Daily Papers

Current coding-agent benchmarks usually pro- vide the full task specification upfront. Real research coding often does not: the intended system is progressively disclosed through in- teraction, requiring the agent to track durable design commitments across a long session. We introduce a benchmark for this setting and study faithfulne Ss Loss U nder eM ergent s Pecification (SLUMP), defined as the reduc- tion in final implementation faithfulness un- der emergent specification relative to a single- shot specification control. The benchmark con- tains 20 recent ML papers (10 ICML 2025, 10 NeurIPS 2025), 371 atomic verifiable compo- nents, and interaction scripts of approximately 60 coding requests that progressively disclose the target design without revealing the paper itself. Final repositories are scored with a five-level component-faithfulness rubric and accompanied by an exposure audit to verify that scored components are recoverable from the visible interaction. Evaluated on Claude Code and Codex, the single-shot specification control achieves higher overall implementation fidelity on 16/20 and 14/20 papers, respectively. Structural integration degrades under emergent specification on both platforms, while seman- tic faithfulness loss is substantial on Claude Code and small on Codex. As a mitigation case study, we introduce ProjectGuard, an exter- nal project-state layer for specification tracking. On Claude Code, ProjectGuard recovers 90% of the faithfulness gap, increases fully faith- ful components from 118 to 181, and reduces severe failures from 72 to 49. These results identify specification tracking as a distinct eval- uation target for long-horizon coding agents.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

Visual illusions traditionally rely on spatial manipulations such as multi-view consistency. In this work, we introduce Progressive Semantic Illusions, a novel vector sketching task where a single sketch undergoes a dramatic semantic transformation through the sequential addition of strokes. We present Stroke of Surprise, a generative framework that optimizes vector strokes to satisfy distinct semantic interpretations at different drawing stages. The core challenge lies in the "dual-constraint": initial prefix strokes must form a coherent object (e.g., a duck) while simultaneously serving as the structural foundation for a second concept (e.g., a sheep) upon adding delta strokes. To address this, we propose a sequence-aware joint optimization framework driven by a dual-branch Score Distillation Sampling (SDS) mechanism. Unlike sequential approaches that freeze the initial state, our method dynamically adjusts prefix strokes to discover a "common structural subspace" valid for both targets. Furthermore, we introduce a novel Overlay Loss that enforces spatial complementarity, ensuring structural integration rather than occlusion. Extensive experiments demonstrate that our method significantly outperforms state-of-the-art baselines in recognizability and illusion strength, successfully expanding visual anagrams from the spatial to the temporal dimension. Project page: https://stroke-of-surprise.github.io/

Conversational semantic role labeling (CSRL) is a newly proposed task that uncovers the shallow semantic structures in a dialogue text. Unfortunately several important characteristics of the CSRL task have been overlooked by the existing works, such as the structural information integration, near-neighbor influence. In this work, we investigate the integration of a latent graph for CSRL. We propose to automatically induce a predicate-oriented latent graph (POLar) with a predicate-centered Gaussian mechanism, by which the nearer and informative words to the predicate will be allocated with more attention. The POLar structure is then dynamically pruned and refined so as to best fit the task need. We additionally introduce an effective dialogue-level pre-trained language model, CoDiaBERT, for better supporting multiple utterance sentences and handling the speaker coreference issue in CSRL. Our system outperforms best-performing baselines on three benchmark CSRL datasets with big margins, especially achieving over 4% F1 score improvements on the cross-utterance argument detection. Further analyses are presented to better understand the effectiveness of our proposed methods.

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the underlying discrete representations are not well understood. In this work, we first demonstrate that the successful utilization of structural tokens in a language model for structure prediction depends on using rich, pre-trained sequence embeddings to bridge the semantic gap between the sequence and structural "language". The analysis of the structural vocabulary itself then reveals significant semantic redundancy, where multiple distinct tokens correspond to nearly identical local geometries, acting as "structural synonyms". This redundancy, rather than being a flaw, can be exploited with a simple "synonym swap" strategy to generate diverse conformational ensembles by perturbing a predicted structure with its structural synonyms. This computationally lightweight method accurately recapitulates protein flexibility, performing competitively with state-of-the-art models. Our study provides fundamental insights into the nature of discrete protein structure representations and introduces a powerful, near-instantaneous method for modeling protein dynamics. Source code is available in https://github.com/IDEA-XL/TokenMD.

Large Language Model (LLM) multi-agent systems are increasingly deployed as interacting agent societies, yet scaling these systems often yields diminishing or unstable returns, the causes of which remain poorly understood. We present the first large-scale empirical study of coordination dynamics in LLM-based multi-agent systems, introducing an atomic event-level formulation that reconstructs reasoning as cascades of coordination. Analyzing over 1.5 Million interactions across tasks, topologies, and scales, we uncover three coupled laws: coordination follows heavy-tailed cascades, concentrates via preferential attachment into intellectual elites, and produces increasingly frequent extreme events as system size grows. We show that these effects are coupled through a single structural mechanism: an integration bottleneck, in which coordination expansion scales with system size while consolidation does not, producing large but weakly integrated reasoning processes. To test this mechanism, we introduce Deficit-Triggered Integration (DTI), which selectively increases integration under imbalance. DTI improves performance precisely where coordination fails, without suppressing large-scale reasoning. Together, our results establish quantitative laws of collective cognition and identify coordination structure as a fundamental, previously unmeasured axis for understanding and improving scalable multi-agent intelligence.

Hepatocellular carcinoma (HCC), ranking as the third leading cause of cancer-related mortality worldwide, demands urgent improvements in early detection to enhance patient survival. While ultrasound remains the preferred screening modality due to its cost-effectiveness and real-time capabilities, its sensitivity (59%-78%) heavily relies on radiologists' expertise, leading to inconsistent diagnostic outcomes and operational inefficiencies. Recent advancements in AI technology offer promising solutions to bridge this gap. This study introduces the Hierarchical Sparse Query Transformer (HSQformer), a novel hybrid architecture that synergizes CNNs' local feature extraction with Vision Transformers' global contextual awareness through latent space representation and sparse learning. By dynamically activating task-specific experts via a Mixture-of-Experts (MoE) framework, HSQformer achieves hierarchical feature integration without structural redundancy. Evaluated across three clinical scenarios: single-center, multi-center, and high-risk patient cohorts, HSQformer outperforms state-of-the-art models (e.g., 95.38% AUC in multi-center testing) and matches senior radiologists' diagnostic accuracy while significantly surpassing junior counterparts. These results highlight the potential of AI-assisted tools to standardize HCC screening, reduce dependency on human expertise, and improve early diagnosis rates. The full code is available at https://github.com/Asunatan/HSQformer.

Predictive process monitoring is a process mining task aimed at forecasting information about a running process trace, such as the most correct next activity to be executed. In medical domains, predictive process monitoring can provide valuable decision support in atypical and nontrivial situations. Decision support and quality assessment in medicine cannot ignore domain knowledge, in order to be grounded on all the available information (which is not limited to data) and to be really acceptable by end users. In this paper, we propose a predictive process monitoring approach relying on the use of a {\em transformer}, a deep learning architecture based on the attention mechanism. A major contribution of our work lies in the incorporation of ontological domain-specific knowledge, carried out through a graph positional encoding technique. The paper presents and discusses the encouraging experimental result we are collecting in the domain of stroke management.

The Knowledge Graph Entity Typing (KGET) task aims to predict missing type annotations for entities in knowledge graphs. Recent works only utilize the \textbf{structural knowledge} in the local neighborhood of entities, disregarding \textbf{semantic knowledge} in the textual representations of entities, relations, and types that are also crucial for type inference. Additionally, we observe that the interaction between semantic and structural knowledge can be utilized to address the false-negative problem. In this paper, we propose a novel \underline{S}emantic and \underline{S}tructure-aware KG \underline{E}ntity \underline{T}yping~{(SSET)} framework, which is composed of three modules. First, the Semantic Knowledge Encoding module encodes factual knowledge in the KG with a Masked Entity Typing task. Then, the Structural Knowledge Aggregation module aggregates knowledge from the multi-hop neighborhood of entities to infer missing types. Finally, the Unsupervised Type Re-ranking module utilizes the inference results from the two models above to generate type predictions that are robust to false-negative samples. Extensive experiments show that SSET significantly outperforms existing state-of-the-art methods.

We introduce a novel neural network, SkyReconNet, which combines the expanded receptive fields of dilated convolutional layers along with standard convolutions, to capture both the global and local features for reconstructing the missing information in an image. We implement our network to inpaint the masked regions in a full-sky Cosmic Microwave Background (CMB) map. Inpainting CMB maps is a particularly formidable challenge when dealing with extensive and irregular masks, such as galactic masks which can obscure substantial fractions of the sky. The hybrid design of SkyReconNet leverages the strengths of standard and dilated convolutions to accurately predict CMB fluctuations in the masked regions, by effectively utilizing the information from surrounding unmasked areas. During training, the network optimizes its weights by minimizing a composite loss function that combines the Structural Similarity Index Measure (SSIM) and mean squared error (MSE). SSIM preserves the essential structural features of the CMB, ensuring an accurate and coherent reconstruction of the missing CMB fluctuations, while MSE minimizes the pixel-wise deviations, enhancing the overall accuracy of the predictions. The predicted CMB maps and their corresponding angular power spectra align closely with the targets, achieving the performance limited only by the fundamental uncertainty of cosmic variance. The network's generic architecture enables application to other physics-based challenges involving data with missing or defective pixels, systematic artefacts etc. Our results demonstrate its effectiveness in addressing the challenges posed by large irregular masks, offering a significant inpainting tool not only for CMB analyses but also for image-based experiments across disciplines where such data imperfections are prevalent.

Named entity disambiguation (NED), which involves mapping textual mentions to structured entities, is particularly challenging in the medical domain due to the presence of rare entities. Existing approaches are limited by the presence of coarse-grained structural resources in biomedical knowledge bases as well as the use of training datasets that provide low coverage over uncommon resources. In this work, we address these issues by proposing a cross-domain data integration method that transfers structural knowledge from a general text knowledge base to the medical domain. We utilize our integration scheme to augment structural resources and generate a large biomedical NED dataset for pretraining. Our pretrained model with injected structural knowledge achieves state-of-the-art performance on two benchmark medical NED datasets: MedMentions and BC5CDR. Furthermore, we improve disambiguation of rare entities by up to 57 accuracy points.

Doorways and passages are critical structural elements for indoor robot navigation, yet they remain underexplored in modern Visual SLAM (VSLAM) frameworks. This paper presents a passage-aware structural mapping approach for RGB-D VSLAM that detects doors and traversable openings by jointly fusing geometric, semantic, and topological cues. Doors are modeled as planar entities embedded within walls and classified as traversable or non-traversable based on their coplanarity with the supporting wall. Passages are inferred through two complementary strategies: traversal evidence accumulated from camera-wall interactions across consecutive keyframes, and geometric opening validation based on discontinuities in the mapped wall geometry. The proposed method is integrated into vS-Graphs as a proof of concept, enriching its scene graph with passage-level abstractions and improving room connectivity modeling. Qualitative evaluations on indoor office sequences demonstrate reliable doorway detection, and the framework lays the foundation for exploiting these elements in BIM-informed VSLAM. The source code is publicly available at https://github.com/snt-arg/visual_sgraphs/tree/doorway_integration.

