I found the phrase 'Java bloatware' to be indicative of a certain sentiment towards the language (or JVM environment) in general (as compared to just 'bloatware'). And, given common use cases for machine learning toolkits, the overhead incurred by the JVM doesn't warrant (IMHO) ruling out Java-based options. I must have misread your comment, thanks for clarifying!

I'll have a look at the underlying C++ classes API (http://waffles.sourceforge.net/apidoc/html/index.html).