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Apr 21

MedVerse: Efficient and Reliable Medical Reasoning via DAG-Structured Parallel Execution

Large language models (LLMs) have demonstrated strong performance and rapid progress in a wide range of medical reasoning tasks. However, their sequential autoregressive decoding forces inherently parallel clinical reasoning, such as differential diagnosis, into a single linear reasoning path, limiting both efficiency and reliability for complex medical problems. To address this, we propose MedVerse, a reasoning framework for complex medical inference that reformulates medical reasoning as a parallelizable directed acyclic graph (DAG) process based on Petri net theory. The framework adopts a full-stack design across data, model architecture, and system execution. For data creation, we introduce the MedVerse Curator, an automated pipeline that synthesizes knowledge-grounded medical reasoning paths and transforms them into Petri net-structured representations. At the architectural level, we propose a topology-aware attention mechanism with adaptive position indices that supports parallel reasoning while preserving logical consistency. Systematically, we develop a customized inference engine that supports parallel execution without additional overhead. Empirical evaluations show that MedVerse improves strong general-purpose LLMs by up to 8.9%. Compared to specialized medical LLMs, MedVerse achieves comparable performance while delivering a 1.3x reduction in inference latency and a 1.7x increase in generation throughput, enabled by its parallel decoding capability.

  • 10 authors
·
Feb 7

Puppeteer: Rig and Animate Your 3D Models

Modern interactive applications increasingly demand dynamic 3D content, yet the transformation of static 3D models into animated assets constitutes a significant bottleneck in content creation pipelines. While recent advances in generative AI have revolutionized static 3D model creation, rigging and animation continue to depend heavily on expert intervention. We present Puppeteer, a comprehensive framework that addresses both automatic rigging and animation for diverse 3D objects. Our system first predicts plausible skeletal structures via an auto-regressive transformer that introduces a joint-based tokenization strategy for compact representation and a hierarchical ordering methodology with stochastic perturbation that enhances bidirectional learning capabilities. It then infers skinning weights via an attention-based architecture incorporating topology-aware joint attention that explicitly encodes inter-joint relationships based on skeletal graph distances. Finally, we complement these rigging advances with a differentiable optimization-based animation pipeline that generates stable, high-fidelity animations while being computationally more efficient than existing approaches. Extensive evaluations across multiple benchmarks demonstrate that our method significantly outperforms state-of-the-art techniques in both skeletal prediction accuracy and skinning quality. The system robustly processes diverse 3D content, ranging from professionally designed game assets to AI-generated shapes, producing temporally coherent animations that eliminate the jittering issues common in existing methods.

  • 9 authors
·
Aug 14, 2025 3

TubeMLLM: A Foundation Model for Topology Knowledge Exploration in Vessel-like Anatomy

Modeling medical vessel-like anatomy is challenging due to its intricate topology and sensitivity to dataset shifts. Consequently, task-specific models often suffer from topological inconsistencies, including artificial disconnections and spurious merges. Motivated by the promise of multimodal large language models (MLLMs) for zero-shot generalization, we propose TubeMLLM, a unified foundation model that couples structured understanding with controllable generation for medical vessel-like anatomy. By integrating topological priors through explicit natural language prompting and aligning them with visual representations in a shared-attention architecture, TubeMLLM significantly enhances topology-aware perception. Furthermore, we construct TubeMData, a pionner multimodal benchmark comprising comprehensive topology-centric tasks, and introduce an adaptive loss weighting strategy to emphasize topology-critical regions during training. Extensive experiments on fifteen diverse datasets demonstrate our superiority. Quantitatively, TubeMLLM achieves state-of-the-art out-of-distribution performance, substantially reducing global topological discrepancies on color fundus photography (decreasing the β_{0} number error from 37.42 to 8.58 compared to baselines). Notably, TubeMLLM exhibits exceptional zero-shot cross-modality transferring ability on unseen X-ray angiography, achieving a Dice score of 67.50% while significantly reducing the β_{0} error to 1.21. TubeMLLM also maintains robustness against degradations such as blur, noise, and low resolution. Furthermore, in topology-aware understanding tasks, the model achieves 97.38% accuracy in evaluating mask topological quality, significantly outperforming standard vision-language baselines.

