Recent advancements in deep learning have significantly enhanced the performance and efficiency of traffic classification in networking systems. However, the lack of transparency in their predictions and decision-making has made network operators reluctant to deploy DL-based solutions in production networks. To tackle this challenge, we propose Traffic-Explainer, a model-agnostic and input-perturbation-based traffic explanation framework. By maximizing the mutual information between predictions on original traffic sequences and their masked counterparts, Traffic-Explainer automatically uncovers the most influential features driving model predictions. Extensive experiments demonstrate that Traffic-Explainer improves upon existing explanation methods by approximately 42%. Practically, we further apply Traffic-Explainer to identify influential features and demonstrate its enhanced transparency across three critical tasks: application classification, traffic localization, and network cartography. For the first two tasks, Traffic-Explainer identifies the most decisive bytes that drive predicted traffic applications and locations, uncovering potential vulnerabilities and privacy concerns. In network cartography, Traffic-Explainer identifies submarine cables that drive the mapping of traceroute to physical path, enabling a traceroute-informed risk analysis.

Real-world graph data often follows long-tailed distributions, making it difficult for Graph Neural Networks (GNNs) to generalize well across both head and tail classes. Recent advances in Vicinal Risk Minimization (VRM) have shown promise in mitigating class imbalance with numeric interpolation; however, existing approaches largely rely on embedding-space arithmetic, which fails to capture the rich semantics inherent in text-attributed graphs. In this work, we propose our method, SaVe-TAG (Semantic-aware Vicinal Risk Minimization for Long-Tailed Text-Attributed Graphs), a novel VRM framework that leverages Large Language Models (LLMs) to perform text-level interpolation, generating on-manifold, boundary-enriching synthetic samples for minority classes. To mitigate the risk of noisy generation, we introduce a confidence-based edge assignment mechanism that uses graph topology as a natural filter to ensure structural consistency. We provide theoretical justification for our method and conduct extensive experiments on benchmark datasets, showing that our approach consistently outperforms both numeric interpolation and prior long-tailed node classification baselines. Our results highlight the importance of integrating semantic and structural signals for balanced and effective learning on text-attributed graphs. The source code is publicly available at: https://github.com/LWang-Laura/SaVe-TAG.

Retrieving external knowledge to Augment Generations of downstream task solutions (RAGs) has become a standard practice in powering knowledge-intensive applications. However, real-world knowledge often manifests in heterogeneous yet distinctive structures (e.g., tabular schemas, social networks, and document trees), the effective modeling of which demands specialized modeling, practical engineering, and domain expertise. Meanwhile, adopting RAGs in high-stakes scenarios underscores rigorous safety considerations. Despite the importance of this structural perspective, the current landscape remains fragmented. Moreover, few approaches adequately consider how structured knowledge shapes RAG's safety. Against this backdrop, our tutorial offers a structural perspective on RAGs. We begin by overviewing structured RAGs across their full lifecycle, highlighting their canonical designs. We then examine how design principles can be specialized for different knowledge structures, showcasing their unique applications and security attack/defense strategies. The tutorial slide is available https://kindlab-fly.github.io/tutorials/WSDM26/

Large Language Models (LLMs) have been increasingly studied as neural knowledge bases for supporting knowledge-intensive applications such as question answering and fact checking. However, the structural organization of their knowledge remains unexplored. Inspired by cognitive neuroscience findings, such as semantic clustering and priming, where knowing one fact increases the likelihood of recalling related facts, we investigate an analogous knowledge homophily pattern in LLMs. To this end, we map LLM knowledge into a graph representation through knowledge checking at both the triplet and entity levels. After that, we analyze the knowledgeability relationship between an entity and its neighbors, discovering that LLMs tend to possess a similar level of knowledge about entities positioned closer in the graph. Motivated by this homophily principle, we propose a Graph Neural Network (GNN) regression model to estimate entity-level knowledgeability scores for triplets by leveraging their neighborhood scores. The predicted knowledgeability enables us to prioritize checking less well-known triplets, thereby maximizing knowledge coverage under the same labeling budget. This not only improves the efficiency of active labeling for fine-tuning to inject knowledge into LLMs but also enhances multi-hop path retrieval in reasoning-intensive question answering.

