Graph Neural Networks (GNNs) have achieved great success on a node classification task. Despite the broad interest in developing and evaluating GNNs, they have been assessed with limited benchmark datasets. As a result, the existing evaluation of GNNs lacks fine-grained analysis from various characteristics of graphs. Motivated by this, we conduct extensive experiments with a synthetic graph generator that can generate graphs having controlled characteristics for fine-grained analysis. Our empirical studies clarify the strengths and weaknesses of GNNs from four major characteristics of real-world graphs with class labels of nodes, i.e., 1) class size distributions (balanced vs. imbalanced), 2) edge connection proportions between classes (homophilic vs. heterophilic), 3) attribute values (biased vs. random), and 4) graph sizes (small vs. large). In addition, to foster future research on GNNs, we publicly release our codebase that allows users to evaluate various GNNs with various graphs. We hope this work offers interesting insights for future research.

Machine learning over graphs has recently attracted growing attention due to its ability to analyze and learn complex relations within critical interconnected systems. However, the disparate impact that is amplified by the use of biased graph structures in these algorithms has raised significant concerns for their deployment in real-world decision systems. In addition, while synthetic graph generation has become pivotal for privacy and scalability considerations, the impact of generative learning algorithms on structural bias has not yet been investigated. Motivated by this, this work focuses on the analysis and mitigation of structural bias for both real and synthetic graphs. Specifically, we first theoretically analyze the sources of structural bias that result in disparity for the predictions of dyadic relations. To alleviate the identified bias factors, we design a novel fairness regularizer that offers a versatile use. Faced with the bias amplification in graph generation models brought to light in this work, we further propose a fair graph generation framework, FairWire, by leveraging our fair regularizer design in a generative model. Experimental results on real-world networks validate that the proposed tools herein deliver effective structural bias mitigation for both real and synthetic graphs.

The volume of graph-structured data has been explosively growing due to the advancement in interconnected systems.

We study the problem of releasing a differentially private (DP) synthetic graph $G'$ that well approximates the triangle-motif sizes of all cuts of any given graph $G$, where a motif in general refers to a frequently occurring subgraph within complex networks. Non-private versions of such graphs have found applications in diverse fields such as graph clustering, graph sparsification, and social network analysis. Specifically, we present the first $(\varepsilon,δ)$-DP mechanism that, given an input graph $G$ with $n$ vertices, $m$ edges and local sensitivity of triangles $\ell_{3}(G)$, generates a synthetic graph $G'$ in polynomial time, approximating the triangle-motif sizes of all cuts $(S,V\setminus S)$ of the input graph $G$ up to an additive error of $\tilde{O}(\sqrt{m\ell_{3}(G)}n/\varepsilon^{3/2})$. Additionally, we provide a lower bound of $Ω(\sqrt{mn}\ell_{3}(G)/\varepsilon)$ on the additive error for any DP algorithm that answers the triangle-motif size queries of all $(S,T)$-cut of $G$. Finally, our algorithm generalizes to weighted graphs, and our lower bound extends to any $K_h$-motif cut for any constant $h\geq 2$.

The rise of graph-structured data has driven interest in graph learning and synthetic data generation. While successful in text and image domains, synthetic graph generation remains challenging -- especially for real-world graphs with complex, heterogeneous schemas. Existing research has focused mostly on homogeneous structures with simple attributes, limiting their usefulness and relevance for application domains requiring semantic fidelity. In this research, we introduce ProvCreator, a synthetic graph framework designed for complex heterogeneous graphs with high-dimensional node and edge attributes. ProvCreator formulates graph synthesis as a sequence generation task, enabling the use of transformer-based large language models. It features a versatile graph-to-sequence encoder-decoder that 1. losslessly encodes graph structure and attributes, 2. efficiently compresses large graphs for contextual modeling, and 3. supports end-to-end, learnable graph generation. To validate our research, we evaluate ProvCreator on two challenging domains: system provenance graphs in cybersecurity and knowledge graphs from IntelliGraph Benchmark Dataset. In both cases, ProvCreator captures intricate dependencies between structure and semantics, enabling the generation of realistic and privacy-aware synthetic datasets.

Graph-structured data is ubiquitous in scientific domains, where models often face imbalanced learning settings. In imbalanced regression, domain preferences focus on specific target value ranges that represent the most scientifically valuable cases; however, we observe a significant lack of research regarding this challenge. In this paper, we present Spectral Manifold Harmonization (SMH), a novel approach to address imbalanced regression challenges on graph-structured data by generating synthetic graph samples that preserve topological properties while focusing on the most relevant target distribution regions. Conventional methods fail in this context because they either ignore graph topology in case generation or do not target specific domain ranges, resulting in models biased toward average target values. Experimental results demonstrate the potential of SMH on chemistry and drug discovery benchmark datasets, showing consistent improvements in predictive performance for target domain ranges. Code is available at https://github.com/brendacnogueira/smh-graph-imbalance.git.

Machine learning over graphs has recently attracted growing attention due to its ability to analyze and learn complex relations within critical interconnected systems. However, the disparate impact that is amplified by the use of biased graph structures in these algorithms has raised significant concerns for their deployment in real-world decision systems. In addition, while synthetic graph generation has become pivotal for privacy and scalability considerations, the impact of generative learning algorithms on structural bias has not yet been investigated. Motivated by this, this work focuses on the analysis and mitigation of structural bias for both real and synthetic graphs. Specifically, we first theoretically analyze the sources of structural bias that result in disparity for the predictions of dyadic relations.

As graph data grows increasingly complicate, training graph neural networks (GNNs) on large-scale datasets presents significant challenges, including computational resource constraints, data redundancy, and transmission inefficiencies. While existing graph condensation techniques have shown promise in addressing these issues, they are predominantly designed for single-label datasets, where each node is associated with a single class label. However, many real-world applications, such as social network analysis and bioinformatics, involve multi-label graph datasets, where one node can have various related labels. To deal with this problem, we extends traditional graph condensation approaches to accommodate multi-label datasets by introducing modifications to synthetic dataset initialization and condensing optimization. Through experiments on eight real-world multi-label graph datasets, we prove the effectiveness of our method. In experiment, the GCond framework, combined with K-Center initialization and binary cross-entropy loss (BCELoss), achieves best performance in general. This benchmark for multi-label graph condensation not only enhances the scalability and efficiency of GNNs for multi-label graph data, but also offering substantial benefits for diverse real-world applications.