  • 5 authors
·
Mar 10

FreeText: Training-Free Text Rendering in Diffusion Transformers via Attention Localization and Spectral Glyph Injection

Large-scale text-to-image (T2I) diffusion models excel at open-domain synthesis but still struggle with precise text rendering, especially for multi-line layouts, dense typography, and long-tailed scripts such as Chinese. Prior solutions typically require costly retraining or rigid external layout constraints, which can degrade aesthetics and limit flexibility. We propose FreeText, a training-free, plug-and-play framework that improves text rendering by exploiting intrinsic mechanisms of Diffusion Transformer (DiT) models. FreeText decomposes the problem into where to write and what to write. For where to write, we localize writing regions by reading token-wise spatial attribution from endogenous image-to-text attention, using sink-like tokens as stable spatial anchors and topology-aware refinement to produce high-confidence masks. For what to write, we introduce Spectral-Modulated Glyph Injection (SGMI), which injects a noise-aligned glyph prior with frequency-domain band-pass modulation to strengthen glyph structure and suppress semantic leakage (rendering the concept instead of the word). Extensive experiments on Qwen-Image, FLUX.1-dev, and SD3 variants across longText-Benchmark, CVTG, and our CLT-Bench show consistent gains in text readability while largely preserving semantic alignment and aesthetic quality, with modest inference overhead.

  • 6 authors
·
Jan 1

STD-PLM: Understanding Both Spatial and Temporal Properties of Spatial-Temporal Data with PLM

Spatial-temporal forecasting and imputation are important for real-world intelligent systems. Most existing methods are tailored for individual forecasting or imputation tasks but are not designed for both. Additionally, they are less effective for zero-shot and few-shot learning. While pre-trained language model (PLM) have exhibited strong pattern recognition and reasoning abilities across various tasks, including few-shot and zero-shot learning, their applications in spatial-temporal data understanding has been constrained by insufficient modeling of complex correlations such as the temporal correlations, spatial connectivity, non-pairwise and high-order spatial-temporal correlations within data. In this paper, we propose STD-PLM for understanding both spatial and temporal properties of Spatial-Temporal Data with PLM, which is capable of implementing both spatial-temporal forecasting and imputation tasks. STD-PLM understands spatial-temporal correlations via explicitly designed spatial and temporal tokenizers. Topology-aware node embeddings are designed for PLM to comprehend and exploit the topology structure of data in inductive manner. Furthermore, to mitigate the efficiency issues introduced by the PLM, we design a sandglass attention module (SGA) combined with a specific constrained loss function, which significantly improves the model's efficiency while ensuring performance. Extensive experiments demonstrate that STD-PLM exhibits competitive performance and generalization capabilities across the forecasting and imputation tasks on various datasets. Moreover, STD-PLM achieves promising results on both few-shot and zero-shot tasks.The code is made available at https://anonymous.4open.science/r/STD-PLM-F3BA{https://anonymous.4open.science/r/STD-PLM-F3BA}

  • 8 authors
·
Jul 12, 2024

Online Navigation Refinement: Achieving Lane-Level Guidance by Associating Standard-Definition and Online Perception Maps

Lane-level navigation is critical for geographic information systems and navigation-based tasks, offering finer-grained guidance than road-level navigation by standard definition (SD) maps. However, it currently relies on expansive global HD maps that cannot adapt to dynamic road conditions. Recently, online perception (OP) maps have become research hotspots, providing real-time geometry as an alternative, but lack the global topology needed for navigation. To address these issues, Online Navigation Refinement (ONR), a new mission is introduced that refines SD-map-based road-level routes into accurate lane-level navigation by associating SD maps with OP maps. The map-to-map association to handle many-to-one lane-to-road mappings under two key challenges: (1) no public dataset provides lane-to-road correspondences; (2) severe misalignment from spatial fluctuations, semantic disparities, and OP map noise invalidates traditional map matching. For these challenges, We contribute: (1) Online map association dataset (OMA), the first ONR benchmark with 30K scenarios and 2.6M annotated lane vectors; (2) MAT, a transformer with path-aware attention to aligns topology despite spatial fluctuations and semantic disparities and spatial attention for integrates noisy OP features via global context; and (3) NR P-R, a metric evaluating geometric and semantic alignment. Experiments show that MAT outperforms existing methods at 34 ms latency, enabling low-cost and up-to-date lane-level navigation.

