UMAP redesign
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Area - Topology 🍩
Area – API
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- Python
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Description
What kind of feature would you like to request?
Additional function parameters / changed functionality / changed defaults?
Please describe your wishes
The UMAP API should be restructured to be class-based to allow for different (e.g. partial) operation modes:
- a function to compute what are now called in scanpy "connectivities" from the distances. This is among other things a symmetrysation of the knn graph.
- a function to compute the embedding from the connectivity graph.
Contributor guide
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
No files or tests are named. Start by reviewing the existing UMAP API and the scanpy handling of distances, connectivities, and embeddings. Clarify the class-based design and the boundaries between computing connectivities and computing the embedding before implementation; done means both partial operation modes are supported without breaking current functionality.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100