Daily Papers

Dynamic pricing in retail requires policies that adapt to shifting demand while coordinating decisions across related products. We present a systematic empirical study of multi-agent reinforcement learning for retail price optimization, comparing a strong MAPPO baseline with a graph-attention-augmented variant (MAPPO+GAT) that leverages learned interactions among products. Using a simulated pricing environment derived from real transaction data, we evaluate profit, stability across random seeds, fairness across products, and training efficiency under a standardized evaluation protocol. The results indicate that MAPPO provides a robust and reproducible foundation for portfolio-level price control, and that MAPPO+GAT further enhances performance by sharing information over the product graph without inducing excessive price volatility. These results indicate that graph-integrated MARL provides a more scalable and stable solution than independent learners for dynamic retail pricing, offering practical advantages in multi-product decision-making.

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).

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.

We present an approach to modifying Transformer architectures by integrating graph-aware relational reasoning into the attention mechanism, merging concepts from graph neural networks and language modeling. Building on the inherent connection between attention and graph theory, we reformulate the Transformer's attention mechanism as a graph operation and propose Graph-Aware Isomorphic Attention. This method leverages advanced graph modeling strategies, including Graph Isomorphism Networks (GIN) and Principal Neighborhood Aggregation (PNA), to enrich the representation of relational structures. Our approach captures complex dependencies and generalizes across tasks, as evidenced by a reduced generalization gap and improved learning performance. Additionally, we expand the concept of graph-aware attention to introduce Sparse GIN-Attention, a fine-tuning approach that employs sparse GINs. By interpreting attention matrices as sparse adjacency graphs, this technique enhances the adaptability of pre-trained foundational models with minimal computational overhead, endowing them with graph-aware capabilities. Sparse GIN-Attention fine-tuning achieves improved training dynamics and better generalization compared to alternative methods like low-rank adaption (LoRA). We discuss latent graph-like structures within traditional attention mechanisms, offering a new lens through which Transformers can be understood. By evolving Transformers as hierarchical GIN models for relational reasoning. This perspective suggests profound implications for foundational model development, enabling the design of architectures that dynamically adapt to both local and global dependencies. Applications in bioinformatics, materials science, language modeling, and beyond could benefit from this synthesis of relational and sequential data modeling, setting the stage for interpretable and generalizable modeling strategies.

Attention-based graph neural networks (GNNs), such as graph attention networks (GATs), have become popular neural architectures for processing graph-structured data and learning node embeddings. Despite their empirical success, these models rely on labeled data and the theoretical properties of these models have yet to be fully understood. In this work, we propose a novel attention-based node embedding framework for graphs. Our framework builds upon a hierarchical kernel for multisets of subgraphs around nodes (e.g. neighborhoods) and each kernel leverages the geometry of a smooth statistical manifold to compare pairs of multisets, by "projecting" the multisets onto the manifold. By explicitly computing node embeddings with a manifold of Gaussian mixtures, our method leads to a new attention mechanism for neighborhood aggregation. We provide theoretical insights into generalizability and expressivity of our embeddings, contributing to a deeper understanding of attention-based GNNs. We propose both efficient unsupervised and supervised methods for learning the embeddings. Through experiments on several node classification benchmarks, we demonstrate that our proposed method outperforms existing attention-based graph models like GATs. Our code is available at https://github.com/BorgwardtLab/fisher_information_embedding.

Attention mechanism in graph neural networks is designed to assign larger weights to important neighbor nodes for better representation. However, what graph attention learns is not understood well, particularly when graphs are noisy. In this paper, we propose a self-supervised graph attention network (SuperGAT), an improved graph attention model for noisy graphs. Specifically, we exploit two attention forms compatible with a self-supervised task to predict edges, whose presence and absence contain the inherent information about the importance of the relationships between nodes. By encoding edges, SuperGAT learns more expressive attention in distinguishing mislinked neighbors. We find two graph characteristics influence the effectiveness of attention forms and self-supervision: homophily and average degree. Thus, our recipe provides guidance on which attention design to use when those two graph characteristics are known. Our experiment on 17 real-world datasets demonstrates that our recipe generalizes across 15 datasets of them, and our models designed by recipe show improved performance over baselines.

Attention Model has now become an important concept in neural networks that has been researched within diverse application domains. This survey provides a structured and comprehensive overview of the developments in modeling attention. In particular, we propose a taxonomy which groups existing techniques into coherent categories. We review salient neural architectures in which attention has been incorporated, and discuss applications in which modeling attention has shown a significant impact. We also describe how attention has been used to improve the interpretability of neural networks. Finally, we discuss some future research directions in attention. We hope this survey will provide a succinct introduction to attention models and guide practitioners while developing approaches for their applications.

Graph Attention Networks (GATs) are one of the most popular GNN architectures and are considered as the state-of-the-art architecture for representation learning with graphs. In GAT, every node attends to its neighbors given its own representation as the query. However, in this paper we show that GAT computes a very limited kind of attention: the ranking of the attention scores is unconditioned on the query node. We formally define this restricted kind of attention as static attention and distinguish it from a strictly more expressive dynamic attention. Because GATs use a static attention mechanism, there are simple graph problems that GAT cannot express: in a controlled problem, we show that static attention hinders GAT from even fitting the training data. To remove this limitation, we introduce a simple fix by modifying the order of operations and propose GATv2: a dynamic graph attention variant that is strictly more expressive than GAT. We perform an extensive evaluation and show that GATv2 outperforms GAT across 11 OGB and other benchmarks while we match their parametric costs. Our code is available at https://github.com/tech-srl/how_attentive_are_gats . GATv2 is available as part of the PyTorch Geometric library, the Deep Graph Library, and the TensorFlow GNN library.

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these structured representations given new sources of information. Although there have been many efforts focusing on improving the performance of the parsers that map text to graphs or parse trees, very few have explored the problem of directly manipulating these representations. In this paper, we explore the novel problem of graph modification, where the systems need to learn how to update an existing scene graph given a new user's command. Our novel models based on graph-based sparse transformer and cross attention information fusion outperform previous systems adapted from the machine translation and graph generation literature. We further contribute our large graph modification datasets to the research community to encourage future research for this new problem.

The Transformer architecture processes sequences by implementing a form of neural message-passing that consists of iterative information retrieval (attention), followed by local processing (position-wise MLP). Two types of information are essential under this general computational paradigm: "sensory" information about individual objects, and "relational" information describing the relationships between objects. Standard attention naturally encodes the former, but does not explicitly encode the latter. In this paper, we present an extension of Transformers where multi-head attention is augmented with two distinct types of attention heads, each routing information of a different type. The first type is the standard attention mechanism of Transformers, which captures object-level features, while the second type is a novel attention mechanism we propose to explicitly capture relational information. The two types of attention heads each possess different inductive biases, giving the resulting architecture greater efficiency and versatility. The promise of this approach is demonstrated empirically across a range of tasks.

Attention mechanisms have been widely used to capture long-range dependencies among nodes in Graph Transformers. Bottlenecked by the quadratic computational cost, attention mechanisms fail to scale in large graphs. Recent improvements in computational efficiency are mainly achieved by attention sparsification with random or heuristic-based graph subsampling, which falls short in data-dependent context reasoning. State space models (SSMs), such as Mamba, have gained prominence for their effectiveness and efficiency in modeling long-range dependencies in sequential data. However, adapting SSMs to non-sequential graph data presents a notable challenge. In this work, we introduce Graph-Mamba, the first attempt to enhance long-range context modeling in graph networks by integrating a Mamba block with the input-dependent node selection mechanism. Specifically, we formulate graph-centric node prioritization and permutation strategies to enhance context-aware reasoning, leading to a substantial improvement in predictive performance. Extensive experiments on ten benchmark datasets demonstrate that Graph-Mamba outperforms state-of-the-art methods in long-range graph prediction tasks, with a fraction of the computational cost in both FLOPs and GPU memory consumption. The code and models are publicly available at https://github.com/bowang-lab/Graph-Mamba.

Graph neural networks (GNNs) have become an indispensable tool for analyzing relational data. In the literature, classical GNNs may be classified into three variants: convolutional, attentional, and message-passing. While the standard message-passing variant is highly expressive, its typical pair-wise messages nevertheless only consider the features of the center node and each neighboring node individually. This design fails to incorporate the rich contextual information contained within the broader local neighborhood, potentially hindering its ability to learn complex relationships within the entire set of neighboring nodes. To address this limitation, this work first formalizes the concept of neighborhood-contextualization, rooted in a key property of the attentional variant. This then serves as the foundation for generalizing the message-passing variant to the proposed neighborhood-contextualized message-passing (NCMP) framework. To demonstrate its utility, a simple, practical, and efficient method to parametrize and operationalize NCMP is presented, leading to the development of the proposed Soft-Isomorphic Neighborhood-Contextualized Graph Convolution Network (SINC-GCN). A preliminary analysis on a synthetic binary node classification problem then underscores both the expressivity and efficiency of the proposed GNN architecture. Overall, the paper lays the foundation for the novel NCMP framework as a practical path toward further enhancing the graph representational power of classical GNNs.

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.

Although Large Language Models (LLMs) have demonstrated potential in processing graphs, they struggle with comprehending graphical structure information through prompts of graph description sequences, especially as the graph size increases. We attribute this challenge to the uneven memory performance of LLMs across different positions in graph description sequences, known as ''positional biases''. To address this, we propose GraphInsight, a novel framework aimed at improving LLMs' comprehension of both macro- and micro-level graphical information. GraphInsight is grounded in two key strategies: 1) placing critical graphical information in positions where LLMs exhibit stronger memory performance, and 2) investigating a lightweight external knowledge base for regions with weaker memory performance, inspired by retrieval-augmented generation (RAG). Moreover, GraphInsight explores integrating these two strategies into LLM agent processes for composite graph tasks that require multi-step reasoning. Extensive empirical studies on benchmarks with a wide range of evaluation tasks show that GraphInsight significantly outperforms all other graph description methods (e.g., prompting techniques and reordering strategies) in understanding graph structures of varying sizes.

In the field of deep learning, Graph Neural Networks (GNNs) and Graph Transformer models, with their outstanding performance and flexible architectural designs, have become leading technologies for processing structured data, especially graph data. Traditional GNNs often face challenges in capturing information from distant vertices effectively. In contrast, Graph Transformer models are particularly adept at managing long-distance node relationships. Despite these advantages, Graph Transformer models still encounter issues with computational and storage efficiency when scaled to large graph datasets. To address these challenges, we propose an innovative Graph Neural Network (GNN) architecture that integrates a Top-m attention mechanism aggregation component and a neighborhood aggregation component, effectively enhancing the model's ability to aggregate relevant information from both local and extended neighborhoods at each layer. This method not only improves computational efficiency but also enriches the node features, facilitating a deeper analysis of complex graph structures. Additionally, to assess the effectiveness of our proposed model, we have applied it to citation sentiment prediction, a novel task previously unexplored in the GNN field. Accordingly, we constructed a dedicated citation network, ArXivNet. In this dataset, we specifically annotated the sentiment polarity of the citations (positive, neutral, negative) to enable in-depth sentiment analysis. Our approach has shown superior performance across a variety of tasks including vertex classification, link prediction, sentiment prediction, graph regression, and visualization. It outperforms existing methods in terms of effectiveness, as demonstrated by experimental results on multiple datasets.

Vision-Language models (VLMs) pre-trained on large corpora have demonstrated notable success across a range of downstream tasks. In light of the rapidly increasing size of pre-trained VLMs, parameter-efficient transfer learning (PETL) has garnered attention as a viable alternative to full fine-tuning. One such approach is the adapter, which introduces a few trainable parameters into the pre-trained models while preserving the original parameters during adaptation. In this paper, we present a novel modeling framework that recasts adapter tuning after attention as a graph message passing process on attention graphs, where the projected query and value features and attention matrix constitute the node features and the graph adjacency matrix, respectively. Within this framework, tuning adapters in VLMs necessitates handling heterophilic graphs, owing to the disparity between the projected query and value space. To address this challenge, we propose a new adapter architecture, p-adapter, which employs p-Laplacian message passing in Graph Neural Networks (GNNs). Specifically, the attention weights are re-normalized based on the features, and the features are then aggregated using the calibrated attention matrix, enabling the dynamic exploitation of information with varying frequencies in the heterophilic attention graphs. We conduct extensive experiments on different pre-trained VLMs and multi-modal tasks, including visual question answering, visual entailment, and image captioning. The experimental results validate our method's significant superiority over other PETL methods.

