PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm
Abstract
Graph neural networks (GNNs) have achieved state-of-the-art performance in various graph-based tasks. However, as mainstream GNNs are designed based on the neural message passing mechanism, they do not scale well to data size and message passing steps. Although there has been an emerging interest in the design of scalable GNNs, current researches focus on specific GNN design, rather than the general design space, limiting the discovery of potential scalable GNN models. This paper proposes PaSca, a new paradigm and system that offers a principled approach to systemically construct and explore the design space for scalable GNNs, rather than studying individual designs. Through deconstructing the message passing mechanism, PaSca presents a novel Scalable Graph Neural Architecture Paradigm (SGAP), together with a general architecture design space consisting of 150k different designs. Following the paradigm, we implement an auto-search engine that can automatically search well-performing and scalable GNN architectures to balance the trade-off between multiple criteria (e.g., accuracy and efficiency) via multi-objective optimization. Empirical studies on ten benchmark datasets demonstrate that the representative instances (i.e., PaSca -V1, V2, and V3) discovered by our system achieve consistent performance among competitive baselines. Concretely, PaSca -V3 outperforms the state-of-the-art GNN method JK-Net by 0.4\
Benchmark Results
Tested on 8 datasets 25 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 20 | APPNP | 0.8142
±0.0026 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 68 | ResGCN | 0.7890 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 96 | SGC | 0.7765
±0.0012 best reported | best at pub: Deep Learning on Graphs: A Survey (2018) |
| 264 | S^2GC | 0.7360
±0.0050 best reported | best today: Diffusion on Graph: Augmentation of Graph Structure for Node Classification (TMLR 2025) |
| 285 | PaSca-V3 | 0.7340
±0.0050 | This paper |
| 295 | AP-GCN | 0.7330
±0.0060 best reported | best at pub: Adversarial Graph Disentanglement with Component-specific Aggregation (2021) |
| 319 | PaSca-V2 | 0.7310
±0.0030 | This paper |
| 342 | GBP | 0.7290
±0.0050 | This paper |
| 350 | MLP | 0.7289
±0.0010 | |
| 412 | SIGN | 0.7240
±0.0080 | This paper |
| 440 | PaSca-V1 | 0.7220
±0.0050 | This paper |
| 578 | JK-Net | 0.7070
±0.0070 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 17 | APPNP | 0.9355
±0.0060 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 36 | ResGCN | 0.9110 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 135 | JK-Net | 0.8841
±0.0001 best reported | |
| 141 | SGC | 0.8832
±0.0055 best reported | best at pub: Learning Conjoint Attentions for Graph Neural Nets (NeurIPS 2021) |
| 210 | MLP | 0.8690
±0.0074 | |
| 389 | PaSca-V3 | 0.8080
±0.0060 | This paper |
| 396 | PaSca-V2 | 0.8070
±0.0070 | This paper |
| 400 | GBP | 0.8060
±0.0040 | This paper |
| 408 | PaSca-V1 | 0.8050
±0.0040 | This paper |
| 433 | S^2GC | 0.8020
±0.0050 best reported | best today: Diffusion on Graph: Augmentation of Graph Structure for Node Classification (TMLR 2025) Difference within reported uncertainty; not counted as underperformance. |
| 444 | AP-GCN | 0.8010
