Daily Papers

Many real-world graphs frequently present challenges for graph learning due to the presence of both heterophily and heterogeneity. However, existing benchmarks for graph learning often focus on heterogeneous graphs with homophily or homogeneous graphs with heterophily, leaving a gap in understanding how methods perform on graphs that are both heterogeneous and heterophilic. To bridge this gap, we introduce H2GB, a novel graph benchmark that brings together the complexities of both the heterophily and heterogeneity properties of graphs. Our benchmark encompasses 9 diverse real-world datasets across 5 domains, 28 baseline model implementations, and 26 benchmark results. In addition, we present a modular graph transformer framework UnifiedGT and a new model variant, H2G-former, that excels at this challenging benchmark. By integrating masked label embeddings, cross-type heterogeneous attention, and type-specific FFNs, H2G-former effectively tackles graph heterophily and heterogeneity. Extensive experiments across 26 baselines on H2GB reveal inadequacies of current models on heterogeneous heterophilic graph learning, and demonstrate the superiority of our H2G-former over existing solutions. Both the benchmark and the framework are available on GitHub (https://github.com/junhongmit/H2GB) and PyPI (https://pypi.org/project/H2GB), and documentation can be found at https://junhongmit.github.io/H2GB/.

Label errors have been found to be prevalent in popular text, vision, and audio datasets, which heavily influence the safe development and evaluation of machine learning algorithms. Despite increasing efforts towards improving the quality of generic data types, such as images and texts, the problem of mislabel detection in graph data remains underexplored. To bridge the gap, we explore mislabelling issues in popular real-world graph datasets and propose GraphCleaner, a post-hoc method to detect and correct these mislabelled nodes in graph datasets. GraphCleaner combines the novel ideas of 1) Synthetic Mislabel Dataset Generation, which seeks to generate realistic mislabels; and 2) Neighborhood-Aware Mislabel Detection, where neighborhood dependency is exploited in both labels and base classifier predictions. Empirical evaluations on 6 datasets and 6 experimental settings demonstrate that GraphCleaner outperforms the closest baseline, with an average improvement of 0.14 in F1 score, and 0.16 in MCC. On real-data case studies, GraphCleaner detects real and previously unknown mislabels in popular graph benchmarks: PubMed, Cora, CiteSeer and OGB-arxiv; we find that at least 6.91% of PubMed data is mislabelled or ambiguous, and simply removing these mislabelled data can boost evaluation performance from 86.71% to 89.11%.

Graph Neural Networks (GNNs) have empowered the advance in graph-structured data analysis. Recently, the rise of Large Language Models (LLMs) like GPT-4 has heralded a new era in deep learning. However, their application to graph data poses distinct challenges due to the inherent difficulty of translating graph structures to language. To this end, we introduce the Large Language and Graph Assistant (LLaGA), an innovative model that effectively integrates LLM capabilities to handle the complexities of graph-structured data. LLaGA retains the general-purpose nature of LLMs while adapting graph data into a format compatible with LLM input. LLaGA achieves this by reorganizing graph nodes to structure-aware sequences and then mapping these into the token embedding space through a versatile projector. LLaGA excels in versatility, generalizability and interpretability, allowing it to perform consistently well across different datasets and tasks, extend its ability to unseen datasets or tasks, and provide explanations for graphs. Our extensive experiments across popular graph benchmarks show that LLaGA delivers outstanding performance across four datasets and three tasks using one single model, surpassing state-of-the-art graph models in both supervised and zero-shot scenarios. Our code is available at https://github.com/VITA-Group/LLaGA.

We present graph attention networks (GATs), novel neural network architectures that operate on graph-structured data, leveraging masked self-attentional layers to address the shortcomings of prior methods based on graph convolutions or their approximations. By stacking layers in which nodes are able to attend over their neighborhoods' features, we enable (implicitly) specifying different weights to different nodes in a neighborhood, without requiring any kind of costly matrix operation (such as inversion) or depending on knowing the graph structure upfront. In this way, we address several key challenges of spectral-based graph neural networks simultaneously, and make our model readily applicable to inductive as well as transductive problems. Our GAT models have achieved or matched state-of-the-art results across four established transductive and inductive graph benchmarks: the Cora, Citeseer and Pubmed citation network datasets, as well as a protein-protein interaction dataset (wherein test graphs remain unseen during training).

We present Graph Neural Diffusion (GRAND) that approaches deep learning on graphs as a continuous diffusion process and treats Graph Neural Networks (GNNs) as discretisations of an underlying PDE. In our model, the layer structure and topology correspond to the discretisation choices of temporal and spatial operators. Our approach allows a principled development of a broad new class of GNNs that are able to address the common plights of graph learning models such as depth, oversmoothing, and bottlenecks. Key to the success of our models are stability with respect to perturbations in the data and this is addressed for both implicit and explicit discretisation schemes. We develop linear and nonlinear versions of GRAND, which achieve competitive results on many standard graph benchmarks.

The era of foundation models has revolutionized AI research, yet Graph Foundation Models (GFMs) remain constrained by the scarcity of large-scale graph corpora. Traditional graph data synthesis techniques primarily focus on simplistic structural operations, lacking the capacity to generate semantically rich nodes with meaningful textual attributes: a critical limitation for real-world applications. While large language models (LLMs) demonstrate exceptional text generation capabilities, their direct application to graph synthesis is impeded by context window limitations, hallucination phenomena, and structural consistency challenges. To address these issues, we introduce GraphMaster, the first multi-agent framework specifically designed for graph data synthesis in data-limited environments. GraphMaster orchestrates four specialized LLM agents (Manager, Perception, Enhancement, and Evaluation) that collaboratively optimize the synthesis process through iterative refinement, ensuring both semantic coherence and structural integrity. To rigorously evaluate our approach, we create new data-limited "Sub" variants of six standard graph benchmarks, specifically designed to test synthesis capabilities under realistic constraints. Additionally, we develop a novel interpretability assessment framework that combines human evaluation with a principled Grassmannian manifold-based analysis, providing both qualitative and quantitative measures of semantic coherence. Experimental results demonstrate that GraphMaster significantly outperforms traditional synthesis methods across multiple datasets, establishing a strong foundation for advancing GFMs in data-scarce environments.

Transformers serve as the backbone architectures of Foundational Models, where a domain-specific tokenizer helps them adapt to various domains. Graph Transformers (GTs) have recently emerged as a leading model in geometric deep learning, outperforming Graph Neural Networks (GNNs) in various graph learning tasks. However, the development of tokenizers for graphs has lagged behind other modalities, with existing approaches relying on heuristics or GNNs co-trained with Transformers. To address this, we introduce GQT (Graph Quantized Tokenizer), which decouples tokenizer training from Transformer training by leveraging multi-task graph self-supervised learning, yielding robust and generalizable graph tokens. Furthermore, the GQT utilizes Residual Vector Quantization (RVQ) to learn hierarchical discrete tokens, resulting in significantly reduced memory requirements and improved generalization capabilities. By combining the GQT with token modulation, a Transformer encoder achieves state-of-the-art performance on 16 out of 18 benchmarks, including large-scale homophilic and heterophilic datasets. The code is available at: https://github.com/limei0307/graph-tokenizer

The inductive bias of a graph neural network (GNN) is largely encoded in its specified graph. Latent graph inference relies on latent geometric representations to dynamically rewire or infer a GNN's graph to maximize the GNN's predictive downstream performance, but it lacks solid theoretical foundations in terms of embedding-based representation guarantees. This paper addresses this issue by introducing a trainable deep learning architecture, coined neural snowflake, that can adaptively implement fractal-like metrics on R^d. We prove that any given finite weights graph can be isometrically embedded by a standard MLP encoder. Furthermore, when the latent graph can be represented in the feature space of a sufficiently regular kernel, we show that the combined neural snowflake and MLP encoder do not succumb to the curse of dimensionality by using only a low-degree polynomial number of parameters in the number of nodes. This implementation enables a low-dimensional isometric embedding of the latent graph. We conduct synthetic experiments to demonstrate the superior metric learning capabilities of neural snowflakes when compared to more familiar spaces like Euclidean space. Additionally, we carry out latent graph inference experiments on graph benchmarks. Consistently, the neural snowflake model achieves predictive performance that either matches or surpasses that of the state-of-the-art latent graph inference models. Importantly, this performance improvement is achieved without requiring random search for optimal latent geometry. Instead, the neural snowflake model achieves this enhancement in a differentiable manner.

Heterophilic Graph Neural Networks (HGNNs) have shown promising results for semi-supervised learning tasks on graphs. Notably, most real-world heterophilic graphs are composed of a mixture of nodes with different neighbor patterns, exhibiting local node-level homophilic and heterophilic structures. However, existing works are only devoted to designing better HGNN backbones or architectures for node classification tasks on heterophilic and homophilic graph benchmarks simultaneously, and their analyses of HGNN performance with respect to nodes are only based on the determined data distribution without exploring the effect caused by this structural difference between training and testing nodes. How to learn invariant node representations on heterophilic graphs to handle this structure difference or distribution shifts remains unexplored. In this paper, we first discuss the limitations of previous graph-based invariant learning methods from the perspective of data augmentation. Then, we propose HEI, a framework capable of generating invariant node representations through incorporating heterophily information to infer latent environments without augmentation, which are then used for invariant prediction, under heterophilic graph structure distribution shifts. We theoretically show that our proposed method can achieve guaranteed performance under heterophilic graph structure distribution shifts. Extensive experiments on various benchmarks and backbones can also demonstrate the effectiveness of our method compared with existing state-of-the-art baselines.

Despite that going deep has proven successful in many neural architectures, the existing graph transformers are relatively shallow. In this work, we explore whether more layers are beneficial to graph transformers, and find that current graph transformers suffer from the bottleneck of improving performance by increasing depth. Our further analysis reveals the reason is that deep graph transformers are limited by the vanishing capacity of global attention, restricting the graph transformer from focusing on the critical substructure and obtaining expressive features. To this end, we propose a novel graph transformer model named DeepGraph that explicitly employs substructure tokens in the encoded representation, and applies local attention on related nodes to obtain substructure based attention encoding. Our model enhances the ability of the global attention to focus on substructures and promotes the expressiveness of the representations, addressing the limitation of self-attention as the graph transformer deepens. Experiments show that our method unblocks the depth limitation of graph transformers and results in state-of-the-art performance across various graph benchmarks with deeper models.

Graph Neural Networks (GNNs) that are based on the message passing (MP) paradigm generally exchange information between 1-hop neighbors to build node representations at each layer. In principle, such networks are not able to capture long-range interactions (LRI) that may be desired or necessary for learning a given task on graphs. Recently, there has been an increasing interest in development of Transformer-based methods for graphs that can consider full node connectivity beyond the original sparse structure, thus enabling the modeling of LRI. However, MP-GNNs that simply rely on 1-hop message passing often fare better in several existing graph benchmarks when combined with positional feature representations, among other innovations, hence limiting the perceived utility and ranking of Transformer-like architectures. Here, we present the Long Range Graph Benchmark (LRGB) with 5 graph learning datasets: PascalVOC-SP, COCO-SP, PCQM-Contact, Peptides-func and Peptides-struct that arguably require LRI reasoning to achieve strong performance in a given task. We benchmark both baseline GNNs and Graph Transformer networks to verify that the models which capture long-range dependencies perform significantly better on these tasks. Therefore, these datasets are suitable for benchmarking and exploration of MP-GNNs and Graph Transformer architectures that are intended to capture LRI.

Foundation models have demonstrated remarkable capabilities across various domains, but developing analogous models for knowledge graphs presents unique challenges due to their dynamic nature and the need for cross-domain reasoning. To address these issues, we introduce \textsc{GraphOracle}, a relation-centric foundation model that unifies reasoning across knowledge graphs by converting them into Relation-Dependency Graphs (RDG), explicitly encoding compositional patterns with fewer edges than prior methods. A query-dependent attention mechanism is further developed to learn inductive representations for both relations and entities. Pre-training on diverse knowledge graphs, followed by minutes-level fine-tuning, enables effective generalization to unseen entities, relations, and entire graphs. Through comprehensive experiments on 31 diverse benchmarks spanning transductive, inductive, and cross-domain settings, we demonstrate consistent state-of-the-art performance with minimal adaptation, improving the prediction performance by up to 35\% compared to the strongest baselines.

Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work (Kim et al., 2022) shows that with proper position embedding, GT can approximate MPNN arbitrarily well, implying that GT is at least as powerful as MPNN. In this paper, we study the inverse connection and show that MPNN with virtual node (VN), a commonly used heuristic with little theoretical understanding, is powerful enough to arbitrarily approximate the self-attention layer of GT. In particular, we first show that if we consider one type of linear transformer, the so-called Performer/Linear Transformer (Choromanski et al., 2020; Katharopoulos et al., 2020), then MPNN + VN with only O(1) depth and O(1) width can approximate a self-attention layer in Performer/Linear Transformer. Next, via a connection between MPNN + VN and DeepSets, we prove the MPNN + VN with O(n^d) width and O(1) depth can approximate the self-attention layer arbitrarily well, where d is the input feature dimension. Lastly, under some assumptions, we provide an explicit construction of MPNN + VN with O(1) width and O(n) depth approximating the self-attention layer in GT arbitrarily well. On the empirical side, we demonstrate that 1) MPNN + VN is a surprisingly strong baseline, outperforming GT on the recently proposed Long Range Graph Benchmark (LRGB) dataset, 2) our MPNN + VN improves over early implementation on a wide range of OGB datasets and 3) MPNN + VN outperforms Linear Transformer and MPNN on the climate modeling task.

Accurate representation of multimodal knowledge is crucial for event forecasting in real-world scenarios. However, existing studies have largely focused on static settings, overlooking the dynamic acquisition and fusion of multimodal knowledge. 1) At the knowledge acquisition level, how to learn time-sensitive information of different modalities, especially the dynamic structural modality. Existing dynamic learning methods are often limited to shallow structures across heterogeneous spaces or simple unispaces, making it difficult to capture deep relation-aware geometric features. 2) At the knowledge fusion level, how to learn evolving multimodal fusion features. Existing knowledge fusion methods based on static coattention struggle to capture the varying historical contributions of different modalities to future events. To this end, we propose DyMRL, a Dynamic Multispace Representation Learning approach to efficiently acquire and fuse multimodal temporal knowledge. 1) For the former issue, DyMRL integrates time-specific structural features from Euclidean, hyperbolic, and complex spaces into a relational message-passing framework to learn deep representations, reflecting human intelligences in associative thinking, high-order abstracting, and logical reasoning. Pretrained models endow DyMRL with time-sensitive visual and linguistic intelligences. 2) For the latter concern, DyMRL incorporates advanced dual fusion-evolution attention mechanisms that assign dynamic learning emphases equally to different modalities at different timestamps in a symmetric manner. To evaluate DyMRL's event forecasting performance through leveraging its learned multimodal temporal knowledge in history, we construct four multimodal temporal knowledge graph benchmarks. Extensive experiments demonstrate that DyMRL outperforms state-of-the-art dynamic unimodal and static multimodal baseline methods.