Accurate ocean modeling and coastal hazard prediction depend on high-resolution bathymetric data; yet, current worldwide datasets are too coarse for exact numerical simulations. While recent deep learning advances have improved earth observation data resolution, existing methods struggle with the unique challenges of producing detailed ocean floor maps, especially in maintaining physical structure consistency and quantifying uncertainties. This work presents a novel uncertainty-aware mechanism using spatial blocks to efficiently capture local bathymetric complexity based on block-based conformal prediction. Using the Vector Quantized Variational Autoencoder (VQ-VAE) architecture, the integration of this uncertainty quantification framework yields spatially adaptive confidence estimates while preserving topographical features via discrete latent representations. With smaller uncertainty widths in well-characterized areas and appropriately larger bounds in areas of complex seafloor structures, the block-based design adapts uncertainty estimates to local bathymetric complexity. Compared to conventional techniques, experimental results over several ocean regions show notable increases in both reconstruction quality and uncertainty estimation reliability. This framework increases the reliability of bathymetric reconstructions by preserving structural integrity while offering spatially adaptive uncertainty estimates, so opening the path for more solid climate modeling and coastal hazard assessment.

Multi-agent systems (MAS) powered by LLMs promise adaptive, reasoning-driven enterprise workflows, yet granting agents autonomous control over tools, memory, and communication introduces attack surfaces absent from deterministic pipelines. While current research largely addresses prompt-level exploits and narrow individual vectors, it lacks a holistic architectural model for enterprise-grade security. We introduce AgenticCyOps (Securing Multi-Agentic AI Integration in Enterprise Cyber Operations), a framework built on a systematic decomposition of attack surfaces across component, coordination, and protocol layers, revealing that documented vectors consistently trace back to two integration surfaces: tool orchestration and memory management. Building on this observation, we formalize these integration surfaces as primary trust boundaries and define five defensive principles: authorized interfaces, capability scoping, verified execution, memory integrity & synchronization, and access-controlled data isolation; each aligned with established compliance standards (NIST, ISO 27001, GDPR, EU AI Act). We apply the framework to a Security Operations Center (SOC) workflow, adopting the Model Context Protocol (MCP) as the structural basis, with phase-scoped agents, consensus validation loops, and per-organization memory boundaries. Coverage analysis, attack path tracing, and trust boundary assessment confirm that the design addresses the documented attack vectors with defense-in-depth, intercepts three of four representative attack chains within the first two steps, and reduces exploitable trust boundaries by a minimum of 72% compared to a flat MAS, positioning AgenticCyOps as a foundation for securing enterprise-grade integration.

Direct Preference Optimization (DPO) is a principled, scalable alternative to RLHF for aligning large language models from pairwise preferences, but its internal geometric footprint remains undercharacterized, limiting audits, checkpoint comparisons, and failure prediction. We introduce SPINAL (Scaling-law and Preference Integration in Neural Alignment Layers), a diagnostic that measures how alignment reshapes representations across depth by tracing localized structural change layer by layer. Across model families, DPO produces a layerwise calibration effect concentrated in the final decoder blocks (often layers 21-30), where preference gradients most directly affect the next-token distribution. SPINAL encodes each checkpoint as a depth trace over (layer index, contraction score, transport score). The contraction score summarizes how quickly the tail of a layer's spectrum decays (how fast small modes vanish); higher values indicate stronger contraction into fewer effective directions. The transport score summarizes how much the token distribution shifts between adjacent layers using a bounded overlap measure; lower values indicate shorter, smoother steps through representation space. Aligned checkpoints show a late-layer ramp-up in contraction and a smooth reduction in transport, consistent with tightened and stabilized policy mass, while unaligned models trace higher-curvature, more entropic, and geometrically incoherent depth paths. Overall, alignment is geometrically localized: the final layers encode the dominant preference-induced corrections. SPINAL turns this localization into a practical audit signal, quantifying where alignment concentrates, how strongly it manifests, and when it begins to destabilize during training.

Models of many engineering and natural systems are imperfect. The discrepancy between the mathematical representations of a true physical system and its imperfect model is called the model error. These model errors can lead to substantial differences between the numerical solutions of the model and the state of the system, particularly in those involving nonlinear, multi-scale phenomena. Thus, there is increasing interest in reducing model errors, particularly by leveraging the rapidly growing observational data to understand their physics and sources. Here, we introduce a framework named MEDIDA: Model Error Discovery with Interpretability and Data Assimilation. MEDIDA only requires a working numerical solver of the model and a small number of noise-free or noisy sporadic observations of the system. In MEDIDA, first the model error is estimated from differences between the observed states and model-predicted states (the latter are obtained from a number of one-time-step numerical integrations from the previous observed states). If observations are noisy, a data assimilation (DA) technique such as ensemble Kalman filter (EnKF) is employed to provide the analysis state of the system, which is then used to estimate the model error. Finally, an equation-discovery technique, here the relevance vector machine (RVM), a sparsity-promoting Bayesian method, is used to identify an interpretable, parsimonious, and closed-form representation of the model error. Using the chaotic Kuramoto-Sivashinsky (KS) system as the test case, we demonstrate the excellent performance of MEDIDA in discovering different types of structural/parametric model errors, representing different types of missing physics, using noise-free and noisy observations.

Recent advances in Video Foundation Models (VFMs) have revolutionized human-centric video synthesis, yet fine-grained and independent editing of subjects and scenes remains a critical challenge. Recent attempts to incorporate richer environment control through rigid 3D geometric compositions often encounter a stark trade-off between precise control and generative flexibility. Furthermore, the heavy 3D pre-processing still limits practical scalability. In this paper, we propose ONE-SHOT, a parameter-efficient framework for compositional human-environment video generation. Our key insight is to factorize the generative process into disentangled signals. Specifically, we introduce a canonical-space injection mechanism that decouples human dynamics from environmental cues via cross-attention. We also propose Dynamic-Grounded-RoPE, a novel positional embedding strategy that establishes spatial correspondences between disparate spatial domains without any heuristic 3D alignments. To support long-horizon synthesis, we introduce a Hybrid Context Integration mechanism to maintain subject and scene consistency across minute-level generations. Experiments demonstrate that our method significantly outperforms state-of-the-art methods, offering superior structural control and creative diversity for video synthesis. Our project has been available on: https://martayang.github.io/ONE-SHOT/.

Verifiable delegation in digital identity systems remains unresolved across centralized, federated, and self-sovereign identity (SSI) environments, particularly where both human users and autonomous AI agents must exercise and transfer authority without exposing primary credentials or private keys. We introduce a unified framework that enables bounded, auditable, and least-privilege delegation across heterogeneous identity ecosystems. The framework includes four key elements: Delegation Grants (DGs), first-class authorization artefacts that encode revocable transfers of authority with enforced scope reduction; a Canonical Verification Context (CVC) that normalizes verification requests into a single structured representation independent of protocols or credential formats; a layered reference architecture that separates trust anchoring, credential and proof validation, policy evaluation, and protocol mediation via a Trust Gateway; and an explicit treatment of blockchain anchoring as an optional integrity layer rather than a structural dependency. Together, these elements advance interoperable delegation and auditability and provide a foundation for future standardization, implementation, and integration of autonomous agents into trusted digital identity infrastructures.

Generalist robot policies built upon 2D visual representations excel at semantic reasoning but inherently lack the explicit 3D spatial awareness required for high-precision tasks. Existing 3D integration methods struggle to bridge this gap due to the structural irregularity of sparse point clouds and the geometric distortion introduced by multi-view orthographic rendering. To overcome these barriers, we present ReMAP-DP, a novel framework synergizing standardized perspective reprojection with a structure-aware dual-stream diffusion policy. By coupling the re-projected views with pixel-aligned PointMaps, our dual-stream architecture leverages learnable modality embeddings to fuse frozen semantic features and explicit geometric descriptors, ensuring precise implicit patch-level alignment. Extensive experiments across simulation and real-world environments demonstrate ReMAP-DP's superior performance in diverse manipulation tasks. On RoboTwin 2.0, it attains a 59.3% average success rate, outperforming the DP3 baseline by +6.6%. On ManiSkill 3, our method yields a 28% improvement over DP3 on the geometrically challenging Stack Cube task. Furthermore, ReMAP-DP exhibits remarkable real-world robustness, executing high-precision and dynamic manipulations with superior data efficiency from only a handful of demonstrations. Project page is available at: https://icr-lab.github.io/ReMAP-DP/

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

Structural Health Monitoring (SHM) plays an indispensable role in ensuring the longevity and safety of infrastructure. With the rapid growth of sensor technology, the volume of data generated from various structures has seen an unprecedented surge, bringing forth challenges in efficient analysis and interpretation. This paper introduces a novel deep learning algorithm tailored for the complexities inherent in multimodal vibration signals prevalent in SHM. By amalgamating convolutional and recurrent architectures, the algorithm adeptly captures both localized and prolonged structural behaviors. The pivotal integration of attention mechanisms further enhances the model's capability, allowing it to discern and prioritize salient structural responses from extraneous noise. Our results showcase significant improvements in predictive accuracy, early damage detection, and adaptability across multiple SHM scenarios. In light of the critical nature of SHM, the proposed approach not only offers a robust analytical tool but also paves the way for more transparent and interpretable AI-driven SHM solutions. Future prospects include real-time processing, integration with external environmental factors, and a deeper emphasis on model interpretability.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Humans abstract experiences into structured representations to facilitate pattern inference and knowledge transfer. While the hippocampal-entorhinal (HPC-MEC) circuit is known to represent both spatial and conceptual spaces, the mechanisms for concurrently extracting abstract structures from continuous, high-dimensional dynamics remain poorly understood. We propose a brain-inspired hierarchical model that simultaneously infers latent transitions and constructs a predictive visual world model. Our architecture employs an inverse model for structural extraction alongside an HPC-MEC coupling model that dissociates relational structures (MEC) from integrated episodic scenes (HPC). Using primitive transformation dynamics as a benchmark, we demonstrate the model's capacity for structural abstraction. By leveraging velocity-driven path integration, the framework enables robust prediction and structural reuse across diverse contexts, thereby achieving structural generalization. This work provides a novel computational framework for understanding how brain-inspired, self-supervised learning of world models facilitates the acquisition of reusable abstract knowledge.

In the study, we present AMFusionNet, an innovative approach to infrared and visible image fusion (IVIF), harnessing the power of multiple kernel sizes and attention mechanisms. By assimilating thermal details from infrared images with texture features from visible sources, our method produces images enriched with comprehensive information. Distinct from prevailing deep learning methodologies, our model encompasses a fusion mechanism powered by multiple convolutional kernels, facilitating the robust capture of a wide feature spectrum. Notably, we incorporate parallel attention mechanisms to emphasize and retain pivotal target details in the resultant images. Moreover, the integration of the multi-scale structural similarity (MS-SSIM) loss function refines network training, optimizing the model for IVIF task. Experimental results demonstrate that our method outperforms state-of-the-art algorithms in terms of quality and quantity. The performance metrics on publicly available datasets also show significant improvement

Retrieval-Augmented Generation (RAG) has become a powerful and widely used approach for improving large language models by grounding generation in retrieved evidence. However, RAG systems still produce incorrect answers in many cases. Why RAG fails despite having access to external information remains poorly understood. We present a model-internal study of retrieval-augmented generation that examines how retrieved evidence influences answer generation. Using circuit tracing, we construct attribution graphs that model the flow of information through transformer layers during decoding. These graphs represent interactions among retrieved context, intermediate model activations, and generated tokens, providing a graph, circuit-level view of how external evidence is integrated into the model's reasoning process across multiple question answering benchmarks, we observe consistent structural differences: correct predictions exhibit deeper reasoning paths, more distributed evidence flow, and a more structured pattern of local connectivity, while failed predictions show shallower, fragmented, and overly concentrated evidence flow. Building on these findings, we develop a graph-based error detection framework that uses attribution-graph topology features. Furthermore, we show that attribution graphs enable targeted interventions. By reinforcing question-constrained evidence grounding, we reshape internal routing so that answer generation remains guided by the question, leading to more effective integration of retrieved information and fewer errors.

