Hi Zhen, For both the forwards and backwards algorithms, you can call them in the same way as viterbi. This will just give you back the score. You can also call them with an explicit dynamic programming matrix. In this case, you get the matrix back with all the values filled in. Both Forward and Backward give you the probability that the sequence was generated in some way (any way) by the model. If you look in the matricies for forwards & backwards, the cells give the probability that the model made all of the sequence up to and including that position (and ending in that state). For the forwards algorithm the probabilities are for all the sequence from the beginning to there, and for backwards it's all the sequence from the end back to there.
Matthew --- "Ren, Zhen" <[EMAIL PROTECTED]> wrote: > Hi, there, > > The three main DP operations are Forwards, Backwards > and Viterbi. Forwards and Backwards calculate the > probability of the sequences having been made in any > way by the model. Viterbi finds the most supported > way that the sequence could have been made. > > I have seen the Dice example that demonstrates how > to use Viterbi algorithm. And I guess it would be > the similar way to use Forward algorithm. However, > it's not like what I thought. Can someone give me a > direction how to use the Forward algorithm in DP > class? Is any tutorial regarding DP and HMM > available? More documentations about DP and HMM > classes in BioJava other than Javadocs are also very > helpful. > > Thank you. > > Zhen > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