  • 10 authors
·
Jul 10, 2025

RelTopo: Multi-Level Relational Modeling for Driving Scene Topology Reasoning

Accurate road topology reasoning is critical for autonomous driving, as it requires both perceiving road elements and understanding how lanes connect to each other (L2L) and to traffic elements (L2T). Existing methods often focus on either perception or L2L reasoning, leaving L2T underexplored and fall short of jointly optimizing perception and reasoning. Moreover, although topology prediction inherently involves relations, relational modeling itself is seldom incorporated into feature extraction or supervision. As humans naturally leverage contextual relationships to recognize road element and infer their connectivity, we posit that relational modeling can likewise benefit both perception and reasoning, and that these two tasks should be mutually enhancing. To this end, we propose RelTopo, a multi-level relational modeling approach that systematically integrates relational cues across three levels: 1) perception-level: a relation-aware lane detector with geometry-biased self-attention and curve-guided cross-attention enriches lane representations; 2) reasoning-level: relation-enhanced topology heads, including a geometry-enhanced L2L head and a cross-view L2T head, enhance topology inference via relational cues; and 3) supervision-level: a contrastive InfoNCE strategy regularizes relational embeddings. This design enables perception and reasoning to be optimized jointly. Extensive experiments on OpenLane-V2 demonstrate that RelTopo significantly improves both detection and topology reasoning, with gains of +3.1 in DET_l, +5.3 in TOP_{ll}, +4.9 in TOP_{lt}, and +4.4 overall in OLS, setting a new state-of-the-art. Code will be released.

  • 8 authors
·
Jun 16, 2025

The Underappreciated Power of Vision Models for Graph Structural Understanding

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.

  • 9 authors
·
Oct 27, 2025 5

TopoPoint: Enhance Topology Reasoning via Endpoint Detection in Autonomous Driving

Topology reasoning, which unifies perception and structured reasoning, plays a vital role in understanding intersections for autonomous driving. However, its performance heavily relies on the accuracy of lane detection, particularly at connected lane endpoints. Existing methods often suffer from lane endpoints deviation, leading to incorrect topology construction. To address this issue, we propose TopoPoint, a novel framework that explicitly detects lane endpoints and jointly reasons over endpoints and lanes for robust topology reasoning. During training, we independently initialize point and lane query, and proposed Point-Lane Merge Self-Attention to enhance global context sharing through incorporating geometric distances between points and lanes as an attention mask . We further design Point-Lane Graph Convolutional Network to enable mutual feature aggregation between point and lane query. During inference, we introduce Point-Lane Geometry Matching algorithm that computes distances between detected points and lanes to refine lane endpoints, effectively mitigating endpoint deviation. Extensive experiments on the OpenLane-V2 benchmark demonstrate that TopoPoint achieves state-of-the-art performance in topology reasoning (48.8 on OLS). Additionally, we propose DET_p to evaluate endpoint detection, under which our method significantly outperforms existing approaches (52.6 v.s. 45.2 on DET_p). The code is released at https://github.com/Franpin/TopoPoint.

  • 6 authors
·
May 23, 2025

Faster Neighborhood Attention: Reducing the O(n^2) Cost of Self Attention at the Threadblock Level

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

  • 3 authors
·
Mar 7, 2024

TopoPerception: A Shortcut-Free Evaluation of Global Visual Perception in Large Vision-Language Models