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.

Recent improvements in KG-to-text generation are due to additional auxiliary pre-training tasks designed to give the fine-tune task a boost in performance. These tasks require extensive computational resources while only suggesting marginal improvements. Here, we demonstrate that by fusing graph-aware elements into existing pre-trained language models, we are able to outperform state-of-the-art models and close the gap imposed by additional pre-training tasks. We do so by proposing a mask structure to capture neighborhood information and a novel type encoder that adds a bias to the graph-attention weights depending on the connection type. Experiments on two KG-to-text benchmark datasets show our models are competitive while involving fewer parameters and no additional pre-training tasks. By formulating the problem as a framework, we can interchange the various proposed components and begin interpreting KG-to-text generative models based on the topological and type information found in a graph.

Graph Transformers (GTs) have achieved impressive results on various graph-related tasks. However, the huge computational cost of GTs hinders their deployment and application, especially in resource-constrained environments. Therefore, in this paper, we explore the feasibility of sparsifying GTs, a significant yet under-explored topic. We first discuss the redundancy of GTs based on the characteristics of existing GT models, and then propose a comprehensive Graph Transformer SParsification (GTSP) framework that helps to reduce the computational complexity of GTs from four dimensions: the input graph data, attention heads, model layers, and model weights. Specifically, GTSP designs differentiable masks for each individual compressible component, enabling effective end-to-end pruning. We examine our GTSP through extensive experiments on prominent GTs, including GraphTrans, Graphormer, and GraphGPS. The experimental results substantiate that GTSP effectively cuts computational costs, accompanied by only marginal decreases in accuracy or, in some cases, even improvements. For instance, GTSP yields a reduction of 30\% in Floating Point Operations while contributing to a 1.8\% increase in Area Under the Curve accuracy on OGBG-HIV dataset. Furthermore, we provide several insights on the characteristics of attention heads and the behavior of attention mechanisms, all of which have immense potential to inspire future research endeavors in this domain.

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

This work studies self-supervised graph learning for text-attributed graphs (TAGs) where nodes are represented by textual attributes. Unlike traditional graph contrastive methods that perturb the numerical feature space and alter the graph's topological structure, we aim to improve view generation through language supervision. This is driven by the prevalence of textual attributes in real applications, which complement graph structures with rich semantic information. However, this presents challenges because of two major reasons. First, text attributes often vary in length and quality, making it difficulty to perturb raw text descriptions without altering their original semantic meanings. Second, although text attributes complement graph structures, they are not inherently well-aligned. To bridge the gap, we introduce GAugLLM, a novel framework for augmenting TAGs. It leverages advanced large language models like Mistral to enhance self-supervised graph learning. Specifically, we introduce a mixture-of-prompt-expert technique to generate augmented node features. This approach adaptively maps multiple prompt experts, each of which modifies raw text attributes using prompt engineering, into numerical feature space. Additionally, we devise a collaborative edge modifier to leverage structural and textual commonalities, enhancing edge augmentation by examining or building connections between nodes. Empirical results across five benchmark datasets spanning various domains underscore our framework's ability to enhance the performance of leading contrastive methods as a plug-in tool. Notably, we observe that the augmented features and graph structure can also enhance the performance of standard generative methods, as well as popular graph neural networks. The open-sourced implementation of our GAugLLM is available at Github.

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.

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.

Simulating physics using Graph Neural Networks (GNNs) is predominantly driven by message-passing architectures, which face challenges in scaling and efficiency, particularly in handling large, complex meshes. These architectures have inspired numerous enhancements, including multigrid approaches and K-hop aggregation (using neighbours of distance K), yet they often introduce significant complexity and suffer from limited in-depth investigations. In response to these challenges, we propose a novel Graph Transformer architecture that leverages the adjacency matrix as an attention mask. The proposed approach incorporates innovative augmentations, including Dilated Sliding Windows and Global Attention, to extend receptive fields without sacrificing computational efficiency. Through extensive experimentation, we evaluate model size, adjacency matrix augmentations, positional encoding and K-hop configurations using challenging 3D computational fluid dynamics (CFD) datasets. We also train over 60 models to find a scaling law between training FLOPs and parameters. The introduced models demonstrate remarkable scalability, performing on meshes with up to 300k nodes and 3 million edges. Notably, the smallest model achieves parity with MeshGraphNet while being 7times faster and 6times smaller. The largest model surpasses the previous state-of-the-art by 38.8\% on average and outperforms MeshGraphNet by 52\% on the all-rollout RMSE, while having a similar training speed. Code and datasets are available at https://github.com/DonsetPG/graph-physics.

Transformers have achieved significant success across various domains, relying on self-attention to capture dependencies. However, the standard first-order attention mechanism is often limited by a low-rank bottleneck, struggling to capture intricate, multi-hop relationships within a single layer. In this paper, we propose the Nexus, a novel architecture designed to enhance representational power through a recursive framework. Unlike standard approaches that use static linear projections for Queries and Keys, Nexus dynamically refines these representations via nested self-attention mechanisms. Specifically, the Query and Key vectors are themselves outputs of inner attention loops, allowing tokens to aggregate global context and model high-order correlations prior to the final attention computation. We enforce a parameter-efficient weight-sharing strategy across recursive steps, ensuring that this enhanced expressivity incurs O(1) additional parameters. We provide theoretical analysis demonstrating that our method breaks the linear bottleneck of standard attention. Empirically, Nexus outperforms standard Transformers on multiple benchmarks.

Graph In-Context Learning, with the ability to adapt pre-trained graph models to novel and diverse downstream graphs without updating any parameters, has gained much attention in the community. The key to graph in-context learning is to perform downstream graphs conditioned on chosen prompt examples. Existing methods randomly select subgraphs or edges as prompts, leading to noisy graph prompts and inferior model performance. Additionally, due to the gap between pre-training and testing graphs, when the number of classes in the testing graphs is much greater than that in the training, the in-context learning ability will also significantly deteriorate. To tackle the aforementioned challenges, we develop a multi-stage adaptive prompt optimization method GraphPrompter, which optimizes the entire process of generating, selecting, and using graph prompts for better in-context learning capabilities. Firstly, Prompt Generator introduces a reconstruction layer to highlight the most informative edges and reduce irrelevant noise for graph prompt construction. Furthermore, in the selection stage, Prompt Selector employs the k-nearest neighbors algorithm and pre-trained selection layers to dynamically choose appropriate samples and minimize the influence of irrelevant prompts. Finally, we leverage a Prompt Augmenter with a cache replacement strategy to enhance the generalization capability of the pre-trained model on new datasets. Extensive experiments show that GraphPrompter effectively enhances the in-context learning ability of graph models. On average across all the settings, our approach surpasses the state-of-the-art baselines by over 8%. Our code is released at https://github.com/karin0018/GraphPrompter.

Attention mechanisms are critical to the success of large language models (LLMs), driving significant advancements in multiple fields. However, for graph-structured data, which requires emphasis on topological connections, they fall short compared to message-passing mechanisms on fixed links, such as those employed by Graph Neural Networks (GNNs). This raises a question: ``Does attention fail for graphs in natural language settings?'' Motivated by these observations, we embarked on an empirical study from the perspective of attention mechanisms to explore how LLMs process graph-structured data. The goal is to gain deeper insights into the attention behavior of LLMs over graph structures. We uncovered unique phenomena regarding how LLMs apply attention to graph-structured data and analyzed these findings to improve the modeling of such data by LLMs. The primary findings of our research are: 1) While LLMs can recognize graph data and capture text-node interactions, they struggle to model inter-node relationships within graph structures due to inherent architectural constraints. 2) The attention distribution of LLMs across graph nodes does not align with ideal structural patterns, indicating a failure to adapt to graph topology nuances. 3) Neither fully connected attention nor fixed connectivity is optimal; each has specific limitations in its application scenarios. Instead, intermediate-state attention windows improve LLM training performance and seamlessly transition to fully connected windows during inference. Source code: https://github.com/millioniron/LLM_exploration{LLM4Exploration}

Message-passing Graph Neural Networks (GNNs) are often criticized for their limited expressiveness, issues like over-smoothing and over-squashing, and challenges in capturing long-range dependencies. Conversely, Graph Transformers (GTs) are regarded as superior due to their employment of global attention mechanisms, which potentially mitigate these challenges. Literature frequently suggests that GTs outperform GNNs in graph-level tasks, especially for graph classification and regression on small molecular graphs. In this study, we explore the untapped potential of GNNs through an enhanced framework, GNN+, which integrates six widely used techniques: edge feature integration, normalization, dropout, residual connections, feed-forward networks, and positional encoding, to effectively tackle graph-level tasks. We conduct a systematic re-evaluation of three classic GNNs (GCN, GIN, and GatedGCN) enhanced by the GNN+ framework across 14 well-known graph-level datasets. Our results reveal that, contrary to prevailing beliefs, these classic GNNs consistently match or surpass the performance of GTs, securing top-three rankings across all datasets and achieving first place in eight. Furthermore, they demonstrate greater efficiency, running several times faster than GTs on many datasets. This highlights the potential of simple GNN architectures, challenging the notion that complex mechanisms in GTs are essential for superior graph-level performance. Our source code is available at https://github.com/LUOyk1999/GNNPlus.

While Graph Neural Networks have gained popularity in multiple domains, graph-structured input remains a major challenge due to (a) over-smoothing, (b) noisy neighbours (heterophily), and (c) the suspended animation problem. To address all these problems simultaneously, we propose a novel graph neural network FDGATII, inspired by attention mechanism's ability to focus on selective information supplemented with two feature preserving mechanisms. FDGATII combines Initial Residuals and Identity Mapping with the more expressive dynamic self-attention to handle noise prevalent from the neighbourhoods in heterophilic data sets. By using sparse dynamic attention, FDGATII is inherently parallelizable in design, whist efficient in operation; thus theoretically able to scale to arbitrary graphs with ease. Our approach has been extensively evaluated on 7 datasets. We show that FDGATII outperforms GAT and GCN based benchmarks in accuracy and performance on fully supervised tasks, obtaining state-of-the-art results on Chameleon and Cornell datasets with zero domain-specific graph pre-processing, and demonstrate its versatility and fairness.

The use of graph neural networks has produced significant advances in point cloud problems, such as those found in high energy physics. The question of how to produce a graph structure in these problems is usually treated as a matter of heuristics, employing fully connected graphs or K-nearest neighbors. In this work, we elevate this question to utmost importance as the Topology Problem. We propose an attention mechanism that allows a graph to be constructed in a learned space that handles geometrically the flow of relevance, providing one solution to the Topology Problem. We test this architecture, called GravNetNorm, on the task of top jet tagging, and show that it is competitive in tagging accuracy, and uses far fewer computational resources than all other comparable models.

Graph transformers are a recent advancement in machine learning, offering a new class of neural network models for graph-structured data. The synergy between transformers and graph learning demonstrates strong performance and versatility across various graph-related tasks. This survey provides an in-depth review of recent progress and challenges in graph transformer research. We begin with foundational concepts of graphs and transformers. We then explore design perspectives of graph transformers, focusing on how they integrate graph inductive biases and graph attention mechanisms into the transformer architecture. Furthermore, we propose a taxonomy classifying graph transformers based on depth, scalability, and pre-training strategies, summarizing key principles for effective development of graph transformer models. Beyond technical analysis, we discuss the applications of graph transformer models for node-level, edge-level, and graph-level tasks, exploring their potential in other application scenarios as well. Finally, we identify remaining challenges in the field, such as scalability and efficiency, generalization and robustness, interpretability and explainability, dynamic and complex graphs, as well as data quality and diversity, charting future directions for graph transformer research.

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.

