Highlights : Analysis and Experimentation Structure scoring during, after learning Graph errors RMSE Log likelihood score Dirichlet structure score Robustness analysis module Data generator: applies existing sampling-based inference algorithms BNJ Highlights :Probabilistic Relational Models: BNJ Highlights : Probabilistic Relational Models Preliminary support for PRM structure learning Accesses relational databases (mySQL, PostgreSQL, ORACLE 9i) via JDBC interface Preliminary local database loading support (without any database engines) Currently: adapt traditional learning algorithms such as K2, Sparse Candidate, etc. to relational models PRM inference: planned for full release of v2 (Spring, 2004) BNJ Highlights : BNJ Highlights  Converter Factory Standalone application GUI front-end Converts among supported network, data formats Database GUI Tool Transfer data files to and from server Submit SQL commands through JDBC interface Currently used for PRM learning BNJ Highlights : BNJ Highlights  Wizards for Inference Learning Others planned GUI for Network Editing Still in redevelopment Currently display-mode only All tools available in command-line mode BNJ Performance: BNJ Performance Relatively fast inference for small to medium networks Tends to slow down when node arity high Optimization underway Very fast learning engine 235 nodes, 76 data points (yeast cell-cycle expression data, Spellman-Gasch) with K2: 3 seconds on AMD Athlon XP 1.6GHz Full alarm (37 nodes, 3000 data points) with K2: 13 seconds on AMD Athlon XP 1.6GHz Applications, New Research:What We Have Done with BNJ: Applications, New Research: What We Have Done with BNJ Computational genomics: learning gene expression pathways Saccharomyces cerevisiae (yeast) [Johanes & Hsu, 2003] Oryza sativa (rice) defense-response – in progress http://www.kddresearch.org/REU/Summer-2003 PRM Learning Experiments: EachMovie data New Developments Variable ordering wrappers [Hsu et al., 2002] Hybrid inference algorithms (AIS-BCC) Software Demo: Software Demo Development using Eclipse platform Open-source IDE From IBM (www.eclipse.org) Standalone applications: coming soon Sources, documentation on SourceForge http://bndev.sourceforge.net References : References  Applications [GHVW98] Grois, E., Hsu, W. H., Voloshin, M., & Wilkins, D. C. (1998). Bayesian Network Models for Automatic Generation of Crisis Management Training Scenarios. In Proceedings of the Tenth Innovative Applications of Artificial Intelligence Conference (IAAI-98), Madison, WI, pp. 1113-1120. Menlo Park, CA: AAAI Press. (PDF / PostScript / .ps.gz) General [Br95] Brooks, F. P. (1995). The Mythical-Man Month, 20th Anniversary Edition: Essays on Software Engineering. Boston, MA: Addison-Wesley. [La00] Langley, P. (2000). Crafting papers on machine learning. In Proceedings of the Seventeenth International Conference on Machine Learning, Stanford, CA, pp. 1207-1211. San Francisco, CA: Morgan Kaufmann Publishers. (HTML / .ps.gz) [La02] Langley, P. (2002). Issues in Research Methodology. Palo Alto, CA: Institute for the Study of Learning and Expertise. Available from URL: http://www.isle.org/~langley/methodology.html. References : References  Recent and Current Research [FGKP99] Friedman, N., Getoor, L., Koller, D., & Pfeffer, A. (1999). Learning Probabilistic Relational Models. In Proceedings of the International Joint Conference on Artificial Intelligence (IJCAI-1999), Stockholm, SWEDEN. San Francisco, CA: Morgan Kaufmann Publishers. (PDF) [GFTK02] Getoor, L., Friedman, N., Koller, D., & Taskar, B. (2002). Learning Probabilistic Models of Link Structure. Journal of Machine Learning Research, 3(2002):679-707. (PDF) [GH02] Guo, H. & Hsu, W. H. (2002). A