thejkayway/kmodes

Python implementations of the k-modes and k-prototypes clustering algorithms, for clustering categorical data

kmodes

Description

Python implementations of the k-modes and k-prototypes clustering algorithms. Relies on numpy for a lot of the heavy lifting.

k-modes is used for clustering categorical variables. It defines clusters based on the number of matching categories between data points. (This is in contrast to the more well-known k-means algorithm, which clusters numerical data based on Euclidean distance.) The k-prototypes algorithm combines k-modes and k-means and is able to cluster mixed numerical / categorical data.

Implemented are:

• k-modes [HUANG97] [HUANG98]
• k-modes with initialization based on density [CAO09]
• k-prototypes [HUANG97]

The code is modeled after the clustering algorithms in scikit-learn and has the same familiar interface.

I would love to have more people play around with this and give me feedback on my implementation. If you come across any issues in running or installing kmodes, please submit a bug report.

Enjoy!

Installation

kmodes can be installed using pip:

pip install kmodes

To upgrade to the latest version (recommended), run it like this:

pip install --upgrade kmodes

Alternatively, you can build the latest development version from source:

git clone https://github.com/nicodv/kmodes.git
cd kmodes
python setup.py install

Usage

import numpy as np
from kmodes.kmodes import KModes

# random categorical data
data = np.random.choice(20, (100, 10))

km = KModes(n_clusters=4, init='Huang', n_init=5, verbose=1)

clusters = km.fit_predict(data)

# Print the cluster centroids
print(km.cluster_centroids_)

The examples directory showcases simple use cases of both k-modes ('soybean.py') and k-prototypes ('stocks.py').

Missing / unseen data

The k-modes algorithm accepts np.NaN values as missing values in the X matrix. However, users are strongly suggested to consider filling in the missing data themselves in a way that makes sense for the problem at hand. This is especially important in case of many missing values.

The k-modes algorithm currently handles missing data as follows. When fitting the model, np.NaN values are encoded into their own category (let's call it "unknown values"). When predicting, the model treats any values in X that (1) it has not seen before during training, or (2) are missing, as being a member of the "unknown values" category. Simply put, the algorithm treats any missing / unseen data as matching with each other but mismatching with non-missing / seen data when determining similarity between points.

The k-prototypes also accepts np.NaN values as missing values for the categorical variables, but does not accept missing values for the numerical values. It is up to the user to come up with a way of handling these missing data that is appropriate for the problem at hand.

Parallel execution

The k-modes and k-prototypes implementations both offer support for multiprocessing via the joblib library, similar to e.g. scikit-learn's implementation of k-means, using the n_jobs parameter. It generally does not make sense to set more jobs than there are processor cores available on your system.

This potentially speeds up any execution with more than one initialization try, n_init > 1, which may be helpful to reduce the execution time for larger problems. Note that it depends on your problem whether multiprocessing actually helps, so be sure to try that out first. You can check out the examples for some benchmarks.

FAQ

Q: I'm seeing errors such as "TypeError: '<' not supported between instances of 'str' and 'float'" when using the kprototypes algorithm.

A: One or more of your numerical feature columns have string values in them. Make sure that all columns have consistent data types.

---

Q: How does k-protypes know which of my features are numerical and which are categorical?

A: You tell it which column indices are categorical using the categorical argument. All others are assumed numerical. E.g., clusters = KPrototypes().fit_predict(X, categorical=[1, 2])

---

Q: I'm getting the following error, what gives? "ModuleNotFoundError: No module named 'kmodes.kmodes'; 'kmodes' is not a package".

A: Make sure your working file is not called 'kmodes.py', because it might overrule the kmodes package.

---

Q: I'm getting the following error: "ValueError: Clustering algorithm could not initialize. Consider assigning the initial clusters manually."

A: This is a feature, not a bug. kmodes is telling you that it can't make sense of the data you are presenting it. At least, not with the parameters you are setting the algorithm with. It is up to you, the data scientist, to figure out why. Some hints to possible solutions:

• Run with fewer clusters as the data might not support a large number of clusters
• Explore and visualize your data, checking for weird distributions, outliers, etc.
• Clean and normalize the data
• Increase the ratio of rows to columns

---

Q: How would like your library to be cited?

A: Something along these lines would do nicely:

@Misc{devos2015,
  author = {Nelis J. de Vos},
  title = {kmodes categorical clustering library},
  howpublished = {\url{https://github.com/nicodv/kmodes}},
  year = {2015--2021}
}

References

CAO09

Cao, F., Liang, J, Bai, L.: A new initialization method for categorical data clustering, Expert Systems with Applications 36(7), pp. 10223-10228., 2009.

HUANG97

Huang, Z.: Clustering large data sets with mixed numeric and categorical values, Proceedings of the First Pacific Asia Knowledge Discovery and Data Mining Conference, Singapore, pp. 21-34, 1997.

HUANG98

Huang, Z.: Extensions to the k-modes algorithm for clustering large data sets with categorical values, Data Mining and Knowledge Discovery 2(3), pp. 283-304, 1998.