VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention

We introduce Topoformer, a lightweight and scalable framework for graph representation learning that encodes topological structure into attention-friendly sequences. At the core of our method is Topo-Scan, a novel module that decomposes a graph into a short, ordered sequence of topological tokens by slicing over node or edge filtrations. These sequences capture multi-scale structural patterns, from local motifs to global organization, and are processed by a Transformer to produce expressive graph-level embeddings. Unlike traditional persistent homology pipelines, Topo-Scan is parallelizable, avoids costly diagram computations, and integrates seamlessly with standard deep learning architectures. We provide theoretical guarantees on the stability of our topological encodings and demonstrate state-of-the-art performance across graph classification and molecular property prediction benchmarks. Our results show that Topoformer matches or exceeds strong GNN and topology-based baselines while offering predictable and efficient compute. This work opens a new path for parallelizable and unifying approaches to graph representation learning that integrate topological inductive biases into attention frameworks.

The success of large pretrained Transformers is closely tied to tokenizers, which convert raw input into discrete symbols. Extending these models to graph-structured data remains a significant challenge. In this work, we introduce a graph tokenization framework that generates sequential representations of graphs by combining reversible graph serialization, which preserves graph information, with Byte Pair Encoding (BPE), a widely adopted tokenizer in large language models (LLMs). To better capture structural information, the graph serialization process is guided by global statistics of graph substructures, ensuring that frequently occurring substructures appear more often in the sequence and can be merged by BPE into meaningful tokens. Empirical results demonstrate that the proposed tokenizer enables Transformers such as BERT to be directly applied to graph benchmarks without architectural modifications. The proposed approach achieves state-of-the-art results on 14 benchmark datasets and frequently outperforms both graph neural networks and specialized graph transformers. This work bridges the gap between graph-structured data and the ecosystem of sequence models. Our code is available at bluehere.

While foundation models have revolutionized natural language processing and computer vision by leveraging universal vocabularies, Graph Machine Learning (GML) remains fractured due to the absence of a unified feature and structural representation across diverse domains. Existing works claiming to be Graph Foundation Models (GFMs) are typically restricted to node-level predictions or require fixed feature dimensions, failing to provide a truly task-agnostic backbone for the full spectrum of graph learning applications. In this paper, we introduce the Universal Classifier (UC), which supports arbitrary feature and class cardinalities, unifying node-, edge-, and graph-level objectives under a single similarity-based classification objective. The UC reformulates all node-, edge-, and graph-level prediction tasks as maximizing similarity in the latent space: by lifting heterogeneous features and labels into 3D latent tensors, the model learns transferable features independent of specific input schemas. This architecture allows a single pre-trained model to generalize to node classification, node regression, and link prediction across unseen graphs with varying feature semantics. Experiments show strong zero-shot transfer performance across node-, link-, and graph-level tasks.