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# dougalsutherland/example.hmm Created Nov 1, 2011

Code for a Hidden Markov Model, along with some sample data / parameters for testing.
 4 # number of states START COLD HOT END 3 # size of vocab 1 2 3 # transition matrix 0.0 0.5 0.5 0.0 # from start 0.0 0.8 0.1 0.1 # from cold 0.0 0.1 0.8 0.1 # from hot 0.0 0.0 0.0 1.0 # from end # emission matrix 0.0 0.0 0.0 # from start 0.7 0.2 0.1 # from cold 0.1 0.2 0.7 # from hot 0.0 0.0 0.0 # from end
 #!/usr/bin/env python """ CS 65 Lab #3 -- 5 Oct 2008 Dougal Sutherland Implements a hidden Markov model, based on Jurafsky + Martin's presentation, which is in turn based off work by Jason Eisner. We test our program with data from Eisner's spreadsheets. """ identity = lambda x: x class HiddenMarkovModel(object): """A hidden Markov model.""" def __init__(self, states, transitions, emissions, vocab): """ states - a list/tuple of states, e.g. ('start', 'hot', 'cold', 'end') start state needs to be first, end state last states are numbered by their order here transitions - the probabilities to go from one state to another transitions[from_state][to_state] = prob emissions - the probabilities of an observation for a given state emissions[state][observation] = prob vocab: a list/tuple of the names of observable values, in order """ self.states = states self.real_states = states[1:-1] self.start_state = 0 self.end_state = len(states) - 1 self.transitions = transitions self.emissions = emissions self.vocab = vocab # functions to get stuff one-indexed state_num = lambda self, n: self.states[n] state_nums = lambda self: xrange(1, len(self.real_states) + 1) vocab_num = lambda self, n: self.vocab[n - 1] vocab_nums = lambda self: xrange(1, len(self.vocab) + 1) num_for_vocab = lambda self, s: self.vocab.index(s) + 1 def transition(self, from_state, to_state): return self.transitions[from_state][to_state] def emission(self, state, observed): return self.emissions[state][observed - 1] # helper stuff def _normalize_observations(self, observations): return [None] + [self.num_for_vocab(o) if o.__class__ == str else o for o in observations] def _init_trellis(self, observed, forward=True, init_func=identity): trellis = [ [None for j in range(len(observed))] for i in range(len(self.real_states) + 1) ] if forward: v = lambda s: self.transition(0, s) * self.emission(s, observed[1]) else: v = lambda s: self.transition(s, self.end_state) init_pos = 1 if forward else -1 for state in self.state_nums(): trellis[state][init_pos] = init_func( v(state) ) return trellis def _follow_backpointers(self, trellis, start): # don't bother branching pointer = start[0] seq = [pointer, self.end_state] for t in reversed(xrange(1, len(trellis[1]))): val, backs = trellis[pointer][t] pointer = backs[0] seq.insert(0, pointer) return seq # actual algorithms def forward_prob(self, observations, return_trellis=False): """ Returns the probability of seeing the given `observations` sequence, using the Forward algorithm. """ observed = self._normalize_observations(observations) trellis = self._init_trellis(observed) for t in range(2, len(observed)): for state in