Daily Papers

Prior work uses linear probes on benchmark prompts as evidence of evaluation awareness in large language models. Because evaluation context is typically entangled with benchmark format and genre, it is unclear whether probe-based signals reflect context or surface structure. We test whether these signals persist under partial control of prompt format using a controlled 2x2 dataset and diagnostic rewrites. We find that probes primarily track benchmark-canonical structure and fail to generalize to free-form prompts independent of linguistic style. Thus, standard probe-based methodologies do not reliably disentangle evaluation context from structural artifacts, limiting the evidential strength of existing results.

Sentences that present a complex syntax act as a major stumbling block for downstream Natural Language Processing applications whose predictive quality deteriorates with sentence length and complexity. The task of Text Simplification (TS) may remedy this situation. It aims to modify sentences in order to make them easier to process, using a set of rewriting operations, such as reordering, deletion, or splitting. State-of-the-art syntactic TS approaches suffer from two major drawbacks: first, they follow a very conservative approach in that they tend to retain the input rather than transforming it, and second, they ignore the cohesive nature of texts, where context spread across clauses or sentences is needed to infer the true meaning of a statement. To address these problems, we present a discourse-aware TS approach that splits and rephrases complex English sentences within the semantic context in which they occur. Based on a linguistically grounded transformation stage that uses clausal and phrasal disembedding mechanisms, complex sentences are transformed into shorter utterances with a simple canonical structure that can be easily analyzed by downstream applications. With sentence splitting, we thus address a TS task that has hardly been explored so far. Moreover, we introduce the notion of minimality in this context, as we aim to decompose source sentences into a set of self-contained minimal semantic units. To avoid breaking down the input into a disjointed sequence of statements that is difficult to interpret because important contextual information is missing, we incorporate the semantic context between the split propositions in the form of hierarchical structures and semantic relationships. In that way, we generate a semantic hierarchy of minimal propositions that leads to a novel representation of complex assertions that puts a semantic layer on top of the simplified sentences.

This work presents a systematic investigation into modernizing Vision Transformer backbones by leveraging architectural advancements from the past five years. While preserving the canonical Attention-FFN structure, we conduct a component-wise refinement involving normalization, activation functions, positional encoding, gating mechanisms, and learnable tokens. These updates form a new generation of Vision Transformers, which we call ViT-5. Extensive experiments demonstrate that ViT-5 consistently outperforms state-of-the-art plain Vision Transformers across both understanding and generation benchmarks. On ImageNet-1k classification, ViT-5-Base reaches 84.2\% top-1 accuracy under comparable compute, exceeding DeiT-III-Base at 83.8\%. ViT-5 also serves as a stronger backbone for generative modeling: when plugged into an SiT diffusion framework, it achieves 1.84 FID versus 2.06 with a vanilla ViT backbone. Beyond headline metrics, ViT-5 exhibits improved representation learning and favorable spatial reasoning behavior, and transfers reliably across tasks. With a design aligned with contemporary foundation-model practices, ViT-5 offers a simple drop-in upgrade over vanilla ViT for mid-2020s vision backbones.

Character video synthesis aims to produce realistic videos of animatable characters within lifelike scenes. As a fundamental problem in the computer vision and graphics community, 3D works typically require multi-view captures for per-case training, which severely limits their applicability of modeling arbitrary characters in a short time. Recent 2D methods break this limitation via pre-trained diffusion models, but they struggle for pose generality and scene interaction. To this end, we propose MIMO, a novel framework which can not only synthesize character videos with controllable attributes (i.e., character, motion and scene) provided by simple user inputs, but also simultaneously achieve advanced scalability to arbitrary characters, generality to novel 3D motions, and applicability to interactive real-world scenes in a unified framework. The core idea is to encode the 2D video to compact spatial codes, considering the inherent 3D nature of video occurrence. Concretely, we lift the 2D frame pixels into 3D using monocular depth estimators, and decompose the video clip to three spatial components (i.e., main human, underlying scene, and floating occlusion) in hierarchical layers based on the 3D depth. These components are further encoded to canonical identity code, structured motion code and full scene code, which are utilized as control signals of synthesis process. The design of spatial decomposed modeling enables flexible user control, complex motion expression, as well as 3D-aware synthesis for scene interactions. Experimental results demonstrate effectiveness and robustness of the proposed method.

The complementarity-determining regions of antibodies are loop structures that are key to their interactions with antigens, and of high importance to the design of novel biologics. Since the 1980s, categorizing the diversity of CDR structures into canonical clusters has enabled the identification of key structural motifs of antibodies. However, existing approaches have limited coverage and cannot be readily incorporated into protein foundation models. Here we introduce ImmunoGlobulin LOOp Tokenizer, Igloo, a multimodal antibody loop tokenizer that encodes backbone dihedral angles and sequence. Igloo is trained using a contrastive learning objective to map loops with similar backbone dihedral angles closer together in latent space. Igloo can efficiently retrieve the closest matching loop structures from a structural antibody database, outperforming existing methods on identifying similar H3 loops by 5.9\%. Igloo assigns tokens to all loops, addressing the limited coverage issue of canonical clusters, while retaining the ability to recover canonical loop conformations. To demonstrate the versatility of Igloo tokens, we show that they can be incorporated into protein language models with IglooLM and IglooALM. On predicting binding affinity of heavy chain variants, IglooLM outperforms the base protein language model on 8 out of 10 antibody-antigen targets. Additionally, it is on par with existing state-of-the-art sequence-based and multimodal protein language models, performing comparably to models with 7times more parameters. IglooALM samples antibody loops which are diverse in sequence and more consistent in structure than state-of-the-art antibody inverse folding models. Igloo demonstrates the benefit of introducing multimodal tokens for antibody loops for encoding the diverse landscape of antibody loops, improving protein foundation models, and for antibody CDR design.

Evolution-based protein structure prediction models have achieved breakthrough success in recent years. However, they struggle to generalize beyond evolutionary priors and on sequences lacking rich homologous data. Here we present a novel, out-of-domain benchmark based on sactipeptides, a rare class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by sulfur-to-alpha-carbon thioether bridges creating cross-links between cysteine residues and backbone. We evaluate recent models on predicting conformations compatible with these cross-links bridges for the 10 known sactipeptides with elucidated post-translational modifications. Crucially, the structures of 5 of them have not yet been experimentally resolved. This makes the task a challenging problem for evolution-based models, which we find exhibit limited performance (0.0% to 19.2% GDT-TS on sulfur-to-alpha-carbon distance). Our results point at the need for physics-informed models to sustain progress in biomolecular structure prediction.

We characterise the dynamics of neuronal activity, in terms of field theory, using neural units placed on a 2D-lattice modelling the cortical surface. The electrical activity of neuronal units was analysed with the aim of deriving a neural field model with a simple functional form that still able to predict or reproduce empirical findings. Each neural unit was modelled using a neural mass and the accompanying field theory was derived in the continuum limit. The field theory comprised coupled (real) Klein-Gordon fields, where predictions of the model fall within the range of experimental findings. These predictions included the frequency spectrum of electric activity measured from the cortex, which was derived using an equipartition of energy over eigenfunctions of the neural fields. Moreover, the neural field model was invariant, within a set of parameters, to the dynamical system used to model each neuronal mass. Specifically, topologically equivalent dynamical systems resulted in the same neural field model when connected in a lattice; indicating that the fields derived could be read as a canonical cortical field theory. We specifically investigated non-dispersive fields that provide a structure for the coding (or representation) of afferent information. Further elaboration of the ensuing neural field theory, including the effect of dispersive forces, could be of importance in the understanding of the cortical processing of information.

Personalized vaccines and T-cell immunotherapies depend critically on identifying peptide-MHC class I (pMHC-I) interactions capable of eliciting potent immune responses. However, current benchmarks and models inherit biases present in mass-spectrometry and binding-assay datasets, limiting discovery of novel peptide ligands. To address this issue, we introduce a structure-guided benchmark of pMHC-I peptides designed using diffusion models conditioned on crystal structure interaction distances. Spanning twenty high-priority HLA alleles, this benchmark is independent of previously characterized peptides yet reproduces canonical anchor residue preferences, indicating structural generalization without experimental dataset bias. Using this resource, we demonstrate that state-of-the-art sequence-based predictors perform poorly at recognizing the binding potential of these structurally stable designs, indicating allele-specific limitations invisible in conventional evaluations. Our geometry-aware design pipeline yields peptides with high predicted structural integrity and higher residue diversity than existing datasets, representing a key resource for unbiased model training and evaluation. Our code, and data are available at: https://github.com/sermare/struct-mhc-dev.

Recent advances in vision-language models (VLMs) have demonstrated remarkable zero-shot capabilities, yet adapting these models to specialized domains remains a significant challenge. Building on recent theoretical insights suggesting that independently trained VLMs are related by a canonical transformation, we extend this understanding to the concept of domains. We hypothesize that image features across disparate domains are related by a canonicalized geometric transformation that can be recovered using a small set of anchors. Few-shot classification provides a natural setting for this alignment, as the limited labeled samples serve as the anchors required to estimate this transformation. Motivated by this hypothesis, we introduce BiCLIP, a framework that applies a targeted transformation to multimodal features to enhance cross-modal alignment. Our approach is characterized by its extreme simplicity and low parameter footprint. Extensive evaluations across 11 standard benchmarks, including EuroSAT, DTD, and FGVCAircraft, demonstrate that BiCLIP consistently achieves state-of-the-art results. Furthermore, we provide empirical verification of existing geometric findings by analyzing the orthogonality and angular distribution of the learned transformations, confirming that structured alignment is the key to robust domain adaptation. Code is available at https://github.com/QuantitativeImagingLaboratory/BilinearCLIP

Visual explanations are often plausible but not structurally faithful. We introduce CAMBench-QR, a structure-aware benchmark that leverages the canonical geometry of QR codes (finder patterns, timing lines, module grid) to test whether CAM methods place saliency on requisite substructures while avoiding background. CAMBench-QR synthesizes QR/non-QR data with exact masks and controlled distortions, and reports structure-aware metrics (Finder/Timing Mass Ratios, Background Leakage, coverage AUCs, Distance-to-Structure) alongside causal occlusion, insertion/deletion faithfulness, robustness, and latency. We benchmark representative, efficient CAMs (LayerCAM, EigenGrad-CAM, XGrad-CAM) under two practical regimes of zero-shot and last-block fine-tuning. The benchmark, metrics, and training recipes provide a simple, reproducible yardstick for structure-aware evaluation of visual explanations. Hence we propose that CAMBENCH-QR can be used as a litmus test of whether visual explanations are truly structure-aware.

