Structured Context
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1 paper in the last four weeks, down 83% on the four weeks before. 0.0% of all new papers.
Latest papers 29
This paper presents the AR fairness metamodel, a framework designed to represent, analyze, and compare different fairness scenarios. The metamodel considers key elements, such as agents, resources, and their attributes, and enables the systematic definition and comparison of various fairness measures. We provide examples involving both discrete and continuous measures, including equality, equity, group fairness, individual fairness, the Gini index, the Theil index, Jain's fairness index, and a detailed fairness measure for Australia's Child Care Subsidy. We also explore relationships among group fairness, individual fairness, and envy-freeness, supported by formal proofs. At the conceptual modeling level, our approach builds on the Tiles framework, which offers modular components that can be connected to capture diverse fairness definitions. The goal is to make AR-based fairness definitions practical and adaptable across contexts, providing a clear way to define, compare, and evaluate them. An implementation of the Tiles framework is available as an open-source tool, and can support fairness modeling and evaluation across a wide range of applications.
FormStruct-Bench:A Hierarchical and Diagnostic Benchmark for Table-Form Document Structure Recognition
Transforming table-form documents into machine-processable records requires recovering not only their visible content but also the multilevel structure that organizes it. However, existing benchmarks evaluate either holistic document outputs or conventional table grids, and their aggregate scores provide little insight into where structural failures occur. We introduce FormStruct-Bench, a hierarchical and diagnostic benchmark that evaluates table-form document structure recognition at both the document level and progressively finer component levels, allowing aggregate performance to be traced back to specific structural failure modes. To construct auditable ground truth at scale, we annotate 70 reusable templates and expand them into 7,000 verified instances through a provenance-preserving Director--Artist--Verifier pipeline; all 1,100 instances in the template-disjoint test set additionally receive human review. Our evaluation protocol uses five primary metrics and three structure-specific diagnostics across page, schema, and component levels, together with slices over difficulty, structural constraints, and visual degradation. Across 14 API-hosted and locally deployable systems plus two SFT variants, the best document-level score reaches 83.85%, whereas the best reported fine-grained structural score remains below 18%. These results reveal a pronounced gap between reading document content and recovering the hierarchy and regional organization required for reliable table-form understanding.
The Announcement Carries the Cue: Markup, Boundaries, and the Notation of Pre-Training Corpora
How a document's arrangement is written down, its notation, is a training variable that no dataset card records. The field has established that text-extraction choices change model behaviour, and has never once measured the notation of what those choices put into the corpus. We define clean-window survival, a deterministic count of how much of a stream still demands the boundary inference, and measure notation on three fronts. What corpora carry: a census of thirteen public corpora, where survival falls to 0.153 in a vision-converted PDF slice against 0.889 in C4; the scarce resource is not unmarked text but long unmarked text; a pre-registered supply test finds what remains institutional, not consumer. Our own pre-registered prediction failed: converters do not fabricate structure on prose, and that null forced the reliability mechanism that survives it. What readers use: across five base models spanning 0.6B to 8.2B and two pipelines, deleting a structural announcement makes the following prose measurably harder to predict, while swapping its notation moves nothing. That zero does not make notation unimportant; it relocates the variable: the operative cue is the announcement, not the sigil. What writers impose: a bounded null. Base models do not impose the marked register above the authored baseline, and handed prose with every announcement deleted they do not put one back, at a rate indistinguishable from zero against an authored reference of zero. We ship the format those measurements imply: the pure frame, paragraphs in authored order, every announcement deleted into a reversible sidecar, mixed against the marked copy over announcement presence rather than notation. Choose format operators by the capability they train, not by the fidelity they preserve, and record extractor identity and survival on data cards.
