# The code below implements a HMM state and symbol sequence simulator.
# You may want to change the data structures used for emission/transition matrices and the state/symbol sequences/names.
# Changes like this would require small changes to the code.
# also note that the start state s needs to be randomly chosen outside of the simulate_HMM method.
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import numpy as np
import pandas
# Transition matrix a, emission matrix e, number of simulations n, starting state s
def simulate_HMM(a, e, n, s):
symbols = []
states = []
for i in range(n):
symbolEmitted = np.random.choice(list(e.T.index), 1, p = list(e.T[s]))[0]
symbols.append(symbolEmitted)
states.append(s)
s = np.random.choice(list(a.T.columns), 1, p = list(a.T[s]))[0]
return “”.join(symbols), “”.join(states)
stateNames = list(“HST”)
symbolNames = list(“BIN”)
# Will transpose the matrices for easier access to rows (which are now columns)
transitionMatrix = pandas.DataFrame(np.matrix(‘0.33 0.33 0.34; 0.33 0.33 0.34; 0.33 0.33 0.34’), index=stateNames, columns=stateNames)
emissionMatrix = pandas.DataFrame(np.matrix(‘0.33 0.33 0.34; 0.33 0.33 0.34; 0.33 0.33 0.34’), index=stateNames, columns=symbolNames)
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