Daily Papers

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have emerged as the preferred method for this challenge, thanks to their ability to harness large sequence databases. Yet, their reliance on expansive sequence data and parameter sets limits their flexibility and practicality in real-world scenarios. Concurrently, the recent surge in computationally predicted protein structures unlocks new opportunities in protein representation learning. While promising, the computational burden carried by such complex data still hinders widely-adopted practical applications. To address these limitations, we introduce a novel framework that enhances protein language models by integrating protein structural data. Drawing from recent advances in graph transformers, our approach refines the self-attention mechanisms of pretrained language transformers by integrating structural information with structure extractor modules. This refined model, termed Protein Structure Transformer (PST), is further pretrained on a small protein structure database, using the same masked language modeling objective as traditional protein language models. Empirical evaluations of PST demonstrate its superior parameter efficiency relative to protein language models, despite being pretrained on a dataset comprising only 542K structures. Notably, PST consistently outperforms the state-of-the-art foundation model for protein sequences, ESM-2, setting a new benchmark in protein function prediction. Our findings underscore the potential of integrating structural information into protein language models, paving the way for more effective and efficient protein modeling Code and pretrained models are available at https://github.com/BorgwardtLab/PST.

Next location prediction plays a crucial role in various real-world applications. Recently, due to the limitation of existing deep learning methods, attempts have been made to apply large language models (LLMs) to zero-shot next location prediction task. However, they directly generate the final output using LLMs without systematic design, which limits the potential of LLMs to uncover complex mobility patterns and underestimates their extensive reserve of global geospatial knowledge. In this paper, we introduce AgentMove, a systematic agentic prediction framework to achieve generalized next location prediction. In AgentMove, we first decompose the mobility prediction task and design specific modules to complete them, including spatial-temporal memory for individual mobility pattern mining, world knowledge generator for modeling the effects of urban structure and collective knowledge extractor for capturing the shared patterns among population. Finally, we combine the results of three modules and conduct a reasoning step to generate the final predictions. Extensive experiments utilizing mobility data from two distinct sources reveal that AgentMove surpasses the leading baseline by 3.33% to 8.57% across 8 out of 12 metrics and it shows robust predictions with various LLMs as base and also less geographical bias across cities. Our codes are available via https://github.com/tsinghua-fib-lab/AgentMove.

This paper introduces VisuCraft, a novel framework designed to significantly enhance the capabilities of Large Vision-Language Models (LVLMs) in complex visual-guided creative content generation. Existing LVLMs often exhibit limitations in maintaining high visual fidelity, genuine creativity, and precise adherence to nuanced user instructions when generating long-form texts. VisuCraft addresses these challenges by integrating a multimodal structured information extractor (E) and a dynamic prompt generation module (G). The extractor distills fine-grained visual attributes from input images into a rich, structured representation, which the dynamic prompt module then combines with user instructions to create highly optimized prompts for underlying LVLMs (e.g., LLaVA, InstructBLIP). Evaluated on the self-constructed ImageStoryGen-500K dataset using VisuGen Metrics (Visual Grounding, Creativity, and Instruction Adherence), VisuCraft consistently outperforms baseline LVLMs across tasks like story generation and poetry composition. Our results demonstrate remarkable improvements, particularly in creativity and instruction adherence, validating VisuCraft's effectiveness in producing imaginative, visually grounded, and user-aligned long-form creative text. This work unlocks new potential for LVLMs in sophisticated creative AI applications.

Graphical User Interface (GUI) datasets are crucial for various downstream tasks. However, GUI datasets often generate annotation information through automatic labeling, which commonly results in inaccurate GUI element BBox annotations, including missing, duplicate, or meaningless BBoxes. These issues can degrade the performance of models trained on these datasets, limiting their effectiveness in real-world applications. Additionally, existing GUI datasets only provide BBox annotations visually, which restricts the development of visually related GUI downstream tasks. To address these issues, we introduce PixelWeb, a large-scale GUI dataset containing over 100,000 annotated web pages. PixelWeb is constructed using a novel automatic annotation approach that integrates visual feature extraction and Document Object Model (DOM) structure analysis through two core modules: channel derivation and layer analysis. Channel derivation ensures accurate localization of GUI elements in cases of occlusion and overlapping elements by extracting BGRA four-channel bitmap annotations. Layer analysis uses the DOM to determine the visibility and stacking order of elements, providing precise BBox annotations. Additionally, PixelWeb includes comprehensive metadata such as element images, contours, and mask annotations. Manual verification by three independent annotators confirms the high quality and accuracy of PixelWeb annotations. Experimental results on GUI element detection tasks show that PixelWeb achieves performance on the mAP95 metric that is 3-7 times better than existing datasets. We believe that PixelWeb has great potential for performance improvement in downstream tasks such as GUI generation and automated user interaction.