self.state_nums(): trellis[state][t] = sum( self.transition(old_state, state) * self.emission(state, observed[t]) * trellis[old_state][t-1] for old_state in self.state_nums() ) final = sum(trellis[state][-1] * self.transition(state, -1) for state in self.state_nums()) return (final, trellis) if return_trellis else final def backward_prob(self, observations, return_trellis=False): """ Returns the probability of seeing the given `observations` sequence, using the Backward algorithm. """ observed = self._normalize_observations(observations) trellis = self._init_trellis(observed, forward=False) for t in reversed(range(1, len(observed) - 1)): for state in self.state_nums(): trellis[state][t] = sum( self.transition(state, next_state) * self.emission(next_state, observed[t+1]) * trellis[next_state][t+1] for next_state in self.state_nums() ) final = sum(self.transition(0, state) * self.emission(state, observed[1]) * trellis[state][1] for state in self.state_nums()) return (final, trellis) if return_trellis else final def viterbi_sequence(self, observations, return_trellis=False): """ Returns the most likely sequence of hidden states, for a given sequence of observations. Uses the Viterbi algorithm. """ observed = self._normalize_observations(observations) trellis = self._init_trellis(observed, init_func=lambda val: (val, [0])) for t in range(2, len(observed)): for state in self.state_nums(): emission_prob = self.emission(state, observed[t]) last = [(old_state, trellis[old_state][t-1][0] * \ self.transition(old_state, state) * \ emission_prob) for old_state in self.state_nums()] highest = max(last, key=lambda p: p[1])[1] backs = [s for s, val in last if val == highest] trellis[state][t] = (highest, backs) last = [(old_state, trellis[old_state][-1][0] * \ self.transition(old_state, self.end_state)) for old_state in self.state_nums()] highest = max(last, key = lambda p: p[1])[1] backs = [s for s, val in last if val == highest] seq = self._follow_backpointers(trellis, backs) return (seq, trellis) if return_trellis else seq def train_on_obs(self, observations, return_probs=False): """ Trains the model once, using the forward-backward algorithm. This function returns a new HMM instance rather than modifying this one. """ observed = self._normalize_observations(observations) forward_prob, forwards = self.forward_prob( observations, True) backward_prob, backwards = self.backward_prob(observations, True) # gamma values prob_of_state_at_time = posat = [None] + [ [0] + [forwards[state][t] * backwards[state][t] / forward_prob for t in range(1, len(observations)+1)] for state in self.state_nums()] # xi values prob_of_transition = pot = [None] + [ [None] + [ [0] + [forwards[state1][t] * self.transition(state1, state2) * self.emission(state2, observed[t+1]) * backwards[state2][t+1] / forward_prob for t in range(1, len(observations))] for state2 in self.state_nums()] for state1 in self.state_nums()] # new transition probabilities trans = [[0 for j in range(len(self.states))] for i in range(len(self.states))] trans[self.end_state][self.end_state] = 1 for state in self.state_nums(): state_prob = sum(posat[state]) trans[0][state] = posat[state][1] trans[state][-1] = posat[state][-1] / state_prob for oth in