Add UMAP to embedding projector #1901

cannoneyed · 2019-02-26T18:46:36Z

Motivation for features / changes

Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE. I've ported the python implementation to JavaScript to add an additional projection method to the embedding projector.

Technical description of changes

The UMAP projection technique pretty much follows the approach for the tSNE projection. The UMAP code is grouped in its own directory for ease of maintenance. There are two things to note about this current implementation of UMAP in the embedding projector:

UMAP's SGD optimization doesn't really animate as nicely as t-SNE. I've addresses this by choosing not to animate the steps and just track progress through a dialog.
I'm currently reusing the GPU computed k-nearest neighbors - there didn't seem to be too big of a difference between using the UMAP CPU knn approach vs the existing GPU approach in the projector. To note, the GPU knn approach uses cosine distance, while the rest of UMAP's implementation uses euclidean distance. Again, the subjective results seem fine with this choice.

Screenshots of UI changes

Detailed steps to verify changes work correctly (as executed by you)
Alternate designs / implementations considered

wchargin · 2019-02-26T20:26:58Z

Hi @cannoneyed! Thanks for the PR. We’ll likely be interested in
integrating this functionality after the TF Dev Summit next week, for
which we’re currently busy preparing.

cannoneyed · 2019-02-26T20:33:47Z

Hey @wchargin! Sounds great, I figured I'd get everything in-place then we can move forward once you're through tf-dev.

wchargin

Partial review—will have to check in again later.

third_party/js.bzl

tensorboard/plugins/projector/vz_projector/vz-projector-projections-panel.html

tensorboard/plugins/projector/vz_projector/vz-projector-projections-panel.ts

tensorboard/plugins/projector/vz_projector/data.ts

tensorboard/plugins/projector/vz_projector/vz-projector-projections-panel.ts

tensorboard/plugins/projector/vz_projector/data.ts

cannoneyed · 2019-03-19T23:23:40Z

OK, I've implemented the requested changes and refactored the projectUmap method to make that control flow a bit more clear. Thanks for working through this so thoroughly!

tensorboard/plugins/projector/vz_projector/data.ts

tensorboard/plugins/projector/vz_projector/vz-projector-projections-panel.ts

tensorboard/plugins/projector/vz_projector/data.ts

tensorboard/plugins/projector/vz_projector/vz-projector-projections-panel.ts

tensorboard/plugins/projector/vz_projector/data.ts

tensorboard/plugins/projector/vz_projector/vz-projector-projections-panel.ts

tensorboard/plugins/projector/vz_projector/data.ts

cannoneyed · 2019-03-25T17:25:46Z

Thanks for getting around to this, and hopefully we can push through the finish line soon! After seeing how much work you've put in / how much work could be done for this and subsequent PRs, I think it's worth revisiting the amount of support that I can provide for the projector. Let me talk with my team a bit to see how much time I can reasonably expect to put into supporting / updating the projector in the near term!

wchargin · 2019-03-25T17:26:29Z

Sounds good; thanks.

googlebot · 2019-03-25T19:56:13Z

So there's good news and bad news.

👍 The good news is that everyone that needs to sign a CLA (the pull request submitter and all commit authors) have done so. Everything is all good there.

😕 The bad news is that it appears that one or more commits were authored or co-authored by someone other than the pull request submitter. We need to confirm that all authors are ok with their commits being contributed to this project. Please have them confirm that here in the pull request.

Note to project maintainer: This is a terminal state, meaning the cla/google commit status will not change from this state. It's up to you to confirm consent of all the commit author(s), set the cla label to yes (if enabled on your project), and then merge this pull request when appropriate.

ℹ️ Googlers: Go here for more info.

wchargin · 2019-03-25T21:31:25Z

You can rebase master (which now includes #2052) to drop the cherry-pick
that Googlebot is complaining about.

More cleanup

googlebot · 2019-03-25T21:35:42Z

CLAs look good, thanks!

ℹ️ Googlers: Go here for more info.

wchargin

Looking good! Just one inline request and a few nits left. (I agree that
automated formatting would be great, but in the meantime let’s keep this
file consistent with its previous style and the rest of the codebase.)

Thanks for your patience! Should be ready to merge after these are addressed.

tensorboard/plugins/projector/vz_projector/vz-projector-projections-panel.ts

tensorboard/plugins/projector/vz_projector/util.ts

tensorboard/plugins/projector/vz_projector/data.ts

tensorboard/plugins/projector/vz_projector/vz-projector-projections-panel.ts

cannoneyed · 2019-03-26T22:22:40Z

Thanks for taking the time for such a thorough review. What's the timeline look like for deployment once these changes are merged?

wchargin

Thanks!

wchargin · 2019-03-26T23:26:32Z

What's the timeline look like for deployment once these changes are
merged?

