Quanming Yao

Shiguang Wu, Yaqing Wang, Quanming Yao · baidu

Molecular property prediction (MPP) plays a crucial role in biomedical applications, but it often encounters challenges due to a scarcity of labeled data. Existing works commonly adopt gradient-based strategy to update a large amount of parameters for task-level adaptation. However, the increase of adaptive parameters can lead to overfitting and poor performance. Observing that graph neural network (GNN) performs well as both encoder and predictor, we propose PACIA, a parameter-efficient GNN adapter for few-shot MPP. We design a unified adapter to generate a few adaptive parameters to modulate the message passing process of GNN. We then adopt a hierarchical adaptation mechanism to adapt the encoder at task-level and the predictor at query-level by the unified GNN adapter. Extensive results show that PACIA obtains the state-of-the-art performance in few-shot MPP problems, and our proposed hierarchical adaptation mechanism is rational and effective.

Zhen Hao Wong, Hansi Yang, Xiaoyi Fu et al.

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/.

Haotong Du, Quanming Yao, Juzheng Zhang et al.

Subgraph-based methods have proven to be effective and interpretable in predicting drug-drug interactions (DDIs), which are essential for medical practice and drug development. Subgraph selection and encoding are critical stages in these methods, yet customizing these components remains underexplored due to the high cost of manual adjustments. In this study, inspired by the success of neural architecture search (NAS), we propose a method to search for data-specific components within subgraph-based frameworks. Specifically, we introduce extensive subgraph selection and encoding spaces that account for the diverse contexts of drug interactions in DDI prediction. To address the challenge of large search spaces and high sampling costs, we design a relaxation mechanism that uses an approximation strategy to efficiently explore optimal subgraph configurations. This approach allows for robust exploration of the search space. Extensive experiments demonstrate the effectiveness and superiority of the proposed method, with the discovered subgraphs and encoding functions highlighting the model's adaptability.

Yu Liu, Shu Yang, Jingtao Ding et al.

By representing knowledge in a primary triple associated with additional attribute-value qualifiers, hyper-relational knowledge graph (HKG) that generalizes triple-based knowledge graph (KG) has been attracting research attention recently. Compared with KG, HKG is enriched with the semantic qualifiers as well as the hyper-relational graph structure. However, to model HKG, existing studies mainly focus on either semantic information or structural information therein, which however fail to capture both simultaneously. To tackle this issue, in this paper, we generalize the hyperedge expansion in hypergraph learning and propose an equivalent transformation for HKG modeling, referred to as TransEQ. Specifically, the equivalent transformation transforms a HKG to a KG, which considers both semantic and structural characteristics. Then an encoder-decoder framework is developed to bridge the modeling research between KG and HKG. In the encoder part, KG-based graph neural networks are leveraged for structural modeling; while in the decoder part, various HKG-based scoring functions are exploited for semantic modeling. Especially, we design the sharing embedding mechanism in the encoder-decoder framework with semantic relatedness captured. We further theoretically prove that TransEQ preserves complete information in the equivalent transformation, and also achieves full expressivity. Finally, extensive experiments on three benchmarks demonstrate the superior performance of TransEQ in terms of both effectiveness and efficiency. On the largest benchmark WikiPeople, TransEQ significantly improves the state-of-the-art models by 15\% on MRR.

Xiaohan Zheng, Lanning Wei, Yong Li et al.

Effective decision-making on networks often relies on learning from graph-structured data, where Graph Neural Networks (GNNs) play a central role, but they take efforts to configure and tune. In this demo, we propose LLMNet, showing how to design GNN automated through Large Language Models. Our system develops a set of agents that construct graph-related knowlege bases and then leverages Retrieval-Augmented Generation (RAG) to support automated configuration and refinement of GNN models through a knowledge-guided evolution process. These agents, equipped with specialized knowledge bases, extract insights into tasks and graph structures by interacting with the knowledge bases. Empirical results show LLMNet excels in twelve datasets across three graph learning tasks, validating its effectiveness of GNN model designing.

Yongqiang Chen, Quanming Yao, Juzheng Zhang et al.

Recently, there has been a surge of interest in extending the success of large language models (LLMs) from texts to molecules. Most existing approaches adopt a graph neural network to represent a molecule as a series of node tokens for molecule-language alignment, which, however, have overlooked the inherent hierarchical structures in molecules. Notably, higher-order molecular structures contain rich semantics of functional groups, which encode crucial biochemical functionalities of the molecules. We show that neglecting the hierarchical information in tokenization will lead to subpar molecule-language alignment and severe hallucination. To address this limitation, we propose HIerarchical GrapH Tokenization (HIGHT). HIGHT employs a hierarchical graph tokenizer that encodes the hierarchy of atom, motif, and molecular levels of informative tokens to improve the molecular perception of LLMs. HIGHT also adopts an augmented instruction tuning dataset, enriched with the hierarchical graph information, to further enhance the molecule-language alignment. Extensive experiments on 14 real-world benchmarks verify the effectiveness of HIGHT in reducing hallucination by 40%, and significant improvements in various molecule-language downstream tasks. The project is available at https: //higraphllm.github.io/.

Juzheng Zhang, Lanning Wei, Zhen Xu et al.

Link prediction is a fundamental task in graph learning, inherently shaped by the topology of the graph. While traditional heuristics are grounded in graph topology, they encounter challenges in generalizing across diverse graphs. Recent research efforts have aimed to leverage the potential of heuristics, yet a unified formulation accommodating both local and global heuristics remains undiscovered. Drawing insights from the fact that both local and global heuristics can be represented by adjacency matrix multiplications, we propose a unified matrix formulation to accommodate and generalize various heuristics. We further propose the Heuristic Learning Graph Neural Network (HL-GNN) to efficiently implement the formulation. HL-GNN adopts intra-layer propagation and inter-layer connections, allowing it to reach a depth of around 20 layers with lower time complexity than GCN. Extensive experiments on the Planetoid, Amazon, and OGB datasets underscore the effectiveness and efficiency of HL-GNN. It outperforms existing methods by a large margin in prediction performance. Additionally, HL-GNN is several orders of magnitude faster than heuristic-inspired methods while requiring only a few trainable parameters. The case study further demonstrates that the generalized heuristics and learned weights are highly interpretable.