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I recently had a homework assignment in my computational biology class to which I had to apply a HMM.
Although I think I understand HMMs, I learn more here manage to apply them to my code.
Basically, I had to apply the to CpG islands in DNA--using observed outcomes to predict hidden states using a transition matrix.
I managed to come fair bet casino problem with a solution that worked fair bet casino problem />I'm not sure how to find the path of highest probability without looking at all the paths, though.
EDIT: I did find a lot of info about the Viterbi algorithm when I was doing the assignment but I was confused as to how it actually gives the best answer.
It seems like Viterbi I was looking at the forward algorithm specifically, I think looks at a specific position, moves forward a position or two, and then decides the "correct" next path increment only having looked at a few subsequent probabilities.
I may be understanding this wrong; is this how the Viterbi works?
One benefit of Hidden Markov Models is that you can generally do what you need without fair bet casino problem all possible paths one by one.
What you are trying to do looks like an expensive way of finding the single most probable path, which you can do by dynamic programming under the name of the Viterbi algorithm - see e.
There are other interesting things covered in documents like this which are not quite the same, such as working out the probabilities for the hidden state at a single position, or at all fair bet casino problem positions.
Very often this involves something called alpha and beta passes, which are a good search term, along with Hidden Markov Models.
There is a large description at with mathematical pseudo-code and what I click at this page is python as well.
Like most of these algorithms, it uses the Markov property that once you know the hidden state at a point you know everything you need to answer questions about that point in fair bet casino problem - you don't need to know the past history.
As in dynamic programming, you work from left to right along the data, using answers computed for output k-1 to work out answers for output k.
What you want to work out at point k, for each state j, is the probability of the observed data up to and including that point, along the most likely path that ends up in state j at point k.
That probability is the product of the probability of the observed data at k given state j, times the probability of the transition from some previous state at time k-1 to j times the probability of all of the observed data up to and including point k-1 given that you ended up at the previous state at time k-1 - this last bit is something you have just computed for time k-1.
That gives you the answer for state j at time k, and you save the previous state that gave you the best answer.
This may look like you are just fiddling around with outputs for k and k-1, but you now have an answer for time k that reflects all the data up to and this web page time k.
You carry this on until k is the last point in your data, at which point you have answers for the probabilities of each final state given all the data.
Pick the go here at this time which gives you the highest probability and then trace all the way back using the info you saved about which previous state in time k-1 you used to compute the probability for data up to k and in state j at time k.
I did find the Viterbi algorithm, but I'm not exactly sure how to apply it.
Additional details are in the question.
Thank you for your answer!
You might also wish to review your notes on alpha-beta passes and consider what you have been asked for.
You don't always want the most likely path.
Sometimes you want estimates of the hidden state at a number of points which come from combining the alpha and beta values.
Provide details and share your research!
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