biperscan 0.1.0

Bi-Persistence Clustering for Applications with Noise.

Bi-Persistence Clustering of Applications with Noise

biperscan adapts HDBSCAN* to extract clusters from bi-filtrations over a distance scale and an centrality scale (other lens-dimensions are untested but might work as well). This type of clustering is particularly useful for detecting (lower-density) branches in a datasets. Such branches are difficult to detect with clustering algorithms because they are connected to a central core with short distances. In other words, there is no gap or low-density region between branches and the central core, so distance-based clustering algorithms cannot detect them. The bi-filtration effectively introduces a gap between the branches by filtering out points with a varying centrality threshold, allowing the branches to be detected as separate connected components (i.e., clusters).

While biperscan is implemented to be fast, it does not scale nicely with data size. For practical applications, we instead recommend pyflasc: our more efficient branch & cluster detection algorithm. The main difference is that pyflasc first extracts HDBSCAN clusters and then extracts branches within the clusters, rather than trying to detect both at the same time. This results in two fast filtrations, instead of one expensive bi-filtration.

How to use BPSCAN

biperscan's API based on the hdbscan package and supports a similar API:

import numpy as np
import matplotlib.pyplot as plt

from biperscan import BPSCAN

data = np.load("./notebooks/data/flared/flared_clusterable_data.npy")

clusterer = BPSCAN(
    lens='negative_distance_to_median', # the lens function to use
    metric='euclidean',                 # same as in HDBSCAN
    min_samples=20,                     # same as in HDBSCAN
    min_cluster_size=80,                # same as in HDBSCAN
    distance_fraction=0.05,             # suppress noise at lower values
).fit(data)

plt.figure()
plt.scatter(
    *data.T, c=clusterer.labels_ % 20, s=5, alpha=0.5, 
    edgecolor="none", cmap="tab20", vmin=0, vmax=19
)
plt.axis("off")
plt.show()

The labelling can be re-computed with a different depth limit using clusterer.labels_at_depth(2) or accessing the clusterer.membership_ property which lists all detected (but overlapping) subgroups. biperscan does not (yet) support weighted cluster membership.

Example Notebooks

A notebook demonstrating how the algorithm works is available at How BPSCAN Works. The other notebooks demonstrate the algorithm on several data sets and contain additional analyses.

Installing

Binary wheels (for x86_64) are available on PyPI. Presuming you have an up-to-date pip:

pip install biperscan

For a manual install of the latest code directly from GitHub:

pip install --upgrade git+https://github.com/vda-lab/biperscan.git#egg=biperscan

The repository contains C++23 code so a suitable compiler is required to install from source. The code is tested to compile with MSVC (build tools version 17), GCC-14 and clang-19.

Citing

To credit this software please cite the Zenodo DOI: ... (TODO).

Licensing

The biperscan package has a 3-Clause BSD license.