Daily Papers

When LLMs exhibit uneven performance across planning tasks, these gaps are often attributed to task difficulty. We argue that this explanation is incomplete, as task-level variation may reflect distinct latent planning competencies rather than differences along a single ability spectrum. We study this question on ACPBench-Hard by evaluating multiple LLM families under varying test-time reasoning budgets and applying a multidimensional item response theory model to uncover the latent competency structure underlying LLM planning. The analysis reveals two principal dimensions that shape planning performance: operational reasoning, the ability to evaluate local action applicability and immediate state transitions, and structural enumeration, the ability to reason about goal reachability and landmark structure. Operational reasoning improving under model scaling and longer reasoning traces, while structural enumeration remains comparatively insensitive. Our findings motivate competency-level evaluation of LLM planning, shifting the focus from whether models improve overall to which planning competencies improve, under what conditions, and why.

Web-agent benchmarks overwhelmingly measure depth -- pinning one obscure answer behind a chain of constraints -- while breadth, exhaustively enumerating a closed set and filling each item's attributes, is barely evaluated, especially outside English. Breadth is also hard to build: certifying that a gold set is complete and every cell correct is far costlier than checking a single answer. I introduce Ko-WideSearch, a Korean breadth-search benchmark built by an automated synthesize-and-verify pipeline. Each task names a set-parent entity -- a TV season, a dynasty, a league, an administrative region, an election -- and asks for its full membership plus a per-item attribute table, graded by Item-, Column-, and Row-F1. It spans 228 tables over 190 entities and sixteen categories across three difficulty tiers, set by two structural knobs I dial independently -- table width and a 2-D composite key -- so cross-product membership climbs from 0\% to 100\% across the tiers. A single normalization-aware comparator is shared between gold construction and grading, so stable date and count columns are not over-dropped on formatting alone. Across twenty web agents, the failure is consistent: agents recover the set but not the rows (e.g.\ Item-F1 92.8 against Row-F1 53.7), accuracy falls steadily as the knobs harden, and neither more search nor more spend closes the gap. Broken down by cell, the hard part is finding the right value, not formatting it: open-ended free-text cells fail most, while cells with a standard answer such as a date or a name usually come out right.

We study Krasner quotient hyperfields arising from finite fields, F_q/G_r, where G_rle F_q^times has index r. Building on the structure theorem of Baker--Jin, we determine the characteristic and C-characteristic of all sufficiently large such quotients: they depend only on the parity of r and, when r is even, on the residue class of q modulo 2r. In particular, the two Baker--Jin stable classes for even r are separated by characteristic 2 versus 3, while the C-characteristic is always 1. We complement this structural result with a computational laboratory: sharp Weil thresholds for Baker--Jin large-q isomorphism, empirical minimal stabilization bounds N_r^{emp}, complete finite-field quotient atlases for hyperfield orders nle 7, and comparisons with the enumerations of Ameri--Eyvazi--Hošková-Mayerová (orders le 6) and Massouros--Massouros (order 7). Among other findings, exactly 15 isomorphism types of order 7 arise as finite-field quotients, out of 277 hyperfields of that order -- a concrete data point toward the Baker--Jin rarity conjecture for quotients. All algorithms and tables are available in an open-source package suitable for independent verification and arXiv ancillary material.

Large language models exhibit a systematic tendency toward early semantic commitment: given ambiguous input, they collapse multiple valid interpretations into a single response before sufficient context is available. This premature collapse discards information that may prove essential as dialogue evolves. We present a formal framework for text-to-state mapping (phi: T -> S) that transforms natural language into a non-collapsing state space where multiple interpretations coexist. The mapping decomposes into three stages: conflict detection, interpretation extraction, and state construction. We instantiate phi with a hybrid extraction pipeline that combines rule-based segmentation for explicit conflict markers (adversative conjunctions, hedging expressions) with LLM-based enumeration of implicit ambiguity (epistemic, lexical, structural). On a test set of 68 ambiguous sentences, the resulting states preserve interpretive multiplicity: using hybrid extraction, we obtain mean state entropy H = 1.087 bits across ambiguity categories, compared to H = 0 for collapse-based baselines that commit to a single interpretation. We additionally instantiate the rule-based conflict detector for Japanese markers (kedo, kamoshirenai, etc.) to illustrate cross-lingual portability of the conflict detection stage. This framework extends Non-Resolution Reasoning (NRR) by providing the missing algorithmic bridge between text and the NRR state space, enabling architectural collapse deferment in LLM inference. Design principles for state-to-state transformations are detailed in the Appendix, with empirical validation on 580 test cases (180 single states, 200 contradictory pairs, 200 temporal pairs), demonstrating 0% collapse for principle-satisfying operators versus up to 17.8% for violating operators.

As LLM agents adopt large skill libraries, selecting the right subset becomes a structural problem rather than a similarity-matching one: skills depend on, conflict with, specialize, or duplicate one another, a structure invisible to both full enumeration and embedding similarity. We present SkillDAG, which models inter-skill relationships as a typed directed graph and exposes it to an LLM agent as an inference-time, agent-callable structural retrieval interface, queried and evolved during execution rather than baked into a fixed retrieval pipeline: each search returns vector matches, typed-edge neighbors, and conflict signals, and a propose-then-commit protocol lets the agent register execution-backed edges so the graph accumulates structure across episodes. On ALFWorld and SkillsBench with MiniMax-M2.7, SkillDAG reaches 67.1% success and 27.3% reward, exceeding the strongest reported Graph-of-Skills baseline by +12.8 and +8.6 points; the advantage ports to gpt-5.2-codex, and intrinsic SkillsBench Ret@K rises from 65.5 to 78.2 under matched queries. These gains trace to isolable mechanisms: candidate ranking that stays robust as the pool grows 10x where a fixed seeding-diffusion pipeline degrades, and set-monotone online edits that enlarge ground-truth recall without evicting prior hits.

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

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.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

We apply category theory to extract multimodal document structure which leads us to develop information theoretic measures, content summarization and extension, and self-supervised improvement of large pretrained models. We first develop a mathematical representation of a document as a category of question-answer pairs. Second, we develop an orthogonalization procedure to divide the information contained in one or more documents into non-overlapping pieces. The structures extracted in the first and second steps lead us to develop methods to measure and enumerate the information contained in a document. We also build on those steps to develop new summarization techniques, as well as to develop a solution to a new problem viz. exegesis resulting in an extension of the original document. Our question-answer pair methodology enables a novel rate distortion analysis of summarization techniques. We implement our techniques using large pretrained models, and we propose a multimodal extension of our overall mathematical framework. Finally, we develop a novel self-supervised method using RLVR to improve large pretrained models using consistency constraints such as composability and closure under certain operations that stem naturally from our category theoretic framework.

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (e.g. graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

Structure information is critical for understanding the semantics of text-rich images, such as documents, tables, and charts. Existing Multimodal Large Language Models (MLLMs) for Visual Document Understanding are equipped with text recognition ability but lack general structure understanding abilities for text-rich document images. In this work, we emphasize the importance of structure information in Visual Document Understanding and propose the Unified Structure Learning to boost the performance of MLLMs. Our Unified Structure Learning comprises structure-aware parsing tasks and multi-grained text localization tasks across 5 domains: document, webpage, table, chart, and natural image. To better encode structure information, we design a simple and effective vision-to-text module H-Reducer, which can not only maintain the layout information but also reduce the length of visual features by merging horizontal adjacent patches through convolution, enabling the LLM to understand high-resolution images more efficiently. Furthermore, by constructing structure-aware text sequences and multi-grained pairs of texts and bounding boxes for publicly available text-rich images, we build a comprehensive training set DocStruct4M to support structure learning. Finally, we construct a small but high-quality reasoning tuning dataset DocReason25K to trigger the detailed explanation ability in the document domain. Our model DocOwl 1.5 achieves state-of-the-art performance on 10 visual document understanding benchmarks, improving the SOTA performance of MLLMs with a 7B LLM by more than 10 points in 5/10 benchmarks. Our codes, models, and datasets are publicly available at https://github.com/X-PLUG/mPLUG-DocOwl/tree/main/DocOwl1.5.

We study the hop-constrained s-t path enumeration (HcPE) problem, which takes a graph G, two distinct vertices s,t and a hop constraint k as input, and outputs all paths from s to t whose length is at most k. The state-of-the-art algorithms suffer from severe performance issues caused by the costly pruning operations during enumeration for the workloads with the large search space. Consequently, these algorithms hardly meet the real-time constraints of many online applications. In this paper, we propose PathEnum, an efficient index-based algorithm towards real-time HcPE. For an input query, PathEnum first builds a light-weight index aiming to reduce the number of edges involved in the enumeration, and develops efficient index-based approaches for enumeration, one based on depth-first search and the other based on joins. We further develop a query optimizer based on a join-based cost model to optimize the search order. We conduct experiments with 15 real-world graphs. Our experiment results show that PathEnum outperforms the state-of-the-art approaches by orders of magnitude in terms of the query time, throughput and response time.

Structural fidelity is essential to scientific methodology diagrams. To communicate research logic, these diagrams must faithfully render components, directional relations, and textual annotations. Since a single error, such as a reversed arrow or an unreadable equation, can invalidate the entire figure, structural fidelity is inherently conjunctive: correctness on one axis cannot compensate for failure on another. Current open-source models fail to satisfy this criterion. Supervised fine-tuning (SFT) learns plausible layouts but cannot reliably ensure structural correctness, while scalar reward-based post-training obscures which structural dimension has failed. To address this, we introduce SciForma, a framework for the structure faithful generation of scientific methodology diagrams. Specifically, SciForma decomposes diagram quality into three structural axes: Component, Arrow, and Text, guided by a structural inventory. Built on this foundation, we curate SciFormaData-700K for structured training and SciFormaBench-2K for logic-verified evaluation. To close the gap left by SFT, we develop Multi-Dimensional Conjunctive Preference Optimization (M-DPO), which enforces simultaneous correctness across all axes and adaptively routes gradients to the most deficient dimension in post-training. The same structural inventory also enables iterative editing at inference time to correct residual errors. This combination allows SciForma-9B to exceed all open-source baselines and GPT-Image-1.5 on both SciFormaBench-2K and AIBench, bringing open scientific diagram generation close to proprietary-level structural fidelity. Our code and data will be available at: https://github.com/microsoft/SciForma.

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce StructTokenBench, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop AminoAseed, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83% and 124.03%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench

State-of-the-art vision-language models (VLMs) still have limited performance in structural knowledge extraction, such as relations between objects. In this work, we present ViStruct, a training framework to learn VLMs for effective visual structural knowledge extraction. Two novel designs are incorporated. First, we propose to leverage the inherent structure of programming language to depict visual structural information. This approach enables explicit and consistent representation of visual structural information of multiple granularities, such as concepts, relations, and events, in a well-organized structured format. Second, we introduce curriculum-based learning for VLMs to progressively comprehend visual structures, from fundamental visual concepts to intricate event structures. Our intuition is that lower-level knowledge may contribute to complex visual structure understanding. Furthermore, we compile and release a collection of datasets tailored for visual structural knowledge extraction. We adopt a weakly-supervised approach to directly generate visual event structures from captions for ViStruct training, capitalizing on abundant image-caption pairs from the web. In experiments, we evaluate ViStruct on visual structure prediction tasks, demonstrating its effectiveness in improving the understanding of visual structures. The code is public at https://github.com/Yangyi-Chen/vi-struct.

Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present opportunities to enhance generative design to directly optimize expensive high-fidelity oracles and provide actionable insights to domain experts. Here, we propose Beam Enumeration to exhaustively enumerate the most probable sub-sequences from language-based molecular generative models and show that molecular substructures can be extracted. When coupled with reinforcement learning, extracted substructures become meaningful, providing a source of explainability and improving sample efficiency through self-conditioned generation. Beam Enumeration is generally applicable to any language-based molecular generative model and notably further improves the performance of the recently reported Augmented Memory algorithm, which achieved the new state-of-the-art on the Practical Molecular Optimization benchmark for sample efficiency. The combined algorithm generates more high reward molecules and faster, given a fixed oracle budget. Beam Enumeration shows that improvements to explainability and sample efficiency for molecular design can be made synergistic.

