Daily Papers

The inference of topological principles is a key problem in structured reconstruction. We observe that wrongly predicted topological relationships are often incurred by the lack of holistic geometry clues in low-level features. Inspired by the fact that massive signals can be compactly described with frequency analysis, we experimentally explore the efficiency and tendency of learning structure geometry in the frequency domain. Accordingly, we propose a frequency-domain feature learning strategy (F-Learn) to fuse scattered geometric fragments holistically for topology-intact structure reasoning. Benefiting from the parsimonious design, the F-Learn strategy can be easily deployed into a deep reconstructor with a lightweight model modification. Experiments demonstrate that the F-Learn strategy can effectively introduce structure awareness into geometric primitive detection and topology inference, bringing significant performance improvement to final structured reconstruction. Code and pre-trained models are available at https://github.com/Geo-Tell/F-Learn.

With the development of large language models (LLMs), particularly with the introduction of the long reasoning chain technique, the reasoning ability of LLMs in complex problem-solving has been significantly enhanced. While acknowledging the power of long reasoning chains, we cannot help but wonder: Why do different reasoning chains perform differently in reasoning? What components of the reasoning chains play a key role? Existing studies mainly focus on evaluating reasoning chains from a functional perspective, with little attention paid to their structural mechanisms. To address this gap, this work is the first to analyze and evaluate the quality of the reasoning chain from a structural perspective. We apply persistent homology from Topological Data Analysis (TDA) to map reasoning steps into semantic space, extract topological features, and analyze structural changes. These changes reveal semantic coherence, logical redundancy, and identify logical breaks and gaps. By calculating homology groups, we assess connectivity and redundancy at various scales, using barcode and persistence diagrams to quantify stability and consistency. Our results show that the topological structural complexity of reasoning chains correlates positively with accuracy. More complex chains identify correct answers sooner, while successful reasoning exhibits simpler topologies, reducing redundancy and cycles, enhancing efficiency and interpretability. This work provides a new perspective on reasoning chain quality assessment and offers guidance for future optimization.

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.

Large language models (LLMs) achieve promising performance, yet their ability to reason remains poorly understood. Existing evaluations largely emphasize task-level accuracy, often conflating pattern matching with reasoning capability. We present X-RAY, an explainable reasoning analysis system that maps the LLM reasoning capability using calibrated, formally verified probes. We model reasoning capability as a function of extractable structure, operationalized through formal properties such as constraint interaction, reasoning depth, and solution-space geometry. X-Ray generates probes via formal tools with controlled structural variations, enabling precise isolation of incremental structural information through formal calibration and verification. We evaluate state-of-the-art LLMs on problems ranging from junior-level to advanced in mathematics, physics, and chemistry. Our analysis reveals a systematic asymmetry in LLM reasoning: models are relatively robust to constraint refinement, where additional conditions shrink an existing solution space, but degrade sharply under solution-space restructuring, where modifications alter the underlying structural form of the solution manifold. Moreover, calibrated formal probes differentiate models that appear indistinguishable on standard benchmarks and reveal failure modes that are structurally interpretable rather than opaque. Beyond evaluation, our framework is contamination-free and supports the training and testing of reasoning models.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

Vision-language models (VLMs) have made significant strides in reasoning, yet they often struggle with complex multimodal tasks and tend to generate overly verbose outputs. A key limitation is their reliance on chain-of-thought (CoT) reasoning, despite many tasks benefiting from alternative topologies like trees or graphs. To address this, we introduce STELAR-Vision, a training framework for topology-aware reasoning. At its core is TopoAug, a synthetic data pipeline that enriches training with diverse topological structures. Using supervised fine-tuning and reinforcement learning, we post-train Qwen2VL models with both accuracy and efficiency in mind. Additionally, we propose Frugal Learning, which reduces output length with minimal accuracy loss. On MATH-V and VLM-S2H, STELAR-Vision improves accuracy by 9.7% over its base model and surpasses the larger Qwen2VL-72B-Instruct by 7.3%. On five out-of-distribution benchmarks, it outperforms Phi-4-Multimodal-Instruct by up to 28.4% and LLaMA-3.2-11B-Vision-Instruct by up to 13.2%, demonstrating strong generalization. Compared to Chain-Only training, our approach achieves 4.3% higher overall accuracy on in-distribution datasets and consistently outperforms across all OOD benchmarks. We have released datasets, and code will be available.

Reverse Chain-of-Thought Generation (RCG) synthesizes reasoning traces from query-answer pairs, but runs the risk of producing post-hoc rationalizations: when models can see the answer during generation, the answer serves as a cognitive anchor that shapes the entire explanation. We formalize this phenomenon through a three-level measurement hierarchy: lexical, entropic, and probabilistic anchoring, each captures surface artifacts, entropy dynamics, and latent answer dependence, respectively. We analyze semantic suppression, the intuitive mitigation strategy that instructs models to ignore the answer, to find out its counterproduction: while it reduces lexical overlap, it paradoxically increases entropic and probabilistic anchoring. Drawing on Ironic Process Theory from cognitive psychology, we attribute this failure to active monitoring of the forbidden answer, which inadvertently deepens dependence on it. To break this cycle, we propose Structural Skeleton-guided Reasoning (SSR), a two-phase approach that first generates an answer-invariant functional skeleton structure, then uses this skeleton to guide full trace generation. By redirecting the information flow to structural planning rather than answer monitoring, SSR consistently reduces anchoring across all three levels. We further introduce Distilled SSR (SSR-D), which fine-tunes models on teacher-generated SSR traces to ensure reliable structural adherence. Experiments across open-ended reasoning benchmarks demonstrate that SSR-D achieves up to 10% improvement over suppression baselines while preserving out-of-distribution (OOD) generalization.

Topology reasoning aims to comprehensively understand road scenes and present drivable routes in autonomous driving. It requires detecting road centerlines (lane) and traffic elements, further reasoning their topology relationship, i.e., lane-lane topology, and lane-traffic topology. In this work, we first present that the topology score relies heavily on detection performance on lane and traffic elements. Therefore, we introduce a powerful 3D lane detector and an improved 2D traffic element detector to extend the upper limit of topology performance. Further, we propose TopoMLP, a simple yet high-performance pipeline for driving topology reasoning. Based on the impressive detection performance, we develop two simple MLP-based heads for topology generation. TopoMLP achieves state-of-the-art performance on OpenLane-V2 benchmark, i.e., 41.2% OLS with ResNet-50 backbone. It is also the 1st solution for 1st OpenLane Topology in Autonomous Driving Challenge. We hope such simple and strong pipeline can provide some new insights to the community. Code is at https://github.com/wudongming97/TopoMLP.

We introduce a novel dataset designed to benchmark the physical and spatial reasoning capabilities of Large Language Models (LLM) based on topology optimization, a method for computing optimal material distributions within a design space under prescribed loads and supports. In this dataset, LLMs are provided with conditions such as 2D boundary, applied forces and supports, and must reason about the resulting optimal material distribution. The dataset includes a variety of tasks, ranging from filling in masked regions within partial structures to predicting complete material distributions. Solving these tasks requires understanding the flow of forces and the required material distribution under given constraints, without access to simulation tools or explicit physical models, challenging models to reason about structural stability and spatial organization. Our dataset targets the evaluation of spatial and physical reasoning abilities in 2D settings, offering a complementary perspective to traditional language and logic benchmarks.

Time series reasoning treats time as a first-class axis and incorporates intermediate evidence directly into the answer. This survey defines the problem and organizes the literature by reasoning topology with three families: direct reasoning in one step, linear chain reasoning with explicit intermediates, and branch-structured reasoning that explores, revises, and aggregates. The topology is crossed with the main objectives of the field, including traditional time series analysis, explanation and understanding, causal inference and decision making, and time series generation, while a compact tag set spans these axes and captures decomposition and verification, ensembling, tool use, knowledge access, multimodality, agent loops, and LLM alignment regimes. Methods and systems are reviewed across domains, showing what each topology enables and where it breaks down in faithfulness or robustness, along with curated datasets, benchmarks, and resources that support study and deployment (https://github.com/blacksnail789521/Time-Series-Reasoning-Survey). Evaluation practices that keep evidence visible and temporally aligned are highlighted, and guidance is distilled on matching topology to uncertainty, grounding with observable artifacts, planning for shift and streaming, and treating cost and latency as design budgets. We emphasize that reasoning structures must balance capacity for grounding and self-correction against computational cost and reproducibility, while future progress will likely depend on benchmarks that tie reasoning quality to utility and on closed-loop testbeds that trade off cost and risk under shift-aware, streaming, and long-horizon settings. Taken together, these directions mark a shift from narrow accuracy toward reliability at scale, enabling systems that not only analyze but also understand, explain, and act on dynamic worlds with traceable evidence and credible outcomes.

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.

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

The natural world is full of complex systems characterized by intricate relations between their components: from social interactions between individuals in a social network to electrostatic interactions between atoms in a protein. Topological Deep Learning (TDL) provides a comprehensive framework to process and extract knowledge from data associated with these systems, such as predicting the social community to which an individual belongs or predicting whether a protein can be a reasonable target for drug development. TDL has demonstrated theoretical and practical advantages that hold the promise of breaking ground in the applied sciences and beyond. However, the rapid growth of the TDL literature has also led to a lack of unification in notation and language across Topological Neural Network (TNN) architectures. This presents a real obstacle for building upon existing works and for deploying TNNs to new real-world problems. To address this issue, we provide an accessible introduction to TDL, and compare the recently published TNNs using a unified mathematical and graphical notation. Through an intuitive and critical review of the emerging field of TDL, we extract valuable insights into current challenges and exciting opportunities for future development.

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is {\em persistent homology}, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. In particular, a central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms. Existing approaches to this problem either ignore most of the multiparameter information to reduce to the one-parameter case or are heuristic and potentially unstable in the face of noise. In this article, we introduce a new general representation framework that leverages recent results on {\em decompositions} of multiparameter persistent homology. This framework is rich in information, fast to compute, and encompasses previous approaches. Moreover, we establish theoretical stability guarantees under this framework as well as efficient algorithms for practical computation, making this framework an applicable and versatile tool for analyzing geometric and point cloud data. We validate our stability results and algorithms with numerical experiments that demonstrate statistical convergence, prediction accuracy, and fast running times on several real data sets.

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

Persistent homology, a technique from computational topology, has recently shown strong empirical performance in the context of graph classification. Being able to capture long range graph properties via higher-order topological features, such as cycles of arbitrary length, in combination with multi-scale topological descriptors, has improved predictive performance for data sets with prominent topological structures, such as molecules. At the same time, the theoretical properties of persistent homology have not been formally assessed in this context. This paper intends to bridge the gap between computational topology and graph machine learning by providing a brief introduction to persistent homology in the context of graphs, as well as a theoretical discussion and empirical analysis of its expressivity for graph learning tasks.

In this paper we introduce a novel family of attributed graphs for the purpose of shape discrimination. Our graphs typically arise from variations on the Mapper graph construction, which is an approximation of the Reeb graph for point cloud data. Our attributions enrich these constructions with (persistent) homology in ways that are provably stable, thereby recording extra topological information that is typically lost in these graph constructions. We provide experiments which illustrate the use of these invariants for shape representation and classification. In particular, we obtain competitive shape classification results when using our topologically attributed graphs as inputs to a simple graph neural network classifier.

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

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

Understanding how Large Language Models (LLMs) perform complex reasoning and their failure mechanisms is a challenge in interpretability research. To provide a measurable geometric analysis perspective, we define the concept of the Reasoning Manifold, a latent low-dimensional geometric structure formed by the internal representations corresponding to all correctly reasoned generations. This structure can be conceptualized as the embodiment of the effective thinking paths that the model has learned to successfully solve a given task. Based on this concept, we build REMA, a framework that explains the origins of failures by quantitatively comparing the spatial relationships of internal model representations corresponding to both erroneous and correct reasoning samples. Specifically, REMA first quantifies the geometric deviation of each erroneous representation by calculating its k-nearest neighbors distance to the approximated manifold formed by correct representations, thereby providing a unified failure signal. It then localizes the divergence points where these deviations first become significant by tracking this deviation metric across the model's layers and comparing it against a baseline of internal fluctuations from correct representations, thus identifying where the reasoning chain begins to go off-track. Our extensive experiments on diverse language and multimodal models and tasks demonstrate the low-dimensional nature of the reasoning manifold and the high separability between erroneous and correct reasoning representations. The results also validate the effectiveness of the REMA framework in analyzing the origins of reasoning failures. This research connects abstract reasoning failures to measurable geometric deviations in representations, providing new avenues for in-depth understanding and diagnosis of the internal computational processes of black-box models.