A prominent paradigm for graph neural networks is based on the message-passing framework. In this framework, information communication is realized only between neighboring nodes. The challenge of approaches that use this paradigm is to ensure efficient and accurate long-distance communication between nodes, as deep convolutional networks are prone to oversmoothing. In this paper, we present a novel method based on time derivative graph diffusion (TIDE) to overcome these structural limitations of the message-passing framework. Our approach allows for optimizing the spatial extent of diffusion across various tasks and network channels, thus enabling medium and long-distance communication efficiently. Furthermore, we show that our architecture design also enables local message-passing and thus inherits from the capabilities of local message-passing approaches. We show that on both widely used graph benchmarks and synthetic mesh and graph datasets, the proposed framework outperforms state-of-the-art methods by a significant margin

Benefiting from the message passing mechanism, Graph Neural Networks (GNNs) have been successful on flourish tasks over graph data. However, recent studies have shown that attackers can catastrophically degrade the performance of GNNs by maliciously modifying the graph structure. A straightforward solution to remedy this issue is to model the edge weights by learning a metric function between pairwise representations of two end nodes, which attempts to assign low weights to adversarial edges. The existing methods use either raw features or representations learned by supervised GNNs to model the edge weights. However, both strategies are faced with some immediate problems: raw features cannot represent various properties of nodes (e.g., structure information), and representations learned by supervised GNN may suffer from the poor performance of the classifier on the poisoned graph. We need representations that carry both feature information and as mush correct structure information as possible and are insensitive to structural perturbations. To this end, we propose an unsupervised pipeline, named STABLE, to optimize the graph structure. Finally, we input the well-refined graph into a downstream classifier. For this part, we design an advanced GCN that significantly enhances the robustness of vanilla GCN without increasing the time complexity. Extensive experiments on four real-world graph benchmarks demonstrate that STABLE outperforms the state-of-the-art methods and successfully defends against various attacks.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

Graph Neural Networks (GNNs), especially message-passing neural networks (MPNNs), have emerged as powerful architectures for learning on graphs in diverse applications. However, MPNNs face challenges when modeling non-local interactions in graphs such as large conjugated molecules, and social networks due to oversmoothing and oversquashing. Although Spectral GNNs and traditional neural networks such as recurrent neural networks and transformers mitigate these challenges, they often lack generalizability, or fail to capture detailed structural relationships or symmetries in the data. To address these concerns, we introduce Matrix Function Neural Networks (MFNs), a novel architecture that parameterizes non-local interactions through analytic matrix equivariant functions. Employing resolvent expansions offers a straightforward implementation and the potential for linear scaling with system size. The MFN architecture achieves stateof-the-art performance in standard graph benchmarks, such as the ZINC and TU datasets, and is able to capture intricate non-local interactions in quantum systems, paving the way to new state-of-the-art force fields.

Self-supervised learning provides a promising path towards eliminating the need for costly label information in representation learning on graphs. However, to achieve state-of-the-art performance, methods often need large numbers of negative examples and rely on complex augmentations. This can be prohibitively expensive, especially for large graphs. To address these challenges, we introduce Bootstrapped Graph Latents (BGRL) - a graph representation learning method that learns by predicting alternative augmentations of the input. BGRL uses only simple augmentations and alleviates the need for contrasting with negative examples, and is thus scalable by design. BGRL outperforms or matches prior methods on several established benchmarks, while achieving a 2-10x reduction in memory costs. Furthermore, we show that BGRL can be scaled up to extremely large graphs with hundreds of millions of nodes in the semi-supervised regime - achieving state-of-the-art performance and improving over supervised baselines where representations are shaped only through label information. In particular, our solution centered on BGRL constituted one of the winning entries to the Open Graph Benchmark - Large Scale Challenge at KDD Cup 2021, on a graph orders of magnitudes larger than all previously available benchmarks, thus demonstrating the scalability and effectiveness of our approach.

We present the Evolving Graph Fourier Transform (EFT), the first invertible spectral transform that captures evolving representations on temporal graphs. We motivate our work by the inadequacy of existing methods for capturing the evolving graph spectra, which are also computationally expensive due to the temporal aspect along with the graph vertex domain. We view the problem as an optimization over the Laplacian of the continuous time dynamic graph. Additionally, we propose pseudo-spectrum relaxations that decompose the transformation process, making it highly computationally efficient. The EFT method adeptly captures the evolving graph's structural and positional properties, making it effective for downstream tasks on evolving graphs. Hence, as a reference implementation, we develop a simple neural model induced with EFT for capturing evolving graph spectra. We empirically validate our theoretical findings on a number of large-scale and standard temporal graph benchmarks and demonstrate that our model achieves state-of-the-art performance.

Large Language Models (LLMs) increasingly rely on agentic capabilities-iterative retrieval, tool use, and decision-making-to overcome the limits of static, parametric knowledge. Yet existing agentic frameworks treat external information as unstructured text and fail to leverage the topological dependencies inherent in real-world data. To bridge this gap, we introduce Agentic Graph Learning (AGL), a paradigm that reframes graph learning as an interleaved process of topology-aware navigation and LLM-based inference. Specifically, we propose AgentGL, the first reinforcement learning (RL)-driven framework for AGL. AgentGL equips an LLM agent with graph-native tools for multi-scale exploration, regulates tool usage via search-constrained thinking to balance accuracy and efficiency, and employs a graph-conditioned curriculum RL strategy to stabilize long-horizon policy learning without step-wise supervision. Across diverse Text-Attributed Graph (TAG) benchmarks and multiple LLM backbones, AgentGL substantially outperforms strong GraphLLMs and GraphRAG baselines, achieving absolute improvements of up to 17.5% in node classification and 28.4% in link prediction. These results demonstrate that AGL is a promising frontier for enabling LLMs to autonomously navigate and reason over complex relational environments. The code is publicly available at https://github.com/sunyuanfu/AgentGL.

Graphs are widely used for modeling relational data in real-world scenarios, such as social networks and urban computing. Existing LLM-based graph analysis approaches either integrate graph neural networks (GNNs) for specific machine learning tasks, limiting their transferability, or rely solely on LLMs' internal reasoning ability, resulting in suboptimal performance. To address these limitations, we take advantage of recent advances in LLM-based agents, which have shown capabilities of utilizing external knowledge or tools for problem solving. By simulating human problem-solving strategies such as analogy and collaboration, we propose a multi-agent system based on LLMs named GraphTeam, for graph analysis. GraphTeam consists of five LLM-based agents from three modules, and the agents with different specialities can collaborate with each other to address complex problems. Specifically, (1) input-output normalization module: the question agent extracts and refines four key arguments from the original question, facilitating the problem understanding, and the answer agent organizes the results to meet the output requirement; (2) external knowledge retrieval module: we first build a knowledge base consisting of relevant documentation and experience information, and then the search agent retrieves the most relevant entries for each question. (3) problem-solving module: given the retrieved information from search agent, the coding agent uses established algorithms via programming to generate solutions, and in case the coding agent does not work, the reasoning agent will directly compute the results without programming. Extensive experiments on six graph analysis benchmarks demonstrate that GraphTeam achieves state-of-the-art performance with an average 25.85% improvement over the best baseline in terms of accuracy. The code and data are available at https://github.com/BUPT-GAMMA/GraphTeam.

Graph Neural Networks (GNNs) have demonstrated remarkable success in various domains such as social networks, molecular chemistry, and more. A crucial component of GNNs is the pooling procedure, in which the node features calculated by the model are combined to form an informative final descriptor to be used for the downstream task. However, previous graph pooling schemes rely on the last GNN layer features as an input to the pooling or classifier layers, potentially under-utilizing important activations of previous layers produced during the forward pass of the model, which we regard as historical graph activations. This gap is particularly pronounced in cases where a node's representation can shift significantly over the course of many graph neural layers, and worsened by graph-specific challenges such as over-smoothing in deep architectures. To bridge this gap, we introduce HISTOGRAPH, a novel two-stage attention-based final aggregation layer that first applies a unified layer-wise attention over intermediate activations, followed by node-wise attention. By modeling the evolution of node representations across layers, our HISTOGRAPH leverages both the activation history of nodes and the graph structure to refine features used for final prediction. Empirical results on multiple graph classification benchmarks demonstrate that HISTOGRAPH offers strong performance that consistently improves traditional techniques, with particularly strong robustness in deep GNNs.

Hierarchical graph pooling(HGP) are designed to consider the fact that conventional graph neural networks(GNN) are inherently flat and are also not multiscale. However, most HGP methods suffer not only from lack of considering global topology of the graph and focusing on the feature learning aspect, but also they do not align local and global features since graphs should inherently be analyzed in a multiscale way. LGRPool is proposed in the present paper as a HGP in the framework of expectation maximization in machine learning that aligns local and global aspects of message passing with each other using a regularizer to force the global topological information to be inline with the local message passing at different scales through the representations at different layers of HGP. Experimental results on some graph classification benchmarks show that it slightly outperforms some baselines.

Associating unstructured data with structured information is crucial for real-world tasks that require relevance search. However, existing graph learning benchmarks often overlook the rich semantic information associate with each node. To bridge such gap, we introduce the Multimodal Graph Benchmark (MM-GRAPH), the first comprehensive multi-modal graph benchmark that incorporates both textual and visual information. MM-GRAPH surpasses previous efforts, which have primarily focused on text-attributed graphs with various connectivity patterns. MM-GRAPH consists of five graph learning datasets of various scales that are appropriate for different learning tasks. Their multimodal node features, enabling a more comprehensive evaluation of graph learning algorithms in real-world scenarios. To facilitate research on multimodal graph learning, we further provide an extensive study on the performance of various graph neural networks in the presence of features from various modalities. MM-GRAPH aims to foster research on multimodal graph learning and drive the development of more advanced and robust graph learning algorithms. By providing a diverse set of datasets and benchmarks, MM-GRAPH enables researchers to evaluate and compare their models in realistic settings, ultimately leading to improved performance on real-world applications that rely on multimodal graph data.

We introduce a randomized topological augmentor based on Schur complements for Graph Contrastive Learning (GCL). Given a graph laplacian matrix, the technique generates unbiased approximations of its Schur complements and treats the corresponding graphs as augmented views. We discuss the benefits of our approach, provide theoretical justifications and present connections with graph diffusion. Unlike previous efforts, we study the empirical effectiveness of the augmentor in a controlled fashion by varying the design choices for subsequent GCL phases, such as encoding and contrasting. Extensive experiments on node and graph classification benchmarks demonstrate that our technique consistently outperforms pre-defined and adaptive augmentation approaches to achieve state-of-the-art results.

Knowledge graph (KG) embeddings have shown great power in learning representations of entities and relations for link prediction tasks. Previous work usually embeds KGs into a single geometric space such as Euclidean space (zero curved), hyperbolic space (negatively curved) or hyperspherical space (positively curved) to maintain their specific geometric structures (e.g., chain, hierarchy and ring structures). However, the topological structure of KGs appears to be complicated, since it may contain multiple types of geometric structures simultaneously. Therefore, embedding KGs in a single space, no matter the Euclidean space, hyperbolic space or hyperspheric space, cannot capture the complex structures of KGs accurately. To overcome this challenge, we propose Geometry Interaction knowledge graph Embeddings (GIE), which learns spatial structures interactively between the Euclidean, hyperbolic and hyperspherical spaces. Theoretically, our proposed GIE can capture a richer set of relational information, model key inference patterns, and enable expressive semantic matching across entities. Experimental results on three well-established knowledge graph completion benchmarks show that our GIE achieves the state-of-the-art performance with fewer parameters.

Recent advances in representation learning on graphs, mainly leveraging graph convolutional networks, have brought a substantial improvement on many graph-based benchmark tasks. While novel approaches to learning node embeddings are highly suitable for node classification and link prediction, their application to graph classification (predicting a single label for the entire graph) remains mostly rudimentary, typically using a single global pooling step to aggregate node features or a hand-designed, fixed heuristic for hierarchical coarsening of the graph structure. An important step towards ameliorating this is differentiable graph coarsening---the ability to reduce the size of the graph in an adaptive, data-dependent manner within a graph neural network pipeline, analogous to image downsampling within CNNs. However, the previous prominent approach to pooling has quadratic memory requirements during training and is therefore not scalable to large graphs. Here we combine several recent advances in graph neural network design to demonstrate that competitive hierarchical graph classification results are possible without sacrificing sparsity. Our results are verified on several established graph classification benchmarks, and highlight an important direction for future research in graph-based neural networks.

Graph Neural Networks (GNNs) are an effective framework for representation learning of graphs. GNNs follow a neighborhood aggregation scheme, where the representation vector of a node is computed by recursively aggregating and transforming representation vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs to capture different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.

Graph Neural Networks (GNNs) show promising results for graph tasks. However, existing GNNs' generalization ability will degrade when there exist distribution shifts between testing and training graph data. The cardinal impetus underlying the severe degeneration is that the GNNs are architected predicated upon the I.I.D assumptions. In such a setting, GNNs are inclined to leverage imperceptible statistical correlations subsisting in the training set to predict, albeit it is a spurious correlation. In this paper, we study the problem of the generalization ability of GNNs in Out-Of-Distribution (OOD) settings. To solve this problem, we propose the Learning to Reweight for Generalizable Graph Neural Network (L2R-GNN) to enhance the generalization ability for achieving satisfactory performance on unseen testing graphs that have different distributions with training graphs. We propose a novel nonlinear graph decorrelation method, which can substantially improve the out-of-distribution generalization ability and compares favorably to previous methods in restraining the over-reduced sample size. The variables of the graph representation are clustered based on the stability of the correlation, and the graph decorrelation method learns weights to remove correlations between the variables of different clusters rather than any two variables. Besides, we interpose an efficacious stochastic algorithm upon bi-level optimization for the L2R-GNN framework, which facilitates simultaneously learning the optimal weights and GNN parameters, and avoids the overfitting problem. Experimental results show that L2R-GNN greatly outperforms baselines on various graph prediction benchmarks under distribution shifts.

Transformers have demonstrated success in graph learning, particularly for node-level tasks. However, existing methods encounter an information bottleneck when generating graph-level representations. The prevalent single token paradigm fails to fully leverage the inherent strength of self-attention in encoding token sequences, and degenerates into a weighted sum of node signals. To address this issue, we design a novel serialized token paradigm to encapsulate global signals more effectively. Specifically, a graph serialization method is proposed to aggregate node signals into serialized graph tokens, with positional encoding being automatically involved. Then, stacked self-attention layers are applied to encode this token sequence and capture its internal dependencies. Our method can yield more expressive graph representations by modeling complex interactions among multiple graph tokens. Experimental results show that our method achieves state-of-the-art results on several graph-level benchmarks. Ablation studies verify the effectiveness of the proposed modules.

Graph Neural Networks (GNN) are inherently limited in their expressive power. Recent seminal works (Xu et al., 2019; Morris et al., 2019b) introduced the Weisfeiler-Lehman (WL) hierarchy as a measure of expressive power. Although this hierarchy has propelled significant advances in GNN analysis and architecture developments, it suffers from several significant limitations. These include a complex definition that lacks direct guidance for model improvement and a WL hierarchy that is too coarse to study current GNNs. This paper introduces an alternative expressive power hierarchy based on the ability of GNNs to calculate equivariant polynomials of a certain degree. As a first step, we provide a full characterization of all equivariant graph polynomials by introducing a concrete basis, significantly generalizing previous results. Each basis element corresponds to a specific multi-graph, and its computation over some graph data input corresponds to a tensor contraction problem. Second, we propose algorithmic tools for evaluating the expressiveness of GNNs using tensor contraction sequences, and calculate the expressive power of popular GNNs. Finally, we enhance the expressivity of common GNN architectures by adding polynomial features or additional operations / aggregations inspired by our theory. These enhanced GNNs demonstrate state-of-the-art results in experiments across multiple graph learning benchmarks.