Tensor network (TN) is a powerful framework in machine learning, but selecting a good TN model, known as TN structure search (TN-SS), is a challenging and computationally intensive task. The recent approach TNLS~li2022permutation showed promising results for this task, however, its computational efficiency is still unaffordable, requiring too many evaluations of the objective function. We propose TnALE, a new algorithm that updates each structure-related variable alternately by local enumeration, greatly reducing the number of evaluations compared to TNLS. We theoretically investigate the descent steps for TNLS and TnALE, proving that both algorithms can achieve linear convergence up to a constant if a sufficient reduction of the objective is reached in each neighborhood. We also compare the evaluation efficiency of TNLS and TnALE, revealing that Omega(2^N) evaluations are typically required in TNLS for reaching the objective reduction in the neighborhood, while ideally O(N^2R) evaluations are sufficient in TnALE, where N denotes the tensor order and R reflects the ``low-rankness'' of the neighborhood. Experimental results verify that TnALE can find practically good TN-ranks and permutations with vastly fewer evaluations than the state-of-the-art algorithms.

Structural priming is a cognitive phenomenon where exposure to a particular syntactic structure increases the likelihood of producing the same structure in subsequent utterances. While humans consistently demonstrate structural priming effects across various linguistic contexts, it remains unclear whether multimodal large language models (MLLMs) exhibit similar syntactic preservation behaviors. We introduce PRISMATIC, the first multimodal structural priming dataset, which advances computational linguistics by providing a standardized benchmark for investigating syntax-vision interactions. We propose the Syntactic Preservation Index (SPI), a novel reference-free evaluation metric designed specifically to assess structural priming effects in sentence level. Using this metric, we constructed and tested models with two different multimodal encoding architectures to investigate their structural preservation capabilities. Our experimental results demonstrate that models with both encoding methods show comparable syntactic priming effects. However, only fusion-encoded models exhibit robust positive correlations between priming effects and visual similarity, suggesting a cognitive process more aligned with human psycholinguistic patterns. This work provides new insights into evaluating and understanding how syntactic information is processed in multimodal language models.

Computational synthesis planning approaches have achieved recent success in organic chemistry, where tabulated synthesis procedures are readily available for supervised learning. The syntheses of inorganic materials, however, exist primarily as natural language narratives contained within scientific journal articles. This synthesis information must first be extracted from the text in order to enable analogous synthesis planning methods for inorganic materials. In this work, we present a system for automatically extracting structured representations of synthesis procedures from the texts of materials science journal articles that describe explicit, experimental syntheses of inorganic compounds. We define the structured representation as a set of linked events made up of extracted scientific entities and evaluate two unsupervised approaches for extracting these structures on expert-annotated articles: a strong heuristic baseline and a generative model of procedural text. We also evaluate a variety of supervised models for extracting scientific entities. Our results provide insight into the nature of the data and directions for further work in this exciting new area of research.

The automated analysis of chemical literature holds promise to accelerate discovery in fields such as material science and drug development. In particular, search capabilities for chemical structures and Markush structures (chemical structure templates) within patent documents are valuable, e.g., for prior-art search. Advancements have been made in the automatic extraction of chemical structures from text and images, yet the Markush structures remain largely unexplored due to their complex multi-modal nature. In this work, we present MarkushGrapher, a multi-modal approach for recognizing Markush structures in documents. Our method jointly encodes text, image, and layout information through a Vision-Text-Layout encoder and an Optical Chemical Structure Recognition vision encoder. These representations are merged and used to auto-regressively generate a sequential graph representation of the Markush structure along with a table defining its variable groups. To overcome the lack of real-world training data, we propose a synthetic data generation pipeline that produces a wide range of realistic Markush structures. Additionally, we present M2S, the first annotated benchmark of real-world Markush structures, to advance research on this challenging task. Extensive experiments demonstrate that our approach outperforms state-of-the-art chemistry-specific and general-purpose vision-language models in most evaluation settings. Code, models, and datasets will be available.

Think about how human handles complex reading tasks: marking key points, inferring their relationships, and structuring information to guide understanding and responses. Likewise, can a large language model benefit from text structure to enhance text-processing performance? To explore it, in this work, we first introduce Structure of Thought (SoT), a prompting technique that explicitly guides models to construct intermediate text structures, consistently boosting performance across eight tasks and three model families. Building upon this insight, we present T2S-Bench, the first benchmark designed to evaluate and improve text-to-structure capabilities of models. T2S-Bench includes 1.8K samples across 6 scientific domains and 32 structural types, rigorously constructed to ensure accuracy, fairness, and quality. Evaluation on 45 mainstream models reveals substantial improvement potential: the average accuracy on the multi-hop reasoning task is only 52.1%, and even the most advanced model achieves 58.1% node accuracy in end-to-end extraction. Furthermore, on Qwen2.5-7B-Instruct, SoT alone yields an average +5.7% improvement across eight diverse text-processing tasks, and fine-tuning on T2S-Bench further increases this gain to +8.6%. These results highlight the value of explicit text structuring and the complementary contributions of SoT and T2S-Bench. Dataset and eval code have been released at https://t2s-bench.github.io/T2S-Bench-Page/.

Recent studies on AMR-to-text generation often formalize the task as a sequence-to-sequence (seq2seq) learning problem by converting an Abstract Meaning Representation (AMR) graph into a word sequence. Graph structures are further modeled into the seq2seq framework in order to utilize the structural information in the AMR graphs. However, previous approaches only consider the relations between directly connected concepts while ignoring the rich structure in AMR graphs. In this paper we eliminate such a strong limitation and propose a novel structure-aware self-attention approach to better modeling the relations between indirectly connected concepts in the state-of-the-art seq2seq model, i.e., the Transformer. In particular, a few different methods are explored to learn structural representations between two concepts. Experimental results on English AMR benchmark datasets show that our approach significantly outperforms the state of the art with 29.66 and 31.82 BLEU scores on LDC2015E86 and LDC2017T10, respectively. To the best of our knowledge, these are the best results achieved so far by supervised models on the benchmarks.

Recent years have seen a paradigm shift in NLP towards using pretrained language models ({PLM}) for a wide range of tasks. However, there are many difficult design decisions to represent structures (e.g. tagged text, coreference chains) in a way such that they can be captured by PLMs. Prior work on structured prediction with PLMs typically flattens the structured output into a sequence, which limits the quality of structural information being learned and leads to inferior performance compared to classic discriminative models. In this work, we describe an approach to model structures as sequences of actions in an autoregressive manner with PLMs, allowing in-structure dependencies to be learned without any loss. Our approach achieves the new state-of-the-art on all the structured prediction tasks we looked at, namely, named entity recognition, end-to-end relation extraction, and coreference resolution.

The question of whether there exists a finite group of order at least three in which every element except one is a commutator has remained unresolved in group theory. In this article, we address this open problem by developing an algorithmic approach that leverages several group theoretic properties of such groups. Specifically, we utilize a result of Frobenius and various necessary properties of such groups, combined with Plesken and Holt's extensive enumeration of finite perfect groups, to systematically examine all finite groups up to a certain order for the desired property. The computational core of our work is implemented using the computer system GAP (Groups, Algorithms, and Programming). We discover two nonisomorphic groups of order 368,640 that exhibit the desired property. Our investigation also establishes that this order is the minimum order for such a group to exist. As a result, this study provides a positive answer to Problem 17.76 in the Kourovka Notebook. In addition to the algorithmic framework, this paper provides a structural description of one of the two groups found.

Machine-learning generative methods for material design are constructed by representing a given chemical structure, either a solid or a molecule, over appropriate atomic features, generally called structural descriptors. These must be fully descriptive of the system, must facilitate the training process and must be invertible, so that one can extract the atomic configurations corresponding to the output of the model. In general, this last requirement is not automatically satisfied by the most efficient structural descriptors, namely the representation is not directly invertible. Such drawback severely limits our freedom of choice in selecting the most appropriate descriptors for the problem, and thus our flexibility to construct generative models. In this work, we present a general optimization method capable of inverting any local many-body descriptor of the chemical environment, back to a cartesian representation. The algorithm is then implemented together with the bispectrum representation of the local structure and demonstrated for a number of molecules. The scheme presented here, thus, represents a general approach to the inversion of structural descriptors, enabling the construction of efficient structural generative models.

Identifying the intent of a citation in scientific papers (e.g., background information, use of methods, comparing results) is critical for machine reading of individual publications and automated analysis of the scientific literature. We propose structural scaffolds, a multitask model to incorporate structural information of scientific papers into citations for effective classification of citation intents. Our model achieves a new state-of-the-art on an existing ACL anthology dataset (ACL-ARC) with a 13.3% absolute increase in F1 score, without relying on external linguistic resources or hand-engineered features as done in existing methods. In addition, we introduce a new dataset of citation intents (SciCite) which is more than five times larger and covers multiple scientific domains compared with existing datasets. Our code and data are available at: https://github.com/allenai/scicite.

Graphs provide a natural representation of relational structure that arises across diverse domains. Despite this ubiquity, graph structure is typically learned in a modality- and task-isolated manner, where graph representations are constructed within individual task contexts and discarded thereafter. As a result, structural regularities across modalities and tasks are repeatedly reconstructed rather than accumulated at the level of intermediate graph representations. This motivates a representation-learning question: how should graph structure be organized so that it can persist and accumulate across heterogeneous modalities and tasks? We adopt a representation-centric perspective in which graph structure is treated as a structural substrate that persists across learning contexts. To instantiate this perspective, we propose G-Substrate, a graph substrate framework that organizes learning around shared graph structures. G-Substrate comprises two complementary mechanisms: a unified structural schema that ensures compatibility among graph representations across heterogeneous modalities and tasks, and an interleaved role-based training strategy that exposes the same graph structure to multiple functional roles during learning. Experiments across multiple domains, modalities, and tasks show that G-Substrate outperforms task-isolated and naive multi-task learning methods. The codebase, model, and datasets are available at https://github.com/zmli6/G-Substrate.

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.

The ongoing development of Lean 4's Mathlib has produced a macroscopic structural complexity that interweaves logical, mathematical, and infrastructural dependencies. We present a network analysis of this library, extracting its dependency structure into a multilayer graph of 308,129 declarations, 8.4 million edges, and 7,563 modules. By introducing graph decompositions that isolate explicit edges from those synthesized by the compiler or driven by proofs, we quantify the structural properties of formalized mathematics. Our analysis reveals three findings. First, taxonomies designed by humans diverge from logical structures, exhibiting a 50.9% coupling across namespaces. Second, developers utilize a median of 1.6% of the imported scope. Third, formalization compresses semantic hierarchies, with network centrality capturing language infrastructure rather than mathematical relevance.

Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into discrete tokens causes substantial loss of fidelity about fine-grained structural details and correlations. In this paper, we systematically elucidate the design space of multimodal PLMs to overcome their limitations. We identify tokenization loss and inaccurate structure token predictions by the PLMs as major bottlenecks. To address these, our proposed design space covers improved generative modeling, structure-aware architectures and representation learning, and data exploration. Our advancements approach finer-grained supervision, demonstrating that token-based multimodal PLMs can achieve robust structural modeling. The effective design methods dramatically improve the structure generation diversity, and notably, folding abilities of our 650M model by reducing the RMSD from 5.52 to 2.36 on PDB testset, even outperforming 3B baselines and on par with the specialized folding models.

Unified multi-modal large language models (MLLMs) have achieved strong text-to-image generation quality, but still struggle with structure-aware prompt following, where object counts, spatial relations, attribute bindings, and coarse layouts must be preserved. We attribute this limitation in part to the entanglement of structural planning and appearance rendering within a single conditioning stream. To address this issue, we propose Implicit Visual Chain-of-Thought (IV-CoT), a latent visual reasoning framework for query-conditioned image generation. IV-CoT decomposes the visual conditioning queries into a structural-to-semantic cascade, where structural queries first form a latent visual plan and semantic queries then render appearance conditioned on this plan. To guide the structural queries, we introduce training-only sketch supervision, which encourages them to capture structure from sketches without requiring sketch extraction or intermediate decoding at inference time. IV-CoT performs implicit CoT reasoning in a single forward pass and achieves superior results on GenEval and T2I-CompBench. Visualizations and analyses demonstrate that the learned structural and semantic queries play complementary roles in structure-aware generation.

