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01.
arXiv (CS.CV) 2026-06-19

SpatialSV: Internalizing Interpretable 3D Spatial Awareness in MLLMs via Task-Oriented Visual Supervision

Unlocking the spatial intelligence of multimodal large language model (MLLMs) is crucial for understanding and interacting with the 3D world. Prevailing approaches typically inject spatial priors via external tools, which impose significant inference overhead, or rely on latent feature distillation, which remains uninterpretable and lacks fine-grained geometric constraints. To address these issues, we propose SpatialSV, a framework designed to internalize robust 3D spatial awareness within MLLMs while simultaneously offering inherent interpretability. Deviating from passive feature imitation, SpatialSV employs task-oriented visual supervision, compelling the model to actively lift its 2D visual features into explicit 3D representations, including depth maps, camera poses, and point clouds. Crucially, this 2D-to-3D lifting process provides a transparent window into the model's representations: the resulting 3D reconstructions serve as an intuitive proxy for visualizing and diagnosing the quality of the model's intrinsic spatial knowledge. Extensive experiments across multiple models and benchmarks demonstrate the effectiveness of SpatialSV in enhancing and interpreting MLLMs' spatial intelligence. Furthermore, the framework exhibits strong generalization in semi-supervised settings, validating its potential to leverage unlabeled visual data for scalable, interpretable spatial representation learning.

02.
arXiv (CS.CL) 2026-06-18

UniECG: Understanding and Generating ECG in One Unified Model

Electrocardiogram (ECG) interpretation is a fundamental skill in medical education, yet students often need more than static examples to connect waveform evidence with diagnostic reasoning. This paper presents UniECG as a step toward interactive ECG education. UniECG supports two complementary learning interactions: given an ECG signal or image, it generates an evidence-based explanation; given a textual learning objective, it generates a corresponding ECG signal example for case-based learning. The model follows a two-stage design. First, it learns grounded ECG explanation from ECG signal–image–text data. Second, it introduces special ECG generation tokens and aligns their hidden representations with a pretrained text-conditioned ECG diffusion model, enabling controllable signal-level ECG generation. We evaluate UniECG through grounded ECG explanation and generation-oriented qualitative analysis, examining its potential to support explanation and case-based learning. UniECG is intended as an educational aid and a research step toward interactive AI-assisted ECG learning, rather than a clinically validated diagnostic system.

03.
arXiv (CS.CL) 2026-06-18

The Personalization Trap: How User Memory Alters Emotional Reasoning in LLMs

When an AI assistant remembers that Sarah is a single mother working two jobs, does it interpret her stress differently than if she were a wealthy executive? As personalized AI systems increasingly incorporate long-term user memory, understanding how this memory shapes emotional reasoning is critical. We investigate how user memory affects emotional intelligence in large language models (LLMs) by evaluating 15 models on human-validated emotional intelligence tests. We find that identical scenarios paired with different user profiles produce systematically divergent emotional interpretations. Across validated user-independent emotional scenarios and diverse user profiles, systematic biases emerged in several high-performing LLMs where advantaged profiles received more accurate emotional interpretations. Moreover, LLMs demonstrate significant disparities across demographic factors in emotion reasoning and supportive recommendations tasks, indicating that personalization mechanisms can embed social hierarchies into models' emotional reasoning. These results highlight a key challenge for memory-enhanced AI: systems designed for personalization may reinforce social inequalities. To mitigate these disparities, we curate a general-purpose preference dataset designed to reduce demographic profiles' influence on emotional understanding.

04.
arXiv (CS.CL) 2026-06-17

Regression Language Models for Code

We study code-to-metric regression: predicting numeric outcomes of code executions, a challenging task due to the open-ended nature of programming languages. While prior methods have resorted to heavy and domain-specific feature engineering, we show that a single unified Regression Language Model (RLM) using a frozen LLM encoder can simultaneously predict directly from text, (i) the memory footprint of code across multiple high-level languages such as Python and C++, (ii) the latency of Triton GPU kernels, and (iii) the accuracy and speed of trained neural networks represented in ONNX. In particular, a relatively small 300M parameter RLM based on T5Gemma, obtains >0.9 Spearman-rank on competitive programming submissions from APPS, and a single unified model achieves >0.5 average Spearman-rank across 24 different programming languages from CodeNet. Furthermore, the RLM can obtain the highest average Kendall-Tau of 0.46 on five classic NAS design spaces previously dominated by graph neural networks, and simultaneously predict architecture latencies on numerous hardware platforms.