Over the last decades, progress in modal analysis has enabled increasingly routine use of modal parameters, including those extracted from in-situ measurements, for applications such as structural health monitoring and finite element model updating. For output-only identification, or Operational Modal Analysis (OMA), widely adopted approaches include Stochastic Subspace Identification (SSI) methods and the Natural Excitation Technique combined with the Eigensystem Realization Algorithm (NExT-ERA). Nevertheless, SSI-based techniques may become cumbersome on large systems, while NExT-ERA fitting can struggle when measurements are contaminated by noise. To alleviate these, this work investigates an OMA frequency-domain formulation for aeronautical structures by coupling the Loewner Framework (LF) with NExT, yielding the proposed NExT-LF method. The method exploits the computational efficiency of LF together with the impulse response function retrieval enabled by NExT. NExT-LF is assessed on two experimental benchmarks: the eXperimental BeaRDS 2 high-aspect-ratio wing main spar and an Airbus Helicopters H135 bearingless main rotor blade. The identified modal parameters are compared against available experimental references and results obtained via SSI with Canonical Variate Analysis and NExT-ERA. The results show that the modes identified by NExT-LF correlate well with benchmark data, particularly for high-amplitude tests and in the low-frequency range.

In this article, we present a structured Kalman filter associated with the transformation matrix for observable Kalman canonical decomposition from conventional Kalman filter (CKF) in order to generate a more accurate time scale. The conventional Kalman filter is a special case of the proposed structured Kalman filter which yields the same predicted unobservable or observable states when some conditions are satisfied. We consider an optimization problem respective to the transformation matrix where the objective function is associated with not only the expected value of prediction error but also its variance. We reveal that such an objective function is a convex function and show some conditions under which CKF is nothing but the optimal algorithm if ideal computation is possible without computation error. A numerical example is presented to show the robustness of the proposed method in terms of the initial error covariance

Deep generative models have shown promise for modeling metal-organic frameworks (MOFs), but existing approaches (1) rely on coarse-grained representations that assume fixed bond lengths and angles, and (2) neglect the MOF-adsorbate interactions, which are critical for downstream applications. We introduce AtomMOF, a scalable flow-based model built on an all-atom Diffusion Transformer that maps 2D molecular graphs of building blocks and adsorbates directly to equilibrium 3D structures without imposing structural constraints. We further present scaling laws for porous crystal generation, indicating predictable performance gains with increased model capacity, and introduce Feynman-Kac steering guided by machine-learned interatomic potentials to improve geometric validity and sampling stability. On the (MOF-only) BW dataset, AtomMOF increases the match rate by 35.00% and reduces RMSD by 32.64%. On the ODAC25 dataset (MOF-adsorbate), AtomMOF is substantially more sample-efficient than grand canonical Monte Carlo in recovering adsorption configurations and can identify candidates with lower adsorption energies than the reference dataset. Code is available at https://github.com/nayoung10/AtomMOF.

The 2017 paper ''Attention Is All You Need'' introduced the Transformer architecture-and inadvertently spawned one of machine learning's most persistent naming conventions. We analyze 717 arXiv preprints containing ''All You Need'' in their titles (2009-2025), finding exponential growth (R^2 > 0.994) following the original paper, with 200 titles in 2025 alone. Among papers following the canonical ''X [Is] All You Need'' structure, ''Attention'' remains the most frequently claimed necessity (28 occurrences). Situating this phenomenon within memetic theory, we argue the pattern's success reflects competitive pressures in scientific communication that increasingly favor memorability over precision. Whether this trend represents harmless academic whimsy or symptomatic sensationalism, we leave-with appropriate self-awareness-to the reader.

We present a novel framework for dynamic 3D scene reconstruction that integrates three key components: an explicit tri-plane deformation field, a view-conditioned canonical radiance field with spherical harmonics (SH) attention, and a temporally-aware latent diffusion prior. Our method encodes 4D scenes using three orthogonal 2D feature planes that evolve over time, enabling efficient and compact spatiotemporal representation. These features are explicitly warped into a canonical space via a deformation offset field, eliminating the need for MLP-based motion modeling. In canonical space, we replace traditional MLP decoders with a structured SH-based rendering head that synthesizes view-dependent color via attention over learned frequency bands improving both interpretability and rendering efficiency. To further enhance fidelity and temporal consistency, we introduce a transformer-guided latent diffusion module that refines the tri-plane and deformation features in a compressed latent space. This generative module denoises scene representations under ambiguous or out-of-distribution (OOD) motion, improving generalization. Our model is trained in two stages: the diffusion module is first pre-trained independently, and then fine-tuned jointly with the full pipeline using a combination of image reconstruction, diffusion denoising, and temporal consistency losses. We demonstrate state-of-the-art results on synthetic benchmarks, surpassing recent methods such as HexPlane and 4D Gaussian Splatting in visual quality, temporal coherence, and robustness to sparse-view dynamic inputs.

Neural networks can accurately forecast complex dynamical systems, yet how they internally represent underlying latent geometry remains poorly understood. We study neural forecasters through the lens of representational alignment, introducing anchor-based, geometry-agnostic relative embeddings that remove rotational and scaling ambiguities in latent spaces. Applying this framework across seven canonical dynamical systems - ranging from periodic to chaotic - we reveal reproducible family-level structure: multilayer perceptrons align with other MLPs, recurrent networks with RNNs, while transformers and echo-state networks achieve strong forecasts despite weaker alignment. Alignment generally correlates with forecasting accuracy, yet high accuracy can coexist with low alignment. Relative geometry thus provides a simple, reproducible foundation for comparing how model families internalize and represent dynamical structure.

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

We present the first comprehensive study on automatic knowledge base construction for two prevalent commonsense knowledge graphs: ATOMIC (Sap et al., 2019) and ConceptNet (Speer et al., 2017). Contrary to many conventional KBs that store knowledge with canonical templates, commonsense KBs only store loosely structured open-text descriptions of knowledge. We posit that an important step toward automatic commonsense completion is the development of generative models of commonsense knowledge, and propose COMmonsEnse Transformers (COMET) that learn to generate rich and diverse commonsense descriptions in natural language. Despite the challenges of commonsense modeling, our investigation reveals promising results when implicit knowledge from deep pre-trained language models is transferred to generate explicit knowledge in commonsense knowledge graphs. Empirical results demonstrate that COMET is able to generate novel knowledge that humans rate as high quality, with up to 77.5% (ATOMIC) and 91.7% (ConceptNet) precision at top 1, which approaches human performance for these resources. Our findings suggest that using generative commonsense models for automatic commonsense KB completion could soon be a plausible alternative to extractive methods.

Creating controllable, photorealistic, and geometrically detailed digital doubles of real humans solely from video data is a key challenge in Computer Graphics and Vision, especially when real-time performance is required. Recent methods attach a neural radiance field (NeRF) to an articulated structure, e.g., a body model or a skeleton, to map points into a pose canonical space while conditioning the NeRF on the skeletal pose. These approaches typically parameterize the neural field with a multi-layer perceptron (MLP) leading to a slow runtime. To address this drawback, we propose TriHuman a novel human-tailored, deformable, and efficient tri-plane representation, which achieves real-time performance, state-of-the-art pose-controllable geometry synthesis as well as photorealistic rendering quality. At the core, we non-rigidly warp global ray samples into our undeformed tri-plane texture space, which effectively addresses the problem of global points being mapped to the same tri-plane locations. We then show how such a tri-plane feature representation can be conditioned on the skeletal motion to account for dynamic appearance and geometry changes. Our results demonstrate a clear step towards higher quality in terms of geometry and appearance modeling of humans as well as runtime performance.

The development of general robotic systems capable of manipulating in unstructured environments is a significant challenge. While Vision-Language Models(VLM) excel in high-level commonsense reasoning, they lack the fine-grained 3D spatial understanding required for precise manipulation tasks. Fine-tuning VLM on robotic datasets to create Vision-Language-Action Models(VLA) is a potential solution, but it is hindered by high data collection costs and generalization issues. To address these challenges, we propose a novel object-centric representation that bridges the gap between VLM's high-level reasoning and the low-level precision required for manipulation. Our key insight is that an object's canonical space, defined by its functional affordances, provides a structured and semantically meaningful way to describe interaction primitives, such as points and directions. These primitives act as a bridge, translating VLM's commonsense reasoning into actionable 3D spatial constraints. In this context, we introduce a dual closed-loop, open-vocabulary robotic manipulation system: one loop for high-level planning through primitive resampling, interaction rendering and VLM checking, and another for low-level execution via 6D pose tracking. This design ensures robust, real-time control without requiring VLM fine-tuning. Extensive experiments demonstrate strong zero-shot generalization across diverse robotic manipulation tasks, highlighting the potential of this approach for automating large-scale simulation data generation.

