Papers › Recurrent Distance Filtering for Graph Representation Learning

Recurrent Distance Filtering for Graph Representation Learning

3 Dec 2023arXiv:2312.01538archive 2025-07-28

Yuhui Ding, Antonio Orvieto, Bobby He, Thomas Hofmann

Graph neural networks based on iterative one-hop message passing have been shown to struggle in harnessing the information from distant nodes effectively. Conversely, graph transformers allow each node to attend to all other nodes directly, but lack graph inductive bias and have to rely on ad-hoc positional encoding. In this paper, we propose a new architecture to reconcile these challenges. Our approach stems from the recent breakthroughs in long-range modeling provided by deep state-space models: for a given target node, our model aggregates other nodes by their shortest distances to the target and uses a linear RNN to encode the sequence of hop representations. The linear RNN is parameterized in a particular diagonal form for stable long-range signal propagation and is theoretically expressive enough to encode the neighborhood hierarchy. With no need for positional encoding, we empirically show that the performance of our model is comparable to or better than that of state-of-the-art graph transformers on various benchmarks, with a significantly reduced computational cost. Our code is open-source at https://github.com/skeletondyh/GRED.

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1ran · violated contract
3ran · our draft was wrong
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LRU skeletondyh/gred/model.py official repository ran no licence file found · pointer only · e01e88637e577256 · report
MLP skeletondyh/gred/model.py official repository ran no licence file found · pointer only · 0f3fd4edd18faabe · report
binary_operator_diag skeletondyh/gred/model.py official repository ran · our draft was wrong no licence file found · pointer only · ba8e9577ac8dfb73 · report
eval_ap skeletondyh/GRED/utils.py official repository ran no licence file found · pointer only · c0d6908dc30f37ec · report
gen_dist_mask skeletondyh/GRED/preprocess_peptides.py official repository ran no licence file found · pointer only · 0a96efa6922a586d · report
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load skeletondyh/GRED/datasets.py official repository ran no licence file found · pointer only · 86e644e878701a9e · report
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load_superpixel skeletondyh/GRED/datasets.py official repository ran no licence file found · pointer only · 9ff9d48e2f6c01d2 · report
map_nested_fn skeletondyh/GRED/utils.py official repository ran no licence file found · pointer only · 1fc8ab51b4d7b0b2 · report
GRED skeletondyh/gred/model.py official repository unverified no licence file found · pointer only · f50e322383b7d10f · report
eval_step skeletondyh/GRED/train_peptides_func.py official repository unverified no licence file found · pointer only · 33f96f60e03d9f4d · report
eval_step skeletondyh/GRED/train_peptides_struct.py official repository unverified no licence file found · pointer only · 573953132860b6c8 · report
eval_step skeletondyh/GRED/train_pixel.py official repository unverified no licence file found · pointer only · 361ca6724f795584 · report
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train_step skeletondyh/GRED/train_pixel.py official repository unverified no licence file found · pointer only · 5ab5f97bf4fe2a26 · report
train_step skeletondyh/GRED/train_sbm.py official repository unverified no licence file found · pointer only · 2f7255aaf56805b4 · report

Tasks

Graph ClassificationGraph Representation LearningInductive BiasLong-range modelingRepresentation LearningState Space Models

Results from the paper archive 2025-07-28

TaskDatasetModelMetricValueRank at snapshotLeaderboardReport
Graph Classification CIFAR10 100k GRED Accuracy (%) 76.853±0.185 #3 of 20 Archive leaderboard report
Graph Classification Peptides-func GRED+LapPE AP 0.7133±0.0011 #10 of 44 Archive leaderboard report
Graph Classification Peptides-func GRED AP 0.7085±0.0027 #12 of 44 Archive leaderboard report

Ranks are positions in the archive's leaderboards as they stood at the 2025-07-28 snapshot. Results published since then are not among these rows, so a rank here is not a current standing.

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