05.
arXiv (CS.CL) 2026-06-15

GitOfThoughts: Version-Controlled Reasoning and Agent Memory You Can Replay, Diff, and Merge

Large language model (LLM) reasoning is ephemeral: chains of thought vanish with the context window, pruned search branches leave no record, and memory buffers cannot be diffed, merged, or audited. Every other complex software process (code, infrastructure, data, experiments) is version-controlled; reasoning is not. We introduce GitOfThoughts, which stores an agent's reasoning tree as a git repository: every scored thought is a commit, scores are notes, outcomes are tags, and retrieval is "git log" over the agent's own history. This makes reasoning replayable, auditable, and mergeable across agents at near-zero engineering cost. We then ask the harder question: does memory, in any substrate, actually improve accuracy? Across five substrates (none, markdown, vector, graph, git), two benchmarks, two model scales, and pre-registered replications, the answer for novel problems is no. No memory format reliably helps, and a promising early result collapsed under its own pre-registered replication. Memory pays only above what we call the copyability threshold: when the retrieved case is a near-duplicate of the current problem (similarity >~ 0.8), accuracy jumps sharply; below it, nothing. The gain is answer retrieval, not method transfer: a 4.5x larger model doubles the near-duplicate payoff yet still cannot extract a transferable method from a worked example. The only general lever we find is test-time sampling. The case for git-as-substrate is therefore auditability, provenance, and mergeability at accuracy parity. We document a retracted result and a refuted hypothesis to model the evaluation standard we hold ourselves to.

06.
medRxiv (Medicine) 2026-06-15

Natural Language Processing Based Solution for Labeling Brain Metastasis Identified in Radiology Reports

Abstract Purpose: Brain metastases (BM) far exceed primary CNS tumours and constitute the majority workload for neuro-oncology care providers. Currently, the cancer registries only capture synchronous BMs, which is only a small proportion of all BMs. We aim to develop and validate a natural language processing (NLP) algorithm that identifies brain metastases in radiology reports, enabling scalable surveillance of asynchronous BMs. Methods: Using population-based cancer registry data in Alberta, Canada, we identified a cancer cohort diagnosed between 2012–2019 with follow-up to 2022. All brain/head radiology reports at and post-cancer diagnosis were identified. Reports were sampled through a multi-phase approach and manually labeled for BM presence. We trained two Bio_ClinicalBERT models on the "Findings" and "Impressions" sections, respectively, and took the maximum predicted probability as the report-level prediction. Internal and external validation used reports from the Canadian provinces of Alberta, Ontario, and British Columbia. Results: The models were trained on 1,879 samples. For internal validation, 1,833 reports from 357 patients were tested. At a probability threshold of 0.4, the model achieved a sensitivity of 0.888 and precision of 0.499. The ensemble substantially outperformed single-section models, which achieved sensitivities of only 67.8% (Findings) and 74.2% (Impressions). On external validation, sensitivity was 0.918 in Ontario and 0.726 in British Columbia, demonstrating robustness across diverse data distributions. Conclusions: An NLP-based pipeline processing both Findings and Impressions sections has been developed and validated in three Canadian provinces. It meets cancer registry operational requirements and to be implemented into the surveillance workflow in Alberta and British Columbia, providing a foundation for population-level BM surveillance.