We study continual skill acquisition in open-ended embodied environments where an agent must construct, refine, and reuse an expanding library of executable skills. We introduce the Programmatic Skill Network (PSN), a framework in which skills are executable symbolic programs forming a compositional network that evolves through experience. PSN defines three core mechanisms instantiated via large language models: (1)REFLECT for structured fault localization over skill compositions, (2) progressive optimization with maturity-aware update gating that stabilizes reliable skills while maintaining plasticity for uncertain ones, and (3) canonical structural refactoring under rollback validation that maintains network compactness. We further show that PSN's learning dynamics exhibit structural parallels to neural network training. Experiments on MineDojo and Crafter demonstrate robust skill reuse, rapid adaptation, and strong generalization across open-ended task distributions.\footnote{We plan to open-source the code.

Sparse-view 3D modeling represents a fundamental tension between reconstruction fidelity and generative plausibility. While feed-forward reconstruction excels in efficiency and input alignment, it often lacks the global priors needed for structural completeness. Conversely, diffusion-based generation provides rich geometric details but struggles with multi-view consistency. We present UniRecGen, a unified framework that integrates these two paradigms into a single cooperative system. To overcome inherent conflicts in coordinate spaces, 3D representations, and training objectives, we align both models within a shared canonical space. We employ disentangled cooperative learning, which maintains stable training while enabling seamless collaboration during inference. Specifically, the reconstruction module is adapted to provide canonical geometric anchors, while the diffusion generator leverages latent-augmented conditioning to refine and complete the geometric structure. Experimental results demonstrate that UniRecGen achieves superior fidelity and robustness, outperforming existing methods in creating complete and consistent 3D models from sparse observations.

In many domains of argumentation, people's arguments are driven by so-called attitude roots, i.e., underlying beliefs and world views, and their corresponding attitude themes. Given the strength of these latent drivers of arguments, recent work in psychology suggests that instead of directly countering surface-level reasoning (e.g., falsifying given premises), one should follow an argumentation style inspired by the Jiu-Jitsu 'soft' combat system (Hornsey and Fielding, 2017): first, identify an arguer's attitude roots and themes, and then choose a prototypical rebuttal that is aligned with those drivers instead of invalidating those. In this work, we are the first to explore Jiu-Jitsu argumentation for peer review by proposing the novel task of attitude and theme-guided rebuttal generation. To this end, we enrich an existing dataset for discourse structure in peer reviews with attitude roots, attitude themes, and canonical rebuttals. To facilitate this process, we recast established annotation concepts from the domain of peer reviews (e.g., aspects a review sentence is relating to) and train domain-specific models. We then propose strong rebuttal generation strategies, which we benchmark on our novel dataset for the task of end-to-end attitude and theme-guided rebuttal generation and two subtasks.

Reconstructing articulated 3D objects from a single image requires jointly inferring object geometry, part structure, and motion parameters from limited visual evidence. A key difficulty lies in the entanglement between motion cues and object structure, which makes direct articulation regression unstable. Existing methods address this challenge through multi-view supervision, retrieval-based assembly, or auxiliary video generation, often sacrificing scalability or efficiency. We present MonoArt, a unified framework grounded in progressive structural reasoning. Rather than predicting articulation directly from image features, MonoArt progressively transforms visual observations into canonical geometry, structured part representations, and motion-aware embeddings within a single architecture. This structured reasoning process enables stable and interpretable articulation inference without external motion templates or multi-stage pipelines. Extensive experiments on PartNet-Mobility demonstrate that OM achieves state-of-the-art performance in both reconstruction accuracy and inference speed. The framework further generalizes to robotic manipulation and articulated scene reconstruction.

We introduce the Consensus-Bottleneck Asset Pricing Model (CB-APM), a framework that reconciles the predictive power of deep learning with the structural transparency of traditional finance. By embedding aggregate analyst consensus as a structural "bottleneck", the model treats professional beliefs as a sufficient statistic for the market's high-dimensional information set. We document a striking "interpretability-accuracy amplification effect" for annual horizons, the structural constraint acts as an endogenous regularizer that significantly improves out-of-sample R2 over unconstrained benchmarks. Portfolios sorted on CB-APM forecasts exhibit a strong monotonic return gradient, delivering an annualized Sharpe ratio of 1.44 and robust performance across macroeconomic regimes. Furthermore, pricing diagnostics reveal that the learned consensus captures priced variation only partially spanned by canonical factor models, identifying structured risk heterogeneity that standard linear models systematically miss. Our results suggest that anchoring machine intelligence to human-expert belief formation is not merely a tool for transparency, but a catalyst for uncovering new dimensions of belief-driven risk premiums.

The existing definitions of graph convolution, either from spatial or spectral perspectives, are inflexible and not unified. Defining a general convolution operator in the graph domain is challenging due to the lack of canonical coordinates, the presence of irregular structures, and the properties of graph symmetries. In this work, we propose a novel and general graph convolution framework by parameterizing the kernels as continuous functions of pseudo-coordinates derived via graph positional encoding. We name this Continuous Kernel Graph Convolution (CKGConv). Theoretically, we demonstrate that CKGConv is flexible and expressive. CKGConv encompasses many existing graph convolutions, and exhibits a stronger expressiveness, as powerful as graph transformers in terms of distinguishing non-isomorphic graphs. Empirically, we show that CKGConv-based Networks outperform existing graph convolutional networks and perform comparably to the best graph transformers across a variety of graph datasets. The code and models are publicly available at https://github.com/networkslab/CKGConv.

Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized benchmark for fair comparison and model development. These methods are evaluated on different SAbDab snapshots, non-overlapping test sets, and incompatible metrics, and the literature fragments the design problem into numerous sub-tasks with no common definition. We introduce Chimera-Bench (CDR Modeling with Epitope-guided Redesign), a unified benchmark built around a single canonical task: epitope-conditioned CDR sequence-structure co-design. Chimera-Bench provides (1) a curated, deduplicated dataset of 2,922 antibody-antigen complexes with epitope and paratope annotations; (2) three biologically motivated splits testing generalization to unseen epitopes, unseen antigen folds, and prospective temporal targets; and (3) a comprehensive evaluation protocol with five metric groups including novel epitope-specificity measures. We benchmark representative methods spanning different generative paradigms and report results across all splits. Chimera-Bench is the largest dataset of its kind for the antibody design problem, allowing the community to develop and test novel methods and evaluate their generalizability. The source code and data are available at: https://github.com/mansoor181/chimera-bench.git

The canonical O(N^2) Transformer remains the empirical performance frontier in sequence modeling, and its training can be further optimized by addressing geometric inefficiency. We propose an optimization framework that leverages an asymmetric projection to decompose the backward-pass gradients into parallel spans and orthogonal violations, while keeping the canonical forward-pass QKV structure intact. Through consistent experimental validation across various decomposition and projection setups, we provide strong theoretical evidence: the standard attention gradient is suboptimal. We demonstrated that selectively scaling these components, focusing primarily on 0^{th} order bidirectional parallel spans, yields the most effective learning signal. On the limited WikiText-2 dataset, and using a crude configuration, this method achieved a 0.56% reduction in validation loss, confirming the framework's fundamental validity and suggesting significant potential gains on larger datasets and deeper training regimes

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

Generating accurate circuit schematics from high-level natural language descriptions remains a persistent challenge in electronics design, as large language models (LLMs) frequently hallucinate in granular details, violate electrical constraints, and produce non-machine-readable outputs. We present CircuitLM, a novel multi-agent LLM-aided circuit design pipeline that translates user prompts into structured, visually interpretable CircuitJSON schematics through five sequential stages: (i) LLM-based component identification, (ii) canonical pinout retrieval, (iii) chain-of-thought reasoning by an electronics expert agent, (iv) JSON schematic synthesis, and (v) force-directed SVG visualization. Anchored by a curated, embedding-powered component knowledge base. While LLMs often violate electrical constraints, CircuitLM bridges this gap by grounding generation in a verified and dynamically extensible component database, initially comprising 50 components. To ensure safety, we incorporate a hybrid evaluation framework, namely Dual-Metric Circuit Validation (DMCV), validated against human-expert assessments, which achieves high fidelity in microcontroller-centric designs. We evaluate the system on 100 diverse embedded-systems prompts across six LLMs and introduce DMCV to assess both structural and electrical validity. This work bridges natural language input to deployable hardware designs, enabling reliable circuit prototyping by non-experts. Our code and data will be made public upon acceptance.

We introduce the category of information structures, whose objects are suitable diagrams of measurable sets that encode the possible outputs of a given family of observables and their mutual relationships of refinement; they serve as mathematical models of contextuality in classical and quantum settings. Each information structure can be regarded as a ringed site with trivial topology; the structure ring is generated by the observables themselves and its multiplication corresponds to joint measurement. We extend Baudot and Bennequin's definition of information cohomology to this setting, as a derived functor in the category of modules over the structure ring, and show explicitly that the bar construction gives a projective resolution in that category, recovering in this way the cochain complexes previously considered in the literature. Finally, we study the particular case of a one-parameter family of coefficients made of functions of probability distributions. The only 1-cocycles are Shannon entropy or Tsallis alpha-entropy, depending on the value of the parameter.

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

We 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.

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

This work addresses two important questions pertinent to Relation Extraction (RE). First, what are all possible relations that could exist between any two given entity types? Second, how do we define an unambiguous taxonomical (is-a) hierarchy among the identified relations? To address the first question, we use three resources Wikipedia Infobox, Wikidata, and DBpedia. This study focuses on relations between person, organization and location entity types. We exploit Wikidata and DBpedia in a data-driven manner, and Wikipedia Infobox templates manually to generate lists of relations. Further, to address the second question, we canonicalize, filter, and combine the identified relations from the three resources to construct a taxonomical hierarchy. This hierarchy contains 623 canonical relations with highest contribution from Wikipedia Infobox followed by DBpedia and Wikidata. The generated relation list subsumes an average of 85% of relations from RE datasets when entity types are restricted.