The Anatomy of a Prompt Injection: A Component Model for Structured Analysis
Four years after prompt injection was first identified in 2022, attacks are still predominantly documented as verbatim strings rather than structured exploits, despite advancing agent capabilities and threat actors embedding injections to subvert AI-assisted security analysis. This paper formalizes the structure of prompt-injection artifacts, enabling defenders, red teamers, and cyber threat intelligence (CTI) teams to label, compare, and mutate attacks without relying on fragile string matching. Because large language models compile varied natural-language realizations into identical executable actions, labeling must track attacker intent (tool targets, sinks, and effects) rather than surface wording. We propose a seven-component model (carrier, delivery vector, concealment, context-break, privilege escalation, payload, and return channel) consisting of five artifact fields and two environment fields. This framework unifies roles partially addressed by HOUYI's payload decomposition, the Promptware Kill Chain, and campaign taxonomies, while framing minimal jailbreak frameworks like ReNeLLM as projections onto a restricted subspace. We provide clear labeling rules, a logical analysis record mapping directly to industry CTI schemas, worked examples including EchoLeak (CVE-2025-32711) and an in-the-wild malware AI-evasion sample, and an illustrative agentic flowchart.
SSC: A Verifiable Structured Representation for Bimanual Manipulation Labelling
Subtask labels decompose a long-horizon manipulation demonstration into shorter semantic segments for policy training and evaluation. Natural language descriptions are easy to read, but their linguistic variability makes automatic verification difficult. Rigid template formats, such as BEHAVIOR-1K's skill_annotation, are linguistically over-segmented, hindering both readability and annotation consistency. We propose the Structured Subtask Chain (SSC), a state-transition representation that bridges these extremes. A demonstration is a sequence of Structured Subtask Template (SST) entries. Each SST stores core action components (subject, predicate, object), flexible conditions (adverbial modifiers such as spatial or instrumental phrases), a base-motion field separate from arm actions, and an after-state scene graph. Built on this format, SSC supports three vision-language assisted functions: rendering SSTs as natural language, checking the assembled chain against four state-transition rules, and completing underspecified fields through a query resolution cascade. We instantiate the pipeline on BEHAVIOR-1K (50 tasks, 3 episodes per task, 2,357 annotated action cells) for logic verification and content completion, evaluating 13 selected state-of-the-art VL models as candidate verifiers and reporting labelling anomalies.
Diffuse to Compress: Leveraging Diffusion LMs for Lossless Compression
We study the problem of lossless text compression, motivated by the rapid growth in the collection and storage of digital textual data - including plain text, source code, and structured formats such as XML - and by recent advances in neural language model-based compression. In particular, recent LLM-based approaches, whether built on symbol-ranking pipelines or paired with a statistical compressor, have demonstrated compression ratios significantly superior to general-purpose compressors such as zstd, gzip, or bzip on text and code. However, these neural approaches suffer from severe throughput limitations, making them not yet practically usable. For the first time in the context of lossless neural text compression, we introduce Diffusion Language Models (DLMs) as an alternative inference paradigm to autoregressive LLM-based approaches. We argue that replacing autoregressive LLMs with DLMs within the same compression framework could overcome the throughput bottleneck caused by their one-symbol-per-step limitation. However, achieving these improvements requires addressing algorithmic challenges introduced by applying DLMs to lossless compression, where the architecture allows the number and positions of symbols encoded at each forward pass to be decided independently. We design efficient and effective strategies to solve these challenges and evaluate them experimentally against LLM-based and general-purpose compressors on enwik8, a well-established textual benchmark. Our results show that the newly proposed DLM-based framework advances the state of the art in lossless text compression. Moreover, as DLMs are still a relatively young paradigm, recent advances toward increasingly capable and efficient models suggest substantial room for further improvements.
