Machine Learning Meetup Notes: 2010-08-18

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[edit] 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)

[edit] 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

[edit] Glen - protein prediction

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)

[edit] 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
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