This document offers a detailed linguistic description of SNACS (Semantic Network of Adposition and Case Supersenses; Schneider et al., 2018), an inventory of 52 semantic labels ("supersenses") that characterize the use of adpositions and case markers at a somewhat coarse level of granularity, as demonstrated in the STREUSLE corpus (https://github.com/nert-nlp/streusle/ ; version 4.5 tracks guidelines version 2.6). Though the SNACS inventory aspires to be universal, this document is specific to English; documentation for other languages will be published separately. Version 2 is a revision of the supersense inventory proposed for English by Schneider et al. (2015, 2016) (henceforth "v1"), which in turn was based on previous schemes. The present inventory was developed after extensive review of the v1 corpus annotations for English, plus previously unanalyzed genitive case possessives (Blodgett and Schneider, 2018), as well as consideration of adposition and case phenomena in Hebrew, Hindi, Korean, and German. Hwang et al. (2017) present the theoretical underpinnings of the v2 scheme. Schneider et al. (2018) summarize the scheme, its application to English corpus data, and an automatic disambiguation task. Liu et al. (2021) offer an English Lexical Semantic Recognition tagger that includes SNACS labels in its output. This documentation can also be browsed alongside corpus data on the Xposition website (Gessler et al., 2022): http://www.xposition.org/

We examine if frontier chat-based large language models (LLMs) adjust their outputs based on neurodivergence (ND) context in system prompts and describe the nature of these adjustments. Specifically, we propose NDBench, a 576-output benchmark involving two frontier models, three system prompt types (baseline, ND-profile assertion, and ND-profile assertion with explicit instructions for adjustments), four canonical ND profiles, and 24 prompts across four categories, one of which involves an adversarial masking strategy. Four trends emerge consistently from our findings. First, LLMs show significant adaptation under ND context, where fully instructed conditions yield lengthier and more structured outputs, characterized by higher token counts, more headings, and more granular steps (p < 10^-8, Holm-corrected). Second, such adaptation is largely structural in nature: although list density does not change much, there is a marked rise in the frequency of headings and per-step detail. Third, ND persona assertion alone fails to suppress potentially harmful tendencies, as masking-reinforcement decreases only in explicitly instructed cases (36-44% reduction); the reduction rate barely changes in persona assertion conditions. Moreover, reliability analysis of LLM-based harm assessment reveals that only two out of the six dimensions (masking and reinforcement, validation quality) exceed the pre-defined inter-judge agreement criterion (alpha >= 0.67) and thus can be considered primary results. NDBench is made publicly available along with its prompts, outputs, code, and other resources, forming a reproducible framework for auditing future LLMs' adaptation to ND awareness.

We announce a shared task on UCCA parsing in English, German and French, and call for participants to submit their systems. UCCA is a cross-linguistically applicable framework for semantic representation, which builds on extensive typological work and supports rapid annotation. UCCA poses a challenge for existing parsing techniques, as it exhibits reentrancy (resulting in DAG structures), discontinuous structures and non-terminal nodes corresponding to complex semantic units. Given the success of recent semantic parsing shared tasks (on SDP and AMR), we expect the task to have a significant contribution to the advancement of UCCA parsing in particular, and semantic parsing in general. Furthermore, existing applications for semantic evaluation that are based on UCCA will greatly benefit from better automatic methods for UCCA parsing. The competition website is https://competitions.codalab.org/competitions/19160

The Novelties corpus is a collection of novels (and parts of novels) annotated for Alias Resolution, among other tasks. This document describes the guidelines applied during the annotation process. It contains the instructions used by the annotators, as well as a number of examples retrieved from the annotated novels, and illustrating how canonical names should be defined, and which names should be considered as referring to the same entity.

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

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

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

We establish combinatorial characterizations of virtually torsion-free and virtually free groups using the canonical graph decomposition theory in DJKK22. Our main results show that a finitely presented, residually finite group Γ is virtually torsion-free if and only if there exists a locality parameter r>0 such that its r-local cover admits a canonical tree-decomposition with finite quotient and finite adhesion, every finite subgroup of Γ fixes a vertex of this decomposition, and the finite subgroups in each bag have uniformly bounded order. Moreover, a finitely generated group Γ is virtually free if and only if for some r>0 its r-global decomposition has a finite model graph with finite bags and the tree-decomposition of the r-local cover is Γ-equivariantly isomorphic to the Bass--Serre tree arising from a splitting of Γ as a finite graph of finite groups.

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

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.

Using a set of LambdaCDM simulations of cosmic structure formation, we study the evolving connectivity and changing topological structure of the cosmic web using state-of-the-art tools of multiscale topological data analysis (TDA). We follow the development of the cosmic web topology in terms of the evolution of Betti number curves and feature persistence diagrams of the three (topological) classes of structural features: matter concentrations, filaments and tunnels, and voids. The Betti curves specify the prominence of features as a function of density level, and their evolution with cosmic epoch reflects the changing network connections between these structural features. The persistence diagrams quantify the longevity and stability of topological features. In this study we establish, for the first time, the link between persistence diagrams, the features they show, and the gravitationally driven cosmic structure formation process. By following the diagrams' development over cosmic time, the link between the multiscale topology of the cosmic web and the hierarchical buildup of cosmic structure is established. The sharp apexes in the diagrams are intimately related to key transitions in the structure formation process. The apex in the matter concentration diagrams coincides with the density level at which, typically, they detach from the Hubble expansion and begin to collapse. At that level many individual islands merge to form the network of the cosmic web and a large number of filaments and tunnels emerge to establish its connecting bridges. The location trends of the apex possess a self-similar character that can be related to the cosmic web's hierarchical buildup. We find that persistence diagrams provide a significantly higher and more profound level of information on the structure formation process than more global summary statistics like Euler characteristic or Betti numbers.

Learning causal structure from observational data often assumes that we observe independent and identically distributed (i.\,i.\,d) data. The traditional approach aims to find a graphical representation that encodes the same set of conditional independence relationships as those present in the observed distribution. It is known that under i.\,i.\,d assumption, even with infinite data, there is a limit to how fine-grained a causal structure we can identify. To overcome this limitation, recent work has explored using data originating from different, related environments to learn richer causal structure. These approaches implicitly rely on the independent causal mechanisms (ICM) principle, which postulates that the mechanism giving rise to an effect given its causes and the mechanism which generates the causes do not inform or influence each other. Thus, components of the causal model can independently change from environment to environment. Despite its wide application in machine learning and causal inference, there is a lack of statistical formalization of the ICM principle and how it enables identification of richer causal structures from grouped data. Here we present new causal de Finetti theorems which offer a first statistical formalization of ICM principle and show how causal structure identification is possible from exchangeable data. Our work provides theoretical justification for a broad range of techniques leveraging multi-environment data to learn causal structure.

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

Retrieval-Augmented Generation (RAG) has become a core paradigm for grounding large language models with external knowledge. Despite extensive efforts exploring diverse retrieval strategies, existing studies predominantly focus on query-side complexity or isolated method improvements, lacking a systematic understanding of how RAG paradigms behave across different query-corpus contexts and effectiveness-efficiency trade-offs. In this work, we introduce RAGRouter-Bench, the first dataset and benchmark designed for adaptive RAG routing. RAGRouter-Bench revisits retrieval from a query-corpus compatibility perspective and standardizes five representative RAG paradigms for systematic evaluation across 7,727 queries and 21,460 documents spanning diverse domains. The benchmark incorporates three canonical query types together with fine-grained semantic and structural corpus metrics, as well as a unified evaluation for both generation quality and resource consumption. Experiments with DeepSeek-V3 and LLaMA-3.1-8B demonstrate that no single RAG paradigm is universally optimal, that paradigm applicability is strongly shaped by query-corpus interactions, and that increased advanced mechanism does not necessarily yield better effectiveness-efficiency trade-offs. These findings underscore the necessity of routing-aware evaluation and establish a foundation for adaptive, interpretable, and generalizable next-generation RAG systems.

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

Understanding architectural differences in language models is challenging, especially at academic-scale pretraining (e.g., 1.3B parameters, 100B tokens), where results are often dominated by noise and randomness. To overcome this, we introduce controlled synthetic pretraining tasks that isolate and evaluate core model capabilities. Within this framework, we discover CANON LAYERS: lightweight architectural components -- named after the musical term "canon" -- that promote horizontal information flow across neighboring tokens. Canon layers compute weighted sums of nearby token representations and integrate seamlessly into Transformers, linear attention, state-space models, or any sequence architecture. We present 12 key results. This includes how Canon layers enhance reasoning depth (e.g., by 2times), reasoning breadth, knowledge manipulation, etc. They lift weak architectures like NoPE to match RoPE, and linear attention to rival SOTA linear models like Mamba2/GDN -- validated both through synthetic tasks and real-world academic-scale pretraining. This synthetic playground offers an economical, principled path to isolate core model capabilities often obscured at academic scales. Equipped with infinite high-quality data, it may even PREDICT how future architectures will behave as training pipelines improve -- e.g., through better data curation or RL-based post-training -- unlocking deeper reasoning and hierarchical inference.

Adeno-associated viruses (AAVs) are promising vectors for gene therapy, but their native serotypes face limitations in tissue tropism, immune evasion, and production efficiency. Engineering capsids to overcome these hurdles is challenging due to the vast sequence space and the difficulty of simultaneously optimizing multiple functional properties. The complexity also adds when it comes to the kidney, which presents unique anatomical barriers and cellular targets that require precise and efficient vector engineering. Here, we present AAVGen, a generative artificial intelligence framework for de novo design of AAV capsids with enhanced multi-trait profiles. AAVGen integrates a protein language model (PLM) with supervised fine-tuning (SFT) and a reinforcement learning technique termed Group Sequence Policy Optimization (GSPO). The model is guided by a composite reward signal derived from three ESM-2-based regression predictors, each trained to predict a key property: production fitness, kidney tropism, and thermostability. Our results demonstrate that AAVGen produces a diverse library of novel VP1 protein sequences. In silico validations revealed that the majority of the generated variants have superior performance across all three employed indices, indicating successful multi-objective optimization. Furthermore, structural analysis via AlphaFold3 confirms that the generated sequences preserve the canonical capsid folding despite sequence diversification. AAVGen establishes a foundation for data-driven viral vector engineering, accelerating the development of next-generation AAV vectors with tailored functional characteristics.

