Machine learning provides a valuable tool for analyzing high-dimensional functional neuroimaging data, and is proving effective in predicting various neurological conditions, psychiatric disorders, and cognitive patterns. In functional magnetic resonance imaging (MRI) research, interactions between brain regions are commonly modeled using graph-based representations. The potency of graph machine learning methods has been established across myriad domains, marking a transformative step in data interpretation and predictive modeling. Yet, despite their promise, the transposition of these techniques to the neuroimaging domain has been challenging due to the expansive number of potential preprocessing pipelines and the large parameter search space for graph-based dataset construction. In this paper, we introduce NeuroGraph, a collection of graph-based neuroimaging datasets, and demonstrated its utility for predicting multiple categories of behavioral and cognitive traits. We delve deeply into the dataset generation search space by crafting 35 datasets that encompass static and dynamic brain connectivity, running in excess of 15 baseline methods for benchmarking. Additionally, we provide generic frameworks for learning on both static and dynamic graphs. Our extensive experiments lead to several key observations. Notably, using correlation vectors as node features, incorporating larger number of regions of interest, and employing sparser graphs lead to improved performance. To foster further advancements in graph-based data driven neuroimaging analysis, we offer a comprehensive open-source Python package that includes the benchmark datasets, baseline implementations, model training, and standard evaluation.

Graph Neural Networks (GNNs) have shown remarkable merit in performing various learning-based tasks in complex networks. The superior performance of GNNs often correlates with the availability and quality of node-level features in the input networks. However, for many network applications, such node-level information may be missing or unreliable, thereby limiting the applicability and efficacy of GNNs. To address this limitation, we present a novel approach denoted as Ego-centric Spectral subGraph Embedding Augmentation (ESGEA), which aims to enhance and design node features, particularly in scenarios where information is lacking. Our method leverages the topological structure of the local subgraph to create topology-aware node features. The subgraph features are generated using an efficient spectral graph embedding technique, and they serve as node features that capture the local topological organization of the network. The explicit node features, if present, are then enhanced with the subgraph embeddings in order to improve the overall performance. ESGEA is compatible with any GNN-based architecture and is effective even in the absence of node features. We evaluate the proposed method in a social network graph classification task where node attributes are unavailable, as well as in a node classification task where node features are corrupted or even absent. The evaluation results on seven datasets and eight baseline models indicate up to a 10% improvement in AUC and a 7% improvement in accuracy for graph and node classification tasks, respectively.

Graph unlearning emerges as a crucial advancement in the pursuit of responsible AI, providing the means to remove sensitive data traces from trained models, thereby upholding the right to be forgotten. It is evident that graph machine learning exhibits sensitivity to data privacy and adversarial attacks, necessitating the application of graph unlearning techniques to address these concerns effectively. In this comprehensive survey paper, we present the first systematic review of graph unlearning approaches, encompassing a diverse array of methodologies and offering a detailed taxonomy and up-to-date literature overview to facilitate the understanding of researchers new to this field. Additionally, we establish the vital connections between graph unlearning and differential privacy, augmenting our understanding of the relevance of privacy-preserving techniques in this context. To ensure clarity, we provide lucid explanations of the fundamental concepts and evaluation measures used in graph unlearning, catering to a broader audience with varying levels of expertise. Delving into potential applications, we explore the versatility of graph unlearning across various domains, including but not limited to social networks, adversarial settings, and resource-constrained environments like the Internet of Things (IoT), illustrating its potential impact in safeguarding data privacy and enhancing AI systems' robustness. Finally, we shed light on promising research directions, encouraging further progress and innovation within the domain of graph unlearning. By laying a solid foundation and fostering continued progress, this survey seeks to inspire researchers to further advance the field of graph unlearning, thereby instilling confidence in the ethical growth of AI systems and reinforcing the responsible application of machine learning techniques in various domains.