Large Vision-Language Models (LVLMs) typically align visual features from an encoder with a pre-trained Large Language Model (LLM). However, this makes the visual perception module a bottleneck, which constrains the overall capabilities of LVLMs. Conventional evaluation benchmarks, while rich in visual semantics, often contain unavoidable local shortcuts that can lead to an overestimation of models' perceptual abilities. Here, we introduce TopoPerception, a benchmark that leverages topological properties to rigorously evaluate the global visual perception capabilities of LVLMs across various granularities. Since topology depends on the global structure of an image and is invariant to local features, TopoPerception enables a shortcut-free assessment of global perception, fundamentally distinguishing it from semantically rich tasks. We evaluate state-of-the-art models on TopoPerception and find that even at the coarsest perceptual granularity, all models perform no better than random chance, indicating a profound inability to perceive global visual features. Notably, a consistent trend emerge within model families: more powerful models with stronger reasoning capabilities exhibit lower accuracy. This suggests that merely scaling up models is insufficient to address this deficit and may even exacerbate it. Progress may require new training paradigms or architectures. TopoPerception not only exposes a critical bottleneck in current LVLMs but also offers a lens and direction for improving their global visual perception. The data and code are publicly available at: https://github.com/Wenhao-Zhou/TopoPerception.

  • 3 authors
·
Nov 14, 2025 2

Attention Mechanisms Perspective: Exploring LLM Processing of Graph-Structured Data

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}

  • 5 authors
·
May 4, 2025 1

OverLoCK: An Overview-first-Look-Closely-next ConvNet with Context-Mixing Dynamic Kernels

Top-down attention plays a crucial role in the human vision system, wherein the brain initially obtains a rough overview of a scene to discover salient cues (i.e., overview first), followed by a more careful finer-grained examination (i.e., look closely next). However, modern ConvNets remain confined to a pyramid structure that successively downsamples the feature map for receptive field expansion, neglecting this crucial biomimetic principle. We present OverLoCK, the first pure ConvNet backbone architecture that explicitly incorporates a top-down attention mechanism. Unlike pyramid backbone networks, our design features a branched architecture with three synergistic sub-networks: 1) a Base-Net that encodes low/mid-level features; 2) a lightweight Overview-Net that generates dynamic top-down attention through coarse global context modeling (i.e., overview first); and 3) a robust Focus-Net that performs finer-grained perception guided by top-down attention (i.e., look closely next). To fully unleash the power of top-down attention, we further propose a novel context-mixing dynamic convolution (ContMix) that effectively models long-range dependencies while preserving inherent local inductive biases even when the input resolution increases, addressing critical limitations in existing convolutions. Our OverLoCK exhibits a notable performance improvement over existing methods. For instance, OverLoCK-T achieves a Top-1 accuracy of 84.2%, significantly surpassing ConvNeXt-B while using only around one-third of the FLOPs/parameters. On object detection, our OverLoCK-S clearly surpasses MogaNet-B by 1% in AP^b. On semantic segmentation, our OverLoCK-T remarkably improves UniRepLKNet-T by 1.7% in mIoU. Code is publicly available at https://github.com/LMMMEng/OverLoCK.

  • 2 authors
·
Feb 27, 2025

TopoMortar: A dataset to evaluate image segmentation methods focused on topology accuracy

We present TopoMortar, a brick wall dataset that is the first dataset specifically designed to evaluate topology-focused image segmentation methods, such as topology loss functions. TopoMortar enables to investigate in two ways whether methods incorporate prior topological knowledge. First, by eliminating challenges seen in real-world data, such as small training set, noisy labels, and out-of-distribution test-set images, that, as we show, impact the effectiveness of topology losses. Second, by allowing to assess in the same dataset topology accuracy across dataset challenges, isolating dataset-related effects from the effect of incorporating prior topological knowledge. In these two experiments, it is deliberately difficult to improve topology accuracy without actually using topology information, thus, permitting to attribute an improvement in topology accuracy to the incorporation of prior topological knowledge. To this end, TopoMortar includes three types of labels (accurate, noisy, pseudo-labels), two fixed training sets (large and small), and in-distribution and out-of-distribution test-set images. We compared eight loss functions on TopoMortar, and we found that clDice achieved the most topologically accurate segmentations, Skeleton Recall loss performed best particularly with noisy labels, and the relative advantageousness of the other loss functions depended on the experimental setting. Additionally, we show that simple methods, such as data augmentation and self-distillation, can elevate Cross entropy Dice loss to surpass most topology loss functions, and that those simple methods can enhance topology loss functions as well. clDice and Skeleton Recall loss, both skeletonization-based loss functions, were also the fastest to train, making this type of loss function a promising research direction. TopoMortar and our code can be found at https://github.com/jmlipman/TopoMortar