Document Structured Extraction (DSE) aims to extract structured content from raw documents. Despite the emergence of numerous DSE systems, their unified evaluation remains inadequate, significantly hindering the field's advancement. This problem is largely attributed to existing benchmark paradigms, which exhibit fragmented and localized characteristics. To address these limitations and offer a thorough evaluation of DSE systems, we introduce a novel benchmark named READoc, which defines DSE as a realistic task of converting unstructured PDFs into semantically rich Markdown. The READoc dataset is derived from 2,233 diverse and real-world documents from arXiv and GitHub. In addition, we develop a DSE Evaluation S^3uite comprising Standardization, Segmentation and Scoring modules, to conduct a unified evaluation of state-of-the-art DSE approaches. By evaluating a range of pipeline tools, expert visual models, and general VLMs, we identify the gap between current work and the unified, realistic DSE objective for the first time. We aspire that READoc will catalyze future research in DSE, fostering more comprehensive and practical solutions.

Multi-view image generation holds significant application value in computer vision, particularly in domains like 3D reconstruction, virtual reality, and augmented reality. Most existing methods, which rely on extending single images, face notable computational challenges in maintaining cross-view consistency and generating high-resolution outputs. To address these issues, we propose the Geometry-guided Multi-View Diffusion Model, which incorporates mechanisms for extracting multi-view geometric information and adjusting the intensity of geometric features to generate images that are both consistent across views and rich in detail. Specifically, we design a multi-view geometry information extraction module that leverages depth maps, normal maps, and foreground segmentation masks to construct a shared geometric structure, ensuring shape and structural consistency across different views. To enhance consistency and detail restoration during generation, we develop a decoupled geometry-enhanced attention mechanism that strengthens feature focus on key geometric details, thereby improving overall image quality and detail preservation. Furthermore, we apply an adaptive learning strategy that fine-tunes the model to better capture spatial relationships and visual coherence between the generated views, ensuring realistic results. Our model also incorporates an iterative refinement process that progressively improves the output quality through multiple stages of image generation. Finally, a dynamic geometry information intensity adjustment mechanism is proposed to adaptively regulate the influence of geometric data, optimizing overall quality while ensuring the naturalness of generated images. More details can be found on the project page: https://sobeymil.github.io/GeoMVD.com.

Document parsing is essential for converting unstructured and semi-structured documents-such as contracts, academic papers, and invoices-into structured, machine-readable data. Document parsing extract reliable structured data from unstructured inputs, providing huge convenience for numerous applications. Especially with recent achievements in Large Language Models, document parsing plays an indispensable role in both knowledge base construction and training data generation. This survey presents a comprehensive review of the current state of document parsing, covering key methodologies, from modular pipeline systems to end-to-end models driven by large vision-language models. Core components such as layout detection, content extraction (including text, tables, and mathematical expressions), and multi-modal data integration are examined in detail. Additionally, this paper discusses the challenges faced by modular document parsing systems and vision-language models in handling complex layouts, integrating multiple modules, and recognizing high-density text. It emphasizes the importance of developing larger and more diverse datasets and outlines future research directions.

Reality is a dance between rigid constraints and deformable structures. For video models, that means generating motion that preserves fidelity as well as structure. Despite progress in diffusion models, producing realistic structure-preserving motion remains challenging, especially for articulated and deformable objects such as humans and animals. Scaling training data alone, so far, has failed to resolve physically implausible transitions. Existing approaches rely on conditioning with noisy motion representations, such as optical flow or skeletons extracted using an external imperfect model. To address these challenges, we introduce an algorithm to distill structure-preserving motion priors from an autoregressive video tracking model (SAM2) into a bidirectional video diffusion model (CogVideoX). With our method, we train SAM2VideoX, which contains two innovations: (1) a bidirectional feature fusion module that extracts global structure-preserving motion priors from a recurrent model like SAM2; (2) a Local Gram Flow loss that aligns how local features move together. Experiments on VBench and in human studies show that SAM2VideoX delivers consistent gains (+2.60\% on VBench, 21-22\% lower FVD, and 71.4\% human preference) over prior baselines. Specifically, on VBench, we achieve 95.51\%, surpassing REPA (92.91\%) by 2.60\%, and reduce FVD to 360.57, a 21.20\% and 22.46\% improvement over REPA- and LoRA-finetuning, respectively. The project website can be found at https://sam2videox.github.io/ .