Two main families of node feature augmentation schemes have been explored for enhancing GNNs: random features and spectral positional encoding. Surprisingly, however, there is still no clear understanding of the relation between these two augmentation schemes. Here we propose a novel family of positional encoding schemes which draws a link between the above two approaches and improves over both. The new approach, named Random Feature Propagation (RFP), is inspired by the power iteration method and its generalizations. It concatenates several intermediate steps of an iterative algorithm for computing the dominant eigenvectors of a propagation matrix, starting from random node features. Notably, these propagation steps are based on graph-dependent propagation operators that can be either predefined or learned. We explore the theoretical and empirical benefits of RFP. First, we provide theoretical justifications for using random features, for incorporating early propagation steps, and for using multiple random initializations. Then, we empirically demonstrate that RFP significantly outperforms both spectral PE and random features in multiple node classification and graph classification benchmarks.

We present CoDEx, a set of knowledge graph completion datasets extracted from Wikidata and Wikipedia that improve upon existing knowledge graph completion benchmarks in scope and level of difficulty. In terms of scope, CoDEx comprises three knowledge graphs varying in size and structure, multilingual descriptions of entities and relations, and tens of thousands of hard negative triples that are plausible but verified to be false. To characterize CoDEx, we contribute thorough empirical analyses and benchmarking experiments. First, we analyze each CoDEx dataset in terms of logical relation patterns. Next, we report baseline link prediction and triple classification results on CoDEx for five extensively tuned embedding models. Finally, we differentiate CoDEx from the popular FB15K-237 knowledge graph completion dataset by showing that CoDEx covers more diverse and interpretable content, and is a more difficult link prediction benchmark. Data, code, and pretrained models are available at https://bit.ly/2EPbrJs.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

Learning powerful data embeddings has become a center piece in machine learning, especially in natural language processing and computer vision domains. The crux of these embeddings is that they are pretrained on huge corpus of data in a unsupervised fashion, sometimes aided with transfer learning. However currently in the graph learning domain, embeddings learned through existing graph neural networks (GNNs) are task dependent and thus cannot be shared across different datasets. In this paper, we present a first powerful and theoretically guaranteed graph neural network that is designed to learn task-independent graph embeddings, thereafter referred to as deep universal graph embedding (DUGNN). Our DUGNN model incorporates a novel graph neural network (as a universal graph encoder) and leverages rich Graph Kernels (as a multi-task graph decoder) for both unsupervised learning and (task-specific) adaptive supervised learning. By learning task-independent graph embeddings across diverse datasets, DUGNN also reaps the benefits of transfer learning. Through extensive experiments and ablation studies, we show that the proposed DUGNN model consistently outperforms both the existing state-of-art GNN models and Graph Kernels by an increased accuracy of 3% - 8% on graph classification benchmark datasets.

Graph neural networks (GNNs) are increasingly applied to physical design tasks such as congestion prediction and wirelength estimation, yet progress is hindered by inconsistent circuit representations and the absence of controlled evaluation protocols. We present R2G (RTL-to-GDSII), a multi-view circuit-graph benchmark suite that standardizes five stage-aware views with information parity (every view encodes the same attribute set, differing only in where features attach) over 30 open-source IP cores (up to 10^6 nodes/edges). R2G provides an end-to-end DEF-to-graph pipeline spanning synthesis, placement, and routing stages, together with loaders, unified splits, domain metrics, and reproducible baselines. By decoupling representation choice from model choice, R2G isolates a confound that prior EDA and graph-ML benchmarks leave uncontrolled. In systematic studies with GINE, GAT, and ResGatedGCN, we find: (i) view choice dominates model choice, with Test R^2 varying by more than 0.3 across representations for a fixed GNN; (ii) node-centric views generalize best across both placement and routing; and (iii) decoder-head depth (3--4 layers) is the primary accuracy driver, turning divergent training into near-perfect predictions (R^2>0.99). Code and datasets are available at https://github.com/ShenShan123/R2G.

Developing models that can learn to reason is a notoriously challenging problem. We focus on reasoning in relational domains, where the use of Graph Neural Networks (GNNs) seems like a natural choice. However, previous work has shown that regular GNNs lack the ability to systematically generalize from training examples on test graphs requiring longer inference chains, which fundamentally limits their reasoning abilities. A common solution relies on neuro-symbolic methods that systematically reason by learning rules, but their scalability is often limited and they tend to make unrealistically strong assumptions, e.g.\ that the answer can always be inferred from a single relational path. We propose the Epistemic GNN (EpiGNN), a novel parameter-efficient and scalable GNN architecture with an epistemic inductive bias for systematic reasoning. Node embeddings in EpiGNNs are treated as epistemic states, and message passing is implemented accordingly. We show that EpiGNNs achieve state-of-the-art results on link prediction tasks that require systematic reasoning. Furthermore, for inductive knowledge graph completion, EpiGNNs rival the performance of state-of-the-art specialized approaches. Finally, we introduce two new benchmarks that go beyond standard relational reasoning by requiring the aggregation of information from multiple paths. Here, existing neuro-symbolic approaches fail, yet EpiGNNs learn to reason accurately. Code and datasets are available at https://github.com/erg0dic/gnn-sg.

Transformers achieve strong performance across diverse domains but implicitly assume Euclidean geometry in their attention mechanisms, limiting their effectiveness on data with non-Euclidean structure. While recent extensions to hyperbolic and spherical spaces show promise for hierarchical and cyclical patterns, respectively, they require committing to a single geometry a priori, reducing flexibility when data exhibits mixed geometric properties. We introduce the Curvature-Adaptive Transformer (CAT), a novel architecture that dynamically learns per-token routing across three geometric attention branches through a lightweight, differentiable gating mechanism. Unlike fixed-geometry approaches, CAT enables adaptive geometric specialization, routing tokens to the appropriate curvature based on their local relational structure. The routing network provides interpretable curvature preferences while each branch employs geometry-specific operations optimized for its respective manifold. On knowledge graph completion benchmarks (FB15k-237, WN18RR), CAT achieves approximately 10% improvements in MRR and Hits@10 over fixed-geometry baselines with minimal overhead (5% parameter increase, comparable inference time). These results demonstrate that learned geometric adaptation outperforms any single fixed geometry for complex relational reasoning, establishing CAT as a scalable and interpretable foundation for mixture-of-geometry architectures across language, vision, and multimodal domains.

Enhancing node-level Out-Of-Distribution (OOD) generalization on graphs remains a crucial area of research. In this paper, we develop a Structural Causal Model (SCM) to theoretically dissect the performance of two prominent invariant learning methods -- Invariant Risk Minimization (IRM) and Variance-Risk Extrapolation (VREx) -- in node-level OOD settings. Our analysis reveals a critical limitation: due to the lack of class-conditional invariance constraints, these methods may struggle to accurately identify the structure of the predictive invariant ego-graph and consequently rely on spurious features. To address this, we propose Cross-environment Intra-class Alignment (CIA), which explicitly eliminates spurious features by aligning cross-environment representations conditioned on the same class, bypassing the need for explicit knowledge of the causal pattern structure. To adapt CIA to node-level OOD scenarios where environment labels are hard to obtain, we further propose CIA-LRA (Localized Reweighting Alignment) that leverages the distribution of neighboring labels to selectively align node representations, effectively distinguishing and preserving invariant features while removing spurious ones, all without relying on environment labels. We theoretically prove CIA-LRA's effectiveness by deriving an OOD generalization error bound based on PAC-Bayesian analysis. Experiments on graph OOD benchmarks validate the superiority of CIA and CIA-LRA, marking a significant advancement in node-level OOD generalization. The codes are available at https://github.com/NOVAglow646/NeurIPS24-Invariant-Learning-on-Graphs.

We propose a new graph neural network (GNN) module, based on relaxations of recently proposed geometric scattering transforms, which consist of a cascade of graph wavelet filters. Our learnable geometric scattering (LEGS) module enables adaptive tuning of the wavelets to encourage band-pass features to emerge in learned representations. The incorporation of our LEGS-module in GNNs enables the learning of longer-range graph relations compared to many popular GNNs, which often rely on encoding graph structure via smoothness or similarity between neighbors. Further, its wavelet priors result in simplified architectures with significantly fewer learned parameters compared to competing GNNs. We demonstrate the predictive performance of LEGS-based networks on graph classification benchmarks, as well as the descriptive quality of their learned features in biochemical graph data exploration tasks. Our results show that LEGS-based networks match or outperforms popular GNNs, as well as the original geometric scattering construction, on many datasets, in particular in biochemical domains, while retaining certain mathematical properties of handcrafted (non-learned) geometric scattering.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

Although Large Language Models (LLMs) have demonstrated remarkable progress, their proficiency in graph-related tasks remains notably limited, hindering the development of truly general-purpose models. Previous attempts, including pretraining graph foundation models or employing supervised fine-tuning, often face challenges such as the scarcity of large-scale, universally represented graph data. We introduce G1, a simple yet effective approach demonstrating that Reinforcement Learning (RL) on synthetic graph-theoretic tasks can significantly scale LLMs' graph reasoning abilities. To enable RL training, we curate Erd\~os, the largest graph reasoning dataset to date comprising 50 diverse graph-theoretic tasks of varying difficulty levels, 100k training data and 5k test data, all drived from real-world graphs. With RL on Erd\~os, G1 obtains substantial improvements in graph reasoning, where our finetuned 3B model even outperforms Qwen2.5-72B-Instruct (24x size). RL-trained models also show strong zero-shot generalization to unseen tasks, domains, and graph encoding schemes, including other graph-theoretic benchmarks as well as real-world node classification and link prediction tasks, without compromising general reasoning abilities. Our findings offer an efficient, scalable path for building strong graph reasoners by finetuning LLMs with RL on graph-theoretic tasks, which combines the strengths of pretrained LLM capabilities with abundant, automatically generated synthetic data, suggesting that LLMs possess graph understanding abilities that RL can elicit successfully.

Finding meaningful representations and distances of hierarchical data is important in many fields. This paper presents a new method for hierarchical data embedding and distance. Our method relies on combining diffusion geometry, a central approach to manifold learning, and hyperbolic geometry. Specifically, using diffusion geometry, we build multi-scale densities on the data, aimed to reveal their hierarchical structure, and then embed them into a product of hyperbolic spaces. We show theoretically that our embedding and distance recover the underlying hierarchical structure. In addition, we demonstrate the efficacy of the proposed method and its advantages compared to existing methods on graph embedding benchmarks and hierarchical datasets.

In contrastive learning, the choice of ``view'' controls the information that the representation captures and influences the performance of the model. However, leading graph contrastive learning methods generally produce views via random corruption or learning, which could lead to the loss of essential information and alteration of semantic information. An anchor view that maintains the essential information of input graphs for contrastive learning has been hardly investigated. In this paper, based on the theory of graph information bottleneck, we deduce the definition of this anchor view; put differently, the anchor view with essential information of input graph is supposed to have the minimal structural uncertainty. Furthermore, guided by structural entropy, we implement the anchor view, termed SEGA, for graph contrastive learning. We extensively validate the proposed anchor view on various benchmarks regarding graph classification under unsupervised, semi-supervised, and transfer learning and achieve significant performance boosts compared to the state-of-the-art methods.

Devising augmentations for graph contrastive learning is challenging due to their irregular structure, drastic distribution shifts, and nonequivalent feature spaces across datasets. We introduce LG2AR, Learning Graph Augmentations to Learn Graph Representations, which is an end-to-end automatic graph augmentation framework that helps encoders learn generalizable representations on both node and graph levels. LG2AR consists of a probabilistic policy that learns a distribution over augmentations and a set of probabilistic augmentation heads that learn distributions over augmentation parameters. We show that LG2AR achieves state-of-the-art results on 18 out of 20 graph-level and node-level benchmarks compared to previous unsupervised models under both linear and semi-supervised evaluation protocols. The source code will be released here: https://github.com/kavehhassani/lg2ar

Large language models (LLMs) have shown significant progress in reasoning tasks. However, recent studies show that transformers and LLMs fail catastrophically once reasoning problems exceed modest complexity. We revisit these findings through the lens of large reasoning models (LRMs) -- LLMs fine-tuned with incentives for step-by-step argumentation and self-verification. LRM performance on graph and reasoning benchmarks such as NLGraph seem extraordinary, with some even claiming they are capable of generalized reasoning and innovation in reasoning-intensive fields such as mathematics, physics, medicine, and law. However, by more carefully scaling the complexity of reasoning problems, we show existing benchmarks actually have limited complexity. We develop a new dataset, the Deep Reasoning Dataset (DeepRD), along with a generative process for producing unlimited examples of scalable complexity. We use this dataset to evaluate model performance on graph connectivity and natural language proof planning. We find that the performance of LRMs drop abruptly at sufficient complexity and do not generalize. We also relate our LRM results to the distributions of the complexities of large, real-world knowledge graphs, interaction graphs, and proof datasets. We find the majority of real-world examples fall inside the LRMs' success regime, yet the long tails expose substantial failure potential. Our analysis highlights the near-term utility of LRMs while underscoring the need for new methods that generalize beyond the complexity of examples in the training distribution.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

Transformer architectures have dramatically advanced representation learning and inference in deep models through self-attention mechanisms. In parallel,associative memory (AM) frameworks map representations onto energy landscapes, offering interpretable retrieval mechanisms. However, their continuous-time inference dynamics lack the biological plausibility of classical Continuous Attractor Neural Networks (CANNs). To bridge this gap, we propose Controlled Dynamics Attractor Transformer (CDAT), which couples a mixture von Mises-Fisher (Mo-vMF) attention energy with a Hopfield refinement energy, while augmenting energy descent with a CANN-inspired excitation-inhibition modulation. CDAT instantiates a topology-constrained dynamical system whose couplings encode relational structure among tokens, thereby linking attractor-style dynamics to modern energy-based attention. We further provide a constructive dissipation analysis to formally establish their controlled inference dynamics. Benefiting from these robust and structured dynamics, CDAT achieves state-of-the-art performance across multiple benchmarks in graph anomaly detection and graph classification.

Large Language Models (LLMs) achieve excellent performance in natural language reasoning tasks through pre-training on vast unstructured text, enabling them to understand the logic in natural language and generate logic-consistent responses. However, the representational differences between unstructured and structured knowledge make LLMs inherently struggle to maintain logic consistency, leading to Logic Drift challenges in structured knowledge reasoning tasks such as Knowledge Graph Question Answering (KGQA). Existing methods address this limitation by designing complex workflows embedded in prompts to guide LLM reasoning. Nevertheless, these approaches only provide input-level guidance and fail to fundamentally address the Logic Drift in LLM outputs. Additionally, their inflexible reasoning workflows cannot adapt to different tasks and knowledge graphs. To enhance LLMs' logic consistency in structured knowledge reasoning, we specifically target the logits output from the autoregressive generation process. We propose the Logits-to-Logic framework, which incorporates logits strengthening and logits filtering as core modules to correct logical defects in LLM outputs. Extensive experiments show that our approach significantly improves LLMs' logic consistency in structured knowledge reasoning and achieves state-of-the-art performance on multiple KGQA benchmarks.

