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[FEA] t-SNE Python API to accept KNN graph directly #1780

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cjnolet opened this issue Mar 2, 2020 · 1 comment · Fixed by #2592
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[FEA] t-SNE Python API to accept KNN graph directly #1780

cjnolet opened this issue Mar 2, 2020 · 1 comment · Fixed by #2592
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@aleksficek
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? - Needs Triage Need team to review and classify Contributions welcome Soliciting for contributions from the community feature request New feature or request

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@cjnolet
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cjnolet commented Mar 2, 2020

This has been separated from #1733 as the UMAP side of this feature is a higher priority at the moment. The same set of changes should be made to the t-SNE API, which should be very similar to the changes made to UMAP.
@cjnolet cjnolet added feature request New feature or request ? - Needs Triage Need team to review and classify labels Mar 2, 2020
@cjnolet cjnolet mentioned this issue Mar 10, 2020
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@cjnolet cjnolet added the Contributions welcome Soliciting for contributions from the community label Mar 11, 2020
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I'll take on this issue

@aleksficek aleksficek mentioned this issue Jul 23, 2020
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rapids-bot bot pushed a commit that referenced this issue Dec 11, 2020
@aleksficek
Add KNN parameter to t-SNE(#2592)
2e2125f 
Closes #1780

Adding kNN graph input functionality to t-SNE, a request broken off of the issue #1733. t-SNE gathers kNN indices and distances in the first stage of it's computation, by allowing the user to input their own kNN graph, they can skip this step. This should follow #1815 as closely as possible.

**Benefits of this**:
- allow user custom run of kNN algorithm
- can use different distance function instead of t-SNE euclidean default
- allows for speedup if performing grid search by storing and reusing kNN graph

**Includes:**
- [x] Abstracted `extract_knn_graph` so it can be used for both UMAP and t-SNE
- [x] Implemented kNN graph input to Python/Cython layer and C++/CUDA layer
- [x] C++/CUDA Barnes Hut and Exact t-SNE tests
- [x] Python t-SNE tests
- [x] General code cleanup wherever needed

Authors:
  - Aleksander Ficek <alex.ficek99@gmail.com>
  - Corey J. Nolet <cjnolet@gmail.com>
  - Ray Douglass <3107146+raydouglass@users.noreply.github.com>
  - Corey J. Nolet <cjnolet@users.noreply.github.com>

Approvers:
  - Corey J. Nolet

URL: #2592
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Add KNN parameter to t-SNE aleksficek/cuml
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