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c12cb08
feat(graph_transformer): add initial skeleton with readout and shape …
omarkhater-school Apr 25, 2025
a395c9d
feat: add super-node ([CLS] token) readout support
omarkhater-school Apr 25, 2025
40c0a0d
feat: add pluggable node_feature_encoder hook
omarkhater-school Apr 25, 2025
4eae6f8
feat(core): wire up EncoderLayers stub and add IdentityLayer
omarkhater-school Apr 25, 2025
8e0b459
Add 2 unit tests
omarkhater-school Apr 25, 2025
3ce766e
test(layers): add tests for activation factory
omarkhater-school Apr 25, 2025
8cf728c
feat(layers): implement PositionwiseFeedForward
omarkhater-school Apr 25, 2025
ed9ba2b
Update feedforward.py
omarkhater-school Apr 25, 2025
65cd0f4
test: expect real GraphTransformerEncoderLayer
omarkhater-school Apr 26, 2025
74d2669
feat(graph_transformer): introduce EncoderLayer/Encoder stack and dro…
omarkhater-school Apr 26, 2025
39f37c3
test(transformer): expect real computation in GraphTransformerEncoder…
omarkhater-school Apr 26, 2025
8b60d43
feat(transformer): add dropout & FFN with residuals to encoder layer
omarkhater-school Apr 26, 2025
ca400cf
test: expect multi-head attention to change values
omarkhater-school Apr 26, 2025
80d65db
feat(transformer): replace Identity with MultiheadAttention + padding…
omarkhater-school Apr 26, 2025
ede26d8
Refactor: Update old test_node_feature_encoder_identity
omarkhater-school Apr 26, 2025
358a5fb
fix(torchscript): model traces with multi-layer encoder
omarkhater-school Apr 26, 2025
0fc62b3
[Fix] Remove isort, yapf skipping primitives
omarkhater-school Apr 26, 2025
ea2303c
test(graph_transformer): Degree Encoder return constant values
omarkhater-school Apr 26, 2025
8c9b50c
feat(graph_transformer): Add Degree Encoder
omarkhater-school Apr 26, 2025
e2bdbce
Refactor: extract degree encoder into private helper
omarkhater-school Apr 26, 2025
056df5f
test(mask utils): prepare for combining padding and attention
omarkhater-school Apr 26, 2025
cf6ab17
feat (mask utils): Enable merging key-padding and attention masks
omarkhater-school Apr 26, 2025
9a8586c
test(graph transformer): add attn-mask integration test
omarkhater-school Apr 26, 2025
f7ec9e7
feat: encoder uses mask_utils.merge_masks
omarkhater-school Apr 26, 2025
dc48906
(fix): test_transformer_block_identity
omarkhater-school Apr 26, 2025
1e5944d
test: cls token must flow through MHA
omarkhater-school Apr 26, 2025
085c23b
feat: feed cls token into encoder
omarkhater-school Apr 26, 2025
01b893a
(fix): Update test_super_node_readout to account for encoder transfor…
omarkhater-school Apr 27, 2025
485d8e7
test: add speed regression guard
omarkhater-school Apr 27, 2025
b79a497
refactor(transformer layer): drop 3-D shortcut, enforce flat input
omarkhater-school Apr 27, 2025
8af1017
perf(transformer): vectorise pad/unpad helpers
omarkhater-school Apr 27, 2025
bf8d829
Refactor(transformer): Avoid flattening the entire tensor while padding
omarkhater-school Apr 27, 2025
e5b54fb
Refactor[transformer]: Update method signatures
omarkhater-school Apr 27, 2025
bda1d2b
Fix(graph transformer): Update encoder initialization and forward pass
omarkhater-school Apr 27, 2025
75370b7
fix(test_graph_transformer): Update the AddOneLayer class to match m…
omarkhater-school Apr 27, 2025
91960b8
fix(transformers): improve key padding caching
