Yuan Fang

Zemin Liu, Xingtong Yu, Yuan Fang et al.

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks(GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily rely on a large amount of task-specific supervision. To reduce labeling requirement, the "pre-train, fine-tune" and "pre-train, prompt" paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-train model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

Deyu Bo, Xiao Wang, Yang Liu et al.

Graph neural networks (GNNs) have attracted considerable attention from the research community. It is well established that GNNs are usually roughly divided into spatial and spectral methods. Despite that spectral GNNs play an important role in both graph signal processing and graph representation learning, existing studies are biased toward spatial approaches, and there is no comprehensive review on spectral GNNs so far. In this paper, we summarize the recent development of spectral GNNs, including model, theory, and application. Specifically, we first discuss the connection between spatial GNNs and spectral GNNs, which shows that spectral GNNs can capture global information and have better expressiveness and interpretability. Next, we categorize existing spectral GNNs according to the spectrum information they use, \ie, eigenvalues or eigenvectors. In addition, we review major theoretical results and applications of spectral GNNs, followed by a quantitative experiment to benchmark some popular spectral GNNs. Finally, we conclude the paper with some future directions.

Zimeng Li, Sa Xiao, Cheng Wang et al. · amazon-science

Magnetic resonance imaging (MRI) using hyperpolarized noble gases provides a way to visualize the structure and function of human lung, but the long imaging time limits its broad research and clinical applications. Deep learning has demonstrated great potential for accelerating MRI by reconstructing images from undersampled data. However, most existing deep conventional neural networks (CNN) directly apply square convolution to k-space data without considering the inherent properties of k-space sampling, limiting k-space learning efficiency and image reconstruction quality. In this work, we propose an encoding enhanced (EN2) complex CNN for highly undersampled pulmonary MRI reconstruction. EN2 employs convolution along either the frequency or phase-encoding direction, resembling the mechanisms of k-space sampling, to maximize the utilization of the encoding correlation and integrity within a row or column of k-space. We also employ complex convolution to learn rich representations from the complex k-space data. In addition, we develop a feature-strengthened modularized unit to further boost the reconstruction performance. Experiments demonstrate that our approach can accurately reconstruct hyperpolarized 129Xe and 1H lung MRI from 6-fold undersampled k-space data and provide lung function measurements with minimal biases compared with fully-sampled image. These results demonstrate the effectiveness of the proposed algorithmic components and indicate that the proposed approach could be used for accelerated pulmonary MRI in research and clinical lung disease patient care.

Zemin Liu, Trung-Kien Nguyen, Yuan Fang

Conventional graph neural networks (GNNs) are often confronted with fairness issues that may stem from their input, including node attributes and neighbors surrounding a node. While several recent approaches have been proposed to eliminate the bias rooted in sensitive attributes, they ignore the other key input of GNNs, namely the neighbors of a node, which can introduce bias since GNNs hinge on neighborhood structures to generate node representations. In particular, the varying neighborhood structures across nodes, manifesting themselves in drastically different node degrees, give rise to the diverse behaviors of nodes and biased outcomes. In this paper, we first define and generalize the degree bias using a generalized definition of node degree as a manifestation and quantification of different multi-hop structures around different nodes. To address the bias in the context of node classification, we propose a novel GNN framework called Generalized Degree Fairness-centric Graph Neural Network (Deg-FairGNN). Specifically, in each GNN layer, we employ a learnable debiasing function to generate debiasing contexts, which modulate the layer-wise neighborhood aggregation to eliminate the degree bias originating from the diverse degrees among nodes. Extensive experiments on three benchmark datasets demonstrate the effectiveness of our model on both accuracy and fairness metrics.

Xingtong Yu, Zemin Liu, Yuan Fang et al.

