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<head> <TITLE>Software Packages for Graphical Models / Bayesian Networks</TITLE> </head> <body> <h1> Software Packages for Graphical Models / Bayesian Networks </h1> <p> Written by Kevin Murphy. <br> Last updated 31 October 2005. <h3>Remarks</h3> <ul> <li> A much more detailed comparison of some of these software packages is available from Appendix B of <a href="http://www.csse.monash.edu.au/bai/">Bayesian AI</a>, by Ann Nicholson and Kevin Korb. This appendix is available <a href="http://www.csse.monash.edu.au/bai/book/appendix_b.pdf">here</a>, and is based on the online comparison below. <li> An online <a href="http://servasi.insa-rouen.fr/enseignement/siteUV/rna/BNT/software.html">French version</a> of this page is also available (not necessarily up-to-date). <!-- <li> Matt Turk has made a <a href="http://ilab.cs.ucsb.edu/BayesNets/Bayesia_Software.pdf">pdf version of this page</a> (not necessarily up-to-date) with some extra comments on the packages. --> <!-- <br> (He also has a <a href="http://ilab.cs.ucsb.edu/BayesNets">cached copy</a> of several of the packages listed below, which you can look at if links are down.) --> </ul> <h3>What do the headers in the table mean?</h3> <ul> <li> Src = source code included? (N=no) If so, what language? <li> API = application program interface included? (N means the program cannot be integrated into your code, i.e., it must be run as a standalone executable.) <li> Exec = Executable runs on W = Windows (95/98/NT), U = Unix, M = Mac, or - = any machine with a compiler. <li> Cts = are continuous (latent) nodes supported? G = (conditionally) Gaussians nodes supported analytically, Cs = continuous nodes supported by sampling, Cd = continuous nodes supported by discretization, Cx = continuous nodes supported by some unspecified method, D = only discrete nodes supported. <li> GUI = Graphical User Interface included? <li> Learns parameters? <li> Learns structure? CI = means uses conditional independency tests <!-- <li> Sample = sampling methods (e.g., likelihood weighting, MCMC) supported? --> <li> Utility = utility and decision nodes (i.e., influence diagrams) supported? <li> Free? 0 = free (although possibly only for academic use). $ = commercial software (although most have free versions which are restricted in various ways, e.g., the model size is limited, or models cannot be saved, or there is no API.) <li> Undir? What kind of graphs are supported? U = only undirected graphs, D = only directed graphs, UD = both undirected and directed, CG = chain graphs (mixed directed/undirected). <li> Inference = which inference algorithm is used? jtree = junction tree, varelim = variable (bucket) elimination, MH = Metropols Hastings, G = Gibbs sampling, IS = importance sampling, sampling = some other Monte Carlo method, polytree = Pearl's algorithm restricted to a graph with no cycles, none = no inference supported (hence the program is only designed for structure learning from completely observed data) <li> Comments. If in "quotes", I am quoting the authors at their request. </ul> <!