The manifold hypothesis, which assumes that data lies on or close to an unknown manifold of low intrinsic dimension, is a staple of modern machine learning research. However, recent work has shown that real-world data exhibits distinct non-manifold structures, i.e. singularities, that can lead to erroneous findings. Detecting such singularities is therefore crucial as a precursor to interpolation and inference tasks. We address this issue by developing a topological framework that (i) quantifies the local intrinsic dimension, and (ii) yields a Euclidicity score for assessing the 'manifoldness' of a point along multiple scales. Our approach identifies singularities of complex spaces, while also capturing singular structures and local geometric complexity in image data.

CoT has significantly enhanced the reasoning ability of LLMs while it faces challenges when extended to multimodal domains, particularly in mathematical tasks. Existing MLLMs typically perform textual reasoning solely from a single static mathematical image, overlooking dynamic visual acquisition during reasoning. In contrast, humans repeatedly examine visual image and employ step-by-step reasoning to prove intermediate propositions. This strategy of decomposing the problem-solving process into key logical nodes adheres to Miller's Law in cognitive science. Inspired by this insight, we propose a ViRC framework for multimodal mathematical tasks, introducing a Reason Chunking mechanism that structures multimodal mathematical CoT into consecutive Critical Reasoning Units (CRUs) to simulate human expert problem-solving patterns. CRUs ensure intra-unit textual coherence for intermediate proposition verification while integrating visual information across units to generate subsequent propositions and support structured reasoning. To this end, we present CRUX dataset by using three visual tools and four reasoning patterns to provide explicitly annotated CRUs across multiple reasoning paths for each mathematical problem. Leveraging the CRUX dataset, we propose a progressive training strategy inspired by human cognitive learning, which includes Instructional SFT, Practice SFT, and Strategic RL, aimed at further strengthening the Reason Chunking ability of the model. The resulting ViRC-7B model achieves a 18.8% average improvement over baselines across multiple mathematical benchmarks. Code is available at https://github.com/Leon-LihongWang/ViRC.

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

The drive for predictable LLM reasoning in their integration with compound systems has popularized structured outputs, yet concerns remain about performance trade-offs compared to unconstrained natural language. At the same time, training on unconstrained Chain of Thought (CoT) traces has brought about a new class of strong reasoning models that nevertheless present novel compute budget and faithfulness challenges. This paper introduces iSelf-Discover, an instance-level adaptation of the Self-Discover framework, and using it compares dynamically generated structured JSON reasoning with its unstructured counterpart. Our empirical evaluation across diverse benchmarks using state-of-the-art open-source models supports a consistent advantage for unstructured reasoning. Notably, on the complex MATH benchmark, unstructured plans achieved relative performance improvements of up to 18.90\% over structured approaches. Zero-shot unstructured iSelf-Discover variants are also shown to outperform their five-shot structured counterparts, underscoring the significance of this gap, even when structured plans are dynamically generated to ensure reasoning precedes the final answer. We further demonstrate that the optimal granularity of plan generation (instance-level vs. task-level) is context-dependent. These findings invite re-evaluation of the reliance on structured formats for complex problem-solving and how compound systems should be organized.

Test-Time Scaling (TTS) has significantly enhanced the capabilities of Large Reasoning Models (LRMs) but introduces a critical side-effect known as Overthinking. We conduct a preliminary study to rethink this phenomenon from a fine-grained perspective. We observe that LRMs frequently conduct repetitive self-verification without revision even after obtaining the final answer during the reasoning process. We formally define this specific position where the answer first stabilizes as the Reasoning Anchor. By analyzing pre- and post-anchor reasoning behaviors, we uncover the structural redundancy fixed in LRMs: the meaningless repetitive verification after deriving the first complete answer, which we term the Answer-Stable Tail (AST). Motivated by this observation, we propose Anchor-based Process Reward (APR), a structure-aware reward shaping method that localizes the reasoning anchor and penalizes exclusively the post-anchor AST. Leveraging the policy optimization algorithm suitable for length penalties, our APR models achieved the performance-efficiency Pareto frontier at 1.5B and 7B scales averaged across five mathematical reasoning datasets while requiring substantially fewer computational resources for RL training.

We introduce Diagram of Thought (DoT), a framework that models iterative reasoning in large language models (LLMs) as the construction of a directed acyclic graph (DAG) within a single model. Unlike traditional approaches that represent reasoning as linear chains or trees, DoT organizes propositions, critiques, refinements, and verifications into a cohesive DAG structure, allowing the model to explore complex reasoning pathways while maintaining logical consistency. Each node in the diagram corresponds to a proposition that has been proposed, critiqued, refined, or verified, enabling the LLM to iteratively improve its reasoning through natural language feedback. By leveraging auto-regressive next-token prediction with role-specific tokens, DoT facilitates seamless transitions between proposing ideas and critically evaluating them, providing richer feedback than binary signals. Furthermore, we formalize the DoT framework using Topos Theory, providing a mathematical foundation that ensures logical consistency and soundness in the reasoning process. This approach enhances both the training and inference processes within a single LLM, eliminating the need for multiple models or external control mechanisms. DoT offers a conceptual framework for designing next-generation reasoning-specialized models, emphasizing training efficiency, robust reasoning capabilities, and theoretical grounding. The code is available at https://github.com/diagram-of-thought/diagram-of-thought.

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.

Reasoning ability is one of the most crucial capabilities of a foundation model, signifying its capacity to address complex reasoning tasks. Chain-of-Thought (CoT) technique is widely regarded as one of the effective methods for enhancing the reasoning ability of foundation models and has garnered significant attention. However, the reasoning process of CoT is linear, step-by-step, similar to personal logical reasoning, suitable for solving general and slightly complicated problems. On the contrary, the thinking pattern of an expert owns two prominent characteristics that cannot be handled appropriately in CoT, i.e., high-order multi-hop reasoning and multimodal comparative judgement. Therefore, the core motivation of this paper is transcending CoT to construct a reasoning paradigm that can think like an expert. The hyperedge of a hypergraph could connect various vertices, making it naturally suitable for modelling high-order relationships. Inspired by this, this paper innovatively proposes a multimodal Hypergraph-of-Thought (HoT) reasoning paradigm, which enables the foundation models to possess the expert-level ability of high-order multi-hop reasoning and multimodal comparative judgement. Specifically, a textual hypergraph-of-thought is constructed utilizing triple as the primary thought to model higher-order relationships, and a hyperedge-of-thought is generated through multi-hop walking paths to achieve multi-hop inference. Furthermore, we devise a visual hypergraph-of-thought to interact with the textual hypergraph-of-thought via Cross-modal Co-Attention Graph Learning for multimodal comparative verification. Experimentations on the ScienceQA benchmark demonstrate the proposed HoT-based T5 outperforms CoT-based GPT3.5 and chatGPT, which is on par with CoT-based GPT4 with a lower model size.

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

The structure of topology underpins much of the research on performance and robustness, yet available topology data are typically scarce, necessitating the generation of synthetic graphs with desired properties for testing or release. Prior diffusion-based approaches either embed conditions into the diffusion model, requiring retraining for each attribute and hindering real-time applicability, or use classifier-based guidance post-training, which does not account for topology scale and practical constraints. In this paper, we show from a discrete perspective that gradients from a pre-trained graph-level classifier can be incorporated into the discrete reverse diffusion posterior to steer generation toward specified structural properties. Based on this insight, we propose Classifier-guided Conditional Topology Generation with Persistent Homology (CoPHo), which builds a persistent homology filtration over intermediate graphs and interprets features as guidance signals that steer generation toward the desired properties at each denoising step. Experiments on four generic/network datasets demonstrate that CoPHo outperforms existing methods at matching target metrics, and we further validate its transferability on the QM9 molecular dataset.

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.

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. For enhancing the accuracy of such machine learning methods, it is often effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we choose a filtration for the point cloud, an increasing sequence of spaces. Since the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we show a theoretical result on a finite-dimensional approximation of filtration functions, which justifies the proposed network architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.

This paper introduces a novel method for merging open-domain terminological knowledge. It takes advantage of the Region Connection Calculus (RCC5), a formalism used to represent regions in a topological space and to reason about their set-theoretic relationships. To this end, we first propose a faithful translation of terminological knowledge provided by several and potentially conflicting sources into region spaces. The merging is then performed on these spaces, and the result is translated back into the underlying language of the input sources. Our approach allows us to benefit from the expressivity and the flexibility of RCC5 while dealing with conflicting knowledge in a principled way.

The pursuit of automated scientific discovery has fueled progress from symbolic logic to modern AI, forging new frontiers in reasoning and pattern recognition. Transformers function as potential systems, where every possible relationship remains latent potentiality until tasks impose constraints, akin to measurement. Yet, refining their sampling requires more than probabilistic selection: solutions must conform to specific structures or rules, ensuring consistency and the invocation of general principles. We present Graph-PReFLexOR (Graph-based Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning), a framework that combines graph reasoning with symbolic abstraction to dynamically expand domain knowledge. Inspired by reinforcement learning, Graph-PReFLexOR defines reasoning as a structured mapping, where tasks yield knowledge graphs, abstract patterns, and ultimately, final answers. Inspired by category theory, it encodes concepts as nodes and their relationships as edges, supporting hierarchical inference and adaptive learning through isomorphic representations. Demonstrations include hypothesis generation, materials design, and creative reasoning, such as discovering relationships between mythological concepts like 'thin places' with materials science. We propose a 'knowledge garden growth' strategy that integrates insights across domains, promoting interdisciplinary connections. Results with a 3-billion-parameter Graph-PReFLexOR model show superior reasoning depth and adaptability, underscoring the potential for transparent, multidisciplinary AI-driven discovery. It lays the groundwork for general autonomous reasoning solutions.

The use of graph neural networks has produced significant advances in point cloud problems, such as those found in high energy physics. The question of how to produce a graph structure in these problems is usually treated as a matter of heuristics, employing fully connected graphs or K-nearest neighbors. In this work, we elevate this question to utmost importance as the Topology Problem. We propose an attention mechanism that allows a graph to be constructed in a learned space that handles geometrically the flow of relevance, providing one solution to the Topology Problem. We test this architecture, called GravNetNorm, on the task of top jet tagging, and show that it is competitive in tagging accuracy, and uses far fewer computational resources than all other comparable models.

This paper introduces an innovative approach to analyzing and improving multi-hop reasoning in AI systems by drawing inspiration from Hamiltonian mechanics. We propose a novel framework that maps reasoning chains in embedding spaces to Hamiltonian systems, allowing us to leverage powerful analytical tools from classical physics. Our method defines a Hamiltonian function that balances the progression of reasoning (kinetic energy) against the relevance to the question at hand (potential energy). Using this framework, we analyze a large dataset of reasoning chains from a multi-hop question-answering task, revealing intriguing patterns that distinguish valid from invalid reasoning. We show that valid reasoning chains have lower Hamiltonian energy and move in ways that make the best trade-off between getting more information and answering the right question. Furthermore, we demonstrate the application of this framework to steer the creation of more efficient reasoning algorithms within AI systems. Our results not only provide new insights into the nature of valid reasoning but also open up exciting possibilities for physics-inspired approaches to understanding and improving artificial intelligence.