Recent research in representation learning utilizes large databases of proteins or molecules to acquire knowledge of drug and protein structures through unsupervised learning techniques. These pre-trained representations have proven to significantly enhance the accuracy of subsequent tasks, such as predicting the affinity between drugs and target proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results on established benchmark datasets. We provide preprocessed and integrated data obtained from 7 public sources, which encompass over 30M triples. Additionally, we make available the pre-trained models based on this data, along with the reported outcomes of their performance on three widely-used benchmark datasets for drug-target binding affinity prediction found in the Therapeutic Data Commons (TDC) benchmarks. Additionally, we make the source code for training models on benchmark datasets publicly available. Our objective in releasing these pre-trained models, accompanied by clean data for model pretraining and benchmark results, is to encourage research in knowledge-enhanced representation learning.

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

Sequential recommendation has increasingly shifted toward generative recommenders that combine sequential patterns with semantic item information. Yet these methods are often evaluated on a small set of widely used benchmarks, raising a key question: do these benchmarks actually require the advanced modeling capabilities that modern generative recommenders claim to provide? We conduct a benchmark audit with an intentionally simple graph heuristic. Starting from only the last one or two interacted items, it retrieves candidates from a few-hop item-transition graph and ranks them by item-feature similarity. Despite using no sequence encoder, generative objective, or training, this heuristic matches or outperforms many modern baselines, with relative NDCG@10 improvements of 38.10% and 44.18% over the best competing baseline on Amazon Review Sports and CDs. We show that this behavior reflects shortcut solvability rather than an artifact of one heuristic. We identify three shortcut structures that can make next-item prediction easier than expected: low-branching local transitions, feature-smooth transitions, and limited dependence on long user histories. These shortcuts need not appear together; even one or two strong signals can make simple local retrieval highly competitive, while weakening them makes the benefits of more sophisticated models clearer. Across 14 datasets, model rankings vary substantially with dataset properties, yet the heuristic remains competitive on 10 of them. Our findings suggest that strong performance on standard benchmarks does not always demonstrate advanced sequential, semantic, or generative modeling ability. We call for more careful dataset selection and dataset-level diagnostic analysis when using benchmarks to support claims about new recommendation models.

Large Language Models (LLMs) are increasingly used for tasks involving Knowledge Graphs (KGs), whose evaluation typically focuses on accuracy and output correctness. We propose a complementary task characterization approach using three complexity frameworks from cognitive psychology. Applying this to the LLM-KG-Bench framework, we highlight value distributions, identify underrepresented demands and motivate richer interpretation and diversity for benchmark evaluation tasks.

Foundational machine learning interatomic potentials that can accurately and efficiently model a vast range of materials are critical for accelerating atomistic discovery. We introduce universal potentials based on the graph atomic cluster expansion (GRACE) framework, trained on several of the largest available materials datasets. Through comprehensive benchmarks, we demonstrate that the GRACE models establish a new Pareto front for accuracy versus efficiency among foundational interatomic potentials. We further showcase their exceptional versatility by adapting them to specialized tasks and simpler architectures via fine-tuning and knowledge distillation, achieving high accuracy while preventing catastrophic forgetting. This work establishes GRACE as a robust and adaptable foundation for the next generation of atomistic modeling, enabling high-fidelity simulations across the periodic table.

Long-horizon Flexible Job-Shop Scheduling~(FJSP) presents a formidable combinatorial challenge due to complex, interdependent decisions spanning extended time horizons. While learning-based Rolling Horizon Optimization~(RHO) has emerged as a promising paradigm to accelerate solving by identifying and fixing invariant operations, its effectiveness is hindered by the structural complexity of FJSP. Existing methods often fail to capture intricate graph-structured dependencies and ignore the asymmetric costs of prediction errors, in which misclassifying critical-path operations is significantly more detrimental than misclassifying non-critical ones. Furthermore, dynamic shifts in predictive confidence during the rolling process make static pruning thresholds inadequate. To address these limitations, we propose Graph-RHO, a novel critical-path-aware graph-based RHO framework. First, we introduce a topology-aware heterogeneous graph network that encodes subproblems as operation-machine graphs with multi-relational edges, leveraging edge-feature-aware message passing to predict operation stability. Second, we incorporate a critical-path-aware mechanism that injects inductive biases during training to distinguish highly sensitive bottleneck operations from robust ones. Third, we devise an adaptive thresholding strategy that dynamically calibrates decision boundaries based on online uncertainty estimation to align model predictions with the solver's search space. Extensive experiments on standard benchmarks demonstrate that Graph-RHO establishes a new state of the art in solution quality and computational efficiency. Remarkably, it exhibits exceptional zero-shot generalization, reducing solve time by over 30\% on large-scale instances (2000 operations) while achieving superior solution quality. Our code is available https://github.com/IntelliSensing/Graph-RHO{here}.

Retrieval-Augmented Generation for software engineering often relies on vector similarity search, which captures topical similarity but can fail on multi-hop architectural reasoning such as controller to service to repository chains, interface-driven wiring, and inheritance. This paper benchmarks three retrieval pipelines on Java codebases (Shopizer, with additional runs on ThingsBoard and OpenMRS Core): (A) vector-only No-Graph RAG, (B) an LLM-generated knowledge graph RAG (LLM-KB), and (C) a deterministic AST-derived knowledge graph RAG (DKB) built with Tree-sitter and bidirectional traversal. Using 15 architecture and code-tracing queries per repository, we measure indexing time, query latency, corpus coverage, cost, and answer correctness. DKB builds its graph in seconds, while LLM-KB requires much longer graph generation. LLM-KB also shows indexing incompleteness: on Shopizer, 377 files are skipped or missed, reducing embedded chunk coverage and graph size compared to DKB. End-to-end cost is modest for DKB relative to the vector-only baseline but much higher for LLM-KB, especially as repository scale increases. Query latency is similar for No-Graph and DKB, while LLM-KB is slower and more variable. On the Shopizer question suite, DKB achieves the highest correctness, LLM-KB is close behind, and the vector-only baseline performs worst on upstream architectural queries and has the highest hallucination risk. Overall, deterministic AST-derived graphs provide more reliable coverage and multi-hop grounding than LLM-extracted graphs at substantially lower indexing cost.

Detecting and localizing leaks in water distribution network systems is an important topic with direct environmental, economic, and social impact. Our paper is the first to explore the use of factor graph optimization techniques for leak localization in water distribution networks, enabling us to perform sensor fusion between pressure and demand sensor readings and to estimate the network's temporal and structural state evolution across all network nodes. The methodology introduces specific water network factors and proposes a new architecture composed of two factor graphs: a leak-free state estimation factor graph and a leak localization factor graph. When a new sensor reading is obtained, unlike Kalman and other interpolation-based methods, which estimate only the current network state, factor graphs update both current and past states. Results on Modena, L-TOWN and synthetic networks show that factor graphs are much faster than nonlinear Kalman-based alternatives such as the UKF, while also providing improvements in localization compared to state-of-the-art estimation-localization approaches. Implementation and benchmarks are available at https://github.com/pirofti/FGLL.

Large language models (LLMs) have demonstrated impressive reasoning abilities, but they still struggle with faithful reasoning due to knowledge gaps and hallucinations. To address these issues, knowledge graphs (KGs) have been utilized to enhance LLM reasoning through their structured knowledge. However, existing KG-enhanced methods, either retrieval-based or agent-based, encounter difficulties in accurately retrieving knowledge and efficiently traversing KGs at scale. In this work, we introduce graph-constrained reasoning (GCR), a novel framework that bridges structured knowledge in KGs with unstructured reasoning in LLMs. To eliminate hallucinations, GCR ensures faithful KG-grounded reasoning by integrating KG structure into the LLM decoding process through KG-Trie, a trie-based index that encodes KG reasoning paths. KG-Trie constrains the decoding process, allowing LLMs to directly reason on graphs and generate faithful reasoning paths grounded in KGs. Additionally, GCR leverages a lightweight KG-specialized LLM for graph-constrained reasoning alongside a powerful general LLM for inductive reasoning over multiple reasoning paths, resulting in accurate reasoning with zero reasoning hallucination. Extensive experiments on several KGQA benchmarks demonstrate that GCR achieves state-of-the-art performance and exhibits strong zero-shot generalizability to unseen KGs without additional training.

Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with preserving node information, depending on whether they use node dropping or node clustering. Additionally, fixed pooling ratios or numbers of pooling layers are predefined for all graphs, which prevents personalized pooling structures from being captured for each individual graph. In this work, inspired by bottom-up grammar induction, we propose an efficient graph parsing algorithm to infer the pooling structure, which then drives graph pooling. The resulting Graph Parsing Network (GPN) adaptively learns personalized pooling structure for each individual graph. GPN benefits from the discrete assignments generated by the graph parsing algorithm, allowing good memory efficiency while preserving node information intact. Experimental results on standard benchmarks demonstrate that GPN outperforms state-of-the-art graph pooling methods in graph classification tasks while being able to achieve competitive performance in node classification tasks. We also conduct a graph reconstruction task to show GPN's ability to preserve node information and measure both memory and time efficiency through relevant tests.

Code localization--identifying precisely where in a codebase changes need to be made--is a fundamental yet challenging task in software maintenance. Existing approaches struggle to efficiently navigate complex codebases when identifying relevant code sections. The challenge lies in bridging natural language problem descriptions with the appropriate code elements, often requiring reasoning across hierarchical structures and multiple dependencies. We introduce LocAgent, a framework that addresses code localization through graph-based representation. By parsing codebases into directed heterogeneous graphs, LocAgent creates a lightweight representation that captures code structures (files, classes, functions) and their dependencies (imports, invocations, inheritance), enabling LLM agents to effectively search and locate relevant entities through powerful multi-hop reasoning. Experimental results on real-world benchmarks demonstrate that our approach significantly enhances accuracy in code localization. Notably, our method with the fine-tuned Qwen-2.5-Coder-Instruct-32B model achieves comparable results to SOTA proprietary models at greatly reduced cost (approximately 86% reduction), reaching up to 92.7% accuracy on file-level localization while improving downstream GitHub issue resolution success rates by 12% for multiple attempts (Pass@10). Our code is available at https://github.com/gersteinlab/LocAgent.

The rapid growth of visual tokens in multimodal large language models (MLLMs) leads to excessive memory consumption and inference latency, especially when handling high-resolution images and videos. Token pruning is a technique used to mitigate this issue by removing redundancy, but existing methods often ignore relevance to the user query or suffer from the limitations of attention mechanisms, reducing their adaptability and effectiveness. To address these challenges, we propose Script, a plug-and-play pruning method that requires no retraining and generalizes across diverse MLLMs. Script comprises two modules: a graph-structured pruning module that removes visually redundant tokens, and a query-conditioned semantic pruning module that preserves query-relevant visual information. Together, they enhance performance on multimodal tasks. Experiments on fourteen benchmarks across image and video understanding tasks show that Script consistently achieves higher model efficiency and predictive accuracy compared to existing pruning methods. On LLaVA-NeXT-7B, it achieves up to 6.8x prefill speedup and 10x FLOP reduction, while retaining 96.88% of the original performance.

Large Language Models (LLMs) have inherent limitations of faithfulness and factuality, commonly referred to as hallucinations. Several benchmarks have been developed that provide a test bed for factuality evaluation within the context of English-centric datasets, while relying on supplementary informative context like web links or text passages but ignoring the available structured factual resources. To this end, Knowledge Graphs (KGs) have been identified as a useful aid for hallucination mitigation, as they provide a structured way to represent the facts about entities and their relations with minimal linguistic overhead. We bridge the lack of KG paths and multilinguality for factual language modeling within the existing hallucination evaluation benchmarks and propose a KG-based multilingual, multihop benchmark called MultiHal framed for generative text evaluation. As part of our data collection pipeline, we mined 140k KG-paths from open-domain KGs, from which we pruned noisy KG-paths, curating a high-quality subset of 25.9k. Our baseline evaluation shows an absolute scale increase by approximately 0.12 to 0.36 points for the semantic similarity score in KG-RAG over vanilla QA across multiple languages and multiple models, demonstrating the potential of KG integration. We anticipate MultiHal will foster future research towards several graph-based hallucination mitigation and fact-checking tasks.

Multimodal recommendation systems typically integrates user behavior with multimodal data from items, thereby capturing more accurate user preferences. Concurrently, with the rise of large models (LMs), multimodal recommendation is increasingly leveraging their strengths in semantic understanding and contextual reasoning. However, LM representations are inherently optimized for general semantic tasks, while recommendation models rely heavily on sparse user/item unique identity (ID) features. Existing works overlook the fundamental representational divergence between large models and recommendation systems, resulting in incompatible multimodal representations and suboptimal recommendation performance. To bridge this gap, we propose RecGOAT, a novel yet simple dual semantic alignment framework for LLM-enhanced multimodal recommendation, which offers theoretically guaranteed alignment capability. RecGOAT first employs graph attention networks to enrich collaborative semantics by modeling item-item, user-item, and user-user relationships, leveraging user/item LM representations and interaction history. Furthermore, we design a dual-granularity progressive multimodality-ID alignment framework, which achieves instance-level and distribution-level semantic alignment via cross-modal contrastive learning (CMCL) and optimal adaptive transport (OAT), respectively. Theoretically, we demonstrate that the unified representations derived from our alignment framework exhibit superior semantic consistency and comprehensiveness. Extensive experiments on three public benchmarks show that our RecGOAT achieves state-of-the-art performance, empirically validating our theoretical insights. Additionally, the deployment on a large-scale online advertising platform confirms the model's effectiveness and scalability in industrial recommendation scenarios. Code available at https://github.com/6lyc/RecGOAT-LLM4Rec.

Optimizing communication topology is fundamental to the efficiency and effectiveness of Large Language Model (LLM)-based Multi-Agent Systems (MAS). While recent approaches utilize reinforcement learning to dynamically construct task-specific graphs, they typically rely on single-sample policy gradients with absolute rewards (e.g., binary correctness). This paradigm suffers from severe gradient variance and the credit assignment problem: simple queries yield non-informative positive rewards for suboptimal structures, while difficult queries often result in failures that provide no learning signal. To address these challenges, we propose Graph-GRPO, a novel topology optimization framework that integrates Group Relative Policy Optimization. Instead of evaluating a single topology in isolation, Graph-GRPO samples a group of diverse communication graphs for each query and computes the advantage of specific edges based on their relative performance within the group. By normalizing rewards across the sampled group, our method effectively mitigates the noise derived from task difficulty variance and enables fine-grained credit assignment. Extensive experiments on reasoning and code generation benchmarks demonstrate that Graph-GRPO significantly outperforms state-of-the-art baselines, achieving superior training stability and identifying critical communication pathways previously obscured by reward noise.

While AI systems have made remarkable progress in processing unstructured text, structured data such as graphs stored in databases, continues to grow rapidly yet remains difficult for neural models to effectively utilize. We introduce NGDBench, a unified benchmark for evaluating neural graph database capabilities across five diverse domains, including finance, medicine, and AI agent tooling. Unlike prior benchmarks limited to elementary logical operations, NGDBench supports the full Cypher query language, enabling complex pattern matching, variable-length paths, and numerical aggregations, while incorporating realistic noise injection and dynamic data management operations. Our evaluation of state-of-the-art LLMs and RAG methods reveals significant limitations in structured reasoning, noise robustness, and analytical precision, establishing NGDBench as a critical testbed for advancing neural graph data management. Our code and data are available at https://github.com/HKUST-KnowComp/NGDBench.