-- The following table is automatically generated as follows bnsoft_to_html.pl < bnsoft.txt > ! soft.html Then soft.html is inserted and the last line is tidied up. --> <table border> <tr> <td> Name <td> Authors <td> Src <td> API <td> Exec <td> Cts <td> GUI <td> Params <td> Struct <td> Utility <td> Free <td> Undir <td> Inference <td> Comments <tr> <td> <!--Name--> <a href=http://www.agenarisk.com > AgenaRisk</a> <td> <!--Authors-->Agena <td> <!--Src-->N <td> <!--API-->Y <td> <!--Exec-->W,U <td> <!--Cts-->Cx <td> <!--GUI-->Y <td> <!--Params-->Y <td> <!--Struct-->N <td> <!--Utility-->N <td> <!--Free-->$ <td> <!--Undir-->D <td> <!--Inference-->JTree <td> <!--Comments-->Simulation by Dynamic discretisation <tr> <td> <!--Name--> <a href=http://www.lumina.com > Analytica</a> <td> <!--Authors-->Lumina <td> <!--Src-->N <td> <!--API-->Y <td> <!--Exec-->W,M <td> <!--Cts-->G <td> <!--GUI-->Y <td> <!--Params-->N <td> <!--Struct-->N <td> <!--Utility-->Y <td> <!--Free-->$ <td> <!--Undir-->D <td> <!--Inference-->sampling <td> <!--Comments-->spread sheet compatible <tr> <td> <!--Name--> <a href=http://www.cs.duke.edu/~amink/software/banjo/> Banjo</a> <td> <!--Authors-->Hartemink <td> <!--Src-->Java <td> <!--API-->Y <td> <!--Exec-->W,U,M <td> <!--Cts-->Cd <td> <!--GUI-->N <td> <!--Params-->N <td> <!--Struct-->Y <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->none <td> <!--Comments--> structure learning of static or dynamic networks of discrete variables <tr> <td><a href=http://www.cs.Helsinki.FI/research/fdk/bassist/> Bassist</a> <td> U. Helsinki <td> C++ <td> Y <td> U <td> G <td> N <td> Y <td> N <td> N <td> 0 <td> D <td> MH <td> Generates C++ for MCMC. <tr> <td><a href=http://www.cs.Helsinki.FI/research/cosco/Projects/NONE/SW/ > Bayda</a> <td> U. Helsinki <td> Java <td> Y <td> WUM <td> G <td> Y <td> Y <td> N <td> N <td> 0 <td> D <td> ? <td> Bayesian Naive Bayes classifier. <tr> <td><a href=http://www.mbfys.kun.nl/snn/Research/bayesbuilder/ > BayesBuilder</a> <td> Nijman (U. Nijmegen) <td> N <td> N <td> W <td> D <td> Y <td> N <td> N <td> N <td> 0 <td> D <td> ? <td> - <tr> <td> <!--Name--> <a href="http://www.bayesia.com">BayesiaLab</a> <td> <!--Authors-->Bayesia Ltd <td> <!--Src-->N <td> <!--API-->N <td> <!--Exec-->- <td> <!--Cts-->Cd <td> <!--GUI-->Y <td> <!--Params-->Y <td> <!--Struct-->Y <td> <!--Utility-->N <td> <!--Free-->$ <td> <!--Undir-->CG <td> <!--Inference-->jtree,G <td> <!--Comments--> <!-- Structural learning (association discovery, classification), Bayesian clustering with analysis report generation, missing values processing, essential graphs, analysis toolbox, adaptive questionnaires, dynamic models --> Structural learning, adaptive questionnaires, dynamic models <tr> <td><a href=http://www.bayesware.com>Bayesware Discoverer</a> <td> Bayesware <td> N <td> N <td> WUM <td> Cd <td> Y <td> Y <td> Y <td> N <td> $ <td> D <td> ? <td> Uses bound and collapse for learning with missing data. <tr> <td><a href=http://B-Course.hiit.fi/> B-course</a> <td> U. Helsinki <td> N <td> N <td> WUM <td> Cd <td> Y <td> Y <td> Y <td> N <td> 0 <td> D <td> ? <td> Runs on their server: view results using a web browser. <!