Retrieval-Augmented Generation (RAG) has emerged as a paradigm for enhancing large language models (LLMs) with external knowledge, yet existing graph-based methods face a fundamental limitation: entity-centric and chunk-centric approaches operate on representations anchored to original text without true knowledge fusion. While entity-centric methods connect logically related content and chunk-centric methods preserve context, both retrieve information separately through similarity search, missing emergent understanding from their synthesis. In this paper, we propose HyGRAG, a hierarchical graph RAG framework that transcends source documents by addressing three core challenges: constructing summaries that genuinely integrate contextual and relational information, leveraging these synthesized representations to access emergent knowledge during retrieval, and efficiently updating hierarchical structures for dynamic corpora. Specifically, we design hierarchical index structures over hybrid graphs with both chunk and entity nodes, then iteratively cluster them and generate LLM-based summaries. Then, we design context and relation-aware retrieval that searches across all abstraction levels while expanding through community membership. Moreover, we enable dynamic knowledge update through attachment-based algorithms with only local re-summarization. Experimental results show that HyGRAG improves the average accuracy of multi-hop reasoning tasks by 9.7%, while maintaining reasonable efficiency.

Graphs are a complex and versatile data structure used across various domains, with possibly multi-label nodes playing a particularly crucial role. Examples include proteins in PPI networks with multiple functions and users in social or e-commerce networks exhibiting diverse interests. Tackling multi-label node classification (MLNC) on graphs has led to the development of various approaches. Some methods leverage graph neural networks (GNNs) to exploit label co-occurrence correlations, while others incorporate label embeddings to capture label proximity. However, these approaches fail to account for the intricate influences between labels in non-Euclidean graph data. To address this issue, we decompose the message passing process in GNNs into two operations: propagation and transformation. We then conduct a comprehensive analysis and quantification of the influence correlations between labels in each operation. Building on these insights, we propose a novel model, Label Influence Propagation (LIP). Specifically, we construct a label influence graph based on the integrated label correlations. Then, we propagate high-order influences through this graph, dynamically adjusting the learning process by amplifying labels with positive contributions and mitigating those with negative influence. Finally, our framework is evaluated on comprehensive benchmark datasets, consistently outperforming SOTA methods across various settings, demonstrating its effectiveness on MLNC tasks.

In recent years, the rapid development of foundation models and graph pre-training technologies has spurred increasing interest in constructing a universal pre-trained graph model or Graph Foundation Model (GFM). However, a significant challenge is that existing models are unable to address feature heterogeneity in graph data without textual information, which hinders the transferability of graph models across different datasets. To bridge this gap, we propose the concept of learnable graph patches, which we regard as the smallest semantic units of any graph data. We decompose the graph into learnable graph patches by unfolding the node features and constructing corresponding patch structures separately. We then design PatchNet, a framework that mines transferable information from graph data across domains. Specifically, after extracting graph patches, we propose a patch encoder to extract knowledge from each unit and a patch aggregator to learn how the units are combined into a whole. Due to its domain-agnostic nature, the model can be applied to downstream data across different domains. Furthermore, we analyze the connection between PatchNet and existing graph models, as well as the transferability of the node embeddings it generates. Empirically, our method not only achieves the capability to use multi-domain graphs for pre-training, but also shows enhanced performance across various downstream datasets and tasks. Moreover, we observe consistent improvement in downstream performance as the volume of pre-training data increases.

Existing foundation models, such as CLIP, aim to learn a unified embedding space for multimodal data, enabling a wide range of downstream web-based applications like search, recommendation, and content classification. However, these models often overlook the inherent graph structures in multimodal datasets, where entities and their relationships are crucial. Multimodal graphs (MMGs) represent such graphs where each node is associated with features from different modalities, while the edges capture the relationships between these entities.On the other hand, existing graph foundation models primarily focus on text-attributed graphs (TAGs) and are not designed to handle the complexities of MMGs. To address these limitations, we propose UniGraph2, a novel cross-domain graph foundation model that enables general representation learning on MMGs, providing a unified embedding space. UniGraph2 employs modality-specific encoders alongside a graph neural network (GNN) to learn a unified low-dimensional embedding space that captures both the multimodal information and the underlying graph structure. We propose a new cross-domain multi-graph pre-training algorithm at scale to ensure effective transfer learning across diverse graph domains and modalities. Additionally, we adopt a Mixture of Experts (MoE) component to align features from different domains and modalities, ensuring coherent and robust embeddings that unify the information across modalities. Extensive experiments on a variety of multimodal graph tasks demonstrate that UniGraph2 significantly outperforms state-of-the-art models in tasks such as representation learning, transfer learning, and multimodal generative tasks, offering a scalable and flexible solution for learning on MMGs.

Recently, the paradigm of pre-training and fine-tuning graph neural networks has been intensively studied and applied in a wide range of graph mining tasks. Its success is generally attributed to the structural consistency between pre-training and downstream datasets, which, however, does not hold in many real-world scenarios. Existing works have shown that the structural divergence between pre-training and downstream graphs significantly limits the transferability when using the vanilla fine-tuning strategy. This divergence leads to model overfitting on pre-training graphs and causes difficulties in capturing the structural properties of the downstream graphs. In this paper, we identify the fundamental cause of structural divergence as the discrepancy of generative patterns between the pre-training and downstream graphs. Furthermore, we propose G-Tuning to preserve the generative patterns of downstream graphs. Given a downstream graph G, the core idea is to tune the pre-trained GNN so that it can reconstruct the generative patterns of G, the graphon W. However, the exact reconstruction of a graphon is known to be computationally expensive. To overcome this challenge, we provide a theoretical analysis that establishes the existence of a set of alternative graphons called graphon bases for any given graphon. By utilizing a linear combination of these graphon bases, we can efficiently approximate W. This theoretical finding forms the basis of our model, as it enables effective learning of the graphon bases and their associated coefficients. Compared with existing algorithms, G-Tuning demonstrates consistent performance improvement in 7 in-domain and 7 out-of-domain transfer learning experiments.

