Differences between revisions 2 and 11 (spanning 9 versions)

Sage Interactions - Statistics and Probability

Contents

A Random Walk

by William Stein

by Marshall Hampton

Based on the classic example in "Biological Sequence Analysis" by Durbin et al.

-  ⇤ ← Revision 2 as of 2010-04-02 15:28:15 → 
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  Editor: MarshallHampton
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+   ← Revision 11 as of 2012-05-09 04:15:11 → ⇥
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  Editor: jason
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+{{{#!sagecell
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+== Hidden Markov Model: The Occasionally Dishonest Casino ==

by Marshall Hampton

Based on the classic example in "Biological Sequence Analysis" by Durbin et al.

{{{#!sagecell
m = hmm.DiscreteHiddenMarkovModel([[0.8,0.2],[0.1,0.9]], [[1/10,1/10,1/10,1/10,1/10,1/2],[1/6,1/6,1/6,1/6,1/6,1/6]], [.2,.8],emission_symbols=[1,2,3,4,5,6])
@interact
def dishonest_casino(auto_update=False):
    test = list(m.generate_sequence(80))
    vit_test = list(m.viterbi(test[0])[0])
    html('<h3>The Occasionally Dishonest Casino</h3>')
    html('Emissions:'+str(test[0]).replace(',','').replace(' ','')[1:-1])
    vit_str = str(vit_test).replace(',','').replace(' ','')
    vit_str = vit_str.replace('1','F').replace('0','<font color="#FF0000">L</font>')[1:-1]
    html('Viterbi:  '+vit_str)
    actual_str = str(list(test[1])).replace(',','').replace(' ','')
    actual_str = actual_str.replace('1','F').replace('0','<font color="#FF0000">L</font>')[1:-1]
    html('Actual:   '+ actual_str)}}} 
{{attachment:hmm_casino.png}}