clusopt-core 1.0.0

Clustream, Streamkm++ and metrics utilities C/C++ bindings for python

ClusOpt Core

This package is used by ClusOpt for it's CPU intensive tasks, but it can be easily imported in any python data stream clustering project, it is coded mainly in C/C++ with bindings for python, and features:

• CluStream (based on MOA implementation)
• StreamKM++ (wrapped around the original paper authors implementation)
• Distance Matrix computation (in place implementation using boost threads)
• Silhouette score (custom in place implementation inspired by BIRCH clustering vector)

Prerequisites

• python >= 3.6
• pip
• boost-thread
• gcc >= 6

boost-thread can be installed in Debian based systems with :

apt install libboost-thread-dev

Usage

See examples folder for more.

CluStream online clustering

from clusopt_core.cluster import CluStream
from sklearn.datasets import make_blobs
import numpy as np
import matplotlib.pyplot as plt

k = 32

dataset, _ = make_blobs(n_samples=64000, centers=k, random_state=42, cluster_std=0.1)

model = CluStream(
    m=k * 10,  # no microclusters
    h=64000,  # horizon
    t=2,  # radius factor
)

chunks = np.split(dataset, len(dataset) / 4000)

model.init_offline(chunks.pop(0), seed=42)

for chunk in chunks:
    model.partial_fit(chunk)

clusters, _ = model.get_macro_clusters(k, seed=42)

plt.scatter(*dataset.T, marker=",", label="datapoints")

plt.scatter(*model.get_partial_cluster_centers().T, marker=".", label="microclusters")

plt.scatter(*clusters.T, marker="x", label="macro clusters", color="black")

plt.legend()
plt.show()

output:

Benchmarks

Some functions in clusopt_core are faster than scikit learn implementations, see the benchmark folder for more info.

Silhouette

Each bar have a tuple of (no_samples,dimension,no_groups), so independently of those 3 factors, clusopt implementation is faster.

Distance Matrix

Each bar shows the dataset dimension, so clusopt_core implemetation is faster when the dataset dimension is small (<~150), even when using 4 processes in scikit-learn.

Installation

You can install it directly from pypi with

pip install clusopt-core

or you can clone this repo and install from the directory

pip install ./clusopt_core

Acknowledgments

Thanks to:

• Marcel R. Ackermann et al. for the StreamKM++ algorithm - link
• The university of Waikato for the MOA framework - link