We propose a novel approach for preserving topological structures of the input space in latent representations of autoencoders. Using persistent homology, a technique from topological data analysis, we calculate topological signatures of both the input and latent space to derive a topological loss term. Under weak theoretical assumptions, we construct this loss in a differentiable manner, such that the encoding learns to retain multi-scale connectivity information. We show that our approach is theoretically well-founded and that it exhibits favourable latent representations on a synthetic manifold as well as on real-world image data sets, while preserving low reconstruction errors.

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

The scarcity of high-quality, logically sound data is a critical bottleneck for advancing the mathematical reasoning of Large Language Models (LLMs). Our work confronts this challenge by turning decades of automated theorem proving research into a scalable data engine. Rather than relying on error-prone LLMs or complex proof-assistant syntax like Lean and Isabelle, our framework leverages E-prover's saturation capabilities on the vast TPTP axiom library to derive a massive, guaranteed-valid corpus of theorems. Our pipeline is principled and simple: saturate axioms, filter for "interesting" theorems, and generate tasks. With no LLMs in the loop, we eliminate factual errors by construction. This purely symbolic data is then transformed into three difficulty-controlled challenges: entailment verification, premise selection, and proof reconstruction. Our zero-shot experiments on frontier models reveal a clear weakness: performance collapses on tasks requiring deep, structural reasoning. Our framework provides both the diagnostic tool to measure this gap and a scalable source of symbolic training data to address it. We make the code and data publicly available. https://github.com/sileod/reasoning_core https://hf.co/datasets/reasoning-core/rc1

Recent advances in large multimodal models suggest that explicit reasoning mechanisms play a critical role in improving model reliability, interpretability, and cross-modal alignment. While such reasoning-centric approaches have been proven effective in language and vision tasks, their extension to 3D remains underdeveloped. CoRe3D introduces a unified 3D understanding and generation reasoning framework that jointly operates over semantic and spatial abstractions, enabling high-level intent inferred from language to directly guide low-level 3D content formation. Central to this design is a spatially grounded reasoning representation that decomposes 3D latent space into localized regions, allowing the model to reason over geometry in a compositional and procedural manner. By tightly coupling semantic chain-of-thought inference with structured spatial reasoning, CoRe3D produces 3D outputs that exhibit strong local consistency and faithful alignment with linguistic descriptions.

We study how large language models (LLMs) ``think'' through their representation space. We propose a novel geometric framework that models an LLM's reasoning as flows -- embedding trajectories evolving where logic goes. We disentangle logical structure from semantics by employing the same natural deduction propositions with varied semantic carriers, allowing us to test whether LLMs internalize logic beyond surface form. This perspective connects reasoning with geometric quantities such as position, velocity, and curvature, enabling formal analysis in representation and concept spaces. Our theory establishes: (1) LLM reasoning corresponds to smooth flows in representation space, and (2) logical statements act as local controllers of these flows' velocities. Using learned representation proxies, we design controlled experiments to visualize and quantify reasoning flows, providing empirical validation of our theoretical framework. Our work serves as both a conceptual foundation and practical tools for studying reasoning phenomenon, offering a new lens for interpretability and formal analysis of LLMs' behavior.

Image-based 3D reconstruction has increasingly stunning results over the past few years with the latest improvements in computer vision and graphics. Geometry and topology are two fundamental concepts when dealing with 3D mesh structures. But the latest often remains a side issue in the 3D mesh-based reconstruction literature. Indeed, performing per-vertex elementary displacements over a 3D sphere mesh only impacts its geometry and leaves the topological structure unchanged and fixed. Whereas few attempts propose to update the geometry and the topology, all need to lean on costly 3D ground-truth to determine the faces/edges to prune. We present in this work a method that aims to refine the topology of any 3D mesh through a face-pruning strategy that extensively relies upon 2D alpha masks and camera pose information. Our solution leverages a differentiable renderer that renders each face as a 2D soft map. Its pixel intensity reflects the probability of being covered during the rendering process by such a face. Based on the 2D soft-masks available, our method is thus able to quickly highlight all the incorrectly rendered faces for a given viewpoint. Because our module is agnostic to the network that produces the 3D mesh, it can be easily plugged into any self-supervised image-based (either synthetic or natural) 3D reconstruction pipeline to get complex meshes with a non-spherical topology.

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

Modern representation learning increasingly relies on unsupervised and self-supervised methods trained on large-scale unlabeled data. While these approaches achieve impressive generalization across tasks and domains, evaluating embedding quality without labels remains an open challenge. In this work, we propose Persistence, a topology-aware metric based on persistent homology that quantifies the geometric structure and topological richness of embedding spaces in a fully unsupervised manner. Unlike metrics that assume linear separability or rely on covariance structure, Persistence captures global and multi-scale organization. Empirical results across diverse domains show that Persistence consistently achieves top-tier correlations with downstream performance, outperforming existing unsupervised metrics and enabling reliable model and hyperparameter selection.

Leaf-lesion segmentation is topology-sensitive: small merges, splits, or false holes can be biologically meaningful descriptors of biochemical pathways, yet they are weakly penalized by standard pixel-wise losses in Euclidean latents. I explore HyperTopo-Adapters, a lightweight, parameter-efficient head trained on top of a frozen vision encoder, which embeds features on a product manifold -- hyperbolic + Euclidean + spherical (H + E + S) -- to encourage hierarchical separation (H), local linear detail (E), and global closure (S). A topology prior complements Dice/BCE in two forms: (i) persistent-homology (PH) distance for evaluation and selection, and (ii) a differentiable surrogate that combines a soft Euler-characteristic match with total variation regularization for stable training. I introduce warm-ups for both the hyperbolic contrastive term and the topology prior, per-sample evaluation of structure-aware metrics (Boundary-F1, Betti errors, PD distance), and a min-PD within top-K Dice rule for checkpoint selection. On a Kaggle leaf-lesion dataset (N=2,940), early results show consistent gains in boundary and topology metrics (reducing Delta beta_1 hole error by 9%) while Dice/IoU remain competitive. The study is diagnostic by design: I report controlled ablations (curvature learning, latent dimensions, contrastive temperature, surrogate settings), and ongoing tests varying encoder strength (ResNet-50, DeepLabV3, DINOv2/v3), input resolution, PH weight, and partial unfreezing of late blocks. The contribution is an open, reproducible train/eval suite (available at https://github.com/ChimdiWalter/HyperTopo-Adapters) that isolates geometric/topological priors and surfaces failure modes to guide stronger, topology-preserving architectures.

There is a growing body of work that leverages features extracted via topological data analysis to train machine learning models. While this field, sometimes known as topological machine learning (TML), has seen some notable successes, an understanding of how the process of learning from topological features differs from the process of learning from raw data is still limited. In this work, we begin to address one component of this larger issue by asking whether a model trained with topological features learns internal representations of data that are fundamentally different than those learned by a model trained with the original raw data. To quantify ``different'', we exploit two popular metrics that can be used to measure the similarity of the hidden representations of data within neural networks, neural stitching and centered kernel alignment. From these we draw a range of conclusions about how training with topological features does and does not change the representations that a model learns. Perhaps unsurprisingly, we find that structurally, the hidden representations of models trained and evaluated on topological features differ substantially compared to those trained and evaluated on the corresponding raw data. On the other hand, our experiments show that in some cases, these representations can be reconciled (at least to the degree required to solve the corresponding task) using a simple affine transformation. We conjecture that this means that neural networks trained on raw data may extract some limited topological features in the process of making predictions.

Current Chain-of-Thought (CoT) verification methods predict reasoning correctness based on outputs (black-box) or activations (gray-box), but offer limited insight into why a computation fails. We introduce a white-box method: Circuit-based Reasoning Verification (CRV). We hypothesize that attribution graphs of correct CoT steps, viewed as execution traces of the model's latent reasoning circuits, possess distinct structural fingerprints from those of incorrect steps. By training a classifier on structural features of these graphs, we show that these traces contain a powerful signal of reasoning errors. Our white-box approach yields novel scientific insights unattainable by other methods. (1) We demonstrate that structural signatures of error are highly predictive, establishing the viability of verifying reasoning directly via its computational graph. (2) We find these signatures to be highly domain-specific, revealing that failures in different reasoning tasks manifest as distinct computational patterns. (3) We provide evidence that these signatures are not merely correlational; by using our analysis to guide targeted interventions on individual transcoder features, we successfully correct the model's faulty reasoning. Our work shows that, by scrutinizing a model's computational process, we can move from simple error detection to a deeper, causal understanding of LLM reasoning.

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.

We give a conceptual treatment of the notion of joints, marginals, and independence in the setting of categorical probability. This is achieved by endowing the usual probability monads (like the Giry monad) with a monoidal and an opmonoidal structure, mutually compatible (i.e. a bimonoidal structure). If the underlying monoidal category is cartesian monoidal, a bimonoidal structure is given uniquely by a commutative strength. However, if the underlying monoidal category is not cartesian monoidal, a strength is not enough to guarantee all the desired properties of joints and marginals. A bimonoidal structure is then the correct requirement for the more general case. We explain the theory and the operational interpretation, with the help of the graphical calculus for monoidal categories. We give a definition of stochastic independence based on the bimonoidal structure, compatible with the intuition and with other approaches in the literature for cartesian monoidal categories. We then show as an example that the Kantorovich monad on the category of complete metric spaces is a bimonoidal monad for a non-cartesian monoidal structure.

We argue that progress toward AGI is theory limited rather than data or scale limited. Building on the critical rationalism of Popper and Deutsch, we challenge the Platonic Representation Hypothesis. Observationally equivalent worlds can diverge under interventions, so observational adequacy alone cannot guarantee interventional competence. We begin by laying foundations, definitions of knowledge, learning, intelligence, counterfactual competence and AGI, and then analyze the limits of observational learning that motivate an error centric shift. We recast the problem as three questions about how explicit and implicit errors evolve under an agent's actions, which errors are unreachable within a fixed hypothesis space, and how conjecture and criticism expand that space. From these questions we propose Causal Mechanics, a mechanisms first program in which hypothesis space change is a first class operation and probabilistic structure is used when useful rather than presumed. We advance structural principles that make error discovery and correction tractable, including a differential Locality and Autonomy Principle for modular interventions, a gauge invariant form of Independent Causal Mechanisms for separability, and the Compositional Autonomy Principle for analogy preservation, together with actionable diagnostics. The aim is a scaffold for systems that can convert unreachable errors into reachable ones and correct them.

Accurately segmenting thin tubular structures, such as vessels, nerves, roads or concrete cracks, is a crucial task in computer vision. Standard deep learning-based segmentation loss functions, such as Dice or Cross-Entropy, focus on volumetric overlap, often at the expense of preserving structural connectivity or topology. This can lead to segmentation errors that adversely affect downstream tasks, including flow calculation, navigation, and structural inspection. Although current topology-focused losses mark an improvement, they introduce significant computational and memory overheads. This is particularly relevant for 3D data, rendering these losses infeasible for larger volumes as well as increasingly important multi-class segmentation problems. To mitigate this, we propose a novel Skeleton Recall Loss, which effectively addresses these challenges by circumventing intensive GPU-based calculations with inexpensive CPU operations. It demonstrates overall superior performance to current state-of-the-art approaches on five public datasets for topology-preserving segmentation, while substantially reducing computational overheads by more than 90%. In doing so, we introduce the first multi-class capable loss function for thin structure segmentation, excelling in both efficiency and efficacy for topology-preservation.

Recently, studies exemplified by Hyper-Connections (HC) have extended the ubiquitous residual connection paradigm established over the past decade by expanding the residual stream width and diversifying connectivity patterns. While yielding substantial performance gains, this diversification fundamentally compromises the identity mapping property intrinsic to the residual connection, which causes severe training instability and restricted scalability, and additionally incurs notable memory access overhead. To address these challenges, we propose Manifold-Constrained Hyper-Connections (mHC), a general framework that projects the residual connection space of HC onto a specific manifold to restore the identity mapping property, while incorporating rigorous infrastructure optimization to ensure efficiency. Empirical experiments demonstrate that mHC is effective for training at scale, offering tangible performance improvements and superior scalability. We anticipate that mHC, as a flexible and practical extension of HC, will contribute to a deeper understanding of topological architecture design and suggest promising directions for the evolution of foundational models.