SeaSlides: Semantic Abstraction Layer for Agentic Slide Generation
Agentic presentation generation must preserve source content, maintain coherent visual design, render specialized objects, and produce usable artifacts. Existing systems meet only part of this requirement: templates preserve regularity but restrict adaptation, whereas free-form HTML or SVG gives models flexibility at the cost of low-level rendering decisions. This mismatch makes long technical decks brittle, especially when slides contain formulas, code, or data graphics. We present SeaSlides, an agentic slide-generation framework built around a semantic abstraction layer. Rather than authoring coordinates, inline styles, or raw SVG geometry, the model writes structured slide content through reusable components and capability modules, while templates own layout, style, and rendering. We instantiate this principle separately in HTML and Typst: SeaSlides-HTML uses template-defined DOM components, whereas SeaSlides-Typst uses template functions and package-backed modules. Capability modules route equations, code, and charts to dedicated renderers, and three feedback stages localize build errors, project-constraint violations, and visual defects before export. The two systems retain backend-specific syntax and contracts while sharing the same authoring boundary. For evaluation, we combine the 128-task UltraPresent validation setting with SeaSlidesBench-Rich, a new 32-task benchmark stressing mathematics, code, pseudocode, tables, charts, and diagrams. Across four generation models, both SeaSlides backends produce more readable, content-oriented source than SVG-heavy generation. A SeaSlides backend attains the highest rich-content macro-average under three of the four models while maintaining competitive overall qualitative performance. These results support semantic abstraction as a practical authoring principle across presentation backends.
Action QFormer: Structured Representation Shaping under Action Supervision in Vision-Language-Action Models
Action supervision in vision-language-action (VLA) models is often treated as a downstream objective for learning action prediction. In this paper, we study it instead as a force that shapes inherited multimodal representations. We show that this shaping has a dual effect: it is necessary for forming action-compatible representations, but when action supervision is applied too directly to the inherited multimodal pathway, it can also destabilize representations that support language-side processing and object grounding. To address this tension, we introduce Action QFormer, a query-based action-facing interface that uses instruction-conditioned queries to reorganize inherited multimodal information into action-facing representations before downstream action generation. In zero-shot sim-to-real navigation, Action QFormer improves average closed-loop task success from 18.8% to 56.3%, raises fixed-instruction action-generation correctness from 22.5% to 75.5%, and nearly eliminates out-of-distribution instruction generations. Further analyses show that Action QFormer changes how action supervision shapes inherited multimodal representations, reducing broad upstream rewriting while preserving targeted and sometimes constructive action-supervised adaptation. These results suggest that improving VLA performance requires not only stronger pretrained backbones, but also better ways of selecting and organizing inherited multimodal information while controlling how it is shaped under action supervision.
Theory-Level Autoformalization: From Isolated Statements to Unified Formal Knowledge Bases
Autoformalization translates informal natural language into formal, machine-verifiable languages. While most work focuses on individual statements, real formalization efforts are inherently theory-level: they require an entire web of axioms, definitions, and lemmas before target theorems can even be stated. In this position paper, we argue for theory-level autoformalization: formalizing complete theories, including all their inter-dependencies, as structured libraries. We examine the significance of this shift, address alternative views, identify open challenges, and propose three promising paths forward. Our survey of autoformalization is available at https://github.com/marcusm117/Awesome-Autoformalization.
A Structural Interpretation of GELU and Threshold-Transmission Activations via the First-Order Loss Function
The Gaussian Error Linear Unit is usually motivated as the expected output of an input-dependent Bernoulli gate. This work gives an alternative interpretation: GELU is the expected output of a hard linear gate with a Gaussian random threshold. This view provides a generative interpretation for the Bernoulli gate: the gate opens once the input clears a latent Gaussian threshold. This interpretation stems from a decomposition based on well-known results in stochastic inventory theory and leads to a threshold-transmission family that includes ReLU, GELU, SiLU/Swish, and hard swish as special cases. By considering a latent uniform threshold, we recover a hard-swish-like piecewise-polynomial gate whose nonlinear transition is confined to a finite interval, yielding fixed- and learned-width variants. Controlled experiments on compact vision and language models show that calibrated or learned uniform-threshold gates are consistently competitive with GELU, ReLU, and SiLU/Swish, improve over them in most tested settings, and use the finite transition region nontrivially.