±0.0070 best reported | best at pub: Adversarial Graph Disentanglement with Component-specific Aggregation (2021) Difference within reported uncertainty; not counted as underperformance. |
| 484 | SIGN | 0.7970
±0.0043 best reported | best today: Gauge-Equivariant Graph Networks via Self-Interference Cancellation (2025) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 21 | APPNP | 0.9573
±0.0012 best reported | |
| 50 | SGC | 0.9511
±0.0009 best reported | best at pub: ROD: Reception-aware Online Distillation for Sparse Graphs (KDD 2021) |
| 259 | \sys-V3 (PaSca-V3) | 0.9270
±0.0080 | This paper |
| 302 | \sys-V2 (PaSca-V2) | 0.9240
±0.0070 | This paper |
| 332 | AP-GCN | 0.9210
±0.0030 | This paper |
| 333 | GBP | 0.9210
±0.0080 | This paper |
| 336 | \sys-V1 (PaSca-V1) | 0.9210
±0.0070 | This paper |
| 349 | JK-Net | 0.9190
±0.0070 | This paper |
| 363 | SIGN | 0.9170
±0.0070 | This paper |
| 367 | S^2GC | 0.9160
±0.0060 | This paper |
| 388 | ResGCN | 0.9130
±0.0090 | This paper |
| 390 | MLP | 0.9128
±0.0063 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Learning on Attribute-Missing Graphs (2020) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 58 | APPNP | 0.9093
±0.0018 best reported | best at pub: A Unified View on Graph Neural Networks as Graph Signal Denoising (2020) |
| 82 | SGC | 0.9022
±0.0021 best reported | |
| 308 | AP-GCN | 0.8518
±0.0023 best reported | best at pub: Adaptive Propagation Graph Convolutional Network (2020) |
| 316 | PaSca-V3 | 0.8480
±0.0070 | This paper |
| 320 | MLP | 0.8463 | |
| 349 | PaSca-V2 | 0.8410
±0.0070 | This paper |
| 361 | PaSca-V1 | 0.8370
±0.0070 | This paper |
| 370 | GBP | 0.8350
±0.0080 | This paper |
| 378 | SIGN | 0.8310
±0.0080 | This paper |
| 379 | S^2GC | 0.8310
±0.0070 | This paper |
| 404 | JK-Net | 0.8200
±0.0060 | This paper |
| 418 | ResGCN | 0.8110
±0.0070 | This paper |
Default metric is F1. The paper reports 2 values on F1 and 5 values on Accuracy .
| # | Model | F1 ↑ default | Accuracy ↑ | Paper |
|---|---|---|---|---|
| 1 | EnGCN | 0.9714
±
0.0003 | — | |
| 2 | SAGN+SLE | 0.9710
±
0.0000 | — | |
| 3 | GAMLP(JK) | 0.9704
±
0.0001 | — | Accuracy
— |
| 10 | PaSca-V3 | —
| 0.9670
±
0.0010 | Accuracy
0.9670
±
0.0010 |
| 14 | GraphSAGE | 0.9660 best reported | — | Accuracy
— best at pub: Accelerating Large Scale Real-Time GNN Inference using Channel Pruning (2021) |
| 4 | GraphSAINT | —
| 0.9660
±
0.0010 | Accuracy
0.9660
±
0.0010 |
| 33 | PaSca-V2 | —
| 0.9630
±
0.0000 | Accuracy
0.9630
±
0.0000 |
| 47 | PaSca-V1 | —
| 0.9580
±
0.0010 | Accuracy
0.9580
±
0.0010 |
| 48 | ClusterGCN | 0.9570 | — | Accuracy
— prev best: GraphSAINT: Graph Sampling Based Inductive Learning Method (ICLR 2019) |
| 58 | GCN | 0.9530
±
0.0010 | — | |
| 91 | FastGCN | —
| 0.9370
±
0.0000 | Accuracy
0.9370
±
0.0000 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GrokFormer | 0.9831
±0.0018 | |
| 2 | PolyFormer | 0.9808
±0.0027 | |
| 3 | SGFormer | 0.9796
±0.0081 | |
| 6 | GAT | 0.9782
±0.0028 best reported | best at pub: SelfGNN: Self-supervised Graph Neural Networks without explicit negative sampling (WWW 2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 9 | GCN | 0.9774
±0.0035 best reported | best at pub: SelfGNN: Self-supervised Graph Neural Networks without explicit negative sampling (WWW 2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 17 | SAGE | 0.9739