Online scene perception and topology reasoning are critical for autonomous vehicles to understand their driving environments, particularly for mapless driving systems that endeavor to reduce reliance on costly High-Definition (HD) maps. However, recent advances in online scene understanding still face limitations, especially in long-range or occluded scenarios, due to the inherent constraints of onboard sensors. To address this challenge, we propose a Standard-Definition (SD) Map Enhanced scene Perception and Topology reasoning (SEPT) framework, which explores how to effectively incorporate the SD map as prior knowledge into existing perception and reasoning pipelines. Specifically, we introduce a novel hybrid feature fusion strategy that combines SD maps with Bird's-Eye-View (BEV) features, considering both rasterized and vectorized representations, while mitigating potential misalignment between SD maps and BEV feature spaces. Additionally, we leverage the SD map characteristics to design an auxiliary intersection-aware keypoint detection task, which further enhances the overall scene understanding performance. Experimental results on the large-scale OpenLane-V2 dataset demonstrate that by effectively integrating SD map priors, our framework significantly improves both scene perception and topology reasoning, outperforming existing methods by a substantial margin.

Dramatic progress has been witnessed in basic vision tasks involving low-level perception, such as object recognition, detection, and tracking. Unfortunately, there is still an enormous performance gap between artificial vision systems and human intelligence in terms of higher-level vision problems, especially ones involving reasoning. Earlier attempts in equipping machines with high-level reasoning have hovered around Visual Question Answering (VQA), one typical task associating vision and language understanding. In this work, we propose a new dataset, built in the context of Raven's Progressive Matrices (RPM) and aimed at lifting machine intelligence by associating vision with structural, relational, and analogical reasoning in a hierarchical representation. Unlike previous works in measuring abstract reasoning using RPM, we establish a semantic link between vision and reasoning by providing structure representation. This addition enables a new type of abstract reasoning by jointly operating on the structure representation. Machine reasoning ability using modern computer vision is evaluated in this newly proposed dataset. Additionally, we also provide human performance as a reference. Finally, we show consistent improvement across all models by incorporating a simple neural module that combines visual understanding and structure reasoning.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

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.

Mathematical geometric reasoning is essential for scientific discovery and educational development, requiring precise logic and rigorous formal verification. While recent advances in Multimodal Large Language Models (MLLMs) have improved reasoning tasks, existing models typically struggle with formal geometric reasoning, particularly when dynamically constructing and verifying auxiliary geometric elements. To address these challenges, we introduce Geoint-R1, a multimodal reasoning framework designed to generate formally verifiable geometric solutions from textual descriptions and visual diagrams. Geoint-R1 uniquely integrates auxiliary elements construction, formal reasoning represented via Lean4, and interactive visualization. To systematically evaluate and advance formal geometric reasoning, we propose the Geoint benchmark, comprising 1,885 rigorously annotated geometry problems across diverse topics such as plane, spatial, and solid geometry. Each problem includes structured textual annotations, precise Lean4 code for auxiliary constructions, and detailed solution steps verified by experts. Extensive experiments demonstrate that Geoint-R1 significantly surpasses existing multimodal and math-specific reasoning models, particularly on challenging problems requiring explicit auxiliary element constructions.

LLMs have demonstrated strong mathematical reasoning abilities by leveraging reinforcement learning with long chain-of-thought, yet they continue to struggle with theorem proving due to the lack of clear supervision signals when solely using natural language. Dedicated domain-specific languages like Lean provide clear supervision via formal verification of proofs, enabling effective training through reinforcement learning. In this work, we propose Seed-Prover, a lemma-style whole-proof reasoning model. Seed-Prover can iteratively refine its proof based on Lean feedback, proved lemmas, and self-summarization. To solve IMO-level contest problems, we design three test-time inference strategies that enable both deep and broad reasoning. Seed-Prover proves 78.1% of formalized past IMO problems, saturates MiniF2F, and achieves over 50\% on PutnamBench, outperforming the previous state-of-the-art by a large margin. To address the lack of geometry support in Lean, we introduce a geometry reasoning engine Seed-Geometry, which outperforms previous formal geometry engines. We use these two systems to participate in IMO 2025 and fully prove 5 out of 6 problems. This work represents a significant advancement in automated mathematical reasoning, demonstrating the effectiveness of formal verification with long chain-of-thought reasoning.

Human reasoning relies on constructing and manipulating mental models-simplified internal representations of situations that we use to understand and solve problems. Conceptual diagrams (for example, sketches drawn by humans to aid reasoning) externalize these mental models, abstracting irrelevant details to efficiently capture relational and spatial information. In contrast, Large Language Models (LLMs) and Large Multimodal Models (LMMs) predominantly reason through textual representations, limiting their effectiveness in complex multi-step combinatorial and planning tasks. In this paper, we propose a zero-shot fully automatic framework that enables LMMs to reason through multiple chains of self-generated intermediate conceptual diagrams, significantly enhancing their combinatorial planning capabilities. Our approach does not require any human initialization beyond a natural language description of the task. It integrates both textual and diagrammatic reasoning within an optimized graph-of-thought inference framework, enhanced by beam search and depth-wise backtracking. Evaluated on multiple challenging PDDL planning domains, our method substantially improves GPT-4o's performance (for example, from 35.5% to 90.2% in Blocksworld). On more difficult planning domains with solution depths up to 40, our approach outperforms even the o1-preview reasoning model (for example, over 13% improvement in Parking). These results highlight the value of conceptual diagrams as a complementary reasoning medium in LMMs.

Though recent advances in vision-language models (VLMs) have achieved remarkable progress across a wide range of multimodal tasks, understanding 3D spatial relationships from limited views remains a significant challenge. Previous reasoning methods typically rely on pure text (e.g., topological cognitive maps) or on 2D visual cues. However, their limited representational capacity hinders performance in specific tasks that require 3D spatial imagination. To address this limitation, we propose 3DThinker, a framework that can effectively exploits the rich geometric information embedded within images while reasoning, like humans do. Our framework is the first to enable 3D mentaling during reasoning without any 3D prior input, and it does not rely on explicitly labeled 3D data for training. Specifically, our training consists of two stages. First, we perform supervised training to align the 3D latent generated by VLM while reasoning with that of a 3D foundation model (e.g., VGGT). Then, we optimize the entire reasoning trajectory solely based on outcome signals, thereby refining the underlying 3D mentaling. Extensive experiments across multiple benchmarks show that 3DThinker consistently outperforms strong baselines and offers a new perspective toward unifying 3D representations into multimodal reasoning. Our code will be available at https://github.com/zhangquanchen/3DThinker.

Vision-Language Models (VLMs) have achieved remarkable progress in integrating visual perception with language understanding. However, effective multimodal reasoning requires both accurate perception and robust reasoning, and weakness in either limits the performance of VLMs. Prior efforts to enhance reasoning often depend on high-quality chain-of-thought (CoT) data, obtained via labor-intensive human annotations, costly proprietary models, or self-training methods that overlook perception. To address these limitations, we propose a simple yet effective self-training framework called See-Think-Learn (STL). At its core, STL introduces a structured reasoning template that encourages the model to see before thinking, first extracting visual attributes in textual form, then using them to guide reasoning. The framework jointly improves perception and reasoning by having the model generate and learn from its own structured rationales in a self-training loop. Furthermore, we augment the training data with negative rationales, i.e. explanations that justify why certain answer choices are incorrect, to enhance the model's ability to distinguish between correct and misleading responses. This fosters more discriminative and robust learning. Experiments across diverse domains show that STL consistently outperforms baselines trained directly only on answers or self-generated reasoning, while qualitative analysis confirms the high quality of its rationales. STL thus provides a cost-effective solution to enhance multimodal reasoning ability of VLMs.

We present EuLearn, the first surface datasets equitably representing a diversity of topological types. We designed our embedded surfaces of uniformly varying genera relying on random knots, thus allowing our surfaces to knot with themselves. EuLearn contributes new topological datasets of meshes, point clouds, and scalar fields in 3D. We aim to facilitate the training of machine learning systems that can discern topological features. We experimented with specific emblematic 3D neural network architectures, finding that their vanilla implementations perform poorly on genus classification. To enhance performance, we developed a novel, non-Euclidean, statistical sampling method adapted to graph and manifold data. We also introduce adjacency-informed adaptations of PointNet and Transformer architectures that rely on our non-Euclidean sampling strategy. Our results demonstrate that incorporating topological information into deep learning workflows significantly improves performance on these otherwise challenging EuLearn datasets.

Complex reasoning problems often involve implicit spatial, geometric, and structural relationships that are not explicitly encoded in text. While recent reasoning models have achieved strong performance across many domains, purely text-based reasoning struggles to represent global structural constraints in complex settings. In this paper, we introduce FIGR, which integrates active visual thinking into multi-turn reasoning via end-to-end reinforcement learning. FIGR externalizes intermediate structural hypotheses by constructing visual representations during problem solving. By adaptively regulating when and how visual reasoning should be invoked, FIGR enables more stable and coherent reasoning over global structural properties that are difficult to capture from text alone. Experiments on challenging mathematical reasoning benchmarks demonstrate that FIGR outperforms strong text-only chain-of-thought baselines. In particular, FIGR improves the base model by 13.12% on AIME 2025 and 11.00% on BeyondAIME, highlighting the effectiveness of figure-guided multimodal reasoning in enhancing the stability and reliability of complex reasoning.

Geometry problem solving (GPS) is a high-level mathematical reasoning requiring the capacities of multi-modal fusion and geometric knowledge application. Recently, neural solvers have shown great potential in GPS but still be short in diagram presentation and modal fusion. In this work, we convert diagrams into basic textual clauses to describe diagram features effectively, and propose a new neural solver called PGPSNet to fuse multi-modal information efficiently. Combining structural and semantic pre-training, data augmentation and self-limited decoding, PGPSNet is endowed with rich knowledge of geometry theorems and geometric representation, and therefore promotes geometric understanding and reasoning. In addition, to facilitate the research of GPS, we build a new large-scale and fine-annotated GPS dataset named PGPS9K, labeled with both fine-grained diagram annotation and interpretable solution program. Experiments on PGPS9K and an existing dataset Geometry3K validate the superiority of our method over the state-of-the-art neural solvers. Our code, dataset and appendix material are available at https://github.com/mingliangzhang2018/PGPS.

Spatial intelligence is crucial for vision--language models (VLMs) in the physical world, yet many benchmarks evaluate largely unconstrained scenes where models can exploit 2D shortcuts. We introduce SSI-Bench, a VQA benchmark for spatial reasoning on constrained manifolds, built from complex real-world 3D structures whose feasible configurations are tightly governed by geometric, topological, and physical constraints. SSI-Bench contains 1,000 ranking questions spanning geometric and topological reasoning and requiring a diverse repertoire of compositional spatial operations, such as mental rotation, cross-sectional inference, occlusion reasoning, and force-path reasoning. It is created via a fully human-centered pipeline: ten researchers spent over 400 hours curating images, annotating structural components, and designing questions to minimize pixel-level cues. Evaluating 31 widely used VLMs reveals a large gap to humans: the best open-source model achieves 22.2% accuracy and the strongest closed-source model reaches 33.6%, while humans score 91.6%. Encouraging models to think yields only marginal gains, and error analysis points to failures in structural grounding and constraint-consistent 3D reasoning. Project page: https://ssi-bench.github.io.

