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01.
medRxiv (Medicine) 2026-06-23

Socioeconomic Determinants of Guideline-Concordant Therapy for Early-Stage Non-Small Cell Lung Cancer: A Population-Based Analysis from Appalachian and Non-Appalachian Ohio, 2004-2015

Purpose: To examine the relative contributions of insurance, county-level poverty, and other socioeconomic factors, as compared with Appalachian geography, to receipt of guideline-concordant therapy for early-stage non-small cell lung cancer (NSCLC) in Appalachian and non-Appalachian Ohio. Methods: Retrospective population-based cohort study using the Ohio Cancer Incidence Surveillance System. We identified adults diagnosed with early-stage NSCLC between 2004 and 2015 (N=26,756). The primary outcome was receipt of guideline-concordant local therapy (surgery or definitive radiation). Rural-urban classification used USDA Rural-Urban Continuum Codes. Multivariable logistic regression and Cox proportional hazards models assessed predictors of treatment and survival, with E-values, race-stratified models, and propensity score weighting as sensitivity analyses. Findings: Median age was 71 years; 50.3% were male, 83.8% non-Hispanic White, and 20.4% Appalachian. Overall, 83.6% received guideline-concordant local therapy (59.6% surgery, 24.0% radiation). In adjusted analysis, Medicaid (adjusted odds ratio [OR] 0.53, 95% confidence interval [CI] 0.44-0.63; adjusted risk ratio [RR] 0.94, 0.91-0.96), county-level poverty >20% (OR 0.77, 95% CI 0.68-0.87; RR 0.96, 0.95-0.98), and unmarried status were independently associated with lower therapy receipt, whereas Appalachian residence was associated with modestly higher receipt (OR 1.17, 95% CI 1.06-1.29; RR 1.02, 1.01-1.04). Therapy rates converged across regions over the study period (year x Appalachian interaction p20% (HR 1.13, 95% CI 1.07-1.20). Conclusions: Socioeconomic factors, particularly Medicaid insurance and county-level poverty, were the patient characteristics most strongly associated with lower receipt of guideline-concordant therapy, whereas Appalachian residence was not a barrier. Findings support targeted interventions addressing insurance-related and poverty-related barriers to lung cancer care in high-poverty communities regardless of geographic designation.

02.
PLOS Computational Biology 2026-06-01

BeetleAtlas 2: An enhanced <i>Tribolium castaneum</i> web resource for tissue and developmental transcriptomics allowing refinement of gene predictions

by David P. Leader, Muhammad T. Naseem, Janina L. Rinke, Kenneth Veland Halberg BeetleAtlas is an online resource for tissue- and stage-specific transcriptomics in the red flour beetle, Tribolium castaneum. On updating from the original Tcas5.2 genome assembly to the more recent improved icTriCast1.1 genome assembly it became evident that there were major discrepancies between the gene models of the two genome annotations in use: the OGS3 and the NCBI gene sets. As neither was clearly superior we implemented a new design in BeetleAtlas 2 (beetleatlas.org) comprising two parallel ‘modes’ — one incorporating results using the NCBI gene models and a second incorporating those using the OGS3 gene models. This allows direct comparison where equivalent gene models exist: 50–57% of cases. To aid resolution of discrepancies between the two gene model sets and verification of results, gene models are linked to a custom visualization of RNA-seq read coverage of the genome in the UCSC Genome Browser. This displays reads from 22 tissues and life stages superimposed on the icTriCast1.1 genome assembly. Reference tracks show the NCBI gene models, the OGS3 gene models after translation of their coordinates from the Tcas5.2 assembly, and 1050 discontinued NCBI gene models from the previous assembly after a similar transfer of coordinates. We document various situations in which distinct patterns of expression of the tissues can be used to confirm and extend correlations between the two gene sets, resolve discrepancies between them, make corrections and identify putative genes or exons absent from the current gene sets. BeetleAtlas 2 allows those involved in Tribolium research to avoid the pitfalls inherent in incorrect gene models when planning experiments on specific genes and interpreting the results. It also demonstrates how BeetleAtlas 2 might play an important role in establishing a revised gene set for Tribolium castaneum in the future.