omarkhater-school Apr 27, 2025
c0071f4
test(graph_transformer): spatial bias affects logits
omarkhater-school Apr 27, 2025
022fbe1
feat: allow data.bias as structural mask
omarkhater-school Apr 27, 2025
68fec53
feat: rename & route struct_mask through merge_masks
omarkhater-school Apr 27, 2025
38eeba1
test: TorchScript trace with structural bias
omarkhater-school Apr 27, 2025
bbc0757
feat: plumb struct_mask through encoder stack
omarkhater-school Apr 27, 2025
2c60122
test: merge_masks handles float bias
omarkhater-school Apr 27, 2025
91efc41
test(bias provider): add failing tests for bias-provider interface
omarkhater-school Apr 28, 2025
24f4e77
feat(bias provider): implement bias-provider wiring in GraphTransformer
omarkhater-school Apr 28, 2025
66c1642
Unify structural bias: support legacy batch.bias and BiasProvider mod…
omarkhater-school Apr 28, 2025
67300da
test(spatial bias provider): complete test suite
omarkhater-school Apr 28, 2025
08969d1
feat(spatial bias provider): implement GraphAttnSpatialBias provider
omarkhater-school Apr 28, 2025
78e4451
Refactor(spatial bias): Make forward method clearer
omarkhater-school Apr 28, 2025
786b584
test: add GraphAttnHopBias tests
omarkhater-school Apr 28, 2025
3cb4c70
feat(hop): add GraphAttnHopBias
omarkhater-school Apr 28, 2025
93f0e0c
test: add GraphAttnHopBias tests
omarkhater-school Apr 28, 2025
0f37bbf
feat(hop): add GraphAttnEdgeBias
omarkhater-school Apr 28, 2025
02801d4
test: bias API & Wiring
omarkhater-school Apr 29, 2025
a68bbd3
test: add super-node bias edge-case tests
omarkhater-school Apr 29, 2025
0831f65
refactor: cache super-node index for bias providers
omarkhater-school Apr 29, 2025
9c4ae91
test: add fusion tests for multiple bias providers with dynamic padding
omarkhater-school Apr 29, 2025
6fc12af
perf: add bias-provider latency benchmark
omarkhater-school Apr 29, 2025
4835d4d
Refactor(Bias Package): Inherit from base class
omarkhater-school Apr 29, 2025
813c7b6
test (gnn integeration): Add unit tests for expected behavior
omarkhater-school Apr 29, 2025
bd02d16
feat( GNN integration): allow using GNN with transformer
omarkhater-school Apr 29, 2025
cdd1687
test (gnn integeration): more unit tests
omarkhater-school Apr 29, 2025
a4c3cec
feat(gnn integeration): Allow parallel case
omarkhater-school Apr 29, 2025
7f0a103
feat: implement __repr__ with full model config
omarkhater-school Apr 29, 2025
9cf5051
Refactor (Graph trnasformer): Improve Readability and modularity
omarkhater-school Apr 29, 2025
a1fce08
Refactor (test_graph_transformer): DRY test cases
omarkhater-school Apr 29, 2025
fcaf116
Refactor (graph transformer): Add doc string to the class
omarkhater-school Apr 29, 2025
5566f97
test (degree encoder): Add failing tests for output shape and values
omarkhater-school Apr 29, 2025
10847a6
feature (degree encoder)
omarkhater-school Apr 29, 2025
f807f33
test (eigenvector embeddings): Add failing tests for output shape and…
omarkhater-school Apr 29, 2025
39cead5
feature (Laplacian eigenvector embeddings)
omarkhater-school Apr 29, 2025
05f111d
refactor (eigen encoder): Refine EigEncoder sign reproducibility
omarkhater-school Apr 29, 2025
c1c0f4a
feat (SVD-based positional encoder)
omarkhater-school Apr 29, 2025
7e305ea
Integrate positional_encoders hook into GraphTransformer