Graph transformers have emerged as a promising architecture for a variety of graph learning and representation tasks. Despite their successes, though, it remains challenging to scale graph transformers to large graphs while maintaining accuracy competitive with message-passing networks. In this paper, we introduce Exphormer, a framework for building powerful and scalable graph transformers. Exphormer consists of a sparse attention mechanism based on two mechanisms: virtual global nodes and expander graphs, whose mathematical characteristics, such as spectral expansion, pseduorandomness, and sparsity, yield graph transformers with complexity only linear in the size of the graph, while allowing us to prove desirable theoretical properties of the resulting transformer models. We show that incorporating Exphormer into the recently-proposed GraphGPS framework produces models with competitive empirical results on a wide variety of graph datasets, including state-of-the-art results on three datasets. We also show that Exphormer can scale to datasets on larger graphs than shown in previous graph transformer architectures. Code can be found at https://github.com/hamed1375/Exphormer.

Many sparse attention mechanisms such as Neighborhood Attention have typically failed to consistently deliver speedup over the self attention baseline. This is largely due to the level of complexity in attention infrastructure, and the rapid evolution of AI hardware architecture. At the same time, many state-of-the-art foundational models, particularly in computer vision, are heavily bound by attention, and need reliable sparsity to escape the O(n^2) complexity. In this paper, we study a class of promising sparse attention mechanisms that focus on locality, and aim to develop a better analytical model of their performance improvements. We first introduce Generalized Neighborhood Attention (GNA), which can describe sliding window, strided sliding window, and blocked attention. We then consider possible design choices in implementing these approaches, and create a simulator that can provide much more realistic speedup upper bounds for any given setting. Finally, we implement GNA on top of a state-of-the-art fused multi-headed attention (FMHA) kernel designed for the NVIDIA Blackwell architecture in CUTLASS. Our implementation can fully realize the maximum speedup theoretically possible in many perfectly block-sparse cases, and achieves an effective utilization of 1.3 petaFLOPs/second in FP16. In addition, we plug various GNA configurations into off-the-shelf generative models, such as Cosmos-7B, HunyuanVideo, and FLUX, and show that it can deliver 28% to 46% end-to-end speedup on B200 without any fine-tuning. We will open source our simulator and Blackwell kernels directly through the NATTEN project.

Over the past 7 years, attention has become one of the most important primitives in deep learning. The primary approach to optimize attention is FlashAttention, which fuses the operation together, drastically improving both the runtime and the memory consumption. However, the importance of FlashAttention combined with its monolithic nature poses a problem for researchers aiming to try new attention variants -- a "software lottery". This problem is exacerbated by the difficulty of writing efficient fused attention kernels, resisting traditional compiler-based approaches. We introduce FlexAttention, a novel compiler-driven programming model that allows implementing the majority of attention variants in a few lines of idiomatic PyTorch code. We demonstrate that many existing attention variants (e.g. Alibi, Document Masking, PagedAttention, etc.) can be implemented via FlexAttention, and that we achieve competitive performance compared to these handwritten kernels. Finally, we demonstrate how FlexAttention allows for easy composition of attention variants, solving the combinatorial explosion of attention variants.

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.

Graph Retrieval-Augmented Generation (GraphRAG) enhances factual reasoning in LLMs by structurally modeling knowledge through graph-based representations. However, existing GraphRAG approaches face two core limitations: shallow retrieval that fails to surface all critical evidence, and inefficient utilization of pre-constructed structural graph data, which hinders effective reasoning from complex queries. To address these challenges, we propose GraphSearch, a novel agentic deep searching workflow with dual-channel retrieval for GraphRAG. GraphSearch organizes the retrieval process into a modular framework comprising six modules, enabling multi-turn interactions and iterative reasoning. Furthermore, GraphSearch adopts a dual-channel retrieval strategy that issues semantic queries over chunk-based text data and relational queries over structural graph data, enabling comprehensive utilization of both modalities and their complementary strengths. Experimental results across six multi-hop RAG benchmarks demonstrate that GraphSearch consistently improves answer accuracy and generation quality over the traditional strategy, confirming GraphSearch as a promising direction for advancing graph retrieval-augmented generation.

Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the computational feasibility of the global attention mechanism is possible. The next goal is to scale up these architectures to handle very large graphs on the scale of millions or even billions of nodes. With large-scale graphs, global attention learning is proven impractical due to its quadratic complexity w.r.t. the number of nodes. On the other hand, neighborhood sampling techniques become essential to manage large graph sizes, yet finding the optimal trade-off between speed and accuracy with sampling techniques remains challenging. This work advances representation learning on single large-scale graphs with a focus on identifying model characteristics and critical design constraints for developing scalable graph transformer (GT) architectures. We argue such GT requires layers that can adeptly learn both local and global graph representations while swiftly sampling the graph topology. As such, a key innovation of this work lies in the creation of a fast neighborhood sampling technique coupled with a local attention mechanism that encompasses a 4-hop reception field, but achieved through just 2-hop operations. This local node embedding is then integrated with a global node embedding, acquired via another self-attention layer with an approximate global codebook, before finally sent through a downstream layer for node predictions. The proposed GT framework, named LargeGT, overcomes previous computational bottlenecks and is validated on three large-scale node classification benchmarks. We report a 3x speedup and 16.8% performance gain on ogbn-products and snap-patents, while we also scale LargeGT on ogbn-papers100M with a 5.9% performance improvement.

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

The execution of graph algorithms using neural networks has recently attracted significant interest due to promising empirical progress. This motivates further understanding of how neural networks can replicate reasoning steps with relational data. In this work, we study the ability of transformer networks to simulate algorithms on graphs from a theoretical perspective. The architecture that we utilize is a looped transformer with extra attention heads that interact with the graph. We prove by construction that this architecture can simulate algorithms such as Dijkstra's shortest path algorithm, Breadth- and Depth-First Search, and Kosaraju's strongly connected components algorithm. The width of the network does not increase with the size of the input graph, which implies that the network can simulate the above algorithms for any graph. Despite this property, we show that there is a limit to simulation in our solution due to finite precision. Finally, we show a Turing Completeness result with constant width when the extra attention heads are utilized.

Transformer models typically calculate attention matrices using dot products, which have limitations when capturing nonlinear relationships between embedding vectors. We propose Neural Attention, a technique that replaces dot products with feed-forward networks, enabling a more expressive representation of relationships between tokens. This approach modifies only the attention matrix calculation while preserving the matrix dimensions, making it easily adaptable to existing transformer-based architectures. We provide a detailed mathematical justification for why Neural Attention increases representational capacity and conduct controlled experiments to validate this claim. When comparing Neural Attention and Dot-Product Attention, NLP experiments on WikiText-103 show a reduction in perplexity of over 5 percent. Similarly, experiments on CIFAR-10 and CIFAR-100 show comparable improvements for image classification tasks. While Neural Attention introduces higher computational demands, we develop techniques to mitigate these challenges, ensuring practical usability without sacrificing the increased expressivity it provides. This work establishes Neural Attention as an effective means of enhancing the predictive capabilities of transformer models across a variety of applications.

In this work, we conduct a systematic analysis of Native Sparse Attention (NSA) and propose targeted improvements that enhance long-context modeling. A key insight is that alternating between local (sliding-window) and global (compression, selective) attention across layers, rather than using fixed patterns, enables more effective propagation of long-range dependencies and substantially boosts performance on long-sequence tasks. Meanwhile, we further refine NSA's branches with Latent Attention that the sliding-window branch is enhanced with Multi-head Latent Attention (MLA) while compression and selective branches adopt Group-head Latent Attention (GLA). These changes reduce KV-cache memory by 50\% versus NSA while improving the model's common-sense reasoning and long-text understanding capabilities. Experiments on models from 340M to 1.3B parameters (trained on 15B and 100B tokens) show our method matches or exceeds full attention and native sparse attention in both common-sense reasoning and long-context understanding tasks.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

Graph learning has become indispensable for interpreting and harnessing relational data in diverse fields, ranging from recommendation systems to social network analysis. In this context, a variety of GNNs have emerged as promising methodologies for encoding the structural information of graphs. By effectively capturing the graph's underlying structure, these GNNs have shown great potential in enhancing performance in graph learning tasks, such as link prediction and node classification. However, despite their successes, a significant challenge persists: these advanced methods often face difficulties in generalizing to unseen graph data that significantly differs from the training instances. In this work, our aim is to advance the graph learning paradigm by developing a general graph foundation model. This model is designed to understand the complex topological patterns present in diverse graph data, enabling it to excel in zero-shot graph learning tasks across different downstream datasets. To achieve this goal, we address several key technical challenges in our OpenGraph model. Firstly, we propose a unified graph tokenizer to adapt our graph model to generalize well on unseen graph data, even when the underlying graph properties differ significantly from those encountered during training. Secondly, we develop a scalable graph transformer as the foundational encoder, which effectively captures node-wise dependencies within the global topological context. Thirdly, we introduce a data augmentation mechanism enhanced by a LLM to alleviate the limitations of data scarcity in real-world scenarios. Extensive experiments validate the effectiveness of our framework. By adapting our OpenGraph to new graph characteristics and comprehending the nuances of diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings and domains.

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

Transformers flexibly operate over sets of real-valued vectors representing task-specific entities and their attributes, where each vector might encode one word-piece token and its position in a sequence, or some piece of information that carries no position at all. But as set processors, transformers are at a disadvantage in reasoning over more general graph-structured data where nodes represent entities and edges represent relations between entities. To address this shortcoming, we generalize transformer attention to consider and update edge vectors in each transformer layer. We evaluate this relational transformer on a diverse array of graph-structured tasks, including the large and challenging CLRS Algorithmic Reasoning Benchmark. There, it dramatically outperforms state-of-the-art graph neural networks expressly designed to reason over graph-structured data. Our analysis demonstrates that these gains are attributable to relational attention's inherent ability to leverage the greater expressivity of graphs over sets.

Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggregated for learning representations of nodes with few neighbors. To address this, we propose a simple and efficient data augmentation strategy, local augmentation, to learn the distribution of the node features of the neighbors conditioned on the central node's feature and enhance GNN's expressive power with generated features. Local augmentation is a general framework that can be applied to any GNN model in a plug-and-play manner. It samples feature vectors associated with each node from the learned conditional distribution as additional input for the backbone model at each training iteration. Extensive experiments and analyses show that local augmentation consistently yields performance improvement when applied to various GNN architectures across a diverse set of benchmarks. For example, experiments show that plugging in local augmentation to GCN and GAT improves by an average of 3.4\% and 1.6\% in terms of test accuracy on Cora, Citeseer, and Pubmed. Besides, our experimental results on large graphs (OGB) show that our model consistently improves performance over backbones. Code is available at https://github.com/SongtaoLiu0823/LAGNN.

When reading books, humans focus primarily on the current page, flipping back to recap prior context only when necessary. Similarly, we demonstrate that Large Language Models (LLMs) can learn to dynamically determine when to attend to global context. We propose All-or-Here Attention (AHA), which utilizes a binary router per attention head to dynamically toggle between full attention and local sliding window attention for each token. Our results indicate that with a window size of 256 tokens, up to 93\% of the original full attention operations can be replaced by sliding window attention without performance loss. Furthermore, by evaluating AHA across various window sizes, we identify a long-tail distribution in context dependency, where the necessity for full attention decays rapidly as the local window expands. By decoupling local processing from global access, AHA reveals that full attention is largely redundant, and that efficient inference requires only on-demand access to the global context.

Vector databases typically rely on approximate nearest neighbor (ANN) search to retrieve the top-k closest vectors to a query in embedding space. While effective, this approach often yields semantically redundant results, missing the diversity and contextual richness required by applications such as retrieval-augmented generation (RAG), multi-hop QA, and memory-augmented agents. We introduce a new retrieval paradigm: semantic compression, which aims to select a compact, representative set of vectors that captures the broader semantic structure around a query. We formalize this objective using principles from submodular optimization and information geometry, and show that it generalizes traditional top-k retrieval by prioritizing coverage and diversity. To operationalize this idea, we propose graph-augmented vector retrieval, which overlays semantic graphs (e.g., kNN or knowledge-based links) atop vector spaces to enable multi-hop, context-aware search. We theoretically analyze the limitations of proximity-based retrieval under high-dimensional concentration and highlight how graph structures can improve semantic coverage. Our work outlines a foundation for meaning-centric vector search systems, emphasizing hybrid indexing, diversity-aware querying, and structured semantic retrieval. We make our implementation publicly available to foster future research in this area.