Subgraph isomorphism counting is an important problem on graphs, as many graph-based tasks exploit recurring subgraph patterns. Classical methods usually boil down to a backtracking framework that needs to navigate a huge search space with prohibitive computational costs. Some recent studies resort to graph neural networks (GNNs) to learn a low-dimensional representation for both the query and input graphs, in order to predict the number of subgraph isomorphisms on the input graph. However, typical GNNs employ a node-centric message passing scheme that receives and aggregates messages on nodes, which is inadequate in complex structure matching for isomorphism counting. Moreover, on an input graph, the space of possible query graphs is enormous, and different parts of the input graph will be triggered to match different queries. Thus, expecting a fixed representation of the input graph to match diversely structured query graphs is unrealistic. In this paper, we propose a novel GNN called Count-GNN for subgraph isomorphism counting, to deal with the above challenges. At the edge level, given that an edge is an atomic unit of encoding graph structures, we propose an edge-centric message passing scheme, where messages on edges are propagated and aggregated based on the edge adjacency to preserve fine-grained structural information. At the graph level, we modulate the input graph representation conditioned on the query, so that the input graph can be adapted to each query individually to improve their matching. Finally, we conduct extensive experiments on a number of benchmark datasets to demonstrate the superior performance of Count-GNN.

Trung-Kien Nguyen, Zemin Liu, Yuan Fang

On graph data, the multitude of node or edge types gives rise to heterogeneous information networks (HINs). To preserve the heterogeneous semantics on HINs, the rich node/edge types become a cornerstone of HIN representation learning. However, in real-world scenarios, type information is often noisy, missing or inaccessible. Assuming no type information is given, we define a so-called latent heterogeneous graph (LHG), which carries latent heterogeneous semantics as the node/edge types cannot be observed. In this paper, we study the challenging and unexplored problem of link prediction on an LHG. As existing approaches depend heavily on type-based information, they are suboptimal or even inapplicable on LHGs. To address the absence of type information, we propose a model named LHGNN, based on the novel idea of semantic embedding at node and path levels, to capture latent semantics on and between nodes. We further design a personalization function to modulate the heterogeneous contexts conditioned on their latent semantics w.r.t. the target node, to enable finer-grained aggregation. Finally, we conduct extensive experiments on four benchmark datasets, and demonstrate the superior performance of LHGNN.

Ruichu Cai, Yuxuan Zhu, Xuexin Chen et al.

The explainability of Graph Neural Networks (GNNs) is critical to various GNN applications, yet it remains a significant challenge. A convincing explanation should be both necessary and sufficient simultaneously. However, existing GNN explaining approaches focus on only one of the two aspects, necessity or sufficiency, or a heuristic trade-off between the two. Theoretically, the Probability of Necessity and Sufficiency (PNS) holds the potential to identify the most necessary and sufficient explanation since it can mathematically quantify the necessity and sufficiency of an explanation. Nevertheless, the difficulty of obtaining PNS due to non-monotonicity and the challenge of counterfactual estimation limit its wide use. To address the non-identifiability of PNS, we resort to a lower bound of PNS that can be optimized via counterfactual estimation, and propose a framework of Necessary and Sufficient Explanation for GNN (NSEG) via optimizing that lower bound. Specifically, we depict the GNN as a structural causal model (SCM), and estimate the probability of counterfactual via the intervention under the SCM. Additionally, we leverage continuous masks with a sampling strategy to optimize the lower bound to enhance the scalability. Empirical results demonstrate that NSEG outperforms state-of-the-art methods, consistently generating the most necessary and sufficient explanations.

Xingtong Yu, Chang Zhou, Yuan Fang et al.

Graphs can inherently model interconnected objects on the Web, thereby facilitating a series of Web applications, such as web analyzing and content recommendation. Recently, Graph Neural Networks (GNNs) have emerged as a mainstream technique for graph representation learning. However, their efficacy within an end-to-end supervised framework is significantly tied to the availabilityof task-specific labels. To mitigate labeling costs and enhance robustness in few-shot settings, pre-training on self-supervised tasks has emerged as a promising method, while prompting has been proposed to further narrow the objective gap between pretext and downstream tasks. Although there has been some initial exploration of prompt-based learning on graphs, they primarily leverage a single pretext task, resulting in a limited subset of general knowledge that could be learned from the pre-training data. Hence, in this paper, we propose MultiGPrompt, a novel multi-task pre-training and prompting framework to exploit multiple pretext tasks for more comprehensive pre-trained knowledge. First, in pre-training, we design a set of pretext tokens to synergize multiple pretext tasks. Second, we propose a dual-prompt mechanism consisting of composed and open prompts to leverage task-specific and global pre-training knowledge, to guide downstream tasks in few-shot settings. Finally, we conduct extensive experiments on six public datasets to evaluate and analyze MultiGPrompt.