I’ll merge this into master, so it will be in tb-nightly starting
tonight. It’s a new feature, so it will be generally available in the
next minor version of TensorBoard: namely, TensorBoard 1.14.0, which
will roughly coincide with the TensorFlow 1.14.0 release.

Summary: This reverts commit 37c5b50. Manual merge of `third_party/js.bzl` was required due to #2079; the file is now identical to its state prior to #1901. This is a temporary measure to keep our GitHub-to-Google sync process green while we work on integrating the `umap-js` library into google3. Test Plan: The embeddings projector now lacks a UMAP option, but still works. wchargin-branch: revert-1901

…ensorflow#2091)" This reverts commit 58df24b.

This reverts commit 58df24b. Other than the reversion, the only changes are non-functional: the UMAP mirror URL is changed (but the sha256 of its contents is not), and a license header is changed from “Google Inc.” to “Google LLC”. Test Plan: As in #1901.

cannoneyed force-pushed the umap-npm branch 3 times, most recently from e58b1c5 to 531ae02 Compare February 26, 2019 19:01

wchargin added type:feature plugin:graph plugin:projector and removed plugin:graph labels Feb 26, 2019

cannoneyed force-pushed the umap-npm branch from 531ae02 to 1c1743b Compare February 26, 2019 20:23

wchargin added the stat:awaiting tensorflower label Feb 26, 2019

cannoneyed force-pushed the umap-npm branch 3 times, most recently from e269d96 to 6a4af2d Compare February 26, 2019 22:30

wchargin self-requested a review March 8, 2019 23:44

wchargin reviewed Mar 19, 2019

View reviewed changes

wchargin reviewed Mar 23, 2019

View reviewed changes

cannoneyed force-pushed the umap-npm branch from 7fae143 to f3d791a Compare March 25, 2019 17:18

cannoneyed force-pushed the umap-npm branch from f3d791a to 5fff698 Compare March 25, 2019 17:42

cannoneyed added 4 commits March 25, 2019 14:35

Add umap-js to embedding projector

581eeef

Update the 3d/2d toggle for UMAP

c8628a0

Update logic, polymer bindings, build rule names

e57c16d

Some more cleanup / fixes

4919305

More cleanup

cannoneyed force-pushed the umap-npm branch from 7f4193b to 4919305 Compare March 25, 2019 21:35

wchargin reviewed Mar 26, 2019

View reviewed changes

Clean up more nits

fbfda58

wchargin approved these changes Mar 26, 2019

View reviewed changes

wchargin changed the title ~~Add umap to embedding projector~~ Add UMAP to embedding projector Mar 26, 2019

wchargin merged commit 37c5b50 into tensorflow:master Mar 26, 2019

This was referenced Apr 1, 2019

Internal k-nearest-neighbors data management is broken #2081

Open

k-nearest-neighbors caching is broken (unsound) #2082

Closed

wchargin mentioned this pull request Apr 3, 2019

Revert "Add UMAP to embedding projector (#1901)" #2091

Merged

cannoneyed added a commit to cannoneyed/tensorboard that referenced this pull request Apr 11, 2019

Revert "Revert "Add UMAP to embedding projector (tensorflow#1901)" (t…

232a17d

…ensorflow#2091)" This reverts commit 58df24b.

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add UMAP to embedding projector #1901

Add UMAP to embedding projector #1901

cannoneyed commented Feb 26, 2019 •

edited

Loading

wchargin commented Feb 26, 2019

cannoneyed commented Feb 26, 2019 •

edited

Loading

wchargin left a comment

cannoneyed commented Mar 19, 2019

cannoneyed commented Mar 25, 2019

wchargin commented Mar 25, 2019

googlebot commented Mar 25, 2019

wchargin commented Mar 25, 2019

googlebot commented Mar 25, 2019

wchargin left a comment

cannoneyed commented Mar 26, 2019

wchargin left a comment

wchargin commented Mar 26, 2019

Add UMAP to embedding projector #1901

Add UMAP to embedding projector #1901

Conversation

cannoneyed commented Feb 26, 2019 • edited Loading

wchargin commented Feb 26, 2019

cannoneyed commented Feb 26, 2019 • edited Loading

wchargin left a comment

Choose a reason for hiding this comment

cannoneyed commented Mar 19, 2019

cannoneyed commented Mar 25, 2019

wchargin commented Mar 25, 2019

googlebot commented Mar 25, 2019

wchargin commented Mar 25, 2019

googlebot commented Mar 25, 2019

wchargin left a comment

Choose a reason for hiding this comment

cannoneyed commented Mar 26, 2019

wchargin left a comment

Choose a reason for hiding this comment

wchargin commented Mar 26, 2019

cannoneyed commented Feb 26, 2019 •

edited

Loading

cannoneyed commented Feb 26, 2019 •

edited

Loading