Structural diagrams are widely used to represent complex systems and relational information across scientific, engineering, procedural, and spatial domains. Recent vision-language models (VLMs) have become increasingly capable of recognizing diagram elements and reasoning about their content, while complete diagram topology extraction remains comparatively underexplored. In this paper, we study diagram-to-graph topology extraction: extracting all diagram entities and the complete relations among them. To enable large-scale supervised training and systematic evaluation of this task, we introduce Knossos, a benchmark of 19,200 diagrams across six diverse domains, with 245,179 nodes and 439,740 edges. Its symbolic generation process provides exact alignment between rendered diagrams and annotations of complete topology, relation types, and connector geometry. To address the modeling challenge of complete topology extraction, we also present Ariadne, a structured framework that decomposes the task into node inventory extraction and source-conditioned edge prediction. Extensive experiments show that training on Knossos substantially improves complete topology extraction in smaller open-source VLMs. Ariadne further improves over one-step extraction under matched supervision, demonstrating the additional benefit of structured decomposition. It achieves the highest average Edge F1 among the evaluated methods on Knossos, while both backbone variants also improve over their unadapted counterparts on the real-world external benchmark. Code and benchmark are available at https://github.com/bangwayne/knossos_Ariadne_Public.

NVIDIA's CUTLASS library provides a robust and expressive set of methods for describing and manipulating multi-dimensional tensor data on the GPU. These methods are conceptually grounded in the abstract notion of a CuTe layout and a rich algebra of such layouts, including operations such as composition, logical product, and logical division. In this paper, we present a categorical framework for understanding this layout algebra by focusing on a naturally occurring class of tractable layouts. To this end, we define two categories Tuple and Nest whose morphisms give rise to layouts. We define a suite of operations on morphisms in these categories and prove their compatibility with the corresponding layout operations. Moreover, we give a complete characterization of the layouts which arise from our construction. Finally, we provide a Python implementation of our categorical constructions, along with tests that demonstrate alignment with CUTLASS behavior. This implementation can be found at our git repository https://github.com/ColfaxResearch/layout-categories.

Structural pruning enables model acceleration by removing structurally-grouped parameters from neural networks. However, the parameter-grouping patterns vary widely across different models, making architecture-specific pruners, which rely on manually-designed grouping schemes, non-generalizable to new architectures. In this work, we study a highly-challenging yet barely-explored task, any structural pruning, to tackle general structural pruning of arbitrary architecture like CNNs, RNNs, GNNs and Transformers. The most prominent obstacle towards this goal lies in the structural coupling, which not only forces different layers to be pruned simultaneously, but also expects all removed parameters to be consistently unimportant, thereby avoiding structural issues and significant performance degradation after pruning. To address this problem, we propose a general and {fully automatic} method, Dependency Graph (DepGraph), to explicitly model the dependency between layers and comprehensively group coupled parameters for pruning. In this work, we extensively evaluate our method on several architectures and tasks, including ResNe(X)t, DenseNet, MobileNet and Vision transformer for images, GAT for graph, DGCNN for 3D point cloud, alongside LSTM for language, and demonstrate that, even with a simple norm-based criterion, the proposed method consistently yields gratifying performances.

Evaluating tabular generators remains a challenging problem, as the unique causal structural prior of heterogeneous tabular data does not lend itself to intuitive human inspection. Recent work has introduced structural fidelity as a tabular-specific evaluation dimension to assess whether synthetic data complies with the causal structures of real data. However, existing benchmarks often neglect the interplay between structural fidelity and conventional evaluation dimensions, thus failing to provide a holistic understanding of model performance. Moreover, they are typically limited to toy datasets, as quantifying existing structural fidelity metrics requires access to ground-truth causal structures, which are rarely available for real-world datasets. In this paper, we propose a novel evaluation framework that jointly considers structural fidelity and conventional evaluation dimensions. We introduce a new evaluation metric, global utility, which enables the assessment of structural fidelity even in the absence of ground-truth causal structures. In addition, we present TabStruct, a comprehensive evaluation benchmark offering large-scale quantitative analysis on 13 tabular generators from nine distinct categories, across 29 datasets. Our results demonstrate that global utility provides a task-independent, domain-agnostic lens for tabular generator performance. We release the TabStruct benchmark suite, including all datasets, evaluation pipelines, and raw results. Code is available at https://github.com/SilenceX12138/TabStruct.

The effective utilization of structured data, integral to corporate data strategies, has been challenged by the rise of large language models (LLMs) capable of processing unstructured information. This shift prompts the question: can LLMs interpret structured data directly in its unstructured form? We propose an automatic evaluation data generation method for assessing LLMs' reasoning capabilities on structure-rich text to explore this. Our approach supports 8 structured languages and 29 tasks, generating data with adjustable complexity through controllable nesting and structural width. We introduce StrucText-Eval, a benchmark containing 5,800 pre-generated and annotated samples designed to evaluate how well LLMs understand and reason through structured text. StrucText-Eval is divided into two suites: a regular Test suite (3,712 samples) and a Test-Hard suite (2,088 samples), the latter emphasizing the gap between human and model performance on more complex tasks. Experimental results show that while open-source LLMs achieve a maximum accuracy of 74.9\% on the standard dataset, their performance drops significantly to 45.8\% on the harder dataset. In contrast, human participants reach an accuracy of 92.6\% on StrucText-Eval-Hard, highlighting LLMs' current limitations in handling intricate structural information. The benchmark and generation codes are open sourced in https://github.com/MikeGu721/StrucText-Eval

We characterise and enumerate permutations that are sortable by n-4 passes through a stack. We conjecture the number of permutations sortable by n-5 passes, and also the form of a formula for the general case n-k, which involves a polynomial expression.

Addressing a structural-engineering request requires more than a single answer; it requires a chain of interdependent artifacts: interpreted requirements, a computable model, validation records, solver outputs, code-check records, and a final report. Evaluations centered on question answering or script generation rarely verify this complete evidence chain and may therefore reward fluent outputs even when the underlying engineering workflow is incomplete, internally inconsistent, or non-executable. To address this limitation, we present StructureClaw, an artifact-centered workbench in which LLM agents operate through governed engineering skills, typed tools, shared artifact state, and local analysis backends. We also introduce StructureClaw-Bench, an executable benchmark of 150 controlled scenarios spanning standard workflow execution, interactive robustness, and multimodal structural-model reconstruction. A scenario succeeds only when all required artifact- and execution-level assertions pass in a single run. Across ten agent-model configurations, each evaluated on the same 50 standard cases, the average Success Rate rises from 56.8% with the generic-skill baseline to 88.6% with the full automatic workflow. The interactive and multimodal evaluations identify two prominent remaining challenges: safe handling of invalid numerical inputs and fixture-consistent reconstruction of structural models. These findings show that artifact-centered evaluation can expose workflow-level failures that are difficult to identify from final responses alone, providing a more rigorous basis for evaluating and improving structural-engineering agents. The code and benchmark are available at https://github.com/structureclaw/structureclaw.

Retrieval-augmented generation systems increasingly rely on document-structure treatments: structure-aligned chunking, LLM-generated chunk contexts, heading-path metadata, and hierarchical two-stage retrieval. Separate studies support each on different corpora, embedders, and metrics, and none control for a shared confound: any text prepended to a chunk perturbs its embedding. We present a mechanism-isolating ablation testing all four treatments under one protocol, matching chunk sizes across conditions and adding a semantically null placebo---heading paths that are structurally valid but shuffled across documents. We score retrieval with a coverage-aware nDCG and test four pre-registered contrasts via document-clustered bootstrap with Holm correction, on two distant corpora: 200 Wikipedia Featured Articles (951 queries) and 1,585 QASPER papers (4,303 questions). Organization helps, and the cause is content, not tokens: structure-aligned chunks with real heading paths beat contextualized fixed windows (+0.022 / +0.012 cov-nDCG@10) and the placebo (+0.010 / +0.016). Naive two-stage hierarchical retrieval hurts (-0.033 / -0.015), traceable to first-stage section recall. Gold structure beats LLM-induced structure on Wikipedia but not on QASPER. Effects are small (dz 0.06-0.11) but Holm-significant and consistent across corpora.

In this paper, we address the challenging task of multimodal mathematical reasoning by incorporating the ability of "slow thinking" into multimodal large language models (MLLMs). Our core idea is that different levels of reasoning abilities can be combined dynamically to tackle questions with different complexity. To this end, we propose a paradigm of Self-structured Chain of Thought (SCoT), which is composed of minimal semantic atomic steps. Different from existing methods that rely on structured templates or free-form paradigms, our method can not only generate cognitive CoT structures for various complex tasks but also mitigates the phenomenon of overthinking. To introduce structured reasoning capabilities into visual understanding models, we further design a novel AtomThink framework with four key modules, including (i) a data engine to generate high-quality multimodal reasoning paths; (ii) a supervised fine-tuning process with serialized inference data; (iii) a policy-guided multi-turn inference method; and (iv) an atomic capability metric to evaluate the single step utilization rate. We conduct extensive experiments to show that the proposed AtomThink significantly improves the performance of baseline MLLMs, achieving more than 10\% average accuracy gains on MathVista and MathVerse. Compared to state-of-the-art structured CoT approaches, our method not only achieves higher accuracy but also improves data utilization by 5 times and boosts inference efficiency by 85.3\%. Our code is now public available in https://github.com/Quinn777/AtomThink.

Model cards describe model behavior through a mixture of textual descriptions and structured artifacts, including performance, configuration, and dataset tables. Existing model search systems rely predominantly on semantic similarity over text, which can produce homogeneous result sets and limit exploration of alternatives. We argue that model search is inherently comparative: users want models that are task-aligned yet differentiated in measurable ways. We hypothesize that this balance requires retrieval over condensed, high-quality evidence rather than verbose descriptions, and much of that evidence is concentrated in structured tables. We present StructuredSemanticSearch, a table-driven model search framework built on the ModelTables benchmark. Given a query, StructuredSemanticSearch combines a semantic baseline for task alignment with a structure-aware pipeline that discovers query-related model-card tables using table discovery operators such as unionability, joinability, and keyword search. Retrieved tables are mapped back to model cards under a controlled top-k budget, enabling fair comparison between text-based and table-based retrieval. Beyond retrieval, StructuredSemanticSearch adapts table integration to the model-table domain through orientation-aware integration, producing compact integrated views of tables from partially overlapping and sometimes transposed evidence tables. For evaluation, we introduce a nugget-based, auditable protocol that extracts compact evidence items from model cards, matches queries to condition- or intent-specific nuggets, and measures evidence coverage and diversity over retrieved model-card candidate sets. This protocol also provides a scalable path toward approximate, evidence-based labeling in dynamic model lakes. Experiments on 597 model-recommendation queries show improved nugget coverage for the structure-aware pipeline than semantic baseline

Multimodal models have demonstrated powerful capabilities in complex tasks requiring multimodal alignment including zero-shot classification and cross-modal retrieval. However, existing models typically rely on millions of paired multimodal samples, which are prohibitively expensive or infeasible to obtain in many domains. In this work, we explore the feasibility of building multimodal models with limited amount of paired data by aligning pretrained unimodal foundation models. We show that high-quality alignment is possible with as few as tens of thousands of paired samplesx2013less than 1% of the data typically used in the field. To achieve this, we introduce STRUCTURE, an effective regularization technique that preserves the neighborhood geometry of the latent space of unimodal encoders. Additionally, we show that aligning last layers is often suboptimal and demonstrate the benefits of aligning the layers with the highest representational similarity across modalities. These two components can be readily incorporated into existing alignment methods, yielding substantial gains across 24 zero-shot image classification and retrieval benchmarks, with average relative improvement of 51.6% in classification and 91.8% in retrieval tasks. Our results highlight the effectiveness and broad applicability of our framework for limited-sample multimodal learning and offer a promising path forward for resource-constrained domains.

Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our representation satisfies all structural, geometric, efficiency, and generalizability constraints. Afterward, we provide a general algorithm to encode any atomistic system. Finally, we report performance comparable to state-of-the-art methods on numerous tasks. We open-source all code and datasets. The code and data are available at https://github.com/rahulkhorana/PolyatomicComplexes.