03.
arXiv (CS.CV) 2026-06-24

Training-Time Optical Priors for Wireless Capsule Endoscopy Classification: Hemoglobin-Aware Input Fusion with Cross-Vendor Evaluation

Background. RGB-trained classifiers for wireless capsule endoscopy (WCE) conflate hemoglobin contrast with bile staining and illumination falloff, limiting sensitivity to small-vessel vascular findings such as Lymphangiectasia. We introduce a physics-informed framework that injects an analytic, Monte-Carlo-inspired hemoglobin prior into a standard classifier purely at training time – to our knowledge the first use of an explicit optical light-transport prior in WCE classification. Methods. On Kvasir-Capsule (47,238 frames, 43 patients, 11 evaluable classes; patient-disjoint split) we test, across 6 seeds against an RGB-only EfficientNet-B0 baseline: (i) a 5-channel input-fusion variant feeding the prior P_blood alongside RGB; (ii) a distillation variant that runs on plain 3-channel RGB at inference; and (iii) a three-stream extension adding a temporal Transformer and an autoencoder-residual stream. We replicate across ResNet-18 and ConvNeXt-Tiny and report cross-vendor zero-shot transfer on the public Galar cohort. Results. Input fusion lifts cross-seed macro-AUC 0.760 -> 0.783 (5/6 seeds positive); distillation reaches 0.773; the three-stream model reaches 0.804 (+0.044 over baseline, paired DeLong p < 1e-4). Lymphangiectasia AUC rises 0.238 -> 0.337, sign-consistent across all 6 seeds. A four-variant ablation reveals a parameterization-mechanism boundary: only the spatial-channel form lifts. Cross-vendor zero-shot on Galar retains ~60% of the ConvNeXt-Tiny lift.

04.
arXiv (quant-ph) 2026-06-16

How Many Shots Are Enough for a Quantum Circuit?

arXiv:2606.16965v1 Announce Type: new Abstract: Quantum algorithms require repeated circuit executions, known as shots, to estimate output distributions accurately. Determining the minimal number of shots needed to meet a target accuracy is crucial to reduce costs and resource usage, especially on today's noisy and expensive quantum hardware. In this paper, we address the shot optimisation problem in a black-box setting, where no assumptions are made about the structure of the quantum circuit or the noise model of the backend. We introduce IncrementalExecution, a novel online framework that dynamically determines when to stop executing shots based on the principle of point of diminishing returns: the point at which additional shots no longer significantly alter the empirical distribution of a fixed circuit. The framework supports customisable policies for shot management, enabling flexible trade-offs between execution cost and result fidelity within static execution scenarios. We assess our proposal through an extensive experimental evaluation spanning 33,750 framework configurations across 180 unique static quantum circuit-backend combinations, for a total of 7.3M independent experiments. Unlike prior work that relies on problem-specific knowledge or algorithm-dependent assumptions (e.g., variational or adaptive workflows), our approach is applicable to a large set of static circuits and immediately deployable on current quantum cloud platforms.

05.
arXiv (CS.CV) 2026-06-18

SAMA: Semantic Anchor-aligned Augmentation for Unified Low-Resource Multimodal Information Extraction

Multimodal Information Extraction (MIE)-covering tasks such as Multimodal Named Entity Recognition (MNER), Relation Extraction (MRE), and Event Extraction (MEE)-is essential for understanding multimedia content but remains constrained by severe data scarcity. Although data augmentation is a promising remedy, existing approaches are impeded by coarse cross-modal alignment and fragmented, task-specific designs that fail to exploit shared semantic knowledge. To overcome these limitations, we introduce Semantic Anchor-aligned Multimodal Augmentation (SAMA), a unified framework for generating high-fidelity, task-aware synthetic data. SAMA constructs structured semantic anchors from ground-truth labels to guide a Collaborative Multi-Experts Multimodal Large Language Model (CME-MLLM), which integrates a Universal Adapter for shared semantics with Task-Specific Adapters to produce diverse yet constraint-compliant textual samples. For image synthesis, SAMA employs an Anchor-Preserving Diffusion mechanism that uses anchor-weighted prompts and latent conditioning to maintain critical semantic anchors while diversifying visual contexts. To eliminate the need for manual verification, SAMA further introduces a Dual-Constraint Filtering module that selects synthetic samples based on both cross-modal consistency and anchor fidelity. Extensive experiments across benchmark datasets for MNER, MRE, and MEE demonstrate that SAMA consistently outperforms state-of-the-art augmentation baselines under both fully supervised and low-resource settings, underscoring its versatility, robustness, and effectiveness.