omarkhater-school Apr 29, 2025
71a8b4d
Test GraphTransformer with different encoders
omarkhater-school Apr 29, 2025
dca0445
Refactor (graph transformer): Include pos_encoders in __repr__
omarkhater-school Apr 29, 2025
09390b5
Refactor (test_transformer.py)
omarkhater-school Apr 29, 2025
0a6d71d
Refactor bias package tests
omarkhater-school Apr 29, 2025
f83e50f
Refactoring: Centralize Test Fixtures
omarkhater-school Apr 29, 2025
73320ce
Improve the coverage for bias package
omarkhater-school Apr 30, 2025
bdade37
[fix] Rename test module to avoid confusion with one library module
omarkhater-school Apr 30, 2025
d773772
test(edge bias): test different path for edge bias
omarkhater-school Apr 30, 2025
b166e7a
test (bias package): ensure that shape errors are accessible
omarkhater-school Apr 30, 2025
033257c
test (mask utils): Ensure accessibility for value errors
omarkhater-school Apr 30, 2025
67d3ccb
test (graph transformer): expect transformer parameters exposure and …
omarkhater-school Apr 30, 2025
f68109a
feat(Graph transformer): Expose Transformer Layer Parameter
omarkhater-school Apr 30, 2025
f183241
test (full model features speed)
omarkhater-school Apr 30, 2025
270d969
refactor(graph transformer): collapse degree encoding into positional…
omarkhater-school Apr 30, 2025
75cf80f
Refactor(graph transformer): vectorized _prepend_cls_token_flat
omarkhater-school Apr 30, 2025
bea4c96
Refactor (graph transformer): unify encoder invocation
omarkhater-school Apr 30, 2025
e85cdcd
Refactor (graph transformer): Register cls_token Properly
omarkhater-school Apr 30, 2025
cd090b7
Refactor (test graph transformer): Remove fixtures from the test module.
omarkhater-school Apr 30, 2025
4abd5a9
refactor (Graph transformer): Remove dead code
omarkhater-school Apr 30, 2025
34cf9a7
Refactor (graph transformer): Traceable _prepend_cls_token_flat
omarkhater-school May 1, 2025
5b1ad83
Refactor (graph transformer): Improve Doc strings
omarkhater-school May 1, 2025
1035196
Refactor (graph transformer): Return Tensor instead of dict from the …
omarkhater-school May 1, 2025
4c3bcf6
Refactor: Improve Doc strings
omarkhater-school May 1, 2025
021fe2a
feat(bias): support heterogeneous block-diagonal spatial_pos in Graph…
omarkhater-school May 10, 2025
fe37f39
feat(bias): support heterogeneous graph sizes in Hop & Edge bias prov…
omarkhater-school May 10, 2025
f964759
[Fix] Ensure that all model parameters move to the same device
May 12, 2025
91cbcfd
(Fix) Bugs in Graph transformer for regression tasks
omarkhater-school Jun 7, 2025
dd9ed9d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 9, 2025
a8045c7
Merge branch 'master' into add_graph_transformer
omarkhater Jun 9, 2025
9d17b70
(fix) Solve 2 bugs
omarkhater-school Jun 9, 2025
748ada3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 10, 2025
efe70ea
(fix): Improve error handling in _encode_nodes
omarkhater-school Jun 10, 2025
af15aae
Merge branch 'add_graph_transformer' of https://github.com/omarkhater…
omarkhater-school Jun 10, 2025
cebd34e
Merge branch 'master' into add_graph_transformer
omarkhater Jun 18, 2025
7ca8a7d
Merge branch 'add_graph_transformer' of https://github.com/omarkhater…
omarkhater-school Jun 18, 2025
96fe7d5
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 18, 2025
e5b9d29
(Refactor): Reduce the cognitive complexity for validate_init_args