Huanyu Bian, Zhilong Jia, Menghan Dou et al.

With the rapid development of classical and quantum machine learning, a large number of machine learning frameworks have been proposed. However, existing machine learning frameworks usually only focus on classical or quantum, rather than both. Therefore, based on VQNet 1.0, we further propose VQNet 2.0, a new generation of unified classical and quantum machine learning framework that supports hybrid optimization. The core library of the framework is implemented in C++, and the user level is implemented in Python, and it supports deployment on quantum and classical hardware. In this article, we analyze the development trend of the new generation machine learning framework and introduce the design principles of VQNet 2.0 in detail: unity, practicality, efficiency, and compatibility, as well as full particulars of implementation. We illustrate the functions of VQNet 2.0 through several basic applications, including classical convolutional neural networks, quantum autoencoders, hybrid classical-quantum networks, etc. After that, through extensive experiments, we demonstrate that the operation speed of VQNet 2.0 is higher than the comparison method. Finally, through extensive experiments, we demonstrate that VQNet 2.0 can deploy on different hardware platforms, the overall calculation speed is faster than the comparison method. It also can be mixed and optimized with quantum circuits composed of multiple quantum computing libraries.

Yuanzhi Cai, Lei Fan, Yuan Fang

Semantic segmentation of Very High Resolution (VHR) remote sensing images is a fundamental task for many applications. However, large variations in the scales of objects in those VHR images pose a challenge for performing accurate semantic segmentation. Existing semantic segmentation networks are able to analyse an input image at up to four resizing scales, but this may be insufficient given the diversity of object scales. Therefore, Multi Scale (MS) test-time data augmentation is often used in practice to obtain more accurate segmentation results, which makes equal use of the segmentation results obtained at the different resizing scales. However, it was found in this study that different classes of objects had their preferred resizing scale for more accurate semantic segmentation. Based on this behaviour, a Stacking-Based Semantic Segmentation (SBSS) framework is proposed to improve the segmentation results by learning this behaviour, which contains a learnable Error Correction Module (ECM) for segmentation result fusion and an Error Correction Scheme (ECS) for computational complexity control. Two ECS, i.e., ECS-MS and ECS-SS, are proposed and investigated in this study. The Floating-point operations (Flops) required for ECS-MS and ECS-SS are similar to the commonly used MS test and the Single-Scale (SS) test, respectively. Extensive experiments on four datasets (i.e., Cityscapes, UAVid, LoveDA and Potsdam) show that SBSS is an effective and flexible framework. It achieved higher accuracy than MS when using ECS-MS, and similar accuracy as SS with a quarter of the memory footprint when using ECS-SS.

Xingtong Yu, Zhenghao Liu, Yuan Fang et al.

Graph neural networks have emerged as a powerful tool for graph representation learning, but their performance heavily relies on abundant task-specific supervision. To reduce labeling requirement, the "pre-train, prompt" paradigms have become increasingly common. However, existing study of prompting on graphs is limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-trained model in a task-specific manner. To further enhance GraphPrompt in these two stages, we extend it into GraphPrompt+ with two major enhancements. First, we generalize several popular graph pre-training tasks beyond simple link prediction to broaden the compatibility with our task template. Second, we propose a more generalized prompt design that incorporates a series of prompt vectors within every layer of the pre-trained graph encoder, in order to capitalize on the hierarchical information across different layers beyond just the readout layer. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt and GraphPrompt+.

Zhongzhou Liu, Hao Zhang, Kuicai Dong et al.