We introduce Image2Struct, a benchmark to evaluate vision-language models (VLMs) on extracting structure from images. Our benchmark 1) captures real-world use cases, 2) is fully automatic and does not require human judgment, and 3) is based on a renewable stream of fresh data. In Image2Struct, VLMs are prompted to generate the underlying structure (e.g., LaTeX code or HTML) from an input image (e.g., webpage screenshot). The structure is then rendered to produce an output image (e.g., rendered webpage), which is compared against the input image to produce a similarity score. This round-trip evaluation allows us to quantitatively evaluate VLMs on tasks with multiple valid structures. We create a pipeline that downloads fresh data from active online communities upon execution and evaluates the VLMs without human intervention. We introduce three domains (Webpages, LaTeX, and Musical Scores) and use five image metrics (pixel similarity, cosine similarity between the Inception vectors, learned perceptual image patch similarity, structural similarity index measure, and earth mover similarity) that allow efficient and automatic comparison between pairs of images. We evaluate Image2Struct on 14 prominent VLMs and find that scores vary widely, indicating that Image2Struct can differentiate between the performances of different VLMs. Additionally, the best score varies considerably across domains (e.g., 0.402 on sheet music vs. 0.830 on LaTeX equations), indicating that Image2Struct contains tasks of varying difficulty. For transparency, we release the full results at https://crfm.stanford.edu/helm/image2struct/v1.0.1/.

As Large Language Models (LLMs) become integral to software development workflows, their ability to generate structured outputs has become critically important. We introduce StructEval, a comprehensive benchmark for evaluating LLMs' capabilities in producing both non-renderable (JSON, YAML, CSV) and renderable (HTML, React, SVG) structured formats. Unlike prior benchmarks, StructEval systematically evaluates structural fidelity across diverse formats through two paradigms: 1) generation tasks, producing structured output from natural language prompts, and 2) conversion tasks, translating between structured formats. Our benchmark encompasses 18 formats and 44 types of task, with novel metrics for format adherence and structural correctness. Results reveal significant performance gaps, even state-of-the-art models like o1-mini achieve only 75.58 average score, with open-source alternatives lagging approximately 10 points behind. We find generation tasks more challenging than conversion tasks, and producing correct visual content more difficult than generating text-only structures.

Semi-structured documents integrate diverse interleaved data elements (e.g., tables, charts, hierarchical paragraphs) arranged in various and often irregular layouts. These documents are widely observed across domains and account for a large portion of real-world data. However, existing methods struggle to support natural language question answering over these documents due to three main technical challenges: (1) The elements extracted by techniques like OCR are often fragmented and stripped of their original semantic context, making them inadequate for analysis. (2) Existing approaches lack effective representations to capture hierarchical structures within documents (e.g., associating tables with nested chapter titles) and to preserve layout-specific distinctions (e.g., differentiating sidebars from main content). (3) Answering questions often requires retrieving and aligning relevant information scattered across multiple regions or pages, such as linking a descriptive paragraph to table cells located elsewhere in the document. To address these issues, we propose MoDora, an LLM-powered system for semi-structured document analysis. First, we adopt a local-alignment aggregation strategy to convert OCR-parsed elements into layout-aware components, and conduct type-specific information extraction for components with hierarchical titles or non-text elements. Second, we design the Component-Correlation Tree (CCTree) to hierarchically organize components, explicitly modeling inter-component relations and layout distinctions through a bottom-up cascade summarization process. Finally, we propose a question-type-aware retrieval strategy that supports (1) layout-based grid partitioning for location-based retrieval and (2) LLM-guided pruning for semantic-based retrieval. Experiments show MoDora outperforms baselines by 5.97%-61.07% in accuracy. The code is at https://github.com/weAIDB/MoDora.

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing F_{max} from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

Heterogeneous tabular data poses unique challenges in generative modelling due to its fundamentally different underlying data structure compared to homogeneous modalities, such as images and text. Although previous research has sought to adapt the successes of generative modelling in homogeneous modalities to the tabular domain, defining an effective generator for tabular data remains an open problem. One major reason is that the evaluation criteria inherited from other modalities often fail to adequately assess whether tabular generative models effectively capture or utilise the unique structural information encoded in tabular data. In this paper, we carefully examine the limitations of the prevailing evaluation framework and introduce TabStruct, a novel evaluation benchmark that positions structural fidelity as a core evaluation dimension. Specifically, TabStruct evaluates the alignment of causal structures in real and synthetic data, providing a direct measure of how effectively tabular generative models learn the structure of tabular data. Through extensive experiments using generators from eight categories on seven datasets with expert-validated causal graphical structures, we show that structural fidelity offers a task-independent, domain-agnostic evaluation dimension. Our findings highlight the importance of tabular data structure and offer practical guidance for developing more effective and robust tabular generative models. Code is available at https://github.com/SilenceX12138/TabStruct.

Despite recent advances in unified multimodal models for multi-reference image generation, existing benchmarks remain organized around predefined task types (e.g., "subject composition"), which are ill-suited to this combinatorial setting and lead to fragmented coverage, uncontrolled complexity, and little diagnostic value. Recognizing that diverse multi-reference tasks share a common set of atomic operations, we adopt a capability-oriented perspective and formalize four operators: Anchor (f), Disentangle (g), Apply (oplus), and Compose (C). Any multi-reference prompt can then be represented as a compositional formula over these operators, whose structural complexity is quantified by the number of operator slots. Building on this formulation, we construct TRACE-Bench, comprising approximately 1,600 evaluation cases across slot counts 1--8, built from 631 formula templates and around 4,000 reference images spanning diverse artistic styles and real-world subjects. The formula structure directly drives an operator-aligned evaluation protocol for per-capability scoring and a diagnostic tree analysis for recursive failure localization. Evaluating 9 leading models reveals insights invisible to holistic scoring: the primary bottleneck lies in disentanglement (g) and attribute binding (oplus) rather than scene-level composition (C), with even the best model scoring only 0.74 on attribute fidelity. Project page: https://amuseum-whr.github.io/TraceBench

Logic Tensor Networks (LTN) provide a neurosymbolic framework in which first-order logic is interpreted through tensor operations, enabling logical constraints to be integrated with differentiable learning. However, the original formulation of LTN is primarily suited to data represented as flat collections of individuals, and does not explicitly capture structural organization such as temporal order, sequential position, or graph connectivity. We introduce sLTN, an extension of LTN that makes structural dimensions first-class elements of the language. Structural dimensions represent named tensor axes associated with domain-specific organization, such as time steps, sequence positions, or graph nodes. They can be quantified explicitly, related through structural relations, and used to express temporal, sequential, and relational constraints directly at the logical level. We formalize the syntax and fuzzy tensor semantics of sLTN and show that, in the absence of structural dimensions, the framework recovers the original LTN semantics as a special case. We further describe a PyTorch implementation based on a declarative signature, formula parsing, and tensorial interpretation. The framework is illustrated on representative temporal and sequential reasoning examples. This paper serves as a companion to the sltn library, available at https://github.com/logictensornetworks/sltn.

Does structure in representations imply structure in computation? We study how Llama-3.1-8B reasons over cyclic concepts (e.g., "what month is six months after August?"). Even though Llama-3.1-8B's representations for these concepts are circularly structured, we find that instead of directly computing modular addition in the period of the cyclic concept (e.g., 12 for months), the model re-uses a generic addition mechanism across tasks that operates independently of concept-specific geometry. First, it computes the sum of its two inputs using base-10 addition (six + August=14). Then, it maps this sum back to cyclic concept space (14->February). We show that Llama-3.1-8B uses task-agnostic Fourier features to compute these sums--in fact, these features have periods that respect standard base-10 addition, e.g., 2, 5, and 10, rather than the cyclic concept period (e.g., 12 for months). Furthermore, we identify a sparse set of 28 MLP neurons re-used across all tasks (approximately 0.2% of the MLP at layer 18) that can be partitioned into disjoint clusters, each computing the sum for a Fourier feature with a different period. Our work highlights how an interplay between causal abstraction and feature geometry can deepen our mechanistic understanding of LMs.

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.

This paper presents a pioneering methodology, termed StructTuning, to efficiently transform foundation Large Language Models (LLMs) into domain specialists. It significantly minimizes the training corpus requirement to a mere 0.3% while achieving an impressive 50% of traditional knowledge injection performance. Our method is inspired by the educational processes for human students, particularly how structured domain knowledge from textbooks is absorbed and then applied to tackle real-world challenges through specific exercises. Based on this, we propose a novel two-stage knowledge injection strategy: Structure-aware Continual Pre-Training (SCPT) and Structure-aware Supervised Fine-Tuning (SSFT). In the SCPT phase, we organize the training data into an auto-generated taxonomy of domain knowledge, enabling LLMs to effectively memorize textual segments linked to specific expertise within the taxonomy's architecture. Subsequently, in the SSFT phase, we explicitly prompt models to reveal the underlying knowledge structure in their outputs, leveraging this structured domain insight to address practical problems adeptly. Our ultimate method has undergone extensive evaluations across model architectures and scales, using closed-book question-answering tasks on LongBench and MMedBench datasets. Remarkably, our method matches 50% of the improvement displayed by the state-of-the-art MMedLM2 on MMedBench, but with only 0.3% quantity of the training corpus. This breakthrough showcases the potential to scale up our StructTuning for stronger domain-specific LLMs. Code will be made public soon.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Structural pruning has emerged as a promising approach for producing more efficient models. Nevertheless, the community suffers from a lack of standardized benchmarks and metrics, leaving the progress in this area not fully comprehended. To fill this gap, we present the first comprehensive benchmark, termed PruningBench, for structural pruning. PruningBench showcases the following three characteristics: 1) PruningBench employs a unified and consistent framework for evaluating the effectiveness of diverse structural pruning techniques; 2) PruningBench systematically evaluates 16 existing pruning methods, encompassing a wide array of models (e.g., CNNs and ViTs) and tasks (e.g., classification and detection); 3) PruningBench provides easily implementable interfaces to facilitate the implementation of future pruning methods, and enables the subsequent researchers to incorporate their work into our leaderboards. We provide an online pruning platform for customizing pruning tasks and reproducing all results in this paper. Leaderboard results can also be available.

Managing extensive context remains a critical bottleneck for Large Language Models (LLMs), particularly in applications like long-document question answering and autonomous agents where lengthy inputs incur high computational costs and introduce noise. Existing compression techniques often disrupt local coherence through discrete token removal or rely on implicit latent encoding that suffers from positional bias and incompatibility with closed-source APIs. To address these limitations, we introduce the EDU-based Context Compressor, a novel explicit compression framework designed to preserve both global structure and fine-grained details. Our approach reformulates context compression as a structure-then-select process. First, our LingoEDU transforms linear text into a structural relation tree of Elementary Discourse Units (EDUs) which are anchored strictly to source indices to eliminate hallucination. Second, a lightweight ranking module selects query-relevant sub-trees for linearization. To rigorously evaluate structural understanding, we release StructBench, a manually annotated dataset of 248 diverse documents. Empirical results demonstrate that our method achieves state-of-the-art structural prediction accuracy and significantly outperforms frontier LLMs while reducing costs. Furthermore, our structure-aware compression substantially enhances performance across downstream tasks ranging from long-context tasks to complex Deep Search scenarios.

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.

The higher Bruhat orders B(n,k) were introduced by Manin-Schechtman to study discriminantal hyperplane arrangements and subsequently studied by Ziegler, who connected B(n,k) to oriented matroids. In this paper, we consider the enumeration of B(n,k) and improve upon Balko's asymptotic lower and upper bounds on |B(n,k)| by a factor exponential in k. A proof of Ziegler's formula for |B(n,n-3)| is given and a bijection between a certain subset of B(n,n-4) and totally symmetric plane partitions is proved. Central to our proofs are deletion and contraction operations for the higher Bruhat orders, defined in analogy with matroids. Dual higher Bruhat orders are also introduced, and we construct isomorphisms relating the higher Bruhat orders and their duals. Additionally, weaving functions are introduced to generalize Felsner's encoding of elements in B(n,2) to all higher Bruhat orders B(n,k).

Tabular documents such as CSV and Excel files are widely used in enterprise data pipelines, yet existing chunking strategies for retrieval-augmented generation (RAG) are primarily designed for unstructured text and do not account for tabular structure. We propose a structure-aware tabular chunking (STC) framework that operates on row-level units by constructing a hierarchical Row Tree representation, where each row is encoded as a key-value block. STC performs token-constrained splitting aligned with structural boundaries and applies overlap-free greedy merging to produce dense, non-overlapping chunks. This design preserves semantic relationships between fields within a row while improving token utilization and reducing fragmentation. Across evaluations on the MAUD dataset, STC reduces chunk count by up to 40% and 56% compared to standard recursive and key-value based baselines, respectively, while improving token utilization and processing efficiency. In retrieval benchmarks, STC improves MRR from 0.3576 to 0.5945 in a hybrid setting and increases Recall@1 from 0.366 to 0.754 in BM25-only retrieval. These results demonstrate that preserving structure during chunking improves retrieval performance, highlighting the importance of structure-aware chunking for RAG over tabular data.

