# State Space Models over Directed Graphs

arXiv: https://arxiv.org/abs/2509.13735 · HTML: https://mlsanity.com/paper/2509.13735/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 46 of its 62 references that are in the map.
- First posted on arXiv 17 Sep 2025.

## Builds on (most cited first, 30 of 46)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation](https://mlsanity.com/paper/1406.1078/) (2014)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Transformers are SSMs: Generalized Models and Efficient Algorithms Through Structured State Space Duality](https://mlsanity.com/paper/2405.21060/) (2024)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [Efficient Neural Architecture Search via Parameter Sharing](https://mlsanity.com/paper/1802.03268/) (2018)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [A Generalization of Transformer Networks to Graphs](https://mlsanity.com/paper/2012.09699/) (2020)
- [HiPPO: Recurrent Memory with Optimal Polynomial Projections](https://mlsanity.com/paper/2008.07669/) (2020)
- [On the Parameterization and Initialization of Diagonal State Space Models](https://mlsanity.com/paper/2206.11893/) (2022)
- [Residual Gated Graph ConvNets](https://mlsanity.com/paper/1711.07553/) (2017)
- [A Survey on Oversmoothing in Graph Neural Networks](https://mlsanity.com/paper/2303.10993/) (2023)
- [NodeFormer: A Scalable Graph Structure Learning Transformer for Node Classification](https://mlsanity.com/paper/2306.08385/) (2023)
- [Structure-Aware Transformer for Graph Representation Learning](https://mlsanity.com/paper/2202.03036/) (2022)
- [Exphormer: Sparse Transformers for Graphs](https://mlsanity.com/paper/2303.06147/) (2023)
- [On Over-Squashing in Message Passing Neural Networks: The Impact of Width, Depth, and Topology](https://mlsanity.com/paper/2302.02941/) (2023)
- [NAGphormer: A Tokenized Graph Transformer for Node Classification in Large Graphs](https://mlsanity.com/paper/2206.04910/) (2022)
- [Graph-Mamba: Towards Long-Range Graph Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2402.00789/) (2024)
- [MagNet: A Neural Network for Directed Graphs](https://mlsanity.com/paper/2102.11391/) (2021)
- [D-VAE: A Variational Autoencoder for Directed Acyclic Graphs](https://mlsanity.com/paper/1904.11088/) (2019)
- [Edge Directionality Improves Learning on Heterophilic Graphs](https://mlsanity.com/paper/2305.10498/) (2023)

## Abstract (arXiv)

Directed graphs are ubiquitous across numerous domains, where the directionality of edges encodes critical causal dependencies. However, existing GNNs and graph Transformers tailored for directed graphs face two major challenges: (1) effectively capturing long-range causal dependencies derived from directed edges; (2) balancing accuracy and training efficiency when processing large-scale graph datasets. In recent years, state space models (SSMs) have achieved substantial progress in causal sequence tasks, and their variants designed for graphs have demonstrated state-of-the-art accuracy while maintaining high efficiency across various graph learning benchmarks. However, existing graph state space models are exclusively designed for undirected graphs, which limits their performance in directed graph learning. To this end, we propose an innovative approach DirEgo2Token which sequentializes directed graphs via k-hop ego graphs. This marks the first systematic extension of state space models to the field of directed graph learning. Building upon this, we develop DirGraphSSM, a novel directed graph neural network architecture that implements state space models on directed graphs via the message-passing mechanism. Experimental results demonstrate that DirGraphSSM achieves state-of-the-art performance on three representative directed graph learning tasks while attaining competitive performance on two additional tasks with 1.5×  to 2×  training speed improvements compared to existing state-of-the-art models.