07.
arXiv (CS.CL) 2026-06-16

PathRouter: Aligning Rewards with Retrieval Quality in Agentic Graph Retrieval-Augmented Generation

Agentic GraphRAG trains language-model agents to iteratively retrieve and reason over graph-structured evidence, enabling more accurate and context-aware decision-making by efficiently navigating complex information networks. However, outcome-only reinforcement learning suffers from answer-path reward aliasing, where correct answers may come from shortcuts rather than useful evidence paths. It also exhibits search-update ambiguity, as scalar trajectory-level feedback does not indicate which retrieval actions to adjust. To mitigate these shortcomings, we present PathRouter, a path-aware training framework for agentic GraphRAG. PathRouter jointly evaluates each trajectory along answer correctness and evidence-path overlap, yielding four trajectory categories with differentiated GRPO advantage scaling that suppresses shortcut reinforcement while preserving evidence-seeking behavior. For evidence-poor trajectories, a frozen gold-evidence teacher provides token-level KL guidance on reasoning and search-query tokens, excluding answer tokens to avoid direct response imitation. Experiments on six QA benchmarks across three model sizes show that PathRouter consistently improves answer F1 and evidence-path overlap, achieving average F1 gains of 3.1 on 3B and 4.9 on 7B models compared to a strong baseline.

08.
arXiv (CS.LG) 2026-06-25

Towards Continuous Power Forecasting: Practical Continual Learning for Real-World Energy Systems in Nonstationary Time Series

arXiv:2606.24955v1 Announce Type: new Abstract: Power forecasting models deployed in real-world energy markets must operate under nonstationary conditions, where data distributions continually evolve due to weather variability, infrastructure upgrades, and changing consumption behaviors. In practice, these models face strict operational constraints: historical data may be limited or unavailable for repeated retraining, and uninterrupted long-term service is often required. This paper addresses these challenges by proposing the paradigm of Continuous Power Forecasting, which views power forecasting as a continual learning problem rather than a static offline task. Based on an adaptive continual learning framework for regression, we systematically investigate the practical effectiveness of six representative continual learning approaches from three methodological categories. These approaches are evaluated under different realistic assumptions regarding data accessibility and update policies. Experimental validation on real-world power datasets demonstrates that continual learning enables forecasting models to self-adapt to distributional drift, accumulate knowledge over time, and mitigate catastrophic forgetting without relying on large-scale historical data storage. Beyond performance gains, our study provides practical insights into the stability and adaptation behaviors of different continual learning approaches under realistic operational constraints. Overall, this work illustrates how continual learning can be pragmatically integrated into industrial power forecasting pipelines, offering a scalable and sustainable solution for long-term deployment in dynamic environments.

09.
arXiv (CS.AI) 2026-06-16

The Faithfulness Gap: Certifying Semantic Equivalence Between Natural-Language and Formal Mathematical Statements

arXiv:2606.16541v1 Announce Type: new Abstract: Autoformalization, translating natural-language mathematics into formal proof assistants, is bottlenecked not by translation fluency but by faithfulness: a formal statement can typecheck and be provable, yet still encode a different theorem than the source intended. We introduce Bidirectional Provability Fingerprinting (\bpf{}), a framework that certifies faithfulness by characterizing each candidate through its forward and backward consequence neighborhoods in the ambient theory and matching these against probes derived from the natural-language statement. We further introduce four novel components: (i) Counterfactual Probe Generation (\cpg{}), a contrastive procedure that synthesizes probes targeting specific drift directions; (ii) the Equivalence Spectrum, a continuous faithfulness score that replaces brittle binary verdicts; (iii) Adaptive Probe Budget Allocation (\apba{}), an information-theoretic budget router; and (iv) Faithfulness-Guided Decoding (\fgd{}), which uses \bpf{} signals as a reward during autoformalization. We prove a drift detection theorem and a PAC-faithfulness result establishing that the equivalence class of a natural language statement is learnable from $\mathcal{O}(\log(1/\delta)/\varepsilon)$ probes under mild assumptions. We release \driftbench{}, a benchmark of $2{,}183$ NL/Lean~4 pairs with controlled drift labels across six subfields of mathlib4. \bpf{}\,+\,\cpg{} detects $89.6\%$ of drifted formalizations at a $3.0\%$ false-positive rate-against $41.2\%$ for typecheck and $63.3\%$ for LLM-judge baselines, and \fgd{} reduces the rate at which a state-of-the-art autoformalizer emits drifted statements by $47\%$. https://pmlrbd.github.io/BPF/

10.
arXiv (CS.CL) 2026-06-11

"Do Not Mention This to the User": Detecting and Understanding Malicious Agent Skills in the Wild