Open-Set Source Tracing as Compositional Factors via Structured Prototypes
Recent research expands beyond binary anti-spoofing with the emergence of Source Tracing, the task of identifying the specific generative origins of synthetic speech. However, current research often equates a "source" with its generative architecture. We propose redefining a source as a compositional tuple of Architecture, Training Data, and other training factors affecting the generated speech. We propose a framework using Structured Orthonormal Prototypes to minimize class overlap and intra-class variance. Our Subspace Partitioning strategy splits the embedding into architecture and data subspaces, while a residual subspace captures stochastic variability, enabling "compositional generalization" for novel factor combinations. This approach improves performance for partially seen sources and maintains robustness in fully open-set scenarios. MLAAD evaluations for Few-Shot open-set Identification show our approach significantly outperforms angular-margin baselines.
A Dual-Track Framework for Template-Constrained LaTeX Conversion
With the increasing demands for advanced document conversion, mapping structured Markdown drafts into template-compliant formats like LaTeX remains a challenge. Existing approaches largely depend on either deterministic rule-based converters or pure end-to-end Large Language Model (LLM) generation. The former fails to correctly handle asset insertions and template-specific constraints, while the latter tends to induce semantic drift, leading to hallucinations that are difficult to debug. To address these limitations, we introduce a robust Dual-Track Framework that systematically decouples template formatting from document processing: an offline track extracts template constraints into a reusable manifest, while an online track implements a hybrid execution pipeline. This pipeline confines LLM usage exclusively to reasoning-intensive components (e.g., semantic metadata, bibliographic references, and complex visual/tabular layouts) while delegating rule-based engines for deterministic processing. Empirical evaluation across 7 LaTeX templates and 56 published research papers demonstrates that our method preserves better structural fidelity, satisfies diverse layout constraints, and achieves a higher compilation success rate compared to the previous baselines.
A Security Analysis of Long-Horizon Agentic AI Systems: Threats, Evaluation, and Framework Development
This paper presents a structured analysis of security challenges in long-horizon agentic AI systems. The study reviews existing threats, evaluation approaches, attack propagation mechanisms, and security frameworks. A taxonomy of security threats and a framework for analyzing attack propagation are proposed to support future research in agentic AI security
Improving Cross-Format Robustness in Language Models with Multi-Format Training
Large language models often remain sensitive to answer format: a question solved correctly in one form may fail in another semantically equivalent form. To study this gap, we define cross-format robustness as the extent to which a model answers the same underlying question consistently across formats. We then compare full-format training with FormatMix, which expands only a subset of training items into multiple equivalent formats using either random or targeted selection. Across GLM4 and Llama-3.1, multi-format supervision consistently improves both task performance and cross-format robustness, whereas Multiple-choice question (MCQ)-only supervision alone brings little benefit and can even reduce robustness. We further find that expanding only about 30% of the training set into multiple formats often recovers most of the gain from full-format training, and this effect appears across the model families and sizes we study. These results suggest that format diversity, rather than additional supervision alone, is the key driver of robustness. That lightweight multi-format augmentation is a practical way to make LLMs less sensitive to answer format without changing the base model.
TABVERSE: Benchmarking Cross-Format Table Understanding in LLMs and VLMs
Large Language Models (LLMs) and Vision-Language Models (VLMs) are increasingly evaluated on table reasoning tasks, but the role of table representation remains under-explored. In practice, the same table content may appear in different structural formats, such as HTML, Markdown, and LaTeX, or as rendered images. However, existing evaluations often let content, format, layout, and modality vary together, making it difficult to isolate representation effects. We introduce TABVERSE, a controlled multimodal table benchmark that aligns the same table content across multiple structural formats and rendered images, with question category and difficulty tags. This design enables systematic evaluation of representation effects while holding table content fixed. We evaluate LLMs and VLMs across three tasks: Question Answering (QA), Structural Understanding Capability (SUC), and Structure Reconstruction (SR). Our results show that representation choice substantially affects table understanding. Models generally perform better with structured text than with rendered images, but the size of this gap depends on the task, model, and format. HTML is often the most robust text format, while row-sensitive structural tasks and syntactically usable LaTeX reconstruction remain challenging. These findings show that table representation is a key factor in reliable table evaluation.
