arXiv subjects

Quanming Yao

Publications and source records attributed to Quanming Yao.

At least 73 records · Page 4Linked to original sources

arXiv2023

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.

q-bio.QM↗

arXiv2023

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.

cs.LG↗

arXiv2023

Ensemble Learning for Graph Neural Networks

Graph Neural Networks (GNNs) have shown success in various fields for learning from graph-structured data. This paper investigates the application of ensemble learning techniques to improve the performance and robustness of Graph Neural Networks (GNNs). By training multiple GNN models with diverse initializations or architectures, we create an ensemble model named ELGNN that captures various aspects of the data and uses the Tree-Structured Parzen Estimator algorithm to determine the ensemble weights. Combining the predictions of these models enhances overall accuracy, reduces bias and variance, and mitigates the impact of noisy data. Our findings demonstrate the efficacy of ensemble learning in enhancing GNN capabilities for analyzing complex graph-structured data. The code is public at https://github.com/wongzhenhao/ELGNN.

cs.LG↗

arXiv2023

Positive-Unlabeled Node Classification with Structure-aware Graph Learning

Node classification on graphs is an important research problem with many applications. Real-world graph data sets may not be balanced and accurate as assumed by most existing works. A challenging setting is positive-unlabeled (PU) node classification, where labeled nodes are restricted to positive nodes. It has diverse applications, e.g., pandemic prediction or network anomaly detection. Existing works on PU node classification overlook information in the graph structure, which can be critical. In this paper, we propose to better utilize graph structure for PU node classification. We first propose a distance-aware PU loss that uses homophily in graphs to introduce more accurate supervision. We also propose a regularizer to align the model with graph structure. Theoretical analysis shows that minimizing the proposed loss also leads to minimizing the expected loss with both positive and negative labels. Extensive empirical evaluation on diverse graph data sets demonstrates its superior performance over existing state-of-the-art methods.

cs.LG↗

arXiv2023

Relation-aware Ensemble Learning for Knowledge Graph Embedding

Knowledge graph (KG) embedding is a fundamental task in natural language processing, and various methods have been proposed to explore semantic patterns in distinctive ways. In this paper, we propose to learn an ensemble by leveraging existing methods in a relation-aware manner. However, exploring these semantics using relation-aware ensemble leads to a much larger search space than general ensemble methods. To address this issue, we propose a divide-search-combine algorithm RelEns-DSC that searches the relation-wise ensemble weights independently. This algorithm has the same computation cost as general ensemble methods but with much better performance. Experimental results on benchmark datasets demonstrate the effectiveness of the proposed method in efficiently searching relation-aware ensemble weights and achieving state-of-the-art embedding performance. The code is public at https://github.com/LARS-research/RelEns.

cs.LG↗

arXiv2023

Topology-aware Tensor Decomposition for Meta-graph Learning

Heterogeneous graphs generally refers to graphs with different types of nodes and edges. A common approach for extracting useful information from heterogeneous graphs is to use meta-graphs, which can be seen as a special kind of directed acyclic graph (DAG) with same node and edge types as the heterogeneous graph. However, how to design proper meta-graphs is challenging. Recently, there have been many works on learning suitable meta-graphs from a heterogeneous graph. Existing methods generally introduce continuous weights for edges that are independent of each other, which ignores the topological stucture of meta-graphs and can be ineffective. To address this issue, we propose a new viewpoint from tensor on learning meta-graphs. Such a viewpoint not only helps interpret the limitation of existing works by CANDECOMP/PARAFAC (CP) decomposition, but also inspires us to propose a topology-aware tensor decomposition, called TENSUS, that reflects the structure of DAGs. The proposed topology-aware tensor decomposition is easy to use and simple to implement, and it can be taken as a plug-in part to upgrade many existing works, including node classification and recommendation on heterogeneous graphs. Experimental results on different tasks demonstrate that the proposed method can significantly improve the state-of-the-arts for all these tasks.