LLM-based coding agents increasingly rely on third-party extensions called skills, which bundle natural language instructions and helper scripts that execute with full user privileges. Community registries have emerged to distribute these skills, but the security implications remain unstudied due to the absence of labeled threat data. This paper presents a systematic security analysis of 98,380 skills collected from two major registries. Through a combination of static pattern matching and dynamic behavioral verification, we identify 157 skills exhibiting confirmed malicious behavior, encompassing 632 distinct vulnerabilities across 13 attack techniques. Our analysis reveals that these threats are deliberate rather than accidental: each malicious skill contains an average of 4.03 vulnerabilities spanning multiple attack phases. We identify two dominant attack strategies with statistically significant negative correlation – credential theft via remote code execution, and agent manipulation through adversarial instructions embedded in documentation. Over half of all confirmed cases originate from a single threat actor employing templated brand impersonation at scale. We further observe that attack sophistication correlates with concealment investment, with advanced skills universally employing undocumented capabilities while also exploiting platform-native trust mechanisms. Following responsible disclosure, registry maintainers removed all 157 (100%) of the reported skills. Our dataset and detection pipeline are publicly available to facilitate future research on securing LLM agent ecosystems.

11.
arXiv (quant-ph) 2026-06-16

Interaction-enabled topological pumping of Rydberg electrons

arXiv:2606.15126v1 Announce Type: cross Abstract: Topological pumping is a paradigmatic realization of quantized transport in band systems, yet its fate in strongly correlated regimes, especially with long-range interactions, remains largely unexplored. Here we report the experimental observation of interaction-enabled topological pumping of correlated Rydberg electrons in a synthetic lattice. We show that dipolar exchange interactions induce a controllable shift of the underlying topological singularity in parameter space, such that a fixed pumping trajectory can be driven through successive topological transitions by tuning the interaction strength alone. This leads to the emergence and breakdown of quantized transport. The observations are consistent with an effective Rice-Mele description with interaction-renormalized onsite potentials and are supported by characterizing the adiabaticity and robustness to control trajectory imperfections. Our results establish a platform for exploring interaction-controlled topological transport beyond perturbative regimes and open a route toward engineering correlated topological matter in synthetic quantum systems.

12.
arXiv (CS.LG) 2026-06-24

Task Vector Bases: A Unified and Scalable Framework for Compressed Task Arithmetic

arXiv:2502.01015v5 Announce Type: replace Abstract: Task arithmetic, representing downstream tasks through linear operations on task vectors, has emerged as a simple yet powerful paradigm for transferring knowledge across diverse settings. However, maintaining a large collection of task vectors introduces scalability challenges in both storage and computation. We propose Task Vector Bases, a framework compressing $T$ task vectors into $M < T$ basis vectors while preserving the functionality of task arithmetic. By representing each task vector as a structured linear combination of basis atoms, our approach supports standard operations such as addition, negation, as well as more advanced arithmetic ones. The framework is orthogonal to other efficiency-oriented improvements in task arithmetic and can be used in combination with them. We provide theoretical analysis showing that basis compression retains addition generalization guarantees and enables principled unlearning, with error bounds depending on reconstruction quality. Empirically, our proposed basis construction methods consistently outperform heuristic basis construction baselines and, in some cases, even surpass the performance of full task vector collections across diverse downstream applications while reducing storage and computational requirements. The code is available at https://github.com/uiuctml/TaskVectorBasis.

13.
arXiv (quant-ph) 2026-06-16

Morphology-resolved scrambling in a chaotic quantum billiard

arXiv:2606.16865v1 Announce Type: new Abstract: Chaotic quantum systems can retain spatial memory through scarred eigenstates, but whether these static structures control scrambling remains unclear. This work establishes a morphology-resolved connection between scarred eigenstates and eigenstate-resolved OTOCs in a peanut-shaped quantum billiard. Scalar localisation diagnostics, including differential entropy and continuum participation ratios, detect anomalous concentration but discard spatial architecture. A scale-normalised density overlap, in contrast, directly compares probability density profiles, revealing families of orthogonal eigenstates with nearly identical spatial morphology. Comparing the complete OTOC time traces of these orthogonal eigenstates reveals that morphological recurrence has dynamical content: moderate density overlap yields no universal prediction, whereas strongly recurring morphologies exhibit nearly identical OTOC growth and saturation. Thus, scarred structures act as spatial templates for operator growth, not merely static violations of ergodicity. This morphology-resolved framework turns eigenstate shape into a quantitative predictor of scrambling and provides a scale-controlled diagnostic of weak ergodicity breaking in quantum chaos.

