Jiliang Tang
Publications
Are Expressive Encoders Necessary for Discrete Graph Generation?
Discrete graph generation has emerged as a powerful paradigm for modeling graph data, often relying on highly expressive neural backbones such as transformers or higher-order architectures. We revisit this design choice by introducing GenGNN, a modular message-passing framework for graph generation. Diffusion models with GenGNN achieve more than 90% validity on Tree and Planar datasets, within margins of graph transformers, at 2-5x faster inference speed. For molecule generation, DiGress with a GenGNN backbone achieves 99.49% Validity. A systematic ablation study shows the benefit provided by each GenGNN component, indicating the need for residual connections to mitigate oversmoothing on complicated graph-structure. Through scaling analyses, we apply a principled metric-space view to investigate learned diffusion representations and uncover whether GNNs can be expressive neural backbones for discrete diffusion.
Plain Transformers are Surprisingly Powerful Link Predictors
Link prediction is a core challenge in graph machine learning, demanding models that capture rich and complex topological dependencies. While Graph Neural Networks (GNNs) are the standard solution, state-of-the-art pipelines often rely on explicit structural heuristics or memory-intensive node embeddings -- approaches that struggle to generalize or scale to massive graphs. Emerging Graph Transformers (GTs) offer a potential alternative but often incur significant overhead due to complex structural encodings, hindering their applications to large-scale link prediction. We challenge these sophisticated paradigms with PENCIL, an encoder-only plain Transformer that replaces hand-crafted priors with attention over sampled local subgraphs, retaining the scalability and hardware efficiency of standard Transformers. Through experimental and theoretical analysis, we show that PENCIL extracts richer structural signals than GNNs, implicitly generalizing a broad class of heuristics and subgraph-based expressivity. Empirically, PENCIL outperforms heuristic-informed GNNs and is far more parameter-efficient than ID-embedding--based alternatives, while remaining competitive across diverse benchmarks -- even without node features. Our results challenge the prevailing reliance on complex engineering techniques, demonstrating that simple design choices are potentially sufficient to achieve the same capabilities.