Graph Transformers (GTs) have emerged as powerful architectures for graph-structured data, yet remain constrained by rigid designs and lack quantifiable interpretability. Current state-of-the-art GTs commit to fixed GNN types across all layers, missing potential benefits of depth-specific component selection, while their complex architectures become opaque where performance gains cannot be distinguished between meaningful patterns and spurious correlations. We redesign GT attention through asymmetry, decoupling structural encoding from feature representation: queries derive from node features while keys and values come from GNN transformations. Within this framework, we use Differentiable ARchiTecture Search (DARTS) to select optimal GNN operators at each layer, enabling depth-wise heterogeneity inside transformer attention itself (DARTS-GT). To understand discovered architectures, we develop the first quantitative interpretability framework for GTs through causal ablation. Our metrics (Head-deviation, Specialization, and Focus), identify which heads and nodes drive predictions while enabling model comparison. Experiments across eight benchmarks show DARTS-GT achieves state-of-the-art on four datasets while remaining competitive on others, with discovered architectures revealing dataset-specific patterns. Our interpretability analysis reveals that visual attention salience and causal importance do not always correlate, indicating widely used visualization approaches may miss components that actually matter. Crucially, heterogeneous architectures found by DARTS-GT consistently produced more interpretable models than baselines, establishing that Graph Transformers need not choose between performance and interpretability.

Knowledge graph (KG) link prediction aims to infer new facts based on existing facts in the KG. Recent studies have shown that using the graph neighborhood of a node via graph neural networks (GNNs) provides more useful information compared to just using the query information. Conventional GNNs for KG link prediction follow the standard message-passing paradigm on the entire KG, which leads to superfluous computation, over-smoothing of node representations, and also limits their expressive power. On a large scale, it becomes computationally expensive to aggregate useful information from the entire KG for inference. To address the limitations of existing KG link prediction frameworks, we propose a novel retrieve-and-read framework, which first retrieves a relevant subgraph context for the query and then jointly reasons over the context and the query with a high-capacity reader. As part of our exemplar instantiation for the new framework, we propose a novel Transformer-based GNN as the reader, which incorporates graph-based attention structure and cross-attention between query and context for deep fusion. This simple yet effective design enables the model to focus on salient context information relevant to the query. Empirical results on two standard KG link prediction datasets demonstrate the competitive performance of the proposed method. Furthermore, our analysis yields valuable insights for designing improved retrievers within the framework.

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.

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

We introduce three new attention mechanisms that outperform standard multi-head attention in terms of efficiency and learning capabilities, thereby improving the performance and broader deployability of Transformer models. Our first contribution is Optimised Attention, which performs similarly to standard attention, but has 3/4 as many parameters and one matrix multiplication fewer per head. Next, we introduce Efficient Attention, which performs on par with standard attention with only 1/2 as many parameters as many parameters and two matrix multiplications fewer per head and is up to twice as fast as standard attention. Lastly, we introduce Super Attention, which surpasses standard attention by a significant margin in both vision and natural language processing tasks while having fewer parameters and matrix multiplications. In addition to providing rigorous mathematical comparisons, we evaluate the presented attention mechanisms on MNIST, CIFAR100, IMDB Movie Reviews, and Amazon Reviews datasets.

Neighborhood attention reduces the cost of self attention by restricting each token's attention span to its nearest neighbors. This restriction, parameterized by a window size and dilation factor, draws a spectrum of possible attention patterns between linear projection and self attention. Neighborhood attention, and more generally sliding window attention patterns, have long been bounded by infrastructure, particularly in higher-rank spaces (2-D and 3-D), calling for the development of custom kernels, which have been limited in either functionality, or performance, if not both. In this work, we first show that neighborhood attention can be represented as a batched GEMM problem, similar to standard attention, and implement it for 1-D and 2-D neighborhood attention. These kernels on average provide 895% and 272% improvement in full precision latency compared to existing naive kernels for 1-D and 2-D neighborhood attention respectively. We find certain inherent inefficiencies in all unfused neighborhood attention kernels that bound their performance and lower-precision scalability. We also developed fused neighborhood attention; an adaptation of fused dot-product attention kernels that allow fine-grained control over attention across different spatial axes. Known for reducing the quadratic time complexity of self attention to a linear complexity, neighborhood attention can now enjoy a reduced and constant memory footprint, and record-breaking half precision latency. We observe that our fused kernels successfully circumvent some of the unavoidable inefficiencies in unfused implementations. While our unfused GEMM-based kernels only improve half precision performance compared to naive kernels by an average of 496% and 113% in 1-D and 2-D problems respectively, our fused kernels improve naive kernels by an average of 1607% and 581% in 1-D and 2-D problems respectively.

Transformers and large language models (LLMs) have revolutionized machine learning, with attention mechanisms at the core of their success. As the landscape of attention variants expands, so too do the challenges of optimizing their performance, particularly across different hardware platforms. Current optimization strategies are often narrowly focused, requiring extensive manual intervention to accommodate changes in model configurations or hardware environments. In this paper, we introduce AttentionEngine, a comprehensive framework designed to streamline the optimization of attention mechanisms across heterogeneous hardware backends. By decomposing attention computation into modular operations with customizable components, AttentionEngine enables flexible adaptation to diverse algorithmic requirements. The framework further automates kernel optimization through a combination of programmable templates and a robust cross-platform scheduling strategy. Empirical results reveal performance gains of up to 10x on configurations beyond the reach of existing methods. AttentionEngine offers a scalable, efficient foundation for developing and deploying attention mechanisms with minimal manual tuning. Our code has been open-sourced and is available at https://github.com/microsoft/AttentionEngine.

In this paper, we propose Superlinear attention, a fully trainable multi-step attention architecture that achieves subquadratic complexity for long sequences while preserving random context access (a.k.a.\ structural non-exclusion): no eligible token position is structurally excluded from being selected for attention. Superlinear attention reformulates standard causal self-attention as a multi-step search problem with N steps, yielding an overall complexity of O(L^{1+1{N}}). To illustrate the architecture, we present a baseline N=2 implementation, which is algorithmically analogous to standard jump search. In this O(L^{3/2}) instantiation, the first step performs O(L^{3/2}) span-search to select relevant spans of the sequence, and the second step applies O(L^{3/2}) span-attention (standard attention restricted to the selected spans). In an upscaled O(L^{1.54}) configuration for robustness, we achieve an average decoding throughput of 114 tokens/sec at 1M context length and 80 tokens/sec at 10M context in our implementation on a modified 30B hybrid MoE model on a single B200 GPU. With limited training, we also obtain strong performance on the NIAH (Needle In A Haystack) task up to 256K context length, demonstrating that the routed span selection is learnable end-to-end. This paper emphasizes architectural formulation, scaling analysis, and systems feasibility, and presents initial validation; comprehensive quality evaluations across diverse long-context tasks are left to future work.

Large language models (LLMs) have demonstrated remarkable in-context reasoning capabilities across a wide range of tasks, particularly with unstructured inputs such as language or images. However, LLMs struggle to handle structured data, such as graphs, due to their lack of understanding of non-Euclidean structures. As a result, without additional fine-tuning, their performance significantly lags behind that of graph neural networks (GNNs) in graph learning tasks. In this paper, we show that learning on graph data can be conceptualized as a retrieval-augmented generation (RAG) process, where specific instances (e.g., nodes or edges) act as queries, and the graph itself serves as the retrieved context. Building on this insight, we propose a series of RAG frameworks to enhance the in-context learning capabilities of LLMs for graph learning tasks. Comprehensive evaluations demonstrate that our proposed RAG frameworks significantly improve LLM performance on graph-based tasks, particularly in scenarios where a pretrained LLM must be used without modification or accessed via an API.

Retrieval-Augmented Generation (RAG) enhances the performance of LLMs across various tasks by retrieving relevant information from external sources, particularly on text-based data. For structured data, such as knowledge graphs, GraphRAG has been widely used to retrieve relevant information. However, recent studies have revealed that structuring implicit knowledge from text into graphs can benefit certain tasks, extending the application of GraphRAG from graph data to general text-based data. Despite their successful extensions, most applications of GraphRAG for text data have been designed for specific tasks and datasets, lacking a systematic evaluation and comparison between RAG and GraphRAG on widely used text-based benchmarks. In this paper, we systematically evaluate RAG and GraphRAG on well-established benchmark tasks, such as Question Answering and Query-based Summarization. Our results highlight the distinct strengths of RAG and GraphRAG across different tasks and evaluation perspectives. Inspired by these observations, we investigate strategies to integrate their strengths to improve downstream tasks. Additionally, we provide an in-depth discussion of the shortcomings of current GraphRAG approaches and outline directions for future research.

Instance selection (IS) is important in machine learning for reducing dataset size while keeping key characteristics. Current IS methods often struggle with capturing complex relationships in high-dimensional spaces and scale with large datasets. This paper introduces a graph attention-based instance selection (GAIS) method that uses attention mechanisms to identify informative instances through their structural relationships in graph representations. We present two approaches for scalable graph construction: a distance-based mini-batch sampling technique that reduces computation through strategic batch processing, and a hierarchical hashing approach that allows for efficient similarity computation through random projections. The mini-batch approach keeps class distributions through stratified sampling, while the hierarchical hashing method captures relationships at multiple granularities through single-level, multi-level, and multi-view variants. Experiments across 39 datasets show that GAIS achieves reduction rates above 96\% while maintaining or improving model performance relative to state-of-the-art IS methods. The findings shows that the distance-based mini-batch approach offers an optimal balance of efficiency and effectiveness for large-scale datasets, while multi-view variants provide superior performance for complex, high-dimensional data, demonstrating that attention-based importance scoring can effectively identify instances crucial for maintaining decision boundaries without requiring exhaustive pairwise comparisons.

Graph representation learning is fundamental for analyzing graph-structured data. Exploring invariant graph representations remains a challenge for most existing graph representation learning methods. In this paper, we propose a cross-view graph consistency learning (CGCL) method that learns invariant graph representations for link prediction. First, two complementary augmented views are derived from an incomplete graph structure through a bidirectional graph structure augmentation scheme. This augmentation scheme mitigates the potential information loss that is commonly associated with various data augmentation techniques involving raw graph data, such as edge perturbation, node removal, and attribute masking. Second, we propose a CGCL model that can learn invariant graph representations. A cross-view training scheme is proposed to train the proposed CGCL model. This scheme attempts to maximize the consistency information between one augmented view and the graph structure reconstructed from the other augmented view. Furthermore, we offer a comprehensive theoretical CGCL analysis. This paper empirically and experimentally demonstrates the effectiveness of the proposed CGCL method, achieving competitive results on graph datasets in comparisons with several state-of-the-art algorithms.

Dot-product attention has wide applications in computer vision and natural language processing. However, its memory and computational costs grow quadratically with the input size. Such growth prohibits its application on high-resolution inputs. To remedy this drawback, this paper proposes a novel efficient attention mechanism equivalent to dot-product attention but with substantially less memory and computational costs. Its resource efficiency allows more widespread and flexible integration of attention modules into a network, which leads to better accuracies. Empirical evaluations demonstrated the effectiveness of its advantages. Efficient attention modules brought significant performance boosts to object detectors and instance segmenters on MS-COCO 2017. Further, the resource efficiency democratizes attention to complex models, where high costs prohibit the use of dot-product attention. As an exemplar, a model with efficient attention achieved state-of-the-art accuracies for stereo depth estimation on the Scene Flow dataset. Code is available at https://github.com/cmsflash/efficient-attention.

Scaling the effective context length is essential for advancing large language models (LLMs) toward artificial general intelligence (AGI). However, the quadratic increase in computational complexity inherent in traditional attention mechanisms presents a prohibitive overhead. Existing approaches either impose strongly biased structures, such as sink or window attention which are task-specific, or radically modify the attention mechanism into linear approximations, whose performance in complex reasoning tasks remains inadequately explored. In this work, we propose a solution that adheres to the ``less structure'' principle, allowing the model to determine where to attend autonomously, rather than introducing predefined biases. We introduce Mixture of Block Attention (MoBA), an innovative approach that applies the principles of Mixture of Experts (MoE) to the attention mechanism. This novel architecture demonstrates superior performance on long-context tasks while offering a key advantage: the ability to seamlessly transition between full and sparse attention, enhancing efficiency without the risk of compromising performance. MoBA has already been deployed to support Kimi's long-context requests and demonstrates significant advancements in efficient attention computation for LLMs. Our code is available at https://github.com/MoonshotAI/MoBA.

