Daily Papers

Weather forecasting offers an ideal testbed for artificial intelligence (AI) to learn complex, multi-scale physical systems. Traditional numerical weather prediction remains computationally costly for frequent regional updates, as high-resolution nests require intensive boundary coupling. We introduce Multi-Resolution Graph Neural Forecasting (MR-GNF), a lightweight, physics-aware model that performs short-term regional forecasts directly on an ellipsoidal, multi-scale graph of the Earth. The framework couples a 0.25° region of interest with a 0.5° context belt and 1.0° outer domain, enabling continuous cross-scale message passing without explicit nested boundaries. Its axial graph-attention network alternates vertical self-attention across pressure levels with horizontal graph attention across surface nodes, capturing implicit 3-D structure in just 1.6 M parameters. Trained on 40 years of ERA5 reanalysis (1980-2024), MR-GNF delivers stable +6 h to +24 h forecasts for near-surface temperature, wind, and precipitation over the UK-Ireland sector. Despite a total compute cost below 80 GPU-hours on a single RTX 6000 Ada, the model matches or exceeds heavier regional AI systems while preserving physical consistency across scales. These results demonstrate that graph-based neural operators can achieve trustworthy, high-resolution weather prediction at a fraction of NWP cost, opening a practical path toward AI-driven early-warning and renewable-energy forecasting systems. Project page and code: https://github.com/AndriiShchur/MR-GNF

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}

Graph Language Models (GLMs) have become a promising direction for adapting Large Language Models (LLMs) to graph learning tasks. By transforming graph topology and node information into graph tokens, GLMs allow LLMs to jointly process structured graph inputs and textual instructions. Yet, it remains unclear how LLMs internally interpret these graph tokens and whether graph tokens act as meaningful carriers of graph structure. In this work, we analyze how LLMs process graph information through graph-token behavior in representative GLM architectures. Findings. We find that the internal saliency of graph tokens in GLMs is not equivalent to graph information utilization. Graph sink tokens consistently emerge as activation-level outliers: they can be identified by massive activation values along a small set of hidden-state dimensions and are biased toward early graph-token positions. However, this activation-level saliency does not imply that these tokens are the main carriers of graph information. Unlike classical attention sinks in language and vision-language models, graph sink tokens do not necessarily attract the largest attention weights from query tokens. Through pruning, repositioning, and swapping interventions, we show that graph sink tokens are not the most important semantic or structural tokens for downstream prediction. Implications. Together, these results suggest that after current GLMs map graph structure into the LLM token space, the resulting graph-token representations do not naturally form a fully usable topology-aware internal representation; instead, they exhibit a decoupling between activation-level saliency and graph-semantic utility. This decoupling points to limitations in existing graph-token construction, placement, and alignment mechanisms.

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.

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.

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.

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.

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.

We study the extent to which rotary position encodings (RoPE), a recent transformer position encoding algorithm broadly adopted in large language models (LLMs) and vision transformers (ViTs), can be applied to graph-structured data. We find that rotating tokens depending on the spectrum of the graph Laplacian efficiently injects structural information into the attention mechanism, boosting performance in synthetic and real-world graph learning tasks. This approach, coined _Wave-Induced Rotary Encodings_ (WIRE), enjoys intriguing theoretical properties: it recovers regular RoPE on grids, and depends asymptotically on the graph effective resistance. Unlike bias-based relative position encodings, WIRE is compatible with linear attention.

Recent advances in search-augmented large reasoning models (LRMs) enable the retrieval of external knowledge to reduce hallucinations in multistep reasoning. However, their ability to operate on graph-structured data, prevalent in domains such as e-commerce, social networks, and scientific citations, remains underexplored. Unlike plain text corpora, graphs encode rich topological signals that connect related entities and can serve as valuable priors for retrieval, enabling more targeted search and improved reasoning efficiency. Yet, effectively leveraging such structure poses unique challenges, including the difficulty of generating graph-expressive queries and ensuring reliable retrieval that balances structural and semantic relevance. To address this gap, we introduce GraphSearch, the first framework that extends search-augmented reasoning to graph learning, enabling zero-shot graph learning without task-specific fine-tuning. GraphSearch combines a Graph-aware Query Planner, which disentangles search space (e.g., 1-hop, multi-hop, or global neighbors) from semantic queries, with a Graph-aware Retriever, which constructs candidate sets based on topology and ranks them using a hybrid scoring function. We further instantiate two traversal modes: GraphSearch-R, which recursively expands neighborhoods hop by hop, and GraphSearch-F, which flexibly retrieves across local and global neighborhoods without hop constraints. Extensive experiments across diverse benchmarks show that GraphSearch achieves competitive or even superior performance compared to supervised graph learning methods, setting state-of-the-art results in zero-shot node classification and link prediction. These findings position GraphSearch as a flexible and generalizable paradigm for agentic reasoning over graphs.

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

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

Interpretable graph learning is in need as many scientific applications depend on learning models to collect insights from graph-structured data. Previous works mostly focused on using post-hoc approaches to interpret pre-trained models (graph neural networks in particular). They argue against inherently interpretable models because the good interpretability of these models is often at the cost of their prediction accuracy. However, those post-hoc methods often fail to provide stable interpretation and may extract features that are spuriously correlated with the task. In this work, we address these issues by proposing Graph Stochastic Attention (GSAT). Derived from the information bottleneck principle, GSAT injects stochasticity to the attention weights to block the information from task-irrelevant graph components while learning stochasticity-reduced attention to select task-relevant subgraphs for interpretation. The selected subgraphs provably do not contain patterns that are spuriously correlated with the task under some assumptions. Extensive experiments on eight datasets show that GSAT outperforms the state-of-the-art methods by up to 20%uparrow in interpretation AUC and 5%uparrow in prediction accuracy. Our code is available at https://github.com/Graph-COM/GSAT.

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}

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.

Graph Neural Networks operate through bottom-up message-passing, fundamentally differing from human visual perception, which intuitively captures global structures first. We investigate the underappreciated potential of vision models for graph understanding, finding they achieve performance comparable to GNNs on established benchmarks while exhibiting distinctly different learning patterns. These divergent behaviors, combined with limitations of existing benchmarks that conflate domain features with topological understanding, motivate our introduction of GraphAbstract. This benchmark evaluates models' ability to perceive global graph properties as humans do: recognizing organizational archetypes, detecting symmetry, sensing connectivity strength, and identifying critical elements. Our results reveal that vision models significantly outperform GNNs on tasks requiring holistic structural understanding and maintain generalizability across varying graph scales, while GNNs struggle with global pattern abstraction and degrade with increasing graph size. This work demonstrates that vision models possess remarkable yet underutilized capabilities for graph structural understanding, particularly for problems requiring global topological awareness and scale-invariant reasoning. These findings open new avenues to leverage this underappreciated potential for developing more effective graph foundation models for tasks dominated by holistic pattern recognition.

Text-attributed graphs integrate semantic information of node texts with topological structure, offering significant value in various applications such as document classification and information extraction. Existing approaches typically encode textual content using language models (LMs), followed by graph neural networks (GNNs) to process structural information. However, during the LM-based text encoding phase, most methods not only perform semantic interaction solely at the word-token granularity, but also neglect the structural dependencies among texts from different nodes. In this work, we propose DuConTE, a dual-granularity text encoder with topology-constrained attention. The model employs a cascaded architecture of two pretrained LMs, encoding semantics first at the word-token granularity and then at the node granularity. During the self-attention computation in each LM, we dynamically adjust the attention mask matrix based on node connectivity, guiding the model to learn semantic correlations informed by the graph structure. Furthermore, when composing node representations from word-token embeddings, we separately evaluate the importance of tokens under the center-node context and the neighborhood context, enabling the capture of more contextually relevant semantic information. Extensive experiments on multiple benchmark datasets demonstrate that DuConTE achieves state-of-the-art performance on the majority of them.

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.

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.

This study aimed to leverage graph information, particularly Rhetorical Structure Theory (RST) and Co-reference (Coref) graphs, to enhance the performance of our baseline summarization models. Specifically, we experimented with a Graph Attention Network architecture to incorporate graph information. However, this architecture did not enhance the performance. Subsequently, we used a simple Multi-layer Perceptron architecture, which improved the results in our proposed model on our primary dataset, CNN/DM. Additionally, we annotated XSum dataset with RST graph information, establishing a benchmark for future graph-based summarization models. This secondary dataset posed multiple challenges, revealing both the merits and limitations of our models.

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 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).

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.

Graph is powerful for representing various types of real-world data. The topology (edges' presence) and edges' features of a graph decides the message passing mechanism among vertices within the graph. While most existing approaches only manually define a single-value edge to describe the connectivity or strength of association between a pair of vertices, task-specific and crucial relationship cues may be disregarded by such manually defined topology and single-value edge features. In this paper, we propose the first general graph representation learning framework (called GRATIS) which can generate a strong graph representation with a task-specific topology and task-specific multi-dimensional edge features from any arbitrary input. To learn each edge's presence and multi-dimensional feature, our framework takes both of the corresponding vertices pair and their global contextual information into consideration, enabling the generated graph representation to have a globally optimal message passing mechanism for different down-stream tasks. The principled investigation results achieved for various graph analysis tasks on 11 graph and non-graph datasets show that our GRATIS can not only largely enhance pre-defined graphs but also learns a strong graph representation for non-graph data, with clear performance improvements on all tasks. In particular, the learned topology and multi-dimensional edge features provide complementary task-related cues for graph analysis tasks. Our framework is effective, robust and flexible, and is a plug-and-play module that can be combined with different backbones and Graph Neural Networks (GNNs) to generate a task-specific graph representation from various graph and non-graph data. Our code is made publicly available at https://github.com/SSYSteve/Learning-Graph-Representation-with-Task-specific-Topology-and-Multi-dimensional-Edge-Features.

