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BAYESIAN NETWORK TOOLS IN JAVA (BNJ)


LATEST RELEASE: V3.004 PRE-ALPHA (21 JULY 2004)

Check out some version 3 screenshots!


[ VERSIÓN EN ESPAÑOL (SPANISH) | CHINESE | JAPANESE ]


WHAT IS BNJ?

> BNJ is an open-source suite of software tools for research and development
> using graphical models of probability. It is implemented in 100% pure Java and
> distributed under the GNU General Public License (GPL) by the Kansas State
> University Laboratory for Knowledge Discovery in Databases (KDD).
> 
> For information on the BNJ project and documentation, see the following pages.
> 
> > 
> 
>  * BNJ Web Discussion Group and Mailing List
>  * Click here to subscribe

> > 
> 
> BNJ also has a community on the weblog (blogging) service LiveJournal:
> bayesnets
> 
> Now online: The BNJ Wiki at K-State


WHO IS ON THE BNJ DEVELOPMENT TEAM?

 * Kansas State University (KSU) KDD Lab
 * KSU Probabilistic Reasoning Group


HOW TO GET BNJ

> > Want the latest source code and docs?
> > Download them from project bnj on SourceForge!
> 
> 
> 
> Please remember to register BNJ online once you have downloaded it.
> Registration is free and takes only a few minutes.


HOW TO USE BNJ

> Software toolkit overview, presented at UAI-2003, by William H. Hsu and Roby
> Joehanes, Fri 08 Aug 2003 [ MS PowerPoint | PDF | HTML ]


USER TUTORIALS

> Read these if you just want to download and compile the basic utilities (the
> GUI-based Bayesian network editor and conversion tools, and the Inference
> Wizard and Learning Wizard tool).
>  * Eclipse setup tutorial, by Roby Joehanes [ HTML ]
>    Note: This is slightly out-of-date (it was written for Eclipse v2.0), and
>    the examples given are for our local setup, so you will have to modify the
>    paths and CVS repository names accordingly.
>    The recommended platform for BNJ v2 development is Eclipse, a very
>    full-featured open-source IDE. We have been using the latest version, which
>    as of Fri 23 Apr 2004 is 3.0 M8. You can download Eclipse here.
>  * Beginner: for new BNJ users - coming soon
>    * Converter utility
>    * Creating and editing graphical models using the GUI editor
>    * Inference Wizard
>    * Learning Wizard
>  * Intermediate: for users in Artificial Intelligence and Machine Learning
>    courses - coming soon
>    * Generating simulated data using a network (e.g., for structure learning)
>    * Inference
>      * Comparisons among exact and approximate inference algorithms
>      * Plotting convergence time for approximations
>      * Deterministic vs. stochastic sampling-based approximation
>    * Structure learning


DEVELOPER TUTORIALS

> Read these if you want to build a new application that uses pre-implemented
> classes for representation of graphical models and inference and learning
> using them, or if you would like to: embed BNJ in your own Java-based
> application, modify or optimize an existing part of the BNJ core clases or
> other modules, or contribute a new module (class), package, or wizard.
> 
>  * Beginner: for new BNJ developers, by Chris Meyer, Tue 09 Dec 2003 [ MS
>    PowerPoint | PDF | HTML ]
>  * Intermediate, by Roby Joehanes, Tue 18 Nov 2003 [ MS PowerPoint | PDF |
>    HTML ]
>  * Advanced - coming soon


SEMINAR ON GRAPHICAL MODELS, KSU MATH DEPARTMENT (09 DEC 2003)


DOCUMENTATION

 * BNJ distribution notes, version 2.03 alpha (05 Nov 2003)
 * BNJ Application Programmer Interface (API) - JavaDoc (HTML), version 2.1 beta
   (16 May 2004)
 * BNJ v2.1b manual


