Masked Language Models are Good Heterogeneous Graph Generalizers

Heterogeneous graph neural networks (HGNNs) excel at capturing structural and semantic information in heterogeneous graphs (HGs), while struggling to generalize across domains and tasks. Recently, some researchers have turned to integrating HGNNs with large language models (LLMs) for more generalizable heterogeneous graph learning. However, these approaches typically extract structural information via HGNNs as HG tokens, and disparities in embedding spaces between HGNNs and LLMs have been shown to bias the LLM's comprehension of HGs. Moreover, as these HG tokens are often derived from node-level tasks, the model's ability to generalize across tasks remains limited. To this end, we propose a simple yet effective Masked Language Modeling-based method, called MLM4HG. MLM4HG introduces metapath-based textual sequences instead of HG tokens to extract structural and semantic information inherent in HGs, and designs customized textual templates to unify different graph tasks into a coherent cloze-style "mask" token prediction paradigm. Specifically, MLM4HG first converts HGs from various domains to texts based on metapaths, and subsequently combines them with the unified task texts to form a HG-based corpus. Moreover, the corpus is fed into a pretrained LM for fine-tuning with a constrained target vocabulary, enabling the fine-tuned LM to generalize to unseen target HGs. Extensive cross-domain and multi-task experiments on four real-world datasets demonstrate the superior generalization performance of MLM4HG over state-of-the-art methods in both few-shot and zero-shot scenarios. Our code is available at https://github.com/BUPT-GAMMA/MLM4HG.

Graph Positional Autoencoders as Self-supervised Learners

Graph self-supervised learning seeks to learn effective graph representations without relying on labeled data. Among various approaches, graph autoencoders (GAEs) have gained significant attention for their efficiency and scalability. Typically, GAEs take incomplete graphs as input and predict missing elements, such as masked nodes or edges. While effective, our experimental investigation reveals that traditional node or edge masking paradigms primarily capture low-frequency signals in the graph and fail to learn the expressive structural information. To address these issues, we propose Graph Positional Autoencoders (GraphPAE), which employs a dual-path architecture to reconstruct both node features and positions. Specifically, the feature path uses positional encoding to enhance the message-passing processing, improving GAE's ability to predict the corrupted information. The position path, on the other hand, leverages node representations to refine positions and approximate eigenvectors, thereby enabling the encoder to learn diverse frequency information. We conduct extensive experiments to verify the effectiveness of GraphPAE, including heterophilic node classification, graph property prediction, and transfer learning. The results demonstrate that GraphPAE achieves state-of-the-art performance and consistently outperforms baselines by a large margin.

Data-centric Federated Graph Learning with Large Language Models

In federated graph learning (FGL), a complete graph is divided into multiple subgraphs stored in each client due to privacy concerns, and all clients jointly train a global graph model by only transmitting model parameters. A pain point of FGL is the heterogeneity problem, where nodes or structures present non-IID properties among clients (e.g., different node label distributions), dramatically undermining the convergence and performance of FGL. To address this, existing efforts focus on design strategies at the model level, i.e., they design models to extract common knowledge to mitigate heterogeneity. However, these model-level strategies fail to fundamentally address the heterogeneity problem as the model needs to be designed from scratch when transferring to other tasks. Motivated by large language models (LLMs) having achieved remarkable success, we aim to utilize LLMs to fully understand and augment local text-attributed graphs, to address data heterogeneity at the data level. In this paper, we propose a general framework LLM4FGL that innovatively decomposes the task of LLM for FGL into two sub-tasks theoretically. Specifically, for each client, it first utilizes the LLM to generate missing neighbors and then infers connections between generated nodes and raw nodes. To improve the quality of generated nodes, we design a novel federated generation-and-reflection mechanism for LLMs, without the need to modify the parameters of the LLM but relying solely on the collective feedback from all clients. After neighbor generation, all the clients utilize a pre-trained edge predictor to infer the missing edges. Furthermore, our framework can seamlessly integrate as a plug-in with existing FGL methods. Experiments on three real-world datasets demonstrate the superiority of our method compared to advanced baselines.

Blend the Separated: Mixture of Synergistic Experts for Data-Scarcity Drug-Target Interaction Prediction

Drug-target interaction prediction (DTI) is essential in various applications including drug discovery and clinical application. There are two perspectives of input data widely used in DTI prediction: Intrinsic data represents how drugs or targets are constructed, and extrinsic data represents how drugs or targets are related to other biological entities. However, any of the two perspectives of input data can be scarce for some drugs or targets, especially for those unpopular or newly discovered. Furthermore, ground-truth labels for specific interaction types can also be scarce. Therefore, we propose the first method to tackle DTI prediction under input data and/or label scarcity. To make our model functional when only one perspective of input data is available, we design two separate experts to process intrinsic and extrinsic data respectively and fuse them adaptively according to different samples. Furthermore, to make the two perspectives complement each other and remedy label scarcity, two experts synergize with each other in a mutually supervised way to exploit the enormous unlabeled data. Extensive experiments on 3 real-world datasets under different extents of input data scarcity and/or label scarcity demonstrate our model outperforms states of the art significantly and steadily, with a maximum improvement of 53.53%. We also test our model without any data scarcity and it still outperforms current methods.