-- <tr> <td><a href="http://www.aist.go.jp/ETL/etl/suri/motomura/BN/bn-java.html">Bayonnet</a> <td> Motomura (ETL) <td> Java <td> Y <td> WUM <td> NN <td> Cx <td> Y <td> N <td> N <td> 0 <td> D <td> ? <td> For learning, represents BN as a neural net. --> <tr> <td><a href=http://www.cs.ualberta.ca/~jcheng/bnpc.htm > Belief net power constructor</a> <td> Cheng (U.Alberta) <td> N <td> W <td> W <td> D <td> Y <td> Y <td> CI <td> N <td> 0 <td> D <td> ? <td> - <tr> <td><a href=http://www.cs.berkeley.edu/~murphyk/Bayes/bnt.html > BNT</a> <td> Murphy (U.C.Berkeley) <td> Matlab/C <td> Y <td> WUM <td> G <td> N <td> Y <td> Y <td> Y <td> 0 <td> D,U <td> Many <td> Also handles dynamic models, like HMMs and Kalman filters. <tr> <td> <!--Name--> <a href="http://bndev.sourceforge.net/">BNJ</a> <td> <!--Authors-->Hsu (Kansas) <td> <!--Src-->Java <td> <!--API-->- <td> <!--Exec-->- <td> <!--Cts-->D <td> <!--GUI-->Y <td> <!--Params-->N <td> <!--Struct-->Y <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->jtree, IS <td> <!--Comments-->- <!-- <tr> <td><a href=http://94.parkview-court.net/project/ > BN Toolkit</a> <td> Gowans (Imperial) <td> Visual Basic <td> Y <td> W <td> D <td> Y <td> N <td> Y <td> N <td> 0 <td> D <td> Polytree <td> Parser and GUI for the XML-BIF format. --> <tr> <td><a href=http://www.ics.uci.edu/~irinar > BucketElim</a> <td> Rish (U.C.Irvine) <td> C++ <td> Y <td> WU <td> D <td> N <td> N <td> N <td> N <td> 0 <td> D <td> Varelim <td> - <tr> <td><a href=http://www.mrc-bsu.cam.ac.uk/bugs > BUGS</a> <td> MRC/Imperial College <td> N <td> N <td> WU <td> Cs <td> W <td> Y <td> N <td> N <td> 0 <td> D <td> Gibbs <td> - <tr> <td><a href=http://www.data-digest.com > Business Navigator 5</a> <td> Data Digest Corp <td> N <td> N <td> W <td> Cd <td> Y <td> Y <td> Y <td> N <td> $ <td> D <td> Jtree <td> - <tr> <td><a href=http://www-pcd.stanford.edu/cousins/caben-1.1.tar.gz > CABeN</a> <td> Cousins et al. (Wash. U.) <td> C <td> Y <td> WU <td> D <td> N <td> N <td> N <td> N <td> 0 <td> D <td> 5 Sampling methods <td> - <tr> <td> <!--Name--> <a href= http://discover1.mc.vanderbilt.edu/discover/public/>Causal discoverer</a> <td> <!--Authors-->Vanderbilt <td> <!--Src-->N <td> <!--API-->N <td> <!--Exec-->W <td> <!--Cts-->- <td> <!--GUI-->- <td> <!--Params-->N <td> <!--Struct-->Y <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->- <td> <!--Comments-->structure learning only <tr> <td><a href=http://www.math.auc.dk/~jhb/CoCo/information.html > CoCo+Xlisp</a> <td> Badsberg (U. Aalborg) <td> C/lisp <td> Y <td> U <td> D <td> Y <td> Y <td> CI <td> N <td> 0 <td> U <td> Jtree <td> Designed for contingency tables. <tr> <td><a href=http://www.cs.ubc.ca/labs/lci/CIspace/ > CIspace</a> <td> Poole et al. (UBC) <td> Java <td> N <td> WU <td> D <td> Y <td> N <td> N <td> N <td> 0 <td> D <td> Varelim <td> - <tr> <td> <!--Name--> <a href="http://www.robots.ox.ac.uk/~parg/software.html">DBNbox</a> <td> <!--Authors-->Roberts et al <td> <!--Src-->Matlab <td> <!--API-->- <td> <!--Exec-->- <td> <!--Cts-->Y <td> <!--GUI-->N <td> <!--Params-->Y <td> <!--Struct-->N <td> <!--Utility-->N <td> <!--Free-->Y <td> <!--Undir-->D <td> <!--Inference-->Various <td> <!