cs.LG↗

arXiv2023

Automated 3D Pre-Training for Molecular Property Prediction

Molecular property prediction is an important problem in drug discovery and materials science. As geometric structures have been demonstrated necessary for molecular property prediction, 3D information has been combined with various graph learning methods to boost prediction performance. However, obtaining the geometric structure of molecules is not feasible in many real-world applications due to the high computational cost. In this work, we propose a novel 3D pre-training framework (dubbed 3D PGT), which pre-trains a model on 3D molecular graphs, and then fine-tunes it on molecular graphs without 3D structures. Based on fact that bond length, bond angle, and dihedral angle are three basic geometric descriptors corresponding to a complete molecular 3D conformer, we first develop a multi-task generative pre-train framework based on these three attributes. Next, to automatically fuse these three generative tasks, we design a surrogate metric using the \textit{total energy} to search for weight distribution of the three pretext task since total energy corresponding to the quality of 3D conformer.Extensive experiments on 2D molecular graphs are conducted to demonstrate the accuracy, efficiency and generalization ability of the proposed 3D PGT compared to various pre-training baselines.

q-bio.QM↗

arXiv2023

Combining Self-Supervised and Supervised Learning with Noisy Labels

Since convolutional neural networks (CNNs) can easily overfit noisy labels, which are ubiquitous in visual classification tasks, it has been a great challenge to train CNNs against them robustly. Various methods have been proposed for this challenge. However, none of them pay attention to the difference between representation and classifier learning of CNNs. Thus, inspired by the observation that classifier is more robust to noisy labels while representation is much more fragile, and by the recent advances of self-supervised representation learning (SSRL) technologies, we design a new method, i.e., CS$^3$NL, to obtain representation by SSRL without labels and train the classifier directly with noisy labels. Extensive experiments are performed on both synthetic and real benchmark datasets. Results demonstrate that the proposed method can beat the state-of-the-art ones by a large margin, especially under a high noisy level.

cs.CV↗

arXiv2023

On Strengthening and Defending Graph Reconstruction Attack with Markov Chain Approximation

Although powerful graph neural networks (GNNs) have boosted numerous real-world applications, the potential privacy risk is still underexplored. To close this gap, we perform the first comprehensive study of graph reconstruction attack that aims to reconstruct the adjacency of nodes. We show that a range of factors in GNNs can lead to the surprising leakage of private links. Especially by taking GNNs as a Markov chain and attacking GNNs via a flexible chain approximation, we systematically explore the underneath principles of graph reconstruction attack, and propose two information theory-guided mechanisms: (1) the chain-based attack method with adaptive designs for extracting more private information; (2) the chain-based defense method that sharply reduces the attack fidelity with moderate accuracy loss. Such two objectives disclose a critical belief that to recover better in attack, you must extract more multi-aspect knowledge from the trained GNN; while to learn safer for defense, you must forget more link-sensitive information in training GNNs. Empirically, we achieve state-of-the-art results on six datasets and three common GNNs. The code is publicly available at: https://github.com/tmlr-group/MC-GRA.

cs.LG↗

arXiv2023

AdaProp: Learning Adaptive Propagation for Graph Neural Network based Knowledge Graph Reasoning

Due to the popularity of Graph Neural Networks (GNNs), various GNN-based methods have been designed to reason on knowledge graphs (KGs). An important design component of GNN-based KG reasoning methods is called the propagation path, which contains a set of involved entities in each propagation step. Existing methods use hand-designed propagation paths, ignoring the correlation between the entities and the query relation. In addition, the number of involved entities will explosively grow at larger propagation steps. In this work, we are motivated to learn an adaptive propagation path in order to filter out irrelevant entities while preserving promising targets. First, we design an incremental sampling mechanism where the nearby targets and layer-wise connections can be preserved with linear complexity. Second, we design a learning-based sampling distribution to identify the semantically related entities. Extensive experiments show that our method is powerful, efficient, and semantic-aware. The code is available at https://github.com/LARS-research/AdaProp.

cs.LG↗

arXiv2023

ColdNAS: Search to Modulate for User Cold-Start Recommendation

Making personalized recommendation for cold-start users, who only have a few interaction histories, is a challenging problem in recommendation systems. Recent works leverage hypernetworks to directly map user interaction histories to user-specific parameters, which are then used to modulate predictor by feature-wise linear modulation function. These works obtain the state-of-the-art performance. However, the physical meaning of scaling and shifting in recommendation data is unclear. Instead of using a fixed modulation function and deciding modulation position by expertise, we propose a modulation framework called ColdNAS for user cold-start problem, where we look for proper modulation structure, including function and position, via neural architecture search. We design a search space which covers broad models and theoretically prove that this search space can be transformed to a much smaller space, enabling an efficient and robust one-shot search algorithm. Extensive experimental results on benchmark datasets show that ColdNAS consistently performs the best. We observe that different modulation functions lead to the best performance on different datasets, which validates the necessity of designing a searching-based method.