Survey of Algorithms for Real-Time Bayesian Network Inference. In Guo, H., Horvitz, E., Hsu, W. H., and Santos, E., eds. Working Notes of the Joint Workshop (WS-18) on Real-Time Decision Support and Diagnosis, AAAI/UAI/KDD-2002. Edmonton, Alberta, CANADA, 29 July 2002. Menlo Park, CA: AAAI Press. (PDF) [Gu02] Guo, H. (2002). A Bayesian Metareasoner for Algorithm Selection for Real-time Bayesian Network Inference Problems (Doctoral Consortium Abstract). In Proceedings of the Eighteenth National Conference on Artificial Intelligence (AAAI-2002), Edmonton, Alberta, CANADA, p. 983. Menlo Park, CA: AAAI Press. (PDF) [HGPS02] Hsu, W. H., Guo, H., Perry, B. B., & Stilson, J. A. (2002). A permutation genetic algorithm for variable ordering in learning Bayesian networks from data. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2002), New York, NY. San Francisco, CA: Morgan Kaufmann Publishers. (PDF / PostScript / .ps.gz) - Nominated for Best of GECCO-2002, Genetic Algorithms Deme (31 nominees, 160 accepted papers out of 320) References : References  Software [Mu03] Murphy, K. P. (2003). Bayes Net Toolbox v5 for MATLAB. Cambridge, MA: MIT AI Lab. Available from URL: http://www.ai.mit.edu/~murphyk/Software/BNT/bnt.html. [PS02] Perry, B. P. & Stilson, J. A. (2002). BN-Tools: A Software Toolkit for Experimentation in BBNs (Student Abstract). In Proceedings of the Eighteenth National Conference on Artificial Intelligence (AAAI-2002), Edmondon, Alberta, CANADA, pp. 963-964. Menlo Park, CA: AAAI Press. (PS) Textbooks and Tutorials [Mu01] Murphy, K. P. (2001). A Brief Introduction to Graphical Models and Bayesian Networks. Berkeley, CA: Department of Computer Science, University of California - Berkeley. Available from URL: http://www.cs.berkeley.edu/~murphyk/Bayes/bayes.html. [Ne90] Neapolitan, R. E. (1990). Probabilistic Reasoning in Expert Systems: Theory and Applications. New York, NY: Wiley-Interscience. (Out of print; Amazon.com reference) [Ne03] Neapolitan, R. E. (2003). Learning Bayesian Networks. Englewood Cliffs, NJ: Prentice Hall. (Amazon.com reference) References : References  Foundational Material and Seminal Research [CH92] Cooper, G. F. & Herskovits, E. (1992). A Bayesian method for the induction of probabilistic networks from data. Machine Learning, 9(4):309-347. [Jo98] Jordan, M. I., ed. (1998). Learning in Graphical Models. Cambridge, MA: MIT Press. (Amazon.com reference) [LS88] Lauritzen, S., & Spiegelhalter, D. J. (1988). Local Computations with Probabilities on Graphical Structures and Their Application to Expert Systems. Journal of the Royal Statistical Society Series B 50:157-224. Theses and Dissertations Related to BNJ [Me99] Mengshoel, O. J. (1999). Efficient Bayesian Network Inference: Genetic Algorthms, Stochastic Local Search and Abstraction. Ph.D. Dissertation, Department of Computer Science, University of Illinois at Urbana-Champaign, May, 1999. Available from URL: http://www-kbs.ai.uiuc.edu/web/kbs/publicLibrary/KBSPubs/Thesis/. References : References  Workshops Relevant to BNJ [GHHS02] Guo, H., Horvitz, E., Hsu, W. H., and Santos, E., eds. (2002). Working Notes of the Joint Workshop (WS-18) on Real-Time Decision Support and Diagnosis, AAAI/UAI/KDD-2002. Edmonton, Alberta, CANADA, 29 July 2002. Menlo Park, CA: AAAI Press. Available from URL: http://www.kddresearch.org/Workshops/RTDSDS-2002. [HJP03] Hsu, W. H., Joehanes, R., & Page, C. D. (2003). Working Notes of the Workshop on Learning Graphical Models in Computational Genomics, International Joint Conference on Artificial Intelligence (IJCAI-2003). Acapulco, MEXICO, 09 Aug 2003. Available from URL: http://www.kddresearch.org/Workshops/IJCAI-2003-Bioinformatics.