Graph self-supervised learning has sparked a research surge in training informative representations without accessing any labeled data. However, our understanding of graph self-supervised learning remains limited, and the inherent relationships between various self-supervised tasks are still unexplored. Our paper aims to provide a fresh understanding of graph self-supervised learning based on task correlations. Specifically, we evaluate the performance of the representations trained by one specific task on other tasks and define correlation values to quantify task correlations. Through this process, we unveil the task correlations between various self-supervised tasks and can measure their expressive capabilities, which are closely related to downstream performance. By analyzing the correlation values between tasks across various datasets, we reveal the complexity of task correlations and the limitations of existing multi-task learning methods. To obtain more capable representations, we propose Graph Task Correlation Modeling (GraphTCM) to illustrate the task correlations and utilize it to enhance graph self-supervised training. The experimental results indicate that our method significantly outperforms existing methods across various downstream tasks.

Pathogenic chromosome abnormalities are very common among the general population. While numerical chromosome abnormalities can be quickly and precisely detected, structural chromosome abnormalities are far more complex and typically require considerable efforts by human experts for identification. This paper focuses on investigating the modeling of chromosome features and the identification of chromosomes with structural abnormalities. Most existing data-driven methods concentrate on a single chromosome and consider each chromosome independently, overlooking the crucial aspect of homologous chromosomes. In normal cases, homologous chromosomes share identical structures, with the exception that one of them is abnormal. Therefore, we propose an adaptive method to align homologous chromosomes and diagnose structural abnormalities through homologous similarity. Inspired by the process of human expert diagnosis, we incorporate information from multiple pairs of homologous chromosomes simultaneously, aiming to reduce noise disturbance and improve prediction performance. Extensive experiments on real-world datasets validate the effectiveness of our model compared to baselines.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our \textit{G-Retriever} method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, \textit{G-Retriever} performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~\footnote{Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}}

Anti-money laundering (AML) systems play a critical role in safeguarding global economy. As money laundering is considered as one of the top group crimes, there is a crucial need to discover money laundering sub-network behind a particular money laundering transaction for a robust AML system. However, existing rule-based methods for money laundering sub-network discovery is heavily based on domain knowledge and may lag behind the modus operandi of launderers. Therefore, in this work, we first address the money laundering sub-network discovery problem with a neural network based approach, and propose an AML framework AMAP equipped with an adaptive sub-network proposer. In particular, we design an adaptive sub-network proposer guided by a supervised contrastive loss to discriminate money laundering transactions from massive benign transactions. We conduct extensive experiments on real-word datasets in AliPay of Ant Group. The result demonstrates the effectiveness of our AMAP in both money laundering transaction detection and money laundering sub-network discovering. The learned framework which yields money laundering sub-network from massive transaction network leads to a more comprehensive risk coverage and a deeper insight to money laundering strategies.

Finding items with potential to increase sales is of great importance in online market. We propose to study this novel and practical problem: rising star prediction. We call these potential items Rising Star, which implies their ability to rise from low-turnover items to bestsellers in the future. Rising stars can be used to help with unfair recommendation in e-commerce platform, balance supply and demand to benefit the retailers and allocate marketing resources rationally. Although the study of rising star can bring great benefits, it also poses challenges to us. The sales trend of rising star fluctuates sharply in the short-term and exhibits more contingency caused by some external events (e.g., COVID-19 caused increasing purchase of the face mask) than other items, which cannot be solved by existing sales prediction methods. To address above challenges, in this paper, we observe that the presence of rising stars is closely correlated with the early diffusion of user interest in social networks, which is validated in the case of Taocode (an intermediary that diffuses user interest in Taobao). Thus, we propose a novel framework, RiseNet, to incorporate the user interest diffusion process with the item dynamic features to effectively predict rising stars. Specifically, we adopt a coupled mechanism to capture the dynamic interplay between items and user interest, and a special designed GNN based framework to quantify user interest. Our experimental results on large-scale real-world datasets provided by Taobao demonstrate the effectiveness of our proposed framework.

Graph neural networks (GNNs) have been intensively studied in various real-world tasks. However, the homophily assumption of GNNs' aggregation function limits their representation learning ability in heterophily graphs. In this paper, we shed light on the path level patterns in graphs that can explicitly reflect rich semantic and structural information. We therefore propose a novel Structure-aware Path Aggregation Graph Neural Network (PathNet) aiming to generalize GNNs for both homophily and heterophily graphs. Specifically, we first introduce a maximal entropy path sampler, which helps us sample a number of paths containing structural context. Then, we introduce a structure-aware recurrent cell consisting of order-preserving and distance-aware components to learn the semantic information of neighborhoods. Finally, we model the preference of different paths to target node after path encoding. Experimental results demonstrate that our model achieves superior performance in node classification on both heterophily and homophily graphs.