cs.AI↗

arXiv2023

Combating Exacerbated Heterogeneity for Robust Models in Federated Learning

Privacy and security concerns in real-world applications have led to the development of adversarially robust federated models. However, the straightforward combination between adversarial training and federated learning in one framework can lead to the undesired robustness deterioration. We discover that the attribution behind this phenomenon is that the generated adversarial data could exacerbate the data heterogeneity among local clients, making the wrapped federated learning perform poorly. To deal with this problem, we propose a novel framework called Slack Federated Adversarial Training (SFAT), assigning the client-wise slack during aggregation to combat the intensified heterogeneity. Theoretically, we analyze the convergence of the proposed method to properly relax the objective when combining federated learning and adversarial training. Experimentally, we verify the rationality and effectiveness of SFAT on various benchmarked and real-world datasets with different adversarial training and federated optimization methods. The code is publicly available at https://github.com/ZFancy/SFAT.

cs.LG↗

arXiv2023

LoSAC: An Efficient Local Stochastic Average Control Method for Federated Optimization

Federated optimization (FedOpt), which targets at collaboratively training a learning model across a large number of distributed clients, is vital for federated learning. The primary concerns in FedOpt can be attributed to the model divergence and communication efficiency, which significantly affect the performance. In this paper, we propose a new method, i.e., LoSAC, to learn from heterogeneous distributed data more efficiently. Its key algorithmic insight is to locally update the estimate for the global full gradient after {each} regular local model update. Thus, LoSAC can keep clients' information refreshed in a more compact way. In particular, we have studied the convergence result for LoSAC. Besides, the bonus of LoSAC is the ability to defend the information leakage from the recent technique Deep Leakage Gradients (DLG). Finally, experiments have verified the superiority of LoSAC comparing with state-of-the-art FedOpt algorithms. Specifically, LoSAC significantly improves communication efficiency by more than $100\%$ on average, mitigates the model divergence problem and equips with the defense ability against DLG.

cs.DC↗

arXiv2023

Search to Capture Long-range Dependency with Stacking GNNs for Graph Classification

In recent years, Graph Neural Networks (GNNs) have been popular in the graph classification task. Currently, shallow GNNs are more common due to the well-known over-smoothing problem facing deeper GNNs. However, they are sub-optimal without utilizing the information from distant nodes, i.e., the long-range dependencies. The mainstream methods in the graph classification task can extract the long-range dependencies either by designing the pooling operations or incorporating the higher-order neighbors, while they have evident drawbacks by modifying the original graph structure, which may result in information loss in graph structure learning. In this paper, by justifying the smaller influence of the over-smoothing problem in the graph classification task, we evoke the importance of stacking-based GNNs and then employ them to capture the long-range dependencies without modifying the original graph structure. To achieve this, two design needs are given for stacking-based GNNs, i.e., sufficient model depth and adaptive skip-connection schemes. By transforming the two design needs into designing data-specific inter-layer connections, we propose a novel approach with the help of neural architecture search (NAS), which is dubbed LRGNN (Long-Range Graph Neural Networks). Extensive experiments on five datasets show that the proposed LRGNN can achieve the best performance, and obtained data-specific GNNs with different depth and skip-connection schemes, which can better capture the long-range dependencies.

cs.LG↗

arXiv2023

Improving Zero-Shot Coordination Performance Based on Policy Similarity

Over these years, multi-agent reinforcement learning has achieved remarkable performance in multi-agent planning and scheduling tasks. It typically follows the self-play setting, where agents are trained by playing with a fixed group of agents. However, in the face of zero-shot coordination, where an agent must coordinate with unseen partners, self-play agents may fail. Several methods have been proposed to handle this problem, but they either take a lot of time or lack generalizability. In this paper, we firstly reveal an important phenomenon: the zero-shot coordination performance is strongly linearly correlated with the similarity between an agent's training partner and testing partner. Inspired by it, we put forward a Similarity-Based Robust Training (SBRT) scheme that improves agents' zero-shot coordination performance by disturbing their partners' actions during training according to a pre-defined policy similarity value. To validate its effectiveness, we apply our scheme to three multi-agent reinforcement learning frameworks and achieve better performance compared with previous methods.