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.

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.

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.

Visual recognition relies on understanding both the semantics of image tokens and the complex interactions among them. Mainstream self-attention methods, while effective at modeling global pair-wise relations, fail to capture high-order associations inherent in real-world scenes and often suffer from redundant computation. Hypergraphs extend conventional graphs by modeling high-order interactions and offer a promising framework for addressing these limitations. However, existing hypergraph neural networks typically rely on static and hard hyperedge assignments, leading to excessive and redundant hyperedges with hard binary vertex memberships that overlook the continuity of visual semantics. To overcome these issues, we present Soft Hypergraph Neural Networks (SoftHGNNs), which extend the methodology of hypergraph computation, to make it truly efficient and versatile in visual recognition tasks. Our framework introduces the concept of soft hyperedges, where each vertex is associated with hyperedges via continuous participation weights rather than hard binary assignments. This dynamic and differentiable association is achieved by using the learnable hyperedge prototype. Through similarity measurements between token features and the prototype, the model generates semantically rich soft hyperedges. SoftHGNN then aggregates messages over soft hyperedges to capture high-order semantics. To further enhance efficiency when scaling up the number of soft hyperedges, we incorporate a sparse hyperedge selection mechanism that activates only the top-k important hyperedges, along with a load-balancing regularizer to ensure balanced hyperedge utilization. Experimental results across three tasks on five datasets demonstrate that SoftHGNN efficiently captures high-order associations in visual scenes, achieving significant performance improvements.

In this paper we provide, to the best of our knowledge, the first comprehensive approach for incorporating various masking mechanisms into Transformers architectures in a scalable way. We show that recent results on linear causal attention (Choromanski et al., 2021) and log-linear RPE-attention (Luo et al., 2021) are special cases of this general mechanism. However by casting the problem as a topological (graph-based) modulation of unmasked attention, we obtain several results unknown before, including efficient d-dimensional RPE-masking and graph-kernel masking. We leverage many mathematical techniques ranging from spectral analysis through dynamic programming and random walks to new algorithms for solving Markov processes on graphs. We provide a corresponding empirical evaluation.

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.

Graphs are a fundamental data structure for representing relationships in real-world scenarios. With the success of Large Language Models (LLMs) across various natural language processing (NLP) tasks, there has been growing interest in integrating LLMs for graph learning. However, applying LLMs to graph-related tasks poses significant challenges, as these models are not inherently designed to capture the complex structural information present in graphs. Existing approaches address this challenge through two strategies: the chain of tasks approach, which uses Graph Neural Networks (GNNs) to encode the graph structure so that LLMs are relieved from understanding spatial positions; and Graph-to-Text Conversion, which translates graph structures into semantic text representations that LLMs can process. Despite their progress, these methods often struggle to fully preserve the topological information of graphs or require extensive computational resources, limiting their practical applicability. In this work, we introduce Node Tokenizer for Large Language Models (NT-LLM), a novel framework that efficiently encodes graph structures by selecting key nodes as anchors and representing each node based on its relative distance to these anchors. This position-anchored encoding effectively captures the graph topology, enabling enhanced reasoning capabilities in LLMs over graph data. Additionally, we implement a task-specific tuning procedure to further improve structural understanding within LLMs. Through extensive empirical evaluations, NT-LLM demonstrates significant performance improvements across a variety of graph-related tasks.

Existing Large Vision-Language Models (LVLMs) exhibit insufficient visual attention, leading to hallucinations. To alleviate this problem, some previous studies adjust and amplify visual attention. These methods present a limitation that boosting attention for all visual tokens inevitably increases attention to task irrelevant tokens. To tackle this challenge, we propose a training free attentional intervention algorithm to enhance the attention of task-relevant tokens based on the argument that task-relevant tokens generally demonstrate high visual-textual similarities. Specifically, the vision-text cross-attention submatrices, which represent visual-textual correlations, are extracted to construct the reweighting matrices to reallocate attention. Besides, to enhance the contribution of visual tokens, we inject visual attention values into the beam search decoding to identify solutions with higher visual attention. Extensive experiments demonstrate that this method significantly reduces hallucinations across mainstream LVLMs, while preserving the accuracy and coherence of generated content.

The advent of Large Language Models (LLMs) has fundamentally reshaped the way we interact with graphs, giving rise to a new paradigm called GraphLLM. As revealed in recent studies, graph learning can benefit from LLMs. However, we observe limited benefits when we directly utilize LLMs to make predictions for graph-related tasks within GraphLLM paradigm, which even yields suboptimal results compared to conventional GNN-based approaches. Through in-depth analysis, we find this failure can be attributed to LLMs' limited capability for processing graph data and their tendency to overlook graph information. To address this issue, we propose LoReC (Look, Remember, and Contrast), a novel plug-and-play method for GraphLLM paradigm, which enhances LLM's understanding of graph data through three stages: (1) Look: redistributing attention to graph; (2) Remember: re-injecting graph information into the Feed-Forward Network (FFN); (3) Contrast: rectifying the vanilla logits produced in the decoding process. Extensive experiments demonstrate that LoReC brings notable improvements over current GraphLLM methods and outperforms GNN-based approaches across diverse datasets. The implementation is available at https://github.com/Git-King-Zhan/LoReC.

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.

The growing importance of textual and relational systems has driven interest in enhancing large language models (LLMs) for graph-structured data, particularly Text-Attributed Graphs (TAGs), where samples are represented by textual descriptions interconnected by edges. While research has largely focused on developing specialized graph LLMs through task-specific instruction tuning, a comprehensive benchmark for evaluating LLMs solely through prompt design remains surprisingly absent. Without such a carefully crafted evaluation benchmark, most if not all, tailored graph LLMs are compared against general LLMs using simplistic queries (e.g., zero-shot reasoning with LLaMA), which can potentially camouflage many advantages as well as unexpected predicaments of them. To achieve more general evaluations and unveil the true potential of LLMs for graph tasks, we introduce Graph In-context Learning (GraphICL) Benchmark, a comprehensive benchmark comprising novel prompt templates designed to capture graph structure and handle limited label knowledge. Our systematic evaluation shows that general-purpose LLMs equipped with our GraphICL outperform state-of-the-art specialized graph LLMs and graph neural network models in resource-constrained settings and out-of-domain tasks. These findings highlight the significant potential of prompt engineering to enhance LLM performance on graph learning tasks without training and offer a strong baseline for advancing research in graph LLMs.

We study the capacity of the self-attention key-query channel: for a fixed budget, how many distinct token-token relations can a single layer reliably encode? We introduce Relational Graph Recognition, where the key-query channel encodes a directed graph and, given a context (a subset of the vertices), must recover the neighbors of each vertex in the context. We measure resources by the total key dimension D_K = h,d_k. In a tractable multi-head model, we prove matching information-theoretic lower bounds and upper bounds via explicit constructions showing that recovering a graph with m' relations in d_{model}-dimensional embeddings requires D_K to grow essentially as m'/d_{model} up to logarithmic factors, and we obtain corresponding guarantees for scaled-softmax attention. This analysis yields a new, capacity-based rationale for multi-head attention: even in permutation graphs, where all queries attend to a single target, splitting a fixed D_K budget into multiple heads increases capacity by reducing interference from embedding superposition. Controlled experiments mirror the theory, revealing sharp phase transitions at the predicted capacity, and the multi-head advantage persists when adding softmax normalization, value routing, and a full Transformer block trained with frozen GPT-2 embeddings.

Higher-order interactions (HOIs) are ubiquitous in real-world complex systems and applications. Investigation of deep learning for HOIs, thus, has become a valuable agenda for the data mining and machine learning communities. As networks of HOIs are expressed mathematically as hypergraphs, hypergraph neural networks (HNNs) have emerged as a powerful tool for representation learning on hypergraphs. Given the emerging trend, we present the first survey dedicated to HNNs, with an in-depth and step-by-step guide. Broadly, the present survey overviews HNN architectures, training strategies, and applications. First, we break existing HNNs down into four design components: (i) input features, (ii) input structures, (iii) message-passing schemes, and (iv) training strategies. Second, we examine how HNNs address and learn HOIs with each of their components. Third, we overview the recent applications of HNNs in recommendation, bioinformatics and medical science, time series analysis, and computer vision. Lastly, we conclude with a discussion on limitations and future directions.

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.

In recent years, the use of multi-modal pre-trained Transformers has led to significant advancements in visually-rich document understanding. However, existing models have mainly focused on features such as text and vision while neglecting the importance of layout relationship between text nodes. In this paper, we propose GraphLayoutLM, a novel document understanding model that leverages the modeling of layout structure graph to inject document layout knowledge into the model. GraphLayoutLM utilizes a graph reordering algorithm to adjust the text sequence based on the graph structure. Additionally, our model uses a layout-aware multi-head self-attention layer to learn document layout knowledge. The proposed model enables the understanding of the spatial arrangement of text elements, improving document comprehension. We evaluate our model on various benchmarks, including FUNSD, XFUND and CORD, and achieve state-of-the-art results among these datasets. Our experimental results demonstrate that our proposed method provides a significant improvement over existing approaches and showcases the importance of incorporating layout information into document understanding models. We also conduct an ablation study to investigate the contribution of each component of our model. The results show that both the graph reordering algorithm and the layout-aware multi-head self-attention layer play a crucial role in achieving the best performance.