Capacity, Not Format: Rethinking Structured Reasoning Failures
Prior work treats structured output as a reasoning tax, but this framing is incomplete: the cost of formatting depends strongly on a model's spare capacity. Using information-matched prose controls and a four-level schema complexity gradient, we separate format-specific effects from prompt-length confounds across 4 models and 5 benchmarks with 0% parse failures on successfully generated responses. We find that structured formats are capacity-dependent. Models with sufficient headroom absorb JSON constraints without degradation (Sonnet: % JSON vs. % CoT on MATH-Hard). In contrast, formats severely degrade models operating near their limits through two distinct mechanisms. First, under standard token budgets, Haiku drops 36.2pp () largely due to truncation. Second, even with extended budgets eliminating truncation, GPT-4o-mini drops 28.0pp (), revealing pure capacity competition independent of token exhaustion. This format penalty scales with schema complexity (McNemar ) and cannot be explained by prompt length alone. Furthermore, these results qualify claims of frontier model immunity: on AIME competition math, Opus 4.7 drops from 96.2% to 91.0% under JSON (pp; the displayed percentages are independently rounded, exact difference is pp pp). A delayed-structure ablation -- reasoning freely before formatting -- recovers most of the lost accuracy (3-run mean: 80--87%), supporting the capacity competition mechanism. The practical implication is not to avoid structured output, but to match it to capacity: when a model is near its limits, think first, format later.
What to Format and How: A Benchmark and Workflow Approach for Document Formatting
Recent advances in large language models (LLMs) have opened up new possibilities for automated document formatting. However, real-world formatting often requires identifying targets based on document content. This content-aware setting remains challenging and underexplored, primarily due to the lack of dedicated evaluation datasets.To enable evaluation in realistic content-aware scenarios, we introduce DocFormBench, a benchmark that extends Text-to-Format evaluation to diverse formatting requirements, along with metrics for both accuracy and efficiency.To mitigate redundant document reading in existing methods during formatting, we propose DocFormFlow, a workflow formatting method that decouples target localization from modification execution into what to format and how. Extensive experiments across multiple LLMs and multimodal models show that DocFormFlow consistently improves formatting accuracy while reducing token consumption compared to representative baselines. Further analysis reveals that precise target localization is the primary factor influencing formatting performance. We hope DocFormBench and DocFormFlow will facilitate future research toward more intelligent and reliable document formatting.
IFMTBench: A Comprehensive Benchmark for Multilingual Translation Instruction Following
Modern translation workflows demand more than semantic equivalence. Users routinely require models to preserve JSON or HTML schemas, honor curated glossaries, disambiguate with provided context, and match prescribed registers, often several at once. Conventional metrics such as BLEU and xCOMET capture semantic fidelity but provide little signal on constraint adherence, while general instruction following benchmarks ignore the cross-lingual nature of translation. We introduce \bench, a benchmark for multilingual translation instruction following covering seven languages, with 4,506 single-constraint and 2,838 multi-constraint items spanning six constraint dimensions and five compositional patterns with instructions issued in all seven languages. Constraints are split into a gating subset verified by deterministic checkers and a continuous subset scored by a rubric-based LLM judge, combined under a multiplicative rule that resists reward hacking. Evaluating 15 models reveals systematic gaps that prior protocols miss: Instruction following scales with size more sharply than translation quality, glossary and structured-format constraints dominate the difficulty gradient, and general instruction following rankings correlate only weakly with translation behavior. Our benchmark are available at https://github.com/Tencent-Hunyuan/Hy-MT2/tree/main/IFMTBench.
Plans for Evaluating Structured Generative Search Summaries
We propose a framework for evaluating structured generative search summaries that are placed atop organic web search results. A structured summary, generated by a large language model, typically consists of an overview, several sections with section titles, and a list of source documents that are cited within the summary. We then describe our plans for implementing and evaluating the framework.