  • 4 authors
·
Mar 5, 2025

Flux Attention: Context-Aware Hybrid Attention for Efficient LLMs Inference

The quadratic computational complexity of standard attention mechanisms presents a severe scalability bottleneck for LLMs in long-context scenarios. While hybrid attention mechanisms combining Full Attention (FA) and Sparse Attention (SA) offer a potential solution, existing methods typically rely on static allocation ratios that fail to accommodate the variable retrieval demands of different tasks. Furthermore, head-level dynamic sparsity often introduces severe computational load imbalance and synchronization long-tails, which hinder hardware acceleration during autoregressive decoding. To bridge this gap, we introduce Flux Attention, a context-aware framework that dynamically optimizes attention computation at the layer level. By integrating a lightweight Layer Router into frozen pretrained LLMs, the proposed method adaptively routes each layer to FA or SA based on the input context. This layer-wise routing preserves high-fidelity information retrieval while ensuring contiguous memory access, translating theoretical computational reductions into practical wall-clock speedups. As a parameter-efficient approach, our framework requires only 12 hours of training on 8timesA800 GPUs. Extensive experiments across multiple long-context and mathematical reasoning benchmarks demonstrate that Flux Attention achieves a superior trade-off between performance and inference speed compared with baseline models, with speed improvements of up to 2.8times and 2.0times in the prefill and decode stages.

Scaling Local Self-Attention for Parameter Efficient Visual Backbones

Self-attention has the promise of improving computer vision systems due to parameter-independent scaling of receptive fields and content-dependent interactions, in contrast to parameter-dependent scaling and content-independent interactions of convolutions. Self-attention models have recently been shown to have encouraging improvements on accuracy-parameter trade-offs compared to baseline convolutional models such as ResNet-50. In this work, we aim to develop self-attention models that can outperform not just the canonical baseline models, but even the high-performing convolutional models. We propose two extensions to self-attention that, in conjunction with a more efficient implementation of self-attention, improve the speed, memory usage, and accuracy of these models. We leverage these improvements to develop a new self-attention model family, HaloNets, which reach state-of-the-art accuracies on the parameter-limited setting of the ImageNet classification benchmark. In preliminary transfer learning experiments, we find that HaloNet models outperform much larger models and have better inference performance. On harder tasks such as object detection and instance segmentation, our simple local self-attention and convolutional hybrids show improvements over very strong baselines. These results mark another step in demonstrating the efficacy of self-attention models on settings traditionally dominated by convolutional models.

  • 6 authors
·
Mar 23, 2021 1

Generalized Neighborhood Attention: Multi-dimensional Sparse Attention at the Speed of Light

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

  • 16 authors
·
Apr 23, 2025

OAT: Object-Level Attention Transformer for Gaze Scanpath Prediction

Visual search is important in our daily life. The efficient allocation of visual attention is critical to effectively complete visual search tasks. Prior research has predominantly modelled the spatial allocation of visual attention in images at the pixel level, e.g. using a saliency map. However, emerging evidence shows that visual attention is guided by objects rather than pixel intensities. This paper introduces the Object-level Attention Transformer (OAT), which predicts human scanpaths as they search for a target object within a cluttered scene of distractors. OAT uses an encoder-decoder architecture. The encoder captures information about the position and appearance of the objects within an image and about the target. The decoder predicts the gaze scanpath as a sequence of object fixations, by integrating output features from both the encoder and decoder. We also propose a new positional encoding that better reflects spatial relationships between objects. We evaluated OAT on the Amazon book cover dataset and a new dataset for visual search that we collected. OAT's predicted gaze scanpaths align more closely with human gaze patterns, compared to predictions by algorithms based on spatial attention on both established metrics and a novel behavioural-based metric. Our results demonstrate the generalization ability of OAT, as it accurately predicts human scanpaths for unseen layouts and target objects.

