Markov Chains#

transition_matrix()#

transition_matrix(sequence, order=1, adjust=True, show=False)[source]#

Transition Matrix

A Transition Matrix (also known as a stochastic matrix or a Markov matrix) is a convenient way of representing and describing a sequence of (discrete) states, also known as discrete Markov chains. Each of its entries is a probability of transitioning from one state to the other.

Note

This function is fairly new and hasn’t be tested extensively. Please help us by double-checking the code and letting us know if everything is correct.

Parameters:
  • sequence (Union[list, np.array, pd.Series]) – A list of discrete states.

  • order (int) – The order of the Markov chain.

  • adjust (bool) – If True, the transition matrix will be adjusted to ensure that the sum of each row is equal to 1. This is useful when the transition matrix is used to represent a probability distribution.

  • show (bool) – Displays the transition matrix heatmap.

Returns:

  • pd.DataFrame – The empirical (observed) transition matrix.

  • dict – A dictionnary containing additional information, such as the Frequency Matrix (fm; accessible via the key "Occurrences"), useful for some tests.

Examples

In [1]: import neurokit2 as nk

In [2]: sequence = ["A", "A", "C", "B", "B", "B", "C", "A", "A", "D"]

In [3]: tm, _ = nk.transition_matrix(sequence, show=True)
savefig/p_transition_matrix1.png
In [4]: tm
Out[4]: 
      A         B         C     D
A  0.50  0.000000  0.250000  0.25
B  0.00  0.666667  0.333333  0.00
C  0.50  0.500000  0.000000  0.00
D  0.25  0.250000  0.250000  0.25

In this example, the transition from D is unknown (it is the last element), resulting in an absence of transitioning probability. As this can cause issues, unknown probabilities are replaced by a uniform distribution, but this can be turned off using the adjust argument.

In [5]: tm, _ = nk.transition_matrix(sequence, adjust=False)

In [6]: tm
Out[6]: 
     A         B         C     D
A  0.5  0.000000  0.250000  0.25
B  0.0  0.666667  0.333333  0.00
C  0.5  0.500000  0.000000  0.00
D  0.0  0.000000  0.000000  0.00

Transition matrix of higher order

In [7]: sequence = ["A", "A", "A", "B", "A", "A", "B", "A", "A", "B"]

In [8]: tm, _ = nk.transition_matrix(sequence, order=2)

In [9]: tm
Out[9]: 
array([[[0.25, 0.75],
        [1.  , 0.  ]],

       [[1.  , 0.  ],
        [0.5 , 0.5 ]]])

markov_simulate()#

markov_simulate(tm, n=10, random_state=None)[source]#

Markov Chain Simulation

Given a transition_matrix(), this function simulates the corresponding sequence of states (also known as a discrete Markov chain).

Parameters:
  • tm (pd.DataFrame) – A probability matrix obtained from transition_matrix().

  • n (int) – Length of the simulated sequence.

  • random_state (None, int, numpy.random.RandomState or numpy.random.Generator) – Seed for the random number generator. See for misc.check_random_state for further information.

Returns:

np.ndarray – Sequence of states.

Examples

In [1]: import neurokit2 as nk

In [2]: sequence = [0, 0, 1, 2, 2, 2, 1, 0, 0, 3]

In [3]: tm, _ = nk.transition_matrix(sequence)

In [4]: x = nk.markov_simulate(tm, n=15)

In [5]: x
Out[5]: array([3, 0, 0, 3, 2, 2, 2, 1, 2, 1, 0, 1, 2, 2, 1])

markov_test_random()#

markov_test_random(fm)[source]#

Is the Markov process random?

This function computes the expected (theoretical) transition matrix if the order of appearance of each state was governed only by their overall prevalence, and that a previous state had no influence on the next state. This “random” matrix is then compered again the observed one, and a Chi2 test is conducted.

If significant (e.g., *p*-value < .05), one can reject the hypothesis that observed Markov process is random, and conclude that past states have an influence on next states.

Parameters:

fm (pd.DataFrame) – A frequency matrix obtained from transition_matrix().

Returns:

dict – Contains indices of the Chi2 test.

Examples

In [1]: import neurokit2 as nk

In [2]: sequence = [0, 0, 1, 2, 2, 2, 1, 0, 0, 3]

In [3]: _, info = nk.transition_matrix(sequence)

In [4]: result = nk.markov_test_random(info["Occurrences"])

In [5]: result["Random_p"]
Out[5]: 0.8815729751590916

markov_test_symmetry()#

markov_test_symmetry(fm)[source]#

Is the Markov process symmetric?

Performs a symmetry test, to test if for instance if the transitions A -> B and B -> A occur with the same probability. If significant (e.g., *p*-value < .05), one can reject the hypothesis that observed Markov process is symmetric, and conclude that it the transition matrix is asymmetric.

Parameters:

fm (pd.DataFrame) – A frequency matrix obtained from transition_matrix().

Returns:

dict – Contains indices of the test.

Examples

In [1]: import neurokit2 as nk

In [2]: sequence = [0, 0, 1, 2, 2, 2, 1, 0, 0, 3]

In [3]: _, info = nk.transition_matrix(sequence)

In [4]: result = nk.markov_test_symmetry(info["Occurrences"])

In [5]: result["Symmetry_p"]
Out[5]: 1.0

References

  • Kullback, S., Kupperman, M., & Ku, H. H. (1962). Tests for contingency tables and Markov chains. Technometrics, 4(4), 573-608.

markov_test_homogeneity()#

markov_test_homogeneity(sequence, size=10)[source]#

Is the Markov process homogeneous?

Performs a homogeneity test that tests the null hypothesis that the samples are homogeneous, i.e., from the same - but unspecified - population, against the alternative hypothesis that at least one pair of samples is from different populations.

Parameters:
  • sequence (Union[list, np.array, pd.Series]) – A list of discrete states.

  • size (int) – The size of the non-overlapping windows to split the sequence.

Returns:

dict – Contains indices of the test.

Examples

In [1]: import neurokit2 as nk

In [2]: sequence = [0, 0, 1, 2, 2, 2, 1, 0, 0, 3]

In [3]: result = nk.markov_test_homogeneity(sequence, size=2)

In [4]: result["Homogeneity_p"]
Out[4]: 0.9999999999999952

References

  • Kullback, S., Kupperman, M., & Ku, H. H. (1962). Tests for contingency tables and Markov chains. Technometrics, 4(4), 573-608.

markov_mixingtime()#

markov_mixingtime(tm)[source]#

Markov Chain Mixing Time

The Mixing time (also known as relaxation time) is the inverse of spectral gap, which is the difference between the two largest eigenvalues of the transition matrix. The Mixing time of a Markov chain tells us how long does it take for a run to go near the stationary distribution (for convergence to happen).

Parameters:

tm (pd.DataFrame) – A transition matrix obtained from transition_matrix().

Returns:

float – Mixing time of the Markov chain.

Examples

In [1]: import neurokit2 as nk

In [2]: sequence = [0, 0, 1, 2, 2, 2, 1, 0, 0, 3]

In [3]: tm, _ = nk.transition_matrix(sequence)

In [4]: nk.markov_mixingtime(tm)
Out[4]: 2.5095870037129875

References

  • Levin, D. A., & Peres, Y. (2017). Markov chains and mixing times (Vol. 107). American Mathematical Society.