Format-Constraint Coupling in Knowledge Graph Construction from Statistical Tables
An extraction schema should not reduce knowledge graph fidelity. On statistical CSV, however, it can. We study country-by-year time-series matrices, a common layout on open-data portals. In this setting, serialization format and schema constraints interact super-additively. Their joint effect exceeds the sum of independent effects by up to +1.180 (2x2 factorial, 6 datasets). Bootstrap 95% CIs are strictly positive on 4/6 datasets, with strongest evidence on wide Type-II matrices. More critically, a schema applied to a mismatched format can trigger catastrophic mismatch. Fact coverage falls below the unconstrained baseline on 4/6 datasets through entity inflation or extraction refusal. We call this observed pattern format-constraint coupling. Probing and token ablation support a surface-form anchoring explanation centred on column-name references. Controlled variants across format-schema pairings, GraphRAG hosts, and LLM families show the same direction within the measured scope; one LLM family shows only partial activation. The observation also has a diagnostic consequence. Three standard retrieval modes largely mask construction quality (delta <= 1pp), whereas direct graph access exposes gaps up to +47.6pp (p < 0.0001). To support fidelity-aware evaluation, we release CSVFidelity-Bench. It contains 15 datasets, 11 Type-II matrices, 4 Type-III tables, and 1,892 Gold Standard facts across 6 domains.
Optimal Representation Size: High-Dimensional Analysis of Pretraining and Linear Probing
Learning to generalise from limited data is a fundamental challenge for both artificial and biological systems. A common strategy is to extract reusable structure from abundant unlabelled data, enabling efficient adaptation to new tasks from limited labelled data. This two-stage paradigm is now standard in modern training pipelines, where pretraining is followed by fine-tuning or linear probing. We provide an analytical model of this process: structure extraction is formalized as principal component analysis on unlabelled data, and downstream learning as linear regression on a separate labelled dataset. In the high-dimensional regime, we derive exact expressions for training and generalisation error showcasing their dependence on representation dimensionality, unlabelled and labelled sample sizes, and task alignment. Our results show that pretrained representations strongly influence downstream generalisation, and we characterize the optimal representation size as a function of task parameters: with abundant pretraining data but scarce downstream data, maximally compressed representations are optimal, whereas with limited pretraining data, higher-dimensional representations generalise better. Furthermore, we establish an exact trade-off between pretraining and supervision, quantifying how much unlabelled data is required to replace a single labelled sample. Beyond our idealised model, we observe similar phenomenology in autoencoders and pretrained LLMs. Altogether, we highlight that optimising representation size is critical, giving conditions for when compression during pretraining improves generalisation.
Sonalyzer-Moz: A Framework for Analyzing the Structure of Mozart's Sonata Form
The sonata form is a musically rich and hierarchically structured form that poses significant challenges for automatic analysis. While music structure analysis has seen strides of progress in recent years, sonata form analysis remains in its early stages. This is largely due to the time-consuming and high barrier of the music background requirement for annotating classical music structures. To advance research in this area, we curated SoSA-Moz, the first large-scale dataset featuring comprehensive hierarchical structure annotations. This work establishes a foundation for systematic sonata form analysis. Leveraging this newly contributed resource, we further propose Sonalyzer-Moz, a baseline model specifically designed for investigating complex sonata structures. This framework integrates feature aggregation with sequential modeling, enabling it to capture both local feature and upper-level structural dependencies. Experiment results show that Sonalyzer-Moz is capable of identifying the components' boundaries of the upper-level structure that are critical to understanding sonata form. Therefore, this method demonstrates, for the first time, the effectiveness of automatic upper-level analysis of sonata form, and provides a robust baseline for future research in the automatic understanding of sonata form while advancing the study of classical music structure analysis.