omarkhater-school Jun 18, 2025
3904df0
(fix): Linting & formatting issues in test_spatial_bias
omarkhater-school Jun 18, 2025
4ed1e7d
Merge remote-tracking branch 'origin/add_graph_transformer'
omarkhater-school Jun 18, 2025
d58debf
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 18, 2025
b94d58c
fix: resolve yapf/isort conflicts in some test modules
omarkhater-school Jun 18, 2025
a141aae
(Refactor): Graph transformer model
omarkhater-school Jun 19, 2025
3efad65
Merge branch 'pyg-team:master' into add_graph_transformer
omarkhater Jul 21, 2025
a08a191
(feat) Add reset parameters to the graph transformer model and all su…
OmarKhater-sws Jul 21, 2025
8e9a434
Refactor bias provider tests to use encoder config fixture
OmarKhater-sws Jul 21, 2025
5140f9b
Refactor bias provider tests to use encoder_cfg param
OmarKhater-sws Jul 21, 2025
86b737e
Add onlyFullTest decorator to performance tests
OmarKhater-sws Jul 21, 2025
e3c8391
Add attention mask caching to GraphTransformer
OmarKhater-sws Jul 22, 2025
3eeaff1
Make caching masks optional
OmarKhater-sws Jul 22, 2025
f963746
Add tests for attention mask caching edge cases
OmarKhater-sws Jul 22, 2025
67e95b0
Refactor key padding mask mocking in GraphTransformer tests
OmarKhater-sws Jul 22, 2025
aa42528
Use DEFAULT_ENCODER and DEFAULT_GNN in tests
OmarKhater-sws Jul 22, 2025
69ddf1f
Refactor variable name in edge bias block creation
OmarKhater-sws Jul 22, 2025
57c0d6a
Add num_nodes to simple_none_batch fixture
OmarKhater-sws Jul 22, 2025
c546597
Align GraphTransformer API with PyG’s node-level-first pattern
OmarKhater-sws Jul 22, 2025
3fa642f
Refactor GraphTransformer output and update tests
OmarKhater-sws Jul 23, 2025
2983052
Reduce complexity for merge_masks method in mask_utils
OmarKhater-sws Jul 23, 2025
25b1aaf
Initialize node features with ones instead of zeros
OmarKhater-sws Jul 23, 2025
7756c9a
Add cast_bias option to GraphTransformer and tests
OmarKhater-sws Jul 24, 2025
3899bb6
Refactor padding logic in GraphTransformerEncoderLayer
OmarKhater-sws Jul 24, 2025
290ba46
graph_transformer: initialise CLS token with 𝒩(0, 1e-2) instead of zeros
OmarKhater-sws Jul 24, 2025
f6555cf
Refactor the padding/unpadding logic to occur only once per forward p…
OmarKhater-sws Jul 24, 2025
fdfdae6
Refactor _prepend_cls_token_flat for efficiency and clarity
OmarKhater-sws Jul 24, 2025
eee428a
Refactor GraphTransformer argument validation tests (coverage increas…
OmarKhater-sws Jul 25, 2025
bf78d78
Add input validation tests for GraphTransformer
OmarKhater-sws Jul 25, 2025
92c33cd
Refactor and expand tests for mask_utils merge_masks (73% to 92% cove…
OmarKhater-sws Jul 25, 2025
bb36f13
Add test for merge_masks with invalid mask dtype (92% to 94% coverage)
OmarKhater-sws Jul 25, 2025
d57c5a3
Remove unused _mixed_batch helper from test_mask_utils.py
OmarKhater-sws Jul 25, 2025
2a9724e
Support GraphTransformer inputs without batch vector
OmarKhater-sws Jul 25, 2025
ec3bd1b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 25, 2025
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4 changes: 4 additions & 0 deletions .env
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
GT_BENCH_BASE_MS=50
CI_LOCAL=1
GT_BENCH_BASE_BIAS_MS=60
GT_BENCH_BASE_FULL_MS=75
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