cs.MA↗

arXiv2022

Enhancing Intra-class Information Extraction for Heterophilous Graphs: One Neural Architecture Search Approach

In recent years, Graph Neural Networks (GNNs) have been popular in graph representation learning which assumes the homophily property, i.e., the connected nodes have the same label or have similar features. However, they may fail to generalize into the heterophilous graphs which in the low/medium level of homophily. Existing methods tend to address this problem by enhancing the intra-class information extraction, i.e., either by designing better GNNs to improve the model effectiveness, or re-designing the graph structures to incorporate more potential intra-class nodes from distant hops. Despite the success, we observe two aspects that can be further improved: (a) enhancing the ego feature information extraction from node itself which is more reliable in extracting the intra-class information; (b) designing node-wise GNNs can better adapt to the nodes with different homophily ratios. In this paper, we propose a novel method IIE-GNN (Intra-class Information Enhanced Graph Neural Networks) to achieve two improvements. A unified framework is proposed based on the literature, in which the intra-class information from the node itself and neighbors can be extracted based on seven carefully designed blocks. With the help of neural architecture search (NAS), we propose a novel search space based on the framework, and then provide an architecture predictor to design GNNs for each node. We further conduct experiments to show that IIE-GNN can improve the model performance by designing node-wise GNNs to enhance intra-class information extraction.

cs.LG↗

arXiv2022

Search to Pass Messages for Temporal Knowledge Graph Completion

Completing missing facts is a fundamental task for temporal knowledge graphs (TKGs). Recently, graph neural network (GNN) based methods, which can simultaneously explore topological and temporal information, have become the state-of-the-art (SOTA) to complete TKGs. However, these studies are based on hand-designed architectures and fail to explore the diverse topological and temporal properties of TKG. To address this issue, we propose to use neural architecture search (NAS) to design data-specific message passing architecture for TKG completion. In particular, we develop a generalized framework to explore topological and temporal information in TKGs. Based on this framework, we design an expressive search space to fully capture various properties of different TKGs. Meanwhile, we adopt a search algorithm, which trains a supernet structure by sampling single path for efficient search with less cost. We further conduct extensive experiments on three benchmark datasets. The results show that the searched architectures by our method achieve the SOTA performances. Besides, the searched models can also implicitly reveal diverse properties in different TKGs. Our code is released in https://github.com/striderdu/SPA.

cs.AI↗

arXiv2022

Heterogeneous Graph-Based Multimodal Brain Network Learning

Graph neural networks (GNNs) provide powerful insights for brain neuroimaging technology from the view of graphical networks. However, most existing GNN-based models assume that the neuroimaging-produced brain connectome network is a homogeneous graph with single types of nodes and edges. In fact, emerging studies have reported and emphasized the significance of heterogeneity among human brain activities, especially between the two cerebral hemispheres. Thus, homogeneous-structured brain network-based graph methods are insufficient for modelling complicated cerebral activity states. To overcome this problem, in this paper, we present a heterogeneous graph neural network (HebrainGNN) for multimodal brain neuroimaging fusion learning. We first model the brain network as a heterogeneous graph with multitype nodes (i.e., left and right hemispheric nodes) and multitype edges (i.e., intra- and interhemispheric edges). Then, we propose a self-supervised pretraining strategy based on a heterogeneous brain network to address the potential overfitting problem caused by the conflict between a large parameter size and a small medical data sample size. Our results show the superiority of the proposed model over other existing methods in brain-related disease prediction tasks. Ablation experiments show that our heterogeneous graph-based model attaches more importance to hemispheric connections that may be neglected due to their low strength by previous homogeneous graph models. Other experiments also indicate that our proposed model with a pretraining strategy alleviates the problem of limited labelled data and yields a significant improvement in accuracy.

cs.LG↗