BNJ FEATURES AND DEVELOPMENT STATUS

> BNJ development began in September, 1997 at the University of Illinois
> Department of Computer Science.
> Development history of BNJ
> 
> BNJ version 2 has been in development since December, 2002. The final alpha
> release was v2.03a on 05 Nov 2003. v2 is now in feature-freeze. The first beta
> release, with a launcher executable for Windows and Linux, appeared on
> Sourceforge on Sun 16 May 2004. The final beta release (v2.2b) with minor
> optimizations is planned for Mon 31 May 2004, and an applications release with
> standalone, platform-specific executables (v2.3) is planned for Fri 11 Jun
> 2004.
> 
> The following new features are planned for BNJ v3 (4th quarter 2004):
> 
>  * Refactored applications programmer interface (API)
>    * Animaton-based tutorials: junction tree, other inference and learning
>      algorithms
>    * Support for pointwise product (maxprop) inference
>  * Reimplementations
>    * Inference algorithms for Bayesian networks other than clustering: bounded
>      cutset conditioning, variable elimination - prototype completed as of
>      v2.02 alpha (20 Aug 2003)
>    * Additional algorithms for structure learning [Jo98, Ne03]: Sparse
>      Candidate, Markov chain Monte Carlo (perturbation-based)
>    * Evaluation modules: error graphic, bootstrap validation
>  * Representation
>    * Continuous state
>    * Dynamic Bayes nets: n-slice temporal BN - in progress for v3 (alpha
>      expected 30 Jun 2004, beta 30 August 2004, full release 30 Nov 2004)
>    * Influence diagrams (decision networks) - in progress for v3
>    * Probabilistic Relational Models (PRMs) - prototype representation,
>      learning modules implemented as of v2.02a (20 Aug 2003)
>  * New development
>    * Converter Factory II: new graphical user interface (GUI) - standalone
>      application completed as of v2.02a (20 Aug 2003)
>    * Graphical editors: for continuous, DBN, ID, PRM representations - in
>      progress for v2.2b (31 May 2004); new GUI base completed as of v2.03a (05
>      Nov 2003)
>    * Gene expression modeling module: Interfaces to TIGR TM4 (especially
>      Multi-Experiment Viewer), EisenLab Cluster/TreeView, Silicon Genetics
>      GeneSpring


BNJ USER COMMUNITY

> As of Fri 21 May 2004, the BNJ source and binaries have been downloaded over
> 4500 times and over 130 offsite users have registered it.
> Descriptive statistics about BNJ versions and users


REGISTERING BNJ (OPTIONAL)

> To receive updates on new releases and to submit requests for documentation
> and new features, click here to register as a BNJ user or developer using the
> online form!
> 
> Your name and e-mail address are requested for major BNJ software development
> and release announcements only, and shall be kept confidential among BNJ
> developers.
> 
> If you have any questions, comments, or requests, please subscribe to the
> Yahoo! Group bndev.


CONTRIBUTING TO BNJ DEVELOPMENT

> We invite contributions from the user community in the following areas:
> 
>  * Research and educational case studies
>  * Source code
>  * Translations of documentation
>  * Builds
>  * Feature requests
>  * Error reports


BNJ TERMS (NO-WARRANTY DISCLAIMER)


ACKNOWLEDGEMENTS


> FUNDING
> 
> BNJ has been and continues to be developed through support from the following
> sponsoring agencies:
> 
> FEDERAL
> 
>  * U.S. National Science Foundation (NSF)
>    * NSF-PGRP-0110154: Research Experience for Undergraduates (REU) supplement
>      to: Inducible Ac elements for activation-tagging and PCR-based detection
>      of deleted genes in rice (J. E. Leach and W. H. Hsu), 15 May 2003 - 31
>      Jul 2003, Plant Genome Research Program
>    * Cooperative agreement 9874732: Algorithms for Discovery of Bayesian
>      Network Models of Gene Regulation in Saccharomyces cerevisiae from
>      Microarray Data (W. H. Hsu), 10 Jun 2002 - 09 Aug 2003; First Award, NSF
>      Experimental Program to Stimulate Competitive Research (EPSCoR),
>      sponsored by NSF and Kansas Technology Enterprise Corporation (KTEC)
>  * U.S Office of Naval Research (ONR)
>    * N00014-01-1-0917: Real-Time Temporal Probabilistic Inference using
>      Bayesian Networks: Decision Support in Manpower and Personnel Management
>      (W. H. Hsu and S.-I Chang, principal investigators), 13 May 2001 – 30 Sep
>      2002; subcontract, University of Mississippi Personnel Research
>      Consortium
>    * N00014-00-1-0769: Distributed Data Mining and Knowledge Discovery System
>      for Navy Personnel Research (W. H. Hsu and S.-I Chang, principal
>      investigators), 01 Jun 2000 – 30 Sep 2001; subcontract, University of
>      Mississippi Personnel Research Consortium
>  * U.S Army Research Lab (ARL)
>    * ARL-PET-IMT-KSU-07: Synthesis, Reduction, and Integration of Test and
>      Evaluation Data for Monitoring Applications (W. H. Hsu), 10 Aug 2000 – 09
>      Aug 2001; subcontract, Raytheon, Inc.
>    * ARL-PET-IMT-NCSA-01: Integration of Data Sources for Time Series Analysis
>      (W. H. Hsu and K. M. Skreiner), 20 Aug 1999 – 09 Aug 2000; subcontract,
>      National Center for Supercomputing Applications
> 
> STATE
> 
>  * Kansas Department of Transportation (KSDOT)
>    * Production of Sub-Standard Stopping Sight Distance Data Set and
>      Development of Highway Design Verification and Passing Sight Distance
>      Analysis via GPS Spatial Models (D. Ben-Arieh, S.-I Chang, M. Rys, W. H.
>      Hsu), 01 Jul 2002 - 30 Sep 2004
> 
> CORPORATE AND INDUSTRIAL PARTNERS
> 
>  * AIdentity Matrix LLC
> 
> 
> WEB LISTINGS
> 
> The BNJ development team gratefully acknowledges the maintainers of the
> following sites for listing our package in their online directories or linking
> to this site:
> 
>  * Java Math Tools, Mathtools.net
>  * Software Packages for Graphical Models / Bayesian Networks - Kevin Murphy,
>    MIT AI Lab
>  * Neural Networks and Fuzzy Logic Packages - GameAI.com
>  * Software for Bayesian and Dependency Networks - KDNuggets.com
> 
> If you have linked to our site on your Bayes nets page and would like a
> reciprocal link, please contact us.
> 
> 
> WEB SITE DESIGN
> 
> Mia Kalogjera