Electronic band structure (BS) and crystal structure are the two complementary identifiers of solid state materials. While convenient instruments and reconstruction algorithms have made large, empirical, crystal structure databases possible, extracting quasiparticle dispersion (closely related to BS) from photoemission band mapping data is currently limited by the available computational methods. To cope with the growing size and scale of photoemission data, we develop a pipeline including probabilistic machine learning and the associated data processing, optimization and evaluation methods for band structure reconstruction, leveraging theoretical calculations. The pipeline reconstructs all 14 valence bands of a semiconductor and shows excellent performance on benchmarks and other materials datasets. The reconstruction uncovers previously inaccessible momentum-space structural information on both global and local scales, while realizing a path towards integration with materials science databases. Our approach illustrates the potential of combining machine learning and domain knowledge for scalable feature extraction in multidimensional data.

We introduce materiomusic as a generative framework linking the hierarchical structures of matter with the compositional logic of music. Across proteins, spider webs and flame dynamics, vibrational and architectural principles recur as tonal hierarchies, harmonic progressions, and long-range musical form. Using reversible mappings, from molecular spectra to musical tones and from three-dimensional networks to playable instruments, we show how sound functions as a scientific probe, an epistemic inversion where listening becomes a mode of seeing and musical composition becomes a blueprint for matter. These mappings excavate deep time: patterns originating in femtosecond molecular vibrations or billion-year evolutionary histories become audible. We posit that novelty in science and art emerges when constraints cannot be satisfied within existing degrees of freedom, forcing expansion of the space of viable configurations. Selective imperfection provides the mechanism restoring balance between coherence and adaptability. Quantitative support comes from exhaustive enumeration of all 2^12 musical scales, revealing that culturally significant systems cluster in a mid-entropy, mid-defect corridor, directly paralleling the Hall-Petch optimum where intermediate defect densities maximize material strength. Iterating these mappings creates productive collisions between human creativity and physics, generating new information as musical structures encounter evolutionary constraints. We show how swarm-based AI models compose music exhibiting human-like structural signatures such as small-world connectivity, modular integration, long-range coherence, suggesting a route beyond interpolation toward invention. We show that science and art are generative acts of world-building under constraint, with vibration as a shared grammar organizing structure across scales.

This work presents a framework based on feature disentanglement to learn speaker embeddings that are robust to environmental variations. Our framework utilises an auto-encoder as a disentangler, dividing the input speaker embedding into components related to the speaker and other residual information. We employ a group of objective functions to ensure that the auto-encoder's code representation - used as the refined embedding - condenses only the speaker characteristics. We show the versatility of our framework through its compatibility with any existing speaker embedding extractor, requiring no structural modifications or adaptations for integration. We validate the effectiveness of our framework by incorporating it into two popularly used embedding extractors and conducting experiments across various benchmarks. The results show a performance improvement of up to 16%. We release our code for this work to be available https://github.com/kaistmm/voxceleb-disentangler

While Multimodal Large Language Models demonstrate impressive semantic capabilities, they often suffer from spatial blindness, struggling with fine-grained geometric reasoning and physical dynamics. Existing solutions typically rely on explicit 3D modalities or complex geometric scaffolding, which are limited by data scarcity and generalization challenges. In this work, we propose a paradigm shift by leveraging the implicit spatial prior within large-scale video generation models. We posit that to synthesize temporally coherent videos, these models inherently learn robust 3D structural priors and physical laws. We introduce VEGA-3D (Video Extracted Generative Awareness), a plug-and-play framework that repurposes a pre-trained video diffusion model as a Latent World Simulator. By extracting spatiotemporal features from intermediate noise levels and integrating them with semantic representations via a token-level adaptive gated fusion mechanism, we enrich MLLMs with dense geometric cues without explicit 3D supervision. Extensive experiments across 3D scene understanding, spatial reasoning, and embodied manipulation benchmarks demonstrate that our method outperforms state-of-the-art baselines, validating that generative priors provide a scalable foundation for physical-world understanding. Code is publicly available at https://github.com/H-EmbodVis/VEGA-3D.

Humans and animals have the ability to continually acquire, fine-tune, and transfer knowledge and skills throughout their lifespan. This ability, referred to as lifelong learning, is mediated by a rich set of neurocognitive mechanisms that together contribute to the development and specialization of our sensorimotor skills as well as to long-term memory consolidation and retrieval. Consequently, lifelong learning capabilities are crucial for autonomous agents interacting in the real world and processing continuous streams of information. However, lifelong learning remains a long-standing challenge for machine learning and neural network models since the continual acquisition of incrementally available information from non-stationary data distributions generally leads to catastrophic forgetting or interference. This limitation represents a major drawback for state-of-the-art deep neural network models that typically learn representations from stationary batches of training data, thus without accounting for situations in which information becomes incrementally available over time. In this review, we critically summarize the main challenges linked to lifelong learning for artificial learning systems and compare existing neural network approaches that alleviate, to different extents, catastrophic forgetting. We discuss well-established and emerging research motivated by lifelong learning factors in biological systems such as structural plasticity, memory replay, curriculum and transfer learning, intrinsic motivation, and multisensory integration.

Due to the presence of the natural gap between Knowledge Graph (KG) structures and the natural language, the effective integration of holistic structural information of KGs with Large Language Models (LLMs) has emerged as a significant question. To this end, we propose a two-stage framework to learn and apply quantized codes for each entity, aiming for the seamless integration of KGs with LLMs. Firstly, a self-supervised quantized representation (SSQR) method is proposed to compress both KG structural and semantic knowledge into discrete codes (\ie, tokens) that align the format of language sentences. We further design KG instruction-following data by viewing these learned codes as features to directly input to LLMs, thereby achieving seamless integration. The experiment results demonstrate that SSQR outperforms existing unsupervised quantized methods, producing more distinguishable codes. Further, the fine-tuned LLaMA2 and LLaMA3.1 also have superior performance on KG link prediction and triple classification tasks, utilizing only 16 tokens per entity instead of thousands in conventional prompting methods.

We present Magic Mirror, a framework for generating identity-preserved videos with cinematic-level quality and dynamic motion. While recent advances in video diffusion models have shown impressive capabilities in text-to-video generation, maintaining consistent identity while producing natural motion remains challenging. Previous methods either require person-specific fine-tuning or struggle to balance identity preservation with motion diversity. Built upon Video Diffusion Transformers, our method introduces three key components: (1) a dual-branch facial feature extractor that captures both identity and structural features, (2) a lightweight cross-modal adapter with Conditioned Adaptive Normalization for efficient identity integration, and (3) a two-stage training strategy combining synthetic identity pairs with video data. Extensive experiments demonstrate that Magic Mirror effectively balances identity consistency with natural motion, outperforming existing methods across multiple metrics while requiring minimal parameters added. The code and model will be made publicly available at: https://github.com/dvlab-research/MagicMirror/

Text embeddings have attracted growing interest due to their effectiveness across a wide range of natural language processing (NLP) tasks, such as retrieval, classification, clustering, bitext mining, and summarization. With the emergence of pretrained language models (PLMs), general-purpose text embeddings (GPTE) have gained significant traction for their ability to produce rich, transferable representations. The general architecture of GPTE typically leverages PLMs to derive dense text representations, which are then optimized through contrastive learning on large-scale pairwise datasets. In this survey, we provide a comprehensive overview of GPTE in the era of PLMs, focusing on the roles PLMs play in driving its development. We first examine the fundamental architecture and describe the basic roles of PLMs in GPTE, i.e., embedding extraction, expressivity enhancement, training strategies, learning objectives, and data construction. Then, we describe advanced roles enabled by PLMs, such as multilingual support, multimodal integration, code understanding, and scenario-specific adaptation. Finally, we highlight potential future research directions that move beyond traditional improvement goals, including ranking integration, safety considerations, bias mitigation, structural information incorporation, and the cognitive extension of embeddings. This survey aims to serve as a valuable reference for both newcomers and established researchers seeking to understand the current state and future potential of GPTE.

In the diverse field of medical imaging, automatic segmentation has numerous applications and must handle a wide variety of input domains, such as different types of Computed Tomography (CT) scans and Magnetic Resonance (MR) images. This heterogeneity challenges automatic segmentation algorithms to maintain consistent performance across different modalities due to the requirement for spatially aligned and paired images. Typically, segmentation models are trained using a single modality, which limits their ability to generalize to other types of input data without employing transfer learning techniques. Additionally, leveraging complementary information from different modalities to enhance segmentation precision often necessitates substantial modifications to popular encoder-decoder designs, such as introducing multiple branched encoding or decoding paths for each modality. In this work, we propose a simple Multi-Modal Segmentation (MulModSeg) strategy to enhance medical image segmentation across multiple modalities, specifically CT and MR. It incorporates two key designs: a modality-conditioned text embedding framework via a frozen text encoder that adds modality awareness to existing segmentation frameworks without significant structural modifications or computational overhead, and an alternating training procedure that facilitates the integration of essential features from unpaired CT and MR inputs. Through extensive experiments with both Fully Convolutional Network and Transformer-based backbones, MulModSeg consistently outperforms previous methods in segmenting abdominal multi-organ and cardiac substructures for both CT and MR modalities. The code is available in this {https://github.com/ChengyinLee/MulModSeg_2024{link}}.

Generating continuous-time, continuous-space stochastic processes (e.g., videos, weather forecasts) conditioned on partial observations (e.g., first and last frames) is a fundamental challenge. Existing approaches, (e.g., diffusion models), suffer from key limitations: (1) noise-to-data evolution fails to capture structural similarity between states close in physical time and has unstable integration in low-step regimes; (2) random noise injected is insensitive to the physical process's time elapsed, resulting in incorrect dynamics; (3) they overlook conditioning on arbitrary subsets of states (e.g., irregularly sampled timesteps, future observations). We propose ABC: Any-Subset Autoregressive Models via Non-Markovian Diffusion Bridges in Continuous Time and Space. Crucially, we model the process with one continual SDE whose time variable and intermediate states track the real time and process states. This has provable advantages: (1) the starting point for generating future states is the already-close previous state, rather than uninformative noise; (2) random noise injection scales with physical time elapsed, encouraging physically plausible dynamics with similar time-adjacent states. We derive SDE dynamics via changes-of-measure on path space, yielding another advantage: (3) path-dependent conditioning on arbitrary subsets of the state history and/or future. To learn these dynamics, we derive a path- and time-dependent extension of denoising score matching. Our experiments show ABC's superiority to competing methods on multiple domains, including video generation and weather forecasting.

The prediction of crystal properties is essential for understanding structure-property relationships and accelerating the discovery of functional materials. However, conventional approaches relying on experimental measurements or density functional theory (DFT) calculations are often resource-intensive, limiting their scalability. Machine learning (ML) models offer a promising alternative by learning complex structure-property relationships from data, enabling faster predictions. Yet, existing ML models often rely on labeled data, adopt representations that poorly capture essential structural characteristics, and lack integration with physical principles--factors that limit their generalizability and interpretability. Here, we introduce CLOUD (Crystal Language mOdel for Unified and Differentiable materials modeling), a transformer-based framework trained on a novel Symmetry-Consistent Ordered Parameter Encoding (SCOPE) that encodes crystal symmetry, Wyckoff positions, and composition in a compact, coordinate-free string representation. Pre-trained on over six million crystal structures, CLOUD is fine-tuned on multiple downstream tasks and achieves competitive performance in predicting a wide range of material properties, demonstrating strong scaling performance. Furthermore, as proof of concept of differentiable materials modeling, CLOUD is applied to predict the phonon internal energy and heat capacity, which integrates the Debye model to preserve thermodynamic consistency. The CLOUD-DEBYE framework enforces thermodynamic consistency and enables temperature-dependent property prediction without requiring additional data. These results demonstrate the potential of CLOUD as a scalable and physics-informed foundation model for crystalline materials, unifying symmetry-consistent representations with physically grounded learning for property prediction and materials discovery.

