Graph Neural Networks Are More Than Filters: Revisiting and Benchmarking from A Spectral Perspective

Graph Neural Networks (GNNs) have achieved remarkable success in various graph-based learning tasks. While their performance is often attributed to the powerful neighborhood aggregation mechanism, recent studies suggest that other components such as non-linear layers may also significantly affecting how GNNs process the input graph data in the spectral domain. Such evidence challenges the prevalent opinion that neighborhood aggregation mechanisms dominate the behavioral characteristics of GNNs in the spectral domain. To demystify such a conflict, this paper introduces a comprehensive benchmark to measure and evaluate GNNs' capability in capturing and leveraging the information encoded in different frequency components of the input graph data. Specifically, we first conduct an exploratory study demonstrating that GNNs can flexibly yield outputs with diverse frequency components even when certain frequencies are absent or filtered out from the input graph data. We then formulate a novel research problem of measuring and benchmarking the performance of GNNs from a spectral perspective. To take an initial step towards a comprehensive benchmark, we design an evaluation protocol supported by comprehensive theoretical analysis. Finally, we introduce a comprehensive benchmark on real-world datasets, revealing insights that challenge prevalent opinions from a spectral perspective. We believe that our findings will open new avenues for future advancements in this area. Our implementations can be found at: https://github.com/yushundong/Spectral-benchmark.

Instance-Aware Graph Prompt Learning

Graph neural networks stand as the predominant technique for graph representation learning owing to their strong expressive power, yet the performance highly depends on the availability of high-quality labels in an end-to-end manner. Thus the pretraining and fine-tuning paradigm has been proposed to mitigate the label cost issue. Subsequently, the gap between the pretext tasks and downstream tasks has spurred the development of graph prompt learning which inserts a set of graph prompts into the original graph data with minimal parameters while preserving competitive performance. However, the current exploratory works are still limited since they all concentrate on learning fixed task-specific prompts which may not generalize well across the diverse instances that the task comprises. To tackle this challenge, we introduce Instance-Aware Graph Prompt Learning (IA-GPL) in this paper, aiming to generate distinct prompts tailored to different input instances. The process involves generating intermediate prompts for each instance using a lightweight architecture, quantizing these prompts through trainable codebook vectors, and employing the exponential moving average technique to ensure stable training. Extensive experiments conducted on multiple datasets and settings showcase the superior performance of IA-GPL compared to state-of-the-art baselines.

Invariant Shape Representation Learning For Image Classification

Geometric shape features have been widely used as strong predictors for image classification. Nevertheless, most existing classifiers such as deep neural networks (DNNs) directly leverage the statistical correlations between these shape features and target variables. However, these correlations can often be spurious and unstable across different environments (e.g., in different age groups, certain types of brain changes have unstable relations with neurodegenerative disease); hence leading to biased or inaccurate predictions. In this paper, we introduce a novel framework that for the first time develops invariant shape representation learning (ISRL) to further strengthen the robustness of image classifiers. In contrast to existing approaches that mainly derive features in the image space, our model ISRL is designed to jointly capture invariant features in latent shape spaces parameterized by deformable transformations. To achieve this goal, we develop a new learning paradigm based on invariant risk minimization (IRM) to learn invariant representations of image and shape features across multiple training distributions/environments. By embedding the features that are invariant with regard to target variables in different environments, our model consistently offers more accurate predictions. We validate our method by performing classification tasks on both simulated 2D images, real 3D brain and cine cardiovascular magnetic resonance images (MRIs). Our code is publicly available at https://github.com/tonmoy-hossain/ISRL.

