# TopoTune : A Framework for Generalized Combinatorial Complex Neural Networks

arXiv: https://arxiv.org/abs/2410.06530 · HTML: https://mlsanity.com/paper/2410.06530/

## Key facts

- Cited by 18 papers in the map (data through 14 Oct 2026).
- Builds on 39 of its 60 references that are in the map.
- First posted on arXiv 9 Oct 2024.

## Builds on (most cited first, 30 of 39)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [Link Prediction Based on Graph Neural Networks](https://mlsanity.com/paper/1802.09691/) (2018)
- [TUDataset: A collection of benchmark datasets for learning with graphs](https://mlsanity.com/paper/2007.08663/) (2020)
- [Hypergraph Neural Networks](https://mlsanity.com/paper/1809.09401/) (2018)
- [Principal Neighbourhood Aggregation for Graph Nets](https://mlsanity.com/paper/2004.05718/) (2020)
- [Provably Powerful Graph Networks](https://mlsanity.com/paper/1905.11136/) (2019)
- [A critical look at the evaluation of GNNs under heterophily: Are we really making progress?](https://mlsanity.com/paper/2302.11640/) (2023)
- [Weisfeiler and Lehman Go Topological: Message Passing Simplicial Networks](https://mlsanity.com/paper/2103.03212/) (2021)
- [Weisfeiler and Lehman Go Cellular: CW Networks](https://mlsanity.com/paper/2106.12575/) (2021)
- [Iterative Deep Graph Learning for Graph Neural Networks: Better and Robust Node Embeddings](https://mlsanity.com/paper/2006.13009/) (2020)
- [Weisfeiler and Leman go Machine Learning: The Story so far](https://mlsanity.com/paper/2112.09992/) (2021)
- [Simplicial Neural Networks](https://mlsanity.com/paper/2010.03633/) (2020)
- [Topological Deep Learning: Going Beyond Graph Data](https://mlsanity.com/paper/2206.00606/) (2022)
- [Principled Simplicial Neural Networks for Trajectory Prediction](https://mlsanity.com/paper/2102.10058/) (2021)
- [Cell Complex Neural Networks](https://mlsanity.com/paper/2010.00743/) (2020)
- [Message passing all the way up](https://mlsanity.com/paper/2202.11097/) (2022)
- [Architectures of Topological Deep Learning: A Survey of Message-Passing Topological Neural Networks](https://mlsanity.com/paper/2304.10031/) (2023)
- [Simplicial Attention Networks](https://mlsanity.com/paper/2204.09455/) (2022)
- [Cell Attention Networks](https://mlsanity.com/paper/2209.08179/) (2022)
- [Convolutional Learning on Simplicial Complexes](https://mlsanity.com/paper/2301.11163/) (2023)

## Built on by (most cited first, 18 of 18)

- [HOPSE: Scalable Higher-Order Positional and Structural Encoder for Combinatorial Representations](https://mlsanity.com/paper/2505.15405/) (2025)
- [HiPoNet: A Multi-View Simplicial Complex Network for High Dimensional Point-Cloud and Single-Cell Data](https://mlsanity.com/paper/2502.07746/) (2025)
- [Ordered Topological Deep Learning: a Network Modeling Case Study](https://mlsanity.com/paper/2503.16746/) (2025)
- [Demystifying Topological Message-Passing with Relational Structures: A Case Study on Oversquashing in Simplicial Message-Passing](https://mlsanity.com/paper/2506.06582/) (2025)
- [GraphUniverse: Synthetic Graph Generation for Evaluating Inductive Generalization](https://mlsanity.com/paper/2509.21097/) (2025)
- [The Logical Expressiveness of Topological Neural Networks](https://mlsanity.com/paper/2604.19212/) (2026)
- [Grothendieck Graph Neural Networks Framework: An Algebraic Platform for Crafting Topology-Aware GNNs](https://mlsanity.com/paper/2412.08835/) (2024)
- [CellCLAT: Preserving Topology and Trimming Redundancy in Self-Supervised Cellular Contrastive Learning](https://mlsanity.com/paper/2505.21587/) (2025)
- [Heat Kernel Goes Topological](https://mlsanity.com/paper/2507.12380/) (2025)
- [Directed Semi-Simplicial Learning with Applications to Brain Activity Decoding](https://mlsanity.com/paper/2505.17939/) (2025)
- [Weisfeiler Lehman Test on Combinatorial Complexes: Generalized Expressive Power of Topological Neural Networks](https://mlsanity.com/paper/2605.00725/) (2026)
- [No Triangulation Without Representation: Generalization in Topological Deep Learning](https://mlsanity.com/paper/2605.06467/) (2026)
- [Neural Point-Forms](https://mlsanity.com/paper/2605.15524/) (2026)
- [Collapsed Effective Operators for Higher-order Structures](https://mlsanity.com/paper/2606.23517/) (2026)
- [Differentiable Lifting for Topological Neural Networks](https://mlsanity.com/paper/2608.01160/) (2026)
- [Look Before You Lift: Visual and Quantitative Diagnostics for Topological Deep Learning](https://mlsanity.com/paper/2608.15388/) (2026)
- [Combinatorial Network-Based Manifold Topological Deep Learning for Image Analysis](https://mlsanity.com/paper/2609.25453/) (2026)
- [Higher-Order Positional Encodings for Graph Representation Learning](https://mlsanity.com/paper/2610.01903/) (2026)

## Abstract (arXiv)

Graph Neural Networks (GNNs) effectively learn from relational data by leveraging graph symmetries. However, many real-world systems -- such as biological or social networks -- feature multi-way interactions that GNNs fail to capture. Topological Deep Learning (TDL) addresses this by modeling and leveraging higher-order structures, with Combinatorial Complex Neural Networks (CCNNs) offering a general and expressive approach that has been shown to outperform GNNs. However, TDL lacks the principled and standardized frameworks that underpin GNN development, restricting its accessibility and applicability. To address this issue, we introduce Generalized CCNNs (GCCNs), a simple yet powerful family of TDL models that can be used to systematically transform any (graph) neural network into its TDL counterpart. We prove that GCCNs generalize and subsume CCNNs, while extensive experiments on a diverse class of GCCNs show that these architectures consistently match or outperform CCNNs, often with less model complexity. In an effort to accelerate and democratize TDL, we introduce TopoTune, a lightweight software for defining, building, and training GCCNs with unprecedented flexibility and ease.