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2010-08-19T04:22:31Z

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====Mike - HMMs====
HMM used for time series data

Markov Chains: matrix of transition probabilities: a_i_j is prob to go from state i to j
the prob funciton is only a function of the previous state

HMM: example is you are trying to predict the weather based on a diary of someone's ice cream eating habits
hidden state = what you are trying to predict (weather)
obs state: ice cream

3 problems HMMs can solve: Likelihood, Decoding, Training
Likelihood: find all the paths
Decoding: whats the best sequence of hidden states that produce your obs seq (Viterbi Algorithm), which is similar to Maximum Likelihood
Training: Given an obs seq, learn the state transition probs and the emission probs of an HMM (Expectation Maximization, Wells-Baum, Forward-Backward Algorithm)

====Thomas - HMM in R====
three packages:
HMM - doesnt allow for multiple chains
hmm.discnp
msm - allows for time based HMMs vs discrete time steps, you can fit in time inbetween states

====Glen - protein prediction====

[http://www.uniprot.org uniprot.org], fasta

>sp|P69906|HBA_PANPA Hemoglobin subunit alpha OS=Pan paniscus GN=HBA1 PE=1 SV=2
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG
KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP
AVHASLDKFLASVSTVLTSKYR

>sp|P69907|HBA_PANTR Hemoglobin subunit alpha OS=Pan troglodytes GN=HBA1 PE=1 SV=2
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG
KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP
AVHASLDKFLASVSTVLTSKYR

>sp|P01942|HBA_MOUSE Hemoglobin subunit alpha OS=Mus musculus GN=Hba PE=1 SV=2
MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG
KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP
AVHASLDKFLASVSTVLTSKYR

*BLOSUM62 is used for determining probabilities for protein mutation (ie. V -> I is more likely than V -> W)

====Mike - Speech recognition====

*fourier transform takes a wave and turns it into frequencies
*spectogram - time frequency representation
*speech and language processing: daniel jurafsky and james martin

Machine Learning Meetup Notes: 2010-08-18 - Revision history

SpammerHellDontDelete: Created page with '====Mike - HMMs==== HMM used for time series data Markov Chains: matrix of transition probabilities: a_i_j is prob to go from state i to j the prob funciton is only a function…'