Text-rich graphs, which integrate complex structural dependencies with abundant textual information, are ubiquitous yet remain challenging for existing learning paradigms. Conventional methods and even LLM-hybrids compress rich text into static embeddings or summaries before structural reasoning, creating an information bottleneck and detaching updates from the raw content. We argue that in text-rich graphs, the text is not merely a node attribute but the primary medium through which structural relationships are manifested. We introduce RAMP, a Raw-text Anchored Message Passing approach that moves beyond using LLMs as mere feature extractors and instead recasts the LLM itself as a graph-native aggregation operator. RAMP exploits the text-rich nature of the graph via a novel dual-representation scheme: it anchors inference on each node's raw text during each iteration while propagating dynamically optimized messages from neighbors. It further handles both discriminative and generative tasks under a single unified generative formulation. Extensive experiments show that RAMP effectively bridges the gap between graph propagation and deep text reasoning, achieving competitive performance and offering new insights into the role of LLMs as graph kernels for general-purpose graph learning.

Graph Attention Network (GAT) focuses on modelling simple undirected and single relational graph data only. This limits its ability to deal with more general and complex multi-relational graphs that contain entities with directed links of different labels (e.g., knowledge graphs). Therefore, directly applying GAT on multi-relational graphs leads to sub-optimal solutions. To tackle this issue, we propose r-GAT, a relational graph attention network to learn multi-channel entity representations. Specifically, each channel corresponds to a latent semantic aspect of an entity. This enables us to aggregate neighborhood information for the current aspect using relation features. We further propose a query-aware attention mechanism for subsequent tasks to select useful aspects. Extensive experiments on link prediction and entity classification tasks show that our r-GAT can model multi-relational graphs effectively. Also, we show the interpretability of our approach by case study.

Recent studies have revealed various manifestations of position bias in transformer architectures, from the "lost-in-the-middle" phenomenon to attention sinks, yet a comprehensive theoretical understanding of how attention masks and positional encodings shape these biases remains elusive. This paper presents a graph-theoretic framework for analyzing position bias in multi-layer attention. Modeling attention masks as directed graphs, we quantify how tokens interact with contextual information based on their sequential positions. We uncover two key insights: First, causal masking inherently biases attention toward earlier positions, as tokens in deeper layers attend to increasingly more contextualized representations of earlier tokens. Second, we characterize the competing effects of the causal mask and relative positional encodings, such as the decay mask and rotary positional encoding (RoPE): while both mechanisms introduce distance-based decay within individual attention maps, their aggregate effect across multiple attention layersx2013coupled with the causal maskx2013leads to a trade-off between the long-term decay effects and the cumulative importance of early sequence positions. Through controlled numerical experiments, we not only validate our theoretical findings but also reproduce position biases observed in real-world LLMs. Our framework offers a principled foundation for understanding positional biases in transformers, shedding light on the complex interplay of attention mechanism components and guiding more informed architectural design.

Transformer models are revolutionizing machine learning, but their inner workings remain mysterious. In this work, we present a new visualization technique designed to help researchers understand the self-attention mechanism in transformers that allows these models to learn rich, contextual relationships between elements of a sequence. The main idea behind our method is to visualize a joint embedding of the query and key vectors used by transformer models to compute attention. Unlike previous attention visualization techniques, our approach enables the analysis of global patterns across multiple input sequences. We create an interactive visualization tool, AttentionViz, based on these joint query-key embeddings, and use it to study attention mechanisms in both language and vision transformers. We demonstrate the utility of our approach in improving model understanding and offering new insights about query-key interactions through several application scenarios and expert feedback.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Graph structure learning aims to learn connectivity in a graph from data. It is particularly important for many computer vision related tasks since no explicit graph structure is available for images for most cases. A natural way to construct a graph among images is to treat each image as a node and assign pairwise image similarities as weights to corresponding edges. It is well known that pairwise similarities between images are sensitive to the noise in feature representations, leading to unreliable graph structures. We address this problem from the viewpoint of statistical tests. By viewing the feature vector of each node as an independent sample, the decision of whether creating an edge between two nodes based on their similarity in feature representation can be thought as a {it single} statistical test. To improve the robustness in the decision of creating an edge, multiple samples are drawn and integrated by {it multiple} statistical tests to generate a more reliable similarity measure, consequentially more reliable graph structure. The corresponding elegant matrix form named B-Attention is designed for efficiency. The effectiveness of multiple tests for graph structure learning is verified both theoretically and empirically on multiple clustering and ReID benchmark datasets. Source codes are available at https://github.com/Thomas-wyh/B-Attention.

As the core building block of vision transformers, attention is a powerful tool to capture long-range dependency. However, such power comes at a cost: it incurs a huge computation burden and heavy memory footprint as pairwise token interaction across all spatial locations is computed. A series of works attempt to alleviate this problem by introducing handcrafted and content-agnostic sparsity into attention, such as restricting the attention operation to be inside local windows, axial stripes, or dilated windows. In contrast to these approaches, we propose a novel dynamic sparse attention via bi-level routing to enable a more flexible allocation of computations with content awareness. Specifically, for a query, irrelevant key-value pairs are first filtered out at a coarse region level, and then fine-grained token-to-token attention is applied in the union of remaining candidate regions (\ie, routed regions). We provide a simple yet effective implementation of the proposed bi-level routing attention, which utilizes the sparsity to save both computation and memory while involving only GPU-friendly dense matrix multiplications. Built with the proposed bi-level routing attention, a new general vision transformer, named BiFormer, is then presented. As BiFormer attends to a small subset of relevant tokens in a query adaptive manner without distraction from other irrelevant ones, it enjoys both good performance and high computational efficiency, especially in dense prediction tasks. Empirical results across several computer vision tasks such as image classification, object detection, and semantic segmentation verify the effectiveness of our design. Code is available at https://github.com/rayleizhu/BiFormer.

Dialog is an effective way to exchange information, but subtle details and nuances are extremely important. While significant progress has paved a path to address visual dialog with algorithms, details and nuances remain a challenge. Attention mechanisms have demonstrated compelling results to extract details in visual question answering and also provide a convincing framework for visual dialog due to their interpretability and effectiveness. However, the many data utilities that accompany visual dialog challenge existing attention techniques. We address this issue and develop a general attention mechanism for visual dialog which operates on any number of data utilities. To this end, we design a factor graph based attention mechanism which combines any number of utility representations. We illustrate the applicability of the proposed approach on the challenging and recently introduced VisDial datasets, outperforming recent state-of-the-art methods by 1.1% for VisDial0.9 and by 2% for VisDial1.0 on MRR. Our ensemble model improved the MRR score on VisDial1.0 by more than 6%.

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.

Object categories are typically organized into a multi-granularity taxonomic hierarchy. When classifying categories at different hierarchy levels, traditional uni-modal approaches focus primarily on image features, revealing limitations in complex scenarios. Recent studies integrating Vision-Language Models (VLMs) with class hierarchies have shown promise, yet they fall short of fully exploiting the hierarchical relationships. These efforts are constrained by their inability to perform effectively across varied granularity of categories. To tackle this issue, we propose a novel framework (HGCLIP) that effectively combines CLIP with a deeper exploitation of the Hierarchical class structure via Graph representation learning. We explore constructing the class hierarchy into a graph, with its nodes representing the textual or image features of each category. After passing through a graph encoder, the textual features incorporate hierarchical structure information, while the image features emphasize class-aware features derived from prototypes through the attention mechanism. Our approach demonstrates significant improvements on 11 diverse visual recognition benchmarks. Our codes are fully available at https://github.com/richard-peng-xia/HGCLIP.

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

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.

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.

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.

Real-world tasks consist of multiple inter-dependent subtasks (e.g., a dirty pan needs to be washed before it can be used for cooking). In this work, we aim to model the causal dependencies between such subtasks from instructional videos describing the task. This is a challenging problem since complete information about the world is often inaccessible from videos, which demands robust learning mechanisms to understand the causal structure of events. We present Multimodal Subtask Graph Generation (MSG2), an approach that constructs a Subtask Graph defining the dependency between a task's subtasks relevant to a task from noisy web videos. Graphs generated by our multimodal approach are closer to human-annotated graphs compared to prior approaches. MSG2 further performs the downstream task of next subtask prediction 85% and 30% more accurately than recent video transformer models in the ProceL and CrossTask datasets, respectively.

Transformers have attained outstanding performance across various modalities, owing to their simple but powerful scaled-dot-product (SDP) attention mechanisms. Researchers have attempted to migrate Transformers to graph learning, but most advanced Graph Transformers (GTs) have strayed far from plain Transformers, exhibiting major architectural differences either by integrating message-passing or incorporating sophisticated attention mechanisms. These divergences hinder the easy adoption of training advances for Transformers developed in other domains. Contrary to previous GTs, this work demonstrates that the plain Transformer architecture can be a powerful graph learner. To achieve this, we propose to incorporate three simple, minimal, and easy-to-implement modifications to the plain Transformer architecture to construct our Powerful Plain Graph Transformers (PPGT): (1) simplified L_2 attention for measuring the magnitude closeness among tokens; (2) adaptive root-mean-square normalization to preserve token magnitude information; and (3) a simple MLP-based stem for graph positional encoding. Consistent with its theoretical expressivity, PPGT demonstrates noteworthy realized expressivity on the empirical graph expressivity benchmark, comparing favorably to more complicated alternatives such as subgraph GNNs and higher-order GNNs. Its empirical performance across various graph datasets also justifies the effectiveness of PPGT. This finding underscores the versatility of plain Transformer architectures and highlights their strong potential as a unified backbone for multimodal learning across language, vision, and graph domains.