PDEs are central to scientific and engineering modeling, yet designing accurate numerical solvers typically requires substantial mathematical expertise and manual tuning. Recent neural network-based approaches improve flexibility but often demand high computational cost and suffer from limited interpretability. We introduce AutoNumerics, a multi-agent framework that autonomously designs, implements, debugs, and verifies numerical solvers for general PDEs directly from natural language descriptions. Unlike black-box neural solvers, our framework generates transparent solvers grounded in classical numerical analysis. We introduce a coarse-to-fine execution strategy and a residual-based self-verification mechanism. Experiments on 24 canonical and real-world PDE problems demonstrate that AutoNumerics achieves competitive or superior accuracy compared to existing neural and LLM-based baselines, and correctly selects numerical schemes based on PDE structural properties, suggesting its viability as an accessible paradigm for automated PDE solving.

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

The integration of syntactic structures into Transformer machine translation has shown positive results, but to our knowledge, no work has attempted to do so with semantic structures. In this work we propose two novel parameter-free methods for injecting semantic information into Transformers, both rely on semantics-aware masking of (some of) the attention heads. One such method operates on the encoder, through a Scene-Aware Self-Attention (SASA) head. Another on the decoder, through a Scene-Aware Cross-Attention (SACrA) head. We show a consistent improvement over the vanilla Transformer and syntax-aware models for four language pairs. We further show an additional gain when using both semantic and syntactic structures in some language pairs.

Evaluating the quality of tables generated by large language models (LLMs) remains an open challenge: existing metrics either flatten tables into text, ignoring structure, or rely on fixed references that limit generalization. We present TabReX, a reference-less, property-driven framework for evaluating tabular generation via graph-based reasoning. TabReX converts both source text and generated tables into canonical knowledge graphs, aligns them through an LLM-guided matching process, and computes interpretable, rubric-aware scores that quantify structural and factual fidelity. The resulting metric provides controllable trade-offs between sensitivity and specificity, yielding human-aligned judgments and cell-level error traces. To systematically asses metric robustness, we introduce TabReX-Bench, a large-scale benchmark spanning six domains and twelve planner-driven perturbation types across three difficulty tiers. Empirical results show that TabReX achieves the highest correlation with expert rankings, remains stable under harder perturbations, and enables fine-grained model-vs-prompt analysis establishing a new paradigm for trustworthy, explainable evaluation of structured generation systems.

We present a new Icelandic-English parallel corpus, the Icelandic Parallel Abstracts Corpus (IPAC), composed of abstracts from student theses and dissertations. The texts were collected from the Skemman repository which keeps records of all theses, dissertations and final projects from students at Icelandic universities. The corpus was aligned based on sentence-level BLEU scores, in both translation directions, from NMT models using Bleualign. The result is a corpus of 64k sentence pairs from over 6 thousand parallel abstracts.

Existing dynamic scene generation methods mostly rely on distilling knowledge from pre-trained 3D generative models, which are typically fine-tuned on synthetic object datasets. As a result, the generated scenes are often object-centric and lack photorealism. To address these limitations, we introduce a novel pipeline designed for photorealistic text-to-4D scene generation, discarding the dependency on multi-view generative models and instead fully utilizing video generative models trained on diverse real-world datasets. Our method begins by generating a reference video using the video generation model. We then learn the canonical 3D representation of the video using a freeze-time video, delicately generated from the reference video. To handle inconsistencies in the freeze-time video, we jointly learn a per-frame deformation to model these imperfections. We then learn the temporal deformation based on the canonical representation to capture dynamic interactions in the reference video. The pipeline facilitates the generation of dynamic scenes with enhanced photorealism and structural integrity, viewable from multiple perspectives, thereby setting a new standard in 4D scene generation.

Modern deep neural networks have achieved impressive performance on tasks from image classification to natural language processing. Surprisingly, these complex systems with massive amounts of parameters exhibit the same structural properties in their last-layer features and classifiers across canonical datasets when training until convergence. In particular, it has been observed that the last-layer features collapse to their class-means, and those class-means are the vertices of a simplex Equiangular Tight Frame (ETF). This phenomenon is known as Neural Collapse (NC). Recent papers have theoretically shown that NC emerges in the global minimizers of training problems with the simplified "unconstrained feature model". In this context, we take a step further and prove the NC occurrences in deep linear networks for the popular mean squared error (MSE) and cross entropy (CE) losses, showing that global solutions exhibit NC properties across the linear layers. Furthermore, we extend our study to imbalanced data for MSE loss and present the first geometric analysis of NC under bias-free setting. Our results demonstrate the convergence of the last-layer features and classifiers to a geometry consisting of orthogonal vectors, whose lengths depend on the amount of data in their corresponding classes. Finally, we empirically validate our theoretical analyses on synthetic and practical network architectures with both balanced and imbalanced scenarios.

Protein language models (PLMs) encode rich biological information, yet their internal neuron representations are poorly understood. We introduce the first automated framework for labeling every neuron in a PLM with biologically grounded natural language descriptions. Unlike prior approaches relying on sparse autoencoders or manual annotation, our method scales to hundreds of thousands of neurons, revealing individual neurons are selectively sensitive to diverse biochemical and structural properties. We then develop a novel neuron activation-guided steering method to generate proteins with desired traits, enabling convergence to target biochemical properties like molecular weight and instability index as well as secondary and tertiary structural motifs, including alpha helices and canonical Zinc Fingers. We finally show that analysis of labeled neurons in different model sizes reveals PLM scaling laws and a structured neuron space distribution.

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

Modern dialog managers face the challenge of having to fulfill human-level conversational skills as part of common user expectations, including but not limited to discourse with no clear objective. Along with these requirements, agents are expected to extrapolate intent from the user's dialogue even when subjected to non-canonical forms of speech. This depends on the agent's comprehension of paraphrased forms of such utterances. Especially in low-resource languages, the lack of data is a bottleneck that prevents advancements of the comprehension performance for these types of agents. In this regard, here we demonstrate the necessity of extracting the intent argument of non-canonical directives in a natural language format, which may yield more accurate parsing, and suggest guidelines for building a parallel corpus for this purpose. Following the guidelines, we construct a Korean corpus of 50K instances of question/command-intent pairs, including the labels for classification of the utterance type. We also propose a method for mitigating class imbalance, demonstrating the potential applications of the corpus generation method and its multilingual extensibility.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

I introduce a novel mathematical framework integrating topological dynamics, operator algebras, and ergodic geometry to study lattices of asynchronous metric dynamical systems. Each node in the lattice carries an internal flow represented by a one-parameter family of operators, evolving on its own time scale. I formalize stratified state spaces capturing multiple levels of synchronized behavior, define an asynchronous evolution metric that quantifies phase-offset distances between subsystems, and characterize emergent coherent topologies arising when subsystems synchronize. Within this framework, I develop formal operators for the evolution of each subsystem and give precise conditions under which phase-aligned synchronization occurs across the lattice. The main results include: (1) the existence and uniqueness of coherent (synchronized) states under a contractive coupling condition, (2) stability of these coherent states and criteria for their emergence as a collective phase transition in a continuous operator topology, and (3) the influence of symmetries, with group-invariant coupling leading to flow-invariant synchrony subspaces and structured cluster dynamics. Proofs are given for each theorem, demonstrating full mathematical rigor. In a final section, I discuss hypothetical applications of this framework to symbolic lattice systems (e.g. subshifts), to invariant group actions on dynamical lattices, and to operator fields over stratified manifolds in the spirit of noncommutative geometry. Throughout, I write in the first person to emphasize the exploratory nature of this work. The paper avoids any reference to cosmology or observers, focusing instead on clean, formal mathematics suitable for a broad array of dynamical systems.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

Information theory, introduced by Shannon, has been extremely successful and influential as a mathematical theory of communication. Shannon's notion of information does not consider the meaning of the messages being communicated but only their probability. Even so, computational approaches regularly appeal to "information processing" to study how meaning is encoded and decoded in natural and artificial systems. Here, we contrast Shannon information theory with integrated information theory (IIT), which was developed to account for the presence and properties of consciousness. IIT considers meaning as integrated information and characterizes it as a structure, rather than as a message or code. In principle, IIT's axioms and postulates allow one to "unfold" a cause-effect structure from a substrate in a state, a structure that fully defines the intrinsic meaning of an experience and its contents. It follows that, for the communication of meaning, the cause-effect structures of sender and receiver must be similar.

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

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

Retrieving relevant documents from a corpus is typically based on the semantic similarity between the document content and query text. The inclusion of structural relationship between documents can benefit the retrieval mechanism by addressing semantic gaps. However, incorporating these relationships requires tractable mechanisms that balance structure with semantics and take advantage of the prevalent pre-train/fine-tune paradigm. We propose here a holistic approach to learning document representations by integrating intra-document content with inter-document relations. Our deep metric learning solution analyzes the complex neighborhood structure in the relationship network to efficiently sample similar/dissimilar document pairs and defines a novel quintuplet loss function that simultaneously encourages document pairs that are semantically relevant to be closer and structurally unrelated to be far apart in the representation space. Furthermore, the separation margins between the documents are varied flexibly to encode the heterogeneity in relationship strengths. The model is fully fine-tunable and natively supports query projection during inference. We demonstrate that it outperforms competing methods on multiple datasets for document retrieval tasks.