--Comments-->DBNs <tr> <td> <!--Name--><a href=http://www.math.auc.dk/novo/deal>Deal</a> <td> <!--Authors-->Bottcher et al <td> <!--Src-->R <td> <!--API-->- <td> <!--Exec-->- <td> <!--Cts-->G <td> <!--GUI-->Y <td> <!--Params-->Y <td> <!--Struct-->Y <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->None <td> <!--Comments--> Structure learning. <tr> <td><a href=http://www.deriveit.com >DeriveIt</a> <td> <!--Authors-->DeriveIt LLC <td> <!--Src-->N <td> <!--API-->- <td> <!--Exec-->- <td> <!--Cts-->? <td> <!--GUI-->? <td> <!--Params-->Y <td> <!--Struct-->Y <td> <!--Utility-->? <td> <!--Free-->$ <td> <!--Undir-->D <td> <!--Inference-->Jtree <td> <!--Comments--> Exploits local structure in CPDs. <tr> <td><a href=http://www.noeticsystems.com>Ergo</> <td> <!--Authors-->Noetic systems <td> <!--Src-->N <td> <!--API-->Y <td> <!--Exec-->W,M <td> <!--Cts-->D <td> <!--GUI-->Y <td> <!--Params-->N <td> <!--Struct-->N <td> <!--Utility-->N <td> <!--Free-->$ <td> <!--Undir-->D <td> <!--Inference-->jtree <td> <!--Comments-->- <!-- <tr> <td><a href=http://www.ens-lyon.fr/~jnarboux/Floue/index.html>FLoUE/BIFtoN</a> <td> ENS Lyon <td> Java <td> Y <td> WUM <td> D <td> N <td> N <td> N <td> N <td> 0 <td> D <td> Jtree <td> - --> <tr> <td><a href=http://www.staff.ncl.ac.uk/d.j.wilkinson/software/gdagsim/ > GDAGsim</a> <td> Wilkinson (U. Newcastle) <td> C <td> Y <td> WUM <td> G <td> N <td> N <td> N <td> N <td> 0 <td> D <td> Exact <td> Bayesian analysis of large linear Gaussian directed models. <tr> <td><a href=http://www2.sis.pitt.edu/~genie > Genie</a> <td> U. Pittsburgh <td> N <td> WU <td> WU <td> D <td> W <td> N <td> N <td> Y <td> 0 <td> D <td> Jtree <td> - <tr> <td><a href=http://www.math.ntnu.no/~hrue/GMRFsim/ > GMRFsim</a> <td> Rue (U. Trondheim) <td> C <td> Y <td> WUM <td> G <td> N <td> N <td> N <td> N <td> 0 <td> U <td> MCMC <td> Bayesian analysis of large linear Gaussian undirected models. <tr> <td> <!--Name--> <a href=http://ssli.ee.washington.edu/~bilmes/gmtk/>GMTk</a> <td> <!--Authors-->Bilmes (UW), Zweig (IBM) <td> <!--Src-->N <td> <!--API-->Y <td> <!--Exec-->U <td> <!--Cts-->D <td> <!--GUI-->N <td> <!--Params-->Y <td> <!--Struct-->Y <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->Jtree <td> <!--Comments--> Designed for speech recognition. <tr> <td> <!--Name--> <a href=http://www.r-project.org/gR>gR</a> <td> <!--Authors-->Lauritzen et al. <td> <!--Src-->R <td> <!--API-->- <td> <!--Exec-->- <td> <!--Cts-->- <td> <!--GUI-->- <td> <!--Params-->- <td> <!--Struct-->- <td> <!--Utility-->- <td> <!--Free-->0 <td> <!--Undir-->- <td> <!--Inference-->- <td> <!--Comments-->Currently vaporware <tr> <td> <!--Name--> <a href=http://www.stats.bris.ac.uk/~peter/Grappa/>Grappa</a> <td> <!--Authors-->Green (Bristol) <td> <!--Src-->R <td> <!--API-->- <td> <!--Exec-->- <td> <!--Cts-->D <td> <!--GUI-->N <td> <!--Params-->N) <td> <!--Struct-->N <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->Jtree <td> <!--Comments-->- <tr> <td><a href=http://www.hugin.com > Hugin Expert</a> <td> Hugin <td> N <td> Y <td> W <td> G <td> W <td> Y <td> CI <td> Y <td> $ <td> CG <td> Jtree <td> - <tr> <td> <!