14.
arXiv (CS.AI) 2026-06-11

The Art of Interrogation: Consistency Amplifies Factuality in Spatial Reasoning

arXiv:2606.11918v1 Announce Type: new Abstract: Current Large Reasoning Models (LRMs) exhibit remarkable general capabilities but significantly underperform in spatial reasoning tasks. Existing approaches treat this gap as a knowledge deficit, relying on supervised fine-tuning (SFT) to ingest labeled spatial data from external vision sources or synthetic engines. In contrast, we argue that for many tasks, spatial reasoning capabilities are already present in pre-trained LRMs but require alignment through logical coherence under geometric 2D and 3D constraints. In this work, we propose a self-supervised reinforcement learning (RL) framework that targets the internal reasoning process without requiring ground-truth annotations. By formalizing the notion of consistency verifiers – reward functions that check for geometric and semantic consistency under transformations – we demonstrate that models can improve their spatial reasoning abilities. We use both image transformations, like flipping, and textual transformations, like swapping the order of objects in the question, and propose a new optimal transport-based RL strategy, OT-GRPO, which is a minimal-matching variant of group relative policy optimization tailored to pairwise verifiers. We show that this label-free consistency training approaches the accuracy of models trained with ground-truth supervision and achieves similar generalization across diverse tasks and data domains.

15.
arXiv (CS.CV) 2026-06-15

CausalMotion: Structured Physical Reasoning as Keyframe and Trajectory Guidance for Training-Free Video Generation

Recent advances in diffusion-based video generation have significantly improved visual quality and short-term temporal coherence. However, existing methods still struggle to produce videos with physically consistent and causally plausible dynamics, especially in scenarios involving long-horizon interactions. This limitation arises from the fact that video diffusion models primarily learn physical consistency implicitly, while vision-language models can directly model physical laws. Based on this idea, in this work, we propose CausalMotion, a training-free framework that injects explicit physical reasoning into video generation through structured intermediate representations. Our key idea is to decouple reasoning from generation by leveraging a vision-language model to decompose a text prompt into a sequence of causally consistent keyframes and object-centric motion trajectories. These representations are then aligned and integrated as soft constraints to guide a pretrained video diffusion model during inference. This design enables explicit modeling of object dynamics and causal transitions without requiring additional training or supervision. Extensive experiments show that our method consistently improves physical plausibility and temporal coherence, particularly in dynamics-intensive scenarios, while maintaining high perceptual video quality.

16.
arXiv (CS.CL) 2026-06-11

External Experience Serving in Production LLM Systems: A Deployment-Oriented Study of Quality-Cost Trade-offs

Production LLM systems accumulate reusable operational experience, but the practical deployment issue is not merely whether such experience can help. It is how different serving strategies trade off quality against online cost under realistic constraints. Injecting external experience can improve task quality, yet it also increases prompt burden, latency, and serving pressure. We study external experience serving as a deployment-oriented quality-cost trade-off problem. We evaluate this question in a real production moderation setting, with tool-use and GPQA as supporting contrast tasks that expose different output-cost regimes. We compare no-experience baselines, random experience controls, global prompt injection, and retrieval-based selective injection, and analyze both task quality and serving cost. The results show that, once experience becomes case-dependent, selective retrieval provides a stronger operating point than unconditional global injection. They further show that retrieval quality matters more than simply increasing Top-$K$, and that the same serving policy can exhibit substantially different cost-benefit profiles across short-output and decode-heavy regimes. These findings suggest that external experience is best treated as a selective, cost-aware serving decision rather than as a universal add-on. Overall, in the settings studied here, external experience pays off only when both the serving interface and the task-specific cost structure make its quality gains worth the online cost.