  • 5 authors
·
Jul 18, 2024

BiFormer: Vision Transformer with Bi-Level Routing 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.

  • 5 authors
·
Mar 15, 2023

The Topology and Geometry of Neural Representations

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis (tRSA), an extension of representational similarity analysis (RSA) that uses a family of geo-topological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this new family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

  • 2 authors
·
Sep 19, 2023

Superlinear Multi-Step Attention

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.

  • 1 authors
·
Jan 26

A Topological Perspective on Demystifying GNN-Based Link Prediction Performance

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.

  • 7 authors
·
Oct 6, 2023

ST-LINK: Spatially-Aware Large Language Models for Spatio-Temporal Forecasting

Traffic forecasting represents a crucial problem within intelligent transportation systems. In recent research, Large Language Models (LLMs) have emerged as a promising method, but their intrinsic design, tailored primarily for sequential token processing, introduces notable challenges in effectively capturing spatial dependencies. Specifically, the inherent limitations of LLMs in modeling spatial relationships and their architectural incompatibility with graph-structured spatial data remain largely unaddressed. To overcome these limitations, we introduce ST-LINK, a novel framework that enhances the capability of Large Language Models to capture spatio-temporal dependencies. Its key components are Spatially-Enhanced Attention (SE-Attention) and the Memory Retrieval Feed-Forward Network (MRFFN). SE-Attention extends rotary position embeddings to integrate spatial correlations as direct rotational transformations within the attention mechanism. This approach maximizes spatial learning while preserving the LLM's inherent sequential processing structure. Meanwhile, MRFFN dynamically retrieves and utilizes key historical patterns to capture complex temporal dependencies and improve the stability of long-term forecasting. Comprehensive experiments on benchmark datasets demonstrate that ST-LINK surpasses conventional deep learning and LLM approaches, and effectively captures both regular traffic patterns and abrupt changes.

  • 4 authors
·
Sep 17, 2025 1

The Blueprints of Intelligence: A Functional-Topological Foundation for Perception and Representation

Real-world phenomena do not generate arbitrary variability: their signals concentrate on compact, low-variability subsets of functional space, enabling rapid generalization from few examples. A small child can recognize a dog after extremely limited exposure because the perceptual manifold of "dog" is compact, structured, and low-dimensional. We formalize this principle through a deterministic functional-topological framework in which the set of valid realizations produced by a physical process forms a compact subset of a Banach space, endowed with stable invariants, a finite Hausdorff radius, and an induced continuous perceptual functional. This geometry provides explicit limits on knowledge, conditions for identifiability, and guarantees for generalization from sparse evidence -- properties fundamental to both natural and artificial intelligence. Across electromechanical, electrochemical, and physiological domains, we show that real-world processes consistently generate compact perceptual manifolds with the same geometric characteristics. Their boundaries can be discovered in a fully self-supervised manner as the empirical radius saturates with increasing sampling, even when the governing equations are unknown. These results demonstrate that deterministic functional topology offers a unified mathematical foundation for perception, representation, and world-model construction. It provides a geometric explanation for why biological learners and self-supervised AI systems can generalize from few observations, and establishes compact perceptual manifolds as a fundamental building block for future AI architectures. Finally, this work unifies biological perception and modern self-supervised models under a single geometric principle: both derive their generalization ability from the compactness and invariants of real-world perceptual manifolds.

  • 1 authors
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Dec 4, 2025

Learning from Historical Activations in Graph Neural Networks

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.

  • 4 authors
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Jan 3

Sparsifiner: Learning Sparse Instance-Dependent Attention for Efficient Vision Transformers

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%.

  • 6 authors
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Mar 23, 2023

Focusing by Contrastive Attention: Enhancing VLMs' Visual Reasoning

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

Graph Transformers for Large Graphs

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.

  • 6 authors
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Dec 18, 2023

Pointer Networks

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence and Neural Turing Machines, because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems -- finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem -- using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.