Text-attributed graphs are widely used across domains, offering rich opportunities for zero-shot learning via graph-text alignment. However, existing methods struggle with tasks requiring fine-grained pattern recognition, particularly on heterophilic graphs. Through empirical and theoretical analysis, we identify an over-abstraction problem: current approaches operate at excessively large hyperbolic radii, compressing multi-scale structural information into uniform high-level abstractions. This abstraction-induced information loss obscures critical local patterns essential for accurate predictions. By analyzing embeddings in hyperbolic space, we demonstrate that optimal graph learning requires faithful preservation of fine-grained structural details, better retained by representations positioned closer to the origin. To address this, we propose H4G, a framework that systematically reduces embedding radii using learnable block-diagonal scaling matrices and M\"obius matrix multiplication. This approach restores access to fine-grained patterns while maintaining global receptive ability with minimal computational overhead. Experiments show H4G achieves state-of-the-art zero-shot performance with 12.8\% improvement on heterophilic graphs and 8.4\% on homophilic graphs, confirming that radius reduction enables faithful multi-scale representation for advancing zero-shot graph learning.

Large language models (LLMs) have recently shown strong potential in modeling relational structures. However, existing approaches remain fundamentally graph-centric: they focus on processing pairwise graph structures into tokens that LLMs can understand. In contrast, many real-world relational patterns do not naturally conform to the pairwise-edge assumption, and are better modeled as high-order associations in hypergraphs. For hypergraph structures, existing methods often fail to preserve the native semantics that multiple objects are jointly connected by the same high-order relation, limiting their ability to exploit complex structures. To address this limitation, we put forth the "Hypergraph as Language" perspective and propose Hyper-Align, a hypergraph-native alignment framework for large language models. Hyper-Align compiles the query-object-centered hypergraph context into hypergraph tokens directly consumable by a base LLM. Specifically, we introduce Hypergraph Incidence Detail Template with Overview (HIDT-O), which serializes high-order association structures into a fixed-shape hybrid template combining local incidence details and overview-level summaries. We then design a Hypergraph Incidence Projector (HIP), which maps native high-order incidence structures into the LLM token space through explicit semantic-structural decoupling and bidirectional message passing between vertices and hyperedges. We further define a concrete Hypergraph-as-Language input protocol, which jointly feeds hypergraph tokens and textual prompts into a frozen base LLM, supporting both vertex-level and hyperedge-level tasks under a unified question-answering paradigm. To systematically evaluate different methods in hypergraph structural modeling, we introduce HyperAlign-Bench. Extensive experiments show that Hyper-Align significantly outperforms existing methods across in-domain and zero-shot evaluations.

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.

Flowcharts are indispensable tools in software design and business-process analysis, yet current vision-language models (VLMs) frequently misinterpret the directional arrows and graph topology that set these diagrams apart from natural images. We introduce a seven-stage pipeline grouped into three broader processes: (1) arrow-aware detection of nodes and arrow endpoints; (2) optical character recognition (OCR) to extract node text; and (3) construction of a structured prompt that guides the VLMs. Tested on a 90-question benchmark distilled from 30 annotated flowcharts, the method raises overall accuracy from 80 % to 89 % (+9 percentage points) without any task-specific fine-tuning. The gain is most pronounced for next-step queries (25/30 -> 30/30; 100 %, +17 pp); branch-result questions improve more modestly, and before-step questions remain difficult. A parallel evaluation with an LLM-as-a-Judge protocol shows the same trends, reinforcing the advantage of explicit arrow encoding. Limitations include dependence on detector and OCR precision, the small evaluation set, and residual errors at nodes with multiple incoming edges. Future work will enlarge the benchmark with synthetic and handwritten flowcharts and assess the approach on Business Process Model and Notation (BPMN) and Unified Modeling Language (UML).

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.

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.

This paper introduces a new approach to extract and analyze vector data from technical drawings in PDF format. Our method involves converting PDF files into SVG format and creating a feature-rich graph representation, which captures the relationships between vector entities using geometrical information. We then apply a graph attention transformer with hierarchical label definition to achieve accurate line-level segmentation. Our approach is evaluated on two datasets, including the public FloorplanCAD dataset, which achieves state-of-the-art results on weighted F1 score, surpassing existing methods. The proposed vector-based method offers a more scalable solution for large-scale technical drawing analysis compared to vision-based approaches, while also requiring significantly less GPU power than current state-of-the-art vector-based techniques. Moreover, it demonstrates improved performance in terms of the weighted F1 (wF1) score on the semantic segmentation task. Our results demonstrate the effectiveness of our approach in extracting meaningful information from technical drawings, enabling new applications, and improving existing workflows in the AEC industry. Potential applications of our approach include automated building information modeling (BIM) and construction planning, which could significantly impact the efficiency and productivity of the industry.

Chart understanding is crucial for deploying multimodal large language models (MLLMs) in real-world scenarios such as analyzing scientific papers and technical reports. Unlike natural images, charts pair a structured visual layout (spatial property) with an underlying data representation (textual property) -- grasping both is essential for precise, fine-grained chart reasoning. Motivated by this observation, we propose START, the Spatial and Textual learning for chART understanding. Specifically, we introduce (i) chart-element grounding and (ii) chart-to-code generation to strengthen an MLLM's understanding of both chart visual layout and data details. To facilitate spatial and textual learning, we propose the START-Dataset generated with a novel data-generation pipeline that first leverages an MLLM to translate real chart images into executable chart code, recovering the underlying data representation while preserving the visual distribution of real-world charts. We then evolve the code with a Large Language Model (LLM) to ascertain the positions of chart elements that capture the chart's visual structure, addressing challenges that existing methods cannot handle. To evaluate a model's ability to understand chart spatial structures, we propose the Chart Spatial understanding Benchmark (CS-Bench), filling a critical gap in comprehensive chart understanding evaluation. Leveraging spatial and textual learning, START delivers consistent gains across model sizes and benchmarks over the base models and surpasses prior state-of-the-art by a clear margin. Code, data and models will be publicly available.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

Integer Linear Programs (ILPs) are powerful tools for modeling and solving a large number of combinatorial optimization problems. Recently, it has been shown that Large Neighborhood Search (LNS), as a heuristic algorithm, can find high quality solutions to ILPs faster than Branch and Bound. However, how to find the right heuristics to maximize the performance of LNS remains an open problem. In this paper, we propose a novel approach, CL-LNS, that delivers state-of-the-art anytime performance on several ILP benchmarks measured by metrics including the primal gap, the primal integral, survival rates and the best performing rate. Specifically, CL-LNS collects positive and negative solution samples from an expert heuristic that is slow to compute and learns a new one with a contrastive loss. We use graph attention networks and a richer set of features to further improve its performance.

Data visualization in the form of charts plays a pivotal role in data analysis, offering critical insights and aiding in informed decision-making. Automatic chart understanding has witnessed significant advancements with the rise of large foundation models in recent years. Foundation models, such as large language models, have revolutionized various natural language processing tasks and are increasingly being applied to chart understanding tasks. This survey paper provides a comprehensive overview of the recent developments, challenges, and future directions in chart understanding within the context of these foundation models. We review fundamental building blocks crucial for studying chart understanding tasks. Additionally, we explore various tasks and their evaluation metrics and sources of both charts and textual inputs. Various modeling strategies are then examined, encompassing both classification-based and generation-based approaches, along with tool augmentation techniques that enhance chart understanding performance. Furthermore, we discuss the state-of-the-art performance of each task and discuss how we can improve the performance. Challenges and future directions are addressed, highlighting the importance of several topics, such as domain-specific charts, lack of efforts in developing evaluation metrics, and agent-oriented settings. This survey paper serves as a comprehensive resource for researchers and practitioners in the fields of natural language processing, computer vision, and data analysis, providing valuable insights and directions for future research in chart understanding leveraging large foundation models. The studies mentioned in this paper, along with emerging new research, will be continually updated at: https://github.com/khuangaf/Awesome-Chart-Understanding.

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.

While Large Language Models (LLMs) excel at generalized reasoning, standard retrieval-augmented approaches fail to address the disconnected nature of long-term agentic memory. To bridge this gap, we introduce Synapse (Synergistic Associative Processing Semantic Encoding), a unified memory architecture that transcends static vector similarity. Drawing from cognitive science, Synapse models memory as a dynamic graph where relevance emerges from spreading activation rather than pre-computed links. By integrating lateral inhibition and temporal decay, the system dynamically highlights relevant sub-graphs while filtering interference. We implement a Triple Hybrid Retrieval strategy that fuses geometric embeddings with activation-based graph traversal. Comprehensive evaluations on the LoCoMo benchmark show that Synapse significantly outperforms state-of-the-art methods in complex temporal and multi-hop reasoning tasks, offering a robust solution to the "Contextual Tunneling" problem. Our code and data will be made publicly available upon acceptance.

