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Hi,
I was trying seqlearn for a realistic problem and the HMM performance was much worse than a structured perceptron (1% vs ~30% F-score). Thinking something was wrong I even tried the implementation in NLTK which performs almost as well as the perceptron.
Upon inspecting the learned parameters I find unexpected results, while NLTK looked sensible. After going through the calculation step by step I think the problem is this; with this patch I get good performance.
I should write a failing test to actually verify that this is correct, and I will try to do so, but it might take a while to find the time...