Large language models have achieved near-expert performance in structured reasoning domains like mathematics and programming, yet their ability to perform compositional multi-hop reasoning in specialized scientific fields remains limited. We propose a bottom-up learning paradigm in which models are grounded in axiomatic domain facts and compose them to solve complex, unseen tasks. To this end, we present a post-training pipeline, based on a combination of supervised fine-tuning and reinforcement learning (RL), in which knowledge graphs act as implicit reward models. By deriving novel reward signals from knowledge graph paths, we provide verifiable, scalable, and grounded supervision that encourages models to compose intermediate axioms rather than optimize only final answers during RL. We validate this approach in the medical domain, training a 14B model on short-hop reasoning paths (1-3 hops) and evaluating its zero-shot generalization to complex multi-hop queries (4-5 hops). Our experiments show that path-derived rewards act as a "compositional bridge", enabling our model to significantly outperform much larger models and frontier systems like GPT-5.2 and Gemini 3 Pro, on the most difficult reasoning tasks. Furthermore, we demonstrate the robustness of our approach to adversarial perturbations against option-shuffling stress tests. This work suggests that grounding the reasoning process in structured knowledge is a scalable and efficient path toward intelligent reasoning.

Can reinforcement learning with hard, verifiable rewards teach a compact language model to reason about physics, or does it primarily learn to pattern-match toward correct answers? We study this question by training a 1.5B-parameter reasoning model on beam statics, a classic engineering problem, using parameter-efficient RLVR with binary correctness rewards from symbolic solvers, without teacher-generated reasoning traces. The best BeamPERL checkpoint achieves a 66.7% improvement in Pass@1 over the base model. However, the learned competence is anisotropic: the model generalizes compositionally (more loads) but fails under topological shifts (moved supports) that require the same equilibrium equations. Intermediate checkpoints yield the strongest reasoning, while continued optimization degrades robustness while maintaining reward. These findings reveal a key limitation of outcome-level alignment: reinforcement learning with exact physics rewards induces procedural solution templates rather than internalization of governing equations. The precision of the reward signal - even when analytically exact - does not by itself guarantee transferable physical reasoning. Our results suggest that verifiable rewards may need to be paired with structured reasoning scaffolding to move beyond template matching toward robust scientific reasoning.

We propose a many-sorted modal logic for reasoning about knowledge in multi-agent systems. Our logic introduces a clear distinction between participating agents and the environment. This allows to express local properties of agents and global properties of worlds in a uniform way, as well as to talk about the presence or absence of agents in a world. The logic subsumes the standard epistemic logic and is a conservative extension of it. The semantics is given in chromatic hypergraphs, a generalization of chromatic simplicial complexes, which were recently used to model knowledge in distributed systems. We show that the logic is sound and complete with respect to the intended semantics. We also show a further connection of chromatic hypergraphs with neighborhood frames.

Large Language Models (LLMs) have made remarkable strides in reasoning tasks, yet their performance often falters on novel and complex problems. Domain-specific continued pretraining (CPT) methods, such as those tailored for mathematical reasoning, have shown promise but lack transferability to broader reasoning tasks. In this work, we pioneer the use of Graph Problem Reasoning (GPR) to enhance the general reasoning capabilities of LLMs. GPR tasks, spanning pathfinding, network analysis, numerical computation, and topological reasoning, require sophisticated logical and relational reasoning, making them ideal for teaching diverse reasoning patterns. To achieve this, we introduce GraphPile, the first large-scale corpus specifically designed for CPT using GPR data. Spanning 10.9 billion tokens across 23 graph tasks, the dataset includes chain-of-thought, program-of-thought, trace of execution, and real-world graph data. Using GraphPile, we train GraphMind on popular base models Llama 3 and 3.1, as well as Gemma 2, achieving up to 4.9 percent higher accuracy in mathematical reasoning and up to 21.2 percent improvement in non-mathematical reasoning tasks such as logical and commonsense reasoning. By being the first to harness GPR for enhancing reasoning patterns and introducing the first dataset of its kind, our work bridges the gap between domain-specific pretraining and universal reasoning capabilities, advancing the adaptability and robustness of LLMs.

Artificial intelligence in construction increasingly depends on structured representations such as Building Information Models and knowledge graphs, yet early-stage building designs are predominantly created as flexible boundary-representation (B-rep) models that lack explicit spatial, semantic, and performance structure. This paper presents a robust, fully automated framework that transforms unstructured B-rep geometry into knowledge-graph-based Building Information Models and further into executable Building Energy Models. The framework enables artificial intelligence to explicitly interpret building elements, spatial topology, and their associated thermal and performance attributes. It integrates automated geometry cleansing, multiple auto space-generation strategies, graph-based extraction of space and element topology, ontology-aligned knowledge modeling, and reversible transformation between ontology-based BIM and EnergyPlus energy models. Validation on parametric, sketch-based, and real-world building datasets demonstrates high robustness, consistent topological reconstruction, and reliable performance-model generation. By bridging design models, BIM, and BEM, the framework provides an AI-oriented infrastructure that extends BIM- and graph-based intelligence pipelines to flexible early-stage design geometry, enabling performance-driven design exploration and optimization by learning-based methods.

Topological Neural Networks (TNNs) incorporate higher-order relational information beyond pairwise interactions, enabling richer representations than Graph Neural Networks (GNNs). Concurrently, topological descriptors based on persistent homology (PH) are being increasingly employed to augment the GNNs. We investigate the benefits of integrating these two paradigms. Specifically, we introduce TopNets as a broad framework that subsumes and unifies various methods in the intersection of GNNs/TNNs and PH such as (generalizations of) RePHINE and TOGL. TopNets can also be readily adapted to handle (symmetries in) geometric complexes, extending the scope of TNNs and PH to spatial settings. Theoretically, we show that PH descriptors can provably enhance the expressivity of simplicial message-passing networks. Empirically, (continuous and E(n)-equivariant extensions of) TopNets achieve strong performance across diverse tasks, including antibody design, molecular dynamics simulation, and drug property prediction.

Large Language Models (LLMs) have achieved impressive performance on complex reasoning tasks with Chain-of-Thought (CoT) prompting. However, conventional CoT relies on reasoning steps explicitly verbalized in natural language, introducing inefficiencies and limiting its applicability to abstract reasoning. To address this, there has been growing research interest in latent CoT reasoning, where inference occurs within latent spaces. By decoupling reasoning from language, latent reasoning promises richer cognitive representations and more flexible, faster inference. Researchers have explored various directions in this promising field, including training methodologies, structural innovations, and internal reasoning mechanisms. This paper presents a comprehensive overview and analysis of this reasoning paradigm. We begin by proposing a unified taxonomy from four perspectives: token-wise strategies, internal mechanisms, analysis, and applications. We then provide in-depth discussions and comparative analyses of representative methods, highlighting their design patterns, strengths, and open challenges. We aim to provide a structured foundation for advancing this emerging direction in LLM reasoning. The relevant papers will be regularly updated at https://github.com/EIT-NLP/Awesome-Latent-CoT.

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

Despite the success of test-time scaling, Large Reasoning Models (LRMs) frequently encounter repetitive loops that lead to computational waste and inference failure. In this paper, we identify a distinct failure mode termed Circular Reasoning. Unlike traditional model degeneration, this phenomenon manifests as a self-reinforcing trap where generated content acts as a logical premise for its own recurrence, compelling the reiteration of preceding text. To systematically analyze this phenomenon, we introduce LoopBench, a dataset designed to capture two distinct loop typologies: numerical loops and statement loops. Mechanistically, we characterize circular reasoning as a state collapse exhibiting distinct boundaries, where semantic repetition precedes textual repetition. We reveal that reasoning impasses trigger the loop onset, which subsequently persists as an inescapable cycle driven by a self-reinforcing V-shaped attention mechanism. Guided by these findings, we employ the Cumulative Sum (CUSUM) algorithm to capture these precursors for early loop prediction. Experiments across diverse LRMs validate its accuracy and elucidate the stability of long-chain reasoning.

Deep iterative chain-of-thought (CoT) reasoning enables LLMs to tackle complex tasks by progressively activating relevant pre-trained knowledge. However, it faces challenges in ensuring continual improvement and determining a stopping criterion. In this paper, we investigate whether the relevant knowledge that contributes directly to solving the given question can be activated from the initial reasoning path, thus circumventing the need for iterative refinement. Our experiments reveal that increasing the diversity of initial reasoning paths can achieve comparable or superior performance, a concept we term breadth reasoning. However, existing breadth reasoning approaches, such as self-consistency, offer limited diversity. To address this limitation, we propose a simple yet effective method that enhances reasoning breadth by integrating contextual exploration with reduced sampling randomness. Extensive experiments demonstrate that our approach significantly outperforms deep iterative reasoning. Our code is provided in https://github.com/zongqianwu/breadth.

Vision-language models (VLMs) achieve strong multimodal performance, yet how computation is organized across populations of neurons remains poorly understood. In this work, we study VLMs through the lens of neural topology, representing each layer as a within-layer correlation graph derived from neuron-neuron co-activations. This view allows us to ask whether population-level structure is behaviorally meaningful, how it changes across modalities and depth, and whether it identifies causally influential internal components under intervention. We show that correlation topology carries recoverable behavioral signal; moreover, cross-modal structure progressively consolidates with depth around a compact set of recurrent hub neurons, whose targeted perturbation substantially alters model output. Neural topology thus emerges as a meaningful intermediate scale for VLM interpretability: richer than local attribution, more tractable than full circuit recovery, and empirically tied to multimodal behavior. Code is publicly available at https://github.com/he-h/vlm-graph-probing.

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

In this paper, we claim that 3D visual grounding is the cornerstone of spatial reasoning and introduce the Grounded-Spatial Reasoner (GS-Reasoner) to explore the effective spatial representations that bridge the gap between them. Existing 3D LLMs suffer from the absence of a unified 3D representation capable of jointly capturing semantic and geometric information. This deficiency is manifested either in poor performance on grounding or in an excessive reliance on external modules, ultimately hindering the seamless integration of grounding and spatial reasoning. To address this, we propose a simple yet effective dual-path pooling mechanism that tightly aligns geometric features with both semantic and positional cues, constructing a unified image patch-based 3D representation that encapsulates all essential information without increasing the number of input tokens. Leveraging this holistic representation, GS-Reasoner is the first 3D LLM that achieves autoregressive grounding entirely without external modules while delivering performance comparable to state-of-the-art models, establishing a unified and self-contained framework for 3D spatial reasoning. To further bridge grounding and spatial reasoning, we introduce the Grounded Chain-of-Thought (GCoT) dataset. This dataset is meticulously curated to include both 3D bounding box annotations for objects referenced in reasoning questions and step-by-step reasoning paths that integrate grounding as a core component of the problem-solving process. Extensive experiments demonstrate that GS-Reasoner achieves impressive results on 3D visual grounding, which in turn significantly enhances its spatial reasoning capabilities, leading to state-of-the-art performance.

The transition from symbolic manipulation to science-grade reasoning represents a pivotal frontier for Large Language Models (LLMs), with physics serving as the critical test anchor for binding abstract logic to physical reality. Physics demands that a model maintain physical consistency with the laws governing the universe, a task that fundamentally requires multimodal perception to ground abstract logic in reality. At the Olympiad level, diagrams are often constitutive rather than illustrative, containing essential constraints, such as boundary conditions and spatial symmetries, that are absent from the text. To bridge this visual-logical gap, we introduce P1-VL, a family of open-source vision-language models engineered for advanced scientific reasoning. Our method harmonizes Curriculum Reinforcement Learning, which employs progressive difficulty expansion to stabilize post-training, with Agentic Augmentation, enabling iterative self-verification at inference. Evaluated on HiPhO, a rigorous benchmark of 13 exams from 2024-2025, our flagship P1-VL-235B-A22B becomes the first open-source Vision-Language Model (VLM) to secure 12 gold medals and achieves the state-of-the-art performance in the open-source models. Our agent-augmented system achieves the No.2 overall rank globally, trailing only Gemini-3-Pro. Beyond physics, P1-VL demonstrates remarkable scientific reasoning capacity and generalizability, establishing significant leads over base models in STEM benchmarks. By open-sourcing P1-VL, we provide a foundational step toward general-purpose physical intelligence to better align visual perceptions with abstract physical laws for machine scientific discovery.

