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Added Graph Encoder Embedding #986

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wants to merge 24 commits into from
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Added Graph Encoder Embedding #986

wants to merge 24 commits into from

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bdpedigo
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@bdpedigo bdpedigo commented Sep 15, 2022

  • Does this PR have a descriptive title that could go in our release notes?
  • Does this PR add any new dependencies?
  • Does this PR modify any existing APIs?
    • Is the change to the API backwards compatible?
  • Have you built the documentation (reference and/or tutorial) and verified the generated documentation is appropriate?

Reference Issues/PRs

Closes #984

What does this do

Implements a new embedding model based on node features/categories

TODOs

  • Should directed graphs yield separate in/out embeddings?
    • Not mentioned in the actual paper or code as far as I can tell, but I think they are just summing what could be thought of as source/target embeddings
  • Should actually discrete features have a separate implementation?
    • Basically, can make this work with indexing instead of adding the entire vector to the embedding
    • However, implementation right now is super super simple, which I like :)
  • Improve documentation, build and make sure it looks good
  • Add tutorial
    • I have notebook with replication of their simulations
  • Add tests

bdpedigo and others added 24 commits September 15, 2022 11:23
I added to line 35. I assumed the asterisk on 3.3 meant all versions of 3.3 ex (3.3.1, 3.3.2) are all excluded from the matplotlib. 

Is this correct?
Removed outdated Zenodo DOI from README.md
)

* Fix seaborn syntax

* fixed padding of a similarity amtrix for graph matching

* fixing mypy complaint from _adj_pad

* use naive padding for similarity

* add a test

* Revert "Fix seaborn syntax"

This reverts commit fd38e05.

* try to fix ipython error in doc generation

* just make sure the original S had the right shape

* run black

* fix tests

Co-authored-by: Benjamin Pedigo <benjamindpedigo@gmail.com>
* Editing contributing guidelines 

My edits were based on my experience with getting set up on GitHub. I added some minor changes of things I wish I had read while I was trying to set up my account.

* fix typo

Co-authored-by: Benjamin Pedigo <benjamindpedigo@gmail.com>
* hard capped networkx version to avoid incompatability

* set networkx to <= 3.0

* Update setup.cfg

Co-authored-by: alyakin314 <antonalyakin@Antons-MacBook-Pro-4.local>
Co-authored-by: Benjamin Pedigo <benjamindpedigo@gmail.com>
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Add graph encoder embedding
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