Many clustering schemes are defined by optimizing an objective function defined on the partitions of the underlying set of a finite metric space. In this paper, we construct a framework for studying what happens when we instead impose various structural conditions on the clustering schemes, under the general heading of functoriality. Functoriality refers to the idea that one should be able to compare the results of clustering algorithms as one varies the data set, for example by adding points or by applying functions to it. We show that within this framework, one can prove a theorems analogous to one of J. Kleinberg, in which for example one obtains an existence and uniqueness theorem instead of a non-existence result. We obtain a full classification of all clustering schemes satisfying a condition we refer to as excisiveness. The classification can be changed by varying the notion of maps of finite metric spaces. The conditions occur naturally when one considers clustering as the statistical version of the geometric notion of connected components. By varying the degree of functoriality that one requires from the schemes it is possible to construct richer families of clustering schemes that exhibit sensitivity to density.

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

We formalize constraint-based structure learning of the "true" causal graph from observed data when unobserved variables are also existent. We provide conditions for a "natural" family of constraint-based structure-learning algorithms that output graphs that are Markov equivalent to the causal graph. Under the faithfulness assumption, this natural family contains all exact structure-learning algorithms. We also provide a set of assumptions, under which any natural structure-learning algorithm outputs Markov equivalent graphs to the causal graph. These assumptions can be thought of as a relaxation of faithfulness, and most of them can be directly tested from (the underlying distribution) of the data, particularly when one focuses on structural causal models. We specialize the definitions and results for structural causal models.

We present a system that uses LLMs as a tool in the development of Constructed Languages. The system is modular in that one first creates a target phonology for the language using an agentic approach that refines its output at each step with commentary feedback on its previous attempt. Next, a set of sentences is 'translated' from their English original into a morphosyntactic markup that reflects the word order and morphosyntactic feature specifications of the desired target language, with affixes represented as morphosyntactic feature bundles. From this translated corpus, a lexicon is constructed using the phonological model and the set of morphemes (stems and affixes) extracted from the 'translated' sentences. The system is then instructed to provide an orthography for the language, using an existing script such as Latin or Cyrillic. Finally, the system writes a brief grammatical handbook of the language. The system can also translate further sentences into the target language. Our goal is twofold. First, we hope that these tools will be fun to use for creating artificially constructed languages. Second, we are interested in exploring what LLMs 'know' about language-not what they know about any particular language or linguistic phenomenon, but how much they know about and understand language and linguistic concepts. As we shall see, there is a fairly wide gulf in capabilities both among different LLMs and among different linguistic specifications, with it being notably easier for systems to deal with more common patterns than rarer ones. An additional avenue that we explore is the application of our approach to translating from high-resource into low-resource languages. While the results so far are mostly negative, we provide some evidence that an improved version of the present system could afford some real gains in such tasks. https://github.com/SakanaAI/IASC

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.

Coecke, Sadrzadeh, and Clark (arXiv:1003.4394v1 [cs.CL]) developed a compositional model of meaning for distributional semantics, in which each word in a sentence has a meaning vector and the distributional meaning of the sentence is a function of the tensor products of the word vectors. Abstractly speaking, this function is the morphism corresponding to the grammatical structure of the sentence in the category of finite dimensional vector spaces. In this paper, we provide a concrete method for implementing this linear meaning map, by constructing a corpus-based vector space for the type of sentence. Our construction method is based on structured vector spaces whereby meaning vectors of all sentences, regardless of their grammatical structure, live in the same vector space. Our proposed sentence space is the tensor product of two noun spaces, in which the basis vectors are pairs of words each augmented with a grammatical role. This enables us to compare meanings of sentences by simply taking the inner product of their vectors.

Document structure analysis, aka document layout analysis, is crucial for understanding both the physical layout and logical structure of documents, serving information retrieval, document summarization, knowledge extraction, etc. Hierarchical Document Structure Analysis (HDSA) specifically aims to restore the hierarchical structure of documents created using authoring software with hierarchical schemas. Previous research has primarily followed two approaches: one focuses on tackling specific subtasks of HDSA in isolation, such as table detection or reading order prediction, while the other adopts a unified framework that uses multiple branches or modules, each designed to address a distinct task. In this work, we propose a unified relation prediction approach for HDSA, called UniHDSA, which treats various HDSA sub-tasks as relation prediction problems and consolidates relation prediction labels into a unified label space. This allows a single relation prediction module to handle multiple tasks simultaneously, whether at a page-level or document-level structure analysis. To validate the effectiveness of UniHDSA, we develop a multimodal end-to-end system based on Transformer architectures. Extensive experimental results demonstrate that our approach achieves state-of-the-art performance on a hierarchical document structure analysis benchmark, Comp-HRDoc, and competitive results on a large-scale document layout analysis dataset, DocLayNet, effectively illustrating the superiority of our method across all sub-tasks. The Comp-HRDoc benchmark and UniHDSA's configurations are publicly available at https://github.com/microsoft/CompHRDoc.

We construct S-linear semiorthogonal decompositions of derived categories of smooth Fano threefold fibrations X/S with relative Picard rank 1 and rational geometric fibers and discuss how the structure of components of these decompositions is related to rationality properties of X/S.

We explore local vs. global evolution of knowledge systems through the framework of socio-epistemic networks (SEN), applying two complementary methods to a corpus of scientific texts. The framework comprises three interconnected layers-social, semiotic (material), and semantic-proposing a multilayered approach to understanding structural developments of knowledge. To analyse diachronic changes on the semantic layer, we first use information-theoretic measures based on relative entropy to detect semantic shifts, assess their significance, and identify key driving features. Second, variations in document embedding densities reveal changes in semantic neighbourhoods, tracking how concentration of similar documents increase, remain stable, or disperse. This enables us to trace document trajectories based on content (topics) or metadata (authorship, institution). Case studies of Joseph Silk and Hans-J\"urgen Treder illustrate how individual scholar's work aligns with broader disciplinary shifts in general relativity and gravitation research, demonstrating the applications, limitations, and further potential of this approach.

We release S\={a}mayik, a dataset of around 53,000 parallel English-Sanskrit sentences, written in contemporary prose. Sanskrit is a classical language still in sustenance and has a rich documented heritage. However, due to the limited availability of digitized content, it still remains a low-resource language. Existing Sanskrit corpora, whether monolingual or bilingual, have predominantly focused on poetry and offer limited coverage of contemporary written materials. S\={a}mayik is curated from a diverse range of domains, including language instruction material, textual teaching pedagogy, and online tutorials, among others. It stands out as a unique resource that specifically caters to the contemporary usage of Sanskrit, with a primary emphasis on prose writing. Translation models trained on our dataset demonstrate statistically significant improvements when translating out-of-domain contemporary corpora, outperforming models trained on older classical-era poetry datasets. Finally, we also release benchmark models by adapting four multilingual pre-trained models, three of them have not been previously exposed to Sanskrit for translating between English and Sanskrit while one of them is multi-lingual pre-trained translation model including English and Sanskrit. The dataset and source code is present at https://github.com/ayushbits/saamayik.

Tangles were originally introduced as a concept to formalize regions of high connectivity in graphs. In recent years, they have also been discovered as a link between structural graph theory and data science: when interpreting similarity in data sets as connectivity between points, finding clusters in the data essentially amounts to finding tangles in the underlying graphs. This paper further explores the potential of tangles in data sets as a means for a formal study of clusters. Real-world data often follow a normal distribution. Accounting for this, we develop a quantitative theory of tangles in data sets drawn from Gaussian mixtures. To this end, we equip the data with a graph structure that models similarity between the points and allows us to apply tangle theory to the data. We provide explicit conditions under which tangles associated with the marginal Gaussian distributions exist asymptotically almost surely. This can be considered as a sufficient formal criterion for the separabability of clusters in the data.

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

An ability that underlies human syntactic knowledge is determining which words can appear in the similar structures (i.e. grouping words by their syntactic categories). These groupings enable humans to combine structures in order to communicate complex meanings. A foundational question is how do children acquire this ability underlying syntactic knowledge. In exploring this process, we will review various engineering approaches whose goal is similar to that of a child's -- without prior syntactic knowledge, correctly identify the parts of speech (POS) of the words in a sample of text. In reviewing these unsupervised tagging efforts, we will discuss common themes that support the advances in the models and their relevance for language acquisition. For example, we discuss how each model judges success (evaluation metrics), the "additional information" that constrains the POS learning (such as orthographic information), and the context used to determine POS (only previous word, words before and after the target, etc). The identified themes pave the way for future investigations into the cognitive processes that underpin the acquisition of syntactic categories and provide a useful layout of current state of the art unsupervised POS tagging models.

Taxonomy is a hierarchically structured knowledge graph that plays a crucial role in machine intelligence. The taxonomy expansion task aims to find a position for a new term in an existing taxonomy to capture the emerging knowledge in the world and keep the taxonomy dynamically updated. Previous taxonomy expansion solutions neglect valuable information brought by the hierarchical structure and evaluate the correctness of merely an added edge, which downgrade the problem to node-pair scoring or mini-path classification. In this paper, we propose the Hierarchy Expansion Framework (HEF), which fully exploits the hierarchical structure's properties to maximize the coherence of expanded taxonomy. HEF makes use of taxonomy's hierarchical structure in multiple aspects: i) HEF utilizes subtrees containing most relevant nodes as self-supervision data for a complete comparison of parental and sibling relations; ii) HEF adopts a coherence modeling module to evaluate the coherence of a taxonomy's subtree by integrating hypernymy relation detection and several tree-exclusive features; iii) HEF introduces the Fitting Score for position selection, which explicitly evaluates both path and level selections and takes full advantage of parental relations to interchange information for disambiguation and self-correction. Extensive experiments show that by better exploiting the hierarchical structure and optimizing taxonomy's coherence, HEF vastly surpasses the prior state-of-the-art on three benchmark datasets by an average improvement of 46.7% in accuracy and 32.3% in mean reciprocal rank.