--Name--> <a href=http://www.warnes.net/GregsSoftwareLinks/index_html?Tab=MCMC>Hydra</a> <td> <!--Authors-->Warnes (U.Wash.) <td> <!--Src-->Java <td> <!--API-->- <td> <!--Exec-->- <td> <!--Cts-->Cs <td> <!--GUI-->Y <td> <!--Params-->Y <td> <!--Struct-->N <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->U,D <td> <!--Inference-->MCMC <td> <!--Comments-->- <tr> <!-- http://www.rpal.rockwell.com/ideal.html --> <td><a href=http://yoda.cis.temple.edu:8080/ideal>Ideal</a> <td> Rockwell <td> Lisp <td> Y <td> WUM <td> D <td> Y <td> N <td> N <td> Y <td> 0 <td> D <td> Jtree <td> GUI requires Allegro Lisp. <tr> <td><a href=http://www.cs.cmu.edu/~javabayes/Home/ > Java Bayes</a> <td> Cozman (CMU) <td> Java <td> Y <td> WUM <td> D <td> Y <td> N <td> N <td> Y <td> 0 <td> D <td> Varelim, jtree <td> - <tr> <td> <!--Name--><a href="http://www.codeas.com/kbaseai.php" >KBaseAI</a> <td> <!--Authors-->Codeas <td> <!--Src-->N <td> <!--API-->Y <td> <!--Exec-->W,U <td> <!--Cts-->D <td> <!--GUI-->N <td> <!--Params-->N <td> <!--Struct-->N <td> <!--Utility-->N <td> <!--Free-->$ <td> <!--Undir-->D <td> <!--Inference-->varelim <td> <!--Comments-->client/server architecture, multiple users, access control, query language <tr> <td> <!--Name--> <a href=http://www.cs.huji.ac.il/labs/compbio/LibB>LibB</a> <td> <!--Authors-->Friedman (Hebrew U) <td> <!--Src-->N <td> <!--API-->Y <td> <!--Exec-->W <td> <!--Cts-->D <td> <!--GUI-->N <td> <!--Params-->Y <td> <!--Struct-->Y <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->none <td> <!--Comments--> Structure learning <tr> <td><a href=http://www.hypergraph.dk/ > MIM</a> <td> HyperGraph Software <td> N <td> N <td> W <td> G <td> Y <td> Y <td> Y <td> N <td> $ <td> CG <td> Jtree <td> Up to 52 variables. <tr> <td><a href=http://research.microsoft.com/adapt/MSBNx/ > MSBNx</a> <td> Microsoft <td> N <td> Y <td> W <td> D <td> W <td> N <td> N <td> Y <td> 0 <td> D <td> Jtree <td> - <tr> <td><a href=http://www.norsys.com > Netica</a> <td> Norsys <td> N <td> WUM <td> W <td> G <td> W <td> Y <td> N <td> Y <td> $ <td> D <td> jtree <td> - <tr> <td> <!--Name--> <a href="http://www.autonlab.org/autonweb/showSoftware/149/">Optimal Reinsertion</a> <td> <!--Authors-->Moore, Wong (CMU) <td> <!--Src-->N <td> <!--API-->N <td> <!--Exec-->W,U <td> <!--Cts-->D <td> <!--GUI-->N <td> <!--Params-->Y <td> <!--Struct-->Y <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->none <td> <!--Comments-->structure learning <tr> <td> <!--Name--> <a href="http://people.bu.edu/vladimir/pmt/index.html">PMT</a> <td> <!--Authors-->Pavlovic (BU) <td> <!--Src-->Matlab/C <td> <!--API-->- <td> <!--Exec-->- <td> <!--Cts-->D <td> <!--GUI-->N <td> <!--Params-->Y <td> <!--Struct-->N <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->special purpose <td> <!--Comments-->- <tr> <td> <!--Name--> <a href=http://www.intel.com/research/mrl/pnl/>PNL</a> <td> <!--Authors-->Eruhimov (Intel) <td> <!--Src-->C++ <td> <!--API-->- <td> <!--Exec-->- <td> <!--Cts-->D <td> <!--GUI-->N <td> <!--Params-->Y <td> <!--Struct-->Y <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->U,D <td> <!--Inference-->Jtree <td> <!