Multi-turn instruction following capability constitutes a core competency of large language models (LLMs) in real-world applications. Existing evaluation benchmarks predominantly focus on fine-grained constraint satisfaction and domain-specific capability assessment, yet overlook the crucial structural dependency between dialogue turns that distinguishes multi-turn from single-turn interactions. This structural dependency not only reflects user intent but also establishes a second dimension for instruction following evaluation beyond constraint satisfaction. To address this gap, we propose StructFlowBench, a multi-turn instruction following benchmark with structural flow modeling. The benchmark innovatively defines a structural flow framework comprising six fundamental inter-turn relationships, which not only introduces novel structural constraints for model evaluation but also serves as generation parameters for creating customized dialogue flows tailored to specific scenarios. Adopting established LLM-based automatic evaluation methodologies, we conduct systematic evaluations of 13 leading open-source and closed-source LLMs. Experimental results reveal significant deficiencies in current models' comprehension of multi-turn dialogue structures. The code is available at https://github.com/MLGroupJLU/StructFlowBench.

This paper investigates the ability of transformer-based models to learn structural recursion from examples. Recursion is a universal concept in both natural and formal languages. Structural recursion is central to the programming language and formal mathematics tasks where symbolic tools currently excel beyond neural models, such as inferring semantic relations between datatypes and emulating program behavior. We introduce a general framework that nicely connects the abstract concepts of structural recursion in the programming language domain to concrete sequence modeling problems and learned models' behavior. The framework includes a representation that captures the general syntax of structural recursion, coupled with two different frameworks for understanding their semantics -- one that is more natural from a programming languages perspective and one that helps bridge that perspective with a mechanistic understanding of the underlying transformer architecture. With our framework as a powerful conceptual tool, we identify different issues under various set-ups. The models trained to emulate recursive computations cannot fully capture the recursion yet instead fit short-cut algorithms and thus cannot solve certain edge cases that are under-represented in the training distribution. In addition, it is difficult for state-of-the-art large language models (LLMs) to mine recursive rules from in-context demonstrations. Meanwhile, these LLMs fail in interesting ways when emulating reduction (step-wise computation) of the recursive function.

Large language models record impressive performance on many natural language processing tasks. However, their knowledge capacity is limited to the pretraining corpus. Retrieval augmentation offers an effective solution by retrieving context from external knowledge sources to complement the language model. However, existing retrieval augmentation techniques ignore the structural relationships between these documents. Furthermore, retrieval models are not explored much in scientific tasks, especially in regard to the faithfulness of retrieved documents. In this paper, we propose a novel structure-aware retrieval augmented language model that accommodates document structure during retrieval augmentation. We create a heterogeneous document graph capturing multiple types of relationships (e.g., citation, co-authorship, etc.) that connect documents from more than 15 scientific disciplines (e.g., Physics, Medicine, Chemistry, etc.). We train a graph neural network on the curated document graph to act as a structural encoder for the corresponding passages retrieved during the model pretraining. Particularly, along with text embeddings of the retrieved passages, we obtain structural embeddings of the documents (passages) and fuse them together before feeding them to the language model. We evaluate our model extensively on various scientific benchmarks that include science question-answering and scientific document classification tasks. Experimental results demonstrate that structure-aware retrieval improves retrieving more coherent, faithful and contextually relevant passages, while showing a comparable performance in the overall accuracy.

Large language models (LLMs) excel in language tasks, especially with supervised fine-tuning after pre-training. However, their substantial memory and computational requirements hinder practical applications. Structural pruning, which reduces less significant weight dimensions, is one solution. Yet, traditional post-hoc pruning often leads to significant performance loss, with limited recovery from further fine-tuning due to reduced capacity. Since the model fine-tuning refines the general and chaotic knowledge in pre-trained models, we aim to incorporate structural pruning with the fine-tuning, and propose the Pruning-Aware Tuning (PAT) paradigm to eliminate model redundancy while preserving the model performance to the maximum extend. Specifically, we insert the innovative Hybrid Sparsification Modules (HSMs) between the Attention and FFN components to accordingly sparsify the upstream and downstream linear modules. The HSM comprises a lightweight operator and a globally shared trainable mask. The lightweight operator maintains a training overhead comparable to that of LoRA, while the trainable mask unifies the channels to be sparsified, ensuring structural pruning. Additionally, we propose the Identity Loss which decouples the transformation and scaling properties of the HSMs to enhance training robustness. Extensive experiments demonstrate that PAT excels in both performance and efficiency. For example, our Llama2-7b model with a 25\% pruning ratio achieves 1.33times speedup while outperforming the LoRA-finetuned model by up to 1.26\% in accuracy with a similar training cost. Code: https://github.com/kriskrisliu/PAT_Pruning-Aware-Tuning

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

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.

Building on our earlier program-evolution workflow guided by large language models (LLMs), we study weight-five bivariate bicycle (BB) and perturbed bivariate bicycle (PBB) codes. The resulting catalogue contains 1,142 distinct code proposals, including 1,081 nonbaseline proposals attributable to LLM-generated programs. Across the catalogue, we certify connected Calderbank--Shor--Steane (CSS) realizations [[96,4,10]], [[140,6,10]], and [[180,4,14]]. A post-search comparison certifies seven imported Lin--Pryadko archive constructions. For leading parameter triples also represented in that archive, we provide exact distance evidence, explicit bivariate presentations, and verified component reductions. A basis-independent connectivity analysis identifies 409 of the 1,142 catalogue entries as disconnected and shows that 73.1\% of the classes with exact distance certificates contain repeated connected components. Algebraic analysis organizes the connected CSS classes into order-3, order-7, and order-15 cyclotomic-kernel strata. The strongest exact connected PBB parameter point is [[216,4,10]], attained by two distinct component classes. Among the 936 distinct CSS proposals from the LLM-guided campaign with a recorded positive distance, 816 (87.18\%) are certified at dgeq5. For comparison, three random-search controls each sample 6,444 CSS code proposals uniformly without replacement, using the same per-lattice and encoded-dimension sample counts as the LLM-guided campaign. In these controls, 4,672--4,785 proposals (72.50--74.26\%) meet the same criterion. The LLM-guided campaign has the higher certified yield, while the random controls cover more connected classes. Together, these results extend LLM-guided discovery to a more constrained code family and provide a reproducible structural and exact-distance account of its strongest candidates.

Current Multimodal Large Language Models (MLLMs) typically integrate a pre-trained LLM with another pre-trained vision transformer through a connector, such as an MLP, endowing the LLM with visual capabilities. However, the misalignment between two embedding strategies in MLLMs -- the structural textual embeddings based on an embedding look-up table and the continuous embeddings generated directly by the vision encoder -- makes challenges for a more seamless fusion of visual and textual information. We propose Ovis, a novel MLLM architecture designed to structurally align visual and textual embeddings. Ovis integrates an additional learnable visual embedding table into the visual encoder's process. To capture rich visual semantics, each image patch indexes the visual embedding table multiple times, resulting in a final visual embedding that is a probabilistic combination of the indexed embeddings. This structural approach mirrors the method used for generating textual embeddings. Empirical evaluations on various multimodal benchmarks demonstrate that Ovis outperforms open-source MLLMs of similar parameter scales and even surpasses the proprietary model Qwen-VL-Plus overall. These results highlight the potential of Ovis' structured visual representation for advancing MLLM architectural design and promoting more effective multimodal learning. Both the source code and the training dataset of Ovis will be made publicly available.

Structured-language models such as SceneScript reconstruct a scene as a short program of parametric commands, an inherently editable and semantically explicit representation. We ask three questions that stand between such models and their most compelling application, automated ingestion of existing buildings into BIM tools, studied here on synthetic scans: what is the scene made of, how fast can it be produced, and exactly where is each element. BIMScript answers all three within one grammar. First, we extend the layout language with per-element material and condition attributes, supervised by a vision-language-model material-passport corpus we build over 100k synthetic scenes (1.9M pseudo-labeled elements), and route image appearance to the material tokens through a lifted-feature point encoder. Second, we show that autoregressive decoding of these programs is dominated not by compute but by kernel-launch and host-synchronization overhead, and remove it with an output-exact CUDA-graph decoder (1.9 vs 6.4\,ms/step, 3.4times) plus a grammar-parallel, tolerance-verified draft-and-verify scheme that exploits the deterministic entity schema. Third, we address the model's 5cm token-grid granularity with training-free geometric snapping and a hybrid discrete--continuous decoder head that regresses a sub-bin offset, and measure how much of the residual error each recovers. Because each command maps one-to-one onto a native Revit object, we validate direct ingestion into a BIM authoring tool end to end with a working add-in and its IFC4 export, and the same program's language form is designed to support LLM-driven, sustainability-aware reasoning over the built asset.

Web search is an essential way for humans to obtain information, but it's still a great challenge for machines to understand the contents of web pages. In this paper, we introduce the task of structural reading comprehension (SRC) on web. Given a web page and a question about it, the task is to find the answer from the web page. This task requires a system not only to understand the semantics of texts but also the structure of the web page. Moreover, we proposed WebSRC, a novel Web-based Structural Reading Comprehension dataset. WebSRC consists of 400K question-answer pairs, which are collected from 6.4K web pages. Along with the QA pairs, corresponding HTML source code, screenshots, and metadata are also provided in our dataset. Each question in WebSRC requires a certain structural understanding of a web page to answer, and the answer is either a text span on the web page or yes/no. We evaluate various baselines on our dataset to show the difficulty of our task. We also investigate the usefulness of structural information and visual features. Our dataset and baselines have been publicly available at https://x-lance.github.io/WebSRC/.

A growing body of research has demonstrated the inability of NLP models to generalize compositionally and has tried to alleviate it through specialized architectures, training schemes, and data augmentation, among other approaches. In this work, we study a different approach: training on instances with diverse structures. We propose a model-agnostic algorithm for subsampling such sets of instances from a labeled instance pool with structured outputs. Evaluating on both compositional template splits and traditional IID splits of 5 semantic parsing datasets of varying complexity, we show that structurally diverse training using our algorithm leads to comparable or better generalization than prior algorithms in 9 out of 10 dataset-split type pairs. In general, we find structural diversity to consistently improve sample efficiency compared to random train sets. Moreover, we show that structurally diverse sampling yields comprehensive test sets that are a lot more challenging than IID test sets. Finally, we provide two explanations for improved generalization from diverse train sets: 1) improved coverage of output substructures, and 2) a reduction in spurious correlations between these substructures.

Structured data sources, such as tables, graphs, and databases, are ubiquitous knowledge sources. Despite the demonstrated capabilities of large language models (LLMs) on plain text, their proficiency in interpreting and utilizing structured data remains limited. Our investigation reveals a notable deficiency in LLMs' ability to process structured data, e.g., ChatGPT lags behind state-of-the-art (SoTA) model by an average of 35%. To augment the Structured Knowledge Grounding (SKG) capabilities in LLMs, we have developed a comprehensive instruction tuning dataset comprising 1.1 million examples. Utilizing this dataset, we train a series of models, referred to as StructLM, based on the Code-LLaMA architecture, ranging from 7B to 34B parameters. Our StructLM series surpasses task-specific models on 14 out of 18 evaluated datasets and establishes new SoTA achievements on 7 SKG tasks. Furthermore, StructLM demonstrates exceptional generalization across 6 novel SKG tasks. Contrary to expectations, we observe that scaling model size offers marginal benefits, with StructLM-34B showing only slight improvements over StructLM-7B. This suggests that structured knowledge grounding is still a challenging task and requires more innovative design to push to a new level.