We introduce meta-factorization, a theory that describes matrix decompositions as solutions of linear matrix equations: the projector and the reconstruction equation. Meta-factorization reconstructs known factorizations, reveals their internal structures, and allows for introducing modifications, as illustrated with SVD, QR, and UTV factorizations. The prospect of meta-factorization also provides insights into computational aspects of generalized matrix inverses and randomized linear algebra algorithms. The relations between the Moore-Penrose pseudoinverse, generalized Nystr\"{o}m method, and the CUR decomposition are revealed here as an illustration. Finally, meta-factorization offers hints on the structure of new factorizations and provides the potential of creating them.

Recent work has demonstrated that semantics specified by pretraining data influence how representations of different concepts are organized in a large language model (LLM). However, given the open-ended nature of LLMs, e.g., their ability to in-context learn, we can ask whether models alter these pretraining semantics to adopt alternative, context-specified ones. Specifically, if we provide in-context exemplars wherein a concept plays a different role than what the pretraining data suggests, do models reorganize their representations in accordance with these novel semantics? To answer this question, we take inspiration from the theory of conceptual role semantics and define a toy "graph tracing" task wherein the nodes of the graph are referenced via concepts seen during training (e.g., apple, bird, etc.) and the connectivity of the graph is defined via some predefined structure (e.g., a square grid). Given exemplars that indicate traces of random walks on the graph, we analyze intermediate representations of the model and find that as the amount of context is scaled, there is a sudden re-organization from pretrained semantic representations to in-context representations aligned with the graph structure. Further, we find that when reference concepts have correlations in their semantics (e.g., Monday, Tuesday, etc.), the context-specified graph structure is still present in the representations, but is unable to dominate the pretrained structure. To explain these results, we analogize our task to energy minimization for a predefined graph topology, providing evidence towards an implicit optimization process to infer context-specified semantics. Overall, our findings indicate scaling context-size can flexibly re-organize model representations, possibly unlocking novel capabilities.

We investigated the evolution and transformation of scientific knowledge in the early modern period, analyzing more than 350 different editions of textbooks used for teaching astronomy in European universities from the late fifteenth century to mid-seventeenth century. These historical sources constitute the Sphaera Corpus. By examining different semantic relations among individual parts of each edition on record, we built a multiplex network consisting of six layers, as well as the aggregated network built from the superposition of all the layers. The network analysis reveals the emergence of five different communities. The contribution of each layer in shaping the communities and the properties of each community are studied. The most influential books in the corpus are found by calculating the average age of all the out-going and in-coming links for each book. A small group of editions is identified as a transmitter of knowledge as they bridge past knowledge to the future through a long temporal interval. Our analysis, moreover, identifies the most disruptive books. These books introduce new knowledge that is then adopted by almost all the books published afterwards until the end of the whole period of study. The historical research on the content of the identified books, as an empirical test, finally corroborates the results of all our analyses.

We show how the Schur-Weyl duality that exists between the partition algebra and the symmetric group results in a stronger theoretical foundation for characterising all of the possible permutation equivariant neural networks whose layers are some tensor power of the permutation representation M_n of the symmetric group S_n. In doing so, we unify two separate bodies of literature, and we correct some of the major results that are now widely quoted by the machine learning community. In particular, we find a basis of matrices for the learnable, linear, permutation equivariant layer functions between such tensor power spaces in the standard basis of M_n by using an elegant graphical representation of a basis of set partitions for the partition algebra and its related vector spaces. Also, we show how we can calculate the number of weights that must appear in these layer functions by looking at certain paths through the McKay quiver for M_n. Finally, we describe how our approach generalises to the construction of neural networks that are equivariant to local symmetries.

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

Large language models (LLMs) can reliably distinguish grammatical from ungrammatical sentences, but how grammatical knowledge is represented within the models remains an open question. We investigate whether different syntactic phenomena recruit shared or distinct components in LLMs. Using a functional localization approach inspired by cognitive neuroscience, we identify the LLM units most responsive to 67 English syntactic phenomena in seven open-weight models. These units are consistently recruited across sentences containing the phenomena and causally support the models' syntactic performance. Critically, different types of syntactic agreement (e.g., subject-verb, anaphor, determiner-noun) recruit overlapping sets of units, suggesting that agreement constitutes a meaningful functional category for LLMs. This pattern holds in English, Russian, and Chinese; and further, in a cross-lingual analysis of 57 diverse languages, structurally more similar languages share more units for subject-verb agreement. Taken together, these findings reveal that syntactic agreement-a critical marker of syntactic dependencies-constitutes a meaningful category within LLMs' representational spaces.

This paper is devoted to the classification and studying properties of complex unital 3-dimensional structurable algebras. We provide a complete list of non-isomorphic classes, identifying five algebras for type (2, 1) and two algebras for type (1, 2). For each obtained algebra, we describe the derivation algebra, the automorphism group, the lattice of subalgebras and ideals, and functional identities of degree 2. Furthermore, we investigate the Allison-Kantor construction for the classified algebras. We determine the structure of the resulting Z-graded Lie algebras, providing their dimensions and Levi decompositions.

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

We compiled a new sentence splitting corpus that is composed of 203K pairs of aligned complex source and simplified target sentences. Contrary to previously proposed text simplification corpora, which contain only a small number of split examples, we present a dataset where each input sentence is broken down into a set of minimal propositions, i.e. a sequence of sound, self-contained utterances with each of them presenting a minimal semantic unit that cannot be further decomposed into meaningful propositions. This corpus is useful for developing sentence splitting approaches that learn how to transform sentences with a complex linguistic structure into a fine-grained representation of short sentences that present a simple and more regular structure which is easier to process for downstream applications and thus facilitates and improves their performance.

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

In this paper, we conduct a holistic exploration of the Universal Decompositional Semantic (UDS) Parsing. We first introduce a cascade model for UDS parsing that decomposes the complex parsing task into semantically appropriate subtasks. Our approach outperforms the prior models, while significantly reducing inference time. We also incorporate syntactic information and further optimized the architecture. Besides, different ways for data augmentation are explored, which further improve the UDS Parsing. Lastly, we conduct experiments to investigate the efficacy of ChatGPT in handling the UDS task, revealing that it excels in attribute parsing but struggles in relation parsing, and using ChatGPT for data augmentation yields suboptimal results. Our code is available at https://github.com/hexuandeng/HExp4UDS.

The categories of open learners (due to Fong, Spivak and Tuy\'eras) and open games (due to the present author, Ghani, Winschel and Zahn) bear a very striking and unexpected similarity. The purpose of this short note is to prove that there is a faithful symmetric monoidal functor from the former to the latter, which means that any supervised neural network (without feedback or other complicating features) can be seen as an open game in a canonical way. Roughly, each parameter is controlled by a different player, and the game's best response relation encodes the dynamics of gradient descent. We suggest paths for further work exploiting the link.

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.

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

Ontologies comprising of concepts, their attributes, and relationships are used in many knowledge based AI systems. While there have been efforts towards populating domain specific ontologies, we examine the role of document structure in learning ontological relationships between concepts in any document corpus. Inspired by ideas from hypernym discovery and explainability, our method performs about 15 points more accurate than a stand-alone R-GCN model for this task.

This thesis introduces quantum natural language processing (QNLP) models based on a simple yet powerful analogy between computational linguistics and quantum mechanics: grammar as entanglement. The grammatical structure of text and sentences connects the meaning of words in the same way that entanglement structure connects the states of quantum systems. Category theory allows to make this language-to-qubit analogy formal: it is a monoidal functor from grammar to vector spaces. We turn this abstract analogy into a concrete algorithm that translates the grammatical structure onto the architecture of parameterised quantum circuits. We then use a hybrid classical-quantum algorithm to train the model so that evaluating the circuits computes the meaning of sentences in data-driven tasks. The implementation of QNLP models motivated the development of DisCoPy (Distributional Compositional Python), the toolkit for applied category theory of which the first chapter gives a comprehensive overview. String diagrams are the core data structure of DisCoPy, they allow to reason about computation at a high level of abstraction. We show how they can encode both grammatical structures and quantum circuits, but also logical formulae, neural networks or arbitrary Python code. Monoidal functors allow to translate these abstract diagrams into concrete computation, interfacing with optimised task-specific libraries. The second chapter uses DisCopy to implement QNLP models as parameterised functors from grammar to quantum circuits. It gives a first proof-of-concept for the more general concept of functorial learning: generalising machine learning from functions to functors by learning from diagram-like data. In order to learn optimal functor parameters via gradient descent, we introduce the notion of diagrammatic differentiation: a graphical calculus for computing the gradients of parameterised diagrams.

This paper will present textual corpora for Serbian (and Serbo-Croatian), usable for the training of large language models and publicly available at one of the several notable online repositories. Each corpus will be classified using multiple methods and its characteristics will be detailed. Additionally, the paper will introduce three new corpora: a new umbrella web corpus of Serbo-Croatian, a new high-quality corpus based on the doctoral dissertations stored within National Repository of Doctoral Dissertations from all Universities in Serbia, and a parallel corpus of abstract translation from the same source. The uniqueness of both old and new corpora will be accessed via frequency-based stylometric methods, and the results will be briefly discussed.

Sentence-level human value detection is typically framed as multi-label classification over Schwartz values, but it remains unclear whether Schwartz higher-order (HO) categories provide usable structure. We study this under a strict compute-frugal budget (single 8 GB GPU) on ValueEval'24 / ValuesML (74K English sentences). We compare (i) direct supervised transformers, (ii) HOrightarrowvalues pipelines that enforce the hierarchy with hard masks, and (iii) PresencerightarrowHOrightarrowvalues cascades, alongside low-cost add-ons (lexica, short context, topics), label-wise threshold tuning, small instruction-tuned LLM baselines (le10B), QLoRA, and simple ensembles. HO categories are learnable from single sentences (e.g., the easiest bipolar pair reaches Macro-F_1approx0.58), but hard hierarchical gating is not a reliable win: it often reduces end-task Macro-F_1 via error compounding and recall suppression. In contrast, label-wise threshold tuning is a high-leverage knob (up to +0.05 Macro-F_1), and small transformer ensembles provide the most consistent additional gains (up to +0.02 Macro-F_1). Small LLMs lag behind supervised encoders as stand-alone systems, yet can contribute complementary errors in cross-family ensembles. Overall, HO structure is useful descriptively, but enforcing it with hard gates hurts sentence-level value detection; robust improvements come from calibration and lightweight ensembling.