Node importance estimation (NIE) in heterogeneous knowledge graphs is a critical yet challenging task, essential for applications such as recommendation, knowledge reasoning, and question answering. Existing methods often rely on pairwise connections, neglecting high-order dependencies among multiple entities and relations, and they treat structural and semantic signals independently, hindering effective cross-modal integration. To address these challenges, we propose MetaHGNIE, a meta-path induced hypergraph contrastive learning framework for disentangling and aligning structural and semantic information. MetaHGNIE constructs a higher-order knowledge graph via meta-path sequences, where typed hyperedges capture multi-entity relational contexts. Structural dependencies are aggregated with local attention, while semantic representations are encoded through a hypergraph transformer equipped with sparse chunking to reduce redundancy. Finally, a multimodal fusion module integrates structural and semantic embeddings under contrastive learning with auxiliary supervision, ensuring robust cross-modal alignment. Extensive experiments on benchmark NIE datasets demonstrate that MetaHGNIE consistently outperforms state-of-the-art baselines. These results highlight the effectiveness of explicitly modeling higher-order interactions and cross-modal alignment in heterogeneous knowledge graphs. Our code is available at https://github.com/SEU-WENJIA/DualHNIE

Recent research on integrating Large Language Models (LLMs) with Graph Neural Networks (GNNs) typically follows two approaches: LLM-centered models, which convert graph data into tokens for LLM processing, and GNN-centered models, which use LLMs to encode text features into node and edge representations for GNN input. LLM-centered models often struggle to capture graph structures effectively, while GNN-centered models compress variable-length textual data into fixed-size vectors, limiting their ability to understand complex semantics. Additionally, GNN-centered approaches require converting tasks into a uniform, manually-designed format, restricting them to classification tasks and preventing language output. To address these limitations, we introduce a new architecture that deeply integrates GNN with LLM, featuring three key innovations: (1) Structure-Aware Transformers, which incorporate GNN's message-passing capabilities directly into LLM's transformer layers, allowing simultaneous processing of textual and structural information and generating outputs from both GNN and LLM; (2) Graph-Text Cross-Attention, which processes full, uncompressed text from graph nodes and edges, ensuring complete semantic integration; and (3) GNN-LLM Twin Predictor, enabling LLM's flexible autoregressive generation alongside GNN's scalable one-pass prediction. GL-Fusion achieves outstand performance on various tasks. Notably, it achieves state-of-the-art performance on OGBN-Arxiv and OGBG-Code2.

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.

Text-rich Graph Knowledge Bases (TG-KBs) have become increasingly crucial for answering queries by providing textual and structural knowledge. However, current retrieval methods often retrieve these two types of knowledge in isolation without considering their mutual reinforcement and some hybrid methods even bypass structural retrieval entirely after neighboring aggregation. To fill in this gap, we propose a Mixture of Structural-and-Textual Retrieval (MoR) to retrieve these two types of knowledge via a Planning-Reasoning-Organizing framework. In the Planning stage, MoR generates textual planning graphs delineating the logic for answering queries. Following planning graphs, in the Reasoning stage, MoR interweaves structural traversal and textual matching to obtain candidates from TG-KBs. In the Organizing stage, MoR further reranks fetched candidates based on their structural trajectory. Extensive experiments demonstrate the superiority of MoR in harmonizing structural and textual retrieval with insights, including uneven retrieving performance across different query logics and the benefits of integrating structural trajectories for candidate reranking. Our code is available at https://github.com/Yoega/MoR.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

Distributional discrepancy between training and test data can lead models to make inaccurate predictions when encountering out-of-distribution (OOD) samples in real-world applications. Although existing graph OOD detection methods leverage data-centric techniques to extract effective representations, their performance remains compromised by structural redundancy that induces semantic shifts. To address this dilemma, we propose RedOUT, an unsupervised framework that integrates structural entropy into test-time OOD detection for graph classification. Concretely, we introduce the Redundancy-aware Graph Information Bottleneck (ReGIB) and decompose the objective into essential information and irrelevant redundancy. By minimizing structural entropy, the decoupled redundancy is reduced, and theoretically grounded upper and lower bounds are proposed for optimization. Extensive experiments on real-world datasets demonstrate the superior performance of RedOUT on OOD detection. Specifically, our method achieves an average improvement of 6.7%, significantly surpassing the best competitor by 17.3% on the ClinTox/LIPO dataset pair.

Retrieval-Augmented Generation systems depend on retrieving semantically relevant document chunks to support accurate, grounded outputs from large language models. In structured and repetitive corpora such as regulatory filings, chunk similarity alone often fails to distinguish between documents with overlapping language. Practitioners often flatten metadata into input text as a heuristic, but the impact and trade-offs of this practice remain poorly understood. We present a systematic study of metadata-aware retrieval strategies, comparing plain-text baselines with approaches that embed metadata directly. Our evaluation spans metadata-as-text (prefix and suffix), a dual-encoder unified embedding that fuses metadata and content in a single index, dual-encoder late-fusion retrieval, and metadata-aware query reformulation. Across multiple retrieval metrics and question types, we find that prefixing and unified embeddings consistently outperform plain-text baselines, with the unified at times exceeding prefixing while being easier to maintain. Beyond empirical comparisons, we analyze embedding space, showing that metadata integration improves effectiveness by increasing intra-document cohesion, reducing inter-document confusion, and widening the separation between relevant and irrelevant chunks. Field-level ablations show that structural cues provide strong disambiguating signals. Our code, evaluation framework, and the RAGMATE-10K dataset are publicly hosted.

Multimodal large language models (MLLMs) have made significant progress in vision-language understanding, yet effectively aligning different modalities remains a fundamental challenge. We present a framework that unifies multimodal understanding by applying byte-pair encoding to visual tokens. Unlike conventional approaches that rely on modality-specific encoders, our method directly incorporates structural information into visual tokens, mirroring successful tokenization strategies in text-only language models. We introduce a priority-guided encoding scheme that considers both frequency and spatial consistency, coupled with a multi-stage training procedure based on curriculum-driven data composition. These enhancements enable the transformer model to better capture cross-modal relationships and reason with visual information. Comprehensive experiments demonstrate improved performance across diverse vision-language tasks. By bridging the gap between visual and textual representations, our approach contributes to the advancement of more capable and efficient multimodal foundation models.

Recent advancements in controllable text-to-image (T2I) diffusion models, such as Ctrl-X and FreeControl, have demonstrated robust spatial and appearance control without requiring auxiliary module training. However, these models often struggle to accurately preserve spatial structures and fail to capture fine-grained conditions related to object poses and scene layouts. To address these challenges, we propose a training-free Dual Recursive Feedback (DRF) system that properly reflects control conditions in controllable T2I models. The proposed DRF consists of appearance feedback and generation feedback that recursively refines the intermediate latents to better reflect the given appearance information and the user's intent. This dual-update mechanism guides latent representations toward reliable manifolds, effectively integrating structural and appearance attributes. Our approach enables fine-grained generation even between class-invariant structure-appearance fusion, such as transferring human motion onto a tiger's form. Extensive experiments demonstrate the efficacy of our method in producing high-quality, semantically coherent, and structurally consistent image generations. Our source code is available at https://github.com/jwonkm/DRF.

Large language models (LLMs) are increasingly adopted for automating survey paper generation wang2406autosurvey, liang2025surveyx, yan2025surveyforge,su2025benchmarking,wen2025interactivesurvey. Existing approaches typically extract content from a large collection of related papers and prompt LLMs to summarize them directly. However, such methods often overlook the structural relationships among papers, resulting in generated surveys that lack a coherent taxonomy and a deeper contextual understanding of research progress. To address these shortcomings, we propose SurveyG, an LLM-based agent framework that integrates hierarchical citation graph, where nodes denote research papers and edges capture both citation dependencies and semantic relatedness between their contents, thereby embedding structural and contextual knowledge into the survey generation process. The graph is organized into three layers: Foundation, Development, and Frontier, to capture the evolution of research from seminal works to incremental advances and emerging directions. By combining horizontal search within layers and vertical depth traversal across layers, the agent produces multi-level summaries, which are consolidated into a structured survey outline. A multi-agent validation stage then ensures consistency, coverage, and factual accuracy in generating the final survey. Experiments, including evaluations by human experts and LLM-as-a-judge, demonstrate that SurveyG outperforms state-of-the-art frameworks, producing surveys that are more comprehensive and better structured to the underlying knowledge taxonomy of a field.

Antibody design is an essential yet challenging task in various domains like therapeutics and biology. There are two major defects in current learning-based methods: 1) tackling only a certain subtask of the whole antibody design pipeline, making them suboptimal or resource-intensive. 2) omitting either the framework regions or side chains, thus incapable of capturing the full-atom geometry. To address these pitfalls, we propose dynamic Multi-channel Equivariant grAph Network (dyMEAN), an end-to-end full-atom model for E(3)-equivariant antibody design given the epitope and the incomplete sequence of the antibody. Specifically, we first explore structural initialization as a knowledgeable guess of the antibody structure and then propose shadow paratope to bridge the epitope-antibody connections. Both 1D sequences and 3D structures are updated via an adaptive multi-channel equivariant encoder that is able to process protein residues of variable sizes when considering full atoms. Finally, the updated antibody is docked to the epitope via the alignment of the shadow paratope. Experiments on epitope-binding CDR-H3 design, complex structure prediction, and affinity optimization demonstrate the superiority of our end-to-end framework and full-atom modeling.

Recently, leveraging pre-trained Large Language Models (LLMs) for time series (TS) tasks has gained increasing attention, which involves activating and enhancing LLMs' capabilities. Many methods aim to activate LLMs' capabilities based on token-level alignment but overlook LLMs' inherent strength on natural language processing -- their deep understanding of linguistic logic and structure rather than superficial embedding processing. We propose Context-Alignment, a new paradigm that aligns TS with a linguistic component in the language environments familiar to LLMs to enable LLMs to contextualize and comprehend TS data, thereby activating their capabilities. Specifically, such context-level alignment comprises structural alignment and logical alignment, which is achieved by a Dual-Scale Context-Alignment GNNs (DSCA-GNNs) applied to TS-language multimodal inputs. Structural alignment utilizes dual-scale nodes to describe hierarchical structure in TS-language, enabling LLMs treat long TS data as a whole linguistic component while preserving intrinsic token features. Logical alignment uses directed edges to guide logical relationships, ensuring coherence in the contextual semantics. Demonstration examples prompt are employed to construct Demonstration Examples based Context-Alignment (DECA) following DSCA-GNNs framework. DECA can be flexibly and repeatedly integrated into various layers of pre-trained LLMs to improve awareness of logic and structure, thereby enhancing performance. Extensive experiments show the effectiveness of DECA and the importance of Context-Alignment across tasks, particularly in few-shot and zero-shot forecasting, confirming that Context-Alignment provide powerful prior knowledge on context.

Large-scale digital platforms generate billions of timestamped user-item interactions (events) that are crucial for predicting user attributes in, e.g., fraud prevention and recommendations. While self-supervised learning (SSL) effectively models the temporal order of events, it typically overlooks the global structure of the user-item interaction graph. To bridge this gap, we propose three model-agnostic strategies for integrating this structural information into contrastive SSL: enriching event embeddings, aligning client representations with graph embeddings, and adding a structural pretext task. Experiments on four financial and e-commerce datasets demonstrate that our approach consistently improves the accuracy (up to a 2.3% AUC) and reveals that graph density is a key factor in selecting the optimal integration strategy.

Category-Agnostic Pose Estimation (CAPE) localizes keypoints across diverse object categories with a single model, using one or a few annotated support images. Recent works have shown that using a pose graph (i.e., treating keypoints as nodes in a graph rather than isolated points) helps handle occlusions and break symmetry. However, these methods assume a static pose graph with equal-weight edges, leading to suboptimal results. We introduce EdgeCape, a novel framework that overcomes these limitations by predicting the graph's edge weights which optimizes localization. To further leverage structural priors, we propose integrating Markovian Structural Bias, which modulates the self-attention interaction between nodes based on the number of hops between them. We show that this improves the model's ability to capture global spatial dependencies. Evaluated on the MP-100 benchmark, which includes 100 categories and over 20K images, EdgeCape achieves state-of-the-art results in the 1-shot setting and leads among similar-sized methods in the 5-shot setting, significantly improving keypoint localization accuracy. Our code is publicly available.