Despite the success of conventional collaborative filtering (CF) approaches for recommendation systems, they exhibit limitations in leveraging semantic knowledge within the textual attributes of users and items. Recent focus on the application of large language models for recommendation (LLM4Rec) has highlighted their capability for effective semantic knowledge capture. However, these methods often overlook the collaborative signals in user behaviors. Some simply instruct-tune a language model, while others directly inject the embeddings of a CF-based model, lacking a synergistic fusion of different modalities. To address these issues, we propose a framework of Collaborative Cross-modal Fusion with Large Language Models, termed CCF-LLM, for recommendation. In this framework, we translate the user-item interactions into a hybrid prompt to encode both semantic knowledge and collaborative signals, and then employ an attentive cross-modal fusion strategy to effectively fuse latent embeddings of both modalities. Extensive experiments demonstrate that CCF-LLM outperforms existing methods by effectively utilizing semantic and collaborative signals in the LLM4Rec context.

Xingtong Yu, Yuan Fang, Zemin Liu et al.

Graph representation learning, a critical step in graph-centric tasks, has seen significant advancements. Earlier techniques often operate in an end-to-end setting, which heavily rely on the availability of ample labeled data. This constraint has spurred the emergence of few-shot learning on graphs, where only a few labels are available for each task. Given the extensive literature in this field, this survey endeavors to synthesize recent developments, provide comparative insights, and identify future directions. We systematically categorize existing studies based on two major taxonomies: (1) Problem taxonomy, which explores different types of data scarcity problems and their applications, and (2) Technique taxonomy, which details key strategies for addressing these data-scarce few-shot problems. The techniques can be broadly categorized into meta-learning, pre-training, and hybrid approaches, with a finer-grained classification in each category to aid readers in their method selection process. Within each category, we analyze the relationships among these methods and compare their strengths and limitations. Finally, we outline prospective directions for few-shot learning on graphs to catalyze continued innovation in this field. The website for this survey can be accessed by \url{https://github.com/smufang/fewshotgraph}.

Tengwei Song, Min Wu, Yuan Fang

Molecular representation learning plays a crucial role in advancing applications such as drug discovery and material design. Existing work leverages 2D and 3D modalities of molecular information for pre-training, aiming to capture comprehensive structural and geometric insights. However, these methods require paired 2D and 3D molecular data to train the model effectively and prevent it from collapsing into a single modality, posing limitations in scenarios where a certain modality is unavailable or computationally expensive to generate. To overcome this limitation, we propose FlexMol, a flexible molecule pre-training framework that learns unified molecular representations while supporting single-modality input. Specifically, inspired by the unified structure in vision-language models, our approach employs separate models for 2D and 3D molecular data, leverages parameter sharing to improve computational efficiency, and utilizes a decoder to generate features for the missing modality. This enables a multistage continuous learning process where both modalities contribute collaboratively during training, while ensuring robustness when only one modality is available during inference. Extensive experiments demonstrate that FlexMol achieves superior performance across a wide range of molecular property prediction tasks, and we also empirically demonstrate its effectiveness with incomplete data. Our code and data are available at https://github.com/tewiSong/FlexMol.

Zhihao Wen, Wenkang Wei, Yuan Fang et al.

Knowledge-based Visual Question Answering (KVQA) requires models to ground entities in images and reason over factual knowledge. Recent work has introduced its implicit-knowledge variant, IK-KVQA, where a multimodal large language model (MLLM) is the sole knowledge source and answers are produced without external retrieval. Existing IK-KVQA approaches, however, are typically trained with answer-only supervision: reasoning remains implicit, justifications are often weak or inconsistent, and generalization after standard supervised fine-tuning (SFT) can be brittle. We propose MODELNAME, a framework that equips IK-KVQA with dual-path structured reasoning traces (symbolic relation paths over text and vision together with path-grounded natural-language explanations) to provide a stronger inductive bias than generic answer-only supervision. These traces act as modality-aware scaffolds that guide the model toward relevant entities and attributes, offering more structure than generic chain-of-thought supervision while not constraining reasoning to any single fixed path. Using a single open-source MLLM, MODELNAME constructs and selects traces to build an offline trace-enriched dataset and then performs structure-aware self-distillation; no external retrievers, verifiers, or curated knowledge bases are used, and inference is a single autoregressive pass. Across benchmarks, MODELNAME consistently improves both answer accuracy and the transparency of intermediate reasoning, achieving up to 11.3% higher answer accuracy on OK-VQA over the strongest baseline.

