URF 0.0.5

Unsupervised Random Forest (Random Forest Clustering)

URF (Unsupervised Random Forest, or Random Forest Clustering) is a python implementation of the paper: Shi, T., & Horvath, S. (2006). Unsupervised learning with random forest predictors. Journal of Computational and Graphical Statistics, 15(1), 118-138.

Prerequisite

conda install -c bioconda pycluster

or:

wget http://bonsai.hgc.jp/~mdehoon/software/cluster/Pycluster-1.54.tar.gz
tar -zxvf Pycluster-1.54.tar.gz
cd Pycluster-1.54
python setup.py install

Installation

pip install URF

Usage

from sklearn.datasets import load_iris
from URF.main import random_forest_cluster, plot_cluster_result
iris = load_iris()
X = iris.data
y = iris.target
print(len(list(set(y))))

clf, prox_mat, cluster_ids = random_forest_cluster(X, k=3, max_depth=20, random_state=0)
plot_cluster_result(prox_mat, cluster_ids, marker=y)

If you encountered an error like

> QXcbConnection: Could not connect to display

then you need to add these codes to the very beginning of your file:

import matplotlib as mpl
mpl.use("Agg")

and you must assign the output file when you call plot_cluster_result, like this:

plot_cluster_result(prox_mat, cluster_ids, marker=y, output="test_123.png")