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

Towards the implementation of a quantum classifier

arXiv:2606.10150v2 Announce Type: replace Abstract: In this work, we investigate the use of a quantum circuit as a binary classification model in the context of quantum machine learning. We call this model, binary quantum classifier. First, we describe fundamental concepts of quantum computing and introduce the computational tool used: Qibo, an open-source framework for efficient quantum simulations and quantum hardware control. Then, we describe how to design a binary quantum classifier for the classification of images and small arrays of variables by showing how to input data in the circuit, defining a quantum circuit model Ansatz with trainable parameters and a loss function, and implementing multiple minimizers. We test our quantum classifier with two data sets. The first one is the MNIST data set which is composed of handwritten digits (reduced to only handwritten zeros and handwritten ones for binary classification). We study the behavior of different minimizers by increasing the number of layers of the Ansatz. The second data set represents two different high energy collisions that can occur at colliders such as LHC (CERN). Due to in-time proton-proton interactions known as pile-up, we distinguish two different data sets: "without pile-up" and "with pile-up". These collisions can be represented by images of size 32x32 or by six high-level variables that we call features. By increasing the size of the training data set and the number of layers of the Ansatz, we search for the best minimizer. Splitting the data set in training set and test set, we compute: ROC curve, AUC score, confusion matrices and test set accuracy. For "with pile-up" images, we compare the results obtained with the quantum classifier with a small convolutional neural network. We conclude that is possible to build a binary quantum classifier with a quantum circuit and we highlight its performances and limitations in comparison with classical technologies.

07.
arXiv (quant-ph) 2026-06-11

Planted-Solution Pauli Hamiltonians as a Quantum Benchmarking Primitive

arXiv:2606.11455v1 Announce Type: new Abstract: We introduce a construction of Pauli Hamiltonians with exactly known ground-state energies, intended as reference instances for ground-state energy estimation algorithms. The construction embeds a planted block-product state as the simultaneous ground state of a sum of frustration-free local clauses on overlapping supports, exposes the resulting model only as a polynomial-size linear combination of Pauli operators, and admits optional Clifford conjugation that preserves the spectrum. The framework subsumes classical planted constraint-satisfaction problems as a diagonal special case, providing a direct embedding channel through which classical hardness properties can be inherited. Open-source software, certification keys, and example instances are made publicly available.

08.
arXiv (CS.AI) 2026-06-12

The Containment Gap: How Deployed Agentic AI Frameworks Fail Public-Facing Safety Requirements

arXiv:2606.12797v1 Announce Type: new Abstract: Agentic large language model systems that autonomously invoke tools, maintain persistent memory, and execute multi-step plans are increasingly deployed in public-facing domains, including government services, healthcare triage, and financial advising. We ask whether the frameworks used to build these systems provide architectural-level structural safety guarantees. Applying six containment principles derived from a compositional model of agentic architectures, we audit three dominant frameworks (LangChain, AutoGPT, and OpenAI Agents SDK) and find no native compliance in any of them. Memory integrity, a defense against one of the most prevalent vulnerability classes, is not observed in any of the three evaluated frameworks. We validate these findings empirically: in a simulated government benefits agent built on LangChain, a single memory-poisoning write induces persistent targeted corruption across all tested seeds and backends, increasing the wrongful denial rate for targeted applicants to 88.9%. Under a complex five-factor policy, the same attack preserves aggregate accuracy while increasing targeted wrongful denials by 3.5x, rendering the corruption difficult to detect through standard monitoring. We then introduce two lightweight containment mechanisms: a memory integrity validator and a policy gate, which eliminate both attack vectors with sub-millisecond overhead (

