arXiv subjects

Quanming Yao

Publications and source records attributed to Quanming Yao.

At least 55 records · Page 3Linked to original sources

arXiv2025

Case-Based Reasoning Enhances the Predictive Power of LLMs in Drug-Drug Interaction

Drug-drug interaction (DDI) prediction is critical for treatment safety. While large language models (LLMs) show promise in pharmaceutical tasks, their effectiveness in DDI prediction remains challenging. Inspired by the well-established clinical practice where physicians routinely reference similar historical cases to guide their decisions through case-based reasoning (CBR), we propose CBR-DDI, a novel framework that distills pharmacological principles from historical cases to improve LLM reasoning for DDI tasks. CBR-DDI constructs a knowledge repository by leveraging LLMs to extract pharmacological insights and graph neural networks (GNNs) to model drug associations. A hybrid retrieval mechanism and dual-layer knowledge-enhanced prompting allow LLMs to effectively retrieve and reuse relevant cases. We further introduce a representative sampling strategy for dynamic case refinement. Extensive experiments demonstrate that CBR-DDI achieves state-of-the-art performance, with a significant 28.7% accuracy improvement over both popular LLMs and CBR baseline, while maintaining high interpretability and flexibility.

cs.AI↗

arXiv2025

Dual Reasoning: A GNN-LLM Collaborative Framework for Knowledge Graph Question Answering

Large Language Models (LLMs) excel at intuitive, implicit reasoning. Guiding LLMs to construct thought chains can enhance their deliberate reasoning abilities, but also faces challenges such as hallucination. Knowledge Graphs (KGs) can provide explicit structured knowledge for LLMs to alleviate these issues. However, existing KG-enhanced methods often overlook explicit graph learning, making it challenging to efficiently provide precise reasoning chains for LLMs. Following dual-process theory, we propose Dual-Reasoning (DualR), a novel framework that integrates an external system based on Graph Neural Network (GNN) for explicit reasoning on KGs, complementing the implicit reasoning of LLMs through externalized reasoning chains. DualR designs an LLM-empowered GNN module for explicit learning on KGs, efficiently extracting high-quality reasoning chains. These reasoning chains are then refined to a knowledge-enhanced multiple-choice prompt, guiding a frozen LLM to reason thoughtfully for final answer determination. Extensive experiments on three benchmark KGQA datasets demonstrate that DualR achieves state-of-the-art performance while maintaining high efficiency and interpretability.

cs.CL↗

arXiv2025

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.

cs.LG↗

arXiv2024

Beyond Scaleup: Knowledge-aware Parsimony Learning from Deep Networks

The brute-force scaleup of training datasets, learnable parameters and computation power, has become a prevalent strategy for developing more robust learning models. However, due to bottlenecks in data, computation, and trust, the sustainability of this strategy is a serious concern. In this paper, we attempt to address this issue in a parsimonious manner (i.e., achieving greater potential with simpler models). The key is to drive models using domain-specific knowledge, such as symbols, logic, and formulas, instead of purely relying on scaleup. This approach allows us to build a framework that uses this knowledge as "building blocks" to achieve parsimony in model design, training, and interpretation. Empirical results show that our methods surpass those that typically follow the scaling law. We also demonstrate our framework in AI for science, specifically in the problem of drug-drug interaction prediction. We hope our research can foster more diverse technical roadmaps in the era of foundation models.

cs.LG↗

arXiv2024

Generalizing Hyperedge Expansion for Hyper-relational Knowledge Graph Modeling

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.

cs.AI↗

arXiv2024

Customized Subgraph Selection and Encoding for Drug-drug Interaction Prediction

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.

cs.LG↗

arXiv2024

Neural Symbolic Regression of Complex Network Dynamics

Complex networks describe important structures in nature and society, composed of nodes and the edges that connect them. The evolution of these networks is typically described by dynamics, which are labor-intensive and require expert knowledge to derive. However, because the complex network involves noisy observations from multiple trajectories of nodes, existing symbolic regression methods are either not applicable or ineffective on its dynamics. In this paper, we propose Physically Inspired Neural Dynamics Symbolic Regression (PI-NDSR), a method based on neural networks and genetic programming to automatically learn the symbolic expression of dynamics. Our method consists of two key components: a Physically Inspired Neural Dynamics (PIND) to augment and denoise trajectories through observed trajectory interpolation; and a coordinated genetic search algorithm to derive symbolic expressions. This algorithm leverages references of node dynamics and edge dynamics from neural dynamics to avoid overfitted expressions in symbolic space. We evaluate our method on synthetic datasets generated by various dynamics and real datasets on disease spreading. The results demonstrate that PI-NDSR outperforms the existing method in terms of both recovery probability and error.