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

The remarkable success of large language models (LLMs) has motivated researchers to adapt them as universal predictors for various graph tasks. As a widely recognized paradigm, Graph-Tokenizing LLMs (GTokenLLMs) compress complex graph data into graph tokens and treat them as prefix tokens for querying LLMs, leading many to believe that LLMs can understand graphs more effectively and efficiently. In this paper, we challenge this belief: Do GTokenLLMs fully understand graph tokens in the natural-language embedding space? Motivated by this question, we formalize a unified framework for GTokenLLMs and propose an evaluation pipeline, GTEval, to assess graph-token understanding via instruction transformations at the format and content levels. We conduct extensive experiments on 6 representative GTokenLLMs with GTEval. The primary findings are as follows: (1) Existing GTokenLLMs do not fully understand graph tokens. They exhibit over-sensitivity or over-insensitivity to instruction changes, and rely heavily on text for reasoning; (2) Although graph tokens preserve task-relevant graph information and receive attention across LLM layers, their utilization varies across models and instruction variants; (3) Additional instruction tuning can improve performance on the original and seen instructions, but it does not fully address the challenge of graph-token understanding, calling for further improvement.

Graphs have emerged as a natural choice to represent and analyze the intricate patterns and rich information of the Web, enabling applications such as online page classification and social recommendation. The prevailing "pre-train, fine-tune" paradigm has been widely adopted in graph machine learning tasks, particularly in scenarios with limited labeled nodes. However, this approach often exhibits a misalignment between the training objectives of pretext tasks and those of downstream tasks. This gap can result in the "negative transfer" problem, wherein the knowledge gained from pre-training adversely affects performance in the downstream tasks. The surge in prompt-based learning within Natural Language Processing (NLP) suggests the potential of adapting a "pre-train, prompt" paradigm to graphs as an alternative. However, existing graph prompting techniques are tailored to homogeneous graphs, neglecting the inherent heterogeneity of Web graphs. To bridge this gap, we propose HetGPT, a general post-training prompting framework to improve the predictive performance of pre-trained heterogeneous graph neural networks (HGNNs). The key is the design of a novel prompting function that integrates a virtual class prompt and a heterogeneous feature prompt, with the aim to reformulate downstream tasks to mirror pretext tasks. Moreover, HetGPT introduces a multi-view neighborhood aggregation mechanism, capturing the complex neighborhood structure in heterogeneous graphs. Extensive experiments on three benchmark datasets demonstrate HetGPT's capability to enhance the performance of state-of-the-art HGNNs on semi-supervised node classification.

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.

The role of the attention mechanism in encoding linguistic knowledge has received special interest in NLP. However, the ability of the attention heads to judge the grammatical acceptability of a sentence has been underexplored. This paper approaches the paradigm of acceptability judgments with topological data analysis (TDA), showing that the geometric properties of the attention graph can be efficiently exploited for two standard practices in linguistics: binary judgments and linguistic minimal pairs. Topological features enhance the BERT-based acceptability classifier scores by 8%-24% on CoLA in three languages (English, Italian, and Swedish). By revealing the topological discrepancy between attention maps of minimal pairs, we achieve the human-level performance on the BLiMP benchmark, outperforming nine statistical and Transformer LM baselines. At the same time, TDA provides the foundation for analyzing the linguistic functions of attention heads and interpreting the correspondence between the graph features and grammatical phenomena.

Large language models (LLMs) enable autonomous agents for reasoning, planning, and tool use. Recent systems increasingly organize these agents as graphs of specialized, interconnected nodes. Although graph-based orchestration supports flexible decomposition and coordination, it creates a key challenge: attention allocation. As workflows grow, existing approaches often execute graph components uniformly, wasting resources on irrelevant or low-impact tasks. We introduce Attention Orchestration, a paradigm that extends Transformer-style attention from token representations to workflow-level agent coordination. Our framework, Adaptive Goal-aware Attention Orchestration (AGAO), dynamically estimates agent importance based on user objectives, graph dependencies, and computational constraints. AGAO combines three components: (1) goal-aware attention, measuring semantic relevance between user goals and agent capabilities; (2) topology-aware attention, modeling structural dependencies in agent graphs; and (3) resource-aware attention, allocating budgets and execution priorities across heterogeneous agents. Together, these mechanisms transform static agent graphs into adaptive systems that focus computation on goal-critical reasoning paths. Experiments across diverse multi-agent workloads show that AGAO improves task effectiveness while reducing unnecessary computation, latency, and token consumption compared with existing graph-based execution strategies. Our work establishes Attention Engineering as a direction for scalable, intelligent multi-agent systems. Code: https://github.com/MingzhouFan97/AGAO.

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.

Modern code intelligence agents operate in contexts exceeding 1 million tokens--far beyond the scale where humans manually locate relevant files. Yet agents consistently fail to discover architecturally critical files when solving real-world coding tasks. We identify the Navigation Paradox: agents perform poorly not due to context limits, but because navigation and retrieval are fundamentally distinct problems. Through 258 automated trials across 30 benchmark tasks on a production FastAPI repository, we demonstrate that graph-based structural navigation via CodeCompass--a Model Context Protocol server exposing dependency graphs--achieves 99.4% task completion on hidden-dependency tasks, a 23.2 percentage-point improvement over vanilla agents (76.2%) and 21.2 points over BM25 retrieval (78.2%).However, we uncover a critical adoption gap: 58% of trials with graph access made zero tool calls, and agents required explicit prompt engineering to adopt the tool consistently. Our findings reveal that the bottleneck is not tool availability but behavioral alignment--agents must be explicitly guided to leverage structural context over lexical heuristics. We contribute: (1) a task taxonomy distinguishing semantic-search, structural, and hidden-dependency scenarios; (2) empirical evidence that graph navigation outperforms retrieval when dependencies lack lexical overlap; and (3) open-source infrastructure for reproducible evaluation of navigation tools.

Large Language Models (LLMs) have achieved impressive performance in text understanding and have become an essential tool for building smart assistants. Originally focusing on text, they have been enhanced with multimodal capabilities in recent works that successfully built visual instruction following assistants. As far as the graph modality goes, however, no such assistants have yet been developed. Graph structures are complex in that they represent relation between different features and are permutation invariant. Moreover, representing them in purely textual form does not always lead to good LLM performance even for finetuned models. As a result, there is a need to develop a new method to integrate graphs in LLMs for general graph understanding. This work explores the integration of the graph modality in LLM for general graph instruction following tasks. It aims at producing a deep learning model that enhances an underlying LLM with graph embeddings and trains it to understand them and to produce, given an instruction, an answer grounded in the graph representation. The approach performs significantly better than a graph to text approach and remains consistent even for larger graphs.

The dominant graph neural networks (GNNs) over-rely on the graph links, several serious performance problems with which have been witnessed already, e.g., suspended animation problem and over-smoothing problem. What's more, the inherently inter-connected nature precludes parallelization within the graph, which becomes critical for large-sized graph, as memory constraints limit batching across the nodes. In this paper, we will introduce a new graph neural network, namely GRAPH-BERT (Graph based BERT), solely based on the attention mechanism without any graph convolution or aggregation operators. Instead of feeding GRAPH-BERT with the complete large input graph, we propose to train GRAPH-BERT with sampled linkless subgraphs within their local contexts. GRAPH-BERT can be learned effectively in a standalone mode. Meanwhile, a pre-trained GRAPH-BERT can also be transferred to other application tasks directly or with necessary fine-tuning if any supervised label information or certain application oriented objective is available. We have tested the effectiveness of GRAPH-BERT on several graph benchmark datasets. Based the pre-trained GRAPH-BERT with the node attribute reconstruction and structure recovery tasks, we further fine-tune GRAPH-BERT on node classification and graph clustering tasks specifically. The experimental results have demonstrated that GRAPH-BERT can out-perform the existing GNNs in both the learning effectiveness and efficiency.

Human mobility prediction is a fundamental task essential for various applications in urban planning, location-based services and intelligent transportation systems. Existing methods often ignore activity information crucial for reasoning human preferences and routines, or adopt a simplified representation of the dependencies between time, activities and locations. To address these issues, we present Hierarchical Graph Attention Recurrent Network (HGARN) for human mobility prediction. Specifically, we construct a hierarchical graph based on past mobility records and employ a Hierarchical Graph Attention Module to capture complex time-activity-location dependencies. This way, HGARN can learn representations with rich human travel semantics to model user preferences at the global level. We also propose a model-agnostic history-enhanced confidence (MAHEC) label to incorporate each user's individual-level preferences. Finally, we introduce a Temporal Module, which employs recurrent structures to jointly predict users' next activities and their associated locations, with the former used as an auxiliary task to enhance the latter prediction. For model evaluation, we test the performance of HGARN against existing state-of-the-art methods in both the recurring (i.e., returning to a previously visited location) and explorative (i.e., visiting a new location) settings. Overall, HGARN outperforms other baselines significantly in all settings based on two real-world human mobility data benchmarks. These findings confirm the important role that human activities play in determining mobility decisions, illustrating the need to develop activity-aware intelligent transportation systems. Source codes of this study are available at https://github.com/YihongT/HGARN.