Abstractive summarization of scientific papers has always been a research focus, yet existing methods face two main challenges. First, most summarization models rely on Encoder-Decoder architectures that treat papers as sequences of words, thus fail to fully capture the structured information inherent in scientific papers. Second, existing research often use keyword mapping or feature engineering to identify the structural information, but these methods struggle with the structural flexibility of scientific papers and lack robustness across different disciplines. To address these challenges, we propose a two-stage abstractive summarization framework that leverages automatic recognition of structural functions within scientific papers. In the first stage, we standardize chapter titles from numerous scientific papers and construct a large-scale dataset for structural function recognition. A classifier is then trained to automatically identify the key structural components (e.g., Background, Methods, Results, Discussion), which provides a foundation for generating more balanced summaries. In the second stage, we employ Longformer to capture rich contextual relationships across sections and generating context-aware summaries. Experiments conducted on two domain-specific scientific paper summarization datasets demonstrate that our method outperforms advanced baselines, and generates more comprehensive summaries. The code and dataset can be accessed at https://github.com/tongbao96/code-for-SFR-AS.

The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and others parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

Directed acyclic graphs (DAGs) encode a lot of information about a particular distribution in their structure. However, compute required to infer these structures is typically super-exponential in the number of variables, as inference requires a sweep of a combinatorially large space of potential structures. That is, until recent advances made it possible to search this space using a differentiable metric, drastically reducing search time. While this technique -- named NOTEARS -- is widely considered a seminal work in DAG-discovery, it concedes an important property in favour of differentiability: transportability. To be transportable, the structures discovered on one dataset must apply to another dataset from the same domain. We introduce D-Struct which recovers transportability in the discovered structures through a novel architecture and loss function while remaining fully differentiable. Because D-Struct remains differentiable, our method can be easily adopted in existing differentiable architectures, as was previously done with NOTEARS. In our experiments, we empirically validate D-Struct with respect to edge accuracy and structural Hamming distance in a variety of settings.

Traditional cooking recipes follow a structure which can be modelled very well if the rules and semantics of the different sections of the recipe text are analyzed and represented accurately. We propose a structure that can accurately represent the recipe as well as a pipeline to infer the best representation of the recipe in this uniform structure. The Ingredients section in a recipe typically lists down the ingredients required and corresponding attributes such as quantity, temperature, and processing state. This can be modelled by defining these attributes and their values. The physical entities which make up a recipe can be broadly classified into utensils, ingredients and their combinations that are related by cooking techniques. The instruction section lists down a series of events in which a cooking technique or process is applied upon these utensils and ingredients. We model these relationships in the form of tuples. Thus, using a combination of these methods we model cooking recipe in the dataset RecipeDB to show the efficacy of our method. This mined information model can have several applications which include translating recipes between languages, determining similarity between recipes, generation of novel recipes and estimation of the nutritional profile of recipes. For the purpose of recognition of ingredient attributes, we train the Named Entity Relationship (NER) models and analyze the inferences with the help of K-Means clustering. Our model presented with an F1 score of 0.95 across all datasets. We use a similar NER tagging model for labelling cooking techniques (F1 score = 0.88) and utensils (F1 score = 0.90) within the instructions section. Finally, we determine the temporal sequence of relationships between ingredients, utensils and cooking techniques for modeling the instruction steps.

Tabular reasoning involves multi-step information extraction and logical inference over tabular data. While recent advances have leveraged large language models (LLMs) for reasoning over structured tables, such high-quality textual representations are often unavailable in real-world settings, where tables typically appear as images. In this paper, we tackle the task of tabular reasoning from table images, leveraging privileged structured information available during training to enhance multimodal large language models (MLLMs). The key challenges lie in the complexity of accurately aligning structured information with visual representations, and in effectively transferring structured reasoning skills to MLLMs despite the input modality gap. To address these, we introduce TabUlar Reasoning with Bridged infOrmation ({\sc Turbo}), a new framework for multimodal tabular reasoning with privileged structured tables. {\sc Turbo} benefits from a structure-aware reasoning trace generator based on DeepSeek-R1, contributing to high-quality modality-bridged data. On this basis, {\sc Turbo} repeatedly generates and selects the advantageous reasoning paths, further enhancing the model's tabular reasoning ability. Experimental results demonstrate that, with limited (9k) data, {\sc Turbo} achieves state-of-the-art performance (+7.2% vs. previous SOTA) across multiple datasets.

Evaluation is the baton for the development of large language models. Current evaluations typically employ a single-item assessment paradigm for each atomic test objective, which struggles to discern whether a model genuinely possesses the required capabilities or merely memorizes/guesses the answers to specific questions. To this end, we propose a novel evaluation framework referred to as StructEval. Starting from an atomic test objective, StructEval deepens and broadens the evaluation by conducting a structured assessment across multiple cognitive levels and critical concepts, and therefore offers a comprehensive, robust and consistent evaluation for LLMs. Experiments on three widely-used benchmarks demonstrate that StructEval serves as a reliable tool for resisting the risk of data contamination and reducing the interference of potential biases, thereby providing more reliable and consistent conclusions regarding model capabilities. Our framework also sheds light on the design of future principled and trustworthy LLM evaluation protocols.

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.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

We present an algorithm for efficiently exploring inequivalent Calabi-Yau threefold hypersurfaces in toric varieties. A direct enumeration of fine, regular, star triangulations (FRSTs) of polytopes in the Kreuzer-Skarke database is foreseeably impossible due to the large count of distinct FRSTs. Moreover, such an enumeration is needlessly redundant because many such triangulations have the same restrictions to 2-faces and hence, by Wall's theorem, lead to equivalent Calabi-Yau threefolds. We show that this redundancy can be circumvented by finding a height vector in the strict interior of the intersection of the secondary cones associated with each 2-face triangulation. We demonstrate that such triangulations are generated with orders of magnitude fewer operations than the naive approach of generating all FRSTs and selecting only those differing on 2-faces. Similar methods are also presented to directly generate (the support of) the secondary subfan of all fine triangulations, relevant for random sampling of FRSTs.

We enhance the calculus of string diagrams for monoidal categories with hierarchical features in order to capture closed monoidal (and cartesian closed) structure. Using this new syntax we formulate an automatic differentiation algorithm for (applied) simply typed lambda calculus in the style of [Pearlmutter and Siskind 2008] and we prove for the first time its soundness. To give an efficient yet principled implementation of the AD algorithm we define a sound and complete representation of hierarchical string diagrams as a class of hierarchical hypergraphs we call hypernets.

Large-scale vision-language pre-training has achieved significant performance in multi-modal understanding and generation tasks. However, existing methods often perform poorly on image-text matching tasks that require structured representations, i.e., representations of objects, attributes, and relations. As illustrated in Fig.~reffig:case (a), the models cannot make a distinction between ``An astronaut rides a horse" and ``A horse rides an astronaut". This is because they fail to fully leverage structured knowledge when learning representations in multi-modal scenarios. In this paper, we present an end-to-end framework Structure-CLIP, which integrates Scene Graph Knowledge (SGK) to enhance multi-modal structured representations. Firstly, we use scene graphs to guide the construction of semantic negative examples, which results in an increased emphasis on learning structured representations. Moreover, a Knowledge-Enhance Encoder (KEE) is proposed to leverage SGK as input to further enhance structured representations. To verify the effectiveness of the proposed framework, we pre-train our model with the aforementioned approaches and conduct experiments on downstream tasks. Experimental results demonstrate that Structure-CLIP achieves state-of-the-art (SOTA) performance on VG-Attribution and VG-Relation datasets, with 12.5% and 4.1% ahead of the multi-modal SOTA model respectively. Meanwhile, the results on MSCOCO indicate that Structure-CLIP significantly enhances the structured representations while maintaining the ability of general representations. Our code is available at https://github.com/zjukg/Structure-CLIP.

Multimodal large language models can expose task-relevant evidence through generation, but producing useful evidence does not by itself determine how it enters a retrieval embedding. We study whether the semantic organization of that evidence can also specify where representations are read. To address this question, we introduce EviAlign, which couples Semantic Evidence Generation with Boundary Readout in a shared multimodal large language model. It organizes evidence into five semantic units, reads the contextualized state at each unit boundary, and aggregates these states into a single normalized embedding. Generation and contrastive retrieval objectives jointly train this shared structure. With the same trailing readout, semantic evidence and free-form CoT yield nearly identical retrieval performance, suggesting that evidence organization alone does not explain the full gain. A controlled 2times3 study compares consistent and permuted evidence organization across three readout strategies, using training targets with matched evidence spans. With five readout states and the same mean pooling, the advantage of consistent semantic organization grows from 0.65 points at length-based training positions to 2.39 at evidence boundaries, yielding a 1.74-point co-design interaction. Across 12 MMEB retrieval tasks, EviAlign achieves 76.9 average Recall@1 with 500K training pairs while retaining single-vector indexing and scoring.

Program source code contains complex structure information, which can be represented in structured data forms like trees or graphs. To acquire the structural information in source code, most existing researches use abstract syntax trees (AST). A group of works add additional edges to ASTs to convert source code into graphs and use graph neural networks to learn representations for program graphs. Although these works provide additional control or data flow information to ASTs for downstream tasks, they neglect an important aspect of structure information in AST itself: the different types of nodes and edges. In ASTs, different nodes contain different kinds of information like variables or control flow, and the relation between a node and all its children can also be different. To address the information of node and edge types, we bring the idea of heterogeneous graphs to learning on source code and present a new formula of building heterogeneous program graphs from ASTs with additional type information for nodes and edges. We use the ASDL grammar of programming language to define the node and edge types of program graphs. Then we use heterogeneous graph neural networks to learn on these graphs. We evaluate our approach on two tasks: code comment generation and method naming. Both tasks require reasoning on the semantics of complete code snippets. Experiment results show that our approach outperforms baseline models, including homogeneous graph-based models, showing that leveraging the type information of nodes and edges in program graphs can help in learning program semantics.

Mathematical reasoning lies at the heart of artificial intelligence, underpinning applications in education, program verification, and research-level mathematical discovery. Mathematical competitions, in particular, present two challenging problem types: theorem proving, which requires rigorous proofs of stated conclusions, and answer construction, which involves hypothesizing and formally verifying mathematical objects. Large Language Models (LLMs) effectively generate creative candidate answers but struggle with formal verification, while symbolic provers ensure rigor but cannot efficiently handle creative conjecture generation. We introduce the Enumerate-Conjecture-Prove (ECP) framework, a modular neuro-symbolic method integrating LLM-based enumeration and pattern-driven conjecturing with formal theorem proving. We present ConstructiveBench, a dataset of 3,431 answer-construction problems in various math competitions with verified Lean formalizations. On the ConstructiveBench dataset, ECP improves the accuracy of answer construction from a Chain-of-Thought (CoT) baseline of 14.54% to 45.06% with the gpt-4.1-mini model. Moreover, combined with ECP's constructed answers, the state-of-the-art DeepSeek-Prover-V2-7B model generates correct proofs for 858 of the 3,431 constructive problems in Lean, achieving 25.01% accuracy compared to 9.86% for symbolic-only baselines. Our code and dataset are publicly available at https://github.com/JackSun200312/ECP.

Recently, the pre-trained language model, BERT (and its robustly optimized version RoBERTa), has attracted a lot of attention in natural language understanding (NLU), and achieved state-of-the-art accuracy in various NLU tasks, such as sentiment classification, natural language inference, semantic textual similarity and question answering. Inspired by the linearization exploration work of Elman [8], we extend BERT to a new model, StructBERT, by incorporating language structures into pre-training. Specifically, we pre-train StructBERT with two auxiliary tasks to make the most of the sequential order of words and sentences, which leverage language structures at the word and sentence levels, respectively. As a result, the new model is adapted to different levels of language understanding required by downstream tasks. The StructBERT with structural pre-training gives surprisingly good empirical results on a variety of downstream tasks, including pushing the state-of-the-art on the GLUE benchmark to 89.0 (outperforming all published models), the F1 score on SQuAD v1.1 question answering to 93.0, the accuracy on SNLI to 91.7.

When reading long-form text, human cognition is complex and structurized. While large language models (LLMs) process input contexts through a causal and sequential perspective, this approach can potentially limit their ability to handle intricate and complex inputs effectively. To enhance LLM's cognition capability, this paper presents a novel concept of context structurization. Specifically, we transform the plain, unordered contextual sentences into well-ordered and hierarchically structurized elements. By doing so, LLMs can better grasp intricate and extended contexts through precise attention and information-seeking along the organized structures. Extensive evaluations are conducted across various model architectures and sizes (including a series of auto-regressive LLMs as well as BERT-like masking models) on a diverse set of NLP tasks (e.g., context-based question-answering, exhaustive hallucination evaluation, and passage-level dense retrieval). Empirical results show consistent and significant performance gains afforded by a single-round structurization. In particular, we boost the open-sourced LLaMA2-70B model to achieve comparable performance against GPT-3.5-Turbo as the hallucination evaluator. Besides, we show the feasibility of distilling advanced LLMs' language processing abilities to a smaller yet effective StruXGPT-7B to execute structurization, addressing the practicality of our approach. Code is available at https://github.com/alibaba/struxgpt.

Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological structures involving branching paths, converging flows, and cyclic dependencies, their reasoning capabilities degrade sharply, even on tasks as basic as counting endpoints. Existing benchmarks fail to probe this gap, focusing on semantic comprehension rather than structural reasoning. We introduce ReactBench, a benchmark that reveals fundamental limitations in structural reasoning through chemical reaction diagrams. These real-world scientific diagrams offer an ideal testbed because they naturally span diverse structures from linear chains to cyclic graphs, while requiring both precise local recognition and coherent global reasoning. Our benchmark comprises 1,618 expert-annotated QA pairs across four hierarchical task dimensions. Extensive evaluation across 17 MLLMs reveals a significant performance gap exceeding 30% between anchor-based tasks and holistic structural reasoning tasks. Controlled ablations confirm this bottleneck lies in reasoning, not perception. These findings expose a fundamental deficit in structural understanding and establish directions for advancing visual reasoning.

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.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

Text and formulas constitute the core informational components of many documents. Accurately and efficiently recognizing both is crucial for developing robust and generalizable document parsing systems. Recently, vision-language models (VLMs) have achieved impressive unified recognition of text and formulas. However, they are large-sized and computationally demanding, restricting their usage in many applications. In this paper, we propose UniRec-0.1B, a unified recognition model with only 0.1B parameters. It is capable of performing text and formula recognition at multiple levels, including characters, words, lines, paragraphs, and documents. To implement this task, we first establish UniRec40M, a large-scale dataset comprises 40 million text, formula and their mix samples, enabling the training of a powerful yet lightweight model. Secondly, we identify two challenges when building such a lightweight but unified expert model. They are: structural variability across hierarchies and semantic entanglement between textual and formulaic content. To tackle these, we introduce a hierarchical supervision training that explicitly guides structural comprehension, and a semantic-decoupled tokenizer that separates text and formula representations. Finally, we develop a comprehensive evaluation benchmark covering Chinese and English documents from multiple domains and with multiple levels. Experimental results on this and public benchmarks demonstrate that UniRec-0.1B outperforms both general-purpose VLMs and leading document parsing expert models, while achieving a 2-9times speedup, validating its effectiveness and efficiency. Codebase and Dataset: https://github.com/Topdu/OpenOCR.

Machine learning (ML) is increasingly used in structural engineering and design, yet its broader adoption is hampered by the lack of openly accessible datasets of structural systems. We introduce BridgeNet, a publicly available graph-based dataset of 20,000 form-found bridge structures aimed at enabling Graph ML and multi-modal learning in the context of conceptual structural design. Each datapoint consists of (i) a pin-jointed equilibrium wireframe model generated with the Combinatorial Equilibrium Modeling (CEM) form-finding method, (ii) a volumetric 3D mesh obtained through force-informed materialization, and (iii) rendered images from two canonical camera angles. The resulting dataset is modality-rich and application-agnostic, supporting tasks such as CEM-specific edge classification and parameter inference, surrogate modeling of form-finding, cross-modal reconstruction between graphs, meshes and images, and generative structural design. BridgeNet addresses a key bottleneck in data-driven applications for structural engineering and design by providing a dataset that facilitates the development of new ML-based approaches for equilibrium bridge structures.

Retrieval-Augmented Generation (RAG) has become essential for large-scale code generation, grounding predictions in external code corpora to improve actuality. However, a critical yet underexplored aspect of RAG pipelines is chunking -- the process of dividing documents into retrievable units. Existing line-based chunking heuristics often break semantic structures, splitting functions or merging unrelated code, which can degrade generation quality. We propose chunking via Abstract Syntax Trees (\ourwork), a structure-aware method that recursively breaks large AST nodes into smaller chunks and merges sibling nodes while respecting size limits. This approach generates self-contained, semantically coherent units across programming languages and tasks, improving performance on diverse code generation tasks, e.g., boosting Recall@5 by 4.3 points on RepoEval retrieval and Pass@1 by 2.67 points on SWE-bench generation. Our work highlights the importance of structure-aware chunking for scaling retrieval-enhanced code intelligence.

This thesis is divided into three parts. The first part deals with cylindric plane partitions. The second with lambda-determinants and the third with commutators in semi-circular systems. For more detailed abstract please see inside. Cylindric plane partitions may be thought of as a natural generalization of reverse plane partitions. A generating series for the enumeration of cylindric plane partitions was recently given by Borodin. The first result of section one is a new bijective proof of Borodin's identity which makes use of Fomin's growth diagram framework for generalized RSK correspondences. The second result is a (q,t)-analog of Borodin's identity which extends previous work by Okada in the reverse plane partition case. The third result is an explicit combinatorial interpretation of the Macdonald weight occurring in the (q,t)-analog using the non-intersecting lattice path model for cylindric plane partitions. Alternating sign matrices were discovered by Robbins and Rumsey whilst studying λ-determinants. In the second part of this thesis we prove a multi-parameter generalization of the λ-determinant, generalizing a recent result by di Francesco. Like the original λ-determinant, our formula exhibits the Laurent phenomenon. Semicircular systems were first introduced by Voiculescu as a part of his study of von Neumann algebras. In the third part of this thesis we study certain commutator subalgebras of the semicircular system. We find a projection matrix with an interesting self-similar structure. Making use of our projection formula we given an alternative, elementary proof that the semicircular system is a factor.

Document parsing has recently advanced with multimodal large language models (MLLMs) that directly map document images to structured outputs. Traditional cascaded pipelines depend on precise layout analysis and often fail under casually captured or non-standard conditions. Although end-to-end approaches mitigate this dependency, they still exhibit repetitive, hallucinated, and structurally inconsistent predictions - primarily due to the scarcity of large-scale, high-quality full-page (document-level) end-to-end parsing data and the lack of structure-aware training strategies. To address these challenges, we propose a data-training co-design framework for robust end-to-end document parsing. A Realistic Scene Synthesis strategy constructs large-scale, structurally diverse full-page end-to-end supervision by composing layout templates with rich document elements, while a Document-Aware Training Recipe introduces progressive learning and structure-token optimization to enhance structural fidelity and decoding stability. We further build Wild-OmniDocBench, a benchmark derived from real-world captured documents for robustness evaluation. Integrated into a 1B-parameter MLLM, our method achieves superior accuracy and robustness across both scanned/digital and real-world captured scenarios. All models, data synthesis pipelines, and benchmarks will be publicly released to advance future research in document understanding.

We establish a fundamental connection between optimal structure learning and optimal conditional independence testing by showing that the minimax optimal rate for structure learning problems is determined by the minimax rate for conditional independence testing in these problems. This is accomplished by establishing a general reduction between these two problems in the case of poly-forests, and demonstrated by deriving optimal rates for several examples, including Bernoulli, Gaussian and nonparametric models. Furthermore, we show that the optimal algorithm in these settings is a suitable modification of the PC algorithm. This theoretical finding provides a unified framework for analyzing the statistical complexity of structure learning through the lens of minimax testing.

We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We also outline the basic principles of the vector formulation of stoichiometry, interpreting reactions as integer vectors in composition space, this geometric view supports compact visualizations of reagent-product interactions and helps surface distinct reaction families. The method enumerates valid balances for arbitrary user-specified species lists without special-case balancing rules or symbolic tricks, and it provides a clean foundation for developing new algorithmic variants (e.g., alternative objectives or constraints). On representative examples (neutralization, double displacement, decomposition, classical redox, small multicomponent sets) and a negative control, the method produced correct integer balances. When multiple balances exist, we report a canonical one - minimizing the total coefficient sum with a simple tie-breaker - without claiming global optimality beyond the solutions the search enumerates. The procedure applies per reaction and extends to reaction networks via consistent per-reaction application. We do not report runtimes, broader benchmarking and code/data release are planned.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Linear sequences of words are implicitly represented in our brains by hierarchical structures that organize the composition of words in sentences. Linguists formalize different frameworks to model this hierarchy; two of the most common syntactic frameworks are Constituency and Dependency. Constituency represents sentences as nested groups of phrases, while dependency represents a sentence by assigning relations between its words. Recently, the pursuit of intelligent machines has produced Language Models (LMs) capable of solving many language tasks with a human-level performance. Many studies now question whether LMs implicitly represent syntactic hierarchies. This thesis focuses on producing constituency and dependency structures from LMs in an unsupervised setting. I review the critical methods in this field and highlight a line of work that utilizes a numerical representation for binary constituency trees (Syntactic Distance). I present a detailed study on StructFormer (SF) (Shen et al., 2021), which retrofits a transformer encoder architecture with a parser network to produce constituency and dependency structures. I present six experiments to analyze and address this field's challenges; experiments include investigating the effect of repositioning the parser network within the SF architecture, evaluating subword-based induced trees, and benchmarking the models developed in the thesis experiments on linguistic tasks. Models benchmarking is performed by participating in the BabyLM challenge, published at CoNLL 2023 (Momen et al., 2023). The results of this thesis encourage further development in the direction of retrofitting transformer-based models to induce syntactic structures, supported by the acceptable performance of SF in different experimental settings and the observed limitations that require innovative solutions to advance the state of syntactic structure induction.

Despite the widespread application of latent factor analysis, existing methods suffer from the following weaknesses: requiring the number of factors to be known, lack of theoretical guarantees for learning the model structure, and nonidentifiability of the parameters due to rotation invariance properties of the likelihood. We address these concerns by proposing a fast correlation thresholding (CT) algorithm that simultaneously learns the number of latent factors and a rotationally identifiable model structure. Our novel approach translates this structure learning problem into the search for so-called independent maximal cliques in a thresholded correlation graph that can be easily constructed from the observed data. Our clique analysis technique scales well up to thousands of variables, while competing methods are not applicable in a reasonable amount of running time. We establish a finite-sample error bound and high-dimensional consistency for the structure learning of our method. Through a series of simulation studies and a real data example, we show that the CT algorithm is an accurate method for learning the structure of factor analysis models and is robust to violations of its assumptions.

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

Language models have the ability to perform in-context learning (ICL), allowing them to flexibly adapt their behavior based on context. This contrasts with in-weights learning, where information is statically encoded in model parameters from iterated observations of the data. Despite this apparent ability to learn in-context, language models are known to struggle when faced with unseen or rarely seen tokens. Hence, we study structural in-context learning, which we define as the ability of a model to execute in-context learning on arbitrary tokens -- so called because the model must generalize on the basis of e.g. sentence structure or task structure, rather than semantic content encoded in token embeddings. An ideal model would be able to do both: flexibly deploy in-weights operations (in order to robustly accommodate ambiguous or unknown contexts using encoded semantic information) and structural in-context operations (in order to accommodate novel tokens). We study structural in-context algorithms in a simple part-of-speech setting using both practical and toy models. We find that active forgetting, a technique that was recently introduced to help models generalize to new languages, forces models to adopt structural in-context learning solutions. Finally, we introduce temporary forgetting, a straightforward extension of active forgetting that enables one to control how much a model relies on in-weights vs. in-context solutions. Importantly, temporary forgetting allows us to induce a dual process strategy where in-context and in-weights solutions coexist within a single model.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

Multi-modal recommendation has gained traction as items possess rich attributes like text and images. Semantic ID-based approaches effectively discretize this information into compact tokens. However, two challenges persist: (1) Suboptimal Tokenization: existing methods (e.g., RQ-VAE) lack disentanglement between shared cross-modal semantics and modality-specific details, causing redundancy or collapse; (2) Architecture-Data Mismatch: vanilla Transformers treat semantic IDs as flat streams, ignoring the hierarchy of user interactions, items, and tokens. Expanding items into multiple tokens amplifies length and noise, biasing attention toward local details over holistic semantics. We propose Hi-SAM, a Hierarchical Structure-Aware Multi-modal framework with two designs: (1) Disentangled Semantic Tokenizer (DST): unifies modalities via geometry-aware alignment and quantizes them via a coarse-to-fine strategy. Shared codebooks distill consensus while modality-specific ones recover nuances from residuals, enforced by mutual information minimization; (2) Hierarchical Memory-Anchor Transformer (HMAT): splits positional encoding into inter- and intra-item subspaces via Hierarchical RoPE to restore hierarchy. It inserts Anchor Tokens to condense items into compact memory, retaining details for the current item while accessing history only through compressed summaries. Experiments on real-world datasets show consistent improvements over SOTA baselines, especially in cold-start scenarios. Deployed on a large-scale social platform serving millions of users, Hi-SAM achieved a 6.55% gain in the core online metric.

