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[DOC] Hierarchical, spectral, or density-based clustering using sklearn and aeon distance metrics #1241
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thanks for this, we have some examples I think of using precomputed with scikit, but if its not clear it would be great if it was clearer. I would like to get density peaks in, iirc we have a java implementation. |
Hey, Can i work on this issue? |
Yes, sure. |
Hey,
Once I have clarification, I’ll proceed with the implementation and submit a PR. |
Please carefully read our Developer Guide and look at the existing documentation.
|
Hey @SebastianSchmidl, |
There is a documentation guide for building the docs locally on the website. For the notebooks themselves where are lots of methods for running them, but I imagine most IDEs (i.e. PyCharm) will support it. |
Describe the issue linked to the documentation
The clustering component in aeon currently supports only partition-based methods. However, there are also hierarchical, spectral, and density-based clustering methods [1].
Suggest a potential alternative/fix
Using the distance metrics in aeon, we can pre-compute the distance matrix for traditional clustering methods. Some methods are already implemented in sklearn, which is a core dependency of eaon and, thus, available to users. I think we should at least link to the sklearn-clusterers in the documentation. With a bit more effort, we could provide examples on how to use sklearn's clusterers with aeon's distance measures (here).
sklearn.cluster.AgglomerativeClustering
withmetric="precomputed"
sklearn.cluster.DBSCAN
withmetric="precomputed"
sklearn.cluster.OPTICS
withmetric="precomputed"
sklearn.cluster.SpectralClustering
withaffinity="precomputed"
and the inverse of the distance matrix (large values indicate greater similarity)[1]: Paparrizos, John, and Luis Gravano. "Fast and Accurate Time-Series Clustering." ACM Transactions on Database Systems 42, no. 2 (2017): 8:1-8:49. https://doi.org/10.1145/3044711.
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