# S2Aligner: Pair-Efficient and Transferable Pre-Training for Sparse Text-Attributed Graphs

arXiv: https://arxiv.org/abs/2605.18579 · HTML: https://mlsanity.com/paper/2605.18579/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 35 of its 43 references that are in the map.
- First posted on arXiv 18 May 2026.

## Builds on (most cited first, 30 of 35)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Domain-Adversarial Training of Neural Networks](https://mlsanity.com/paper/1505.07818/) (2015)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Invariant Risk Minimization](https://mlsanity.com/paper/1907.02893/) (2019)
- [MiniLM: Deep Self-Attention Distillation for Task-Agnostic Compression of Pre-Trained Transformers](https://mlsanity.com/paper/2002.10957/) (2020)
- [Learning Transferable Features with Deep Adaptation Networks](https://mlsanity.com/paper/1502.02791/) (2015)
- [Text Embeddings by Weakly-Supervised Contrastive Pre-training](https://mlsanity.com/paper/2212.03533/) (2022)
- [Distributionally Robust Neural Networks for Group Shifts: On the Importance of Regularization for Worst-Case Generalization](https://mlsanity.com/paper/1911.08731/) (2019)
- [Deep CORAL: Correlation Alignment for Deep Domain Adaptation](https://mlsanity.com/paper/1607.01719/) (2016)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [Out-of-Distribution Generalization via Risk Extrapolation (REx)](https://mlsanity.com/paper/2003.00688/) (2020)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [Deep Graph Contrastive Representation Learning](https://mlsanity.com/paper/2006.04131/) (2020)
- [Causal inference using invariant prediction: identification and confidence intervals](https://mlsanity.com/paper/1501.01332/) (2015)
- [GraphMAE: Self-Supervised Masked Graph Autoencoders](https://mlsanity.com/paper/2205.10803/) (2022)
- [Wiki-CS: A Wikipedia-Based Benchmark for Graph Neural Networks](https://mlsanity.com/paper/2007.02901/) (2020)
- [One for All: Towards Training One Graph Model for All Classification Tasks](https://mlsanity.com/paper/2310.00149/) (2023)
- [GraphGPT: Graph Instruction Tuning for Large Language Models](https://mlsanity.com/paper/2310.13023/) (2023)
- [LLaGA: Large Language and Graph Assistant](https://mlsanity.com/paper/2402.08170/) (2024)
- [Handling Distribution Shifts on Graphs: An Invariance Perspective](https://mlsanity.com/paper/2202.02466/) (2022)
- [ZeroG: Investigating Cross-dataset Zero-shot Transferability in Graphs](https://mlsanity.com/paper/2402.11235/) (2024)
- [A Survey of Large Language Models for Graphs](https://mlsanity.com/paper/2405.08011/) (2024)
- [Can GNN be Good Adapter for LLMs?](https://mlsanity.com/paper/2402.12984/) (2024)
- [Augmenting Low-Resource Text Classification with Graph-Grounded Pre-training and Prompting](https://mlsanity.com/paper/2305.03324/) (2023)
- [GraphCLIP: Enhancing Transferability in Graph Foundation Models for Text-Attributed Graphs](https://mlsanity.com/paper/2410.10329/) (2024)
- [Text-space Graph Foundation Models: Comprehensive Benchmarks and New Insights](https://mlsanity.com/paper/2406.10727/) (2024)
- [ConGraT: Self-Supervised Contrastive Pretraining for Joint Graph and Text Embeddings](https://mlsanity.com/paper/2305.14321/) (2023)
- [Multi-level Graph Convolutional Networks for Cross-platform Anchor Link Prediction](https://mlsanity.com/paper/2006.01963/) (2020)

## Abstract (arXiv)

Pre-training on text-attributed graphs (TAGs) is central to building transferable graph foundation models, where LLM-as-Aligner methods align graph and text representations through the semantic knowledge of large language models. However, these methods usually assume that node texts provide sufficient and reliable supervision, an assumption often violated in real-world sparse TAGs. When textual anchors are missing, noisy, or uneven across domains, graph structures must be aligned with weak semantic evidence, leading to unreliable structure-semantics correspondence and sparsity-induced transfer bias. This paper presents S2Aligner, a sparsity-aware and structure-enhanced LLM-as-Aligner framework for graph-text pre-training on sparse TAGs. The key idea is to decouple semantic alignment from structural modeling, allowing topology-aware signals to enhance alignment without contaminating the shared semantic space. Specifically, S2Aligner decomposes graph-text representations into semantic and structural components, uses structure-oriented reconstruction with consistency control to inject reliable topology cues into text representations, and suppresses inconsistent structural signals under textual sparsity. Moreover, S2Aligner introduces sparsity-aware cross-domain risk balancing, which calibrates domain risks through a global-domain density ratio and downweights unreliable sparse samples via graph reliability estimation. Theoretical analysis shows that this objective reduces cross-domain generalization gaps by controlling domain risk discrepancy. Extensive experiments across diverse graph domains, sparsity levels, and downstream tasks demonstrate that S2Aligner consistently outperforms existing baselines.