Test in Python 3.12

pykda (you say "pie-k-d-a") is a Python package for the Kemeny Decomposition Algorithm (KDA) which allows to decompose a Markov chain into clusters of states, where states within a cluster are relatively more connected to each other than states outside the cluster. This is useful for analyzing influence graphs, such as social networks and internet networks. KDA was developed in the paper from Berkhout and Heidergott (2019) and uses the Kemeny constant as a connectivity measure.

Installing `pykda`

Package pykda depends on numpy, tarjan and pyvis. Use the package manager pip to install PyKDA

pip install pykda

Getting started

The first step is to load a Markov chain as a MarkovChain object using a transition matrix P.

from pykda.Markov_chain import MarkovChain

P = [[0, 0.3, 0.7, 0, 0],
     [0.7, 0.2, 0.1, 0, 0],
     [0.5, 0.25, 0.25, 0, 0],
     [0, 0, 0, 0.5, 0.5],
     [0, 0, 0, 0.75, 0.25]]  # artificial transition matrix
MC = MarkovChain(P)

We can study some properties of the Markov chain, such as the stationary distribution:

print(MC.stationary_distribution.flatten())

This gives [0.226 0.156 0.23 0.232 0.156]. We can also plot the Markov chain:

MC.plot(file_name="An artificial Markov chain")

Now, let us decompose the Markov chain into clusters using KDA. We start by initializing a KDA object using the Markov chain and the KDA settings (such as the number of clusters). For more details about setting choices, see the KDA documentation or Berkhout and Heidergott (2019). Here, we apply the default settings, which is to cut all edges with a negative Kemeny constant derivative and normalizing the transition matrix afterward.

kda = KDA(
    original_MC=MC, CO_A="CO_A_1(1)", CO_B="CO_B_3(0)", symmetric_cut=False
    )

Now, let us run the KDA algorithm and visualize the results.

kda.run()
kda.plot(file_name="An artificial Markov chain after KDA_A1_1_B3_0")

We can study the resulting Markov chain in more detail via the current Markov chain attribute MC of the KDA object.

print(kda.MC)

This gives the following output:

MC with 5 states.
Ergodic classes: [[2, 0], [3]].
Transient classes: [[1], [4]].

So KDA led to a Markov multi-chain with two ergodic classes and two transient classes. We can also study the edges that KDA cut via the log attribute of the KDA object.

print(kda.log['edges cut'])

This gives the following output:

[[None], [(4, 0), (1, 4), (2, 1), (0, 1), (3, 4)]]

We can also study the Markov chains that KDA found in each (outer) iteration via kda.log['Markov chains'])`.

As another KDA application example, let us apply KDA until we find two ergodic classes explicitly. We will also ensure that the Kemeny constant derivatives are recalculated after each cut (and normalize the cut transition matrix to ensure it is a stochastic matrix again). To that end, we use:

kda2 = KDA(
    original_MC=MC, CO_A="CO_A_2(2)", CO_B="CO_B_1(1)", symmetric_cut=False
    )
kda2.run()
kda2.plot(file_name="An artificial Markov chain after KDA_A2_2_B1_1")

which gives (edges (4, 0) and (1, 4) are cut in two iterations):

How to learn more about `pykda`?

To learn more about pykda have a look at the documentation. There, you can also find links to interactive Google Colab notebooks in examples. If you have any questions, feel free to open an issue here on Github Issues.

How to cite `pykda`?

If you use pykda in your research, please consider citing the following paper:

Joost Berkhout, Bernd F. Heidergott (2019). Analysis of Markov influence graphs. Operations Research, 67(3):892-904. https://doi.org/10.1287/opre.2018.1813

Or, using the following BibTeX entry:

@article{Berkhout_Heidergott_2019,
	title = {Analysis of {Markov} influence graphs},
	volume = {67},
	number = {3},
	journal = {Operations Research},
	author = {Berkhout, J. and Heidergott, B. F.},
	year = {2019},
	pages = {892--904},
}

joostberkhout / pykda Goto Github PK

pykda's Introduction

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