self.state_nums(): trans[state][oth] = sum(pot[state][oth]) / state_prob # new emission probabilities emit = [[0 for j in range(len(self.vocab))] for i in range(len(self.states))] for state in self.state_nums(): for output in range(1, len(self.vocab) + 1): n = sum(posat[state][t] for t in range(1, len(observations)+1) if observed[t] == output) emit[state][output-1] = n / sum(posat[state]) trained = HiddenMarkovModel(self.states, trans, emit, self.vocab) return (trained, posat, pot) if return_probs else trained # ====================== # = reading from files = # ====================== def normalize(string): if '#' in string: string = string[:string.index('#')] return string.strip() def make_hmm_from_file(f): def nextline(): line = f.readline() if line == '': # EOF return None else: return normalize(line) or nextline() n = int(nextline()) states = [nextline() for i in range(n)] # <3 list comprehension abuse num_vocab = int(nextline()) vocab = [nextline() for i in range(num_vocab)] transitions = [[float(x) for x in nextline().split()] for i in range(n)] emissions = [[float(x) for x in nextline().split()] for i in range(n)] assert nextline() is None return HiddenMarkovModel(states, transitions, emissions, vocab) def read_observations_from_file(f): return filter(lambda x: x, [normalize(line) for line in f.readlines()]) # ========= # = tests = # ========= import unittest class TestHMM(unittest.TestCase): def setUp(self): # it's complicated to pass args to a testcase, so just use globals self.hmm = make_hmm_from_file(file(HMM_FILENAME)) self.obs = read_observations_from_file(file(OBS_FILENAME)) def test_forward(self): prob, trellis = self.hmm.forward_prob(self.obs, True) self.assertAlmostEqual(prob, 9.1276e-19, 21) self.assertAlmostEqual(trellis[1][1], 0.1, 4) self.assertAlmostEqual(trellis[1][3], 0.00135, 5) self.assertAlmostEqual(trellis[1][6], 8.71549e-5, 9) self.assertAlmostEqual(trellis[1][13], 5.70827e-9, 9) self.assertAlmostEqual(trellis[1][20], 1.3157e-10, 14) self.assertAlmostEqual(trellis[1][27], 3.1912e-14, 13) self.assertAlmostEqual(trellis[1][33], 2.0498e-18, 22) self.assertAlmostEqual(trellis[2][1], 0.1, 4) self.assertAlmostEqual(trellis[2][3], 0.03591, 5) self.assertAlmostEqual(trellis[2][6], 5.30337e-4, 8) self.assertAlmostEqual(trellis[2][13], 1.37864e-7, 11) self.assertAlmostEqual(trellis[2][20], 2.7819e-12, 15) self.assertAlmostEqual(trellis[2][27], 4.6599e-15, 18) self.assertAlmostEqual(trellis[2][33], 7.0777e-18, 22) def test_backward(self): prob, trellis = self.hmm.backward_prob(self.obs, True) self.assertAlmostEqual(prob, 9.1276e-19, 21) self.assertAlmostEqual(trellis[1][1], 1.1780e-18, 22) self.assertAlmostEqual(trellis[1][3], 7.2496e-18, 22) self.assertAlmostEqual(trellis[1][6], 3.3422e-16, 20) self.assertAlmostEqual(trellis[1][13], 3.5380e-11, 15) self.assertAlmostEqual(trellis[1][20], 6.77837e-9, 14) self.assertAlmostEqual(trellis[1][27], 1.44877e-5, 10) self.assertAlmostEqual(trellis[1][33], 0.1, 4) self.assertAlmostEqual(trellis[2][1], 7.9496e-18, 22) self.assertAlmostEqual(trellis[2][3], 2.5145e-17, 21) self.assertAlmostEqual(trellis[2][6], 1.6662e-15, 19) self.assertAlmostEqual(trellis[2][13], 5.1558e-12, 16) self.assertAlmostEqual(trellis[2][20], 