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.

Retrieval-Augmented Generation (RAG) is widely used to mitigate hallucinations of Large Language Models (LLMs) by leveraging external knowledge. While effective for simple queries, traditional RAG systems struggle with large-scale, unstructured corpora where information is fragmented. Recent advances incorporate knowledge graphs to capture relational structures, enabling more comprehensive retrieval for complex, multi-hop reasoning tasks. However, existing graph-based RAG (GraphRAG) methods rely on unstable and costly relation extraction for graph construction, often producing noisy graphs with incorrect or inconsistent relations that degrade retrieval quality. In this paper, we revisit the pipeline of existing GraphRAG systems and propose LinearRAG (Linear Graph-based Retrieval-Augmented Generation), an efficient framework that enables reliable graph construction and precise passage retrieval. Specifically, LinearRAG constructs a relation-free hierarchical graph, termed Tri-Graph, using only lightweight entity extraction and semantic linking, avoiding unstable relation modeling. This new paradigm of graph construction scales linearly with corpus size and incurs no extra token consumption, providing an economical and reliable indexing of the original passages. For retrieval, LinearRAG adopts a two-stage strategy: (i) relevant entity activation via local semantic bridging, followed by (ii) passage retrieval through global importance aggregation. Extensive experiments on four datasets demonstrate that LinearRAG significantly outperforms baseline models.

When manipulating three-dimensional data, it is possible to ensure that rotational and translational symmetries are respected by applying so-called SE(3)-equivariant models. Protein structure prediction is a prominent example of a task which displays these symmetries. Recent work in this area has successfully made use of an SE(3)-equivariant model, applying an iterative SE(3)-equivariant attention mechanism. Motivated by this application, we implement an iterative version of the SE(3)-Transformer, an SE(3)-equivariant attention-based model for graph data. We address the additional complications which arise when applying the SE(3)-Transformer in an iterative fashion, compare the iterative and single-pass versions on a toy problem, and consider why an iterative model may be beneficial in some problem settings. We make the code for our implementation available to the community.

The rapidly growing number and variety of Large Language Models (LLMs) present significant challenges in efficiently selecting the appropriate LLM for a given query, especially considering the trade-offs between performance and computational cost. Current LLM selection methods often struggle to generalize across new LLMs and different tasks because of their limited ability to leverage contextual interactions among tasks, queries, and LLMs, as well as their dependence on a transductive learning framework. To address these shortcomings, we introduce a novel inductive graph framework, named as GraphRouter, which fully utilizes the contextual information among tasks, queries, and LLMs to enhance the LLM selection process. GraphRouter constructs a heterogeneous graph comprising task, query, and LLM nodes, with interactions represented as edges, which efficiently captures the contextual information between the query's requirements and the LLM's capabilities. Through an innovative edge prediction mechanism, GraphRouter is able to predict attributes (the effect and cost of LLM response) of potential edges, allowing for optimized recommendations that adapt to both existing and newly introduced LLMs without requiring retraining. Comprehensive experiments across three distinct effect-cost weight scenarios have shown that GraphRouter substantially surpasses existing routers, delivering a minimum performance improvement of 12.3%. In addition, it achieves enhanced generalization across new LLMs settings and supports diverse tasks with at least a 9.5% boost in effect and a significant reduction in computational demands. This work endeavors to apply a graph-based approach for the contextual and adaptive selection of LLMs, offering insights for real-world applications. Our codes for GraphRouter is released at https://github.com/ulab-uiuc/GraphRouter.

Task planning in language agents is emerging as an important research topic alongside the development of large language models (LLMs). It aims to break down complex user requests in natural language into solvable sub-tasks, thereby fulfilling the original requests. In this context, the sub-tasks can be naturally viewed as a graph, where the nodes represent the sub-tasks, and the edges denote the dependencies among them. Consequently, task planning is a decision-making problem that involves selecting a connected path or subgraph within the corresponding graph and invoking it. In this paper, we explore graph learning-based methods for task planning, a direction that is orthogonal to the prevalent focus on prompt design. Our interest in graph learning stems from a theoretical discovery: the biases of attention and auto-regressive loss impede LLMs' ability to effectively navigate decision-making on graphs, which is adeptly addressed by graph neural networks (GNNs). This theoretical insight led us to integrate GNNs with LLMs to enhance overall performance. Extensive experiments demonstrate that GNN-based methods surpass existing solutions even without training, and minimal training can further enhance their performance. The performance gain increases with a larger task graph size.

Despite the impressive advancements of Large Language Models (LLMs) in generating text, they are often limited by the knowledge contained in the input and prone to producing inaccurate or hallucinated content. To tackle these issues, Retrieval-augmented Generation (RAG) is employed as an effective strategy to enhance the available knowledge base and anchor the responses in reality by pulling additional texts from external databases. In real-world applications, texts are often linked through entities within a graph, such as citations in academic papers or comments in social networks. This paper exploits these topological relationships to guide the retrieval process in RAG. Specifically, we explore two kinds of topological connections: proximity-based, focusing on closely connected nodes, and role-based, which looks at nodes sharing similar subgraph structures. Our empirical research confirms their relevance to text relationships, leading us to develop a Topology-aware Retrieval-augmented Generation framework. This framework includes a retrieval module that selects texts based on their topological relationships and an aggregation module that integrates these texts into prompts to stimulate LLMs for text generation. We have curated established text-attributed networks and conducted comprehensive experiments to validate the effectiveness of this framework, demonstrating its potential to enhance RAG with topological awareness.

Large Language Models (LLMs) have demonstrated remarkable performance across various tasks but remain prone to hallucinations. Detecting hallucinations is essential for safety-critical applications, and recent methods leverage attention map properties to this end, though their effectiveness remains limited. In this work, we investigate the spectral features of attention maps by interpreting them as adjacency matrices of graph structures. We propose the LapEigvals method, which utilises the top-k eigenvalues of the Laplacian matrix derived from the attention maps as an input to hallucination detection probes. Empirical evaluations demonstrate that our approach achieves state-of-the-art hallucination detection performance among attention-based methods. Extensive ablation studies further highlight the robustness and generalisation of LapEigvals, paving the way for future advancements in the hallucination detection domain.

Image classification is a computer vision task where a model analyzes an image to categorize it into a specific label. Vision Transformers (ViT) improve this task by leveraging self-attention to capture complex patterns and long range relationships between image patches. However, a key challenge for ViTs is efficiently incorporating multiscale feature representations, which is inherent in CNNs through their hierarchical structure. In this paper, we introduce the Scale-Aware Graph Attention Vision Transformer (SAG-ViT), a novel framework that addresses this challenge by integrating multi-scale features. Using EfficientNet as a backbone, the model extracts multi-scale feature maps, which are divided into patches to preserve semantic information. These patches are organized into a graph based on spatial and feature similarities, with a Graph Attention Network (GAT) refining the node embeddings. Finally, a Transformer encoder captures long-range dependencies and complex interactions. The SAG-ViT is evaluated on benchmark datasets, demonstrating its effectiveness in enhancing image classification performance.

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field.

In this study, we propose a novel graph neural network called propagate-selector (PS), which propagates information over sentences to understand information that cannot be inferred when considering sentences in isolation. First, we design a graph structure in which each node represents an individual sentence, and some pairs of nodes are selectively connected based on the text structure. Then, we develop an iterative attentive aggregation and a skip-combine method in which a node interacts with its neighborhood nodes to accumulate the necessary information. To evaluate the performance of the proposed approaches, we conduct experiments with the standard HotpotQA dataset. The empirical results demonstrate the superiority of our proposed approach, which obtains the best performances, compared to the widely used answer-selection models that do not consider the intersentential relationship.

Transformer-based architectures have become the prevailing backbone of large language models. However, the quadratic time and memory complexity of self-attention remains a fundamental obstacle to efficient long-context modeling. To address this limitation, recent research has introduced two principal categories of efficient attention mechanisms. Linear attention methods achieve linear complexity through kernel approximations, recurrent formulations, or fastweight dynamics, thereby enabling scalable inference with reduced computational overhead. Sparse attention techniques, in contrast, limit attention computation to selected subsets of tokens based on fixed patterns, block-wise routing, or clustering strategies, enhancing efficiency while preserving contextual coverage. This survey provides a systematic and comprehensive overview of these developments, integrating both algorithmic innovations and hardware-level considerations. In addition, we analyze the incorporation of efficient attention into largescale pre-trained language models, including both architectures built entirely on efficient attention and hybrid designs that combine local and global components. By aligning theoretical foundations with practical deployment strategies, this work aims to serve as a foundational reference for advancing the design of scalable and efficient language models.

Gating mechanisms have been widely utilized, from early models like LSTMs and Highway Networks to recent state space models, linear attention, and also softmax attention. Yet, existing literature rarely examines the specific effects of gating. In this work, we conduct comprehensive experiments to systematically investigate gating-augmented softmax attention variants. Specifically, we perform a comprehensive comparison over 30 variants of 15B Mixture-of-Experts (MoE) models and 1.7B dense models trained on a 3.5 trillion token dataset. Our central finding is that a simple modification-applying a head-specific sigmoid gate after the Scaled Dot-Product Attention (SDPA)-consistently improves performance. This modification also enhances training stability, tolerates larger learning rates, and improves scaling properties. By comparing various gating positions and computational variants, we attribute this effectiveness to two key factors: (1) introducing non-linearity upon the low-rank mapping in the softmax attention, and (2) applying query-dependent sparse gating scores to modulate the SDPA output. Notably, we find this sparse gating mechanism mitigates 'attention sink' and enhances long-context extrapolation performance, and we also release related https://github.com/qiuzh20/gated_attention{codes} and https://huggingface.co/QwQZh/gated_attention{models} to facilitate future research.

Graph transformers (GTs) have emerged as a promising architecture that is theoretically more expressive than message-passing graph neural networks (GNNs). However, typical GT models have at least quadratic complexity and thus cannot scale to large graphs. While there are several linear GTs recently proposed, they still lag behind GNN counterparts on several popular graph datasets, which poses a critical concern on their practical expressivity. To balance the trade-off between expressivity and scalability of GTs, we propose Polynormer, a polynomial-expressive GT model with linear complexity. Polynormer is built upon a novel base model that learns a high-degree polynomial on input features. To enable the base model permutation equivariant, we integrate it with graph topology and node features separately, resulting in local and global equivariant attention models. Consequently, Polynormer adopts a linear local-to-global attention scheme to learn high-degree equivariant polynomials whose coefficients are controlled by attention scores. Polynormer has been evaluated on 13 homophilic and heterophilic datasets, including large graphs with millions of nodes. Our extensive experiment results show that Polynormer outperforms state-of-the-art GNN and GT baselines on most datasets, even without the use of nonlinear activation functions.

Retrieval-Augmented Generation (RAG) enhances the response quality and domain-specific performance of large language models (LLMs) by incorporating external knowledge to combat hallucinations. In recent research, graph structures have been integrated into RAG to enhance the capture of semantic relations between entities. However, it primarily focuses on low-order pairwise entity relations, limiting the high-order associations among multiple entities. Hypergraph-enhanced approaches address this limitation by modeling multi-entity interactions via hyperedges, but they are typically constrained to inter-chunk entity-level representations, overlooking the global thematic organization and alignment across chunks. Drawing inspiration from the top-down cognitive process of human reasoning, we propose a theme-aligned dual-hypergraph RAG framework (Cog-RAG) that uses a theme hypergraph to capture inter-chunk thematic structure and an entity hypergraph to model high-order semantic relations. Furthermore, we design a cognitive-inspired two-stage retrieval strategy that first activates query-relevant thematic content from the theme hypergraph, and then guides fine-grained recall and diffusion in the entity hypergraph, achieving semantic alignment and consistent generation from global themes to local details. Our extensive experiments demonstrate that Cog-RAG significantly outperforms existing state-of-the-art baseline approaches.