Xingtong Yu, Yuan Fang, Zemin Liu et al.

Graph neural networks (GNNs) and heterogeneous graph neural networks (HGNNs) are prominent techniques for homogeneous and heterogeneous graph representation learning, yet their performance in an end-to-end supervised framework greatly depends on the availability of task-specific supervision. To reduce the labeling cost, pre-training on self-supervised pretext tasks has become a popular paradigm,but there is often a gap between the pre-trained model and downstream tasks, stemming from the divergence in their objectives. To bridge the gap, prompt learning has risen as a promising direction especially in few-shot settings, without the need to fully fine-tune the pre-trained model. While there has been some early exploration of prompt-based learning on graphs, they primarily deal with homogeneous graphs, ignoring the heterogeneous graphs that are prevalent in downstream applications. In this paper, we propose HGPROMPT, a novel pre-training and prompting framework to unify not only pre-training and downstream tasks but also homogeneous and heterogeneous graphs via a dual-template design. Moreover, we propose dual-prompt in HGPROMPT to assist a downstream task in locating the most relevant prior to bridge the gaps caused by not only feature variations but also heterogeneity differences across tasks. Finally, we thoroughly evaluate and analyze HGPROMPT through extensive experiments on three public datasets.

Amitoz Azad, Yuan Fang

Geodesic distances on manifolds have numerous applications in image processing, computer graphics and computer vision. In this work, we introduce an approach called `LGGD' (Learned Generalized Geodesic Distances). This method involves generating node features by learning a generalized geodesic distance function through a training pipeline that incorporates training data, graph topology and the node content features. The strength of this method lies in the proven robustness of the generalized geodesic distances to noise and outliers. Our contributions encompass improved performance in node classification tasks, competitive results with state-of-the-art methods on real-world graph datasets, the demonstration of the learnability of parameters within the generalized geodesic equation on graph, and dynamic inclusion of new labels.

Xingtong Yu, Chang Zhou, Yuan Fang et al.

Given the ubiquity of graph data, it is intriguing to ask: Is it possible to train a graph foundation model on a broad range of graph data across diverse domains? A major hurdle toward this goal lies in the fact that graphs from different domains often exhibit profoundly divergent characteristics. Although there have been some initial efforts in integrating multi-domain graphs for pre-training, they primarily rely on textual descriptions to align the graphs, limiting their application to text-attributed graphs. Moreover, different source domains may conflict or interfere with each other, and their relevance to the target domain can vary significantly. To address these issues, we propose MDGPT, a text free Multi-Domain Graph Pre-Training and adaptation framework designed to exploit multi-domain knowledge for graph learning. First, we propose a set of domain tokens to to align features across source domains for synergistic pre-training. Second, we propose a dual prompts, consisting of a unifying prompt and a mixing prompt, to further adapt the target domain with unified multi-domain knowledge and a tailored mixture of domain-specific knowledge. Finally, we conduct extensive experiments involving six public datasets to evaluate and analyze MDGPT, which outperforms prior art by up to 37.9%.

Jianyuan Bo, Yuan Fang

In the rapidly evolving field of self-supervised learning on graphs, generative and contrastive methodologies have emerged as two dominant approaches. Our study focuses on masked feature reconstruction (MFR), a generative technique where a model learns to restore the raw features of masked nodes in a self-supervised manner. We observe that both MFR and graph contrastive learning (GCL) aim to maximize agreement between similar elements. Building on this observation, we reveal a novel theoretical insight: under specific conditions, the objectives of MFR and node-level GCL converge, despite their distinct operational mechanisms. This theoretical connection suggests these approaches are complementary rather than fundamentally different, prompting us to explore their integration to enhance self-supervised learning on graphs. Our research presents Contrastive Masked Feature Reconstruction (CORE), a novel graph self-supervised learning framework that integrates contrastive learning into MFR. Specifically, we form positive pairs exclusively between the original and reconstructed features of masked nodes, encouraging the encoder to prioritize contextual information over the node's own features. Additionally, we leverage the masked nodes themselves as negative samples, combining MFR's reconstructive power with GCL's discriminative ability to better capture intrinsic graph structures. Empirically, our proposed framework CORE significantly outperforms MFR across node and graph classification tasks, demonstrating state-of-the-art results. In particular, CORE surpasses GraphMAE and GraphMAE2 by up to 2.80% and 3.72% on node classification tasks, and by up to 3.82% and 3.76% on graph classification tasks.