--Comments--> A C++ version of BNT; will be released 12/03. <tr> <td><a href=http://iridia.ulb.ac.be/pulcinella/Welcome.html > Pulcinella</a> <td> IRIDIA <td> Lisp <td> Y <td> WUM <td> D <td> Y <td> N <td> N <td> N <td> 0 <td> D <td> ? <td> Uses valuation systems for non-probabilistic calculi. <tr> <!-- http://civil.colorado.edu/~dodier/sonero-mirror/index.html --> <td><a href=http://sourceforge.net/projects/riso>RISO</a> <td> Dodier (U.Colorado) <td> Java <td> Y <td> WUM <td> G <td> Y <td> N <td> N <td> N <td> 0 <td> D <td> Polytree <td> Distributed implementation. <tr> <td> <!--Name--> <a href=http://reasoning.cs.ucla.edu/samiam/> Sam Iam</a> <td> <!--Authors-->Darwiche (UCLA) <td> <!--Src-->N <td> <!--API-->N ? <td> <!--Exec-->WU ? (Java executable) <td> <!--Cts-->G ? <td> <!--GUI-->Y <td> <!--Params-->Y <td> <!--Struct-->N ? <td> <!--Utility-->Y <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->Recursive conditioning <td> <!--Comments-->Also does sensitivity Analysis <tr> <td><a href=http://www.phil.cmu.edu/tetrad/>Tetrad</a> <td> CMU <td> N <td> N <td> WU <td> G <td> N <td> Y <td> CI <td> N <td> 0 <td> U,D <td> None <td> - <tr> <td> <!--Name--> <a href="https://sourceforge.net/projects/unbbayes/">UnBBayes</a> <td> <!--Authors-->? <td> <!--Src-->Java <td> <!--API-->- <td> <!--Exec-->- <td> <!--Cts-->D <td> <!--GUI-->Y <td> <!--Params-->N <td> <!--Struct-->Y <td> <!--Utility-->N <td> <!--Free-->0 <td> <!--Undir-->D <td> <!--Inference-->jtree <td> <!--Comments-->K2 for struct learning <tr> <td><a href=http://www.inference.phy.cam.ac.uk/jmw39/>Vibes</a> <td> Winn & Bishop (U. Cambridge) <td> Java <td> Y <td> WU <td> Cx <td> Y <td> Y <td> N <td> N <td> 0 <td> D <td> Variational <td> Not yet available. <tr> <td><a href=http://snowhite.cis.uoguelph.ca/faculty_info/yxiang/ww3/> Web Weaver</a> <td> Xiang (U.Regina) <td> Java <td> Y <td> WUM <td> D <td> Y <td> N <td> N <td> Y <td> 0 <td> D <td> ? <td> - <tr> <td><a href=http://research.microsoft.com/~dmax/WinMine/tooldoc.htm > WinMine</a> <td> Microsoft <td> N <td> N <td> W <td> Cx <td> Y <td> Y <td> Y <td> N <td> 0 <td> U,D <td> None <td> Learns BN or dependency net structure. <tr> <td><a href=http://www.staff.city.ac.uk/~rgc/webpages/xbpage.html > XBAIES 2.0</a> <td> Cowell (City U.) <td> N <td> N <td> W <td> G <td> Y <td> Y <td> N <td> Y <td> 0 <td> CG <td> Jtree <td> - <tr> </table> <p> <h2>Other sites related to (software for) graphical models</h2> <ul> <li> <a href="http://directory.google.com/Top/Computers/Artificial_Intelligence/Belief_Networks/Software/"> Google's list</a> of Bayes net software. <!-- <li> <a href="http://www.sis.pitt.edu/~dsl/da-software.html"> Decision analysis programs</a>, list maintained by Marek Druzdzel. --> <li> <a href="http://www.cs.cmu.edu/~lorens/papers/mscthesis.html"> Comparison of decision analysis software packages</a> by Håkan L. Younes. The emphasis is on real-time decision making. <li> <a href="http://bayes.stat.washington.edu/almond/belief.html"> Older belief net programs</a> (c 1996), a list created (but no longer maintained) by Russ Almond. <li> <a href="http://www.cs.huji.ac.il/labs/compbio/Repository"> Repository of Bayes nets</a>. </document>