EgoExo-WM: Unlocking Exo Video for Ego World Models
Egocentric world models present a promising direction for enabling agents to predict and plan, but their performance is constrained by the limited availability of egocentric training data and its inherent partial observability of humans' physical actions. In contrast, exocentric video is abundant and reveals body poses well, but lacks direct alignment with an agent's action space -- and is not egocentric. We propose a method to bridge this gap by extracting structured body pose from exocentric video as a representation of action and transforming the exocentric video to egocentric video, informed by a human kinematics prior. This process unlocks the integration of in-the-wild exocentric data for egocentric world model training. We show that training whole-body action-conditioned egocentric world models with our converted data significantly improves both prediction quality and downstream planning performance, where we infer the sequence of body poses needed to achieve a visual goal state. Our approach paves the way to enlist arbitrary in-the-wild videos for building powerful egocentric world models, furthering applications in robot planning and augmented-reality guidance.
Coherency through formalisations of Structured Natural Language, A case study on FRETish
Formalisation is the process of writing system requirements in a formal language. These requirements mostly originate in Natural Language. In the field of Formal Methods, formalisation is often identified as one of the most delicate and complicated steps in the verification process. Not seldomly, formalisation tools and environments choose various levels of requirement descriptions: Natural Language, Technical Language, Diagram Representations and Formal Language, to mention a few. In the literature, there are various maxims and principles of good practice to guide the process of requirement formalisation. In this paper we propose a new guideline: Coherency through Formalisations. The guideline states that the different levels of formalisation mentioned above should roughly follow the same logical structure. The principle seems particularly relevant in the setting where LLMs are prompted to perform reasoning tasks that can be checked by formal tools using Structured Natural Language to act as an intermediate layer bridging both paradigms. In the light of coherency, we analyze NASA's Formal Requirement Elicitation Tool FRET and propose an alternative automated translation of the Controlled Natural Language FRETish to the formal language of MTL. We compare our translation to the original translation and prove equivalence using model checking. Some statistics are performed which seem to favor the new translation. As expected, the translation process yielded interesting reflections and revealed inconsistencies which we present and discuss.
Structural Interpretations of Protein Language Model Representations via Differentiable Graph Partitioning
Protein language models such as ESM-2 learn rich residue representations that achieve strong performance on protein function prediction, but their features remain difficult to interpret as structural evolutionary signals are encoded in dense latent spaces. We propose a plug--play framework that projects ESM-2 representations onto protein contact graphs applies , a lightweight Graph Isomorphism Network with differentiable Gumbel-softmax substructure pooling, to perform structure-aware message passing learn coarse functional substructures for downstream prediction tasks. Across enzyme classification, SoftBlobGIN achieves 92.8% accuracy 0.898 macro-F1. Unlike post hoc analysis of protein language models alone, our method produces directly auditable structural explanations: GNNExplainer recovers biologically meaningful active-site residues, spatially localized functional clusters, catalytic contact patterns. On binding-site detection, SoftBlobGIN improves residue AUROC from using an ESM-2 linear probe to , indicating that these structural explanations are not recoverable from language-model features alone. Learned blob partitions provide an additional layer of interpretability by automatically grouping residues into functional substructures, with blobs containing annotated active-site residues showing higher importance than other blobs (, ), without any active-site supervision. Our framework requires no retraining of the language model, adds only 1.1M parameters, generalises across ProteinShake tasks, achieving of on Gene Ontology prediction AUROC of on binding-site detection. We position this as an interpretable structural companion to protein language models that makes their predictions more transparent auditable.
Mise en Place for Agentic Coding: Deliberate Preparation as Context Engineering Methodology
The rapid adoption of AI coding agents has produced a dominant workflow pattern -- often called "vibe coding" -- that prioritizes speed of implementation over deliberate preparation. We argue that this approach creates a systematic alignment problem: agents that lack sufficient context produce code requiring extensive debugging and refactoring, consuming substantial development time. Drawing on the culinary concept of mise en place (everything in its place; abbreviated MEP), we propose a three-phase preparation methodology for agentic coding: (1) contextual grounding, where domain expertise and tacit knowledge are externalized into structured documents; (2) collaborative specification, where human-agent dialogue produces detailed design artifacts; and (3) task decomposition, where specifications are converted into structured, dependency-aware task records. We report on the application of MEP during a competitive hackathon, where roughly two hours of preparation enabled a rapid parallel implementation of a full-stack educational platform by concurrent AI agents. We introduce the concept of context fluency as an emerging developer skill -- the ability to create rich, structured context that agents can act on -- and connect it to established frameworks in backward design and tacit knowledge externalization. We conclude with a research agenda for empirically validating preparation-phase methodologies in AI-assisted software development.