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

Bridging data-driven priors via the score function for posterior sampling – Comparative review and experimental study

arXiv:2606.14800v1 Announce Type: cross Abstract: This paper reviews how a diverse set of popular data-driven priors commonly used in Bayesian inverse problems can be unified through their respective score functions. By framing these priors under this common perspective, we show that they can benefit from their straightfoward and effective integration into a recently proposed sampling algorithm. The applicability of this common framework is illustrated by considering several data-driven priors, namely regularization-by-denoising, normalizing flow-based priors, score-based generative models, and convex-ridge regularizers. For these four particular priors, the performance of the method is evaluated when conducting image inpainting and single image super-resolution. These results, as well as those obtained when restoring real images acquired in a geological context, demonstrate the efficiency of the method. This unified framework proves versatile enough to handle any posterior distribution defined by a broad class of score function-based priors, beyond the specific cases considered in this paper.

10.
arXiv (CS.AI) 2026-06-12

PhononBench:A Large-Scale Phonon-Based Benchmark for Dynamical Stability in Crystal Generation

arXiv:2512.21227v3 Announce Type: replace-cross Abstract: In recent years, generative artificial intelligence has made significant advances in the design of crystalline materials, giving rise to approaches based on graph neural networks, diffusion models, and large language models. Existing evaluations commonly follow the stability-uniqueness-novelty (S.U.N.) framework, where stability is primarily assessed using thermodynamic criteria, which do not fully capture the dynamical stability essential for a material's practical existence. Dynamical stability is a key determinant of whether a material can be synthesized and persist, with phonon spectrum calculations serving as the standard for its evaluation. However, the high computational cost of such calculations has prevented large-scale assessment of dynamical stability in generated crystals. In this work, we introduce PhononBench, the first large-scale benchmark for dynamical stability in AI-generated crystals. Leveraging the recently developed MatterSim interatomic potential, which achieves density-functional-theory (DFT)-level accuracy in phonon predictions across more than 10,000 materials, PhononBench enables efficient phonon calculations and dynamical-stability analysis for 133,838 crystal structures generated by 7 leading crystal generation models. PhononBench reveals a widespread limitation of current generative models: unless otherwise specified, all reported dynamical-stability metrics are evaluated at a phonon-frequency threshold of -0.1 THz, with the average dynamical-stability rate across all generated structures being only 32.15%, and the top-performing model, MatterGen, reaching just 45.05%.In addition, we identify 32,995 crystal structures that are phonon-stable across the entire Brillouin zone under a strict threshold of -0.001 THz. In addition, a web-based service is accessible at http://phononbench.cn/, enabling minute-level ultra-fast phonon predictions.

11.
bioRxiv (Bioinfo) 2026-06-11

A high-quality chromosome-scale reference genome assembly for Asparagus racemosus var. CIM-Shakti (Shatavari), a medicinal plant of Ayurvedic importance

Asparagus racemosus Wild., commonly known as Shatavari, is an important medicinal plant in Ayurveda and is valued for its steroidal saponins, particularly shatavarin compounds, which contribute to its adaptogenic, galactagogue, immunomodulatory, and therapeutic properties. Despite its medicinal and economic importance, genomic resources for this species have remained limited, restricting molecular breeding, pathway discovery, and comparative evolutionary studies within Asparagaceae. Here, we report a high quality chromosome scale reference genome assembly of A. racemosus var. CIM Shakti generated using PacBio HiFi long read sequencing and Omni C chromatin conformation scaffolding. The pseudo haploid assembly spans 817 Mb across 53 scaffolds, with a scaffold N50 of 98.50 Mb, L50 of 5, and a largest scaffold of 113.80 Mb. Ten major chromosome scale pseudomolecules were resolved, corresponding to the haploid chromosome complement of A. racemosus. The assembly showed high gene space completeness, with BUSCO completeness of 99.8% against the Eukaryota dataset and 98.0% against the Embryophyta dataset. BlobToolKit profiling further supported assembly quality, with GC content of approximately 39 to 40% and no major evidence of contamination. EDTA based repeat annotation identified 580.93 Mb of interspersed repetitive elements, accounting for 71.06% of the 817.57 Mb genome assembly. The repeat landscape was dominated by LTR retrotransposons, particularly Gypsy elements, which accounted for 25.01% of the assembly, followed by unclassified LTR elements at 26.58% and Copia elements at 4.84%. Structural and functional annotation identified 29,199 protein coding genes represented by 29,199 transcript models, 138,433 exons, and 125,201 CDS features. The annotation was structurally robust, with an average gene length of 4,605.1 bp, 4.74 exons per transcript, and 97.80% of transcripts containing multiple exons. The CIM Shakti reference genome provides a foundational genomic resource for investigating steroidal saponin biosynthesis, sex chromosome evolution, repeat driven genome expansion, and comparative genomics in Asparagaceae. This assembly will support future studies on medicinal trait improvement, conservation genomics, and genomics assisted breeding of climate resilient Shatavari cultivars.

