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branch-detection paper references #674

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38 changes: 21 additions & 17 deletions README.rst
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Expand Up @@ -168,7 +168,7 @@ Branch detection
----------------

The hdbscan package supports a branch-detection post-processing step
by `Bot et al. <https://arxiv.org/abs/2311.15887>`_. Cluster shapes,
by `Bot et al. <https://peerj.com/articles/cs-2792/>`_. Cluster shapes,
such as branching structures, can reveal interesting patterns
that are not expressed in density-based cluster hierarchies. The
BranchDetector class mimics the HDBSCAN API and can be used to
Expand All @@ -192,10 +192,10 @@ Example usage:


Based on the paper:
D. M. Bot, J. Peeters, J. Liesenborgs and J. Aerts
*"FLASC: A Flare-Sensitive Clustering Algorithm: Extending HDBSCAN\* for Detecting Branches in Clusters"*
Arxiv 2311.15887, 2023.

D.M. Bot, J. Peeters, J. Liesenborgs and J. Aerts
*FLASC: a flare-sensitive clustering algorithm.*
PeerJ Computer Science, Vol 11, April 2025, e2792.
https://doi.org/10.7717/peerj-cs.2792/.

----------
Installing
Expand Down Expand Up @@ -334,22 +334,26 @@ To reference the high performance algorithm developed in this library please cit
organization={IEEE}
}

If you used the branch-detection functionality in this codebase in a scientific publication and which to cite it, please use the `Arxiv preprint <https://arxiv.org/abs/2311.15887>`_:
If you used the branch-detection functionality in this library please cite our `PeerJ paper <https://peerj.com/articles/cs-2792/>`_:

D. M. Bot, J. Peeters, J. Liesenborgs and J. Aerts
*"FLASC: A Flare-Sensitive Clustering Algorithm: Extending HDBSCAN\* for Detecting Branches in Clusters"*
Arxiv 2311.15887, 2023.
Bot DM, Peeters J, Liesenborgs J, Aerts J.
*FLASC: a flare-sensitive clustering algorithm.*
In: PeerJ Computer Science, Volume 11, e2792, 2025.
https://doi.org/10.7717/peerj-cs.2792

.. code:: bibtex

@misc{bot2023flasc,
title={FLASC: A Flare-Sensitive Clustering Algorithm: Extending HDBSCAN* for Detecting Branches in Clusters},
author={D. M. Bot and J. Peeters and J. Liesenborgs and J. Aerts},
year={2023},
eprint={2311.15887},
archivePrefix={arXiv},
primaryClass={cs.LG},
url={https://arxiv.org/abs/2311.15887},
@article{bot2025flasc,
title = {{FLASC: a flare-sensitive clustering algorithm}},
author = {Bot, Dani{\"{e}}l M. and Peeters, Jannes and Liesenborgs, Jori and Aerts, Jan},
year = {2025},
month = {apr},
journal = {PeerJ Comput. Sci.},
volume = {11},
pages = {e2792},
issn = {2376-5992},
doi = {10.7717/peerj-cs.2792},
url = {https://peerj.com/articles/cs-2792},
}

---------
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26 changes: 25 additions & 1 deletion docs/how_to_detect_branches.rst
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Expand Up @@ -81,7 +81,7 @@ tell us how those clusters combine into a larger shape.

This is where the branch detection post-processing step comes into play.
The functionality is described in detail by `Bot et
al <https://arxiv.org/abs/2311.15887>`__ (please reference this paper
al <https://peerj.com/articles/cs-2792/>`__ (please cite this paper
when using this functionality). It operates on the detected clusters and
extracts a branch-hierarchy analogous to HDBSCAN\*’s condensed cluster
hierarchy. The process is very similar to HDBSCAN\* clustering, except
Expand Down Expand Up @@ -388,3 +388,27 @@ branches!!

.. image:: images/how_to_detect_branches_25_0.png


Citing
------

If you used the branch-detection functionality in this library please cite our `PeerJ paper <https://peerj.com/articles/cs-2792/>`_:

Bot DM, Peeters J, Liesenborgs J, Aerts J. 2025. FLASC: a flare-sensitive
clustering algorithm. PeerJ Computer Science 11:e2792
https://doi.org/10.7717/peerj-cs.2792

.. code:: bibtex

@article{bot2025flasc,
title = {{FLASC: a flare-sensitive clustering algorithm}},
author = {Bot, Dani{\"{e}}l M. and Peeters, Jannes and Liesenborgs, Jori and Aerts, Jan},
year = {2025},
month = {apr},
journal = {PeerJ Comput. Sci.},
volume = {11},
pages = {e2792},
issn = {2376-5992},
doi = {10.7717/peerj-cs.2792},
url = {https://peerj.com/articles/cs-2792},
}
12 changes: 6 additions & 6 deletions hdbscan/branches.py
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Expand Up @@ -179,9 +179,9 @@ def detect_branches_in_clusters(

References
----------
.. [1] Bot, D. M., Peeters, J., Liesenborgs J., & Aerts, J. (2023, November).
FLASC: A Flare-Sensitive Clustering Algorithm: Extending HDBSCAN* for
Detecting Branches in Clusters. arXiv:2311.15887
.. [1] Bot D.M., Peeters J., Liesenborgs J., Aerts J. 2025. FLASC: a
flare-sensitive clustering algorithm. PeerJ Computer Science 11:e2792
https://doi.org/10.7717/peerj-cs.2792.
"""
# Check clusterer state
if clusterer._min_spanning_tree is None:
Expand Down Expand Up @@ -872,9 +872,9 @@ class BranchDetector(BaseEstimator, ClusterMixin):

References
----------
.. [1] Bot, D. M., Peeters, J., Liesenborgs J., & Aerts, J. (2023, November).
FLASC: A Flare-Sensitive Clustering Algorithm: Extending HDBSCAN* for
Detecting Branches in Clusters. arXiv:2311.15887
.. [1] Bot D.M., Peeters J., Liesenborgs J., Aerts J. 2025. FLASC: a
flare-sensitive clustering algorithm. PeerJ Computer Science 11:e2792
https://doi.org/10.7717/peerj-cs.2792.
"""

def __init__(
Expand Down