Trung-Kien Nguyen, Yuan Fang

Link prediction is a fundamental task for graph analysis with important applications on the Web, such as social network analysis and recommendation systems, etc. Modern graph link prediction methods often employ a contrastive approach to learn robust node representations, where negative sampling is pivotal. Typical negative sampling methods aim to retrieve hard examples based on either predefined heuristics or automatic adversarial approaches, which might be inflexible or difficult to control. Furthermore, in the context of link prediction, most previous methods sample negative nodes from existing substructures of the graph, missing out on potentially more optimal samples in the latent space. To address these issues, we investigate a novel strategy of multi-level negative sampling that enables negative node generation with flexible and controllable ``hardness'' levels from the latent space. Our method, called Conditional Diffusion-based Multi-level Negative Sampling (DMNS), leverages the Markov chain property of diffusion models to generate negative nodes in multiple levels of variable hardness and reconcile them for effective graph link prediction. We further demonstrate that DMNS follows the sub-linear positivity principle for robust negative sampling. Extensive experiments on several benchmark datasets demonstrate the effectiveness of DMNS.

Xingtong Yu, Zhenghao Liu, Xinming Zhang et al.

Dynamic graphs capture evolving interactions between entities, such as in social networks, online learning platforms, and crowdsourcing projects. For dynamic graph modeling, dynamic graph neural networks (DGNNs) have emerged as a mainstream technique. However, they are generally pre-trained on the link prediction task, leaving a significant gap from the objectives of downstream tasks such as node classification. To bridge the gap, prompt-based learning has gained traction on graphs, but most existing efforts focus on static graphs, neglecting the evolution of dynamic graphs. In this paper, we propose DYGPROMPT, a novel pre-training and prompt learning framework for dynamic graph modeling. First, we design dual prompts to address the gap in both task objectives and temporal variations across pre-training and downstream tasks. Second, we recognize that node and time features mutually characterize each other, and propose dual condition-nets to model the evolving node-time patterns in downstream tasks. Finally, we thoroughly evaluate and analyze DYGPROMPT through extensive experiments on four public datasets.

Zhihao Wen, Yuan Fang, Pengcheng Wei et al.

Predicting Remaining Useful Life (RUL) plays a crucial role in the prognostics and health management of industrial systems that involve a variety of interrelated sensors. Given a constant stream of time series sensory data from such systems, deep learning models have risen to prominence at identifying complex, nonlinear temporal dependencies in these data. In addition to the temporal dependencies of individual sensors, spatial dependencies emerge as important correlations among these sensors, which can be naturally modelled by a temporal graph that describes time-varying spatial relationships. However, the majority of existing studies have relied on capturing discrete snapshots of this temporal graph, a coarse-grained approach that leads to loss of temporal information. Moreover, given the variety of heterogeneous sensors, it becomes vital that such inherent heterogeneity is leveraged for RUL prediction in temporal sensor graphs. To capture the nuances of the temporal and spatial relationships and heterogeneous characteristics in an interconnected graph of sensors, we introduce a novel model named Temporal and Heterogeneous Graph Neural Networks (THGNN). Specifically, THGNN aggregates historical data from neighboring nodes to accurately capture the temporal dynamics and spatial correlations within the stream of sensor data in a fine-grained manner. Moreover, the model leverages Feature-wise Linear Modulation (FiLM) to address the diversity of sensor types, significantly improving the model's capacity to learn the heterogeneity in the data sources. Finally, we have validated the effectiveness of our approach through comprehensive experiments. Our empirical findings demonstrate significant advancements on the N-CMAPSS dataset, achieving improvements of up to 19.2% and 31.6% in terms of two different evaluation metrics over state-of-the-art methods.

Shujie Li, Yuxia Wu, Chuan Shi et al.

