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Incorporate Graphormer #21

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@ttolhurst ttolhurst commented Oct 31, 2025

Addition of Graphormer from Do Transformers Really Perform Bad for Graph Representation?, C. Ying et al., 2021.

@ttolhurst
add graphormer file
b88cb76 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
graphormer data formatting
dde35de 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
graphormer data formatting
0e46f02 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
graphormer data formatting
0f07900 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
basic reworking of model to match formatting
00d0987 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
rearrange the Data preprocessing to match existing
7da6b28 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
changes up to decision between collator or to_dense_batch, will try t…
b125061 
…o_dense batch first

Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
changes up to decision between collator or to_dense_batch, will try t…
7fa1508 
…o_dense batch first

Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
cython - replace long by int for python 3 compat
8125e04 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
cython - adjust version to use long
a513b1a 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
replace cython by networkx version of floyd_warshall
d7a6193 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
put in place holder for pos embed to speed up development
10bc942 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
passed positional embedding
e1f8cd5 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
pass to loss
4bd0845 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
pass loss, but note that AddGrEnc breaks multi-graph batch
2fff231 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
wrap up before testing new batching
4e995e9 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
confirmation that flat tensors do not break batching
f9da3c0 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
add padding of attributes
0976cba 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
corrected cython integer
de141d7 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
confirmation that route with cython and masking functions
9d834a3 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
propogate mask to loss calculation for all models
903708c 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
clean up and include cython code for encoding
4014034 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
clean up
6cc690e 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
rework function head and parameters
87ef065 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
clean up Graphormer code
74486b3 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
clean up
e9a4d04 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
flow dataset parameters from the config
e343049 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
baseline dataset finalized
ddb0ff8 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
flow over baseline logic for edge encodings
6124403 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
added model parameters for managing edge data
61fd07e 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
work in progress for incorporating edge data
32c19f3 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
multi-hop functional with N nodes upper limit
bf1e221 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
set max hops for edge encoding
fc5a93e 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
add buffer for single hop case
04aed10 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
checkpoint before cleanup and testing
b9e9efd 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
TODOs cleared from transforms
98e1b12 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
TODOs cleared from transforms
a3b5b61 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
TODOs cleared from graphormer
498709b 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
add raw graphormer config
7f0e285 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
rename graphormer config
d3abe1f 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
adjust calc of mask
f63a760 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
clean up comments
47a7cef 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
add swith for windows and linux for cython algos
893146b 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
add layer norm to decoder
8c44e25 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
adjust edge encoding to accomodate better switching and negative values
1478b3b 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
checkpoint in testing
518f549 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
verified fix to edge encoding range
b4c1a6f 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
checkpoint before rework of tensor shapes
1b63f2b 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
mask based on dense batch tested
1f6fe59 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
clean up
03f4f7a 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
clean up
c988fbb 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
clean up
f3c0f60 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
update comments
e8ec043 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
specify cython version in toml
23f0119 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
@ttolhurst
changed default of args for dataset
43a5e3c 
Signed-off-by: Thomas Tolhurst <99353435+ttolhurst@users.noreply.github.com>
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