Graphs, which encode pairwise relations between entities, serve as a fundamental data structure across real-world domains. Many critical applications can be formulated as graph-based tasks, and graph machine learning (GML), from the shallow embedding models to graph neural networks and further advanced to the most powerful graph transformers, has been well-established to automate knowledge discovery and decision-making on graphs. In parallel, the recent emergence of large foundational models has driven machine learning into a new era of Generative Artificial Intelligence (Gen-AI), and this revolution presents both unprecedented opportunities and profound challenges for the well-established GML paradigms. However, few investigations have analyzed and envisioned how GML should evolve to harness these opportunities, address these challenges, and embrace this new Gen-AI era. To fill in this gap, we organize the first international Workshop on Machine Learning on Graphs in the Era of Generative Artificial Intelligence (MLoG-GenAI), held in connection with the 31st ACM Conference on Knowledge Discovery and Data Mining, which provides a venue to gather academic researchers and industry practitioners to discuss and picture the development of GML in the new Gen-AI era.

The rapid rise of online social networks underscores the need to understand the heterogeneous strengths of online relationships. Yet, efforts to assess tie strength (TS) are hindered by the lack of ground-truth labels, differing research perspectives, and limited model performance in real-world settings. To address this gap, we introduce BTS, a comprehensive Benchmark for Tie Strength prediction, aiming to establish a standardized foundation for evaluating and advancing TS prediction methodologies. Specifically, our contributions are: TS Pseudo-Label Techniques -- we categorize TS into seven standardized pseudo-labeling techniques based on prior literature; TS Dataset Collection -- we present a representative collection of three social networks and perform data analysis by investigating the class distributions and correlations across the generated pseudo-labels; TS Pseudo-Label Evaluation Framework -- we propose a standardized framework to evaluate the pseudo-label quality from the perspective of tie resilience; Benchmarking -- we evaluate existing tie strength prediction model performance using the BTS dataset collection, exploring the effects of different experiment settings, models, and evaluation criteria on the results. Furthermore, we derive key insights to enhance existing methods and shed light on promising directions for future research in this domain. The BTS dataset collection, along with the curation codes and experimental scripts, is all available at: https://github.com/XueqiC/Awesome-Tie-Strength-Prediction.

Recent years have witnessed the remarkable success of applying Graph Machine Learning (GML) to node/graph classification and link prediction. However, edge classification task that enjoys numerous real-world applications such as social network analysis and cybersecurity, has not seen significant advancement with the progress of GML. To address this gap, our study pioneers a comprehensive approach to edge classification. We identify a novel 'Topological Imbalance Issue,' which arises from the skewed distribution of edges across different classes, affecting the local subgraph of each edge and harming the performance of edge classifications. Inspired by recent node-level studies observing performance discrepancies with varying local structural patterns, we aim to investigate if the topological imbalanced edge classification tasks can also be mitigated by characterizing the local class distribution variance. Thus, we introduce Topological Entropy (TE), a novel topological-based metric that measures the topological imbalance for each edge. Our empirical studies confirm that TE effectively measures local class distribution variance, and indicate that prioritizing edges with high TE values can help address the issue of topological imbalance. Inspired by this observation, we develop two strategies - Topological Reweighting and TE Wedge-based Mixup - to adaptively focus training on (synthetic) edges based on their TEs. While topological reweighting directly manipulates training edge weights according to TE, our wedge-based mixup interpolates synthetic edges between high TE wedges. To further enhance performance, we integrate these strategies into a novel topological imbalance strategy for edge classification: TopoEdge. Extensive experiments on real-world datasets demonstrate the efficacy of our proposed strategies. Our code and data are available at https://github.com/XueqiC/TopoEdge. Additionally, our curated datasets and designed experimental settings establish a new benchmark for future edge classification research, particularly in addressing imbalance issues.