Despite rapid advancements in the capabilities of generative models, pretrained text-to-image models still struggle in capturing the semantics conveyed by complex prompts that compound multiple objects and instance-level attributes. Consequently, we are witnessing growing interests in integrating additional structural constraints, typically in the form of coarse bounding boxes, to better guide the generation process in such challenging cases. In this work, we take the idea of structural guidance a step further by making the observation that contemporary image generation models can directly provide a plausible fine-grained structural initialization. We propose a technique that couples this image-based structural guidance with LLM-based instance-level instructions, yielding output images that adhere to all parts of the text prompt, including object counts, instance-level attributes, and spatial relations between instances.

Multimodal Large Language Models (MLLMs) have advanced image and video understanding and can increasingly handle longer visual inputs. Long-horizon tasks such as autonomous driving and robotic navigation require more than recognizing the current view, as models must remember and retrieve previously observed spatial layouts, routes, viewpoint changes, and object states. To evaluate this capability, we introduce LongSpace-Bench, a room-tour video benchmark for long-horizon spatial memory, covering scene perception, spatial relations, and spatial memory. In this work, we further propose LongSpace, a memory framework for long-video spatial reasoning. LongSpace models long videos as sequential chunks, incorporates 3D structural cues into early decoder layers, and constructs layer-aware memory for question-guided retrieval. Experiments on multiple spatial reasoning benchmarks show that LongSpace improves long-video spatial understanding, further demonstrating explicit spatial memory as a key capability for long-horizon video MLLMs.

While deep learning models play a crucial role in predicting antibody-antigen interactions (AAI), the scarcity of publicly available sequence-structure pairings constrains their generalization. Current AAI methods often focus on residue-level static details, overlooking fine-grained structural representations of antibodies and their inter-antibody similarities. To tackle this challenge, we introduce a multi-modality representation approach that integates 3D structural and 1D sequence data to unravel intricate intra-antibody hierarchical relationships. By harnessing these representations, we present MuLAAIP, an AAI prediction framework that utilizes graph attention networks to illuminate graph-level structural features and normalized adaptive graph convolution networks to capture inter-antibody sequence associations. Furthermore, we have curated an AAI benchmark dataset comprising both structural and sequence information along with interaction labels. Through extensive experiments on this benchmark, our results demonstrate that MuLAAIP outperforms current state-of-the-art methods in terms of predictive performance. The implementation code and dataset are publicly available at https://github.com/trashTian/MuLAAIP for reproducibility.

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availability of experimental 3D protein structures have accelerated structure prediction, the dynamic nature of protein structures has received limited attention. This study introduces an innovative 4D diffusion model incorporating molecular dynamics (MD) simulation data to learn dynamic protein structures. Our approach is distinguished by the following components: (1) a unified diffusion model capable of generating dynamic protein structures, including both the backbone and side chains, utilizing atomic grouping and side-chain dihedral angle predictions; (2) a reference network that enhances structural consistency by integrating the latent embeddings of the initial 3D protein structures; and (3) a motion alignment module aimed at improving temporal structural coherence across multiple time steps. To our knowledge, this is the first diffusion-based model aimed at predicting protein trajectories across multiple time steps simultaneously. Validation on benchmark datasets demonstrates that our model exhibits high accuracy in predicting dynamic 3D structures of proteins containing up to 256 amino acids over 32 time steps, effectively capturing both local flexibility in stable states and significant conformational changes.

Text-Attributed Graphs (TAGs) enhance graph structures with natural language descriptions, enabling detailed representation of data and their relationships across a broad spectrum of real-world scenarios. Despite the potential for deeper insights, existing TAG representation learning primarily relies on supervised methods, necessitating extensive labeled data and limiting applicability across diverse contexts. This paper introduces a new self-supervised learning framework, Text-And-Graph Multi-View Alignment (TAGA), which overcomes these constraints by integrating TAGs' structural and semantic dimensions. TAGA constructs two complementary views: Text-of-Graph view, which organizes node texts into structured documents based on graph topology, and the Graph-of-Text view, which converts textual nodes and connections into graph data. By aligning representations from both views, TAGA captures joint textual and structural information. In addition, a novel structure-preserving random walk algorithm is proposed for efficient training on large-sized TAGs. Our framework demonstrates strong performance in zero-shot and few-shot scenarios across eight real-world datasets.

Automated analysis for engineering structures offers considerable potential for boosting efficiency by minimizing repetitive tasks. Although AI-driven methods are increasingly common, no systematic framework yet leverages Large Language Models (LLMs) for automatic structural analysis. To address this gap, we propose a novel framework that integrates LLMs with structural analysis software. LLMs serve as the core engine: they parse structural descriptions from text and translate them into executable Python scripts. Moreover, the framework integrates the generative capabilities of LLMs with code-based finite element (FE) tools like OpenSeesPy. It employs domain-specific prompt design and in-context learning strategies to enhance the LLM's problem-solving capabilities and generative stability, enabling fully automated structural analysis from descriptive text to model outputs. In our experiments, we introduce a well-curated small-scale benchmark dataset of 20 structural analysis word problems (SAWPs) with ground-truth solutions and evaluate the performance of different LLMs within our framework in solving these SAWPs. The role of system instructions, crafted by structural engineers, is also investigated to understand their impact on LLM-driven structural analysis. Additionally, the generative stability of our framework is examined. Through multiple validation experiments on the benchmark, our results demonstrate that the proposed framework can substantially increase the level of automation in solving SAWPs compared to traditional methods. Quantitatively, the framework, built on GPT-4o, achieved 100% accuracy, surpassing GPT-4 (85%), Gemini 1.5 Pro (80%), and Llama-3.3 (30%) on the test examples. Furthermore, integrating domain-specific instructions enhanced performance by 30% on problems with asymmetrical structural configurations.

To address the limitations of Transformer decoders in capturing edge details, recognizing local textures and modeling spatial continuity, this paper proposes a novel decoder framework specifically designed for medical image segmentation, comprising three core modules. First, the Adaptive Cross-Fusion Attention (ACFA) module integrates channel feature enhancement with spatial attention mechanisms and introduces learnable guidance in three directions (planar, horizontal, and vertical) to enhance responsiveness to key regions and structural orientations. Second, the Triple Feature Fusion Attention (TFFA) module fuses features from Spatial, Fourier and Wavelet domains, achieving joint frequency-spatial representation that strengthens global dependency and structural modeling while preserving local information such as edges and textures, making it particularly effective in complex and blurred boundary scenarios. Finally, the Structural-aware Multi-scale Masking Module (SMMM) optimizes the skip connections between encoder and decoder by leveraging multi-scale context and structural saliency filtering, effectively reducing feature redundancy and improving semantic interaction quality. Working synergistically, these modules not only address the shortcomings of traditional decoders but also significantly enhance performance in high-precision tasks such as tumor segmentation and organ boundary extraction, improving both segmentation accuracy and model generalization. Experimental results demonstrate that this framework provides an efficient and practical solution for medical image segmentation.

Current Visual Simultaneous Localization and Mapping (VSLAM) systems often struggle to create maps that are both semantically rich and easily interpretable. While incorporating semantic scene knowledge aids in building richer maps with contextual associations among mapped objects, representing them in structured formats like scene graphs has not been widely addressed, encountering complex map comprehension and limited scalability. This paper introduces visual S-Graphs (vS-Graphs), a novel real-time VSLAM framework that integrates vision-based scene understanding with map reconstruction and comprehensible graph-based representation. The framework infers structural elements (i.e., rooms and corridors) from detected building components (i.e., walls and ground surfaces) and incorporates them into optimizable 3D scene graphs. This solution enhances the reconstructed map's semantic richness, comprehensibility, and localization accuracy. Extensive experiments on standard benchmarks and real-world datasets demonstrate that vS-Graphs outperforms state-of-the-art VSLAM methods, reducing trajectory error by an average of 3.38% and up to 9.58% on real-world data. Furthermore, the proposed framework achieves environment-driven semantic entity detection accuracy comparable to precise LiDAR-based frameworks using only visual features. A web page containing more media and evaluation outcomes is available on https://snt-arg.github.io/vsgraphs-results/.

Relational structures such as schema linking and schema encoding have been validated as a key component to qualitatively translating natural language into SQL queries. However, introducing these structural relations comes with prices: they often result in a specialized model structure, which largely prohibits using large pretrained models in text-to-SQL. To address this problem, we propose RASAT: a Transformer seq2seq architecture augmented with relation-aware self-attention that could leverage a variety of relational structures while inheriting the pretrained parameters from the T5 model effectively. Our model can incorporate almost all types of existing relations in the literature, and in addition, we propose introducing co-reference relations for the multi-turn scenario. Experimental results on three widely used text-to-SQL datasets, covering both single-turn and multi-turn scenarios, have shown that RASAT could achieve state-of-the-art results across all three benchmarks (75.5% EX on Spider, 52.6% IEX on SParC, and 37.4% IEX on CoSQL).

Human-level contact-rich manipulation relies on the distinct roles of two key modalities: vision provides spatially rich but temporally slow global context, while force sensing captures rapid, high-frequency local contact dynamics. Integrating these signals is challenging due to their fundamental frequency and informational disparities. In this work, we propose ImplicitRDP, a unified end-to-end visual-force diffusion policy that integrates visual planning and reactive force control within a single network. We introduce Structural Slow-Fast Learning, a mechanism utilizing causal attention to simultaneously process asynchronous visual and force tokens, allowing the policy to perform closed-loop adjustments at the force frequency while maintaining the temporal coherence of action chunks. Furthermore, to mitigate modality collapse where end-to-end models fail to adjust the weights across different modalities, we propose Virtual-target-based Representation Regularization. This auxiliary objective maps force feedback into the same space as the action, providing a stronger, physics-grounded learning signal than raw force prediction. Extensive experiments on contact-rich tasks demonstrate that ImplicitRDP significantly outperforms both vision-only and hierarchical baselines, achieving superior reactivity and success rates with a streamlined training pipeline. Code and videos will be publicly available at https://implicit-rdp.github.io.

Knowledge Graphs, such as Wikidata, comprise structural and textual knowledge in order to represent knowledge. For each of the two modalities dedicated approaches for graph embedding and language models learn patterns that allow for predicting novel structural knowledge. Few approaches have integrated learning and inference with both modalities and these existing ones could only partially exploit the interaction of structural and textual knowledge. In our approach, we build on existing strong representations of single modalities and we use hypercomplex algebra to represent both, (i), single-modality embedding as well as, (ii), the interaction between different modalities and their complementary means of knowledge representation. More specifically, we suggest Dihedron and Quaternion representations of 4D hypercomplex numbers to integrate four modalities namely structural knowledge graph embedding, word-level representations (e.g.\ Word2vec, Fasttext), sentence-level representations (Sentence transformer), and document-level representations (sentence transformer, Doc2vec). Our unified vector representation scores the plausibility of labelled edges via Hamilton and Dihedron products, thus modeling pairwise interactions between different modalities. Extensive experimental evaluation on standard benchmark datasets shows the superiority of our two new models using abundant textual information besides sparse structural knowledge to enhance performance in link prediction tasks.

Episodic memory allows LLM agents to accumulate and retrieve experience, but current methods treat each memory independently, i.e., evaluating retrieval quality in isolation without accounting for the dependency chains through which memories enable the creation of future memories. We introduce MemQ, which applies TD(λ) eligibility traces to memory Q-values, propagating credit backward through a provenance DAG that records which memories were retrieved when each new memory was created. Credit weight decays as (γλ)^d with DAG depth d, replacing temporal distance with structural proximity. We formalize the setting as an Exogenous-Context MDP, whose factored transition decouples the exogenous task stream from the endogenous memory store. Across six benchmarks, spanning OS interaction, function calling, code generation, multimodal reasoning, embodied reasoning, and expert-level QA, MemQ achieves the highest success rate on all six in generalization evaluation and runtime learning, with gains largest on multi-step tasks that produce deep and relevant provenance chains (up to +5.7~pp) and smallest on single-step classification (+0.77~pp) where single-step updates already suffice. We further study how γ and λ interact with the EC-MDP structure, providing principled guidance for parameter selection and future research. Code is available at https://github.com/jwliao-ai/MemQ.

