Is there any API for building bayesian networks of influence diagram with java?
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It's not free, but Norsys Netica has a Java API. It's not pretty, either.
http://www.norsys.com/netica-j.html
I've found two influence diagram engines with Java API which are free & open source:
http://genie.sis.pitt.edu/
http://sourceforge.net/projects/unbbayes/
From the Jayes website: