CIN++: Enhancing Topological Message Passing
Abstract
Graph Neural Networks (GNNs) have demonstrated remarkable success in learning from graph-structured data. However, they face significant limitations in expressive power, struggling with long-range interactions and lacking a principled approach to modeling higher-order structures and group interactions. Cellular Isomorphism Networks (CINs) recently addressed most of these challenges with a message passing scheme based on cell complexes. Despite their advantages, CINs make use only of boundary and upper messages which do not consider a direct interaction between the rings present in the underlying complex. Accounting for these interactions might be crucial for learning representations of many real-world complex phenomena such as the dynamics of supramolecular assemblies, neural activity within the brain, and gene regulation processes. In this work, we propose CIN++, an enhancement of the topological message passing scheme introduced in CINs. Our message passing scheme accounts for the aforementioned limitations by letting the cells to receive also lower messages within each layer. By providing a more comprehensive representation of higher-order and long-range interactions, our enhanced topological message passing scheme achieves state-of-the-art results on large-scale and long-range chemistry benchmarks.
Benchmark Results
Tested on 6 datasets 12 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | MAE ↓ | Paper |
|---|---|---|---|
| 1 | TIGT | 0.0140
±0.0010 | |
| 2 | FloydNet | 0.0160 | |
| 3 | GSSC | 0.0190
±0.0010 | |
| 7 | CIN | 0.0210
±0.0010 | prev best: Weisfeiler and Lehman Go Cellular: CW Networks (NeurIPS 2021) Improvement within reported uncertainty; not highlighted. |
| 53 | CIN++-small | 0.0440
±0.0040 | This paper |
| 69 | GIN | 0.0880
±0.0020 |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 26 | CIN | 0.9440
±0.0370 | prev best: Weisfeiler and Lehman Go Cellular: CW Networks (NeurIPS 2021) Improvement within reported uncertainty; not highlighted. |
| 29 | CAN | 0.9410
±0.0480 | This paper |
| 39 | GIN | 0.9330
±0.0290 best reported | best at pub: ProtGNN: Towards Self-Explaining Graph Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 64 | GSN | 0.9220
±0.0750 | This paper |
| 63 | GCN | 0.9220
±0.0440 | |
| 139 | PPGNs | 0.9060
±0.0870 | This paper |
| 164 | WL kernel | 0.9040
±0.0570 | This paper |
| 244 | Natural GN | 0.8940
±0.0160 | This paper |
| 403 | MLP | 0.8660
±0.0495 | |
| 425 | DGCNN | 0.8583
±0.0116 best reported | best at pub: Deep Learning on Attributed Graphs: A Journey from Graphs to Their Embeddings and Back (2018) best today: Graph Structure Refinement with Energy-based Contrastive Learning (AAAI 2024) Difference within reported uncertainty; not counted as underperformance. |
| 467 | PK | 0.8450
±0.0060 best reported | best at pub: Propagation Kernels (2014) |
| 492 | IGN | 0.8390
±0.1300 | This paper |
| 584 | GK (k=3) | 0.8140
±0.0170 | This paper |
| 643 | RWK | 0.7920
±0.0210 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 best reported | best at pub: 1-WL Expressiveness Is (Almost) All You Need (2022) |
| 3 | GCN | 0.9727 | |
| 10 | WL kernel | 0.8600
±0.0180 | This paper |
| 19 | CIN | 0.8530
±0.0120 | prev best: Weisfeiler and Lehman Go Cellular: CW Networks (NeurIPS 2021) Improvement within reported uncertainty; not highlighted. |
| 28 | PK | 0.8450
±0.0010 best reported | best at pub: Propagation Kernels (2014) |
| 29 | CAN | 0.8450
±0.0160 | This paper |
| 50 | GSN | 0.8350
±0.0200 | This paper |
| 64 | PPGNs | 0.8320
±0.0110 | This paper |
| 82 | SIN | 0.8280
±0.0220 best reported | best at pub: Weisfeiler and Lehman Go Topological: Message Passing Simplicial Networks (ICML 2021) Difference within reported uncertainty; not counted as underperformance. |
| 109 | Natural GN | 0.8240
±0.0130 | This paper |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 373 | DGCNN | 0.7650
±0.0190 best reported | best at pub: GraphCrop: Subgraph Cropping for Graph Classification (2020) Difference within reported uncertainty; not counted as underperformance. |
| 428 | IGN | 0.7433
±0.0271 best reported | best at pub: Towards Better Graph Representation Learning with Parameterized Decomposition & Filtering (ICML 2023) Difference within reported uncertainty; not counted as underperformance. |
| 540 | DCNN | 0.6261 best reported | |
| 541 | GK (k=3) | 0.6250
±0.0030 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 12 | CIN | 0.8050
±0.0390 | prev best: Weisfeiler and Lehman Go Cellular: CW Networks (NeurIPS 2021) Improvement within reported uncertainty; not highlighted. |
| 32 | GIN | 0.7880
±0.0410 best reported | best at pub: CI-GNN: A Granger Causality-Inspired Graph Neural Network for Interpretable Brain Network-Based Psychiatric Diagnosis (2023) best today: Permutation-Invariant graph partitioning: How graph neural networks capture structural interactions? (2023) Difference within reported uncertainty; not counted as underperformance. |
| 44 | CAN | 0.7820
±0.0200 | This paper |
| 67 | SAGE | 0.7726
±0.0228 | |
| 74 | PPGNs | 0.7720
±0.0470 | This paper |
| 100 | IGN | 0.7660
±0.0550 | prev best: Towards Better Graph Representation Learning with Parameterized Decomposition & Filtering (ICML 2023) Improvement within reported uncertainty; not highlighted. |
| 102 | GSN | 0.7660
±0.0500 | prev best: On Structural Expressive Power of Graph Transformers (KDD 2023) Improvement within reported uncertainty; not highlighted. |
| 118 | SIN | 0.7640
±0.0330 | This paper |
| 132 | DGCNN | 0.7626 best reported | best at pub: Orthogonal Graph Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 149 | MLP | 0.7600
±0.0320 | |
| 252 | WL kernel | 0.7500
±0.0310 | This paper |
| 328 | PK | 0.7370
±0.0070 | This paper |
| 421 | Natural GN | 0.7170
±0.0100 | This paper |
| 430 | GK (k=3) | 0.7140
±0.0030 | This paper |
| 501 | DCNN | 0.6130
±0.0160 | prev best: Graph Capsule Convolutional Neural Networks (ICML 2018) Improvement within reported uncertainty; not highlighted. |
| 510 | RWK | 0.5960
±0.0010 | This paper |
LRGB
| # | Model | MAE ↓ | Paper |
|---|---|---|---|
| 1 | GCN | 0.2421
±0.0016 best reported | best at pub: On the Connection Between MPNN and Graph Transformer (ICML 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 2 | IPR-MPNN | 0.2422
±0.0007 | |
| 3 | TANGO-GPS | 0.2422
±0.0014 | |
| 5 | GIN | 0.2429
±0.0019 | |
| 7 | GatedGCN | 0.2431
±0.0020 best reported | best at pub: On the Connection Between MPNN and Graph Transformer (ICML 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 49 | GINE | 0.2473
±0.0017 best reported | best at pub: On the Connection Between MPNN and Graph Transformer (ICML 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 69 | GatedGCN+RWSE | 0.2485
±0.0022 best reported | best at pub: On the Connection Between MPNN and Graph Transformer (ICML 2023) best today: Benchmarking Positional Encodings for GNNs and Graph Transformers (KDD 2024) |
| 110 | CIN | 0.2523
±0.0013 | This paper |
| 113 | Transformer+LapPE | 0.2529
±0.0016 | This paper |
| 123 | SAN+RWSE | 0.2545
±0.0012 | This paper |
| 155 | SAN+LapPE | 0.2680
±0.0040 best reported | best at pub: LRGB (NeurIPS 2022) best today: Learning Efficient Positional Encodings with Graph Neural Networks (ICLR 2025) Difference within reported uncertainty; not counted as underperformance. |
| 183 | GCNII | 0.3471
±0.0010 | This paper |
| 201 | MLP | 0.4351
±0.0008 | This paper |
| # | Model | AP ↑ | Paper |
|---|---|---|---|
| 1 | S^2GCN | 0.7311
±0.0066 | |
| 2 | S4G | 0.7293
±0.0004 | |
| 3 | BuNN | 0.7276
±0.0065 | |
| 4 | GCN | 0.7261
±0.0011 best reported | best at pub: On the Connection Between MPNN and Graph Transformer (ICML 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 26 | GIN | 0.7059
±0.0089 | |
| 34 | GatedGCN | 0.7006
±0.0033 best reported | best at pub: On the Connection Between MPNN and Graph Transformer (ICML 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 35 | GCNII | 0.6990
±0.0030 best reported | best at pub: LRGB (NeurIPS 2022) |
| 73 | GatedGCN+RWSE | 0.6685
±0.0062 best reported | best at pub: On the Connection Between MPNN and Graph Transformer (ICML 2023) |
| 78 | GINE | 0.6621
±0.0067 best reported | best at pub: On the Connection Between MPNN and Graph Transformer (ICML 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 86 | CIN | 0.6569
±0.0117 | This paper |
| 89 | SAN+RWSE | 0.6562
±0.0075 best reported | best at pub: Multiresolution Graph Transformers and Wavelet Positional Encoding for Learning Hierarchical Structures (2023) Difference within reported uncertainty; not counted as underperformance. |
| 116 | SAN+LapPE | 0.6384
±0.0121 | This paper |
| 118 | Transformer+LapPE | 0.6326
±0.0126 | This paper |
| 181 | MLP | 0.4060
±0.0021 | This paper |