17.
arXiv (quant-ph) 2026-06-16

Worst-case depth hierarchy for shallow quantum circuits

arXiv:2606.16425v1 Announce Type: new Abstract: Circuit depth is a central resource in complexity theory. While bounded-depth classical circuits admit well-understood hierarchy theorems, the internal structure of constant-depth quantum computation remains comparatively unexplored. We prove an explicit depth hierarchy theorem for $\mathsf{QNC}^0$. For each $d\ge 12$, we construct a family of two-round interactive problems on which no depth-$(d-1)$ quantum circuit can achieve near-perfect success, regardless of gate set, circuit size, or ancillary qubits. In contrast, we prove that our construction admits realizations by simple bounded fan-in quantum circuits of depth larger than $d$ by a small constant factor. Moreover, all bounded fan-in classical circuits of sublogarithmic depth (in the input size) fail to achieve perfect success on these tasks for every $d$, yielding a hierarchy of problems that show unconditional quantum advantage of $\mathsf{QNC}^0$ over $\mathsf{NC}^0$. A key obstacle is the scarcity of lower bound techniques for quantum circuits. To address this, we develop methods to analyze how depth affects a circuit's ability to realize nonlocal correlations amongst its output qubits in a fine-grained manner. Our approach exploits the correspondence between constraint systems and nonlocal games, translating group-theoretic constructions into rigid operator-valued constraint systems and then into non-local games. In particular, we construct constraint systems whose unique faithful operator-valued solutions require every perfect strategy, and every near-perfect strategy to a fixed precision, to implement multi-controlled phase operations. This reduces to a nonlocal unitary-synthesis problem, yielding depth lower bounds for both shallow quantum and classical circuits. These results show that increasing depth strictly increases computational power within $\mathsf{QNC}^0$, establishing a genuinely quantum hierarchy.

18.
arXiv (CS.LG) 2026-06-11

Querying Counterfactuals on Tissue Graphs with Supervised Disentanglement

arXiv:2606.08493v2 Announce Type: replace-cross Abstract: Tissue graph counterfactuals ask how a cell's expression would change under altered spatial neighbor contexts. Such queries are central to predicting cell behavior in tissues, but lack a unified definition, with existing methods targeting specific intervention types or treating cells as i.i.d. In this work, we first formalize tissue graph counterfactuals as a class of spatial interventions that either rewire connections between cells (edge perturbation) or modify the expression of their neighbors (node perturbation). We then introduce Cellina (https://cellina.readthedocs.io) - a framework that uses supervised disentanglement to decompose a cell's intrinsic state from its spatial context, using the latter as a conditioning input for counterfactual predictions. Across benchmarks spanning over 2.5 million spatially-resolved cells in colorectal cancer and mouse brain, Cellina outperforms spatially-informed and non-spatial competitors in in-silico graph perturbations, disentanglement, and scalability. Additionally, we show that Cellina reveals biologically distinct cancer subdomains in an unsupervised manner and enables targeted neighbor perturbation simulations.

19.
Nature (Science) 2026-06-10

Lignin to adipic acid in a high-yield chemical and biological redox process

Viable manufacturing pathways to produce bio-based chemicals from renewable feedstocks, such as lignin derived from plant biomass, are needed to decarbonize the chemicals manufacturing sector. Converting the recalcitrant lignin polymer to valuable bioproducts remains a longstanding challenge in biorefining, with the highest reported single-product yield from lignin currently around 20 wt% (refs. 1–4). Most existing lignin depolymerization strategies target aryl–ether bond cleavage, which can produce aromatic monomers in yields of only about 30 wt%, and&nbsp;still as complex mixtures with C–C-linked dimers and oligomers5,6. The recalcitrance of these C–C linkages between aromatic moieties fundamentally limits single-product yields from lignin, prompting the development of strategies to efficiently cleave these C–C bonds3,7–9. Here we show how reductive processing of lignin from poplar accesses a hydrocarbon mixture of alkyl-aromatic monomers and oligomers that is privileged for oxidative conversion to monomeric aromatic carboxylic acids, comprising mostly benzoic acid and phthalic acid isomers in up to 73 wt% monomer yields, using a Co/Mn/Br catalyst. The soil bacterium Pseudomonas putida KT2440 was engineered to convert this mixture of aromatic carboxylic acids to muconolactone, a precursor to bio-based nylons, enabling final adipic acid yields up to 26 wt% (gram adipic acid per gram lignin) with a maximum theoretical yield of 57&nbsp;wt%. This pairing of reductive and oxidative steps with lignin resembles processes in petrochemical refining and shows how lignin may be converted into a single, valuable bioproduct in high yields. A chemical and biological redox process that resembles processes in petrochemical refining is used to convert lignin from poplar into a single, valuable bioproduct, adipic acid, in high yields.