Federated Graph Learning with Graphless Clients

Federated Graph Learning (FGL) is tasked with training machine learning models, such as Graph Neural Networks (GNNs), for multiple clients, each with its own graph data. Existing methods usually assume that each client has both node features and graph structure of its graph data. In real-world scenarios, however, there exist federated systems where only a part of the clients have such data while other clients (i.e. graphless clients) may only have node features. This naturally leads to a novel problem in FGL: how to jointly train a model over distributed graph data with graphless clients? In this paper, we propose a novel framework FedGLS to tackle the problem in FGL with graphless clients. In FedGLS, we devise a local graph learner on each graphless client which learns the local graph structure with the structure knowledge transferred from other clients. To enable structure knowledge transfer, we design a GNN model and a feature encoder on each client. During local training, the feature encoder retains the local graph structure knowledge together with the GNN model via knowledge distillation, and the structure knowledge is transferred among clients in global update. Our extensive experiments demonstrate the superiority of the proposed FedGLS over five baselines.

Global Graph Counterfactual Explanation: A Subgraph Mapping Approach

Graph Neural Networks (GNNs) have been widely deployed in various real-world applications. However, most GNNs are black-box models that lack explanations. One strategy to explain GNNs is through counterfactual explanation, which aims to find minimum perturbations on input graphs that change the GNN predictions. Existing works on GNN counterfactual explanations primarily concentrate on the local-level perspective (i.e., generating counterfactuals for each individual graph), which suffers from information overload and lacks insights into the broader cross-graph relationships. To address such issues, we propose GlobalGCE, a novel global-level graph counterfactual explanation method. GlobalGCE aims to identify a collection of subgraph mapping rules as counterfactual explanations for the target GNN. According to these rules, substituting certain significant subgraphs with their counterfactual subgraphs will change the GNN prediction to the desired class for most graphs (i.e., maximum coverage). Methodologically, we design a significant subgraph generator and a counterfactual subgraph autoencoder in our GlobalGCE, where the subgraphs and the rules can be effectively generated. Extensive experiments demonstrate the superiority of our GlobalGCE compared to existing baselines. Our code can be found at https://anonymous.4open.science/r/GlobalGCE-92E8.

A Survey of Deep Graph Learning under Distribution Shifts: from Graph Out-of-Distribution Generalization to Adaptation

Distribution shifts on graphs -- the discrepancies in data distribution between training and employing a graph machine learning model -- are ubiquitous and often unavoidable in real-world scenarios. These shifts may severely deteriorate model performance, posing significant challenges for reliable graph machine learning. Consequently, there has been a surge in research on graph machine learning under distribution shifts, aiming to train models to achieve satisfactory performance on out-of-distribution (OOD) test data. In our survey, we provide an up-to-date and forward-looking review of deep graph learning under distribution shifts. Specifically, we cover three primary scenarios: graph OOD generalization, training-time graph OOD adaptation, and test-time graph OOD adaptation. We begin by formally formulating the problems and discussing various types of distribution shifts that can affect graph learning, such as covariate shifts and concept shifts. To provide a better understanding of the literature, we systematically categorize the existing models based on our proposed taxonomy and investigate the adopted techniques behind. We also summarize commonly used datasets in this research area to facilitate further investigation. Finally, we point out promising research directions and the corresponding challenges to encourage further study in this vital domain. Additionally, we provide a continuously updated reading list at https://github.com/kaize0409/Awesome-Graph-OOD.

Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction

In recent years, Graph Neural Networks (GNNs) have become successful in molecular property prediction tasks such as toxicity analysis. However, due to the black-box nature of GNNs, their outputs can be concerning in high-stakes decision-making scenarios, e.g., drug discovery. Facing such an issue, Graph Counterfactual Explanation (GCE) has emerged as a promising approach to improve GNN transparency. However, current GCE methods usually fail to take domain-specific knowledge into consideration, which can result in outputs that are not easily comprehensible by humans. To address this challenge, we propose a novel GCE method, LLM-GCE, to unleash the power of large language models (LLMs) in explaining GNNs for molecular property prediction. Specifically, we utilize an autoencoder to generate the counterfactual graph topology from a set of counterfactual text pairs (CTPs) based on an input graph. Meanwhile, we also incorporate a CTP dynamic feedback module to mitigate LLM hallucination, which provides intermediate feedback derived from the generated counterfactuals as an attempt to give more faithful guidance. Extensive experiments demonstrate the superior performance of LLM-GCE. Our code is released on https://github.com/YinhanHe123/new\_LLM4GNNExplanation.