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

Spatial reasoning is a crucial component of both biological and artificial intelligence. In this work, we present a comprehensive study of the capability of current state-of-the-art large language models (LLMs) on spatial reasoning. To support our study, we created and contribute a novel Spatial Reasoning Characterization (SpaRC) framework and Spatial Reasoning Paths (SpaRP) datasets, to enable an in-depth understanding of the spatial relations and compositions as well as the usefulness of spatial reasoning chains. We found that all the state-of-the-art LLMs do not perform well on the datasets -- their performances are consistently low across different setups. The spatial reasoning capability improves substantially as model sizes scale up. Finetuning both large language models (e.g., Llama-2-70B) and smaller ones (e.g., Llama-2-13B) can significantly improve their F1-scores by 7--32 absolute points. We also found that the top proprietary LLMs still significantly outperform their open-source counterparts in topological spatial understanding and reasoning.

Current paradigms for code verification rely heavily on external mechanisms-such as execution-based unit tests or auxiliary LLM judges-which are often labor-intensive or limited by the judging model's own capabilities. This raises a fundamental, yet unexplored question: Can an LLM's functional correctness be assessed purely from its internal computational structure? Our primary objective is to investigate whether the model's neural dynamics encode internally decodable signals that are predictive of logical validity during code generation. Inspired by mechanistic interpretability, we propose to treat code verification as a mechanistic diagnostic task, mapping the model's explicit algorithmic trajectory into line-level attribution graphs. By decomposing complex residual flows, we aim to identify the structural signatures that distinguish sound reasoning from logical failure within the model's internal circuits. Analysis across Python, C++, and Java confirms that intrinsic correctness signals are robust across diverse syntaxes. Topological features from these internal graphs predict correctness more reliably than surface heuristics and enable targeted causal interventions to fix erroneous logic. These findings establish internal introspection as a decodable property for verifying generated code. Our code is at https:// github.com/bruno686/CodeCircuit.

The chain-of-though (CoT) prompting methods were successful in various natural language processing (NLP) tasks thanks to their ability to unveil the underlying complex reasoning processes. Such reasoning processes typically exhibit implicitly structured steps. Recent efforts also started investigating methods to encourage more explicitly structured reasoning procedures to be captured. In this work, we propose Tab-CoT, a novel tabular-format CoT prompting method, which allows the complex reasoning process to be explicitly modelled in a highly structured manner. Despite its simplicity, we show that our approach is capable of performing reasoning across multiple dimensions (i.e., both rows and columns). We demonstrate our approach's strong zero-shot and few-shot capabilities through extensive experiments on a range of reasoning tasks.

While large language models (LLMs) have demonstrated impressive capabilities in formal theorem proving, current benchmarks fail to adequately measure library-grounded abstraction -- the ability to reason with high-level interfaces and reusable structures central to modern mathematics and software engineering. We introduce LeanCat, a challenging benchmark comprising 100 fully formalized category-theory tasks in Lean. Unlike algebra or arithmetic, category theory serves as a rigorous stress test for structural, interface-level reasoning. Our evaluation reveals a severe abstraction gap: the best state-of-the-art model solves only 12.0% of tasks at pass@4, with performance collapsing from 55.0% on Easy tasks to 0.0% on High-difficulty tasks, highlighting a failure in compositional generalization. To overcome this, we evaluate LeanBridge, a retrieval-augmented agent that employs a retrieve-generate-verify loop. LeanBridge achieves a peak success rate of 24.0% -- doubling the performance of the best static baseline. These results empirically demonstrate that iterative refinement and dynamic library retrieval are not merely optimizations but strict necessities for neuro-symbolic reasoning in abstract domains. LeanCat offers a compact, reusable testbed for tracking progress toward reliable, research-level formalization.

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.

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

Understanding and reasoning over diagrams is a fundamental aspect of human intelligence. While Large Multimodal Models (LMMs) have demonstrated impressive capabilities across various tasks, existing benchmarks lack comprehensive evaluation of their diagram interpretation and reasoning abilities, particularly in coding contexts. We present HumanEval-V, a rigorous benchmark of human-annotated coding tasks that spans six task types and evaluates diverse visual reasoning capabilities. Each task features carefully crafted diagrams paired with function signatures and test cases, employing novel code generation tasks to thoroughly assess models' diagram comprehension. Through extensive experiments with 22 LMMs, we find that even top-performing models achieve modest success rates, with Claude 3.5 Sonnet reaching only 36.8% pass@1, highlighting substantial room for improvement. Our analysis reveals that current LMMs struggle with spatial transformations, topological relationships, and dynamic patterns that humans find intuitive. These findings provide valuable insights for advancing LMMs' visual reasoning abilities. We have open-sourced our code and benchmark at https://github.com/HumanEval-V/HumanEval-V-Benchmark.

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.

Topological deep learning has emerged for modeling higher-order relational structures beyond pairwise interactions that standard graph neural networks fail to capture. Although combinatorial complexes offer a unified topological framework, most existing topological deep learning methods rely on local message passing via attention mechanisms, which incur quadratic complexity and remain low-dimensional, limiting scalability and rank-aware information aggregation in higher-order complexes.We propose Combinatorial Complex Mamba (CCMamba), the first unified mamba-based neural framework for learning on combinatorial complexes. CCMamba reformulates message passing as a selective state-space modeling problem by organizing multi-rank incidence relations into structured sequences processed by rank-aware state-space models. This enables adaptive, directional, and long range information propagation in linear time without self attention. We further establish the theoretical analysis that the expressive power upper-bound of CCMamba message passing is the 1-Weisfeiler-Lehman test. Experiments on graph, hypergraph, and simplicial benchmarks demonstrate that CCMamba consistently outperforms existing methods while exhibiting improved scalability and robustness to depth.

Chain-of-Thought (CoT) prompting enhances the reasoning of large language models (LLMs) by decomposing problems into sequential steps, mimicking human logic and reducing errors. However, complex tasks with vast solution spaces and vague constraints often exceed the capacity of a single reasoning chain. Inspired by Minimal Free Resolution (MFR) in commutative algebra and algebraic geometry, we propose Syzygy of Thoughts (SoT)-a novel framework that extends CoT by introducing auxiliary, interrelated reasoning paths. SoT captures deeper logical dependencies, enabling more robust and structured problem-solving. MFR decomposes a module into a sequence of free modules with minimal rank, providing a structured analytical approach to complex systems. This method introduces the concepts of "Module", "Betti numbers","Freeness", "Mapping", "Exactness" and "Minimality", enabling the systematic decomposition of the original complex problem into logically complete minimal subproblems while preserving key problem features and reducing reasoning length. We tested SoT across diverse datasets (e.g., GSM8K, MATH) and models (e.g., GPT-4o-mini, Qwen2.5), achieving inference accuracy that matches or surpasses mainstream CoTs standards. Additionally, by aligning the sampling process with algebraic constraints, our approach enhances the scalability of inference time in LLMs, ensuring both transparent reasoning and high performance. Our code will be publicly available at https://github.com/dlMARiA/Syzygy-of-thoughts.

Existing benchmarks fail to capture a crucial aspect of intelligence: physical reasoning, the integrated ability to combine domain knowledge, symbolic reasoning, and understanding of real-world constraints. To address this gap, we introduce PhyX: the first large-scale benchmark designed to assess models capacity for physics-grounded reasoning in visual scenarios. PhyX includes 3K meticulously curated multimodal questions spanning 6 reasoning types across 25 sub-domains and 6 core physics domains: thermodynamics, electromagnetism, mechanics, modern physics, optics, and wave\&acoustics. In our comprehensive evaluation, even state-of-the-art models struggle significantly with physical reasoning. GPT-4o, Claude3.7-Sonnet, and GPT-o4-mini achieve only 32.5\%, 42.2\%, and 45.8\% accuracy respectively-performance gaps exceeding 29\% compared to human experts. Our analysis exposes critical limitations in current models: over-reliance on memorized disciplinary knowledge, excessive dependence on mathematical formulations, and surface-level visual pattern matching rather than genuine physical understanding. We provide in-depth analysis through fine-grained statistics, detailed case studies, and multiple evaluation paradigms to thoroughly examine physical reasoning capabilities. To ensure reproducibility, we implement a compatible evaluation protocol based on widely-used toolkits such as VLMEvalKit, enabling one-click evaluation.

While Large Reasoning Models (LRMs) generate extensive chain-of-thought reasoning, we lack a principled framework for understanding how these thoughts are structured. In this paper, we introduce a novel approach by applying Schoenfeld's Episode Theory, a classic cognitive framework for human mathematical problem-solving, to analyze the reasoning traces of LRMs. We annotated thousands of sentences and paragraphs from model-generated solutions to math problems using seven cognitive labels (e.g., Plan, Implement, Verify). The result is the first publicly available benchmark for the fine-grained analysis of machine reasoning, including a large annotated corpus and detailed annotation guidebooks. Our preliminary analysis reveals distinct patterns in LRM reasoning, such as the transition dynamics between cognitive states. This framework provides a theoretically grounded methodology for interpreting LRM cognition and enables future work on more controllable and transparent reasoning systems.

Large reasoning models (e.g., R1, o3) have demonstrated remarkable mathematical problem-solving abilities. However, the high reported accuracy of these advanced models on popular datasets, reliance on purely numerical evaluation and potential benchmark leakage, often masks their true reasoning shortcomings. To address this, we propose leveraging the inherent rigor and methodological complexity of mathematical proofs as a diagnostic tool to expose these hidden failures. Specifically, we introduce the RFMDataset (Reveal Failure Modes), a collection of 200 diverse mathematical proof problems, and thoroughly evaluate advanced models' performance on it. Our in-depth analysis of their failures uncovers 10 fine-grained error types, which shows fundamental limitations in current large reasoning models: 1) large reasoning models grapple profoundly with mathematical proofs, with some generating entirely correct proofs for less than 20% of problems and failing even on basic ones; 2) models exhibit a diverse spectrum of reasoning failures, prominently demonstrating the lack of guarantees for the correctness and rigor of single-step reasoning; and 3) models show hallucination and incompleteness during the reasoning process. Our findings reveal that models' self-reflection is insufficient to resolve the current logical dilemmas, necessitating formalized and fine-grained logical training.

We introduce a new generative model that combines latent diffusion with persistent homology to create 3D shapes with high diversity, with a special emphasis on their topological characteristics. Our method involves representing 3D shapes as implicit fields, then employing persistent homology to extract topological features, including Betti numbers and persistence diagrams. The shape generation process consists of two steps. Initially, we employ a transformer-based autoencoding module to embed the implicit representation of each 3D shape into a set of latent vectors. Subsequently, we navigate through the learned latent space via a diffusion model. By strategically incorporating topological features into the diffusion process, our generative module is able to produce a richer variety of 3D shapes with different topological structures. Furthermore, our framework is flexible, supporting generation tasks constrained by a variety of inputs, including sparse and partial point clouds, as well as sketches. By modifying the persistence diagrams, we can alter the topology of the shapes generated from these input modalities.

Large reasoning models (LRMs) have achieved remarkable progress on complex tasks by generating extended chains of thought (CoT). However, their uncontrolled output lengths pose significant challenges for real-world deployment, where inference-time budgets on tokens, latency, or compute are strictly constrained. We propose Elastic Reasoning, a novel framework for scalable chain of thoughts that explicitly separates reasoning into two phases--thinking and solution--with independently allocated budgets. At test time, Elastic Reasoning prioritize that completeness of solution segments, significantly improving reliability under tight resource constraints. To train models that are robust to truncated thinking, we introduce a lightweight budget-constrained rollout strategy, integrated into GRPO, which teaches the model to reason adaptively when the thinking process is cut short and generalizes effectively to unseen budget constraints without additional training. Empirical results on mathematical (AIME, MATH500) and programming (LiveCodeBench, Codeforces) benchmarks demonstrate that Elastic Reasoning performs robustly under strict budget constraints, while incurring significantly lower training cost than baseline methods. Remarkably, our approach also produces more concise and efficient reasoning even in unconstrained settings. Elastic Reasoning offers a principled and practical solution to the pressing challenge of controllable reasoning at scale.