Recommender systems (RS) are effective tools for mitigating information overload and have seen extensive applications across various domains. However, the single focus on utility goals proves to be inadequate in addressing real-world concerns, leading to increasing attention to fairness-aware and diversity-aware RS. While most existing studies explore fairness and diversity independently, we identify strong connections between these two domains. In this survey, we first discuss each of them individually and then dive into their connections. Additionally, motivated by the concepts of user-level and item-level fairness, we broaden the understanding of diversity to encompass not only the item level but also the user level. With this expanded perspective on user and item-level diversity, we re-interpret fairness studies from the viewpoint of diversity. This fresh perspective enhances our understanding of fairness-related work and paves the way for potential future research directions. Articles discussed in this survey along with public code links are available at: https://github.com/YuyingZhao/Awesome-Fairness-and-Diversity-Papers-in-Recommender-Systems

Recent years have seen a significant shift in Artificial Intelligence from model-centric to data-centric approaches, highlighted by the success of large foundational models. Following this trend, despite numerous innovations in graph machine learning model design, graph-structured data often suffers from data quality issues, jeopardizing the progress of Data-centric AI in graph-structured applications. Our proposed tutorial addresses this gap by raising awareness about data quality issues within the graph machine-learning community. We provide an overview of existing topology, imbalance, bias, limited data, and abnormality issues in graph data. Additionally, we highlight recent developments in foundational graph models that focus on identifying, investigating, mitigating, and resolving these issues.

Recommender systems (RSs) have gained widespread applications across various domains owing to the superior ability to capture users' interests. However, the complexity and nuanced nature of users' interests, which span a wide range of diversity, pose a significant challenge in delivering fair recommendations. In practice, user preferences vary significantly; some users show a clear preference toward certain item categories, while others have a broad interest in diverse ones. Even though it is expected that all users should receive high-quality recommendations, the effectiveness of RSs in catering to this disparate interest diversity remains under-explored.

Graph Neural Networks (GNNs) have become increasingly important due to their representational power and state-of-the-art predictive performance on many fundamental learning tasks. Despite this success, GNNs suffer from fairness issues that arise as a result of the underlying graph data and the fundamental aggregation mechanism that lies at the heart of the large class of GNN models. In this article, we examine and categorize fairness techniques for improving the fairness of GNNs. We categorize these techniques by whether they focus on improving fairness in the pre-processing, in-processing (during training), or post-processing phases. We discuss how such techniques can be used together whenever appropriate and highlight the advantages and intuition as well. We also introduce an intuitive taxonomy for fairness evaluation metrics, including graph-level fairness, neighborhood-level fairness, embedding-level fairness, and prediction-level fairness metrics. In addition, graph datasets that are useful for benchmarking the fairness of GNN models are summarized succinctly. Finally, we highlight key open problems and challenges that remain to be addressed.

Graph Neural Networks (GNNs) have gained significant attention owing to their ability to handle graph-structured data and the improvement in practical applications. However, many of these models prioritize high utility performance, such as accuracy, with a lack of privacy consideration, which is a major concern in modern society where privacy attacks are rampant. To address this issue, researchers have started to develop privacy-preserving GNNs. Despite this progress, there is a lack of a comprehensive overview of the attacks and the techniques for preserving privacy in the graph domain. In this survey, we aim to address this gap by summarizing the attacks on graph data according to the targeted information, categorizing the privacy preservation techniques in GNNs, and reviewing the datasets and applications that could be used for analyzing/solving privacy issues in GNNs. We also outline potential directions for future research in order to build better privacy-preserving GNNs.