Graph neural networks (GNNs) have demonstrated success in modeling relational data primarily under the assumption of homophily. However, many real-world graphs exhibit heterophily, where linked nodes belong to different categories or possess diverse attributes. Additionally, nodes in many domains are associated with textual descriptions, forming heterophilic text-attributed graphs (TAGs). Despite their significance, the study of heterophilic TAGs remains underexplored due to the lack of comprehensive benchmarks. To address this gap, we introduce the Heterophilic Text-attributed Graph Benchmark (HeTGB), a novel benchmark comprising five real-world heterophilic graph datasets from diverse domains, with nodes enriched by extensive textual descriptions. HeTGB enables systematic evaluation of GNNs, pre-trained language models (PLMs) and co-training methods on the node classification task. Through extensive benchmarking experiments, we showcase the utility of text attributes in heterophilic graphs, analyze the challenges posed by heterophilic TAGs and the limitations of existing models, and provide insights into the interplay between graph structures and textual attributes. We have publicly released HeTGB with baseline implementations to facilitate further research in this field.

Yang Liu, Deyu Bo, Wenxuan Cao et al.

Graph self-supervised learning seeks to learn effective graph representations without relying on labeled data. Among various approaches, graph autoencoders (GAEs) have gained significant attention for their efficiency and scalability. Typically, GAEs take incomplete graphs as input and predict missing elements, such as masked nodes or edges. While effective, our experimental investigation reveals that traditional node or edge masking paradigms primarily capture low-frequency signals in the graph and fail to learn the expressive structural information. To address these issues, we propose Graph Positional Autoencoders (GraphPAE), which employs a dual-path architecture to reconstruct both node features and positions. Specifically, the feature path uses positional encoding to enhance the message-passing processing, improving GAE's ability to predict the corrupted information. The position path, on the other hand, leverages node representations to refine positions and approximate eigenvectors, thereby enabling the encoder to learn diverse frequency information. We conduct extensive experiments to verify the effectiveness of GraphPAE, including heterophilic node classification, graph property prediction, and transfer learning. The results demonstrate that GraphPAE achieves state-of-the-art performance and consistently outperforms baselines by a large margin.

Xingtong Yu, Chang Zhou, Xinming Zhang et al.

Molecular graph representation learning is widely used in chemical and biomedical research. While pre-trained 2D graph encoders have demonstrated strong performance, they overlook the rich molecular domain knowledge associated with submolecular instances (atoms and bonds). While molecular pre-training approaches incorporate such knowledge into their pre-training objectives, they typically employ designs tailored to a specific type of knowledge, lacking the flexibility to integrate diverse knowledge present in molecules. Hence, reusing widely available and well-validated pre-trained 2D encoders, while incorporating molecular domain knowledge during downstream adaptation, offers a more practical alternative. In this work, we propose MolGA, which adapts pre-trained 2D graph encoders to downstream molecular applications by flexibly incorporating diverse molecular domain knowledge. First, we propose a molecular alignment strategy that bridge the gap between pre-trained topological representations with domain-knowledge representations. Second, we introduce a conditional adaptation mechanism that generates instance-specific tokens to enable fine-grained integration of molecular domain knowledge for downstream tasks. Finally, we conduct extensive experiments on eleven public datasets, demonstrating the effectiveness of MolGA.

Xuexin Chen, Ruichu Cai, Yuan Fang et al.

Graphs can model complicated interactions between entities, which naturally emerge in many important applications. These applications can often be cast into standard graph learning tasks, in which a crucial step is to learn low-dimensional graph representations. Graph neural networks (GNNs) are currently the most popular model in graph embedding approaches. However, standard GNNs in the neighborhood aggregation paradigm suffer from limited discriminative power in distinguishing \emph{high-order} graph structures as opposed to \emph{low-order} structures. To capture high-order structures, researchers have resorted to motifs and developed motif-based GNNs. However, existing motif-based GNNs still often suffer from less discriminative power on high-order structures. To overcome the above limitations, we propose Motif Graph Neural Network (MGNN), a novel framework to better capture high-order structures, hinging on our proposed motif redundancy minimization operator and injective motif combination. First, MGNN produces a set of node representations w.r.t. each motif. The next phase is our proposed redundancy minimization among motifs which compares the motifs with each other and distills the features unique to each motif. Finally, MGNN performs the updating of node representations by combining multiple representations from different motifs. In particular, to enhance the discriminative power, MGNN utilizes an injective function to combine the representations w.r.t. different motifs. We further show that our proposed architecture increases the expressive power of GNNs with a theoretical analysis. We demonstrate that MGNN outperforms state-of-the-art methods on seven public benchmarks on both node classification and graph classification tasks.