Arbitrary-scale video super-resolution (AVSR) aims to enhance the resolution of video frames, potentially at various scaling factors, which presents several challenges regarding spatial detail reproduction, temporal consistency, and computational complexity. In this paper, we first describe a strong baseline for AVSR by putting together three variants of elementary building blocks: 1) a flow-guided recurrent unit that aggregates spatiotemporal information from previous frames, 2) a flow-refined cross-attention unit that selects spatiotemporal information from future frames, and 3) a hyper-upsampling unit that generates scaleaware and content-independent upsampling kernels. We then introduce ST-AVSR by equipping our baseline with a multi-scale structural and textural prior computed from the pre-trained VGG network. This prior has proven effective in discriminating structure and texture across different locations and scales, which is beneficial for AVSR. Comprehensive experiments show that ST-AVSR significantly improves super-resolution quality, generalization ability, and inference speed over the state-of-theart. The code is available at https://github.com/shangwei5/ST-AVSR.

The automated generation of imaging reports proves invaluable in alleviating the workload of radiologists. A clinically applicable reports generation algorithm should demonstrate its effectiveness in producing reports that accurately describe radiology findings and attend to patient-specific indications. In this paper, we introduce a novel method, Structural Entities extraction and patient indications Incorporation (SEI) for chest X-ray report generation. Specifically, we employ a structural entities extraction (SEE) approach to eliminate presentation-style vocabulary in reports and improve the quality of factual entity sequences. This reduces the noise in the following cross-modal alignment module by aligning X-ray images with factual entity sequences in reports, thereby enhancing the precision of cross-modal alignment and further aiding the model in gradient-free retrieval of similar historical cases. Subsequently, we propose a cross-modal fusion network to integrate information from X-ray images, similar historical cases, and patient-specific indications. This process allows the text decoder to attend to discriminative features of X-ray images, assimilate historical diagnostic information from similar cases, and understand the examination intention of patients. This, in turn, assists in triggering the text decoder to produce high-quality reports. Experiments conducted on MIMIC-CXR validate the superiority of SEI over state-of-the-art approaches on both natural language generation and clinical efficacy metrics.

This work investigates the production of high-resolution images of typical support elements in concrete structures by means of the muon tomography (muography). By exploiting detailed Monte Carlo radiation-matter simulations, we demonstrate the feasibility of the reconstruction of 1 cm--thick iron tubes inside 30 cm--deep concrete blocks, regarded as an important testbed within the structural diagnostics community. In addition, we present a new method for integrating simulated data with advanced deep learning techniques in order to improve the muon imaging of concrete structures. Through deep learning enhancement techniques, this results into a dramatic improvement of the image quality, as well as into a significant reduction of the data acquisition time, which are two critical limitations within the usual practice of muography for civil engineering diagnostics.

Transformer-based models have demonstrated significant success in various source code representation tasks. Nonetheless, traditional positional embeddings employed by these models inadequately capture the hierarchical structure intrinsic to source code, typically represented as Abstract Syntax Trees (ASTs). To address this, we propose a novel tree-based positional embedding approach that explicitly encodes hierarchical relationships derived from ASTs, including node depth and sibling indices. These hierarchical embeddings are integrated into the transformer architecture, specifically enhancing the CodeBERTa model. We thoroughly evaluate our proposed model through masked language modeling (MLM) pretraining and clone detection fine-tuning tasks. Experimental results indicate that our Tree-Enhanced CodeBERTa consistently surpasses the baseline model in terms of loss, accuracy, F1 score, precision, and recall, emphasizing the importance of incorporating explicit structural information into transformer-based representations of source code.

With the rapid advancement of large language models (LLMs), discrete speech representations have become crucial for integrating speech into LLMs. Existing methods for speech representation discretization rely on a predefined codebook size and Euclidean distance-based quantization. However, 1) the size of codebook is a critical parameter that affects both codec performance and downstream task training efficiency. 2) The Euclidean distance-based quantization may lead to audio distortion when the size of the codebook is controlled within a reasonable range. In fact, in the field of information compression, structural information and entropy guidance are crucial, but previous methods have largely overlooked these factors. Therefore, we address the above issues from an information-theoretic perspective, we present SECodec, a novel speech representation codec based on structural entropy (SE) for building speech language models. Specifically, we first model speech as a graph, clustering the speech features nodes within the graph and extracting the corresponding codebook by hierarchically and disentangledly minimizing 2D SE. Then, to address the issue of audio distortion, we propose a new quantization method. This method still adheres to the 2D SE minimization principle, adaptively selecting the most suitable token corresponding to the cluster for each incoming original speech node. Furthermore, we develop a Structural Entropy-based Speech Language Model (SESLM) that leverages SECodec. Experimental results demonstrate that SECodec performs comparably to EnCodec in speech reconstruction, and SESLM surpasses VALL-E in zero-shot text-to-speech tasks. Code, demo speeches, speech feature graph, SE codebook, and models are available at https://github.com/wlq2019/SECodec.

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.

Generative Recommendation (GR) has emerged as a transformative paradigm that reformulates the traditional cascade ranking system into a sequence-to-item generation task, facilitated by the use of discrete Semantic IDs (SIDs). However, current SIDs are suboptimal as the indexing objectives (Stage 1) are misaligned with the actual recommendation goals (Stage 2). Since these identifiers remain static (Stage 2), the backbone model lacks the flexibility to adapt them to the evolving complexities of user interactions. Furthermore, the prevailing strategy of flattening hierarchical SIDs into token sequences leads to sequence length inflation, resulting in prohibitive computational overhead and inference latency. To address these challenges, we propose IntRR, a novel framework that integrates objective-aligned SID Redistribution and structural Length Reduction. By leveraging item-specific Unique IDs (UIDs) as collaborative anchors, this approach dynamically redistributes semantic weights across hierarchical codebook layers. Concurrently, IntRR handles the SID hierarchy recursively, eliminating the need to flatten sequences. This ensures a fixed cost of one token per item. Extensive experiments on benchmark datasets demonstrate that IntRR yields substantial improvements over representative generative baselines, achieving superior performance in both recommendation accuracy and efficiency.

We present Probabilistic Structure Integration (PSI), a system for learning richly controllable and flexibly promptable world models from data. PSI consists of a three-step cycle. The first step, Probabilistic prediction, involves building a probabilistic graphical model Psi of the data, in the form of a random-access autoregressive sequence model. Psi supports a complete set of learned conditional distributions describing the dependence of any variables in the data on any other set of variables. In step 2, Structure extraction, we show how to extract underlying low-dimensional properties in the data, corresponding to a diverse set of meaningful "intermediate structures", in a zero-shot fashion via causal inference on Psi. Step 3, Integration, completes the cycle by converting these structures into new token types that are then continually mixed back into the training diet as conditioning signals and prediction targets. Each such cycle augments the capabilities of Psi, both allowing it to model the underlying data better, and creating new control handles -- akin to an LLM-like universal prompting language. We train an instance of Psi on 1.4 trillion tokens of internet video data; we use it to perform a variety of useful video prediction and understanding inferences; we extract state-of-the-art optical flow, self-supervised depth and object segmentation; and we use these structures to support a full cycle of predictive improvements.

Modern CI/CD pipelines integrating agent-generated code exhibit a structural failure in responsibility attribution. Decisions are executed through formally correct approval processes, yet no entity possesses both the authority to approve those decisions and the epistemic capacity to meaningfully understand their basis. We define this condition as responsibility vacuum: a state in which decisions occur, but responsibility cannot be attributed because authority and verification capacity do not coincide. We show that this is not a process deviation or technical defect, but a structural property of deployments where decision generation throughput exceeds bounded human verification capacity. We identify a scaling limit under standard deployment assumptions, including parallel agent generation, CI-based validation, and individualized human approval gates. Beyond a throughput threshold, verification ceases to function as a decision criterion and is replaced by ritualized approval based on proxy signals. Personalized responsibility becomes structurally unattainable in this regime. We further characterize a CI amplification dynamic, whereby increasing automated validation coverage raises proxy signal density without restoring human capacity. Under fixed time and attention constraints, this accelerates cognitive offloading in the broad sense and widens the gap between formal approval and epistemic understanding. Additional automation therefore amplifies, rather than mitigates, the responsibility vacuum. We conclude that unless organizations explicitly redesign decision boundaries or reassign responsibility away from individual decisions toward batch- or system-level ownership, responsibility vacuum remains an invisible but persistent failure mode in scaled agent deployments.

Reliable facial expression learning (FEL) involves the effective learning of distinctive facial expression characteristics for more reliable, unbiased and accurate predictions in real-life settings. However, current systems struggle with FEL tasks because of the variance in people's facial expressions due to their unique facial structures, movements, tones, and demographics. Biased and imbalanced datasets compound this challenge, leading to wrong and biased prediction labels. To tackle these, we introduce GReFEL, leveraging Vision Transformers and a facial geometry-aware anchor-based reliability balancing module to combat imbalanced data distributions, bias, and uncertainty in facial expression learning. Integrating local and global data with anchors that learn different facial data points and structural features, our approach adjusts biased and mislabeled emotions caused by intra-class disparity, inter-class similarity, and scale sensitivity, resulting in comprehensive, accurate, and reliable facial expression predictions. Our model outperforms current state-of-the-art methodologies, as demonstrated by extensive experiments on various datasets.

Knowledge Graph Completion (KGC), which aims to infer missing or incomplete facts, is a crucial task for KGs. However, integrating the vital structural information of KGs into Large Language Models (LLMs) and outputting predictions deterministically remains challenging. To address this, we propose a new method called GLTW, which encodes the structural information of KGs and merges it with LLMs to enhance KGC performance. Specifically, we introduce an improved Graph Transformer (iGT) that effectively encodes subgraphs with both local and global structural information and inherits the characteristics of language model, bypassing training from scratch. Also, we develop a subgraph-based multi-classification training objective, using all entities within KG as classification objects, to boost learning efficiency.Importantly, we combine iGT with an LLM that takes KG language prompts as input.Our extensive experiments on various KG datasets show that GLTW achieves significant performance gains compared to SOTA baselines.

The application of artificial intelligence (AI) in three-dimensional (3D) agricultural research, particularly for maize, has been limited by the scarcity of large-scale, diverse datasets. While 2D image datasets are abundant, they fail to capture essential structural details such as leaf architecture, plant volume, and spatial arrangements that 3D data provide. To address this limitation, we present AgriField3D (https://baskargroup.github.io/AgriField3D/), a curated dataset of 3D point clouds of field-grown maize plants from a diverse genetic panel, designed to be AI-ready for advancing agricultural research. Our dataset comprises over 1,000 high-quality point clouds collected using a Terrestrial Laser Scanner, complemented by procedural models that provide structured, parametric representations of maize plants. These procedural models, generated using Non-Uniform Rational B-Splines (NURBS) and optimized via a two-step process combining Particle Swarm Optimization (PSO) and differentiable programming, enable precise, scalable reconstructions of leaf surfaces and plant architectures. To enhance usability, we performed graph-based segmentation to isolate individual leaves and stalks, ensuring consistent labeling across all samples. We also conducted rigorous manual quality control on all datasets, correcting errors in segmentation, ensuring accurate leaf ordering, and validating metadata annotations. The dataset further includes metadata detailing plant morphology and quality, alongside multi-resolution subsampled versions (100k, 50k, 10k points) optimized for various computational needs. By integrating point cloud data of field grown plants with high-fidelity procedural models and ensuring meticulous manual validation, AgriField3D provides a comprehensive foundation for AI-driven phenotyping, plant structural analysis, and 3D applications in agricultural research.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Subcellular localization is a crucial biological task for drug target identification and function annotation. Although it has been biologically realized that subcellular localization is closely associated with protein structure, no existing dataset offers comprehensive 3D structural information with detailed subcellular localization annotations, thus severely hindering the application of promising structure-based models on this task. To address this gap, we introduce a new benchmark called CAPSUL, a Comprehensive humAn Protein benchmark for SUbcellular Localization. It features a dataset that integrates diverse 3D structural representations with fine-grained subcellular localization annotations carefully curated by domain experts. We evaluate this benchmark using a variety of state-of-the-art sequence-based and structure-based models, showcasing the importance of involving structural features in this task. Furthermore, we explore reweighting and single-label classification strategies to facilitate future investigation on structure-based methods for this task. Lastly, we showcase the powerful interpretability of structure-based methods through a case study on the Golgi apparatus, where we discover a decisive localization pattern α-helix from attention mechanisms, demonstrating the potential for bridging the gap with intuitive biological interpretability and paving the way for data-driven discoveries in cell biology.

