# Heterogeneous Graph Alignment for Joint Reasoning and Interpretability

arXiv: https://arxiv.org/abs/2601.22593 · HTML: https://mlsanity.com/paper/2601.22593/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 42 of its 64 references that are in the map.
- First posted on arXiv 30 Jan 2026.

## Builds on (most cited first, 30 of 42)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Multimodal Machine Learning: A Survey and Taxonomy](https://mlsanity.com/paper/1705.09406/) (2017)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [Graph Neural Networks for Social Recommendation](https://mlsanity.com/paper/1902.07243/) (2019)
- [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)
- [Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classification](https://mlsanity.com/paper/2009.03509/) (2020)
- [Rethinking Graph Transformers with Spectral Attention](https://mlsanity.com/paper/2106.03893/) (2021)
- [MixHop: Higher-Order Graph Convolutional Architectures via Sparsified Neighborhood Mixing](https://mlsanity.com/paper/1905.00067/) (2019)
- [Multimodal Deep Learning](https://mlsanity.com/paper/2301.04856/) (2023)
- [Iterative Deep Graph Learning for Graph Neural Networks: Better and Robust Node Embeddings](https://mlsanity.com/paper/2006.13009/) (2020)
- [Representing Long-Range Context for Graph Neural Networks with Global Attention](https://mlsanity.com/paper/2201.08821/) (2022)
- [Pure Transformers are Powerful Graph Learners](https://mlsanity.com/paper/2207.02505/) (2022)
- [Are Multimodal Transformers Robust to Missing Modality?](https://mlsanity.com/paper/2204.05454/) (2022)
- [Exphormer: Sparse Transformers for Graphs](https://mlsanity.com/paper/2303.06147/) (2023)
- [Graph Inductive Biases in Transformers without Message Passing](https://mlsanity.com/paper/2305.17589/) (2023)
- [Global Self-Attention as a Replacement for Graph Convolution](https://mlsanity.com/paper/2108.03348/) (2021)
- [Causal Attention for Interpretable and Generalizable Graph Classification](https://mlsanity.com/paper/2112.15089/) (2021)
- [On the Unreasonable Effectiveness of Feature propagation in Learning on Graphs with Missing Node Features](https://mlsanity.com/paper/2111.12128/) (2021)
- [MedFuse: Multi-modal fusion with clinical time-series data and chest X-ray images](https://mlsanity.com/paper/2207.07027/) (2022)
- [UniGraph2: Learning a Unified Embedding Space to Bind Multimodal Graphs](https://mlsanity.com/paper/2502.00806/) (2025)
- [Multi-modal Graph Learning for Disease Prediction](https://mlsanity.com/paper/2203.05880/) (2022)
- [Evidence-aware Fake News Detection with Graph Neural Networks](https://mlsanity.com/paper/2201.06885/) (2022)
- [Counterfactual Learning on Graphs: A Survey](https://mlsanity.com/paper/2304.01391/) (2023)
- [AMIGO: Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images](https://mlsanity.com/paper/2303.00865/) (2023)
- [Enhancing Graph Transformers with Hierarchical Distance Structural Encoding](https://mlsanity.com/paper/2308.11129/) (2023)

## Abstract (arXiv)

Multi-graph learning is crucial for extracting meaningful signals from collections of heterogeneous graphs. However, effectively integrating information across graphs with differing topologies, scales, and semantics, often in the absence of shared node identities, remains a significant challenge. We present the Multi-Graph Meta-Transformer (MGMT), a unified, scalable, and interpretable framework for cross-graph learning. MGMT first applies Graph Transformer encoders to each graph, mapping structure and attributes into a shared latent space. It then selects task-relevant supernodes via attention and builds a meta-graph that connects functionally aligned supernodes across graphs using similarity in the latent space. Additional Graph Transformer layers on this meta-graph enable joint reasoning over intra- and inter-graph structure. The meta-graph provides built-in interpretability: supernodes and superedges highlight influential substructures and cross-graph alignments. Evaluating MGMT on both synthetic datasets and real-world neuroscience applications, we show that MGMT consistently outperforms existing state-of-the-art models in graph-level prediction tasks while offering interpretable representations that facilitate scientific discoveries. Our work establishes MGMT as a unified framework for structured multi-graph learning, advancing representation techniques in domains where graph-based data plays a central role.