±0.0018 | |
| 42 | APPNP | 0.9654
±0.0007 best reported | best at pub: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) best today: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 58 | MLP | 0.9597
±0.0007 | |
| 70 | SGC | 0.9580
±0.0010 best reported | best at pub: Towards Graph Self-Supervised Learning with Contrastive Adjusted Zooming (2021) best today: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) |
| 205 | PaSca-V3 | 0.9380
±0.0090 | This paper |
| 210 | PaSca-V2 | 0.9360
±0.0080 | This paper |
| 223 | GBP | 0.9330
±0.0070 | This paper |
| 232 | PaSca-V1 | 0.9320
±0.0060 | This paper |
| 236 | AP-GCN | 0.9310
±0.0090 | This paper |
| 237 | S^2GC | 0.9310
±0.0080 | This paper |
| 240 | SIGN | 0.9303
±0.0115 best reported | best at pub: ROD: Reception-aware Online Distillation for Sparse Graphs (KDD 2021) best today: Alternately Optimized Graph Neural Networks (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 254 | JK-Net | 0.9250
±0.0040 | This paper |
| 260 | ResGCN | 0.9220
±0.0150 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DoG | 0.9690
±0.0030 | |
| 2 | GWN-fa | 0.9667
±0.0026 | |
| 3 | GWN-sym | 0.9666
±0.0026 | |
| 6 | GraphSAGE | 0.9593
±0.0025 | |
| 12 | GCN | 0.9514
±0.0025 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 21 | GAT | 0.9437
±0.0028 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 25 | APPNP | 0.9400
±0.0030 best reported | best at pub: A Unified View on Graph Neural Networks as Graph Signal Denoising (2020) best today: Diffusion on Graph: Augmentation of Graph Structure for Node Classification (TMLR 2025) |
| 31 | S^2GC | 0.9380
±0.0010 best reported | best today: Diffusion on Graph: Augmentation of Graph Structure for Node Classification (TMLR 2025) |
| 88 | MLP | 0.9280
±0.0020 | |
| 92 | PaSca-V3 | 0.9280
±0.0050 | This paper |
| 96 | SGC | 0.9270
±0.0010 best reported | best at pub: Towards Graph Self-Supervised Learning with Contrastive Adjusted Zooming (2021) |
| 101 | PaSca-V2 | 0.9260
±0.0040 | This paper |
| 106 | JK-Net | 0.9240
±0.0040 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) |
| 110 | GBP | 0.9230
±0.0040 | This paper |
| 129 | PaSca-V1 | 0.9190
±0.0030 | This paper |
| 128 | SIGN | 0.9190
±0.0030 | This paper |
| 136 | AP-GCN | 0.9160
±0.0070 | This paper |
| 174 | ResGCN | 0.8790
±0.0060 | This paper |
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Jacobi | 0.8968 | |
| 2 | GPR | 0.8953 | |
| 3 | LEMP4HG | 0.8939 | |
| 4 | SAGE | 0.8933 | |
| 6 | GCN | 0.8240
±0.0040 | prev best: Calibrating and Improving Graph Contrastive Learning (TMLR 2021) |
| 9 | GAT | 0.8010
±0.0060 | |
| 29 | APPNP | 0.8634 best reported | |
| 46 | PaSca-V3 | 0.8480
±0.0070 | This paper |
| 61 | PaSca-V2 | 0.8410
±0.0070 | This paper |
| 68 | PaSca-V1 | 0.8370
±0.0070 | This paper |
| 67 | AP-GCN | 0.8370
±0.0060 | This paper |
| 72 | GBP | 0.8350
±0.0080 | prev best: Evaluating Deep Graph Neural Networks (2021) |
| 77 | SIGN | 0.8310
±0.0080 | |
| 78 | S^2GC | 0.8310
±0.0070 | prev best: Evaluating Deep Graph Neural Networks (2021) |
| 94 | SGC | 0.8220
±0.0090 | prev best: Evaluating Deep Graph Neural Networks (2021) |
| 100 | JK-Net | 0.8200
±0.0060 | This paper |
| 123 | ResGCN | 0.8110
±0.0070 | This paper |
| 351 | MLP | 0.6605
±0.0020 |
