SpikeInterface / SpikeInterface/spikeinterface
UMAP instead of PCA
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Description
Hi!
I was playing a bit with spikecomponents, and I was wondering if someone was already working on it, or if it could be worth it that I add a clustering class (https://github.com/SpikeInterface/spikeinterface/blob/main/src/spikeinterface/sortingcomponents/clustering/method_list.py), with UMAP as a dimensionality reduction method. Indeed, this thesis shows that UMAP is promising https://dalspace.library.dal.ca/handle/10222/83717 if we manage to compute it efficiently.
Best,
Florent
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading src/spikeinterface/sortingcomponents/clustering/method_list.py and examining how dimensionality-reduction methods are currently represented. Assess the proposed UMAP approach, including whether its computation can be efficient enough for spikecomponents. Done means the project has a defined UMAP method and an agreed way to evaluate its practicality.
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Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100