Convolutional Neural Networks (CNNs) have been the standard for image classification tasks for a long time, but more recently attention-based mechanisms have gained traction. This project aims to compare traditional CNNs with attention-augmented CNNs across an image classification task. By evaluating and comparing their performance, accuracy and computational efficiency, the project will highlight benefits and trade-off of the localized feature extraction of traditional CNNs and the global context capture in attention-augmented CNNs. By doing this, we can reveal further insights into their respective strengths and weaknesses, guide the selection of models based on specific application needs and ultimately, enhance understanding of these architectures in the deep learning community. This was our final project for CS7643 Deep Learning course at Georgia Tech.

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of these neighborhood aggregation methods only consider immediate neighbors, and the performance decreases when going deeper to enable larger receptive fields. Several recent studies attribute this performance deterioration to the over-smoothing issue, which states that repeated propagation makes node representations of different classes indistinguishable. In this work, we study this observation systematically and develop new insights towards deeper graph neural networks. First, we provide a systematical analysis on this issue and argue that the key factor compromising the performance significantly is the entanglement of representation transformation and propagation in current graph convolution operations. After decoupling these two operations, deeper graph neural networks can be used to learn graph node representations from larger receptive fields. We further provide a theoretical analysis of the above observation when building very deep models, which can serve as a rigorous and gentle description of the over-smoothing issue. Based on our theoretical and empirical analysis, we propose Deep Adaptive Graph Neural Network (DAGNN) to adaptively incorporate information from large receptive fields. A set of experiments on citation, co-authorship, and co-purchase datasets have confirmed our analysis and insights and demonstrated the superiority of our proposed methods.

Utilizing pre-trained language models has achieved great success for neural document ranking. Limited by the computational and memory requirements, long document modeling becomes a critical issue. Recent works propose to modify the full attention matrix in Transformer by designing sparse attention patterns. However, most of them only focus on local connections of terms within a fixed-size window. How to build suitable remote connections between terms to better model document representation remains underexplored. In this paper, we propose the model Socialformer, which introduces the characteristics of social networks into designing sparse attention patterns for long document modeling in document ranking. Specifically, we consider several attention patterns to construct a graph like social networks. Endowed with the characteristic of social networks, most pairs of nodes in such a graph can reach with a short path while ensuring the sparsity. To facilitate efficient calculation, we segment the graph into multiple subgraphs to simulate friend circles in social scenarios. Experimental results confirm the effectiveness of our model on long document modeling.

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional 'Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

Graph neural networks (GNNs) have been successfully applied to learning representation on graphs in many relational tasks. Recently, researchers study neural architecture search (NAS) to reduce the dependence of human expertise and explore better GNN architectures, but they over-emphasize entity features and ignore latent relation information concealed in the edges. To solve this problem, we incorporate edge features into graph search space and propose Edge-featured Graph Neural Architecture Search to find the optimal GNN architecture. Specifically, we design rich entity and edge updating operations to learn high-order representations, which convey more generic message passing mechanisms. Moreover, the architecture topology in our search space allows to explore complex feature dependence of both entities and edges, which can be efficiently optimized by differentiable search strategy. Experiments at three graph tasks on six datasets show EGNAS can search better GNNs with higher performance than current state-of-the-art human-designed and searched-based GNNs.

Benefiting from the capability of building inter-dependencies among channels or spatial locations, attention mechanisms have been extensively studied and broadly used in a variety of computer vision tasks recently. In this paper, we investigate light-weight but effective attention mechanisms and present triplet attention, a novel method for computing attention weights by capturing cross-dimension interaction using a three-branch structure. For an input tensor, triplet attention builds inter-dimensional dependencies by the rotation operation followed by residual transformations and encodes inter-channel and spatial information with negligible computational overhead. Our method is simple as well as efficient and can be easily plugged into classic backbone networks as an add-on module. We demonstrate the effectiveness of our method on various challenging tasks including image classification on ImageNet-1k and object detection on MSCOCO and PASCAL VOC datasets. Furthermore, we provide extensive in-sight into the performance of triplet attention by visually inspecting the GradCAM and GradCAM++ results. The empirical evaluation of our method supports our intuition on the importance of capturing dependencies across dimensions when computing attention weights. Code for this paper can be publicly accessed at https://github.com/LandskapeAI/triplet-attention

Retrieval-augmented generation (RAG) has proven effective in integrating knowledge into large language models (LLMs). However, conventional RAGs struggle to capture complex relationships between pieces of knowledge, limiting their performance in intricate reasoning that requires integrating knowledge from multiple sources. Recently, graph-enhanced retrieval augmented generation (GraphRAG) builds graph structure to explicitly model these relationships, enabling more effective and efficient retrievers. Nevertheless, its performance is still hindered by the noise and incompleteness within the graph structure. To address this, we introduce GFM-RAG, a novel graph foundation model (GFM) for retrieval augmented generation. GFM-RAG is powered by an innovative graph neural network that reasons over graph structure to capture complex query-knowledge relationships. The GFM with 8M parameters undergoes a two-stage training process on large-scale datasets, comprising 60 knowledge graphs with over 14M triples and 700k documents. This results in impressive performance and generalizability for GFM-RAG, making it the first graph foundation model applicable to unseen datasets for retrieval without any fine-tuning required. Extensive experiments on three multi-hop QA datasets and seven domain-specific RAG datasets demonstrate that GFM-RAG achieves state-of-the-art performance while maintaining efficiency and alignment with neural scaling laws, highlighting its potential for further improvement.

Retrieval-augmented generation (RAG) empowers large language models to access external and private corpus, enabling factually consistent responses in specific domains. By exploiting the inherent structure of the corpus, graph-based RAG methods further enrich this process by building a knowledge graph index and leveraging the structural nature of graphs. However, current graph-based RAG approaches seldom prioritize the design of graph structures. Inadequately designed graph not only impede the seamless integration of diverse graph algorithms but also result in workflow inconsistencies and degraded performance. To further unleash the potential of graph for RAG, we propose NodeRAG, a graph-centric framework introducing heterogeneous graph structures that enable the seamless and holistic integration of graph-based methodologies into the RAG workflow. By aligning closely with the capabilities of LLMs, this framework ensures a fully cohesive and efficient end-to-end process. Through extensive experiments, we demonstrate that NodeRAG exhibits performance advantages over previous methods, including GraphRAG and LightRAG, not only in indexing time, query time, and storage efficiency but also in delivering superior question-answering performance on multi-hop benchmarks and open-ended head-to-head evaluations with minimal retrieval tokens. Our GitHub repository could be seen at https://github.com/Terry-Xu-666/NodeRAG.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

Humans possess a versatile mechanism for extracting structured representations of our visual world. When looking at an image, we can decompose the scene into entities and their parts as well as obtain the dependencies between them. To mimic such capability, we propose Visual Dependency Transformers (DependencyViT) that can induce visual dependencies without any labels. We achieve that with a novel neural operator called reversed attention that can naturally capture long-range visual dependencies between image patches. Specifically, we formulate it as a dependency graph where a child token in reversed attention is trained to attend to its parent tokens and send information following a normalized probability distribution rather than gathering information in conventional self-attention. With such a design, hierarchies naturally emerge from reversed attention layers, and a dependency tree is progressively induced from leaf nodes to the root node unsupervisedly. DependencyViT offers several appealing benefits. (i) Entities and their parts in an image are represented by different subtrees, enabling part partitioning from dependencies; (ii) Dynamic visual pooling is made possible. The leaf nodes which rarely send messages can be pruned without hindering the model performance, based on which we propose the lightweight DependencyViT-Lite to reduce the computational and memory footprints; (iii) DependencyViT works well on both self- and weakly-supervised pretraining paradigms on ImageNet, and demonstrates its effectiveness on 8 datasets and 5 tasks, such as unsupervised part and saliency segmentation, recognition, and detection.

Heterogeneous graph learning aims to capture complex relationships and diverse relational semantics among entities in a heterogeneous graph to obtain meaningful representations for nodes and edges. Recent advancements in heterogeneous graph neural networks (HGNNs) have achieved state-of-the-art performance by considering relation heterogeneity and using specialized message functions and aggregation rules. However, existing frameworks for heterogeneous graph learning have limitations in generalizing across diverse heterogeneous graph datasets. Most of these frameworks follow the "pre-train" and "fine-tune" paradigm on the same dataset, which restricts their capacity to adapt to new and unseen data. This raises the question: "Can we generalize heterogeneous graph models to be well-adapted to diverse downstream learning tasks with distribution shifts in both node token sets and relation type heterogeneity?'' To tackle those challenges, we propose HiGPT, a general large graph model with Heterogeneous graph instruction-tuning paradigm. Our framework enables learning from arbitrary heterogeneous graphs without the need for any fine-tuning process from downstream datasets. To handle distribution shifts in heterogeneity, we introduce an in-context heterogeneous graph tokenizer that captures semantic relationships in different heterogeneous graphs, facilitating model adaptation. We incorporate a large corpus of heterogeneity-aware graph instructions into our HiGPT, enabling the model to effectively comprehend complex relation heterogeneity and distinguish between various types of graph tokens. Furthermore, we introduce the Mixture-of-Thought (MoT) instruction augmentation paradigm to mitigate data scarcity by generating diverse and informative instructions. Through comprehensive evaluations, our proposed framework demonstrates exceptional performance in terms of generalization performance.

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.

Large Language Models (LLMs) face efficiency bottlenecks due to the quadratic complexity of the attention mechanism when processing long contexts. Sparse attention methods offer a promising solution, but existing approaches often suffer from incomplete effective context and/or require complex implementation of pipeline. We present a comprehensive analysis of sparse attention for autoregressive LLMs from the respective of receptive field, recognize the suboptimal nature of existing methods for expanding the receptive field, and introduce PowerAttention, a novel sparse attention design that facilitates effective and complete context extension through the theoretical analysis. PowerAttention achieves exponential receptive field growth in d-layer LLMs, allowing each output token to attend to 2^d tokens, ensuring completeness and continuity of the receptive field. Experiments demonstrate that PowerAttention outperforms existing static sparse attention methods by 5sim 40%, especially on tasks demanding long-range dependencies like Passkey Retrieval and RULER, while maintaining a comparable time complexity to sliding window attention. Efficiency evaluations further highlight PowerAttention's superior speedup in both prefilling and decoding phases compared with dynamic sparse attentions and full attention (3.0times faster on 128K context), making it a highly effective and user-friendly solution for processing long sequences in LLMs.

Feature-based image matching has extensive applications in computer vision. Keypoints detected in images can be naturally represented as graph structures, and Graph Neural Networks (GNNs) have been shown to outperform traditional deep learning techniques. Consequently, the paradigm of image matching via GNNs has gained significant prominence in recent academic research. In this paper, we first introduce an innovative adaptive graph construction method that utilizes a filtering mechanism based on distance and dynamic threshold similarity. This method dynamically adjusts the criteria for incorporating new vertices based on the characteristics of existing vertices, allowing for the construction of more precise and robust graph structures while avoiding redundancy. We further combine the vertex processing capabilities of GNNs with the global awareness capabilities of Transformers to enhance the model's representation of spatial and feature information within graph structures. This hybrid model provides a deeper understanding of the interrelationships between vertices and their contributions to the matching process. Additionally, we employ the Sinkhorn algorithm to iteratively solve for optimal matching results. Finally, we validate our system using extensive image datasets and conduct comprehensive comparative experiments. Experimental results demonstrate that our system achieves an average improvement of 3.8x-40.3x in overall matching performance. Additionally, the number of vertices and edges significantly impacts training efficiency and memory usage; therefore, we employ multi-GPU technology to accelerate the training process. Our code is available at https://github.com/songxf1024/GIMS.

Recent advancements in large language models (LLMs) have shown impressive versatility across various tasks. To eliminate its hallucinations, retrieval-augmented generation (RAG) has emerged as a powerful approach, leveraging external knowledge sources like knowledge graphs (KGs). In this paper, we study the task of KG-driven RAG and propose a novel Similar Graph Enhanced Retrieval-Augmented Generation (SimGRAG) method. It effectively addresses the challenge of aligning query texts and KG structures through a two-stage process: (1) query-to-pattern, which uses an LLM to transform queries into a desired graph pattern, and (2) pattern-to-subgraph, which quantifies the alignment between the pattern and candidate subgraphs using a graph semantic distance (GSD) metric. We also develop an optimized retrieval algorithm that efficiently identifies the top-k subgraphs within 1-second latency on a 10-million-scale KG. Extensive experiments show that SimGRAG outperforms state-of-the-art KG-driven RAG methods in both question answering and fact verification, offering superior plug-and-play usability and scalability.