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.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

Large language models (LLMs) are increasingly adopted for a variety of tasks with implicit graphical structures, such as planning in robotics, multi-hop question answering or knowledge probing, structured commonsense reasoning, and more. While LLMs have advanced the state-of-the-art on these tasks with structure implications, whether LLMs could explicitly process textual descriptions of graphs and structures, map them to grounded conceptual spaces, and perform structured operations remains underexplored. To this end, we propose NLGraph (Natural Language Graph), a comprehensive benchmark of graph-based problem solving designed in natural language. NLGraph contains 29,370 problems, covering eight graph reasoning tasks with varying complexity from simple tasks such as connectivity and shortest path up to complex problems such as maximum flow and simulating graph neural networks. We evaluate LLMs (GPT-3/4) with various prompting approaches on the NLGraph benchmark and find that 1) language models do demonstrate preliminary graph reasoning abilities, 2) the benefit of advanced prompting and in-context learning diminishes on more complex graph problems, while 3) LLMs are also (un)surprisingly brittle in the face of spurious correlations in graph and problem settings. We then propose Build-a-Graph Prompting and Algorithmic Prompting, two instruction-based approaches to enhance LLMs in solving natural language graph problems. Build-a-Graph and Algorithmic prompting improve the performance of LLMs on NLGraph by 3.07% to 16.85% across multiple tasks and settings, while how to solve the most complicated graph reasoning tasks in our setup with language models remains an open research question. The NLGraph benchmark and evaluation code are available at https://github.com/Arthur-Heng/NLGraph.

Self-attention is a ubiquitous primitive in modern sequence models, yet its operator-level geometry is only partially understood. We view a token sequence as a vector field over the token-position graph and identify attention as a connection walk: messages are aggregated by a nonnegative walk matrix while being transported along each edge by a learned linear map. Within this framework, we prove that single-head attention (SHA) is exactly a connection propagation step with constant transport, and that multi-head attention (MHA) is exactly a single edge-dependent connection walk whose effective transport is an attention-gated mixture of headwise transports. We further clarify the conditions under which the corresponding generator reduces to a random-walk connection Laplacian, highlighting the roles of stochasticity, reversibility, and metric-compatible transports. Empirically, we find that trained Transformers across scales (from 124M to 8B) and structures (encoder/decoder) exhibit geometric structure consistent with our theory: effective attention graphs converge to stable geometric operators in deeper layers, learned transports self-organize into approximate scaled isometries, and both phenomena strengthen consistently with scale. Overall, the paper provides a precise connection-walk formalism that links self-attention to classical geometric operators, along with a set of operator-level tools for analyzing transformer models from a geometric perspective.

Transformers were originally proposed as a sequence-to-sequence model for text but have become vital for a wide range of modalities, including images, audio, video, and undirected graphs. However, transformers for directed graphs are a surprisingly underexplored topic, despite their applicability to ubiquitous domains including source code and logic circuits. In this work, we propose two direction- and structure-aware positional encodings for directed graphs: (1) the eigenvectors of the Magnetic Laplacian - a direction-aware generalization of the combinatorial Laplacian; (2) directional random walk encodings. Empirically, we show that the extra directionality information is useful in various downstream tasks, including correctness testing of sorting networks and source code understanding. Together with a data-flow-centric graph construction, our model outperforms the prior state of the art on the Open Graph Benchmark Code2 relatively by 14.7%.

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.

Search is an ability foundational in many important tasks, and recent studies have shown that large language models (LLMs) struggle to perform search robustly. It is unknown whether this inability is due to a lack of data, insufficient model parameters, or fundamental limitations of the transformer architecture. In this work, we use the foundational graph connectivity problem as a testbed to generate effectively limitless high-coverage data to train small transformers and test whether they can learn to perform search. We find that, when given the right training distribution, the transformer is able to learn to search. We analyze the algorithm that the transformer has learned through a novel mechanistic interpretability technique that enables us to extract the computation graph from the trained model. We find that for each vertex in the input graph, transformers compute the set of vertices reachable from that vertex. Each layer then progressively expands these sets, allowing the model to search over a number of vertices exponential in the number of layers. However, we find that as the input graph size increases, the transformer has greater difficulty in learning the task. This difficulty is not resolved even as the number of parameters is increased, suggesting that increasing model scale will not lead to robust search abilities. We also find that performing search in-context (i.e., chain-of-thought) does not resolve this inability to learn to search on larger graphs.

Recently, graph neural networks (GNNs) have shown prominent performance in semi-supervised node classification by leveraging knowledge from the graph database. However, most existing GNNs follow the homophily assumption, where connected nodes are more likely to exhibit similar feature distributions and the same labels, and such an assumption has proven to be vulnerable in a growing number of practical applications. As a supplement, heterophily reflects dissimilarity in connected nodes, which has gained significant attention in graph learning. To this end, data engineers aim to develop a powerful GNN model that can ensure performance under both homophily and heterophily. Despite numerous attempts, most existing GNNs struggle to achieve optimal node representations due to the constraints of undirected graphs. The neglect of directed edges results in sub-optimal graph representations, thereby hindering the capacity of GNNs. To address this issue, we introduce AMUD, which quantifies the relationship between node profiles and topology from a statistical perspective, offering valuable insights for Adaptively Modeling the natural directed graphs as the Undirected or Directed graph to maximize the benefits from subsequent graph learning. Furthermore, we propose Adaptive Directed Pattern Aggregation (ADPA) as a new directed graph learning paradigm for AMUD. Empirical studies have demonstrated that AMUD guides efficient graph learning. Meanwhile, extensive experiments on 14 benchmark datasets substantiate the impressive performance of ADPA, outperforming baselines by significant margins of 3.96\%.

Transformer-based pre-training techniques of text and layout have proven effective in a number of document understanding tasks. Despite this success, multimodal pre-training models suffer from very high computational and memory costs. Motivated by human reading strategies, this paper presents Skim-Attention, a new attention mechanism that takes advantage of the structure of the document and its layout. Skim-Attention only attends to the 2-dimensional position of the words in a document. Our experiments show that Skim-Attention obtains a lower perplexity than prior works, while being more computationally efficient. Skim-Attention can be further combined with long-range Transformers to efficiently process long documents. We also show how Skim-Attention can be used off-the-shelf as a mask for any Pre-trained Language Model, allowing to improve their performance while restricting attention. Finally, we show the emergence of a document structure representation in Skim-Attention.

Large Vision-Language Models (LVLMs) achieve impressive visual reasoning and dialogue capabilities, yet frequently hallucinate content unsupported by the visual input. Effective mitigation requires token-level localization, enabling targeted intervention without discarding the entire response. Existing detectors require expensive full-model fine-tuning, rely on external verifiers that ignore the model's generation process, or reduce internal signals to isolated features and hand-crafted statistics, discarding spatial, sequential, and relational structure. We introduce UniProbe, a lightweight, unified, learnable detector that models a frozen LVLM's heterogeneous computational trace from a single forward pass. UniProbe constructs a directed graph over image patches, query tokens, and generated tokens, with attention weights encoding their relations. It processes this trace with alternating structure-aware modules: a GNN for relational evidence, a ViT for 2-D visual geometry, and a GRU for response order. Interleaving them allows spatial, relational, and sequential evidence to interact throughout the detector. We further develop a streaming variant for hallucination-aware decoding, which detects and resamples hallucinated tokens during generation, and a self-adaptation strategy aligning the detector with the LVLM's own generations. Across diverse LVLM backbones, UniProbe achieves state-of-the-art token-level and object-hallucination detection. During decoding, it reduces object hallucinations by up to 55\% at 1.06times the latency of standard generation.

Transformer models underpin many recent advances in practical machine learning applications, yet understanding their internal behavior continues to elude researchers. Given the size and complexity of these models, forming a comprehensive picture of their inner workings remains a significant challenge. To this end, we set out to understand small transformer models in a more tractable setting: that of solving mazes. In this work, we focus on the abstractions formed by these models and find evidence for the consistent emergence of structured internal representations of maze topology and valid paths. We demonstrate this by showing that the residual stream of only a single token can be linearly decoded to faithfully reconstruct the entire maze. We also find that the learned embeddings of individual tokens have spatial structure. Furthermore, we take steps towards deciphering the circuity of path-following by identifying attention heads (dubbed adjacency heads), which are implicated in finding valid subsequent tokens.

Multimodal Large Language Models (MLLMs) demonstrate impressive reasoning capabilities, but often fail to perceive fine-grained visual details, limiting their applicability in precision-demanding tasks. While methods that crop salient regions of an image offer a partial solution, we identify a critical limitation they introduce: "Contextual Blindness". This failure occurs due to structural disconnect between high-fidelity details (from the crop) and the broader global context (from the original image), even when all necessary visual information is present. We argue that this limitation stems not from a lack of information 'Quantity', but from a lack of 'Structural Diversity' in the model's input. To resolve this, we propose Visual Funnel, a training-free, two-step approach. Visual Funnel first performs Contextual Anchoring to identify the region of interest in a single forward pass. It then constructs an Entropy-Scaled Portfolio that preserves the hierarchical context - ranging from focal detail to broader surroundings - by dynamically determining crop sizes based on attention entropy and refining crop centers. Through extensive experiments, we demonstrate that Visual Funnel significantly outperforms naive single-crop and unstructured multi-crop baselines. Our results further validate that simply adding more unstructured crops provides limited or even detrimental benefits, confirming that the hierarchical structure of our portfolio is key to resolving Contextual Blindness.

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.

