Explore then Determine: A GNN-LLM Synergy Framework for Reasoning over Knowledge Graph

The task of reasoning over Knowledge Graphs (KGs) poses a significant challenge for Large Language Models (LLMs) due to the complex structure and large amounts of irrelevant information. Existing LLM reasoning methods overlook the importance of compositional learning on KG to supply with precise knowledge. Besides, the fine-tuning and frequent interaction with LLMs incur substantial time and resource costs. This paper focuses on the Question Answering over Knowledge Graph (KGQA) task and proposes an Explore-then-Determine (EtD) framework that synergizes LLMs with graph neural networks (GNNs) for reasoning over KGs. The Explore stage employs a lightweight GNN to explore promising candidates and relevant fine-grained knowledge to the questions, while the Determine stage utilizes the explored information to construct a knowledge-enhanced multiple-choice prompt, guiding a frozen LLM to determine the final answer. Extensive experiments on three benchmark KGQA datasets demonstrate that EtD achieves state-of-the-art performance and generates faithful reasoning results.

Knowledge-Enhanced Recommendation with User-Centric Subgraph Network

Recommendation systems, as widely implemented nowadays on various platforms, recommend relevant items to users based on their preferences. The classical methods which rely on user-item interaction matrices has limitations, especially in scenarios where there is a lack of interaction data for new items. Knowledge graph (KG)-based recommendation systems have emerged as a promising solution. However, most KG-based methods adopt node embeddings, which do not provide personalized recommendations for different users and cannot generalize well to the new items. To address these limitations, we propose Knowledge-enhanced User-Centric subgraph Network (KUCNet), a subgraph learning approach with graph neural network (GNN) for effective recommendation. KUCNet constructs a U-I subgraph for each user-item pair that captures both the historical information of user-item interactions and the side information provided in KG. An attention-based GNN is designed to encode the U-I subgraphs for recommendation. Considering efficiency, the pruned user-centric computation graph is further introduced such that multiple U-I subgraphs can be simultaneously computed and that the size can be pruned by Personalized PageRank. Our proposed method achieves accurate, efficient, and interpretable recommendations especially for new items. Experimental results demonstrate the superiority of KUCNet over state-of-the-art KG-based and collaborative filtering (CF)-based methods.

Graph Unitary Message Passing

Message passing mechanism contributes to the success of GNNs in various applications, but also brings the oversquashing problem. Recent works combat oversquashing by improving the graph spectrums with rewiring techniques, disrupting the structural bias in graphs, and having limited improvement on oversquashing in terms of oversquashing measure. Motivated by unitary RNN, we propose Graph Unitary Message Passing (GUMP) to alleviate oversquashing in GNNs by applying unitary adjacency matrix for message passing. To design GUMP, a transformation is first proposed to make general graphs have unitary adjacency matrix and keep its structural bias. Then, unitary adjacency matrix is obtained with a unitary projection algorithm, which is implemented by utilizing the intrinsic structure of unitary adjacency matrix and allows GUMP to be permutation-equivariant. Experimental results show the effectiveness of GUMP in improving the performance on various graph learning tasks.

Less is More: One-shot Subgraph Reasoning on Large-scale Knowledge Graphs

To deduce new facts on a knowledge graph (KG), a link predictor learns from the graph structure and collects local evidence to find the answer to a given query. However, existing methods suffer from a severe scalability problem due to the utilization of the whole KG for prediction, which hinders their promise on large scale KGs and cannot be directly addressed by vanilla sampling methods. In this work, we propose the one-shot-subgraph link prediction to achieve efficient and adaptive prediction. The design principle is that, instead of directly acting on the whole KG, the prediction procedure is decoupled into two steps, i.e., (i) extracting only one subgraph according to the query and (ii) predicting on this single, query dependent subgraph. We reveal that the non-parametric and computation-efficient heuristics Personalized PageRank (PPR) can effectively identify the potential answers and supporting evidence. With efficient subgraph-based prediction, we further introduce the automated searching of the optimal configurations in both data and model spaces. Empirically, we achieve promoted efficiency and leading performances on five large-scale benchmarks. The code is publicly available at: https://github.com/tmlr-group/one-shot-subgraph.

Loss-aware Curriculum Learning for Heterogeneous Graph Neural Networks

Heterogeneous Graph Neural Networks (HGNNs) are a class of deep learning models designed specifically for heterogeneous graphs, which are graphs that contain different types of nodes and edges. This paper investigates the application of curriculum learning techniques to improve the performance and robustness of Heterogeneous Graph Neural Networks (GNNs). To better classify the quality of the data, we design a loss-aware training schedule, named LTS that measures the quality of every nodes of the data and incorporate the training dataset into the model in a progressive manner that increases difficulty step by step. LTS can be seamlessly integrated into various frameworks, effectively reducing bias and variance, mitigating the impact of noisy data, and enhancing overall accuracy. Our findings demonstrate the efficacy of curriculum learning in enhancing HGNNs capabilities for analyzing complex graph-structured data. The code is public at https: //github.com/LARS-research/CLGNN/.