The increasing context length of modern language models has created a need for evaluating their ability to retrieve and process information across extensive documents. While existing benchmarks test long-context capabilities, they often lack a structured way to systematically vary question complexity. We introduce KG-QAGen (Knowledge-Graph-based Question-Answer Generation), a framework that (1) extracts QA pairs at multiple complexity levels (2) by leveraging structured representations of financial agreements (3) along three key dimensions -- multi-hop retrieval, set operations, and answer plurality -- enabling fine-grained assessment of model performance across controlled difficulty levels. Using this framework, we construct a dataset of 20,139 QA pairs (the largest number among the long-context benchmarks) and open-source a part of it. We evaluate 13 proprietary and open-source LLMs and observe that even the best-performing models are struggling with set-based comparisons and multi-hop logical inference. Our analysis reveals systematic failure modes tied to semantic misinterpretation and inability to handle implicit relations.

Self-evolving search agents reduce reliance on human-written training questions by generating and solving their own search tasks. We build on Search Self-Play (SSP), a representative Proposer and Solver framework in which questions are generated and answered via multi-step search and reasoning. In practice, however, SSP faces two bottlenecks: the Proposer constructs questions from isolated answer entities without relational context, yielding many invalid or unverifiable questions in early self-play training, while the Solver receives only a binary outcome reward that discards useful signal from partially on-track search trajectories. We address both bottlenecks by reusing knowledge-graph paths as construction-derived intermediate supervision for both question construction and reward shaping. First, we ground question construction in LLM-guided knowledge-graph subgraphs, providing relational context for the Proposer. Second, we observe that constructing and solving a multi-hop question can involve overlapping intermediate entities: the factual bridges used to formulate the question may provide approximate waypoints for answering it. Exploiting this overlap, we introduce Waypoint Coverage Reward (WCR), which grants graded partial credit to incorrect Solver trajectories according to their coverage of entities on the construction path, while preserving full reward for correct answers. Across seven QA benchmarks and nine model configurations, our approach improves the average score over standard SSP in all configurations, including notable gains on multi-hop QA tasks. These results suggest that knowledge-graph paths can be reused as lightweight intermediate supervision, providing both relational guidance and process feedback without additional task-specific human annotations or manually labeled process steps.

With an ever-growing zoo of LLMs and benchmarks, the need to orchestrate multiple models for improved task performance has never been more pressing. While frameworks like Mixture-of-Agents (MoA) attempt to coordinate LLMs, they often fall short in terms of (1) selecting relevant agents, (2) facilitating effective intra-agent communication, and (3) integrating responses efficiently. In this work, we propose Graph-of-Agents (GoA), a new graph-based framework for modeling multi-agent LLM communication. Our approach begins with node sampling, selecting only the most relevant agents by leveraging model cards that summarize each model's domain, task specialization, and other characteristics. Next, we construct edges between the selected agents by evaluating their responses against one another to determine relevance ordering. Directed message passing is then performed from highly relevant agents to less relevant ones to enhance their responses, followed by reverse message passing to refine the original responses of the more relevant agents. Finally, the updated responses are aggregated via graph-based pooling (e.g., max or mean pooling) to produce a single, unified answer. We evaluate GoA on diverse multi-domain benchmarks (MMLU, MMLU-Pro, GPQA) and domain-specific benchmarks (MATH, HumanEval, MedMCQA), with an agent pool of 6 LLMs spanning multiple domains. Surprisingly, GoA achieves superior performance using only 3 selected agents, outperforming recent multi-agent LLM baselines that utilize all 6 agents simultaneously. By adopting a graph structure, GoA offers both scalability and effectiveness through structured message passing-positioning it as a strong candidate for navigating the challenges of the ever-growing LLM zoo. Code is available at: https://github.com/UNITES-Lab/GoA.

Retrieval-Augmented Generation (RAG) has emerged as a dominant paradigm for mitigating hallucinations in Large Language Models (LLMs) by incorporating external knowledge. Nevertheless, effectively integrating and interpreting key evidence scattered across noisy documents remains a critical challenge for existing RAG systems. In this paper, we propose GraphAnchor, a novel Graph-Anchored Knowledge Indexing approach that reconceptualizes graph structures from static knowledge representations into active, evolving knowledge indices. GraphAnchor incrementally updates a graph during iterative retrieval to anchor salient entities and relations, yielding a structured index that guides the LLM in evaluating knowledge sufficiency and formulating subsequent subqueries. The final answer is generated by jointly leveraging all retrieved documents and the final evolved graph. Experiments on four multi-hop question answering benchmarks demonstrate the effectiveness of GraphAnchor, and reveal that GraphAnchor modulates the LLM's attention to more effectively associate key information distributed in retrieved documents. All code and data are available at https://github.com/NEUIR/GraphAnchor.

Long-horizon applications increasingly require large language models (LLMs) to answer queries when relevant evidence is sparse and dispersed across very long contexts. Existing memory systems largely follow two paradigms: explicit structured memories offer interpretability but often become brittle under long-context overload, while latent memory mechanisms are efficient and stable yet difficult to inspect. We propose LatentGraphMem, a memory framework that combines implicit graph memory with explicit subgraph retrieval. LatentGraphMem stores a graph-structured memory in latent space for stability and efficiency, and exposes a task-specific subgraph retrieval interface that returns a compact symbolic subgraph under a fixed budget for downstream reasoning and human inspection. During training, an explicit graph view is materialized to interface with a frozen reasoner for question-answering supervision. At inference time, retrieval is performed in latent space and only the retrieved subgraph is externalized. Experiments on long-horizon benchmarks across multiple model scales show that LatentGraphMem consistently outperforms representative explicit-graph and latent-memory baselines, while enabling parameter-efficient adaptation and flexible scaling to larger reasoners without introducing large symbolic artifacts.

We introduce **EvoGraph**, a framework that enables software systems to evolve their own source code, build pipelines, documentation, and tickets. EvoGraph represents every artefact in a typed directed graph, applies learned mutation operators driven by specialized small language models (SLMs), and selects survivors with a multi-objective fitness. On three benchmarks, EvoGraph fixes 83% of known security vulnerabilities, translates COBOL to Java with 93% functional equivalence (test verified), and maintains documentation freshness within two minutes. Experiments show a 40% latency reduction and a sevenfold drop in feature lead time compared with strong baselines. We extend our approach to **evoGraph**, leveraging language-specific SLMs for modernizing .NET, Lisp, CGI, ColdFusion, legacy Python, and C codebases, achieving 82-96% semantic equivalence across languages while reducing computational costs by 90% compared to large language models. EvoGraph's design responds to empirical failure modes in legacy modernization, such as implicit contracts, performance preservation, and integration evolution. Our results suggest a practical path toward Software 3.0, where systems adapt continuously yet remain under measurable control.

Recent large language model (LLM) reasoning, despite its success, suffers from limited domain knowledge, susceptibility to hallucinations, and constrained reasoning depth, particularly in small-scale models deployed in resource-constrained environments. This paper presents the first investigation into integrating step-wise knowledge graph retrieval with step-wise reasoning to address these challenges, introducing a novel paradigm termed as graph-augmented reasoning. Our goal is to enable frozen, small-scale LLMs to retrieve and process relevant mathematical knowledge in a step-wise manner, enhancing their problem-solving abilities without additional training. To this end, we propose KG-RAR, a framework centered on process-oriented knowledge graph construction, a hierarchical retrieval strategy, and a universal post-retrieval processing and reward model (PRP-RM) that refines retrieved information and evaluates each reasoning step. Experiments on the Math500 and GSM8K benchmarks across six models demonstrate that KG-RAR yields encouraging results, achieving a 20.73\% relative improvement with Llama-3B on Math500.

Large language models are extensively applied across a wide range of tasks, such as customer support, content creation, educational tutoring, and providing financial guidance. However, a well-known drawback is their predisposition to generate hallucinations. This damages the trustworthiness of the information these models provide, impacting decision-making and user confidence. We propose a method to detect hallucinations by looking at the structure of the latent space and finding associations within hallucinated and non-hallucinated generations. We create a graph structure that connects generations that lie closely in the embedding space. Moreover, we employ a Graph Attention Network which utilizes message passing to aggregate information from neighboring nodes and assigns varying degrees of importance to each neighbor based on their relevance. Our findings show that 1) there exists a structure in the latent space that differentiates between hallucinated and non-hallucinated generations, 2) Graph Attention Networks can learn this structure and generalize it to unseen generations, and 3) the robustness of our method is enhanced when incorporating contrastive learning. When evaluated against evidence-based benchmarks, our model performs similarly without access to search-based methods.

Answering complex questions about textual narratives requires reasoning over both stated context and the world knowledge that underlies it. However, pretrained language models (LM), the foundation of most modern QA systems, do not robustly represent latent relationships between concepts, which is necessary for reasoning. While knowledge graphs (KG) are often used to augment LMs with structured representations of world knowledge, it remains an open question how to effectively fuse and reason over the KG representations and the language context, which provides situational constraints and nuances. In this work, we propose GreaseLM, a new model that fuses encoded representations from pretrained LMs and graph neural networks over multiple layers of modality interaction operations. Information from both modalities propagates to the other, allowing language context representations to be grounded by structured world knowledge, and allowing linguistic nuances (e.g., negation, hedging) in the context to inform the graph representations of knowledge. Our results on three benchmarks in the commonsense reasoning (i.e., CommonsenseQA, OpenbookQA) and medical question answering (i.e., MedQA-USMLE) domains demonstrate that GreaseLM can more reliably answer questions that require reasoning over both situational constraints and structured knowledge, even outperforming models 8x larger.

Recent advances in large language models (LLMs) have opened new avenues for multimodal reasoning. Yet, most existing methods still rely on pretrained vision-language models (VLMs) to encode image-text pairs in isolation, ignoring the relational structure that real-world multimodal data naturally form. This motivates reasoning on multimodal graphs (MMGs), where each node has textual and visual attributes and edges provide structural cues. Enabling LLM-based reasoning on such heterogeneous multimodal signals while preserving graph topology introduces two key challenges: resolving weak cross-modal consistency and handling heterogeneous modality preference. To address this, we propose Mario, a unified framework that simultaneously resolves the two above challenges and enables effective LLM-based reasoning over MMGs. Mario consists of two innovative stages. Firstly, a graph-conditioned VLM design that jointly refines textual and visual features through fine-grained cross-modal contrastive learning guided by graph topology. Secondly, a modality-adaptive graph instruction tuning mechanism that organizes aligned multimodal features into graph-aware instruction views and employs a learnable router to surface, for each node and its neighborhood, the most informative modality configuration to the LLM. Extensive experiments across diverse MMG benchmarks demonstrate that Mario consistently outperforms state-of-the-art graph models in both supervised and zero-shot scenarios for node classification and link prediction. The code will be made available at https://github.com/sunyuanfu/Mario.

Knowledge graph question answering (KGQA) presents significant challenges due to the structural and semantic variations across input graphs. Existing works rely on Large Language Model (LLM) agents for graph traversal and retrieval; an approach that is sensitive to traversal initialization, as it is prone to entity linking errors and may not generalize well to custom ("bring-your-own") KGs. We introduce BYOKG-RAG, a framework that enhances KGQA by synergistically combining LLMs with specialized graph retrieval tools. In BYOKG-RAG, LLMs generate critical graph artifacts (question entities, candidate answers, reasoning paths, and OpenCypher queries), and graph tools link these artifacts to the KG and retrieve relevant graph context. The retrieved context enables the LLM to iteratively refine its graph linking and retrieval, before final answer generation. By retrieving context from different graph tools, BYOKG-RAG offers a more general and robust solution for QA over custom KGs. Through experiments on five benchmarks spanning diverse KG types, we demonstrate that BYOKG-RAG outperforms the second-best graph retrieval method by 4.5% points while showing better generalization to custom KGs. BYOKG-RAG framework is open-sourced at https://github.com/awslabs/graphrag-toolkit.

Large multimodal models (LMMs) have exhibited proficiencies across many visual tasks. Although numerous well-known benchmarks exist to evaluate model performance, they increasingly have insufficient headroom. As such, there is a pressing need for a new generation of benchmarks challenging enough for the next generation of LMMs. One area that LMMs show potential is graph analysis, specifically, the tasks an analyst might typically perform when interpreting figures such as estimating the mean, intercepts or correlations of functions and data series. In this work, we introduce GRAB, a graph analysis benchmark, fit for current and future frontier LMMs. Our benchmark is entirely synthetic, ensuring high-quality, noise-free questions. GRAB is comprised of 2170 questions, covering four tasks and 23 graph properties. We evaluate 20 LMMs on GRAB, finding it to be a challenging benchmark, with the highest performing model attaining a score of just 21.7%. Finally, we conduct various ablations to investigate where the models succeed and struggle. We release GRAB to encourage progress in this important, growing domain.

Recent advances in Retrieval-Augmented Generation (RAG) have shifted from simple vector similarity to structure-aware approaches like HippoRAG, which leverage Knowledge Graphs (KGs) and Personalized PageRank (PPR) to capture multi-hop dependencies. However, these methods suffer from a "Static Graph Fallacy": they rely on fixed transition probabilities determined during indexing. This rigidity ignores the query-dependent nature of edge relevance, causing semantic drift where random walks are diverted into high-degree "hub" nodes before reaching critical downstream evidence. Consequently, models often achieve high partial recall but fail to retrieve the complete evidence chain required for multi-hop queries. To address this, we propose CatRAG, Context-Aware Traversal for robust RAG, a framework that builds on the HippoRAG 2 architecture and transforms the static KG into a query-adaptive navigation structure. We introduce a multi-faceted framework to steer the random walk: (1) Symbolic Anchoring, which injects weak entity constraints to regularize the random walk; (2) Query-Aware Dynamic Edge Weighting, which dynamically modulates graph structure, to prune irrelevant paths while amplifying those aligned with the query's intent; and (3) Key-Fact Passage Weight Enhancement, a cost-efficient bias that structurally anchors the random walk to likely evidence. Experiments across four multi-hop benchmarks demonstrate that CatRAG consistently outperforms state of the art baselines. Our analysis reveals that while standard Recall metrics show modest gains, CatRAG achieves substantial improvements in reasoning completeness, the capacity to recover the entire evidence path without gaps. These results reveal that our approach effectively bridges the gap between retrieving partial context and enabling fully grounded reasoning. Resources are available at https://github.com/kwunhang/CatRAG.

While Retrieval-Augmented Generation (RAG) enhances the accuracy and relevance of responses by generative language models, it falls short in graph-based contexts where both textual and topological information are important. Naive RAG approaches inherently neglect the structural intricacies of textual graphs, resulting in a critical gap in the generation process. To address this challenge, we introduce Graph Retrieval-Augmented Generation (GRAG), which significantly enhances both the retrieval and generation processes by emphasizing the importance of subgraph structures. Unlike RAG approaches that focus solely on text-based entity retrieval, GRAG maintains an acute awareness of graph topology, which is crucial for generating contextually and factually coherent responses. Our GRAG approach consists of four main stages: indexing of k-hop ego-graphs, graph retrieval, soft pruning to mitigate the impact of irrelevant entities, and generation with pruned textual subgraphs. GRAG's core workflow-retrieving textual subgraphs followed by soft pruning-efficiently identifies relevant subgraph structures while avoiding the computational infeasibility typical of exhaustive subgraph searches, which are NP-hard. Moreover, we propose a novel prompting strategy that achieves lossless conversion from textual subgraphs to hierarchical text descriptions. Extensive experiments on graph multi-hop reasoning benchmarks demonstrate that in scenarios requiring multi-hop reasoning on textual graphs, our GRAG approach significantly outperforms current state-of-the-art RAG methods while effectively mitigating hallucinations.