20.
arXiv (CS.CL) 2026-06-16

A large-scale pipeline for LLM-assisted corpus annotation: variation and change in the English consider construction

As natural language corpora expand at an unprecedented rate, manual annotation remains a significant methodological bottleneck in corpus linguistic work. We address this challenge by presenting a scalable pipeline for automating grammatical annotation in voluminous corpora using large language models (LLMs). Unlike previous supervised and iterative approaches, our method employs a four-phase workflow: prompt engineering, pre-hoc evaluation, automated batch processing, and post-hoc validation. We demonstrate the pipeline's accessibility and effectiveness through a diachronic case study of variation in the English evaluative consider construction (consider X as/to be/{\O} Y). We annotate 143,933 'consider' concordance lines from the Corpus of Historical American English (COHA) via the OpenAI API in under 60 hours, achieving 98%+ accuracy on two sophisticated annotation procedures. A Bayesian multinomial GAM fitted to 44,527 true positives of the evaluative construction reveals previously undocumented genre-specific trajectories of change, enabling us to advance new hypotheses about the relationship between register formality and competing pressures of morphosyntactic reduction and enhancement. Our results suggest that LLMs can perform a range of data preparation tasks at scale with minimal human intervention, unlocking substantive research questions previously beyond practical reach, though implementation requires attention to costs, licensing, and other ethical considerations.

21.
arXiv (CS.LG) 2026-06-12

The Mathematics of AI Winters: The mathematical Taxonomy of Paradigm Fragility in AI Winter

arXiv:2606.12610v1 Announce Type: new Abstract: Two major periods of reduced funding and confidence in artificial intelligence research, commonly called the first and second AI winters, are usually explained through engineering failure, commercial disappointment, and inflated expectations. This article develops a complementary thesis: that the dominant paradigms of those periods also met genuine formal barriers, including limitations of representation, optimisation, computational complexity, statistical learnability, and high-dimensional approximation. The contribution is synthetic rather than archival. We do not claim that particular theorems mechanically caused the winters; rather, we show that several central disappointments of early AI were aligned with mathematically precise bottlenecks. We analyse these bottlenecks through the perceptron impossibility results of Minsky and Papert, the complexity-theoretic hardness of exact neural-network training established by Blum and Rivest, minimax rates for nonparametric estimation in high dimension due to Stone, vanishing-gradient analyses by Hochreiter and by Bengio and collaborators, and classical statistical learning theory in the tradition of Vapnik and Chervonenkis, Valiant, and Blumer and collaborators. We then relate these barriers to the later breakthroughs that mitigated, rather than eliminated, them.

22.
arXiv (CS.LG) 2026-06-16

The Data Manifold under the Microscope

arXiv:2606.15760v1 Announce Type: new Abstract: A significant gap exists between theory and practice in deep learning. Generalization and approximation error bounds are often derived for simplified models or are too loose to be informative. Many rely on the manifold hypothesis and on geometric regularity such as intrinsic dimension, curvature, and reach. Progress requires insight into data-manifold geometry and suitable benchmarks, yet existing options are polarized: analytic manifolds with known geometry but limited applicability, or real-world datasets where geometry is only coarsely estimable. We introduce a benchmarking framework for studying data geometry. We repurpose and extend dSprites and COIL-20 with additional transformation dimensions and dense, axis-aligned sampling, and pair them with finite-difference estimators that recover curvature, reach, and volume at near-ground-truth accuracy in a regime where general-purpose estimators are unreliable or difficult to deploy. The framework is intended as a controlled testbed, useful as a calibration environment for geometric estimators and a sandbox for probing theoretical assumptions. To illustrate its use, we present two application studies, namely assessing the scaling behavior of the bounds of Genovese et al. and Fefferman et al., and tracking the layer-wise geometry of a $\beta$-VAE, highlighting the behavior of current bounds and the value of controlled benchmarks for guiding and validating future theory. A reference implementation is available at https://github.com/koulakis/manifold-microscope.