cs.LG↗

arXiv2024

A Versatile Graph Learning Approach through LLM-based Agent

Designing versatile graph learning approaches is important, considering the diverse graphs and tasks existing in real-world applications. Existing methods have attempted to achieve this target through automated machine learning techniques, pre-training and fine-tuning strategies, and large language models. However, these methods are not versatile enough for graph learning, as they work on either limited types of graphs or a single task. In this paper, we propose to explore versatile graph learning approaches with LLM-based agents, and the key insight is customizing the graph learning procedures for diverse graphs and tasks. To achieve this, we develop several LLM-based agents, equipped with diverse profiles, tools, functions and human experience. They collaborate to configure each procedure with task and data-specific settings step by step towards versatile solutions, and the proposed method is dubbed GL-Agent. By evaluating on diverse tasks and graphs, the correct results of the agent and its comparable performance showcase the versatility of the proposed method, especially in complex scenarios.The low resource cost and the potential to use open-source LLMs highlight the efficiency of GL-Agent.

cs.LG↗

arXiv2024

Warming Up Cold-Start CTR Prediction by Learning Item-Specific Feature Interactions

In recommendation systems, new items are continuously introduced, initially lacking interaction records but gradually accumulating them over time. Accurately predicting the click-through rate (CTR) for these items is crucial for enhancing both revenue and user experience. While existing methods focus on enhancing item ID embeddings for new items within general CTR models, they tend to adopt a global feature interaction approach, often overshadowing new items with sparse data by those with abundant interactions. Addressing this, our work introduces EmerG, a novel approach that warms up cold-start CTR prediction by learning item-specific feature interaction patterns. EmerG utilizes hypernetworks to generate an item-specific feature graph based on item characteristics, which is then processed by a Graph Neural Network (GNN). This GNN is specially tailored to provably capture feature interactions at any order through a customized message passing mechanism. We further design a meta learning strategy that optimizes parameters of hypernetworks and GNN across various item CTR prediction tasks, while only adjusting a minimal set of item-specific parameters within each task. This strategy effectively reduces the risk of overfitting when dealing with limited data. Extensive experiments on benchmark datasets validate that EmerG consistently performs the best given no, a few and sufficient instances of new items.

cs.IR↗

arXiv2024

Heuristic Learning with Graph Neural Networks: A Unified Framework for Link Prediction

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.

cs.LG↗

arXiv2024

PACIA: Parameter-Efficient Adapter for Few-Shot Molecular Property Prediction

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.

cs.LG↗

arXiv2024

Understanding Expressivity of GNN in Rule Learning

Rule learning is critical to improving knowledge graph (KG) reasoning due to their ability to provide logical and interpretable explanations. Recently, Graph Neural Networks (GNNs) with tail entity scoring achieve the state-of-the-art performance on KG reasoning. However, the theoretical understandings for these GNNs are either lacking or focusing on single-relational graphs, leaving what the kind of rules these GNNs can learn an open problem. We propose to fill the above gap in this paper. Specifically, GNNs with tail entity scoring are unified into a common framework. Then, we analyze their expressivity by formally describing the rule structures they can learn and theoretically demonstrating their superiority. These results further inspire us to propose a novel labeling strategy to learn more rules in KG reasoning. Experimental results are consistent with our theoretical findings and verify the effectiveness of our proposed method. The code is publicly available at https://github.com/LARS-research/Rule-learning-expressivity.

cs.LG↗

arXiv2024

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.

cs.IR↗

arXiv2024

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.

cs.LG↗

arXiv2024

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/.

cs.LG↗

arXiv2024

Automated Machine Learning: From Principles to Practices

Machine learning (ML) methods have been developing rapidly, but configuring and selecting proper methods to achieve a desired performance is increasingly difficult and tedious. To address this challenge, automated machine learning (AutoML) has emerged, which aims to generate satisfactory ML configurations for given tasks in a data-driven way. In this paper, we provide a comprehensive survey on this topic. We begin with the formal definition of AutoML and then introduce its principles, including the bi-level learning objective, the learning strategy, and the theoretical interpretation. Then, we summarize the AutoML practices by setting up the taxonomy of existing works based on three main factors: the search space, the search algorithm, and the evaluation strategy. Each category is also explained with the representative methods. Then, we illustrate the principles and practices with exemplary applications from configuring ML pipeline, one-shot neural architecture search, and integration with foundation models. Finally, we highlight the emerging directions of AutoML and conclude the survey.

cs.AI↗

arXiv2024

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.

cs.LG↗

arXiv2023

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.

cs.MA↗