Large Language Models (LLMs) have demonstrated impressive reasoning capabilities, yet their performance is highly dependent on the prompting strategy and model scale. While reinforcement learning and fine-tuning have been deployed to boost reasoning, these approaches incur substantial computational and data overhead. In this work, we introduce Adaptive Graph of Thoughts (AGoT), a dynamic, graph-based inference framework that enhances LLM reasoning solely at test time. Rather than relying on fixed-step methods like Chain of Thought (CoT) or Tree of Thoughts (ToT), AGoT recursively decomposes complex queries into structured subproblems, forming an dynamic directed acyclic graph (DAG) of interdependent reasoning steps. By selectively expanding only those subproblems that require further analysis, AGoT unifies the strengths of chain, tree, and graph paradigms into a cohesive framework that allocates computation where it is most needed. We validate our approach on diverse benchmarks spanning multi-hop retrieval, scientific reasoning, and mathematical problem-solving, achieving up to 46.2% improvement on scientific reasoning tasks (GPQA) - comparable to gains achieved through computationally intensive reinforcement learning approaches and outperforming state-of-the-art iterative approaches. These results suggest that dynamic decomposition and structured recursion offer a scalable, cost-effective alternative to post-training modifications, paving the way for more robust, general-purpose reasoning in LLMs.

We introduce PersonalAI 2.0 (PAI-2), a novel framework, designed to enhance large language model (LLM) based systems through integration of external knowledge graphs (KG). The proposed approach addresses key limitations of existing Graph Retrieval-Augmented Generation (GraphRAG) methods by incorporating a dynamic, multistage query processing pipeline. The central point of PAI-2 design is its ability to perform adaptive, iterative information search, guided by extracted entities, matched graph vertices and generated clue-queries. Conducted evaluation over six benchmarks (Natural Questions, TriviaQA, HotpotQA, 2WikiMultihopQA, MuSiQue and DiaASQ) demonstrates improvement in factual correctness of generating answers compared to analogues methods (LightRAG, RAPTOR, and HippoRAG 2). PAI-2 achieves 4% average gain by LLM-as-a-Judge across four benchmarks, reflecting its effectiveness in reducing hallucination rates and increasing precision. We show that use of graph traversal algorithms (e.g. BeamSearch, WaterCircles) gain superior results compared to standard flatten retriever on average 6%, while enabled search plan enhancement mechanism gain 18% boost compared to disabled one by LLM-as-a-Judge across six datasets. In addition, ablation study reveals that PAI-2 achieves the SOTA result on MINE-1 benchmark, achieving 89% information-retention score, using LLMs from 7-14B tiers. Collectively, these findings underscore the potential of PAI-2 to serve as a foundational model for next-generation personalized AI applications, requiring scalable, context-aware knowledge representation and reasoning capabilities.

Approximate Nearest Neighbor Search (ANNS) is a core primitive for unstructured data retrieval. Real-world applications--such as temporal databases, financial data analysis, and retrieval-augmented generation--often require hybrid queries whose valid objects are constrained by continuous interval attributes, such as lifespans or price ranges. We study Interval-Predicate ANNS (IPANNS), where validity is determined by a predicate between an object interval and a query interval. Existing range-filtering ANNS (RFANNS) methods are designed for single-dimensional scalar filters, but interval predicates such as containment and overlap rely on two coupled endpoint constraints. Treating endpoints as independent scalar attributes can incur large intersection overhead, while containment-specific methods lack a generalized indexing abstraction. In this paper, we propose the Unified Dominance Graph (UDG), a graph-indexing framework for the closed two-bound conjunctive fragment of IPANNS. For a chosen interval predicate, UDG maps object and query endpoints into a normalized two-dimensional dominance space and builds a dominance-labeled graph over the transformed coordinates. Containment, overlap, and other supported endpoint-bound predicates therefore reuse the same construction and search algorithms after semantic mapping, while each UDG instance remains tied to its selected predicate. UDG compresses query-state-specific proximity graphs into one compact index. To improve graph search under restrictive interval filters, we add validity-preserving patch edges that provide routing choices when few objects remain valid. Extensive evaluations on standard benchmarks and real-world datasets show that UDG achieves stable query performance across multiple interval relations and workloads, significantly outperforming existing hybrid search baselines while maintaining low indexing overhead.

Knowledge Graph Question Answering (KGQA) has shown promise for grounded and interpretable reasoning, yet existing approaches often fail to provide reliable coverage guarantees over retrieved answers. While Conformal Prediction (CP) offers a principled framework for producing prediction sets with statistical guarantees, prior methods suffer from critical limitations in both calibration validity and score discriminability, resulting in violated coverage guarantees and excessively large prediction sets. To address these pitfalls, we propose Conformal Path Reasoning (CPR), a trustworthy KGQA framework with two key innovations. First, we perform query-level conformal calibration over path-level scores, preserving the exchangeability while generating path prediction sets. Second, we introduce the Residual Conformal Value Network (RCVNet), a lightweight module trained via PUCT-guided exploration to learn discriminative path-level nonconformity scores. Experiments on benchmarks show that CPR significantly improves the Empirical Coverage Rate by 34% while reducing average prediction set size by 40% compared to conformal baselines. These results validate the efficacy of CPR in satisfying coverage guarantees with substantially more compact answer sets.

Graph-based Retrieval-Augmented Generation (GraphRAG) enhances the reasoning capabilities of Large Language Models (LLMs) by grounding their responses in structured knowledge graphs. Leveraging community detection and relation filtering techniques, GraphRAG systems demonstrate inherent resistance to traditional RAG attacks, such as text poisoning and prompt injection. However, in this paper, we find that the security of GraphRAG systems fundamentally relies on the topological integrity of the underlying graph, which can be undermined by implicitly corrupting the logical connections, without altering surface-level text semantics. To exploit this vulnerability, we propose LogicPoison, a novel attack framework that targets logical reasoning rather than injecting false contents. Specifically, LogicPoison employs a type-preserving entity swapping mechanism to perturb both global logic hubs for disrupting overall graph connectivity and query-specific reasoning bridges for severing essential multi-hop inference paths. This approach effectively reroutes valid reasoning into dead ends while maintaining surface-level textual plausibility. Comprehensive experiments across multiple benchmarks demonstrate that LogicPoison successfully bypasses GraphRAG's defenses, significantly degrading performance and outperforming state-of-the-art baselines in both effectiveness and stealth. Our code is available at bluehttps://github.com/Jord8061/logicPoison.

Dynamic graph representation learning requires capturing both structural relationships and temporal evolution, yet existing approaches face a fundamental trade-off: attention-based methods achieve expressiveness at O(T^2) complexity, while recurrent architectures suffer from gradient pathologies and dense state storage. Spiking neural networks offer event-driven efficiency but remain limited by sequential propagation, binary information loss, and local aggregation that misses global context. We propose ChronoSpike, an adaptive spiking graph neural network that integrates learnable LIF neurons with per-channel membrane dynamics, multi-head attentive spatial aggregation on continuous features, and a lightweight Transformer temporal encoder, enabling both fine-grained local modeling and long-range dependency capture with linear memory complexity O(T cdot d). On three large-scale benchmarks, ChronoSpike outperforms twelve state-of-the-art baselines by 2.0% Macro-F1 and 2.4% Micro-F1 while achieving 3-10times faster training than recurrent methods with a constant 105K-parameter budget independent of graph size. We provide theoretical guarantees for membrane potential boundedness, gradient flow stability under contraction factor ρ< 1, and BIBO stability; interpretability analyses reveal heterogeneous temporal receptive fields and a learned primacy effect with 83-88% sparsity.

Graph Neural Networks (GNNs) have demonstrated impressive performance on task-specific benchmarks, yet their ability to generalize across diverse domains and tasks remains limited. Existing approaches often struggle with negative transfer, scalability issues, and high adaptation costs. To address these challenges, we propose GMoPE (Graph Mixture of Prompt-Experts), a novel framework that seamlessly integrates the Mixture-of-Experts (MoE) architecture with prompt-based learning for graphs. GMoPE leverages expert-specific prompt vectors and structure-aware MoE routing to enable each expert to specialize in distinct subdomains and dynamically contribute to predictions. To promote diversity and prevent expert collapse, we introduce a soft orthogonality constraint across prompt vectors, encouraging expert specialization and facilitating a more balanced expert utilization. Additionally, we adopt a prompt-only fine-tuning strategy that significantly reduces spatiotemporal complexity during transfer. We validate GMoPE through extensive experiments under various pretraining strategies and multiple downstream tasks. Results show that GMoPE consistently outperforms state-of-the-art baselines and achieves performance comparable to full parameter fine-tuning-while requiring only a fraction of the adaptation overhead. Our work provides a principled and scalable framework for advancing generalizable and efficient graph foundation models.

Modern large language models (LLMs) are inherently auto-regressive, requiring input to be serialized into flat sequences regardless of their structural dependencies. This serialization hinders the model's ability to leverage structural inductive biases, especially in tasks such as retrieval-augmented generation (RAG) and reasoning on data with native graph structures, where inter-segment dependencies are crucial. We introduce Graph-KV with the potential to overcome this limitation. Graph-KV leverages the KV-cache of text segments as condensed representations and governs their interaction through structural inductive biases. In this framework, 'target' segments selectively attend only to the KV-caches of their designated 'source' segments, rather than all preceding segments in a serialized sequence. This approach induces a graph-structured block mask, sparsifying attention and enabling a message-passing-like step within the LLM. Furthermore, strategically allocated positional encodings for source and target segments reduce positional bias and context window consumption. We evaluate Graph-KV across three scenarios: (1) seven RAG benchmarks spanning direct inference, multi-hop reasoning, and long-document understanding; (2) Arxiv-QA, a novel academic paper QA task with full-text scientific papers structured as citation ego-graphs; and (3) paper topic classification within a citation network. By effectively reducing positional bias and harnessing structural inductive biases, Graph-KV substantially outperforms baselines, including standard costly sequential encoding, across various settings. Code and the Graph-KV data are publicly available.

Reasoning system dynamics is one of the most important analytical approaches for many scientific studies. With the initial state of a system as input, the recent graph neural networks (GNNs)-based methods are capable of predicting the future state distant in time with high accuracy. Although these methods have diverse designs in modeling the coordinates and interacting forces of the system, we show that they actually share a common paradigm that learns the integration of the velocity over the interval between the initial and terminal coordinates. However, their integrand is constant w.r.t. time. Inspired by this observation, we propose a new approach to predict the integration based on several velocity estimations with Newton-Cotes formulas and prove its effectiveness theoretically. Extensive experiments on several benchmarks empirically demonstrate consistent and significant improvement compared with the state-of-the-art methods.

Spiking Neural Networks (SNNs) have emerged as an energy-efficient alternative to conventional neural networks, demonstrating strong performance in computer vision and robotics. More recently, SNNs have been applied to time series forecasting (TSF), with methods exploring spiking temporal backbones, spike-compatible positional encodings, Fourier-domain processing, and redesigned neuron dynamics. However, existing SNN forecasting approaches process variables independently, lacking explicit mechanisms for modeling inter-variable dependencies. This is a critical limitation in multivariate settings, where cross-variable correlations carry substantial predictive information. We propose Spiking Fourier Graph Operators (SpikF-GO), which addresses this gap by combining a hypervariate graph formulation in which every scalar observation becomes a graph node with spike-driven spectral processing. SpikF-GO introduces a Hard Concrete frequency gate for learnable sparse frequency selection and a Complex LIF gate that applies independent spiking neurons to real and imaginary Fourier components, preserving binary, event-driven computation throughout the spectral domain. We further present a variant incorporating Central Pattern Generator-based positional encodings for stronger long-range temporal modeling. Evaluated on eight benchmarks under a unified experimental protocol, SpikF-GO achieves the best average rank among all SNN methods and outperforms its ANN counterpart, FourierGNN, at reduced energy cost. SpikF-GO maintains competitive accuracy even at substantially smaller embedding dimensions, thereby achieving significant energy reductions. To our knowledge, this is among the first works to bring graph-based multivariate modeling into the spiking domain for TSF and the first to provide a unified comparison across SNN forecasting architectures under a common experimental protocol.

Graph Self-Supervised Learning (GSSL) offers a powerful paradigm for learning graph representations without labeled data. However, existing work assumes clean, manually curated graphs. Recent advances in NLP enable the large-scale automatic extraction of knowledge graphs from text, opening new opportunities for GSSL while introducing substantial real-world noise. This type of noise remains largely unexplored, as prior robustness studies typically rely on synthetic perturbations. To address this gap, we present the first comprehensive evaluation of GSSL methods on text-driven graphs for unsupervised term typing. We introduce Noise-Aware Text-Driven Graph GSSL (NATD-GSSL), a unified framework that combines automatic graph construction, graph refinement, and GSSL. Our evaluation follows a dual-graph protocol that contrasts a noisy graph derived from MedMentions with a clean Unified Medical Language System (UMLS) reference graph, aligned through a shared gold standard. Our results reveal variability in robustness across both pretext tasks and Graph Neural Network (GNN) architectures. Relation reconstruction is highly sensitive to noise and benefits from well-defined schemas, whereas feature reconstruction is considerably more robust, achieving performance comparable to clean-graph settings. Contrastive objectives are generally less affected by noise but depend strongly on alignment with downstream tasks. GNN architecture also plays a critical role: bidirectional relational message-passing designs are better suited to noisy, text-driven graphs, while unidirectional relational ones perform best on clean graphs. Overall, NATD-GSSL provides practical guidance for applying GSSL to real-world, noisy graphs and achieves up to a 7\% improvement over pretrained language model baselines. All code and benchmarks are publicly available at https://github.com/OthmaneKabal/MC2GAE.

Neuronal morphology encodes critical information about circuit function, development, and disease, yet current methods analyze topology or graph structure in isolation. We introduce GraPHFormer, a multimodal architecture that unifies these complementary views through CLIP-style contrastive learning. Our vision branch processes a novel three-channel persistence image encoding unweighted, persistence-weighted, and radius-weighted topological densities via DINOv2-ViT-S. In parallel, a TreeLSTM encoder captures geometric and radial attributes from skeleton graphs. Both project to a shared embedding space trained with symmetric InfoNCE loss, augmented by persistence-space transformations that preserve topological semantics. Evaluated on six benchmarks (BIL-6, ACT-4, JML-4, N7, M1-Cell, M1-REG) spanning self-supervised and supervised settings, GraPHFormer achieves state-of-the-art performance on five benchmarks, significantly outperforming topology-only, graph-only, and morphometrics baselines. We demonstrate practical utility by discriminating glial morphologies across cortical regions and species, and detecting signatures of developmental and degenerative processes. Code: https://github.com/Uzshah/GraPHFormer

Multimodal recommendation enhances ranking by integrating user-item interactions with item content, which is particularly effective under sparse feedback and long-tail distributions. However, multimodal signals are inherently heterogeneous and can conflict in specific contexts, making effective fusion both crucial and challenging. Existing approaches often rely on shared fusion pathways, leading to entangled representations and modality imbalance. To address these issues, we propose MAGNET, a Modality-Guided Mixture of Adaptive Graph Experts Network with Progressive Entropy-Triggered Routing for Multimodal Recommendation, designed to enhance controllability, stability, and interpretability in multimodal fusion. MAGNET couples interaction-conditioned expert routing with structure-aware graph augmentation, so that both what to fuse and how to fuse are explicitly controlled and interpretable. At the representation level, a dual-view graph learning module augments the interaction graph with content-induced edges, improving coverage for sparse and long-tail items while preserving collaborative structure via parallel encoding and lightweight fusion. At the fusion level, MAGNET employs structured experts with explicit modality roles-dominant, balanced, and complementary-enabling a more interpretable and adaptive combination of behavioral, visual, and textual cues. To further stabilize sparse routing and prevent expert collapse, we introduce a two-stage entropy-weighting mechanism that monitors routing entropy. This mechanism automatically transitions training from an early coverage-oriented regime to a later specialization-oriented regime, progressively balancing expert utilization and routing confidence. Extensive experiments on public benchmarks demonstrate consistent improvements over strong baselines.

