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added Graphormer.jl #265

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5hv5hvnk
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@5hv5hvnk 5hv5hvnk commented Mar 16, 2023

fixes #251
To do:

  • struct based layers
  • doc-string
  • example pipeline
  • unit tests
  • pass build tests

@CarloLucibello is there anything else to work on?

@5hv5hvnk
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Is there a contributing guideline doc so I can fix the build tests at least?

@CarloLucibello
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test failures is probably related to some changes in dependencies like FiniteDifferences.jl, I'll have to investigate

@@ -1670,3 +1670,67 @@ function Base.show(io::IO, l::TransformerConv)
(in, ein), out = l.channels
print(io, "TransformerConv(($in, $ein) => $out, heads=$(l.heads))")
end

struct GraphomerLayer{DX <: Dense, DE <: Union{Dense, Nothing}, T, A <: AbstractMatrix, F, B} <: GNNLayer
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we can start adding a docstring and some tests

@CarloLucibello
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I think it would be good to add an example to the example folder showing the full pipeline,
since there are some ingredients in the graphormer pipeline which are not part of the layer (e.g. the edge encodings) https://proceedings.neurips.cc/paper/2021/file/f1c1592588411002af340cbaedd6fc33-Paper.pdf

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Anyways, this looks very good already

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codecov bot commented Mar 19, 2023

Codecov Report

Merging #265 (53efa7d) into master (c5bd656) will decrease coverage by 1.43%.
The diff coverage is 13.51%.

❗ Current head 53efa7d differs from pull request most recent head 6aa987d. Consider uploading reports for the commit 6aa987d to get more accurate results

@@            Coverage Diff             @@
##           master     #265      +/-   ##
==========================================
- Coverage   81.70%   80.28%   -1.43%     
==========================================
  Files          17       17              
  Lines        1864     1902      +38     
==========================================
+ Hits         1523     1527       +4     
- Misses        341      375      +34     
Impacted Files Coverage Δ
src/layers/conv.jl 74.65% <13.51%> (-4.83%) ⬇️

... and 1 file with indirect coverage changes

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@5hv5hvnk
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@CarloLucibello where should I add the tests ? Secondly is adding tests here similar too PyTest ?

@CarloLucibello
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CarloLucibello commented Mar 20, 2023

take a look at the test folder. The entry point is test/runtests.jl. All julia packages are similarly structured.
The organization of the test files reflects the organization of the src files.

@5hv5hvnk 5hv5hvnk closed this Mar 22, 2023
@5hv5hvnk
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Hi @CarloLucibello due to some conflicts that I was trying to resolve the PR is closed now. Let me try fix it and raise another PR

@5hv5hvnk 5hv5hvnk mentioned this pull request Mar 22, 2023
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@CarloLucibello
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Sure, sorry for that, I made some pretty extensive changes

@5hv5hvnk
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No problem you can have a look on #275

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implement Graphormer
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