Graph Neural Networks (GNNs) have been successfully adopted in recommender systems by virtue of the message-passing that implicitly captures collaborative effect. Nevertheless, most of the existing message-passing mechanisms for recommendation are directly inherited from GNNs without scrutinizing whether the captured collaborative effect would benefit the prediction of user preferences. In this paper, we first analyze how message-passing captures the collaborative effect and propose a recommendation-oriented topological metric, Common Interacted Ratio (CIR), which measures the level of interaction between a specific neighbor of a node with the rest of its neighbors. After demonstrating the benefits of leveraging collaborations from neighbors with higher CIR, we propose a recommendation-tailored GNN, Collaboration-Aware Graph Convolutional Network (CAGCN), that goes beyond 1-Weisfeiler-Lehman(1-WL) test in distinguishing non-bipartite-subgraph-isomorphic graphs. Experiments on six benchmark datasets show that the best CAGCN variant outperforms the most representative GNN-based recommendation model, LightGCN, by nearly 10% in Recall@20 and also achieves around 80% speedup. Our code/supplementary is at https://github.com/YuWVandy/CAGCN.

Graph Neural Networks (GNNs) have achieved unprecedented success in identifying categorical labels of graphs. However, most existing graph classification problems with GNNs follow the protocol of balanced data splitting, which misaligns with many real-world scenarios in which some classes have much fewer labels than others. Directly training GNNs under this imbalanced scenario may lead to uninformative representations of graphs in minority classes, and compromise the overall classification performance, which signifies the importance of developing effective GNNs towards handling imbalanced graph classification. Existing methods are either tailored for non-graph structured data or designed specifically for imbalanced node classification while few focus on imbalanced graph classification. To this end, we introduce a novel framework, Graph-of-Graph Neural Networks (G2GNN), which alleviates the graph imbalance issue by deriving extra supervision globally from neighboring graphs and locally from stochastic augmentations of graphs. Globally, we construct a graph of graphs (GoG) based on kernel similarity and perform GoG propagation to aggregate neighboring graph representations. Locally, we employ topological augmentation via masking node features or dropping edges with self-consistency regularization to generate stochastic augmentations of each graph that improve the model generalizability. Extensive graph classification experiments conducted on seven benchmark datasets demonstrate our proposed G2GNN outperforms numerous baselines by roughly 5% in both F1-macro and F1-micro scores.

Graph Neural Networks (GNNs) have shown satisfying performance in various graph analytical problems. Hence, they have become the de facto solution in a variety of decision-making scenarios. However, GNNs could yield biased results against certain demographic subgroups. Some recent works have empirically shown that the biased structure of the input network is a significant source of bias for GNNs. Nevertheless, no studies have systematically scrutinized which part of the input network structure leads to biased predictions for any given node. The low transparency on how the structure of the input network influences the bias in GNN outcome largely limits the safe adoption of GNNs in various decision-critical scenarios. In this paper, we study a novel research problem of structural explanation of bias in GNNs. Specifically, we propose a novel post-hoc explanation framework to identify two edge sets that can maximally account for the exhibited bias and maximally contribute to the fairness level of the GNN prediction for any given node, respectively. Such explanations not only provide a comprehensive understanding of bias/fairness of GNN predictions but also have practical significance in building an effective yet fair GNN model. Extensive experiments on real-world datasets validate the effectiveness of the proposed framework towards delivering effective structural explanations for the bias of GNNs. Open-source code can be found at https://github.com/yushundong/REFEREE.

In this paper, we introduce ChemicalX, a PyTorch-based deep learning library designed for providing a range of state of the art models to solve the drug pair scoring task. The primary objective of the library is to make deep drug pair scoring models accessible to machine learning researchers and practitioners in a streamlined framework. The design of ChemicalX reuses existing high level model training utilities, geometric deep learning, and deep chemistry layers from the PyTorch ecosystem. Our system provides neural network layers, custom pair scoring architectures, data loaders, and batch iterators for end users. We showcase these features with example code snippets and case studies to highlight the characteristics of ChemicalX. A range of experiments on real world drug-drug interaction, polypharmacy side effect, and combination synergy prediction tasks demonstrate that the models available in ChemicalX are effective at solving the pair scoring task. Finally, we show that ChemicalX could be used to train and score machine learning models on large drug pair datasets with hundreds of thousands of compounds on commodity hardware.