We introduce a novel 3D generation method for versatile and high-quality 3D asset creation. The cornerstone is a unified Structured LATent (SLAT) representation which allows decoding to different output formats, such as Radiance Fields, 3D Gaussians, and meshes. This is achieved by integrating a sparsely-populated 3D grid with dense multiview visual features extracted from a powerful vision foundation model, comprehensively capturing both structural (geometry) and textural (appearance) information while maintaining flexibility during decoding. We employ rectified flow transformers tailored for SLAT as our 3D generation models and train models with up to 2 billion parameters on a large 3D asset dataset of 500K diverse objects. Our model generates high-quality results with text or image conditions, significantly surpassing existing methods, including recent ones at similar scales. We showcase flexible output format selection and local 3D editing capabilities which were not offered by previous models. Code, model, and data will be released.

Conventional point cloud semantic segmentation methods usually employ an encoder-decoder architecture, where mid-level features are locally aggregated to extract geometric information. However, the over-reliance on these class-agnostic local geometric representations may raise confusion between local parts from different categories that are similar in appearance or spatially adjacent. To address this issue, we argue that mid-level features can be further enhanced with semantic information, and propose semantic-affine transformation that transforms features of mid-level points belonging to different categories with class-specific affine parameters. Based on this technique, we propose SemAffiNet for point cloud semantic segmentation, which utilizes the attention mechanism in the Transformer module to implicitly and explicitly capture global structural knowledge within local parts for overall comprehension of each category. We conduct extensive experiments on the ScanNetV2 and NYUv2 datasets, and evaluate semantic-affine transformation on various 3D point cloud and 2D image segmentation baselines, where both qualitative and quantitative results demonstrate the superiority and generalization ability of our proposed approach. Code is available at https://github.com/wangzy22/SemAffiNet.

In this work, we present CCEdit, a versatile framework designed to address the challenges of creative and controllable video editing. CCEdit accommodates a wide spectrum of user editing requirements and enables enhanced creative control through an innovative approach that decouples video structure and appearance. We leverage the foundational ControlNet architecture to preserve structural integrity, while seamlessly integrating adaptable temporal modules compatible with state-of-the-art personalization techniques for text-to-image generation, such as DreamBooth and LoRA.Furthermore, we introduce reference-conditioned video editing, empowering users to exercise precise creative control over video editing through the more manageable process of editing key frames. Our extensive experimental evaluations confirm the exceptional functionality and editing capabilities of the proposed CCEdit framework. Demo video is available at https://www.youtube.com/watch?v=UQw4jq-igN4.

Understanding the underlying linguistic rules of plant genomes remains a fundamental challenge in computational biology. Recent advances including AgroNT and PDLLMs have made notable progress although, they suffer from excessive parameter size and limited ability to model the bidirectional nature of DNA strands respectively. To address these limitations, we propose PlantBiMoE, a lightweight and expressive plant genome language model that integrates bidirectional Mamba and a Sparse Mixture-of-Experts (SparseMoE) framework. The bidirectional Mamba enables the model to effectively capture structural dependencies across both the forward and reverse DNA strands, while SparseMoE significantly reduces the number of active parameters, improving computational efficiency without sacrificing modeling capacity. We evaluated and tested our model on the Modified Plants Genome Benchmark (MPGB), an enhanced genomic benchmark, which consolidates 31 datasets across 11 representative tasks, with input sequence lengths ranging from 50 to 6,000 bp. Experimental results demonstrate that PlantBiMoE achieves the best performance on 20 out of 31 datasets and the average best when comparing with existing models. In summary, all above results demonstrate that our model can effectively represent plant genomic sequences, serving as a robust computational tool for diverse genomic tasks, while making substantive contributions to plant genomics, gene editing, and synthetic biology. The code is available at: https://github.com/HUST-Keep-Lin/PlantBiMoE

To migrate the remarkable successes of Large Language Models (LLMs), the community has made numerous efforts to generalize them to the table reasoning tasks for the widely deployed tabular data. Despite that, in this work, by showing a probing experiment on our proposed StructQA benchmark, we postulate that even the most advanced LLMs (such as GPTs) may still fall short of coping with tabular data. More specifically, the current scheme often simply relies on serializing the tabular data, together with the meta information, then inputting them through the LLMs. We argue that the loss of structural information is the root of this shortcoming. In this work, we further propose TAMO, which bears an ideology to treat the tables as an independent modality integrated with the text tokens. The resulting model in TAMO is a multimodal framework consisting of a hypergraph neural network as the global table encoder seamlessly integrated with the mainstream LLM. Empirical results on various benchmarking datasets, including HiTab, WikiTQ, WikiSQL, FeTaQA, and StructQA, have demonstrated significant improvements on generalization with an average relative gain of 42.65%.

Document layout understanding remains data-intensive despite advances in semi-supervised learning. We present a framework that enhances semi-supervised detection by fusing visual predictions with structural priors from text-pretrained LLMs via principled probabilistic weighting. Given unlabeled documents, an OCR-LLM pipeline infers hierarchical regions which are combined with teacher detector outputs through inverse-variance fusion to generate refined pseudo-labels.Our method demonstrates consistent gains across model scales. With a lightweight SwiftFormer backbone (26M params), we achieve 88.2pm0.3 AP using only 5\% labels on PubLayNet. When applied to document-pretrained LayoutLMv3 (133M params), our fusion framework reaches 89.7pm0.4 AP, surpassing both LayoutLMv3 with standard semi-supervised learning (89.1pm0.4 AP, p=0.02) and matching UDOP~udop (89.8 AP) which requires 100M+ pages of multimodal pretraining. This demonstrates that LLM structural priors are complementary to both lightweight and pretrained architectures. Key findings include: (1) learned instance-adaptive gating improves over fixed weights by +0.9 AP with data-dependent PAC bounds correctly predicting convergence; (2) open-source LLMs enable privacy-preserving deployment with minimal loss (Llama-3-70B: 87.1 AP lightweight, 89.4 AP with LayoutLMv3); (3) LLMs provide targeted semantic disambiguation (18.7\% of cases, +3.8 AP gain) beyond simple text heuristics.Total system cost includes \$12 for GPT-4o-mini API or 17 GPU-hours for local Llama-3-70B per 50K pages, amortized across training runs.

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism. Our model integrates local evolutionary context from homologous sequences, the global evolutionary context encoding rich semantic from the universal protein sequence space and the structure information accounting for the microenvironment around each residue in a protein. We show that SESNet outperforms state-of-the-art models for predicting the sequence-function relationship on 26 deep mutational scanning datasets. More importantly, we propose a data augmentation strategy by leveraging the data from unsupervised models to pre-train our model. After that, our model can achieve strikingly high accuracy in prediction of the fitness of protein mutants, especially for the higher order variants (> 4 mutation sites), when finetuned by using only a small number of experimental mutation data (<50). The strategy proposed is of great practical value as the required experimental effort, i.e., producing a few tens of experimental mutation data on a given protein, is generally affordable by an ordinary biochemical group and can be applied on almost any protein.

Generating long-range, geometrically consistent video presents a fundamental dilemma: while consistency demands strict adherence to 3D geometry in pixel space, state-of-the-art generative models operate most effectively in a camera-conditioned latent space. This disconnect causes current methods to struggle with occluded areas and complex camera trajectories. To bridge this gap, we propose WorldWarp, a framework that couples a 3D structural anchor with a 2D generative refiner. To establish geometric grounding, WorldWarp maintains an online 3D geometric cache built via Gaussian Splatting (3DGS). By explicitly warping historical content into novel views, this cache acts as a structural scaffold, ensuring each new frame respects prior geometry. However, static warping inevitably leaves holes and artifacts due to occlusions. We address this using a Spatio-Temporal Diffusion (ST-Diff) model designed for a "fill-and-revise" objective. Our key innovation is a spatio-temporal varying noise schedule: blank regions receive full noise to trigger generation, while warped regions receive partial noise to enable refinement. By dynamically updating the 3D cache at every step, WorldWarp maintains consistency across video chunks. Consequently, it achieves state-of-the-art fidelity by ensuring that 3D logic guides structure while diffusion logic perfects texture. Project page: https://hyokong.github.io/worldwarp-page/{https://hyokong.github.io/worldwarp-page/}.

3D Human motion generation is pivotal across film, animation, gaming, and embodied intelligence. Traditional 3D motion synthesis relies on costly motion capture, while recent work shows that 2D videos provide rich, temporally coherent observations of human behavior. Existing approaches, however, either map high-level text descriptions to motion or rely solely on video conditioning, leaving a gap between generated dynamics and real-world motion statistics. We introduce MotionDuet, a multimodal framework that aligns motion generation with the distribution of video-derived representations. In this dual-conditioning paradigm, video cues extracted from a pretrained model (e.g., VideoMAE) ground low-level motion dynamics, while textual prompts provide semantic intent. To bridge the distribution gap across modalities, we propose Dual-stream Unified Encoding and Transformation (DUET) and a Distribution-Aware Structural Harmonization (DASH) loss. DUET fuses video-informed cues into the motion latent space via unified encoding and dynamic attention, while DASH aligns motion trajectories with both distributional and structural statistics of video features. An auto-guidance mechanism further balances textual and visual signals by leveraging a weakened copy of the model, enhancing controllability without sacrificing diversity. Extensive experiments demonstrate that MotionDuet generates realistic and controllable human motions, surpassing strong state-of-the-art baselines.

Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based tasks. However, pLMs lack structural context. Conversely, graph neural networks (GNNs) designed to leverage 3D structural information have shown promising generalization in protein-related prediction tasks, but their effectiveness is often constrained by the scarcity of labeled structural data. Recognizing that sequence and structural representations are complementary perspectives of the same protein entity, we propose a multimodal bidirectional hierarchical fusion framework to effectively merge these modalities. Our framework employs attention and gating mechanisms to enable effective interaction between pLMs-generated sequential representations and GNN-extracted structural features, improving information exchange and enhancement across layers of the neural network. This bidirectional and hierarchical (Bi-Hierarchical) fusion approach leverages the strengths of both modalities to capture richer and more comprehensive protein representations. Based on the framework, we further introduce local Bi-Hierarchical Fusion with gating and global Bi-Hierarchical Fusion with multihead self-attention approaches. Our method demonstrates consistent improvements over strong baselines and existing fusion techniques in a variety of protein representation learning benchmarks, including enzyme EC classification, model quality assessment, protein-ligand binding affinity prediction, protein-protein binding site prediction, and B cell epitopes prediction. Our method establishes a new state-of-the-art for multimodal protein representation learning, emphasizing the efficacy of Bi-Hierarchical Fusion in bridging sequence and structural modalities.

