Hi Robin, Isabel and Shannon: Thank you for your responses--I've been learning more about Mahout by reading the code and the wiki, and running the examples.
While I'm still learning about Mahout, I'd like to elaborate further on my ideas: 1) Hidden Markov Models: Applications are, as Shannon mentioned, in Spliced Alignment for Gene Prediction where Viterbi's Algorithm can be applied. The other application, which I'm investigating for the Bioinformatics course project could be to predict the side chain structure of proteins. This has been traditionally done using the rotamer libraries and I think HMMs could be of use there. I've also noticed that the current HMM does not use MapReduce, so one possible project would be to provide that functionality, although it is not trivial... 2) Reinforcement Learning using Markov Decision Process for Recommender Systems: Solve Optimal Control (Planning) and/or Q Learning. For planning problems where transition probabilities and reward function is known in advance, the task remains to solve for optimal policy using the Bellman Ford/Policy Iteration/Matrix Inversion methods. For cases where this information is not available a priori, one can implement the Q Learning algorithm. I'm also curious where Haloop (http://code.google.com/p/haloop/) stands in relation to Mahout because a lot of Machine Learning algorithms are iterative. Any feedback on my approaches are welcome, especially any information on fitting HMM/MDPs with MapReduce. Thank you. Dhruv. On Tue, Feb 15, 2011 at 10:43 AM, Shannon Quinn <[email protected]> wrote: > Hi Dhruv, > > > It would be interesting to see how the current implementation can be > > integrated into your Bioinformatics course work, what extensions you > > need for this particular domain. > > I assume your HMM would be for the purpose of protein/nucleic acid sequence > analysis and alignment. HMMs/MDPs are fairly domain-independent, but this > would definitely be an interesting pursuit; I'm a grad student in comp bio, > and I know a lot of folks who would love to use this. > > On the topic of GSoC, I meant to mention: I'm happy to volunteer my > services as a potential mentor for the summer. > > Shannon > > Apologies for the brevity, this was sent from my iPhone