Despite impressive advances in agent systems, multi-turn tool-use scenarios remain challenging. It is mainly because intent is clarified progressively and the environment evolves with each tool call. While reusing past experience is natural, current LLM agents either treat entire trajectories or pre-defined subtasks as indivisible units, or solely exploit tool-to-tool dependencies, hindering adaptation as states and information evolve across turns. In this paper, we propose a State Integrated Tool Graph (SIT-Graph), which enhances multi-turn tool use by exploiting partially overlapping experience. Inspired by human decision-making that integrates episodic and procedural memory, SIT-Graph captures both compact state representations (episodic-like fragments) and tool-to-tool dependencies (procedural-like routines) from historical trajectories. Specifically, we first build a tool graph from accumulated tool-use sequences, and then augment each edge with a compact state summary of the dialog and tool history that may shape the next action. At inference time, SIT-Graph enables a human-like balance between episodic recall and procedural execution: when the next decision requires recalling prior context, the agent retrieves the state summaries stored on relevant edges and uses them to guide its next action; when the step is routine, it follows high-confidence tool dependencies without explicit recall. Experiments across multiple stateful multi-turn tool-use benchmarks show that SIT-Graph consistently outperforms strong memory- and graph-based baselines, delivering more robust tool selection and more effective experience transfer.

Accurate and efficient simulations of physical phenomena governed by partial differential equations (PDEs) are important for scientific and engineering progress. While traditional numerical solvers are powerful, they are often computationally expensive. Recently, data-driven methods have emerged as alternatives, but they frequently suffer from error accumulation and limited physical consistency, especially in multiphysics and complex geometries. To address these challenges, we propose PEGNet, a Physics-Embedded Graph Network that incorporates PDE-guided message passing to redesign the graph neural network architecture. By embedding key PDE dynamics like convection, viscosity, and diffusion into distinct message functions, the model naturally integrates physical constraints into its forward propagation, producing more stable and physically consistent solutions. Additionally, a hierarchical architecture is employed to capture multi-scale features, and physical regularization is integrated into the loss function to further enforce adherence to governing physics. We evaluated PEGNet on benchmarks, including custom datasets for respiratory airflow and drug delivery, showing significant improvements in long-term prediction accuracy and physical consistency over existing methods. Our code is available at https://github.com/Yanghuoshan/PEGNet.

Detecting intrusions in network traffic is a challenging task, particularly under limited supervision and constantly evolving attack patterns. While recent works have leveraged graph neural networks for network intrusion detection, they often decouple representation learning from anomaly detection, limiting the utility of the embeddings for identifying attacks. We propose GraphIDS, a self-supervised intrusion detection model that unifies these two stages by learning local graph representations of normal communication patterns through a masked autoencoder. An inductive graph neural network embeds each flow with its local topological context to capture typical network behavior, while a Transformer-based encoder-decoder reconstructs these embeddings, implicitly learning global co-occurrence patterns via self-attention without requiring explicit positional information. During inference, flows with unusually high reconstruction errors are flagged as potential intrusions. This end-to-end framework ensures that embeddings are directly optimized for the downstream task, facilitating the recognition of malicious traffic. On diverse NetFlow benchmarks, GraphIDS achieves up to 99.98% PR-AUC and 99.61% macro F1-score, outperforming baselines by 5-25 percentage points.

Knowledge graph (KG) reasoning is an important problem for knowledge graphs. In this paper, we propose a novel and principled framework called RulE (stands for {Rul}e {E}mbedding) to effectively leverage logical rules to enhance KG reasoning. Unlike knowledge graph embedding (KGE) methods, RulE learns rule embeddings from existing triplets and first-order {rules} by jointly representing entities, relations and logical rules in a unified embedding space. Based on the learned rule embeddings, a confidence score can be calculated for each rule, reflecting its consistency with the observed triplets. This allows us to perform logical rule inference in a soft way, thus alleviating the brittleness of logic. On the other hand, RulE injects prior logical rule information into the embedding space, enriching and regularizing the entity/relation embeddings. This makes KGE alone perform better too. RulE is conceptually simple and empirically effective. We conduct extensive experiments to verify each component of RulE. Results on multiple benchmarks reveal that our model outperforms the majority of existing embedding-based and rule-based approaches.

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D molecular graph or a single 3D structure, existing works often overlook the flexible nature of molecules, which continuously interconvert across conformations via chemical bond rotations and minor vibrational perturbations. To better account for molecular flexibility, some recent works formulate MRL as an ensemble learning problem, focusing on explicitly learning from a set of conformer structures. However, most of these studies have limited datasets, tasks, and models. In this work, we introduce the first MoleculAR Conformer Ensemble Learning (MARCEL) benchmark to thoroughly evaluate the potential of learning on conformer ensembles and suggest promising research directions. MARCEL includes four datasets covering diverse molecule- and reaction-level properties of chemically diverse molecules including organocatalysts and transition-metal catalysts, extending beyond the scope of common GNN benchmarks that are confined to drug-like molecules. In addition, we conduct a comprehensive empirical study, which benchmarks representative 1D, 2D, and 3D molecular representation learning models, along with two strategies that explicitly incorporate conformer ensembles into 3D MRL models. Our findings reveal that direct learning from an accessible conformer space can improve performance on a variety of tasks and models.

Graph Contrastive Learning (GCL) has emerged as a popular training approach for learning node embeddings from augmented graphs without labels. Despite the key principle that maximizing the similarity between positive node pairs while minimizing it between negative node pairs is well established, some fundamental problems are still unclear. Considering the complex graph structure, are some nodes consistently well-trained and following this principle even with different graph augmentations? Or are there some nodes more likely to be untrained across graph augmentations and violate the principle? How to distinguish these nodes and further guide the training of GCL? To answer these questions, we first present experimental evidence showing that the training of GCL is indeed imbalanced across all nodes. To address this problem, we propose the metric "node compactness", which is the lower bound of how a node follows the GCL principle related to the range of augmentations. We further derive the form of node compactness theoretically through bound propagation, which can be integrated into binary cross-entropy as a regularization. To this end, we propose the PrOvable Training (POT) for GCL, which regularizes the training of GCL to encode node embeddings that follows the GCL principle better. Through extensive experiments on various benchmarks, POT consistently improves the existing GCL approaches, serving as a friendly plugin.

Aspect-based sentiment analysis (ABSA) is a fine-grained task of sentiment analysis. To better comprehend long complicated sentences and obtain accurate aspect-specific information, linguistic and commonsense knowledge are generally required in this task. However, most current methods employ complicated and inefficient approaches to incorporate external knowledge, e.g., directly searching the graph nodes. Additionally, the complementarity between external knowledge and linguistic information has not been thoroughly studied. To this end, we propose a knowledge graph augmented network KGAN, which aims to effectively incorporate external knowledge with explicitly syntactic and contextual information. In particular, KGAN captures the sentiment feature representations from multiple different perspectives, i.e., context-, syntax- and knowledge-based. First, KGAN learns the contextual and syntactic representations in parallel to fully extract the semantic features. Then, KGAN integrates the knowledge graphs into the embedding space, based on which the aspect-specific knowledge representations are further obtained via an attention mechanism. Last, we propose a hierarchical fusion module to complement these multi-view representations in a local-to-global manner. Extensive experiments on five popular ABSA benchmarks demonstrate the effectiveness and robustness of our KGAN. Notably, with the help of the pretrained model of RoBERTa, KGAN achieves a new record of state-of-the-art performance among all datasets.

Knowledge graph (KG) embeddings learn low-dimensional representations of entities and relations to predict missing facts. KGs often exhibit hierarchical and logical patterns which must be preserved in the embedding space. For hierarchical data, hyperbolic embedding methods have shown promise for high-fidelity and parsimonious representations. However, existing hyperbolic embedding methods do not account for the rich logical patterns in KGs. In this work, we introduce a class of hyperbolic KG embedding models that simultaneously capture hierarchical and logical patterns. Our approach combines hyperbolic reflections and rotations with attention to model complex relational patterns. Experimental results on standard KG benchmarks show that our method improves over previous Euclidean- and hyperbolic-based efforts by up to 6.1% in mean reciprocal rank (MRR) in low dimensions. Furthermore, we observe that different geometric transformations capture different types of relations while attention-based transformations generalize to multiple relations. In high dimensions, our approach yields new state-of-the-art MRRs of 49.6% on WN18RR and 57.7% on YAGO3-10.

Learning vector representations (aka. embeddings) of users and items lies at the core of modern recommender systems. Ranging from early matrix factorization to recently emerged deep learning based methods, existing efforts typically obtain a user's (or an item's) embedding by mapping from pre-existing features that describe the user (or the item), such as ID and attributes. We argue that an inherent drawback of such methods is that, the collaborative signal, which is latent in user-item interactions, is not encoded in the embedding process. As such, the resultant embeddings may not be sufficient to capture the collaborative filtering effect. In this work, we propose to integrate the user-item interactions -- more specifically the bipartite graph structure -- into the embedding process. We develop a new recommendation framework Neural Graph Collaborative Filtering (NGCF), which exploits the user-item graph structure by propagating embeddings on it. This leads to the expressive modeling of high-order connectivity in user-item graph, effectively injecting the collaborative signal into the embedding process in an explicit manner. We conduct extensive experiments on three public benchmarks, demonstrating significant improvements over several state-of-the-art models like HOP-Rec and Collaborative Memory Network. Further analysis verifies the importance of embedding propagation for learning better user and item representations, justifying the rationality and effectiveness of NGCF. Codes are available at https://github.com/xiangwang1223/neural_graph_collaborative_filtering.

To provide more accurate, diverse, and explainable recommendation, it is compulsory to go beyond modeling user-item interactions and take side information into account. Traditional methods like factorization machine (FM) cast it as a supervised learning problem, which assumes each interaction as an independent instance with side information encoded. Due to the overlook of the relations among instances or items (e.g., the director of a movie is also an actor of another movie), these methods are insufficient to distill the collaborative signal from the collective behaviors of users. In this work, we investigate the utility of knowledge graph (KG), which breaks down the independent interaction assumption by linking items with their attributes. We argue that in such a hybrid structure of KG and user-item graph, high-order relations --- which connect two items with one or multiple linked attributes --- are an essential factor for successful recommendation. We propose a new method named Knowledge Graph Attention Network (KGAT) which explicitly models the high-order connectivities in KG in an end-to-end fashion. It recursively propagates the embeddings from a node's neighbors (which can be users, items, or attributes) to refine the node's embedding, and employs an attention mechanism to discriminate the importance of the neighbors. Our KGAT is conceptually advantageous to existing KG-based recommendation methods, which either exploit high-order relations by extracting paths or implicitly modeling them with regularization. Empirical results on three public benchmarks show that KGAT significantly outperforms state-of-the-art methods like Neural FM and RippleNet. Further studies verify the efficacy of embedding propagation for high-order relation modeling and the interpretability benefits brought by the attention mechanism.

Graph retrieval-augmented generation (GraphRAG) has effectively enhanced large language models in complex reasoning by organizing fragmented knowledge into explicitly structured graphs. Prior efforts have been made to improve either graph construction or graph retrieval in isolation, yielding suboptimal performance, especially when domain shifts occur. In this paper, we propose a vertically unified agentic paradigm, Youtu-GraphRAG, to jointly connect the entire framework as an intricate integration. Specifically, (i) a seed graph schema is introduced to bound the automatic extraction agent with targeted entity types, relations and attribute types, also continuously expanded for scalability over unseen domains; (ii) To obtain higher-level knowledge upon the schema, we develop novel dually-perceived community detection, fusing structural topology with subgraph semantics for comprehensive knowledge organization. This naturally yields a hierarchical knowledge tree that supports both top-down filtering and bottom-up reasoning with community summaries; (iii) An agentic retriever is designed to interpret the same graph schema to transform complex queries into tractable and parallel sub-queries. It iteratively performs reflection for more advanced reasoning; (iv) To alleviate the knowledge leaking problem in pre-trained LLM, we propose a tailored anonymous dataset and a novel 'Anonymity Reversion' task that deeply measures the real performance of the GraphRAG frameworks. Extensive experiments across six challenging benchmarks demonstrate the robustness of Youtu-GraphRAG, remarkably moving the Pareto frontier with up to 90.71% saving of token costs and 16.62% higher accuracy over state-of-the-art baselines. The results indicate our adaptability, allowing seamless domain transfer with minimal intervention on schema.

Graph neural networks (GNNs) learn the representation of graph-structured data, and their expressiveness can be further enhanced by inferring node relations for propagation. Attention-based GNNs infer neighbor importance to manipulate the weight of its propagation. Despite their popularity, the discussion on deep graph attention and its unique challenges has been limited. In this work, we investigate some problematic phenomena related to deep graph attention, including vulnerability to over-smoothed features and smooth cumulative attention. Through theoretical and empirical analyses, we show that various attention-based GNNs suffer from these problems. Motivated by our findings, we propose AEROGNN, a novel GNN architecture designed for deep graph attention. AERO-GNN provably mitigates the proposed problems of deep graph attention, which is further empirically demonstrated with (a) its adaptive and less smooth attention functions and (b) higher performance at deep layers (up to 64). On 9 out of 12 node classification benchmarks, AERO-GNN outperforms the baseline GNNs, highlighting the advantages of deep graph attention. Our code is available at https://github.com/syleeheal/AERO-GNN.

Recent advances in Graph Neural Networks (GNNs) and Graph Transformers (GTs) have been driven by innovations in architectures and Positional Encodings (PEs), which are critical for augmenting node features and capturing graph topology. PEs are essential for GTs, where topological information would otherwise be lost without message-passing. However, PEs are often tested alongside novel architectures, making it difficult to isolate their effect on established models. To address this, we present a comprehensive benchmark of PEs in a unified framework that includes both message-passing GNNs and GTs. We also establish theoretical connections between MPNNs and GTs and introduce a sparsified GRIT attention mechanism to examine the influence of global connectivity. Our findings demonstrate that previously untested combinations of GNN architectures and PEs can outperform existing methods and offer a more comprehensive picture of the state-of-the-art. To support future research and experimentation in our framework, we make the code publicly available.