Privacy attack is a popular and well-developed topic in various fields such as social network analysis, healthcare, finance, system, etc. [88], [89], [90]. During recent years, the surge of machine learning has provided powerful tools to solve many practical problems. However, data-driven approaches also threaten users' privacy due to the associated risks of data leakage and inference [85]. Consequently, a substantial amount of work has been devoted to investigate the vulnerabilities of ML models and the risks of privacy leakage [47]. A branch of privacy research is to develop privacy attack models, which has received much attention during the past few years. However, attack models with respect to GNNs have only been explored very recently because GNN techniques are relatively new compared with CNN/transformers in image/natural language processing(NLP) domains, and the irregular graph structure poses unique challenges to transfer existing attack techniques that are well-established in other domains. In this section, we summarize papers that have developed attack models specifically targeting GNNs. Figure 1: Illustrations of the four categories of privacy attack We classify the privacy attack models on GNN into models on graphs: a) Model extraction attacks (MEA); b) four categories (which are visualized in Figure 4): a) model Graph structure reconstruction (GSR); c) Attribute inference extraction attack (MEA), b) graph structure reconstruction attacks (AIA); and d) Membership inference attacks (MIA).

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 is publicly available at https://github.com/YuWVandy/CAGCN.

While machine learning models have achieved unprecedented success in real-world applications, they might make biased/unfair decisions for specific demographic groups and hence result in discriminative outcomes. Although research efforts have been devoted to measuring and mitigating bias, they mainly study bias from the result-oriented perspective while neglecting the bias encoded in the decision-making procedure. This results in their inability to capture procedure-oriented bias, which therefore limits the ability to have a fully debiasing method. Fortunately, with the rapid development of explainable machine learning, explanations for predictions are now available to gain insights into the procedure. In this work, we bridge the gap between fairness and explainability by presenting a novel perspective of procedure-oriented fairness based on explanations. We identify the procedure-based bias by measuring the gap of explanation quality between different groups with Ratio-based and Value-based Explanation Fairness. The new metrics further motivate us to design an optimization objective to mitigate the procedure-based bias where we observe that it will also mitigate bias from the prediction. Based on our designed optimization objective, we propose a Comprehensive Fairness Algorithm (CFA), which simultaneously fulfills multiple objectives - improving traditional fairness, satisfying explanation fairness, and maintaining the utility performance. Extensive experiments on real-world datasets demonstrate the effectiveness of our proposed CFA and highlight the importance of considering fairness from the explainability perspective. Our code is publicly available at https://github.com/YuyingZhao/FairExplanations-CFA .

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 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. Code of TDGNN: http://github.com/YuWVandy/TDGNN

While image understanding on recognition-level has achieved remarkable advancements, reliable visual scene understanding requires comprehensive image understanding on recognition-level but also cognition-level, which calls for exploiting the multi-source information as well as learning different levels of understanding and extensive commonsense knowledge. In this paper, we propose a novel Cognitive Attention Network (CAN) for visual commonsense reasoning to achieve interpretable visual understanding. Specifically, we first introduce an image-text fusion module to fuse information from images and text collectively. Second, a novel inference module is designed to encode commonsense among image, query and response. Extensive experiments on large-scale Visual Commonsense Reasoning (VCR) benchmark dataset demonstrate the effectiveness of our approach. The implementation is publicly available at https://github.com/tanjatang/CAN

Graph neural networks (GNNs) have received tremendous attention due to their power in learning effective representations for graphs. Most GNNs follow a message-passing scheme where the node representations are updated by aggregating and transforming the information from the neighborhood. Meanwhile, they adopt the same strategy in aggregating the information from different feature dimensions. However, suggested by social dimension theory and spectral embedding, there are potential benefits to treat the dimensions differently during the aggregation process. In this work, we investigate to enable heterogeneous contributions of feature dimensions in GNNs. In particular, we propose a general graph feature gating network (GFGN) based on the graph signal denoising problem and then correspondingly introduce three graph filters under GFGN to allow different levels of contributions from feature dimensions. Extensive experiments on various real-world datasets demonstrate the effectiveness and robustness of the proposed frameworks.