Partition logics -- non-Boolean event structures obtained by pasting Boolean algebras -- provide a natural language for situations in which a system has a definite latent state but can be accessed and resolved only through mutually incompatible coarse-grained modes of observation. We show that this structure arises in a range of social-science settings by constructing six explicit examples from personnel assessment, survey framing, clinical diagnosis, espionage coordination, legal pluralism, and organizational auditing. For each case we identify the latent state space, the observational contexts as partitions, and the shared atoms that intertwine contexts, yielding instances of the L_{12} bowtie, triangle, pentagon, and automaton partition logics. These examples make precise a notion of social complementarity: different modes of inquiry can be incompatible even though the underlying system remains fully value-definite. Complementarity in this sense does not entail contextuality or ontic indeterminacy. We further compare the classical probabilities generated by convex mixtures of dispersion-free states with the quantum-like Born probabilities available when the same exclusivity graph admits a faithful orthogonal representation. The framework thus separates logical structure from probabilistic realization and suggests empirically testable benchmarks for quantum-cognition models.

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

Scientific posters play a vital role in academic communication by presenting ideas through visual summaries. Analyzing reading order and parent-child relations of posters is essential for building structure-aware interfaces that facilitate clear and accurate understanding of research content. Despite their prevalence in academic communication, posters remain underexplored in structural analysis research, which has primarily focused on papers. To address this gap, we constructed SciPostLayoutTree, a dataset of approximately 8,000 posters annotated with reading order and parent-child relations. Compared to an existing structural analysis dataset, SciPostLayoutTree contains more instances of spatially challenging relations, including upward, horizontal, and long-distance relations. As a solution to these challenges, we develop Layout Tree Decoder, which incorporates visual features as well as bounding box features including position and category information. The model also uses beam search to predict relations while capturing sequence-level plausibility. Experimental results demonstrate that our model improves the prediction accuracy for spatially challenging relations and establishes a solid baseline for poster structure analysis. The dataset is publicly available at https://huggingface.co/datasets/omron-sinicx/scipostlayouttree. The code is also publicly available at https://github.com/omron-sinicx/scipostlayouttree.

In order to avoid well-know paradoxes associated with self-referential definitions, higher-order dependent type theories stratify the theory using a countably infinite hierarchy of universes (also known as sorts), Type_0 : Type_1 : cdots . Such type systems are called cumulative if for any type A we have that A : Type_{i} implies A : Type_{i+1}. The predicative calculus of inductive constructions (pCIC) which forms the basis of the Coq proof assistant, is one such system. In this paper we present and establish the soundness of the predicative calculus of cumulative inductive constructions (pCuIC) which extends the cumulativity relation to inductive types.

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

Mathematical researchers, especially those in early-career positions, face critical decisions about topic specialization with limited information about the collaborative environments of different research areas. The aim of this paper is to study how the popularity of a research topic is associated with the structure of that topic's collaboration network, as observed by a suite of measures capturing organizational structure at several scales. We apply these measures to 1,938 algorithmically discovered topics across 121,391 papers sourced from arXiv metadata during the period 2020--2025. Our analysis, which controls for the confounding effects of network size, reveals a structural dichotomy--we find that popular topics organize into modular "schools of thought," while niche topics maintain hierarchical core-periphery structures centered around established experts. This divide is not an artifact of scale, but represents a size-independent structural pattern correlated with popularity. We also document a "constraint reversal": after controlling for size, researchers in popular fields face greater structural constraints on collaboration opportunities, contrary to conventional expectations. Our findings suggest that topic selection is an implicit choice between two fundamentally different collaborative environments, each with distinct implications for a researcher's career. To make these structural patterns transparent to the research community, we developed the Math Research Compass (https://mathresearchcompass.com), an interactive platform providing data on topic popularity and collaboration patterns across mathematical topics.

In this paper, we introduce fundamental notions of homotopy theory, including homotopy excision and the Freudenthal suspension theorem. We then explore framed cobordism and its connection to stable homotopy groups of spheres through the Pontryagin-Thom construction. Using this framework, we compute the stable stems in dimensions 0, 1, and 2. This work is primarily expository, revisiting proofs from Pont1 with slight modifications incorporating modern notation. Furthermore, in the final section, we discuss 2-dimensional framed manifolds with Arf invariant one and examine why the result of Pont2 regarding π_2^S is incorrect.

Subject classification schemes are foundational to the organization, evaluation, and navigation of scientific knowledge. While expert-curated systems like Scopus provide widely used taxonomies, they often suffer from coarse granularity, subjectivity, and limited adaptability to emerging interdisciplinary fields. Data-driven alternatives based on citation networks show promise but lack rigorous, external validation against the semantic content of scientific literature. Here, we propose a novel quantitative framework that leverages classification tasks to evaluate the effectiveness of journal classification schemes. Using over 23 million paper abstracts, we demonstrate that labels derived from k-means clustering on Periodical2Vec (P2V)--a periodical embedding learned from paper-level citations--yield significantly higher classification performance than both Scopus and other data-driven baselines (e.g., citation, co-citation, and Node2Vec variants). By comparing journal partitions across classification schemes, two structural patterns emerge on the map of science: (1) the reorganization of disciplinary boundaries--splitting overly broad categories (e.g., "Medicine" into "Oncology", "Cardiology", and other specialties) while merging artificially fragmented ones (e.g., "Chemistry" and "Chemical Engineering"); and (2) the identification of coherent interdisciplinary clusters--such as "Biomedical Engineering", "Medical Ethics", and "Information Management"--that are dispersed across multiple categories but unified in citation space. These findings underscore that citation-derived periodical embeddings not only outperform traditional taxonomies in predictive validity but also offer a dynamic, fine-grained map of science that better reflects both the specialization and interdisciplinarity inherent in contemporary research.

Long document question answering (DocQA) aims to answer questions from long documents over 10k words. They usually contain content structures such as sections, sub-sections, and paragraph demarcations. However, the indexing methods of long documents remain under-explored, while existing systems generally employ fixed-length chunking. As they do not consider content structures, the resultant chunks can exclude vital information or include irrelevant content. Motivated by this, we propose the Multi-view Content-aware indexing (MC-indexing) for more effective long DocQA via (i) segment structured document into content chunks, and (ii) represent each content chunk in raw-text, keywords, and summary views. We highlight that MC-indexing requires neither training nor fine-tuning. Having plug-and-play capability, it can be seamlessly integrated with any retrievers to boost their performance. Besides, we propose a long DocQA dataset that includes not only question-answer pair, but also document structure and answer scope. When compared to state-of-art chunking schemes, MC-indexing has significantly increased the recall by 42.8%, 30.0%, 23.9%, and 16.3% via top k= 1.5, 3, 5, and 10 respectively. These improved scores are the average of 8 widely used retrievers (2 sparse and 6 dense) via extensive experiments.

SiPaKosa is a comprehensive corpus of Sinhala and Pali doctrinal texts comprising approximately 786K sentences and 9.25M words, incorporating 16 copyright-cleared historical Buddhist documents alongside the complete web-scraped Tripitaka canonical texts. The corpus was created through high-quality OCR using Google Document AI on historical manuscripts, combined with systematic web scraping of canonical repositories, followed by rigorous quality control and metadata annotation. The corpus is organised into language-specific subcorpora: Sinhala and Mixed Sinhala-Pali. We evaluate the performance of language models using ten pretrained models, with perplexity scores ranging from 1.09 to 189.67 on our corpus. This analysis shows that proprietary models significantly outperform open-source alternatives by factors of three to six times. This corpus supports the pretraining of domain-adapted language models, facilitates historical language analysis, and aids in the development of information retrieval systems for Buddhist scholarship while preserving Sinhala cultural heritage.

Bayes' rule tells us how to invert a causal process in order to update our beliefs in light of new evidence. If the process is believed to have a complex compositional structure, we may observe that the inversion of the whole can be computed piecewise in terms of the component processes. We study the structure of this compositional rule, noting that it relates to the lens pattern in functional programming. Working in a suitably general axiomatic presentation of a category of Markov kernels, we see how we can think of Bayesian inversion as a particular instance of a state-dependent morphism in a fibred category. We discuss the compositional nature of this, formulated as a functor on the underlying category and explore how this can used for a more type-driven approach to statistical inference.

Document structure analysis (aka document layout analysis) is crucial for understanding the physical layout and logical structure of documents, with applications in information retrieval, document summarization, knowledge extraction, etc. In this paper, we concentrate on Hierarchical Document Structure Analysis (HDSA) to explore hierarchical relationships within structured documents created using authoring software employing hierarchical schemas, such as LaTeX, Microsoft Word, and HTML. To comprehensively analyze hierarchical document structures, we propose a tree construction based approach that addresses multiple subtasks concurrently, including page object detection (Detect), reading order prediction of identified objects (Order), and the construction of intended hierarchical structure (Construct). We present an effective end-to-end solution based on this framework to demonstrate its performance. To assess our approach, we develop a comprehensive benchmark called Comp-HRDoc, which evaluates the above subtasks simultaneously. Our end-to-end system achieves state-of-the-art performance on two large-scale document layout analysis datasets (PubLayNet and DocLayNet), a high-quality hierarchical document structure reconstruction dataset (HRDoc), and our Comp-HRDoc benchmark. The Comp-HRDoc benchmark will be released to facilitate further research in this field.