Human perception of 3D shapes goes beyond reconstructing them as a set of points or a composition of geometric primitives: we also effortlessly understand higher-level shape structure such as the repetition and reflective symmetry of object parts. In contrast, recent advances in 3D shape sensing focus more on low-level geometry but less on these higher-level relationships. In this paper, we propose 3D shape programs, integrating bottom-up recognition systems with top-down, symbolic program structure to capture both low-level geometry and high-level structural priors for 3D shapes. Because there are no annotations of shape programs for real shapes, we develop neural modules that not only learn to infer 3D shape programs from raw, unannotated shapes, but also to execute these programs for shape reconstruction. After initial bootstrapping, our end-to-end differentiable model learns 3D shape programs by reconstructing shapes in a self-supervised manner. Experiments demonstrate that our model accurately infers and executes 3D shape programs for highly complex shapes from various categories. It can also be integrated with an image-to-shape module to infer 3D shape programs directly from an RGB image, leading to 3D shape reconstructions that are both more accurate and more physically plausible.

The relentless pursuit of enhancing Large Language Models (LLMs) has led to the advent of Super Retrieval-Augmented Generation (Super RAGs), a novel approach designed to elevate the performance of LLMs by integrating external knowledge sources with minimal structural modifications. This paper presents the integration of Super RAGs into the Mistral 8x7B v1, a state-of-the-art LLM, and examines the resultant improvements in accuracy, speed, and user satisfaction. Our methodology uses a fine-tuned instruct model setup and a cache tuning fork system, ensuring efficient and relevant data retrieval. The evaluation, conducted over several epochs, demonstrates significant enhancements across all metrics. The findings suggest that Super RAGs can effectively augment LLMs, paving the way for more sophisticated and reliable AI systems. This research contributes to the field by providing empirical evidence of the benefits of Super RAGs and offering insights into their potential applications.

The rapid progress of Multimodal Large Language Models(MLLMs) has transformed the AI landscape. These models combine pre-trained LLMs with various modality encoders. This integration requires a systematic understanding of how different modalities connect to the language backbone. Our survey presents an LLM-centric analysis of current approaches. We examine methods for transforming and aligning diverse modal inputs into the language embedding space. This addresses a significant gap in existing literature. We propose a classification framework for MLLMs based on three key dimensions. First, we examine architectural strategies for modality integration. This includes both the specific integration mechanisms and the fusion level. Second, we categorize representation learning techniques as either joint or coordinate representations. Third, we analyze training paradigms, including training strategies and objective functions. By examining 125 MLLMs developed between 2021 and 2025, we identify emerging patterns in the field. Our taxonomy provides researchers with a structured overview of current integration techniques. These insights aim to guide the development of more robust multimodal integration strategies for future models built on pre-trained foundations.

Unified multi-model representation spaces are the foundation of multimodal understanding and generation. However, the billions of model parameters and catastrophic forgetting problems make it challenging to further enhance pre-trained unified spaces. In this work, we propose FreeBind, an idea that treats multimodal representation spaces as basic units, and freely augments pre-trained unified space by integrating knowledge from extra expert spaces via "space bonds". Specifically, we introduce two kinds of basic space bonds: 1) Space Displacement Bond and 2) Space Combination Bond. Based on these basic bonds, we design Complex Sequential & Parallel Bonds to effectively integrate multiple spaces simultaneously. Benefiting from the modularization concept, we further propose a coarse-to-fine customized inference strategy to flexibly adjust the enhanced unified space for different purposes. Experimentally, we bind ImageBind with extra image-text and audio-text expert spaces, resulting in three main variants: ImageBind++, InternVL_IB, and InternVL_IB++. These resulting spaces outperform ImageBind on 5 audio-image-text downstream tasks across 9 datasets. Moreover, via customized inference, it even surpasses the advanced audio-text and image-text expert spaces.

Textured 3D morphing seeks to generate smooth and plausible transitions between two 3D assets, preserving both structural coherence and fine-grained appearance. This ability is crucial not only for advancing 3D generation research but also for practical applications in animation, editing, and digital content creation. Existing approaches either operate directly on geometry, limiting them to shape-only morphing while neglecting textures, or extend 2D interpolation strategies into 3D, which often causes semantic ambiguity, structural misalignment, and texture blurring. These challenges underscore the necessity to jointly preserve geometric consistency, texture alignment, and robustness throughout the transition process. To address this, we propose Interp3D, a novel training-free framework for textured 3D morphing. It harnesses generative priors and adopts a progressive alignment principle to ensure both geometric fidelity and texture coherence. Starting from semantically aligned interpolation in condition space, Interp3D enforces structural consistency via SLAT (Structured Latent)-guided structure interpolation, and finally transfers appearance details through fine-grained texture fusion. For comprehensive evaluations, we construct a dedicated dataset, Interp3DData, with graded difficulty levels and assess generation results from fidelity, transition smoothness, and plausibility. Both quantitative metrics and human studies demonstrate the significant advantages of our proposed approach over previous methods. Source code is available at https://github.com/xiaolul2/Interp3D.

Data comes in many forms. From a shallow perspective, they can be viewed as being either in structured (e.g., as a relation, as key-value pairs) or unstructured (e.g., text, image) formats. So far, machines have been fairly good at processing and reasoning over structured data that follows a precise schema. However, the heterogeneity of data poses a significant challenge on how well diverse categories of data can be meaningfully stored and processed. Data Integration, a crucial part of the data engineering pipeline, addresses this by combining disparate data sources and providing unified data access to end-users. Until now, most data integration systems have leaned on only combining structured data sources. Nevertheless, unstructured data (a.k.a. free text) also contains a plethora of knowledge waiting to be utilized. Thus, in this chapter, we firstly make the case for the integration of textual data, to later present its challenges, state of the art and open problems.

Artificial intelligence has become a crucial tool for medical image analysis. As an advanced cerebral angiography technique, Digital Subtraction Angiography (DSA) poses a challenge where the radiation dose to humans is proportional to the image count. By reducing images and using AI interpolation instead, the radiation can be cut significantly. However, DSA images present more complex motion and structural features than natural scenes, making interpolation more challenging. We propose MoSt-DSA, the first work that uses deep learning for DSA frame interpolation. Unlike natural scene Video Frame Interpolation (VFI) methods that extract unclear or coarse-grained features, we devise a general module that models motion and structural context interactions between frames in an efficient full convolution manner by adjusting optimal context range and transforming contexts into linear functions. Benefiting from this, MoSt-DSA is also the first method that directly achieves any number of interpolations at any time steps with just one forward pass during both training and testing. We conduct extensive comparisons with 7 representative VFI models for interpolating 1 to 3 frames, MoSt-DSA demonstrates robust results across 470 DSA image sequences (each typically 152 images), with average SSIM over 0.93, average PSNR over 38 (standard deviations of less than 0.030 and 3.6, respectively), comprehensively achieving state-of-the-art performance in accuracy, speed, visual effect, and memory usage. Our code is available at https://github.com/ZyoungXu/MoSt-DSA.

Structural modeling is a fundamental component of computational engineering science, in which even minor physical inconsistencies or specification violations may invalidate downstream simulations. The potential of large language models (LLMs) for automatic generation of modeling code has been demonstrated. However, non-executable or physically inconsistent outputs remain prevalent under stringent engineering constraints. A framework for physics-consistent automatic building modeling is therefore proposed, integrating domain knowledge construction, constraint-oriented model alignment, and verification-driven evaluation. CivilInstruct is introduced as a domain-specific dataset that formalizes structural engineering knowledge and constraint reasoning to enable simulation-ready model generation. A two-stage fine-tuning strategy is further employed to enforce constraint satisfaction and application programming interface compliance, substantially reducing hallucinated and non-conforming outputs. MBEval is presented as a verification-driven benchmark that evaluates executability and structural dynamics consistency through closed-loop validation. Experimental results show consistent improvements over baselines across rigorous verification metrics. Our code is available at https://github.com/Jovanqing/AutoBM.

Structural topology optimization (TO) is central to engineering design but remains computationally intensive due to complex physics and hard constraints. Existing deep-learning methods are limited to fixed square grids, a few hand-coded boundary conditions, and post-hoc optimization, preventing general deployment. We introduce Optimize Any Topology (OAT), a foundation-model framework that directly predicts minimum-compliance layouts for arbitrary aspect ratios, resolutions, volume fractions, loads, and fixtures. OAT combines a resolution- and shape-agnostic autoencoder with an implicit neural-field decoder and a conditional latent-diffusion model trained on OpenTO, a new corpus of 2.2 million optimized structures covering 2 million unique boundary-condition configurations. On four public benchmarks and two challenging unseen tests, OAT lowers mean compliance up to 90% relative to the best prior models and delivers sub-1 second inference on a single GPU across resolutions from 64 x 64 to 256 x 256 and aspect ratios as high as 10:1. These results establish OAT as a general, fast, and resolution-free framework for physics-aware topology optimization and provide a large-scale dataset to spur further research in generative modeling for inverse design. Code & data can be found at https://github.com/ahnobari/OptimizeAnyTopology.

Vision-Language Pretraining (VLP) has achieved remarkable success across various downstream tasks, but such gains are largely driven by scaling up on training data. Yet, literature methods treat image-text pairs as isolated training examples; this neglects the rich relational structure naturally present in many domains, such as e-commerce product co-purchase graphs and social recommendation networks. Inspired by neuroscientific evidence that human encodes knowledge as relationship cognitive maps, we introduce Structure-aware Language-Image Pretraining (SLIP). SLIP integrates a structural contrastive loss to align modalities while also modeling relationships between neighboring entities in a structured graph. To support this paradigm, we construct a large-scale Amazon Product Co-purchase Multimodal Graph Dataset, enabling structured cross-modality supervision at scale. Experiment results show that SLIP consistently outperforms CLIP on cross-modal retrieval and classification tasks in both zero-shot and few-shot settings, showing the value of relational supervision for cross-modal alignment.

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared representation space using contrastive learning. However, systematic evaluations reveal significant performance degradation at structural boundaries where distinct topological patterns converge, with accuracy losses exceeding 20 percentage points. This issue arises from a key limitation: current methods assume all graph structures can be encoded within a single Euclidean space. In reality, tree structures require hyperbolic geometry to preserve hierarchical branching, while cyclic patterns depend on spherical geometry for closure properties. At structural boundaries, nodes experience conflicting geometric constraints that uniform encoding spaces cannot resolve. This raises a crucial challenge: Can alignment frameworks be designed to respect the intrinsic geometric diversity of graph structures? We introduce GraphShaper, a geometry-aware framework that enhances graph encoding through multi-geometric specialization. Our approach employs expert networks tailored to different geometric spaces, dynamically computing fusion weights to adaptively integrate geometric properties based on local structural characteristics. This adaptive fusion preserves structural integrity before alignment with text embeddings. Extensive experiments demonstrate that GraphShaper achieves 9.47\% accuracy improvements on citation networks and 7.63\% on social networks in zero-shot settings.

Understanding the physical structure is essential for real-world applications such as embodied agents, interactive design, and long-horizon manipulation. Yet, prevailing Vision-Language Model (VLM) evaluations still center on structure-agnostic, single-turn setups (e.g., VQA), which fail to assess agents' ability to reason about how geometry, contact, and support relations jointly constrain what actions are possible in a dynamic environment. To address this gap, we introduce the Causal Hierarchy of Actions and Interactions (CHAIN) benchmark, an interactive 3D, physics-driven testbed designed to evaluate whether models can understand, plan, and execute structured action sequences grounded in physical constraints. CHAIN shifts evaluation from passive perception to active problem solving, spanning tasks such as interlocking mechanical puzzles and 3D stacking and packing. We conduct a comprehensive study of state-of-the-art VLMs and diffusion-based models under unified interactive settings. Our results show that top-performing models still struggle to internalize physical structure and causal constraints, often failing to produce reliable long-horizon plans and cannot robustly translate perceived structure into effective actions. The project is available at https://social-ai-studio.github.io/CHAIN/.