  • 3 authors
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Jun 9, 2015

RoboHop: Segment-based Topological Map Representation for Open-World Visual Navigation

Mapping is crucial for spatial reasoning, planning and robot navigation. Existing approaches range from metric, which require precise geometry-based optimization, to purely topological, where image-as-node based graphs lack explicit object-level reasoning and interconnectivity. In this paper, we propose a novel topological representation of an environment based on "image segments", which are semantically meaningful and open-vocabulary queryable, conferring several advantages over previous works based on pixel-level features. Unlike 3D scene graphs, we create a purely topological graph with segments as nodes, where edges are formed by a) associating segment-level descriptors between pairs of consecutive images and b) connecting neighboring segments within an image using their pixel centroids. This unveils a "continuous sense of a place", defined by inter-image persistence of segments along with their intra-image neighbours. It further enables us to represent and update segment-level descriptors through neighborhood aggregation using graph convolution layers, which improves robot localization based on segment-level retrieval. Using real-world data, we show how our proposed map representation can be used to i) generate navigation plans in the form of "hops over segments" and ii) search for target objects using natural language queries describing spatial relations of objects. Furthermore, we quantitatively analyze data association at the segment level, which underpins inter-image connectivity during mapping and segment-level localization when revisiting the same place. Finally, we show preliminary trials on segment-level `hopping' based zero-shot real-world navigation. Project page with supplementary details: oravus.github.io/RoboHop/

  • 7 authors
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May 9, 2024

ConnNet: A Long-Range Relation-Aware Pixel-Connectivity Network for Salient Segmentation

Salient segmentation aims to segment out attention-grabbing regions, a critical yet challenging task and the foundation of many high-level computer vision applications. It requires semantic-aware grouping of pixels into salient regions and benefits from the utilization of global multi-scale contexts to achieve good local reasoning. Previous works often address it as two-class segmentation problems utilizing complicated multi-step procedures including refinement networks and complex graphical models. We argue that semantic salient segmentation can instead be effectively resolved by reformulating it as a simple yet intuitive pixel-pair based connectivity prediction task. Following the intuition that salient objects can be naturally grouped via semantic-aware connectivity between neighboring pixels, we propose a pure Connectivity Net (ConnNet). ConnNet predicts connectivity probabilities of each pixel with its neighboring pixels by leveraging multi-level cascade contexts embedded in the image and long-range pixel relations. We investigate our approach on two tasks, namely salient object segmentation and salient instance-level segmentation, and illustrate that consistent improvements can be obtained by modeling these tasks as connectivity instead of binary segmentation tasks for a variety of network architectures. We achieve state-of-the-art performance, outperforming or being comparable to existing approaches while reducing inference time due to our less complex approach.

  • 5 authors
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Apr 20, 2018

TopoReformer: Mitigating Adversarial Attacks Using Topological Purification in OCR Models

Adversarially perturbed images of text can cause sophisticated OCR systems to produce misleading or incorrect transcriptions from seemingly invisible changes to humans. Some of these perturbations even survive physical capture, posing security risks to high-stakes applications such as document processing, license plate recognition, and automated compliance systems. Existing defenses, such as adversarial training, input preprocessing, or post-recognition correction, are often model-specific, computationally expensive, and affect performance on unperturbed inputs while remaining vulnerable to unseen or adaptive attacks. To address these challenges, TopoReformer is introduced, a model-agnostic reformation pipeline that mitigates adversarial perturbations while preserving the structural integrity of text images. Topology studies properties of shapes and spaces that remain unchanged under continuous deformations, focusing on global structures such as connectivity, holes, and loops rather than exact distance. Leveraging these topological features, TopoReformer employs a topological autoencoder to enforce manifold-level consistency in latent space and improve robustness without explicit gradient regularization. The proposed method is benchmarked on EMNIST, MNIST, against standard adversarial attacks (FGSM, PGD, Carlini-Wagner), adaptive attacks (EOT, BDPA), and an OCR-specific watermark attack (FAWA).

  • 5 authors
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Nov 19, 2025

Various Lengths, Constant Speed: Efficient Language Modeling with Lightning Attention

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

  • 6 authors
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May 27, 2024 2

Scalable Graph Attention-based Instance Selection via Mini-Batch Sampling and Hierarchical Hashing

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

  • 3 authors
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Feb 27, 2025