HeTGB: A Comprehensive Benchmark for Heterophilic Text-Attributed Graphs

Graph neural networks (GNNs) have demonstrated success in modeling relational data primarily under the assumption of homophily. However, many real-world graphs exhibit heterophily, where linked nodes belong to different categories or possess diverse attributes. Additionally, nodes in many domains are associated with textual descriptions, forming heterophilic text-attributed graphs (TAGs). Despite their significance, the study of heterophilic TAGs remains underexplored due to the lack of comprehensive benchmarks. To address this gap, we introduce the Heterophilic Text-attributed Graph Benchmark (HeTGB), a novel benchmark comprising five real-world heterophilic graph datasets from diverse domains, with nodes enriched by extensive textual descriptions. HeTGB enables systematic evaluation of GNNs, pre-trained language models (PLMs) and co-training methods on the node classification task. Through extensive benchmarking experiments, we showcase the utility of text attributes in heterophilic graphs, analyze the challenges posed by heterophilic TAGs and the limitations of existing models, and provide insights into the interplay between graph structures and textual attributes. We have publicly released HeTGB with baseline implementations to facilitate further research in this field.

Between Circuits and Chomsky: Pre-pretraining on Formal Languages Imparts Linguistic Biases

Pretraining language models on formal languages can improve their acquisition of natural language, but it is unclear which features of the formal language impart an inductive bias that leads to effective transfer. Drawing on insights from linguistics and complexity theory, we hypothesize that effective transfer occurs when the formal language both captures dependency structures in natural language and remains within the computational limitations of the model architecture. Focusing on transformers, we find that formal languages with both these properties enable language models to achieve lower loss on natural language and better linguistic generalization compared to other languages. In fact, pre-pretraining, or training on formal-then-natural language, reduces loss more efficiently than the same amount of natural language. For a 1B-parameter language model trained on roughly 1.6B tokens of natural language, pre-pretraining achieves the same loss and better linguistic generalization with a 33% smaller token budget. We also give mechanistic evidence of cross-task transfer from formal to natural language: attention heads acquired during formal language pretraining remain crucial for the model's performance on syntactic evaluations.

PathRAG: Pruning Graph-based Retrieval Augmented Generation with Relational Paths

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG

Graph Foundation Models for Recommendation: A Comprehensive Survey

Recommender systems (RS) serve as a fundamental tool for navigating the vast expanse of online information, with deep learning advancements playing an increasingly important role in improving ranking accuracy. Among these, graph neural networks (GNNs) excel at extracting higher-order structural information, while large language models (LLMs) are designed to process and comprehend natural language, making both approaches highly effective and widely adopted. Recent research has focused on graph foundation models (GFMs), which integrate the strengths of GNNs and LLMs to model complex RS problems more efficiently by leveraging the graph-based structure of user-item relationships alongside textual understanding. In this survey, we provide a comprehensive overview of GFM-based RS technologies by introducing a clear taxonomy of current approaches, diving into methodological details, and highlighting key challenges and future directions. By synthesizing recent advancements, we aim to offer valuable insights into the evolving landscape of GFM-based recommender systems.

Rethinking Byzantine Robustness in Federated Recommendation from Sparse Aggregation Perspective

To preserve user privacy in recommender systems, federated recommendation (FR) based on federated learning (FL) emerges, keeping the personal data on the local client and updating a model collaboratively. Unlike FL, FR has a unique sparse aggregation mechanism, where the embedding of each item is updated by only partial clients, instead of full clients in a dense aggregation of general FL. Recently, as an essential principle of FL, model security has received increasing attention, especially for Byzantine attacks, where malicious clients can send arbitrary updates. The problem of exploring the Byzantine robustness of FR is particularly critical since in the domains applying FR, e.g., e-commerce, malicious clients can be injected easily by registering new accounts. However, existing Byzantine works neglect the unique sparse aggregation of FR, making them unsuitable for our problem. Thus, we make the first effort to investigate Byzantine attacks on FR from the perspective of sparse aggregation, which is non-trivial: it is not clear how to define Byzantine robustness under sparse aggregations and design Byzantine attacks under limited knowledge/capability. In this paper, we reformulate the Byzantine robustness under sparse aggregation by defining the aggregation for a single item as the smallest execution unit. Then we propose a family of effective attack strategies, named Spattack, which exploit the vulnerability in sparse aggregation and are categorized along the adversary's knowledge and capability. Extensive experimental results demonstrate that Spattack can effectively prevent convergence and even break down defenses under a few malicious clients, raising alarms for securing FR systems.

Invariant debiasing learning for recommendation via biased imputation

Previous debiasing studies utilize unbiased data to make supervision of model training. They suffer from the high trial risks and experimental costs to obtain unbiased data. Recent research attempts to use invariant learning to detach the invariant preference of users for unbiased recommendations in an unsupervised way. However, it faces the drawbacks of low model accuracy and unstable prediction performance due to the losing cooperation with variant preference. In this paper, we experimentally demonstrate that invariant learning causes information loss by directly discarding the variant information, which reduces the generalization ability and results in the degradation of model performance in unbiased recommendations. Based on this consideration, we propose a novel lightweight knowledge distillation framework (KDDebias) to automatically learn the unbiased preference of users from both invariant and variant information. Specifically, the variant information is imputed to the invariant user preference in the distance-aware knowledge distillation process. Extensive experiments on three public datasets, i.e., Yahoo!R3, Coat, and MIND, show that with the biased imputation from the variant preference of users, our proposed method achieves significant improvements with less than 50% learning parameters compared to the SOTA unsupervised debiasing model in recommender systems. Our code are publicly available at https://github.com/BAI-LAB/KD-Debias.