I am using LDA in mallet to explore my data. I do not have any problem with running, just I need to have the probability of top words (let's say 20 words)
I use this query:
bin\mallet train-topics --input tutorial.mallet --num-topics 40 --optimize-interval 20 --output-state topic-state_doc_40t.gz --output-topic-keys tutorial_keys_doc_40t.txt --output-doc-topics tutorial_composition_doc_40t.txt
I do not know what would be the query for words' probabilities.
Late answer, but who knows, it might help someone else.
MALLET 2.0.8 has a new feature to output a very interesting diagnostics file containing a bunch of metrics for each topic and its top words. Word probability is one of them.
Simply add --diagnostics-file FILENAME to your train-topics command.
Number of words described for each topic is the same than defined by "--num-top-words".
Here is the link to a detailed documentation: http://mallet.cs.umass.edu/diagnostics.php. If you don't want to re-train your topic, you can output the diagnostics file anyway by using your "state" file. Everything is described in the link.