Towards Versatile Graph Learning Approach: from the Perspective of Large Language Models

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

Robust Communicative Multi-Agent Reinforcement Learning with Active Defense

Communication in multi-agent reinforcement learning (MARL) has been proven to effectively promote cooperation among agents recently. Since communication in real-world scenarios is vulnerable to noises and adversarial attacks, it is crucial to develop robust communicative MARL technique. However, existing research in this domain has predominantly focused on passive defense strategies, where agents receive all messages equally, making it hard to balance performance and robustness. We propose an active defense strategy, where agents automatically reduce the impact of potentially harmful messages on the final decision. There are two challenges to implement this strategy, that are defining unreliable messages and adjusting the unreliable messages' impact on the final decision properly. To address them, we design an Active Defense Multi-Agent Communication framework (ADMAC), which estimates the reliability of received messages and adjusts their impact on the final decision accordingly with the help of a decomposable decision structure. The superiority of ADMAC over existing methods is validated by experiments in three communication-critical tasks under four types of attacks.

Accurate and interpretable drug-drug interaction prediction enabled by knowledge subgraph learning

Background: Discovering potential drug-drug interactions (DDIs) is a long-standing challenge in clinical treatments and drug developments. Recently, deep learning techniques have been developed for DDI prediction. However, they generally require a huge number of samples, while known DDIs are rare. Methods: In this work, we present KnowDDI, a graph neural network-based method that addresses the above challenge. KnowDDI enhances drug representations by adaptively leveraging rich neighborhood information from large biomedical knowledge graphs. Then, it learns a knowledge subgraph for each drug-pair to interpret the predicted DDI, where each of the edges is associated with a connection strength indicating the importance of a known DDI or resembling strength between a drug-pair whose connection is unknown. Thus, the lack of DDIs is implicitly compensated by the enriched drug representations and propagated drug similarities. Results: We evaluate KnowDDI on two benchmark DDI datasets. Results show that KnowDDI obtains the state-of-the-art prediction performance with better interpretability. We also find that KnowDDI suffers less than existing works given a sparser knowledge graph. This indicates that the propagated drug similarities play a more important role in compensating for the lack of DDIs when the drug representations are less enriched. Conclusions: KnowDDI nicely combines the efficiency of deep learning techniques and the rich prior knowledge in biomedical knowledge graphs. As an original open-source tool, KnowDDI can help detect possible interactions in a broad range of relevant interaction prediction tasks, such as protein-protein interactions, drug-target interactions and disease-gene interactions, eventually promoting the development of biomedicine and healthcare.

Emerging Drug Interaction Prediction Enabled by Flow-based Graph Neural Network with Biomedical Network

Accurately predicting drug-drug interactions (DDI) for emerging drugs, which offer possibilities for treating and alleviating diseases, with computational methods can improve patient care and contribute to efficient drug development. However, many existing computational methods require large amounts of known DDI information, which is scarce for emerging drugs. In this paper, we propose EmerGNN, a graph neural network (GNN) that can effectively predict interactions for emerging drugs by leveraging the rich information in biomedical networks. EmerGNN learns pairwise representations of drugs by extracting the paths between drug pairs, propagating information from one drug to the other, and incorporating the relevant biomedical concepts on the paths. The different edges on the biomedical network are weighted to indicate the relevance for the target DDI prediction. Overall, EmerGNN has higher accuracy than existing approaches in predicting interactions for emerging drugs and can identify the most relevant information on the biomedical network.

Combating Bilateral Edge Noise for Robust Link Prediction

Although link prediction on graphs has achieved great success with the development of graph neural networks (GNNs), the potential robustness under the edge noise is still less investigated. To close this gap, we first conduct an empirical study to disclose that the edge noise bilaterally perturbs both input topology and target label, yielding severe performance degradation and representation collapse. To address this dilemma, we propose an information-theory-guided principle, Robust Graph Information Bottleneck (RGIB), to extract reliable supervision signals and avoid representation collapse. Different from the basic information bottleneck, RGIB further decouples and balances the mutual dependence among graph topology, target labels, and representation, building new learning objectives for robust representation against the bilateral noise. Two instantiations, RGIB-SSL and RGIB-REP, are explored to leverage the merits of different methodologies, i.e., self-supervised learning and data reparameterization, for implicit and explicit data denoising, respectively. Extensive experiments on six datasets and three GNNs with diverse noisy scenarios verify the effectiveness of our RGIB instantiations. The code is publicly available at: https://github.com/tmlr-group/RGIB.