Knowledge Graph Question Answering (KGQA) aims to answer user-questions from a knowledge graph (KG) by identifying the reasoning relations between topic entity and answer. As a complex branch task of KGQA, multi-hop KGQA requires reasoning over the multi-hop relational chain preserved in KG to arrive at the right answer. Despite recent successes, the existing works on answering multi-hop complex questions still face the following challenges: i) The absence of an explicit relational chain order reflected in user-question stems from a misunderstanding of a user's intentions. ii) Incorrectly capturing relational types on weak supervision of which dataset lacks intermediate reasoning chain annotations due to expensive labeling cost. iii) Failing to consider implicit relations between the topic entity and the answer implied in structured KG because of limited neighborhoods size constraint in subgraph retrieval-based algorithms.To address these issues in multi-hop KGQA, we propose a novel model herein, namely Relational Chain based Embedded KGQA (Rce-KGQA), which simultaneously utilizes the explicit relational chain revealed in natural language question and the implicit relational chain stored in structured KG. Our extensive empirical study on three open-domain benchmarks proves that our method significantly outperforms the state-of-the-art counterparts like GraftNet, PullNet and EmbedKGQA. Comprehensive ablation experiments also verify the effectiveness of our method on the multi-hop KGQA task. We have made our model's source code available at github: https://github.com/albert-jin/Rce-KGQA.

Large reasoning models (LRMs) have shown significant progress in test-time scaling through chain-of-thought prompting. Current approaches like search-o1 integrate retrieval augmented generation (RAG) into multi-step reasoning processes but rely on a single, linear reasoning chain while incorporating unstructured textual information in a flat, context-agnostic manner. As a result, these approaches can lead to error accumulation throughout the reasoning chain, which significantly limits its effectiveness in medical question-answering (QA) tasks where both accuracy and traceability are critical requirements. To address these challenges, we propose MIRAGE (Multi-chain Inference with Retrieval-Augmented Graph Exploration), a novel test-time scalable reasoning framework that performs dynamic multi-chain inference over structured medical knowledge graphs. Specifically, MIRAGE 1) decomposes complex queries into entity-grounded sub-questions, 2) executes parallel inference chains, 3) retrieves evidence adaptively via neighbor expansion and multi-hop traversal, and 4) integrates answers using cross-chain verification to resolve contradictions. Experiments on three medical QA benchmarks (GenMedGPT-5k, CMCQA, and ExplainCPE) show that MIRAGE consistently outperforms GPT-4o, Tree-of-Thought variants, and other retrieval-augmented baselines in both automatic and human evaluations. Additionally, MIRAGE improves interpretability by generating explicit reasoning chains that trace each factual claim to concrete chains within the knowledge graph, making it well-suited for complex medical reasoning scenarios. The code will be available for further research.

Retrieval-Augmented Generation (RAG) plays a crucial role in grounding Large Language Models by leveraging external knowledge, whereas the effectiveness is often compromised by the retrieval of contextually flawed or incomplete information. To address this, knowledge graph-based RAG methods have evolved towards hierarchical structures, organizing knowledge into multi-level summaries. However, these approaches still suffer from two critical, unaddressed challenges: high-level conceptual summaries exist as disconnected ``semantic islands'', lacking the explicit relations needed for cross-community reasoning; and the retrieval process itself remains structurally unaware, often degenerating into an inefficient flat search that fails to exploit the graph's rich topology. To overcome these limitations, we introduce LeanRAG, a framework that features a deeply collaborative design combining knowledge aggregation and retrieval strategies. LeanRAG first employs a novel semantic aggregation algorithm that forms entity clusters and constructs new explicit relations among aggregation-level summaries, creating a fully navigable semantic network. Then, a bottom-up, structure-guided retrieval strategy anchors queries to the most relevant fine-grained entities and then systematically traverses the graph's semantic pathways to gather concise yet contextually comprehensive evidence sets. The LeanRAG can mitigate the substantial overhead associated with path retrieval on graphs and minimizes redundant information retrieval. Extensive experiments on four challenging QA benchmarks with different domains demonstrate that LeanRAG significantly outperforming existing methods in response quality while reducing 46\% retrieval redundancy. Code is available at: https://github.com/RaZzzyz/LeanRAG

Despite the remarkable progress of Large Language Models (LLMs), their performance in question answering (QA) remains limited by the lack of domain-specific and up-to-date knowledge. Retrieval-Augmented Generation (RAG) addresses this limitation by incorporating external information, often from graph-structured data. However, existing graph-based RAG methods suffer from poor graph quality due to incomplete extraction and insufficient utilization of query information during retrieval. To overcome these limitations, we propose Clue-RAG, a novel approach that introduces (1) a multi-partite graph index incorporates Chunk, knowledge unit, and entity to capture semantic content at multiple levels of granularity, coupled with a hybrid extraction strategy that reduces LLM token usage while still producing accurate and disambiguated knowledge units, and (2) Q-Iter, a query-driven iterative retrieval strategy that enhances relevance through semantic search and constrained graph traversal. Experiments on three QA benchmarks show that Clue-RAG significantly outperforms state-of-the-art baselines, achieving up to 99.33% higher Accuracy and 113.51% higher F1 score while reducing indexing costs by 72.58%. Remarkably, Clue-RAG matches or outperforms baselines even without using an LLM for indexing. These results demonstrate the effectiveness and cost-efficiency of Clue-RAG in advancing graph-based RAG systems.

Recent advances in large language models (LLMs) have intensified efforts to fuse heterogeneous open-source models into a unified system that inherits their complementary strengths. Existing logit-based fusion methods maintain inference efficiency but treat vocabulary dimensions independently, overlooking semantic dependencies encoded by cross-dimension interactions. These dependencies reflect how token types interact under a model's internal reasoning and are essential for aligning models with diverse generation behaviors. To explicitly model these dependencies, we propose InfiGFusion, the first structure-aware fusion framework with a novel Graph-on-Logits Distillation (GLD) loss. Specifically, we retain the top-k logits per output and aggregate their outer products across sequence positions to form a global co-activation graph, where nodes represent vocabulary channels and edges quantify their joint activations. To ensure scalability and efficiency, we design a sorting-based closed-form approximation that reduces the original O(n^4) cost of Gromov-Wasserstein distance to O(n log n), with provable approximation guarantees. Experiments across multiple fusion settings show that GLD consistently improves fusion quality and stability. InfiGFusion outperforms SOTA models and fusion baselines across 11 benchmarks spanning reasoning, coding, and mathematics. It shows particular strength in complex reasoning tasks, with +35.6 improvement on Multistep Arithmetic and +37.06 on Causal Judgement over SFT, demonstrating superior multi-step and relational inference.

The advent of Large Language Models (LLMs) has revolutionized natural language processing. However, these models face challenges in retrieving precise information from vast datasets. Retrieval-Augmented Generation (RAG) was developed to combining LLMs with external information retrieval systems to enhance the accuracy and context of responses. Despite improvements, RAG still struggles with comprehensive retrieval in high-volume, low-information-density databases and lacks relational awareness, leading to fragmented answers. To address this, this paper introduces the Pseudo-Knowledge Graph (PKG) framework, designed to overcome these limitations by integrating Meta-path Retrieval, In-graph Text and Vector Retrieval into LLMs. By preserving natural language text and leveraging various retrieval techniques, the PKG offers a richer knowledge representation and improves accuracy in information retrieval. Extensive evaluations using Open Compass and MultiHop-RAG benchmarks demonstrate the framework's effectiveness in managing large volumes of data and complex relationships.

We present Simplified Text-Attributed Graph Embeddings (STAGE), a straightforward yet effective method for enhancing node features in Graph Neural Network (GNN) models that encode Text-Attributed Graphs (TAGs). Our approach leverages Large-Language Models (LLMs) to generate embeddings for textual attributes. STAGE achieves competitive results on various node classification benchmarks while also maintaining a simplicity in implementation relative to current state-of-the-art (SoTA) techniques. We show that utilizing pre-trained LLMs as embedding generators provides robust features for ensemble GNN training, enabling pipelines that are simpler than current SoTA approaches which require multiple expensive training and prompting stages. We also implement diffusion-pattern GNNs in an effort to make this pipeline scalable to graphs beyond academic benchmarks.

Recently, there has been a surge of interest in extending the success of large language models (LLMs) from texts to molecules. Most existing approaches adopt a graph neural network to represent a molecule as a series of node tokens for molecule-language alignment, which, however, have overlooked the inherent hierarchical structures in molecules. Notably, higher-order molecular structures contain rich semantics of functional groups, which encode crucial biochemical functionalities of the molecules. We show that neglecting the hierarchical information in tokenization will lead to subpar molecule-language alignment and severe hallucination. To address this limitation, we propose HIerarchical GrapH Tokenization (HIGHT). HIGHT employs a hierarchical graph tokenizer that encodes the hierarchy of atom, motif, and molecular levels of informative tokens to improve the molecular perception of LLMs. HIGHT also adopts an augmented instruction tuning dataset, enriched with the hierarchical graph information, to further enhance the molecule-language alignment. Extensive experiments on 14 real-world benchmarks verify the effectiveness of HIGHT in reducing hallucination by 40%, and significant improvements in various molecule-language downstream tasks. The project is available at https: //higraphllm.github.io/.

Weakly-supervised temporal action localization (WTAL) is a practical yet challenging task. Due to large-scale datasets, most existing methods use a network pretrained in other datasets to extract features, which are not suitable enough for WTAL. To address this problem, researchers design several modules for feature enhancement, which improve the performance of the localization module, especially modeling the temporal relationship between snippets. However, all of them neglect the adverse effects of ambiguous information, which would reduce the discriminability of others. Considering this phenomenon, we propose Discriminability-Driven Graph Network (DDG-Net), which explicitly models ambiguous snippets and discriminative snippets with well-designed connections, preventing the transmission of ambiguous information and enhancing the discriminability of snippet-level representations. Additionally, we propose feature consistency loss to prevent the assimilation of features and drive the graph convolution network to generate more discriminative representations. Extensive experiments on THUMOS14 and ActivityNet1.2 benchmarks demonstrate the effectiveness of DDG-Net, establishing new state-of-the-art results on both datasets. Source code is available at https://github.com/XiaojunTang22/ICCV2023-DDGNet.

Accurate Urban SpatioTemporal Prediction (USTP) is of great importance to the development and operation of the smart city. As an emerging building block, multi-sourced urban data are usually integrated as urban knowledge graphs (UrbanKGs) to provide critical knowledge for urban spatiotemporal prediction models. However, existing UrbanKGs are often tailored for specific downstream prediction tasks and are not publicly available, which limits the potential advancement. This paper presents UUKG, the unified urban knowledge graph dataset for knowledge-enhanced urban spatiotemporal predictions. Specifically, we first construct UrbanKGs consisting of millions of triplets for two metropolises by connecting heterogeneous urban entities such as administrative boroughs, POIs, and road segments. Moreover, we conduct qualitative and quantitative analysis on constructed UrbanKGs and uncover diverse high-order structural patterns, such as hierarchies and cycles, that can be leveraged to benefit downstream USTP tasks. To validate and facilitate the use of UrbanKGs, we implement and evaluate 15 KG embedding methods on the KG completion task and integrate the learned KG embeddings into 9 spatiotemporal models for five different USTP tasks. The extensive experimental results not only provide benchmarks of knowledge-enhanced USTP models under different task settings but also highlight the potential of state-of-the-art high-order structure-aware UrbanKG embedding methods. We hope the proposed UUKG fosters research on urban knowledge graphs and broad smart city applications. The dataset and source code are available at https://github.com/usail-hkust/UUKG/.

Learning a shared policy that guides the locomotion of different agents is of core interest in Reinforcement Learning (RL), which leads to the study of morphology-agnostic RL. However, existing benchmarks are highly restrictive in the choice of starting point and target point, constraining the movement of the agents within 2D space. In this work, we propose a novel setup for morphology-agnostic RL, dubbed Subequivariant Graph RL in 3D environments (3D-SGRL). Specifically, we first introduce a new set of more practical yet challenging benchmarks in 3D space that allows the agent to have full Degree-of-Freedoms to explore in arbitrary directions starting from arbitrary configurations. Moreover, to optimize the policy over the enlarged state-action space, we propose to inject geometric symmetry, i.e., subequivariance, into the modeling of the policy and Q-function such that the policy can generalize to all directions, improving exploration efficiency. This goal is achieved by a novel SubEquivariant Transformer (SET) that permits expressive message exchange. Finally, we evaluate the proposed method on the proposed benchmarks, where our method consistently and significantly outperforms existing approaches on single-task, multi-task, and zero-shot generalization scenarios. Extensive ablations are also conducted to verify our design. Code and videos are available on our project page: https://alpc91.github.io/SGRL/.

Conversational AI and Question-Answering systems (QASs) for knowledge graphs (KGs) are both emerging research areas: they empower users with natural language interfaces for extracting information easily and effectively. Conversational AI simulates conversations with humans; however, it is limited by the data captured in the training datasets. In contrast, QASs retrieve the most recent information from a KG by understanding and translating the natural language question into a formal query supported by the database engine. In this paper, we present a comprehensive study of the characteristics of the existing alternatives towards combining both worlds into novel KG chatbots. Our framework compares two representative conversational models, ChatGPT and Galactica, against KGQAN, the current state-of-the-art QAS. We conduct a thorough evaluation using four real KGs across various application domains to identify the current limitations of each category of systems. Based on our findings, we propose open research opportunities to empower QASs with chatbot capabilities for KGs. All benchmarks and all raw results are available1 for further analysis.

Recent studies often exploit Graph Convolutional Network (GCN) to model label dependencies to improve recognition accuracy for multi-label image recognition. However, constructing a graph by counting the label co-occurrence possibilities of the training data may degrade model generalizability, especially when there exist occasional co-occurrence objects in test images. Our goal is to eliminate such bias and enhance the robustness of the learnt features. To this end, we propose an Attention-Driven Dynamic Graph Convolutional Network (ADD-GCN) to dynamically generate a specific graph for each image. ADD-GCN adopts a Dynamic Graph Convolutional Network (D-GCN) to model the relation of content-aware category representations that are generated by a Semantic Attention Module (SAM). Extensive experiments on public multi-label benchmarks demonstrate the effectiveness of our method, which achieves mAPs of 85.2%, 96.0%, and 95.5% on MS-COCO, VOC2007, and VOC2012, respectively, and outperforms current state-of-the-art methods with a clear margin. All codes can be found at https://github.com/Yejin0111/ADD-GCN.

Point clouds provide a flexible geometric representation suitable for countless applications in computer graphics; they also comprise the raw output of most 3D data acquisition devices. While hand-designed features on point clouds have long been proposed in graphics and vision, however, the recent overwhelming success of convolutional neural networks (CNNs) for image analysis suggests the value of adapting insight from CNN to the point cloud world. Point clouds inherently lack topological information so designing a model to recover topology can enrich the representation power of point clouds. To this end, we propose a new neural network module dubbed EdgeConv suitable for CNN-based high-level tasks on point clouds including classification and segmentation. EdgeConv acts on graphs dynamically computed in each layer of the network. It is differentiable and can be plugged into existing architectures. Compared to existing modules operating in extrinsic space or treating each point independently, EdgeConv has several appealing properties: It incorporates local neighborhood information; it can be stacked applied to learn global shape properties; and in multi-layer systems affinity in feature space captures semantic characteristics over potentially long distances in the original embedding. We show the performance of our model on standard benchmarks including ModelNet40, ShapeNetPart, and S3DIS.