Text-attributed graphs (TAGs) present unique challenges in representation learning by requiring models to capture both the semantic richness of node-associated texts and the structural dependencies of the graph. While graph neural networks (GNNs) excel at modeling topological information, they lack the capacity to process unstructured text. Conversely, large language models (LLMs) are proficient in text understanding but are typically unaware of graph structure. In this work, we propose BiGTex (Bidirectional Graph Text), a novel architecture that tightly integrates GNNs and LLMs through stacked Graph-Text Fusion Units. Each unit allows for mutual attention between textual and structural representations, enabling information to flow in both directions, text influencing structure and structure guiding textual interpretation. The proposed architecture is trained using parameter-efficient fine-tuning (LoRA), keeping the LLM frozen while adapting to task-specific signals. Extensive experiments on five benchmark datasets demonstrate that BiGTex achieves state-of-the-art performance in node classification and generalizes effectively to link prediction. An ablation study further highlights the importance of soft prompting and bi-directional attention in the model's success.

In recent years, graph prompting has emerged as a promising research direction, enabling the learning of additional tokens or subgraphs appended to the original graphs without requiring retraining of pre-trained graph models across various applications. This novel paradigm, shifting from the traditional pretraining and finetuning to pretraining and prompting has shown significant empirical success in simulating graph data operations, with applications ranging from recommendation systems to biological networks and graph transferring. However, despite its potential, the theoretical underpinnings of graph prompting remain underexplored, raising critical questions about its fundamental effectiveness. The lack of rigorous theoretical proof of why and how much it works is more like a dark cloud over the graph prompt area to go further. To fill this gap, this paper introduces a theoretical framework that rigorously analyzes graph prompting from a data operation perspective. Our contributions are threefold: First, we provide a formal guarantee theorem, demonstrating graph prompts capacity to approximate graph transformation operators, effectively linking upstream and downstream tasks. Second, we derive upper bounds on the error of these data operations by graph prompts for a single graph and extend this discussion to batches of graphs, which are common in graph model training. Third, we analyze the distribution of data operation errors, extending our theoretical findings from linear graph models (e.g., GCN) to non-linear graph models (e.g., GAT). Extensive experiments support our theoretical results and confirm the practical implications of these guarantees.

Why do large pre-trained transformer-based models perform so well across a wide variety of NLP tasks? Recent research suggests the key may lie in multi-headed attention mechanism's ability to learn and represent linguistic information. Understanding how these models represent both syntactic and semantic knowledge is vital to investigate why they succeed and fail, what they have learned, and how they can improve. We present Dodrio, an open-source interactive visualization tool to help NLP researchers and practitioners analyze attention mechanisms in transformer-based models with linguistic knowledge. Dodrio tightly integrates an overview that summarizes the roles of different attention heads, and detailed views that help users compare attention weights with the syntactic structure and semantic information in the input text. To facilitate the visual comparison of attention weights and linguistic knowledge, Dodrio applies different graph visualization techniques to represent attention weights scalable to longer input text. Case studies highlight how Dodrio provides insights into understanding the attention mechanism in transformer-based models. Dodrio is available at https://poloclub.github.io/dodrio/.

We introduce Hyperdimensional Graph Learner (HDGL), a novel method for node classification and link prediction in graphs. HDGL maps node features into a very high-dimensional space (hyperdimensional or HD space for short) using the injectivity property of node representations in a family of Graph Neural Networks (GNNs) and then uses HD operators such as bundling and binding to aggregate information from the local neighborhood of each node yielding latent node representations that can support both node classification and link prediction tasks. HDGL, unlike GNNs that rely on computationally expensive iterative optimization and hyperparameter tuning, requires only a single pass through the data set. We report results of experiments using widely used benchmark datasets which demonstrate that, on the node classification task, HDGL achieves accuracy that is competitive with that of the state-of-the-art GNN methods at substantially reduced computational cost; and on the link prediction task, HDGL matches the performance of DeepWalk and related methods, although it falls short of computationally demanding state-of-the-art GNNs.

Vision Transformers (ViT) have shown their competitive advantages performance-wise compared to convolutional neural networks (CNNs) though they often come with high computational costs. To this end, previous methods explore different attention patterns by limiting a fixed number of spatially nearby tokens to accelerate the ViT's multi-head self-attention (MHSA) operations. However, such structured attention patterns limit the token-to-token connections to their spatial relevance, which disregards learned semantic connections from a full attention mask. In this work, we propose a novel approach to learn instance-dependent attention patterns, by devising a lightweight connectivity predictor module to estimate the connectivity score of each pair of tokens. Intuitively, two tokens have high connectivity scores if the features are considered relevant either spatially or semantically. As each token only attends to a small number of other tokens, the binarized connectivity masks are often very sparse by nature and therefore provide the opportunity to accelerate the network via sparse computations. Equipped with the learned unstructured attention pattern, sparse attention ViT (Sparsifiner) produces a superior Pareto-optimal trade-off between FLOPs and top-1 accuracy on ImageNet compared to token sparsity. Our method reduces 48% to 69% FLOPs of MHSA while the accuracy drop is within 0.4%. We also show that combining attention and token sparsity reduces ViT FLOPs by over 60%.

Modern vision models have achieved remarkable success in benchmarks where local features provide critical information about the target. There is now a growing interest in solving tasks that require more global reasoning, where local features offer no significant information. These tasks are reminiscent of the connectivity tasks discussed by Minsky and Papert in 1969, which exposed the limitations of the perceptron model and contributed to the first AI winter. In this paper, we revisit such tasks by introducing four global visual benchmarks involving path findings and mazes. We show that: (1) although today's large vision models largely surpass the expressivity limitations of the early models, they still struggle with the learning efficiency; we put forward the "globality degree" notion to understand this limitation; (2) we then demonstrate that the picture changes and global reasoning becomes feasible with the introduction of "visual scratchpads"; similarly to the text scratchpads and chain-of-thoughts used in language models, visual scratchpads help break down global tasks into simpler ones; (3) we finally show that some scratchpads are better than others, in particular, "inductive scratchpads" that take steps relying on less information afford better out-of-distribution generalization and succeed for smaller model sizes.

Linear attention is an efficient attention mechanism that has recently emerged as a promising alternative to conventional softmax attention. With its ability to process tokens in linear computational complexities, linear attention, in theory, can handle sequences of unlimited length without sacrificing speed, i.e., maintaining a constant training speed for various sequence lengths with a fixed memory consumption. However, due to the issue with cumulative summation (cumsum), current linear attention algorithms cannot demonstrate their theoretical advantage in a causal setting. In this paper, we present Lightning Attention-2, the first linear attention implementation that enables linear attention to realize its theoretical computational benefits. To achieve this, we leverage the thought of tiling, separately handling the intra-block and inter-block components in linear attention calculation. Specifically, we utilize the conventional attention computation mechanism for the intra-blocks and apply linear attention kernel tricks for the inter-blocks. A tiling technique is adopted through both forward and backward procedures to take full advantage of the GPU hardware. We implement our algorithm in Triton to make it IO-aware and hardware-friendly. Various experiments are conducted on different model sizes and sequence lengths. Lightning Attention-2 retains consistent training and inference speed regardless of input sequence length and is significantly faster than other attention mechanisms. The source code is available at https://github.com/OpenNLPLab/lightning-attention.

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/

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.

Vision-Language Models (VLMs) have been shown to be blind, often underutilizing their visual inputs even on tasks that require visual reasoning. In this work, we demonstrate that VLMs are selectively blind. They modulate the amount of attention applied to visual inputs based on linguistic framing even when alternative framings demand identical visual reasoning. Using visual attention as a probe, we quantify how framing alters both the amount and distribution of attention over the image. Constrained framings, such as multiple choice and yes/no, induce substantially lower attention to image context compared to open-ended, reduce focus on task-relevant regions, and shift attention towards uninformative tokens. We further demonstrate that this attention misallocation is the principal cause of degraded accuracy and cross-framing inconsistency. Building on this mechanistic insight, we introduce a lightweight prompt-tuning method using learnable tokens that encourages the robust, visually grounded attention patterns observed in open-ended settings, improving visual grounding and improving performance across framings.

Automatic Sign Language (SL) recognition is an important task in the computer vision community. To build a robust SL recognition system, we need a considerable amount of data which is lacking particularly in Indian sign language (ISL). In this paper, we introduce a large-scale isolated ISL dataset and a novel SL recognition model based on skeleton graph structure. The dataset covers 2002 daily used common words in the deaf community recorded by 20 (10 male and 10 female) deaf adult signers (contains 40033 videos). We propose a SL recognition model namely Hierarchical Windowed Graph Attention Network (HWGAT) by utilizing the human upper body skeleton graph. The HWGAT tries to capture distinctive motions by giving attention to different body parts induced by the human skeleton graph. The utility of the proposed dataset and the usefulness of our model are evaluated through extensive experiments. We pre-trained the proposed model on the presented dataset and fine-tuned it across different sign language datasets further boosting the performance of 1.10, 0.46, 0.78, and 6.84 percentage points on INCLUDE, LSA64, AUTSL and WLASL respectively compared to the existing state-of-the-art keypoints-based models.

Attention sink (AS) is a consistent pattern in transformer attention maps where certain tokens (often special tokens or positional anchors) disproportionately attract attention from other tokens. We show that in transformers, AS is not an architectural artifact, but it is the manifestation of a fundamental geometric principle: the establishment of reference frames that anchor representational spaces. We analyze several architectures and identify three distinct reference frame types, centralized, distributed, and bidirectional, that correlate with the attention sink phenomenon. We show that they emerge during the earliest stages of training as optimal solutions to the problem of establishing stable coordinate systems in high-dimensional spaces. We show the influence of architecture components, particularly position encoding implementations, on the specific type of reference frame. This perspective transforms our understanding of transformer attention mechanisms and provides insights for both architecture design and the relationship with AS.

