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Which open-source software (toolbox) do you think is the best for modelling graphical models (e.g. factor graphs), and doing inference on them? (the language doesn't matter)

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Another is the gRain package in R.

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I found LibDai very useful: http://staff.science.uva.nl/~jmooij1/libDAI/

Also Factorie is very easy to use.

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