Recent large language models have shown promising capabilities in long-form reasoning, following structured chains of thought before arriving at a final answer. However, we observe that these reasoning paths tend to include substantial redundancy; analyzing attention patterns reveals that attention scores are widely scattered, particularly incorrect answers exhibit greater attention sparsity. In this paper, we demonstrate that deliberately removing this redundancy in the reasoning process significantly improves performance through clear thinking, i.e., removing distraction. Specifically, we systematically identify reasoning redundancy by measuring token-level attention scores to a special end-of-thinking token, which is appended to an explicit instruction inserted to conclude each intermediate reasoning step. Furthermore, we propose structure-aware pruning that prioritizes removing tokens in low-contributing reasoning chunks over individual tokens. After evicting redundant tokens, we remove the injected end-of-thinking instruction, then resume the reasoning generation. We demonstrate that our method significantly improves overall accuracy across reasoning-intensive benchmarks without any training involved. In particular, our method shows strong performance on challenging mathematical competition benchmarks such as AIME and AMC, where reasoning redundancy is more prevalent.

Large vision language models exhibit notable limitations on Geometry Problem Solving (GPS) because of their unreliable diagram interpretation and pure natural-language reasoning. A recent line of work mitigates this by using symbolic solvers: the model directly generates a formal program that a geometry solver can execute. However, this direct program generation lacks intermediate reasoning, making the decision process opaque and prone to errors. In this work, we explore a new approach that integrates Chain-of-Thought (CoT) with formal language. The model interleaves natural language reasoning with incremental emission of solver-executable code, producing a hybrid reasoning trace in which critical derivations are expressed in formal language. To teach this behavior at scale, we combine (1) supervised fine-tuning on an 11K newly developed synthetic dataset with interleaved natural language reasoning and automatic formalization, and (2) solver-in-the-loop reinforcement learning that jointly optimizes both the CoT narrative and the resulting program through outcome-based rewards. Built on Qwen2.5-VL-7B, our new model, named GF-Reasoner, achieves up to 15% accuracy improvements on standard GPS benchmarks, surpassing both 7B-scale peers and the much larger model Qwen2.5-VL-72B. By exploiting high-order geometric knowledge and offloading symbolic computation to the solver, the generated reasoning traces are noticeably shorter and cleaner. Furthermore, we present a comprehensive analysis of method design choices (e.g., reasoning paradigms, data synthesis, training epochs, etc.), providing actionable insights for future research.

Latent Graph Inference (LGI) relaxed the reliance of Graph Neural Networks (GNNs) on a given graph topology by dynamically learning it. However, most of LGI methods assume to have a (noisy, incomplete, improvable, ...) input graph to rewire and can solely learn regular graph topologies. In the wake of the success of Topological Deep Learning (TDL), we study Latent Topology Inference (LTI) for learning higher-order cell complexes (with sparse and not regular topology) describing multi-way interactions between data points. To this aim, we introduce the Differentiable Cell Complex Module (DCM), a novel learnable function that computes cell probabilities in the complex to improve the downstream task. We show how to integrate DCM with cell complex message passing networks layers and train it in a end-to-end fashion, thanks to a two-step inference procedure that avoids an exhaustive search across all possible cells in the input, thus maintaining scalability. Our model is tested on several homophilic and heterophilic graph datasets and it is shown to outperform other state-of-the-art techniques, offering significant improvements especially in cases where an input graph is not provided.

Unlocking spatial reasoning in Large Multimodal Models (LMMs) is crucial for enabling intelligent interaction with 3D environments. While prior efforts often rely on explicit 3D inputs or specialized model architectures, we ask: can LMMs reason about 3D space using only structured 2D representations derived from perception? We introduce Struct2D, a perception-guided prompting framework that combines bird's-eye-view (BEV) images with object marks and object-centric metadata, optionally incorporating egocentric keyframes when needed. Using Struct2D, we conduct an in-depth zero-shot analysis of closed-source LMMs (e.g., GPT-o3) and find that they exhibit surprisingly strong spatial reasoning abilities when provided with structured 2D inputs, effectively handling tasks such as relative direction estimation and route planning. Building on these insights, we construct Struct2D-Set, a large-scale instruction tuning dataset with 200K fine-grained QA pairs across eight spatial reasoning categories, generated automatically from 3D indoor scenes. We fine-tune an open-source LMM (Qwen2.5VL) on Struct2D-Set, achieving competitive performance on multiple benchmarks, including 3D question answering, dense captioning, and object grounding. Our approach demonstrates that structured 2D inputs can effectively bridge perception and language reasoning in LMMs-without requiring explicit 3D representations as input. We will release both our code and dataset to support future research.

In this paper, we present a deep learning-based framework for solving geometric construction problems through visual reasoning, which is useful for automated geometry theorem proving. Constructible problems in geometry often ask for the sequence of straightedge-and-compass constructions to construct a given goal given some initial setup. Our EuclidNet framework leverages the neural network architecture Mask R-CNN to extract the visual features from the initial setup and goal configuration with extra points of intersection, and then generate possible construction steps as intermediary data models that are used as feedback in the training process for further refinement of the construction step sequence. This process is repeated recursively until either a solution is found, in which case we backtrack the path for a step-by-step construction guide, or the problem is identified as unsolvable. Our EuclidNet framework is validated on complex Japanese Sangaku geometry problems, demonstrating its capacity to leverage backtracking for deep visual reasoning of challenging problems.

Large Language Models (LLMs) show strong reasoning ability in open-domain question answering, yet their reasoning processes are typically linear and often logically inconsistent. In contrast, real-world reasoning requires integrating multiple premises and solving subproblems in parallel. Existing methods, such as Chain-of-Thought (CoT), express reasoning in a linear textual form, which may appear coherent but frequently leads to inconsistent conclusions. Recent approaches rely on externally provided graphs and do not explore how LLMs can construct and use their own graph-structured reasoning, particularly in open-domain QA. To fill this gap, we novelly explore graph-structured reasoning of LLMs in general-domain question answering. We propose Self-Graph Reasoning (SGR), a framework that enables LLMs to explicitly represent their reasoning process as a structured graph before producing the final answer. We further construct a graph-structured reasoning dataset that merges multiple candidate reasoning graphs into refined graph structures for model training. Experiments on five QA benchmarks across both general and specialized domains show that SGR consistently improves reasoning consistency and yields a 17.74% gain over the base model. The LLaMA-3.3-70B model fine-tuned with SGR performs comparably to GPT-4o and surpasses Claude-3.5-Haiku, demonstrating the effectiveness of graph-structured reasoning.

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.

Remarkable progress has been made on automated reasoning with natural text, by using Language Models (LMs) and methods such as Chain-of-Thought and Selection-Inference. These techniques search for proofs in the forward direction from axioms to the conclusion, which suffers from a combinatorial explosion of the search space, and thus high failure rates for problems requiring longer chains of reasoning. The classical automated reasoning literature has shown that reasoning in the backward direction (i.e. from the intended conclusion to supporting axioms) is significantly more efficient at proof-finding. Importing this intuition into the LM setting, we develop a Backward Chaining algorithm, called LAMBADA, that decomposes reasoning into four sub-modules. These sub-modules are simply implemented by few-shot prompted LM inference. We show that LAMBADA achieves sizable accuracy boosts over state-of-the-art forward reasoning methods on challenging logical reasoning datasets, particularly when deep and accurate proof chains are required.

The field of face recognition (FR) has undergone significant advancements with the rise of deep learning. Recently, the success of unsupervised learning and graph neural networks has demonstrated the effectiveness of data structure information. Considering that the FR task can leverage large-scale training data, which intrinsically contains significant structure information, we aim to investigate how to encode such critical structure information into the latent space. As revealed from our observations, directly aligning the structure information between the input and latent spaces inevitably suffers from an overfitting problem, leading to a structure collapse phenomenon in the latent space. To address this problem, we propose TopoFR, a novel FR model that leverages a topological structure alignment strategy called PTSA and a hard sample mining strategy named SDE. Concretely, PTSA uses persistent homology to align the topological structures of the input and latent spaces, effectively preserving the structure information and improving the generalization performance of FR model. To mitigate the impact of hard samples on the latent space structure, SDE accurately identifies hard samples by automatically computing structure damage score (SDS) for each sample, and directs the model to prioritize optimizing these samples. Experimental results on popular face benchmarks demonstrate the superiority of our TopoFR over the state-of-the-art methods. Code and models are available at: https://github.com/modelscope/facechain/tree/main/face_module/TopoFR.

Successful robotic grasping in cluttered environments not only requires a model to visually ground a target object but also to reason about obstructions that must be cleared beforehand. While current vision-language embodied reasoning models show emergent spatial understanding, they remain limited in terms of obstruction reasoning and accessibility planning. To bridge this gap, we present UNOGrasp, a learning-based vision-language model capable of performing visually-grounded obstruction reasoning to infer the sequence of actions needed to unobstruct the path and grasp the target object. We devise a novel multi-step reasoning process based on obstruction paths originated by the target object. We anchor each reasoning step with obstruction-aware visual cues to incentivize reasoning capability. UNOGrasp combines supervised and reinforcement finetuning through verifiable reasoning rewards. Moreover, we construct UNOBench, a large-scale dataset for both training and benchmarking, based on MetaGraspNetV2, with over 100k obstruction paths annotated by humans with obstruction ratios, contact points, and natural-language instructions. Extensive experiments and real-robot evaluations show that UNOGrasp significantly improves obstruction reasoning and grasp success across both synthetic and real-world environments, outperforming generalist and proprietary alternatives. Project website: https://tev-fbk.github.io/UnoGrasp/.

Recent advancements in Generative Reward Models (GRMs) have demonstrated that scaling the length of Chain-of-Thought (CoT) reasoning considerably enhances the reliability of evaluation. However, current works predominantly rely on unstructured length scaling, ignoring the divergent efficacy of different reasoning mechanisms: Breadth-CoT (B-CoT, i.e., multi-dimensional principle coverage) and Depth-CoT (D-CoT, i.e., substantive judgment soundness). To address this, we introduce Mix-GRM, a framework that reconfigures raw rationales into structured B-CoT and D-CoT through a modular synthesis pipeline, subsequently employing Supervised Fine-Tuning (SFT) and Reinforcement Learning with Verifiable Rewards (RLVR) to internalize and optimize these mechanisms. Comprehensive experiments demonstrate that Mix-GRM establishes a new state-of-the-art across five benchmarks, surpassing leading open-source RMs by an average of 8.2\%. Our results reveal a clear divergence in reasoning: B-CoT benefits subjective preference tasks, whereas D-CoT excels in objective correctness tasks. Consequently, misaligning the reasoning mechanism with the task directly degrades performance. Furthermore, we demonstrate that RLVR acts as a switching amplifier, inducing an emergent polarization where the model spontaneously allocates its reasoning style to match task demands. The synthesized data and models are released at https://huggingface.co/collections/DonJoey/mix-grm{Hugging Face}, and the code is released at https://github.com/Don-Joey/Mix-GRM{Github}.

In this article, we introduce a new parameterized family of topological invariants, taking the form of candidate decompositions, for multi-parameter persistence modules. We prove that our candidate decompositions are controllable approximations: when restricting to modules that can be decomposed into interval summands, we establish theoretical results about the approximation error between our candidate decompositions and the true underlying module in terms of the standard interleaving and bottleneck distances. Moreover, even when the underlying module does not admit such a decomposition, our candidate decompositions are nonetheless stable invariants; small perturbations in the underlying module lead to small perturbations in the candidate decomposition. Then, we introduce MMA (Multipersistence Module Approximation): an algorithm for computing stable instances of such invariants, which is based on fibered barcodes and exact matchings, two constructions that stem from the theory of single-parameter persistence. By design, MMA can handle an arbitrary number of filtrations, and has bounded complexity and running time. Finally, we present empirical evidence validating the generalization capabilities and running time speed-ups of MMA on several data sets.