TabPFN v2 achieves better results than tree-based models on several tabular benchmarks, which is notable since tree-based models are usually the strongest choice for tabular data. However, it cannot handle more than 10K context tokens because transformers have quadratic computation and memory costs. Unlike existing approaches that rely on context compression, such as selecting representative samples via K-nearest neighbors (KNN), we introduce a tiled-block strategy to compute attention within the TabPFN framework. This design is compatible with standard GPU setups and, to the best of our knowledge, is the first to enable TabPFN to process long contexts without any pre-processing. We demonstrate the effectiveness of our approach on the standard TabArena benchmark.

Neural attention has become central to many state-of-the-art models in natural language processing and related domains. Attention networks are an easy-to-train and effective method for softly simulating alignment; however, the approach does not marginalize over latent alignments in a probabilistic sense. This property makes it difficult to compare attention to other alignment approaches, to compose it with probabilistic models, and to perform posterior inference conditioned on observed data. A related latent approach, hard attention, fixes these issues, but is generally harder to train and less accurate. This work considers variational attention networks, alternatives to soft and hard attention for learning latent variable alignment models, with tighter approximation bounds based on amortized variational inference. We further propose methods for reducing the variance of gradients to make these approaches computationally feasible. Experiments show that for machine translation and visual question answering, inefficient exact latent variable models outperform standard neural attention, but these gains go away when using hard attention based training. On the other hand, variational attention retains most of the performance gain but with training speed comparable to neural attention.

We explore different ways to utilize position-based cross-attention in seq2seq networks to enable length generalization in algorithmic tasks. We show that a simple approach of interpolating the original and reversed encoded representations combined with relative attention allows near-perfect length generalization for both forward and reverse lookup tasks or copy tasks that had been generally hard to tackle. We also devise harder diagnostic tasks where the relative distance of the ideal attention position varies with timestep. In such settings, the simple interpolation trick with relative attention is not sufficient. We introduce novel variants of location attention building on top of Dubois et al. (2020) to address the new diagnostic tasks. We also show the benefits of our approaches for length generalization in SCAN (Lake & Baroni, 2018) and CFQ (Keysers et al., 2020). Our code is available on GitHub.

Motivated by the factorization inherent in the original fast multipole method and the improved fast Gauss transform we introduce a factorable form of attention that operates efficiently in high dimensions. This approach reduces the computational and memory complexity of the attention mechanism in transformers from O(N^2) to O(N). In comparison to previous attempts, our work presents a linearly scaled attention mechanism that maintains the full representation of the attention matrix without compromising on sparsification and incorporates the all-to-all relationship between tokens. We explore the properties of our new attention metric and conduct tests in various standard settings. Results indicate that our attention mechanism has a robust performance and holds significant promise for diverse applications where self-attention is used.

We introduce Block-Attention, an attention mechanism designed to address the increased inference latency and cost in Retrieval-Augmented Generation (RAG) scenarios. Traditional approaches often encode the entire context. Instead, Block-Attention divides retrieved documents into discrete blocks, with each block independently calculating key-value (KV) states except for the final block. In RAG scenarios, by defining each passage as a block, Block-Attention enables us to reuse the KV states of passages that have been seen before, thereby significantly reducing the latency and the computation overhead during inference. The implementation of Block-Attention involves block segmentation, position re-encoding, and fine-tuning the LLM to adapt to the Block-Attention mechanism. Experiments on four RAG benchmarks demonstrate that after block fine-tuning, the Block-Attention model achieves performance comparable to self-attention models (68.4\% vs 67.9\% on Llama3) or even superior performance (62.8\% vs 59.6\% on Mistral). Notably, Block-Attention significantly reduces the time to first token (TTFT) and floating point operations (FLOPs) to a very low level. It only takes 45 ms to output the first token for an input sequence with a total length of 32K. Compared to the self-attention models, the time consumption and corresponding FLOPs are reduced by 98.7\% and 99.8\%, respectively.

Although attention mechanisms have been applied to a variety of deep learning models and have been shown to improve the prediction performance, it has been reported to be vulnerable to perturbations to the mechanism. To overcome the vulnerability to perturbations in the mechanism, we are inspired by adversarial training (AT), which is a powerful regularization technique for enhancing the robustness of the models. In this paper, we propose a general training technique for natural language processing tasks, including AT for attention (Attention AT) and more interpretable AT for attention (Attention iAT). The proposed techniques improved the prediction performance and the model interpretability by exploiting the mechanisms with AT. In particular, Attention iAT boosts those advantages by introducing adversarial perturbation, which enhances the difference in the attention of the sentences. Evaluation experiments with ten open datasets revealed that AT for attention mechanisms, especially Attention iAT, demonstrated (1) the best performance in nine out of ten tasks and (2) more interpretable attention (i.e., the resulting attention correlated more strongly with gradient-based word importance) for all tasks. Additionally, the proposed techniques are (3) much less dependent on perturbation size in AT. Our code is available at https://github.com/shunk031/attention-meets-perturbation

Recently, Retrieval-Augmented Generation (RAG) has achieved remarkable success in addressing the challenges of Large Language Models (LLMs) without necessitating retraining. By referencing an external knowledge base, RAG refines LLM outputs, effectively mitigating issues such as ``hallucination'', lack of domain-specific knowledge, and outdated information. However, the complex structure of relationships among different entities in databases presents challenges for RAG systems. In response, GraphRAG leverages structural information across entities to enable more precise and comprehensive retrieval, capturing relational knowledge and facilitating more accurate, context-aware responses. Given the novelty and potential of GraphRAG, a systematic review of current technologies is imperative. This paper provides the first comprehensive overview of GraphRAG methodologies. We formalize the GraphRAG workflow, encompassing Graph-Based Indexing, Graph-Guided Retrieval, and Graph-Enhanced Generation. We then outline the core technologies and training methods at each stage. Additionally, we examine downstream tasks, application domains, evaluation methodologies, and industrial use cases of GraphRAG. Finally, we explore future research directions to inspire further inquiries and advance progress in the field.

Text-guided image editing aims to modify specific regions of an image according to natural language instructions while maintaining the general structure and the background fidelity. Existing methods utilize masks derived from cross-attention maps generated from diffusion models to identify the target regions for modification. However, since cross-attention mechanisms focus on semantic relevance, they struggle to maintain the image integrity. As a result, these methods often lack spatial consistency, leading to editing artifacts and distortions. In this work, we address these limitations and introduce LOCATEdit, which enhances cross-attention maps through a graph-based approach utilizing self-attention-derived patch relationships to maintain smooth, coherent attention across image regions, ensuring that alterations are limited to the designated items while retaining the surrounding structure. \method consistently and substantially outperforms existing baselines on PIE-Bench, demonstrating its state-of-the-art performance and effectiveness on various editing tasks. Code can be found on https://github.com/LOCATEdit/LOCATEdit/

The heterogeneous network is a robust data abstraction that can model entities of different types interacting in various ways. Such heterogeneity brings rich semantic information but presents nontrivial challenges in aggregating the heterogeneous relationships between objects - especially those of higher-order indirect relations. Recent graph neural network approaches for representation learning on heterogeneous networks typically employ the attention mechanism, which is often only optimized for predictions based on direct links. Furthermore, even though most deep learning methods can aggregate higher-order information by building deeper models, such a scheme can diminish the degree of interpretability. To overcome these challenges, we explore an architecture - Layer-stacked ATTention Embedding (LATTE) - that automatically decomposes higher-order meta relations at each layer to extract the relevant heterogeneous neighborhood structures for each node. Additionally, by successively stacking layer representations, the learned node embedding offers a more interpretable aggregation scheme for nodes of different types at different neighborhood ranges. We conducted experiments on several benchmark heterogeneous network datasets. In both transductive and inductive node classification tasks, LATTE can achieve state-of-the-art performance compared to existing approaches, all while offering a lightweight model. With extensive experimental analyses and visualizations, the framework can demonstrate the ability to extract informative insights on heterogeneous networks.

Although graph-based learning has attracted a lot of attention, graph representation learning is still a challenging task whose resolution may impact key application fields such as chemistry or biology. To this end, we introduce GRALE, a novel graph autoencoder that encodes and decodes graphs of varying sizes into a shared embedding space. GRALE is trained using an Optimal Transport-inspired loss that compares the original and reconstructed graphs and leverages a differentiable node matching module, which is trained jointly with the encoder and decoder. The proposed attention-based architecture relies on Evoformer, the core component of AlphaFold, which we extend to support both graph encoding and decoding. We show, in numerical experiments on simulated and molecular data, that GRALE enables a highly general form of pre-training, applicable to a wide range of downstream tasks, from classification and regression to more complex tasks such as graph interpolation, editing, matching, and prediction.

Answer grounding is the task of locating relevant visual evidence for the Visual Question Answering task. While a wide variety of attention methods have been introduced for this task, they suffer from the following three problems: designs that do not allow the usage of pre-trained networks and do not benefit from large data pre-training, custom designs that are not based on well-grounded previous designs, therefore limiting the learning power of the network, or complicated designs that make it challenging to re-implement or improve them. In this paper, we propose a novel architectural block, which we term Sentence Attention Block, to solve these problems. The proposed block re-calibrates channel-wise image feature-maps by explicitly modeling inter-dependencies between the image feature-maps and sentence embedding. We visually demonstrate how this block filters out irrelevant feature-maps channels based on sentence embedding. We start our design with a well-known attention method, and by making minor modifications, we improve the results to achieve state-of-the-art accuracy. The flexibility of our method makes it easy to use different pre-trained backbone networks, and its simplicity makes it easy to understand and be re-implemented. We demonstrate the effectiveness of our method on the TextVQA-X, VQS, VQA-X, and VizWiz-VQA-Grounding datasets. We perform multiple ablation studies to show the effectiveness of our design choices.

Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined "LLMs-as-Consultants," which integrates LLMs with GNNs in an interactive manner. A framework named LOGIN (LLM Consulted GNN training) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of LOGIN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at https://github.com/QiaoYRan/LOGIN.

This paper builds off recent work from Kiperwasser & Goldberg (2016) using neural attention in a simple graph-based dependency parser. We use a larger but more thoroughly regularized parser than other recent BiLSTM-based approaches, with biaffine classifiers to predict arcs and labels. Our parser gets state of the art or near state of the art performance on standard treebanks for six different languages, achieving 95.7% UAS and 94.1% LAS on the most popular English PTB dataset. This makes it the highest-performing graph-based parser on this benchmark---outperforming Kiperwasser Goldberg (2016) by 1.8% and 2.2%---and comparable to the highest performing transition-based parser (Kuncoro et al., 2016), which achieves 95.8% UAS and 94.6% LAS. We also show which hyperparameter choices had a significant effect on parsing accuracy, allowing us to achieve large gains over other graph-based approaches.

We present Lightning Attention, the first linear attention implementation that maintains a constant training speed for various sequence lengths under fixed memory consumption. Due to the issue with cumulative summation operations (cumsum), previous linear attention implementations cannot achieve their theoretical advantage in a casual setting. However, this issue can be effectively solved by utilizing different attention calculation strategies to compute the different parts of attention. Specifically, we split the attention calculation into intra-blocks and inter-blocks and use conventional attention computation for intra-blocks and linear attention kernel tricks for inter-blocks. This eliminates the need for cumsum in the linear attention calculation. Furthermore, a tiling technique is adopted through both forward and backward procedures to take full advantage of the GPU hardware. To enhance accuracy while preserving efficacy, we introduce TransNormerLLM (TNL), a new architecture that is tailored to our lightning attention. We conduct rigorous testing on standard and self-collected datasets with varying model sizes and sequence lengths. TNL is notably more efficient than other language models. In addition, benchmark results indicate that TNL performs on par with state-of-the-art LLMs utilizing conventional transformer structures. The source code is released at github.com/OpenNLPLab/TransnormerLLM.