Channel-Wise Mixed-Precision Quantization for Large Language Models

Large Language Models (LLMs) have demonstrated remarkable success across a wide range of language tasks, but their deployment on edge devices remains challenging due to the substantial memory requirements imposed by their large parameter sizes. Weight-only quantization presents a promising solution to reduce the memory footprint of LLMs. However, existing approaches primarily focus on integer-bit quantization, limiting their adaptability to fractional-bit quantization tasks and preventing the full utilization of available storage space on devices. In this paper, we introduce Channel-Wise Mixed-Precision Quantization (CMPQ), a novel mixed-precision quantization method that allocates quantization precision in a channel-wise pattern based on activation distributions. By assigning different precision levels to different weight channels, CMPQ can adapt to any bit-width constraint. CMPQ employs a non-uniform quantization strategy and incorporates two outlier extraction techniques that collaboratively preserve the critical information, thereby minimizing the quantization loss. Experiments on different sizes of LLMs demonstrate that CMPQ not only enhances performance in integer-bit quantization tasks but also achieves significant performance gains with a modest increase in memory usage. CMPQ thus represents an adaptive and effective approach to LLM quantization, offering substantial benefits across diverse device capabilities.

Federated Graph Learning with Structure Proxy Alignment

Federated Graph Learning (FGL) aims to learn graph learning models over graph data distributed in multiple data owners, which has been applied in various applications such as social recommendation and financial fraud detection. Inherited from generic Federated Learning (FL), FGL similarly has the data heterogeneity issue where the label distribution may vary significantly for distributed graph data across clients. For instance, a client can have the majority of nodes from a class, while another client may have only a few nodes from the same class. This issue results in divergent local objectives and impairs FGL convergence for node-level tasks, especially for node classification. Moreover, FGL also encounters a unique challenge for the node classification task: the nodes from a minority class in a client are more likely to have biased neighboring information, which prevents FGL from learning expressive node embeddings with Graph Neural Networks (GNNs). To grapple with the challenge, we propose FedSpray, a novel FGL framework that learns local class-wise structure proxies in the latent space and aligns them to obtain global structure proxies in the server. Our goal is to obtain the aligned structure proxies that can serve as reliable, unbiased neighboring information for node classification. To achieve this, FedSpray trains a global feature-structure encoder and generates unbiased soft targets with structure proxies to regularize local training of GNN models in a personalized way. We conduct extensive experiments over four datasets, and experiment results validate the superiority of FedSpray compared with other baselines. Our code is available at https://github.com/xbfu/FedSpray.

Understanding and Modeling Job Marketplace with Pretrained Language Models

Job marketplace is a heterogeneous graph composed of interactions among members (job-seekers), companies, and jobs. Understanding and modeling job marketplace can benefit both job seekers and employers, ultimately contributing to the greater good of the society. However, existing graph neural network (GNN)-based methods have shallow understandings of the associated textual features and heterogeneous relations. To address the above challenges, we propose PLM4Job, a job marketplace foundation model that tightly couples pretrained language models (PLM) with job market graph, aiming to fully utilize the pretrained knowledge and reasoning ability to model member/job textual features as well as various member-job relations simultaneously. In the pretraining phase, we propose a heterogeneous ego-graph-based prompting strategy to model and aggregate member/job textual features based on the topological structure around the target member/job node, where entity type embeddings and graph positional embeddings are introduced accordingly to model different entities and their heterogeneous relations. Meanwhile, a proximity-aware attention alignment strategy is designed to dynamically adjust the attention of the PLM on ego-graph node tokens in the prompt, such that the attention can be better aligned with job marketplace semantics. Extensive experiments at LinkedIn demonstrate the effectiveness of PLM4Job.