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

Large Language Models (LLMs) and Vision-Language Models (VLMs) are increasingly evaluated on table reasoning tasks, but the role of table representation remains under-explored. In practice, the same table content may appear in different structural formats, such as HTML, Markdown, and LaTeX, or as rendered images. However, existing evaluations often let content, format, layout, and modality vary together, making it difficult to isolate representation effects. We introduce TABVERSE, a controlled multimodal table benchmark that aligns the same table content across multiple structural formats and rendered images, with question category and difficulty tags. This design enables systematic evaluation of representation effects while holding table content fixed. We evaluate LLMs and VLMs across three tasks: Question Answering (QA), Structural Understanding Capability (SUC), and Structure Reconstruction (SR). Our results show that representation choice substantially affects table understanding. Models generally perform better with structured text than with rendered images, but the size of this gap depends on the task, model, and format. HTML is often the most robust text format, while row-sensitive structural tasks and syntactically usable LaTeX reconstruction remain challenging. These findings show that table representation is a key factor in reliable table evaluation.

Computer-Aided Design (CAD) is a foundational component of industrial prototyping, where models are defined not by raw coordinates but by construction sequences such as sketches and extrusions. This sequential structure enables both efficient prototype initialization and subsequent editing. Text-guided CAD prototyping, which unifies Text-to-CAD generation and CAD editing, has the potential to streamline the entire design pipeline. However, prior work has not explored this setting, largely because standard large language model (LLM) tokenizers decompose CAD sequences into natural-language word pieces, failing to capture primitive-level CAD semantics and hindering attention modules from modeling geometric structure. We conjecture that a multimodal tokenization strategy, aligned with CAD's primitive and structural nature, can provide more effective representations. To this end, we propose CAD-Tokenizer, a framework that represents CAD data with modality-specific tokens using a sequence-based VQ-VAE with primitive-level pooling and constrained decoding. This design produces compact, primitive-aware representations that align with CAD's structural nature. Applied to unified text-guided CAD prototyping, CAD-Tokenizer significantly improves instruction following and generation quality, achieving better quantitative and qualitative performance over both general-purpose LLMs and task-specific baselines.

In an unpublished preprint batanin, Batanin conjectures that it is possible to take `slices' of a globular operad, thereby isolating the algebraic structure in each dimension. It was further hypothesised that the slices of a globular operad for some theory of higher category contain essential information about those higher categories, namely whether or not they are equivalent to the fully weak variety. In this paper, we use the theory of presentations for globular operads developed in Me to provide a concrete definition of slices, and calculate the slices for several key theories of n-category.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

Recent Vision-Language Models (e.g., ColPali) enable fine-grained Visual Document Retrieval (VDR) but incur prohibitive multi-vector index storage overhead. Existing training-free pruning methods either rely on heuristic layer choices or degrade sharply under aggressive compression, leading prior work to argue that effective high-compression pruning requires query-dependent training. We challenge this view with Structural Anchor Pruning (SAP), a self-calibrating, training-free, and query-agnostic index-time pruning framework with three components: (i) Score Retention (SR), a white-box per-layer compression diagnostic; (ii) SR-guided window selection, a procedure that automatically locates the structural pruning region for any backbone with no per-model hyperparameters; and (iii) a visual in-degree centrality scorer that identifies anchor patches within the selected window. On the ViDoRe v1/v2 benchmarks across three architectures spanning 18, 28, and 36 backbone layers, SAP retains over 90\% of NDCG@5 while pruning more than 90\% of visual tokens, without any per-model parameter tuning. Our layer-resolved SR analysis reveals an Alignment-Aggregation Divergence: the document's visual structure is preserved as a stable ``Structural Plateau'' within the backbone, but the final layers reshape this representation into a sparse, query-aligned form that is no longer suitable for pruning. This is the mechanistic reason SAP succeeds where final-layer methods fail.

Multimodal models for text-to-image generation have achieved strong visual fidelity, yet they remain brittle under compositional structural constraints-notably generative numeracy, attribute binding, and part-level relations. To address these challenges, we propose Shape-of-Thought (SoT), a visual CoT framework that enables progressive shape assembly via coherent 2D projections without external engines at inference time. SoT trains a unified multimodal autoregressive model to generate interleaved textual plans and rendered intermediate states, helping the model capture shape-assembly logic without producing explicit geometric representations. To support this paradigm, we introduce SoT-26K, a large-scale dataset of grounded assembly traces derived from part-based CAD hierarchies, and T2S-CompBench, a benchmark for evaluating structural integrity and trace faithfulness. Fine-tuning on SoT-26K achieves 88.4% on component numeracy and 84.8% on structural topology, outperforming text-only baselines by around 20%. SoT establishes a new paradigm for transparent, process-supervised compositional generation. The code is available at https://anonymous.4open.science/r/16FE/. The SoT-26K dataset will be released upon acceptance.

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

Modeling and designing urban building layouts is of significant interest in computer vision, computer graphics, and urban applications. A building layout consists of a set of buildings in city blocks defined by a network of roads. We observe that building layouts are discrete structures, consisting of multiple rows of buildings of various shapes, and are amenable to skeletonization for mapping arbitrary city block shapes to a canonical form. Hence, we propose a fully automatic approach to building layout generation using graph attention networks. Our method generates realistic urban layouts given arbitrary road networks, and enables conditional generation based on learned priors. Our results, including user study, demonstrate superior performance as compared to prior layout generation networks, support arbitrary city block and varying building shapes as demonstrated by generating layouts for 28 large cities.

Complex tables with multi-level headers, merged cells and heterogeneous layouts pose persistent challenges for LLMs in both understanding and reasoning. Existing approaches typically rely on table linearization or normalized grid modeling. However, these representations struggle to explicitly capture hierarchical structures and cross-dimensional dependencies, which can lead to misalignment between structural semantics and textual representations for non-standard tables. To address this issue, we propose an Orthogonal Hierarchical Decomposition (OHD) framework that constructs structure-preserving input representations of complex tables for LLMs. OHD introduces an Orthogonal Tree Induction (OTI) method based on spatial--semantic co-constraints, which decomposes irregular tables into a column tree and a row tree to capture vertical and horizontal hierarchical dependencies, respectively. Building on this representation, we design a dual-pathway association protocol to symmetrically reconstruct semantic lineage of each cell, and incorporate an LLM as a semantic arbitrator to align multi-level semantic information. We evaluate OHD framework on two complex table question answering benchmarks, AITQA and HiTab. Experimental results show that OHD consistently outperforms existing representation paradigms across multiple evaluation metrics.

Different from the flow semantics of natural languages, programming languages are inherently rigid in structure and grammar. Existing fine-tuning methodologies for code vulnerability detection generally treat code as long text sequences, stripping away structural elements such as newlines ('/n') and whitespace. However, this approach inadvertently results in the loss of crucial structural information, diminishing the distinct characteristics of code and impairing the accuracy of vulnerability detection. To address these challenges, we propose a novel network architecture method based on pre-trained code models, which incorporates structural information awareness. We propose an enhanced code text processing workflow that retains structural elements prior to modeling. This refinement allows the model to retain and exploit line-level structural information and semantic information during the modeling process. Furthermore, we introduce a new network architecture, the Code Structure-Aware Network through Line-level Semantic Learning (CSLS), which integrates three key components: global vulnerability awareness, line-structural awareness, and sensitive-line awareness. We have conducted comprehensive experiments using vulnerability detection datasets from real-world projects. Extensive experiments were conducted on vulnerability detection datasets derived from real-world projects. The results demonstrate that our new code pre-processing flow significantly improves existing baselines (e.g., a 3\% accuracy improvement on the Devign dataset when applied to popular models such as CoderBert and UniXcoder). The proposed network architecture also demonstrates superior accuracy in detecting vulnerabilities, surpassing newly established benchmarks. These findings underscore the importance of structural information in enhancing the efficacy of code vulnerability detection models.

Mathematical reasoning remains challenging for LLMs due to complex logic and the need for precise computation. Existing methods enhance LLM reasoning by synthesizing datasets through problem rephrasing, but face issues with generation quality and problem complexity. To address this, we propose to extract structural information with generated problem-solving code from mathematical reasoning and guide data generation with structured solutions. Applied to MATH and GSM8K, our approach produces 39K problems with labeled intermediate steps and a 6.1K-problem benchmark of higher difficulty. Results on our benchmark show that model performance declines as reasoning length increases. Additionally, we conducted fine-tuning experiments using the proposed training data on a range of LLMs, and the results validate the effectiveness of our dataset. We hope the proposed method and dataset will contribute to future research in enhancing LLM reasoning capabilities. Our code and data are available at https://github.com/OpenCausaLab/StructuralGeneration.

Knowledge Graph-based Question Answering (KGQA) plays a pivotal role in complex reasoning tasks but remains constrained by two persistent challenges: the structural heterogeneity of Knowledge Graphs(KGs) often leads to semantic mismatch during retrieval, while existing reasoning path retrieval methods lack a global structural perspective. To address these issues, we propose Structure-Tracing Evidence Mining (STEM), a novel framework that reframes multi-hop reasoning as a schema-guided graph search task. First, we design a Semantic-to-Structural Projection pipeline that leverages KG structural priors to decompose queries into atomic relational assertions and construct an adaptive query schema graph. Subsequently, we execute globally-aware node anchoring and subgraph retrieval to obtain the final evidence reasoning graph from KG. To more effectively integrate global structural information during the graph construction process, we design a Triple-Dependent GNN (Triple-GNN) to generate a Global Guidance Subgraph (Guidance Graph) that guides the construction. STEM significantly improves both the accuracy and evidence completeness of multi-hop reasoning graph retrieval, and achieves State-of-the-Art performance on multiple multi-hop benchmarks.

Graph neural networks (GNNs) have shown great potential in learning on graphs, but they are known to perform sub-optimally on link prediction tasks. Existing GNNs are primarily designed to learn node-wise representations and usually fail to capture pairwise relations between target nodes, which proves to be crucial for link prediction. Recent works resort to learning more expressive edge-wise representations by enhancing vanilla GNNs with structural features such as labeling tricks and link prediction heuristics, but they suffer from high computational overhead and limited scalability. To tackle this issue, we propose to learn structural link representations by augmenting the message-passing framework of GNNs with Bloom signatures. Bloom signatures are hashing-based compact encodings of node neighborhoods, which can be efficiently merged to recover various types of edge-wise structural features. We further show that any type of neighborhood overlap-based heuristic can be estimated by a neural network that takes Bloom signatures as input. GNNs with Bloom signatures are provably more expressive than vanilla GNNs and also more scalable than existing edge-wise models. Experimental results on five standard link prediction benchmarks show that our proposed model achieves comparable or better performance than existing edge-wise GNN models while being 3-200 times faster and more memory-efficient for online inference.

While large language models (LLMs) demonstrate impressive capabilities, their reliance on parametric knowledge often leads to factual inaccuracies. Retrieval-Augmented Generation (RAG) mitigates this by leveraging external documents, yet existing approaches treat retrieved passages as isolated chunks, ignoring valuable structure that is crucial for document organization. Motivated by this gap, we propose Retrieve-DocumentRoute-Read (RDR2), a novel framework that explicitly incorporates structural information throughout the RAG process. RDR2 employs an LLM-based router to dynamically navigate document structure trees, jointly evaluating content relevance and hierarchical relationships to assemble optimal evidence. Our key innovation lies in formulating document routing as a trainable task, with automatic action curation and structure-aware passage selection inspired by human reading strategies. Through comprehensive evaluation on five challenging datasets, RDR2 achieves state-of-the-art performance, demonstrating that explicit structural awareness significantly enhances RAG systems' ability to acquire and utilize knowledge, particularly in complex scenarios requiring multi-document synthesis.