Graph Neural Networks (GNNs) have shown great power in learning node representations on graphs. However, they may inherit historical prejudices from training data, leading to discriminatory bias in predictions. Although some work has developed fair GNNs, most of them directly borrow fair representation learning techniques from non-graph domains without considering the potential problem of sensitive attribute leakage caused by feature propagation in GNNs. However, we empirically observe that feature propagation could vary the correlation of previously innocuous non-sensitive features to the sensitive ones. This can be viewed as a leakage of sensitive information which could further exacerbate discrimination in predictions. Thus, we design two feature masking strategies according to feature correlations to highlight the importance of considering feature propagation and correlation variation in alleviating discrimination. Motivated by our analysis, we propose Fair View Graph Neural Network (FairVGNN) to generate fair views of features by automatically identifying and masking sensitive-correlated features considering correlation variation after feature propagation. Given the learned fair views, we adaptively clamp weights of the encoder to avoid using sensitive-related features. Experiments on real-world datasets demonstrate that FairVGNN enjoys a better trade-off between model utility and fairness.

Graph-structured data is omnipresent in various fields, such as biology, chemistry, social media and transportation. Learning informative graph representations are crucial in effectively completing downstream graph-related tasks such as node/graph classification and link prediction. Graph Neural Networks (GNNs), due to their inclusiveness on handling graph-structured data and distinguished data-mining power inherited from deep learning, have achieved significant success in learning graph representations. Nonetheless, most existing GNNs are mainly designed with unrealistic data assumptions, such as the balanced and unbiased data distributions while abounding real-world networks exhibit skewed (i.e., long-tailed) node/graph class distributions and may also encode patterns of previous discriminatory decisions dominated by sensitive attributes. Even further, extensive research efforts have been invested in developing GNN architectures towards improving model utility while most of the time totally ignoring whether the obtained node/graph representations conceal any discriminatory bias, which could lead to prejudicial decisions as GNN-based machine learning models are increasingly being utilized in real-world applications. In light of the prevalence of the above two types of unfairness originated from quantity-imbalanced and discriminatory bias, my research expects to propose novel node/graph representation learning frameworks through constructing innovative GNN architectures and devising novel graph-mining algorithms to learn both fair and expressive node/graph representations that can enjoy a favorable fairness-utility tradeoff.

Graph Neural Networks (GNNs) have achieved significant success in learning better representations by performing feature propagation and transformation iteratively to leverage neighborhood information. Nevertheless, iterative propagation restricts the information of higher-layer neighborhoods to be transported through and fused with the lower-layer neighborhoods', which unavoidably results in feature smoothing between neighborhoods in different layers and can thus compromise the performance, especially on heterophily networks. Furthermore, most deep GNNs only recognize the importance of higher-layer neighborhoods while yet to fully explore the importance of multi-hop dependency within the context of different layer neighborhoods in learning better representations. In this work, we first theoretically analyze the feature smoothing between neighborhoods in different layers and empirically demonstrate the variance of the homophily level across neighborhoods at different layers. Motivated by these analyses, we further propose a tree decomposition method to disentangle neighborhoods in different layers to alleviate feature smoothing among these layers. Moreover, we characterize the multi-hop dependency via graph diffusion within our tree decomposition formulation to construct Tree Decomposed Graph Neural Network (TDGNN), which can flexibly incorporate information from large receptive fields and aggregate this information utilizing the multi-hop dependency. Comprehensive experiments demonstrate the superior performance of TDGNN on both homophily and heterophily networks under a variety of node classification settings. Extensive parameter analysis highlights the ability of TDGNN to prevent over-smoothing and incorporate features from shallow layers with deeper multi-hop dependencies, which provides new insights towards deeper graph neural networks.