GRAVITY: Architecture-Agnostic Structured Anchoring for Long-Horizon Conversational Memory
Long-horizon memory systems increasingly improve how evidence is stored and retrieved, yet the generator must still reason over fragments whose cross-session relationships are implicit. We study generation-time memory organization as a distinct design dimension and introduce GRAVITY (Generation-time Relational Anchoring Via Injected Topological MemorY), a host-independent auxiliary memory layer. GRAVITY consolidates raw dialogue into entity profiles, temporal event traces, and cross-session topic summaries, then retrieves and injects query-relevant records through the prompt interface. Across five heterogeneous memory systems on LongMemEval and LoCoMo, it improves every host--benchmark baseline under two distinct LLM configurations. Controlled analyses separate gains from organizing already available evidence and from consolidating information across the full history. Under a matched LightMem pipeline, the entity--event--topic representation reaches 83.9% on LoCoMo, 3.6% above the strongest of six alternative auxiliary representations. These results show that generation-time structure is a portable complement to existing memory retrieval, while its interaction with host evidence depends on the benchmark and host.
When 2D Tasks Meet 1D Serialization: On Serialization Friction in Structured Tasks
In the LLM era, many symbolic and structured problems are presented to models through 1D text serialization. Yet some such problems are natively two-dimensional: their relevant relations, such as row--column correspondence or spatial adjacency, are defined by position in a 2D layout rather than by sequential order. This raises a representational question: does preserving the same symbolic entries in a 1D sequence also preserve the relational structure needed for computation? We study this issue through the lens of serialization friction: the representational mismatch in which the same underlying task instances and entries are still present, but relations that depend on layout become implicit under 1D serialization. The study uses a controlled synthetic testbed of three tasks: matrix transpose, Conway's Game of Life, and LU decomposition. In each task, the same instances are presented either as 1D text serialization or as their native 2D layout rendered as an image. Across this testbed, 1D serialization degrades more sharply as task size grows, and errors under serialization exhibit spatially structured patterns, suggesting that this presentation choice is consequential within our testbed. To further interpret these results, we add supplementary analyses that include a within-visual probe and an additional comparison of the two input presentations under the mixed-training transpose setting. These findings suggest that, for layout-defined tasks, reducing inputs to 1D serialization is not a neutral choice of representation.
Token Space: A Category Theory Framework for AI Computations
We introduce Token Space, a categorical framework for AI computations based on explicit structural records. Five theses guide it: object interiors should be data; category theory should compute with its own objects; computational interfaces should specify structural obligations; equal vectors need not identify the same Token occurrence; and computation should admit an unbounded, dynamically organized population of Token computing cores. A Token is a finite tuple of carrier elements and fixed symbols. A Token class pairs a carrier with a heap of records; Token maps preserve those records. The elementary category has finite limits, finite coproducts and exponentials, but is not a topos. Algebraic tokenization is fully faithful for a fixed finitary signature with all homomorphisms. Small categories and functors have record encodings, natural transformations have endpoint-constrained encodings, and finite categorical constructions are executable. Operators and supported tree reification expose internal structure. For represented finite mappings, valid acyclic graphs evaluate through unique Token maps. Completed parts glue by pullback-pushout squares, sharing induces an adjunction on completion lattices, frontier interfaces form a functor, and certified residual replacement preserves the remaining result. Effective finite transitions preserve finite configurations; a uniform generator yields arbitrarily wide ready populations. Requests with finite dependency closures complete under stated progress conditions. Transformers are one implementation family: permutation heaps characterize equivariance and prefix-agreement heaps characterize causality under specified interfaces. Structural distillation uses teacher-induced heaps; relation-saturating quotients characterize exact preservation and reflection of recorded structure.