23.
arXiv (CS.AI) 2026-06-11

HERO: Hindsight-Enhanced Reflection from Environment Observations for Agentic Self-Distillation

arXiv:2606.11559v1 Announce Type: new Abstract: Reinforcement learning typically improves multi-turn agent capabilities through the terminal outcome of the trajectories, which makes it difficult to determine credit assignments for each intermediate turns. Recent on-policy self-distillation methods offer a promising alternative by converting privileged feedback into dense token-level supervision through a self-teacher. Our study is motivated by the unexpected performance degradation observed when naively extending this paradigm to multi-turn settings, which we attribute to a lack of alignment between privileged feedback, such as successful trajectories or terminal outcomes, and the student's current decision context. We introduce HERO, a hindsight-enhanced self-distillation framework that uses next environment observations as locally aligned feedback. After each rollout, HERO reflects on the completed interaction to convert each observation into a compact turn-level diagnosis, that captures actionable feedback about the original action such as its necessity, validity or failure cause. On TauBench and WebShop, HERO improves task success and reduces unnecessary turns over environment-feedback-only self-distillation and GRPO. It is especially effective under limited training turn budgets, where successful rollouts are rare and GRPO provides weak reward-contrast signals.

24.
bioRxiv (Bioinfo) 2026-06-23

Model-based inference of gene expression noise from single-cell RNA-sequencing data

The heterogeneity of expression levels among genetically identical cells, termed gene expression noise, is a property of the gene expression process whose importance in the biology of organisms and their evolution is increasingly recognized. Measuring gene expression noise requires single-cell expression data, as obtained from single-cell RNA sequencing (scRNASeq). Its estimation, however, is challenging owing to (i) the presence of technical noise in addition to biological noise, and (ii) the heterogeneity of cell types in the sampled population. We propose a maximum-likelihood framework to infer biological noise from scRNASeq data, while accounting for technical noise, dropout probabilities, and distinct cell sequencing depths. We demonstrate the parameter identifiability using simulations and that the resulting noise estimates are uncorrelated from the mean gene expression, and therefore do not need extra correction in downstream analyses, easing intra- and inter- genome comparisons. Using two technical replicates of scRNASeq data from the wild yeast *Saccharomyces paradoxus*, we show that expression noise can be inferred in a reproducible manner.

25.
medRxiv (Medicine) 2026-06-11

Advancing Clinical Implementation of Cardiovascular Polygenic Risk Scores Through Patient-Level Robustness Assessment

Background and Aims: Polygenic risk scores (PRSs) for atherosclerotic cardiovascular disease (ASCVD) can perform equivalently at the population level yet disagree for individual patients. We examined whether such intra-individual variability reflects genuinely complementary risk information or mainly statistical and methodological uncertainty, and whether it affects clinical classification once PRSs are integrated into SCORE2-OP. Methods: In 4,137 ASCVD-free participants of the CoLaus|PsyCoLaus cohort (478 incident events over a median 14.4 years), we identified 16 ASCVD-PRSs with practically equivalent population-level performance using Bayesian equivalence testing. We quantified intra-individual variability (standard deviation, coefficient of variation, intraclass correlation, Cohen's kappa, extreme discordance), tested whether discordance exceeded chance, decomposed scores into shared and unique genetic components, and assessed variability after integration into SCORE2-OP, benchmarked against perturbation of systolic blood pressure. Results: For a typical individual, risk estimates varied by 18 percentile points across PRSs. Discordance matched chance expectations under a shared-signal model, with no distinct phenotypic profile among discordant individuals, and predictive power resided overwhelmingly in the shared genetic component. Variability tracked PRS size and weighting rather than distinct variants. After integration into SCORE2-OP, 75.6% of participants were placed in different categories by at least one model and 54.6% as both low and high risk; instability was concentrated near guideline thresholds and far exceeded that from blood-pressure measurement error. Conclusions: Equivalent population-level performance is not sufficient to treat PRSs as interchangeable at the individual level, and methodological standardisation and pragmatic clinical trials remain necessary to determine whether PRS integration improves long-term cardiovascular outcomes.