7.52345e-9, 14) self.assertAlmostEqual(trellis[2][27], 9.66609e-5, 9) self.assertAlmostEqual(trellis[2][33], 0.1, 4) def test_viterbi(self): path, trellis = self.hmm.viterbi_sequence(self.obs, True) self.assertEqual(path, [0] + [2]*13 + [1]*14 + [2]*6 + [3]) self.assertAlmostEqual(trellis[1][1] [0], 0.1, 4) self.assertAlmostEqual(trellis[1][6] [0], 5.62e-05, 7) self.assertAlmostEqual(trellis[1][7] [0], 4.50e-06, 8) self.assertAlmostEqual(trellis[1][16][0], 1.99e-09, 11) self.assertAlmostEqual(trellis[1][17][0], 3.18e-10, 12) self.assertAlmostEqual(trellis[1][23][0], 4.00e-13, 15) self.assertAlmostEqual(trellis[1][25][0], 1.26e-13, 15) self.assertAlmostEqual(trellis[1][29][0], 7.20e-17, 19) self.assertAlmostEqual(trellis[1][30][0], 1.15e-17, 19) self.assertAlmostEqual(trellis[1][32][0], 7.90e-19, 21) self.assertAlmostEqual(trellis[1][33][0], 1.26e-19, 21) self.assertAlmostEqual(trellis[2][ 1][0], 0.1, 4) self.assertAlmostEqual(trellis[2][ 4][0], 0.00502, 5) self.assertAlmostEqual(trellis[2][ 6][0], 0.00045, 5) self.assertAlmostEqual(trellis[2][12][0], 1.62e-07, 9) self.assertAlmostEqual(trellis[2][18][0], 3.18e-12, 14) self.assertAlmostEqual(trellis[2][19][0], 1.78e-12, 14) self.assertAlmostEqual(trellis[2][23][0], 5.00e-14, 16) self.assertAlmostEqual(trellis[2][28][0], 7.87e-16, 18) self.assertAlmostEqual(trellis[2][29][0], 4.41e-16, 18) self.assertAlmostEqual(trellis[2][30][0], 7.06e-17, 19) self.assertAlmostEqual(trellis[2][33][0], 1.01e-18, 20) def test_learning_probs(self): trained, gamma, xi = self.hmm.train_on_obs(self.obs, True) self.assertAlmostEqual(gamma[1][1], 0.129, 3) self.assertAlmostEqual(gamma[1][3], 0.011, 3) self.assertAlmostEqual(gamma[1][7], 0.022, 3) self.assertAlmostEqual(gamma[1][14], 0.887, 3) self.assertAlmostEqual(gamma[1][18], 0.994, 3) self.assertAlmostEqual(gamma[1][23], 0.961, 3) self.assertAlmostEqual(gamma[1][27], 0.507, 3) self.assertAlmostEqual(gamma[1][33], 0.225, 3) self.assertAlmostEqual(gamma[2][1], 0.871, 3) self.assertAlmostEqual(gamma[2][3], 0.989, 3) self.assertAlmostEqual(gamma[2][7], 0.978, 3) self.assertAlmostEqual(gamma[2][14], 0.113, 3) self.assertAlmostEqual(gamma[2][18], 0.006, 3) self.assertAlmostEqual(gamma[2][23], 0.039, 3) self.assertAlmostEqual(gamma[2][27], 0.493, 3) self.assertAlmostEqual(gamma[2][33], 0.775, 3) self.assertAlmostEqual(xi[1][1][1], 0.021, 3) self.assertAlmostEqual(xi[1][1][12], 0.128, 3) self.assertAlmostEqual(xi[1][1][32], 0.13, 3) self.assertAlmostEqual(xi[2][1][1], 0.003, 3) self.assertAlmostEqual(xi[2][1][22], 0.017, 3) self.assertAlmostEqual(xi[2][1][32], 0.095, 3) self.assertAlmostEqual(xi[1][2][4], 0.02, 3) self.assertAlmostEqual(xi[1][2][16], 0.018, 3) self.assertAlmostEqual(xi[1][2][29], 0.010, 3) self.assertAlmostEqual(xi[2][2][2], 0.972, 3) self.assertAlmostEqual(xi[2][2][12], 0.762, 3) self.assertAlmostEqual(xi[2][2][28], 0.907, 3) def test_learning_results(self): trained = self.hmm.train_on_obs(self.obs) tr = trained.transition self.assertAlmostEqual(tr(0, 0), 0, 5) self.assertAlmostEqual(tr(0, 1), 0.1291, 4) self.assertAlmostEqual(tr(0, 2), 0.8709, 4) self.assertAlmostEqual(tr(0, 3), 0, 4) self.assertAlmostEqual(tr(1, 0), 0, 5) self.assertAlmostEqual(tr(1, 