Chenghao Liu, Zhihao Wang, Doyen Sahoo et al.

Meta-learning methods have been extensively studied and applied in computer vision, especially for few-shot classification tasks. The key idea of meta-learning for few-shot classification is to mimic the few-shot situations faced at test time by randomly sampling classes in meta-training data to construct few-shot tasks for episodic training. While a rich line of work focuses solely on how to extract meta-knowledge across tasks, we exploit the complementary problem on how to generate informative tasks. We argue that the randomly sampled tasks could be sub-optimal and uninformative (e.g., the task of classifying "dog" from "laptop" is often trivial) to the meta-learner. In this paper, we propose an adaptive task sampling method to improve the generalization performance. Unlike instance based sampling, task based sampling is much more challenging due to the implicit definition of the task in each episode. Therefore, we accordingly propose a greedy class-pair based sampling method, which selects difficult tasks according to class-pair potentials. We evaluate our adaptive task sampling method on two few-shot classification benchmarks, and it achieves consistent improvements across different feature backbones, meta-learning algorithms and datasets.

Sezin Kircali Ata, Yuan Fang, Min Wu et al.

Real-world networks often exist with multiple views, where each view describes one type of interaction among a common set of nodes. For example, on a video-sharing network, while two user nodes are linked if they have common favorite videos in one view, they can also be linked in another view if they share common subscribers. Unlike traditional single-view networks, multiple views maintain different semantics to complement each other. In this paper, we propose MANE, a multi-view network embedding approach to learn low-dimensional representations. Similar to existing studies, MANE hinges on diversity and collaboration - while diversity enables views to maintain their individual semantics, collaboration enables views to work together. However, we also discover a novel form of second-order collaboration that has not been explored previously, and further unify it into our framework to attain superior node representations. Furthermore, as each view often has varying importance w.r.t. different nodes, we propose MANE+, an attention-based extension of MANE to model node-wise view importance. Finally, we conduct comprehensive experiments on three public, real-world multi-view networks, and the results demonstrate that our models consistently outperform state-of-the-art approaches.

Fang Yuan, Zhe Wang, Jie Lin et al.

Video understanding has attracted much research attention especially since the recent availability of large-scale video benchmarks. In this paper, we address the problem of multi-label video classification. We first observe that there exists a significant knowledge gap between how machines and humans learn. That is, while current machine learning approaches including deep neural networks largely focus on the representations of the given data, humans often look beyond the data at hand and leverage external knowledge to make better decisions. Towards narrowing the gap, we propose to incorporate external knowledge graphs into video classification. In particular, we unify traditional "knowledgeless" machine learning models and knowledge graphs in a novel end-to-end framework. The framework is flexible to work with most existing video classification algorithms including state-of-the-art deep models. Finally, we conduct extensive experiments on the largest public video dataset YouTube-8M. The results are promising across the board, improving mean average precision by up to 2.9%.

Zhe Wang, Kingsley Kuan, Mathieu Ravaut et al.

The YouTube-8M video classification challenge requires teams to classify 0.7 million videos into one or more of 4,716 classes. In this Kaggle competition, we placed in the top 3% out of 650 participants using released video and audio features. Beyond that, we extend the original competition by including text information in the classification, making this a truly multi-modal approach with vision, audio and text. The newly introduced text data is termed as YouTube-8M-Text. We present a classification framework for the joint use of text, visual and audio features, and conduct an extensive set of experiments to quantify the benefit that this additional mode brings. The inclusion of text yields state-of-the-art results, e.g. 86.7% GAP on the YouTube-8M-Text validation dataset.