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.

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

Transformer models have achieved remarkable results in a wide range of applications. However, their scalability is hampered by the quadratic time and memory complexity of the self-attention mechanism concerning the sequence length. This limitation poses a substantial obstacle when dealing with long documents or high-resolution images. In this work, we study the self-attention mechanism by analyzing the distribution of the attention matrix and its concentration ability. Furthermore, we propose instruments to measure these quantities and introduce a novel self-attention mechanism, Linear Log-Normal Attention, designed to emulate the distribution and concentration behavior of the original self-attention. Our experimental results on popular natural language benchmarks reveal that our proposed Linear Log-Normal Attention outperforms other linearized attention alternatives, offering a promising avenue for enhancing the scalability of transformer models. Our code is available in supplementary materials.

Attention sinks, representation collapse, and norm stratification are treated as transformer-specific pathologies. We show they are not specific to attention: they are what content-based routing does under a fixed similarity metric. We give a reframing identity: softmax attention is Boltzmann-weighted aggregation over Euclidean distances with constant key norms, so its score omits a -|k|^2 term and is blind to key magnitude. This predicts that any router whose metric is ill-matched to its representations should compensate, by concentrating its routing and collapsing the routed representations. We test it on routers that score and aggregate over different axes: softmax attention over tokens (nine pretrained transformers), graph attention over nodes, a selective state-space model and a recurrent mixer over time, and learned residuals over depth. All develop the same signature, and two within-model ablations show it is caused by the routing mechanism rather than by incidental dynamics. The form is contingent, set by the strength of the positional brake each router carries alongside its content score; we sweep that brake and move the onset across its whole range. The mechanism is not contingent, and it does not require norm stratification: a router with norm-normalized keys concentrates just the same. We do not claim these models implement Riemannian geometry; the geometric view is a diagnostic that names the inadequacy of the flat, norm-blind metric.

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.

Text-to-image (T2I) generation has made remarkable progress in producing high-quality images, but a fundamental challenge remains: creating backgrounds that naturally accommodate text placement without compromising image quality. This capability is non-trivial for real-world applications like graphic design, where clear visual hierarchy between content and text is essential. Prior work has primarily focused on arranging layouts within existing static images, leaving unexplored the potential of T2I models for generating text-friendly backgrounds. We present TextCenGen, a training-free dynamic background adaptation in the blank region for text-friendly image generation. Instead of directly reducing attention in text areas, which degrades image quality, we relocate conflicting objects before background optimization. Our method analyzes cross-attention maps to identify conflicting objects overlapping with text regions and uses a force-directed graph approach to guide their relocation, followed by attention excluding constraints to ensure smooth backgrounds. Our method is plug-and-play, requiring no additional training while well balancing both semantic fidelity and visual quality. Evaluated on our proposed text-friendly T2I benchmark of 27,000 images across four seed datasets, TextCenGen outperforms existing methods by achieving 23% lower saliency overlap in text regions while maintaining 98% of the semantic fidelity measured by CLIP score and our proposed Visual-Textual Concordance Metric (VTCM).

Hypergraphs are widely being employed to represent complex higher-order relations in real-world applications. Most existing research on hypergraph learning focuses on node-level or edge-level tasks. A practically relevant and more challenging task, edge-dependent node classification (ENC), is still under-explored. In ENC, a node can have different labels across different hyperedges, which requires the modeling of node features unique to each hyperedge. The state-of-the-art ENC solution, WHATsNet, only outputs single node and edge representations, leading to the limitations of entangled edge-specific features and non-adaptive representation sizes when applied to ENC. Additionally, WHATsNet suffers from the common oversmoothing issue in most HGNNs. To address these limitations, we propose CoNHD, a novel HGNN architecture specifically designed to model edge-specific features for ENC. Instead of learning separate representations for nodes and edges, CoNHD reformulates within-edge and within-node interactions as a hypergraph diffusion process over node-edge co-representations. We develop a neural implementation of the proposed diffusion process, leveraging equivariant networks as diffusion operators to effectively learn the diffusion dynamics from data. Extensive experiments demonstrate that CoNHD achieves the best performance across all benchmark ENC datasets and several downstream tasks without sacrificing efficiency. Our implementation is available at https://github.com/zhengyijia/CoNHD.

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.

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.

While visual question-answering (VQA) benchmarks have catalyzed the development of reasoning techniques, they have focused on vertical thinking. Effective problem-solving also necessitates lateral thinking, which remains understudied in AI and has not been used to test visual perception systems. To bridge this gap, we formulate visual lateral thinking as a multiple-choice question-answering task and describe a three-step taxonomy-driven methodology for instantiating task examples. Then, we develop COLUMBUS, a synthetic benchmark that applies the task pipeline to create QA sets with text and icon rebus puzzles based on publicly available collections of compounds and common phrases. COLUMBUS comprises over 1,000 puzzles, each with four answer candidates. While the SotA vision-language models (VLMs) achieve decent performance, our evaluation demonstrates a substantial gap between humans and models. VLMs benefit from human-curated descriptions but struggle to self-generate such representations at the right level of abstraction.

Large Vision Language Models (VLMs) have long struggled with spatial reasoning tasks. Surprisingly, even simple spatial reasoning tasks, such as recognizing "under" or "behind" relationships between only two objects, pose significant challenges for current VLMs. In this work, we study the spatial reasoning challenge from the lens of mechanistic interpretability, diving into the model's internal states to examine the interactions between image and text tokens. By tracing attention distribution over the image through out intermediate layers, we observe that successful spatial reasoning correlates strongly with the model's ability to align its attention distribution with actual object locations, particularly differing between familiar and unfamiliar spatial relationships. Motivated by these findings, we propose ADAPTVIS based on inference-time confidence scores to sharpen the attention on highly relevant regions when confident, while smoothing and broadening the attention window to consider a wider context when confidence is lower. This training-free decoding method shows significant improvement (e.g., up to a 50 absolute point improvement) on spatial reasoning benchmarks such as WhatsUp and VSR with negligible cost. We make code and data publicly available for research purposes at https://github.com/shiqichen17/AdaptVis.

Recent studies have shown that Large Language Models (LLMs) can achieve strong reasoning performance by incorporating functional symbolic representations that abstractly describe graph traversal algorithms and step-by-step reasoning in few-shot learning settings. However, it remains unclear how LLMs genuinely understand the abstract meaning of each reasoning step and the overall algorithm from only a limited number of demonstrations. This work aims to localize the attention heads responsible for individual reasoning steps and characterize the types of information transferred among them. We first align constituent reasoning steps with their corresponding token logits under a symbolic-aided Chain-of-Thought (CoT) prompting framework. Our analysis shows that token positions that steer the reasoning process are associated with low confidence scores caused by constraints on satisfying reasoning behavior patterns in demonstrations. We then adopt causal mediation analysis techniques to identify the attention heads responsible for these patterns. In addition, our findings indicate that LLMs retrieve factual and rule-based information for individual sub-reasoning tasks through specialized attention heads (approximately 3% total heads), whereas higher layers predominantly facilitate information integration and the emergence of global reasoning strategies (e.g., graph traversal algorithms) that coordinate multiple intermediate reasoning steps to solve the overall task.

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 have recently gained significant attention in the computer vision community. However, the lack of scalability of self-attention mechanisms with respect to image size has limited their wide adoption in state-of-the-art vision backbones. In this paper we introduce an efficient and scalable attention model we call multi-axis attention, which consists of two aspects: blocked local and dilated global attention. These design choices allow global-local spatial interactions on arbitrary input resolutions with only linear complexity. We also present a new architectural element by effectively blending our proposed attention model with convolutions, and accordingly propose a simple hierarchical vision backbone, dubbed MaxViT, by simply repeating the basic building block over multiple stages. Notably, MaxViT is able to ''see'' globally throughout the entire network, even in earlier, high-resolution stages. We demonstrate the effectiveness of our model on a broad spectrum of vision tasks. On image classification, MaxViT achieves state-of-the-art performance under various settings: without extra data, MaxViT attains 86.5% ImageNet-1K top-1 accuracy; with ImageNet-21K pre-training, our model achieves 88.7% top-1 accuracy. For downstream tasks, MaxViT as a backbone delivers favorable performance on object detection as well as visual aesthetic assessment. We also show that our proposed model expresses strong generative modeling capability on ImageNet, demonstrating the superior potential of MaxViT blocks as a universal vision module. The source code and trained models will be available at https://github.com/google-research/maxvit.

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being local, global or relative. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges O(N+E) by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework GraphGPS that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.

When an image generation process is guided by both a text prompt and spatial cues, such as a set of bounding boxes, do these elements work in harmony, or does one dominate the other? Our analysis of a pretrained image diffusion model that integrates gated self-attention into the U-Net reveals that spatial grounding often outweighs textual grounding due to the sequential flow from gated self-attention to cross-attention. We demonstrate that such bias can be significantly mitigated without sacrificing accuracy in either grounding by simply rewiring the network architecture, changing from sequential to parallel for gated self-attention and cross-attention. This surprisingly simple yet effective solution does not require any fine-tuning of the network but significantly reduces the trade-off between the two groundings. Our experiments demonstrate significant improvements from the original GLIGEN to the rewired version in the trade-off between textual grounding and spatial grounding.