1), 0.8757, 4) self.assertAlmostEqual(tr(1, 2), 0.1090, 4) self.assertAlmostEqual(tr(1, 3), 0.0153, 4) self.assertAlmostEqual(tr(2, 0), 0, 5) self.assertAlmostEqual(tr(2, 1), 0.0925, 4) self.assertAlmostEqual(tr(2, 2), 0.8652, 4) self.assertAlmostEqual(tr(2, 3), 0.0423, 4) self.assertAlmostEqual(tr(3, 0), 0, 5) self.assertAlmostEqual(tr(3, 1), 0, 4) self.assertAlmostEqual(tr(3, 2), 0, 4) self.assertAlmostEqual(tr(3, 3), 1, 4) em = trained.emission self.assertAlmostEqual(em(0, 1), 0, 4) self.assertAlmostEqual(em(0, 2), 0, 4) self.assertAlmostEqual(em(0, 3), 0, 4) self.assertAlmostEqual(em(1, 1), 0.6765, 4) self.assertAlmostEqual(em(1, 2), 0.2188, 4) self.assertAlmostEqual(em(1, 3), 0.1047, 4) self.assertAlmostEqual(em(2, 1), 0.0584, 4) self.assertAlmostEqual(em(2, 2), 0.4251, 4) self.assertAlmostEqual(em(2, 3), 0.5165, 4) self.assertAlmostEqual(em(3, 1), 0, 4) self.assertAlmostEqual(em(3, 2), 0, 4) self.assertAlmostEqual(em(3, 3), 0, 4) # train 9 more times for i in range(9): trained = trained.train_on_obs(self.obs) tr = trained.transition self.assertAlmostEqual(tr(0, 0), 0, 4) self.assertAlmostEqual(tr(0, 1), 0, 4) self.assertAlmostEqual(tr(0, 2), 1, 4) self.assertAlmostEqual(tr(0, 3), 0, 4) self.assertAlmostEqual(tr(1, 0), 0, 4) self.assertAlmostEqual(tr(1, 1), 0.9337, 4) self.assertAlmostEqual(tr(1, 2), 0.0663, 4) self.assertAlmostEqual(tr(1, 3), 0, 4) self.assertAlmostEqual(tr(2, 0), 0, 4) self.assertAlmostEqual(tr(2, 1), 0.0718, 4) self.assertAlmostEqual(tr(2, 2), 0.8650, 4) self.assertAlmostEqual(tr(2, 3), 0.0632, 4) self.assertAlmostEqual(tr(3, 0), 0, 4) self.assertAlmostEqual(tr(3, 1), 0, 4) self.assertAlmostEqual(tr(3, 2), 0, 4) self.assertAlmostEqual(tr(3, 3), 1, 4) em = trained.emission self.assertAlmostEqual(em(0, 1), 0, 4) self.assertAlmostEqual(em(0, 2), 0, 4) self.assertAlmostEqual(em(0, 3), 0, 4) self.assertAlmostEqual(em(1, 1), 0.6407, 4) self.assertAlmostEqual(em(1, 2), 0.1481, 4) self.assertAlmostEqual(em(1, 3), 0.2112, 4) self.assertAlmostEqual(em(2, 1), 0.00016,5) self.assertAlmostEqual(em(2, 2), 0.5341, 4) self.assertAlmostEqual(em(2, 3), 0.4657, 4) self.assertAlmostEqual(em(3, 1), 0, 4) self.assertAlmostEqual(em(3, 2), 0, 4) self.assertAlmostEqual(em(3, 3), 0, 4) if __name__ == '__main__': import sys HMM_FILENAME = sys.argv[1] if len(sys.argv) >= 2 else 'example.hmm' OBS_FILENAME = sys.argv[2] if len(sys.argv) >= 3 else 'observations.txt' unittest.main()
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### Balharbi commented Jul 11, 2018

 Hello, Thanx for sharing, I'm learning python, I want to disengage a stochastic process of 4 states ( start , open , close , end) your work is the most relevant however I couldn't run the code nor I could find (Jurafsky + Martin's presentation) or Jason Eisner , which caused me to disconnect from what the actually the code is doing and what the data represent , I know this is old , but if you kindly could help me with how to get the presentation or the theoretical part , it will be really great , thanx

### Balharbi commented Jul 11, 2018

 where I should put the file names ? inside the code itself ?

### vermaujjwal14 commented Dec 17, 2018

 Sir how can I use Hmm for stemming?