Existing research on 3D Large Language Models (LLMs) still struggles to achieve grounded question-answering, primarily due to the under-exploration of the mechanism of human-like scene-object grounded reasoning. This paper bridges the gap by presenting a novel framework. We first introduce a grounded Chain-of-Thought reasoning method in 3D scenes (SCENECOT), decoupling a complex reasoning task into simpler and manageable problems, and building corresponding visual clues based on multimodal expert modules. To enable such a method, we develop SCENECOT-185K, the first large-scale grounded CoT reasoning dataset, consisting of 185K high-quality instances. Extensive experiments across various complex 3D scene reasoning benchmarks demonstrate that our new framework achieves strong performance with high grounding-QA coherence. To the best of our knowledge, this is the first successful application of CoT reasoning to 3D scene understanding, enabling step-by-step human-like reasoning and showing potential for extension to broader 3D scene understanding scenarios.

Deductive reasoning is the process of deriving conclusions strictly from the given premises, without relying on external knowledge. We define honesty in this setting as a model's ability to respond only when the conclusion is logically entailed by the premises, and to abstain otherwise. However, current language models often fail to reason honestly, producing unwarranted answers when the input is insufficient. To study this challenge, we formulate honest deductive reasoning as multi-step tasks where models must either derive the correct conclusion or abstain. We curate two datasets from graph structures, one for linear algebra and one for logical inference, and introduce unanswerable cases by randomly perturbing an edge in half of the instances. We find that prompting and existing training methods, including GRPO with or without supervised fine-tuning initialization, struggle on these tasks. In particular, GRPO optimize only for final task outcomes, leaving models vulnerable to collapse when negative rewards dominate early training. To address this, we propose ACNCHOR, a reinforcement learning method that injects ground truth trajectories into rollouts, preventing early training collapse. Our results demonstrate that this method stabilizes learning and significantly improves the overall reasoning performance, underscoring the importance of training dynamics for enabling honest deductive reasoning in language models.

In this paper, we study the content-aware layout generation problem, which aims to automatically generate layouts that are harmonious with a given background image. Existing methods usually deal with this task with a single-step reasoning framework. The lack of a feedback-based self-correction mechanism leads to their failure rates significantly increasing when faced with complex element layout planning. To address this challenge, we introduce SEGA, a novel Stepwise Evolution Paradigm for Content-Aware Layout Generation. Inspired by the systematic mode of human thinking, SEGA employs a hierarchical reasoning framework with a coarse-to-fine strategy: first, a coarse-level module roughly estimates the layout planning results; then, another refining module performs fine-level reasoning regarding the coarse planning results. Furthermore, we incorporate layout design principles as prior knowledge into the model to enhance its layout planning ability. Besides, we present GenPoster-100K that is a new large-scale poster dataset with rich meta-information annotation. The experiments demonstrate the effectiveness of our approach by achieving the state-of-the-art results on multiple benchmark datasets. Our project page is at: https://brucew91.github.io/SEGA.github.io/

A deep understanding of kinematic structures and movable components is essential for enabling robots to manipulate objects and model their own articulated forms. Such understanding is captured through articulated objects, which are essential for tasks such as physical simulation, motion planning, and policy learning. However, creating these models, particularly for objects with high degrees of freedom (DoF), remains a significant challenge. Existing methods typically rely on motion sequences or strong assumptions from hand-curated datasets, which hinders scalability. In this paper, we introduce Kinematify, an automated framework that synthesizes articulated objects directly from arbitrary RGB images or textual descriptions. Our method addresses two core challenges: (i) inferring kinematic topologies for high-DoF objects and (ii) estimating joint parameters from static geometry. To achieve this, we combine MCTS search for structural inference with geometry-driven optimization for joint reasoning, producing physically consistent and functionally valid descriptions. We evaluate Kinematify on diverse inputs from both synthetic and real-world environments, demonstrating improvements in registration and kinematic topology accuracy over prior work.

While Large Language Models (LLMs) achieve expert-level performance on standard medical benchmarks through single-hop factual recall, they severely struggle with the complex, multi-hop diagnostic reasoning required in real-world clinical settings. A primary obstacle is "shortcut learning", where models exploit highly connected, generic hub nodes (e.g., "inflammation") in knowledge graphs to bypass authentic micro-pathological cascades. To address this, we introduce ShatterMed-QA, a bilingual benchmark of 10,558 multi-hop clinical questions designed to rigorously evaluate deep diagnostic reasoning. Our framework constructs a topology-regularized medical Knowledge Graph using a novel k-Shattering algorithm, which physically prunes generic hubs to explicitly sever logical shortcuts. We synthesize the evaluation vignettes by applying implicit bridge entity masking and topology-driven hard negative sampling, forcing models to navigate biologically plausible distractors without relying on superficial elimination. Comprehensive evaluations of 21 LLMs reveal massive performance degradation on our multi-hop tasks, particularly among domain-specific models. Crucially, restoring the masked evidence via Retrieval-Augmented Generation (RAG) triggers near-universal performance recovery, validating ShatterMed-QA's structural fidelity and proving its efficacy in diagnosing the fundamental reasoning deficits of current medical AI. Explore the dataset, interactive examples, and full leaderboards at our project website: https://shattermed-qa-web.vercel.app/

We propose SAM-Road, an adaptation of the Segment Anything Model (SAM) for extracting large-scale, vectorized road network graphs from satellite imagery. To predict graph geometry, we formulate it as a dense semantic segmentation task, leveraging the inherent strengths of SAM. The image encoder of SAM is fine-tuned to produce probability masks for roads and intersections, from which the graph vertices are extracted via simple non-maximum suppression. To predict graph topology, we designed a lightweight transformer-based graph neural network, which leverages the SAM image embeddings to estimate the edge existence probabilities between vertices. Our approach directly predicts the graph vertices and edges for large regions without expensive and complex post-processing heuristics, and is capable of building complete road network graphs spanning multiple square kilometers in a matter of seconds. With its simple, straightforward, and minimalist design, SAM-Road achieves comparable accuracy with the state-of-the-art method RNGDet++, while being 40 times faster on the City-scale dataset. We thus demonstrate the power of a foundational vision model when applied to a graph learning task. The code is available at https://github.com/htcr/sam_road.

Large language models (LLMs) have demonstrated remarkable success across a wide range of tasks; however, they still encounter challenges in reasoning tasks that require understanding and inferring relationships between distinct pieces of information within text sequences. This challenge is particularly pronounced in tasks involving multi-step processes, such as logical reasoning and multi-hop question answering, where understanding implicit relationships between entities and leveraging multi-hop connections in the given context are crucial. Graphs, as fundamental data structures, explicitly represent pairwise relationships between entities, thereby offering the potential to enhance LLMs' reasoning capabilities. External graphs have proven effective in supporting LLMs across multiple tasks. However, in many reasoning tasks, no pre-existing graph structure is provided. Can we structure implicit knowledge derived from context into graphs to assist LLMs in reasoning? In this paper, we propose Reasoning with Graphs (RwG) by first constructing explicit graphs from the context and then leveraging these graphs to enhance LLM reasoning performance on reasoning tasks. Extensive experiments demonstrate the effectiveness of the proposed method in improving both logical reasoning and multi-hop question answering tasks.

Geometry problem solving (GPS) represents a critical frontier in artificial intelligence, with profound applications in education, computer-aided design, and computational graphics. Despite its significance, automating GPS remains challenging due to the dual demands of spatial understanding and rigorous logical reasoning. Recent advances in large models have enabled notable breakthroughs, particularly for SAT-level problems, yet the field remains fragmented across methodologies, benchmarks, and evaluation frameworks. This survey systematically synthesizes GPS advancements through three core dimensions: (1) benchmark construction, (2) textual and diagrammatic parsing, and (3) reasoning paradigms. We further propose a unified analytical paradigm, assess current limitations, and identify emerging opportunities to guide future research toward human-level geometric reasoning, including automated benchmark generation and interpretable neuro-symbolic integration.

LLM-based formal proof assistants (e.g., in Lean) hold great promise for automating mathematical discovery. But beyond syntactic correctness, do these systems truly understand mathematical structure as humans do? We investigate this question through the lens of mathematical inequalities -- a fundamental tool across many domains. While modern provers can solve basic inequalities, we probe their ability to handle human-intuitive compositionality. We introduce Ineq-Comp, a benchmark built from elementary inequalities through systematic transformations, including variable duplication, algebraic rewriting, and multi-step composition. Although these problems remain easy for humans, we find that most provers -- including Goedel, STP, and Kimina-7B -- struggle significantly. DeepSeek-Prover-V2-7B shows relative robustness -- possibly because it is trained to decompose the problems into sub-problems -- but still suffers a 20\% performance drop (pass@32). Strikingly, performance remains poor for all models even when formal proofs of the constituent parts are provided in context, revealing that the source of weakness is indeed in compositional reasoning. Our results expose a persisting gap between the generalization behavior of current AI provers and human mathematical intuition.

Reasoning Large Language Models (RLLMs) have recently achieved remarkable progress on complex reasoning tasks, largely enabled by their long chain-of-thought (Long CoT) capabilities. However, developing these Long CoT behaviors relies heavily on post-training with high-quality datasets, which are typically costly and human-curated (e.g., mathematics and code), leaving scalable alternatives unexplored. In this work, we introduce NP-hard (NPH) graph problems as a novel synthetic training corpus, as they inherently require deep reasoning, extensive exploration, and reflective strategies, which are core characteristics of Long CoT reasoning. Building on this insight, we develop a two-stage post-training framework: (i) Long CoT Supervised Fine-Tuning (SFT) on rejection-sampled NPH graph instances, which substantially enhances reasoning depth, and (ii) Reinforcement Learning (RL) with a fine-grained reward design, which sharpens reasoning efficiency. Our flagship model, Graph-R1-7B, demonstrates strong generalization across mathematics, coding, STEM, and logic, and surpasses QwQ-32B on NPH graph problems in both accuracy and reasoning efficiency. These results position NPH graph problems as an effective and scalable resource for advancing Long CoT reasoning in LLMs, opening a new frontier for LLM post-training. Our implementation is available at https://github.com/Graph-Reasoner/Graph-R1, with models and datasets hosted in our Hugging Face collection HKUST-DSAIL/Graph-R1.

Scientific reasoning relies not only on logical inference but also on activating prior knowledge and experiential structures. Memory can efficiently reuse knowledge and enhance reasoning consistency and stability. However, existing benchmarks mainly evaluate final answers or step-by-step coherence, overlooking the memory-driven mechanisms that underlie human reasoning, which involves activating anchors and attractors, then integrating them into multi-step inference. To address this gap, we propose A^3-Bench~ https://a3-bench.github.io, a benchmark designed to evaluate scientific reasoning through dual-scale memory-driven activation, grounded in Anchor and Attractor Activation. First, we annotate 2,198 science reasoning problems across domains using the SAPM process(subject, anchor & attractor, problem, and memory developing). Second, we introduce a dual-scale memory evaluation framework utilizing anchors and attractors, along with the AAUI(Anchor--Attractor Utilization Index) metric to measure memory activation rates. Finally, through experiments with various base models and paradigms, we validate A^3-Bench and analyze how memory activation impacts reasoning performance, providing insights into memory-driven scientific reasoning.

In "Backprop as functor", the authors show that the fundamental elements of deep learning -- gradient descent and backpropagation -- can be conceptualized as a strong monoidal functor Para(Euc)toLearn from the category of parameterized Euclidean spaces to that of learners, a category developed explicitly to capture parameter update and backpropagation. It was soon realized that there is an isomorphism LearncongPara(Slens), where Slens is the symmetric monoidal category of simple lenses as used in functional programming. In this note, we observe that Slens is a full subcategory of Poly, the category of polynomial functors in one variable, via the functor Amapsto Ay^A. Using the fact that (Poly,otimes) is monoidal closed, we show that a map Ato B in Para(Slens) has a natural interpretation in terms of dynamical systems (more precisely, generalized Moore machines) whose interface is the internal-hom type [Ay^A,By^B]. Finally, we review the fact that the category p-Coalg of dynamical systems on any p in Poly forms a topos, and consider the logical propositions that can be stated in its internal language. We give gradient descent as an example, and we conclude by discussing some directions for future work.