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.

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.

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.

Hierarchical Adaptation with Hypernetworks for Few-shot Molecular Property Prediction

Molecular property prediction (MPP) is important in biomedical applications, which naturally suffers from a lack of labels, thus forming a few-shot learning problem. State-of-the-art approaches are usually based on gradient-based meta learning strategy, which ignore difference in model parameter and molecule's learning difficulty. To address above problems, we propose a novel hierarchical adaptation mechanism for few-shot MPP (HiMPP). The model follows a encoder-predictor framework. First, to make molecular representation property-adaptive, we selectively adapt encoder's parameter by designing a hypernetwork to modulate node embeddings during message propagation. Next, we make molecule-level adaptation by design another hypernetwork, which assigns larger propagating steps for harder molecules in predictor. In this way, molecular representation is transformed by HiMPP hierarchically from property-level to molecular level. Extensive results show that HiMPP obtains the state-of-the-art performance in few-shot MPP problems, and our proposed hierarchical adaptation mechanism is rational and effective.

Unleashing the Power of Graph Learning through LLM-based Autonomous Agents

Graph structured data are widely existed and applied in the real-world applications, while it is a challenge to handling these diverse data and learning tasks on graph in an efficient manner. When facing the complicated graph learning tasks, experts have designed diverse Graph Neural Networks (GNNs) in recent years. They have also implemented AutoML in Graph, also known as AutoGraph, to automatically generate data-specific solutions. Despite their success, they encounter limitations in (1) managing diverse learning tasks at various levels, (2) dealing with different procedures in graph learning beyond architecture design, and (3) the huge requirements on the prior knowledge when using AutoGraph. In this paper, we propose to use Large Language Models (LLMs) as autonomous agents to simplify the learning process on diverse real-world graphs. Specifically, in response to a user request which may contain varying data and learning targets at the node, edge, or graph levels, the complex graph learning task is decomposed into three components following the agent planning, namely, detecting the learning intent, configuring solutions based on AutoGraph, and generating a response. The AutoGraph agents manage crucial procedures in automated graph learning, including data-processing, AutoML configuration, searching architectures, and hyper-parameter fine-tuning. With these agents, those components are processed by decomposing and completing step by step, thereby generating a solution for the given data automatically, regardless of the learning task on node or graph. The proposed method is dubbed Auto$^2$Graph, and the comparable performance on different datasets and learning tasks. Its effectiveness is demonstrated by its comparable performance on different datasets and learning tasks, as well as the human-like decisions made by the agents.

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.

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.

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.

Logical Expressiveness of Graph Neural Network for Knowledge Graph Reasoning

Graph Neural Networks (GNNs) have been recently introduced to learn from knowledge graph (KG) and achieved state-of-the-art performance in KG reasoning. However, a theoretical certification for their good empirical performance is still absent. Besides, while logic in KG is important for inductive and interpretable inference, existing GNN-based methods are just designed to fit data distributions with limited knowledge of their logical expressiveness. We propose to fill the above gap in this paper. Specifically, we theoretically analyze GNN from logical expressiveness and find out what kind of logical rules can be captured from KG. Our results first show that GNN can capture logical rules from graded modal logic, providing a new theoretical tool for analyzing the expressiveness of GNN for KG reasoning; and a query labeling trick makes it easier for GNN to capture logical rules, explaining why SOTA methods are mainly based on labeling trick. Finally, insights from our theory motivate the development of an entity labeling method for capturing difficult logical rules. Experimental results are consistent with our theoretical results and verify the effectiveness of our proposed method.

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.