We propose the Multi-Head Gaussian Adaptive Attention Mechanism (GAAM), a novel probabilistic attention framework, and the Gaussian Adaptive Transformer (GAT), designed to enhance information aggregation across multiple modalities, including Speech, Text and Vision. GAAM integrates learnable mean and variance into its attention mechanism, implemented in a Multi-Headed framework enabling it to collectively model any Probability Distribution for dynamic recalibration of feature significance. This method demonstrates significant improvements, especially with highly non-stationary data, surpassing the state-of-the-art attention techniques in model performance (up to approximately +20% in accuracy) by identifying key elements within the feature space. GAAM's compatibility with dot-product-based attention models and relatively low number of parameters showcases its adaptability and potential to boost existing attention frameworks. Empirically, GAAM exhibits superior adaptability and efficacy across a diverse range of tasks, including emotion recognition in speech, image classification, and text classification, thereby establishing its robustness and versatility in handling multi-modal data. Furthermore, we introduce the Importance Factor (IF), a new learning-based metric that enhances the explainability of models trained with GAAM-based methods. Overall, GAAM represents an advancement towards development of better performing and more explainable attention models across multiple modalities.

The performance of Large Language Models (LLMs) is significantly sensitive to the contextual position of information in the input. To investigate the mechanism behind this positional bias, our extensive experiments reveal a consistent phenomenon we term the attention basin: when presented with a sequence of structured items (e.g., retrieved documents or few-shot examples), models systematically assign higher attention to the items at the beginning and end of the sequence, while neglecting those in the middle. Crucially, our analysis further reveals that allocating higher attention to critical information is key to enhancing model performance. Based on these insights, we introduce Attention-Driven Reranking (AttnRank), a two-stage framework that (i) estimates a model's intrinsic positional attention preferences using a small calibration set, and (ii) reorders retrieved documents or few-shot examples to align the most salient content with these high-attention positions. AttnRank is a model-agnostic, training-free, and plug-and-play method with minimal computational overhead. Experiments on multi-hop QA and few-shot in-context learning tasks demonstrate that AttnRank achieves substantial improvements across 10 large language models of varying architectures and scales, without modifying model parameters or training procedures.

The Softmax attention mechanism in Transformer models is notoriously computationally expensive, particularly due to its quadratic complexity, posing significant challenges in vision applications. In contrast, linear attention provides a far more efficient solution by reducing the complexity to linear levels. However, compared to Softmax attention, linear attention often experiences significant performance degradation. Our experiments indicate that this performance drop is due to the low-rank nature of linear attention's feature map, which hinders its ability to adequately model complex spatial information. In this paper, to break the low-rank dilemma of linear attention, we conduct rank analysis from two perspectives: the KV buffer and the output features. Consequently, we introduce Rank-Augmented Linear Attention (RALA), which rivals the performance of Softmax attention while maintaining linear complexity and high efficiency. Based on RALA, we construct the Rank-Augmented Vision Linear Transformer (RAVLT). Extensive experiments demonstrate that RAVLT achieves excellent performance across various vision tasks. Specifically, without using any additional labels, data, or supervision during training, RAVLT achieves an 84.4% Top-1 accuracy on ImageNet-1k with only 26M parameters and 4.6G FLOPs. This result significantly surpasses previous linear attention mechanisms, fully illustrating the potential of RALA. Code will be available at https://github.com/qhfan/RALA.

We propose a novel attention mechanism, named Cog Attention, that enables attention weights to be negative for enhanced expressiveness, which stems from two key factors: (1) Cog Attention can shift the token deletion and copying function from a static OV matrix to dynamic QK inner products, with the OV matrix now focusing more on refinement or modification. The attention head can simultaneously delete, copy, or retain tokens by assigning them negative, positive, or minimal attention weights, respectively. As a result, a single attention head becomes more flexible and expressive. (2) Cog Attention improves the model's robustness against representational collapse, which can occur when earlier tokens are over-squashed into later positions, leading to homogeneous representations. Negative weights reduce effective information paths from earlier to later tokens, helping to mitigate this issue. We develop Transformer-like models which use Cog Attention as attention modules, including decoder-only models for language modeling and U-ViT diffusion models for image generation. Experiments show that models using Cog Attention exhibit superior performance compared to those employing traditional softmax attention modules. Our approach suggests a promising research direction for rethinking and breaking the entrenched constraints of traditional softmax attention, such as the requirement for non-negative weights.

Attention matrices are fundamental to transformer research, supporting a broad range of applications including interpretability, visualization, manipulation, and distillation. Yet, most existing analyses focus on individual attention heads or layers, failing to account for the model's global behavior. While prior efforts have extended attention formulations across multiple heads via averaging and matrix multiplications or incorporated components such as normalization and FFNs, a unified and complete representation that encapsulates all transformer blocks is still lacking. We address this gap by introducing TensorLens, a novel formulation that captures the entire transformer as a single, input-dependent linear operator expressed through a high-order attention-interaction tensor. This tensor jointly encodes attention, FFNs, activations, normalizations, and residual connections, offering a theoretically coherent and expressive linear representation of the model's computation. TensorLens is theoretically grounded and our empirical validation shows that it yields richer representations than previous attention-aggregation methods. Our experiments demonstrate that the attention tensor can serve as a powerful foundation for developing tools aimed at interpretability and model understanding. Our code is attached as a supplementary.

Long-document QA presents challenges with large-scale text and long-distance dependencies. Recent advances in Large Language Models (LLMs) enable entire documents to be processed in a single pass. However, their computational cost is significantly high. Retrieval-Augmented Generation (RAG) methods split text into smaller chunks, but they often yield inferior results and may lose global context. Recent approaches that integrate LLMs into RAG via iterative summarization either underutilize LLM capabilities or still incur high computational costs. In this paper, we combine the high accuracy of LLMs with the efficiency of RAG and propose LLM-Guided Dynamic Progress Control with Attention-Based Hierarchical Weighted Graph (PECAN). Our method introduces two key improvements: (1) LLM-Guided Dynamic Progress Control: We leverage LLMs to dynamically control the retrieval process, adjusting the amount of retrieved information based on different queries to achieve a better balance of effectiveness and efficiency. (2) Attention-Guided Retrieval: We propose a novel retrieval method that constructs a hierarchical graph where edges are derived by LLM attention weights. Experimental results demonstrate that PECAN achieves LLM-level performance while maintaining computational complexity comparable to that of RAG methods on two single-document and two multi-document QA datasets.

Cross Attention is a popular method for retrieving information from a set of context tokens for making predictions. At inference time, for each prediction, Cross Attention scans the full set of O(N) tokens. In practice, however, often only a small subset of tokens are required for good performance. Methods such as Perceiver IO are cheap at inference as they distill the information to a smaller-sized set of latent tokens L < N on which cross attention is then applied, resulting in only O(L) complexity. However, in practice, as the number of input tokens and the amount of information to distill increases, the number of latent tokens needed also increases significantly. In this work, we propose Tree Cross Attention (TCA) - a module based on Cross Attention that only retrieves information from a logarithmic O(log(N)) number of tokens for performing inference. TCA organizes the data in a tree structure and performs a tree search at inference time to retrieve the relevant tokens for prediction. Leveraging TCA, we introduce ReTreever, a flexible architecture for token-efficient inference. We show empirically that Tree Cross Attention (TCA) performs comparable to Cross Attention across various classification and uncertainty regression tasks while being significantly more token-efficient. Furthermore, we compare ReTreever against Perceiver IO, showing significant gains while using the same number of tokens for inference.

Vision-Language Models (VLMs) have demonstrated remarkable success across diverse visual tasks, yet their performance degrades in complex visual environments. While existing enhancement approaches require additional training, rely on external segmentation tools, or operate at coarse-grained levels, they overlook the innate ability within VLMs. To bridge this gap, we investigate VLMs' attention patterns and discover that: (1) visual complexity strongly correlates with attention entropy, negatively impacting reasoning performance; (2) attention progressively refines from global scanning in shallow layers to focused convergence in deeper layers, with convergence degree determined by visual complexity. (3) Theoretically, we prove that the contrast of attention maps between general queries and task-specific queries enables the decomposition of visual signal into semantic signals and visual noise components. Building on these insights, we propose Contrastive Attention Refinement for Visual Enhancement (CARVE), a training-free method that extracts task-relevant visual signals through attention contrasting at the pixel level. Extensive experiments demonstrate that CARVE consistently enhances performance, achieving up to 75% improvement on open-source models. Our work provides critical insights into the interplay between visual complexity and attention mechanisms, offering an efficient pathway for improving visual reasoning with contrasting attention.

Retrieval-Augmented Generation (RAG) mitigates hallucination in LLMs by incorporating external knowledge, but relies on chunk-based retrieval that lacks structural semantics. GraphRAG methods improve RAG by modeling knowledge as entity-relation graphs, but still face challenges in high construction cost, fixed one-time retrieval, and reliance on long-context reasoning and prompt design. To address these challenges, we propose Graph-R1, an agentic GraphRAG framework via end-to-end reinforcement learning (RL). It introduces lightweight knowledge hypergraph construction, models retrieval as a multi-turn agent-environment interaction, and optimizes the agent process via an end-to-end reward mechanism. Experiments on standard RAG datasets show that Graph-R1 outperforms traditional GraphRAG and RL-enhanced RAG methods in reasoning accuracy, retrieval efficiency, and generation quality.

Language Models (LMs) are increasingly challenging the dominance of domain-specific models, including Graph Neural Networks (GNNs) and Graph Transformers (GTs), in graph learning tasks. Following this trend, we propose a novel approach that empowers off-the-shelf LMs to achieve performance comparable to state-of-the-art GNNs on node classification tasks, without requiring any architectural modification. By preserving the LM's original architecture, our approach retains a key benefit of LM instruction tuning: the ability to jointly train on diverse datasets, fostering greater flexibility and efficiency. To achieve this, we introduce two key augmentation strategies: (1) Enriching LMs' input using topological and semantic retrieval methods, which provide richer contextual information, and (2) guiding the LMs' classification process through a lightweight GNN classifier that effectively prunes class candidates. Our experiments on real-world datasets show that backbone Flan-T5 models equipped with these augmentation strategies outperform state-of-the-art text-output node classifiers and are comparable to top-performing vector-output node classifiers. By bridging the gap between specialized task-specific node classifiers and general LMs, this work paves the way for more versatile and widely applicable graph learning models. We will open-source the code upon publication.

Recent studies show that graph neural networks (GNNs) are prevalent to model high-order relationships for collaborative filtering (CF). Towards this research line, graph contrastive learning (GCL) has exhibited powerful performance in addressing the supervision label shortage issue by learning augmented user and item representations. While many of them show their effectiveness, two key questions still remain unexplored: i) Most existing GCL-based CF models are still limited by ignoring the fact that user-item interaction behaviors are often driven by diverse latent intent factors (e.g., shopping for family party, preferred color or brand of products); ii) Their introduced non-adaptive augmentation techniques are vulnerable to noisy information, which raises concerns about the model's robustness and the risk of incorporating misleading self-supervised signals. In light of these limitations, we propose a Disentangled Contrastive Collaborative Filtering framework (DCCF) to realize intent disentanglement with self-supervised augmentation in an adaptive fashion. With the learned disentangled representations with global context, our DCCF is able to not only distill finer-grained latent factors from the entangled self-supervision signals but also alleviate the augmentation-induced noise. Finally, the cross-view contrastive learning task is introduced to enable adaptive augmentation with our parameterized interaction mask generator. Experiments on various public datasets demonstrate the superiority of our method compared to existing solutions. Our model implementation is released at the link https://github.com/HKUDS/DCCF.

Graph-based Retrieval-Augmented Generation (RAG) has proven effective in integrating external knowledge into large language models (LLMs), improving their factual accuracy, adaptability, interpretability, and trustworthiness. A number of graph-based RAG methods have been proposed in the literature. However, these methods have not been systematically and comprehensively compared under the same experimental settings. In this paper, we first summarize a unified framework to incorporate all graph-based RAG methods from a high-level perspective. We then extensively compare representative graph-based RAG methods over a range of questing-answering (QA) datasets -- from specific questions to abstract questions -- and examine the effectiveness of all methods, providing a thorough analysis of graph-based RAG approaches. As a byproduct of our experimental analysis, we are also able to identify new variants of the graph-based RAG methods over specific QA and abstract QA tasks respectively, by combining existing techniques, which outperform the state-of-the-art methods. Finally, based on these findings, we offer promising research opportunities. We believe that a deeper understanding of the behavior of existing methods can provide new valuable insights for future research.