BNJ DEVELOPMENT AND EVALUATION TEAM


> CURRENT DEVELOPERS
> 
>  * Dr. William H. Hsu (team leader) - KSU Department of Computing and
>    Information Sciences
>  * Scott J. Harmon - KSU Department of Computing and Information Sciences
>  * Jeffrey M. Barber - KSU Department of Computing and Information Sciences
>  * Christopher H. Meyer - KSU Department of Computing and Information Sciences
>  * Silpan Patel - KSU Department of Electrical Engineering and Computer
>    Engineering
>  * James W. Plummer - KSU Department of Electrical Engineering and Computer
>    Engineering
>  * Andrew King - KSU Department of Computing and Information Sciences
> 
> 
> TEST SITE INSTRUCTORS
> 
>  * Dr. Tom Dietterich - Oregon State University Department of Computer Science
>  * Dr. Vasant Honavar - Iowa State University Department of Computer Science
> 
> 
> AFFILIATES
> 
>  * Dr. Sanjoy Das - KSU Department of Electrical Engineering and Computer
>    Engineering
>  * Dr. Lev Kapitanski - University of Miami Department of Mathematics
>  * Dr. Jan E. Leach - KSU Department of Plant Pathology
>  * Dr. Clare Nelson - KSU Department of Plant Pathology
>  * Bart Peinter - University of Michigan Department of Computer Science and
>    Engineering
>  * Edwin Rodríguez - KSU Department of Computing and Information Sciences
>  * Dr. Judith L. Roe - KSU Division of Biology
>  * Christopher Zhong - KSU Department of Computing and Information Sciences
>  * Dr. Stephen M. Welch - KSU Department of Agronomy
>  * Julie A. Thornton - KSU Deparment of Computing and Information Sciences


> PAST DEVELOPERS
> 
>  * Nathan D. Gettings
>    B.S. Mathematics, University of Illinois, 1998
>    PayPal, Palo Alto, CA, USA
>  * Dr. Haipeng Guo
>    Ph.D. Computer Science, KSU, 2003
>    Hong Kong University of Science and Technology Department of Computer
>    Science, Hong Kong
>  * Laura M. (Kruse) Haverkamp
>    B.S. Computer Science, KSU, 2000
>    Sprint, Kansas City, KS, USA
>  * Ben B. Perry
>    M.S. Computer Science, KSU, 2003
>    Quantum Leap Innovations, Newark, DE, USA
>  * Julie A. (Stilson) Thornton
>    B.S. Computer Science / Mathematics, KSU, 2003
>    KSU Department of Computing and Information Sciences, Manhattan, KS
>  * Roby Joehanes - KSU Department of Computing and Information Sciences
> 
> 
> PAST AFFILIATES
> 
>  * Sonal S. Junnarkar - M.S.E. Computer Science, KSU, 2002
>  * Rengakrishnan Subramanian - M.S. Computer Science, KSU, 2002
>  * Siddharth S. Chandak - M.S. Computer Science, KSU, 2003
>  * Charles L. Thornton - B.S. Computer Science, KSU, 2003


RELEVANT PUBLICATIONS AND REFERENCES

 



Page created: Thu 22 Aug 2002
Last updated: Wed 28 July 2004
William H. Hsu
BNJ Development Team