12.
arXiv (CS.CL) 2026-06-19

Large Language Models Do Not Always Need Readable Language

Large language models (LLMs) are commonly prompted and interfaced with human-readable natural language, even when the intended reader is another model. This paper investigates whether semantic information can be encoded in compact, non-standard textual forms that sacrifice human readability while remaining recoverable by LLMs. We refer to this class of model-centric textual representations as BabelTele, approached here not as a fixed protocol but as an empirical probe into LLMs' capacity to generate and interpret such representations. Through readability diagnostics, model likelihood measures, human questionnaires, and downstream task evaluations, we find that BabelTele can substantially depart from ordinary natural language while preserving core semantics for instruction-tuned LLMs. As a task-agnostic representational paradigm, BabelTele demonstrates high information density, maintaining 99.5% semantic fidelity even when the text volume is condensed to 27.9% of its original length. We further evaluate its semantic robustness in cross-model transfer, agent memory, and multi-agent communication. Results suggest that BabelTele can reduce context overhead while generally maintaining reliable downstream performance, although its effectiveness depends on the compressor-reader pair and task setting. These findings indicate that human readability, natural-language typicality, and model-side semantic recoverability can be partially decoupled, opening a path toward model-native representations in future exploration of LLM systems.

13.
arXiv (CS.AI) 2026-06-16

CONCORD: Asynchronous Sparse Aggregation for Device-Cloud RAG under Document Isolation

arXiv:2606.15179v1 Announce Type: new Abstract: Retrieval-augmented generation (RAG) has emerged as a pivotal technique for improving language models by incorporating external knowledge at inference time. As device-cloud collaborative inference makes it feasible to deploy small language models on edge devices, a new setting arises in which private documents remain on the device and public knowledge resides in the cloud. Privacy and policy constraints often forbid raw document exchange, creating a document-isolated dual-end RAG setting. However, existing methods rely on frequent remote synchronization and dense evidence transfer, limiting throughput under realistic latency and bandwidth conditions. To address this issue, we propose CONCORD, an asynchronous sparse aggregation framework for dual-end RAG under document isolation. CONCORD treats the cloud as an asynchronously arriving evidence source rather than a continuously synchronized co-generator. Specifically, we introduce waiting debt control to decide whether each decoding step should continue waiting for remote participation based on the observed return of waiting. We also design a certificate-guided minimal supplementation mechanism that requests only the remote evidence needed to determine the current greedy decision. Steps that consult the cloud preserve the same greedy token as dense dual-end aggregation, while the remaining steps commit locally without remote evidence. Experiments on Natural Questions and WikiText-2 show that CONCORD improves end-to-end throughput over baselines by $1.66\times$ and $2.15\times$, respectively, while reducing per-token communication by over two orders of magnitude and maintaining comparable answer quality and perplexity.

14.
PLOS Computational Biology 2026-06-03

IsoPepTracker: An interactive web application for peptide-driven isoform analysis

作者:

by Araf Mahmud, Chen Huang Alternative splicing affects 95% of multi-exon genes, generating protein isoforms with distinct functions. While current alternative splicing analyses effectively identify splice events at the RNA level, they provide limited protein-level insight. To address this gap, we developed IsoPepTracker (https://www.isopeptracker.org), a user-friendly web application for analyzing and visualizing differential peptides across canonical and novel isoforms that are theoretically detectable by shotgun mass spectrometry-based proteomics. IsoPepTracker features four modules: Canonical Isoform Analysis, Novel Isoform Discovery, Peptide Sequence Search, and Alternative Splicing Analysis. Each module is tailored for distinct and complementary proteogenomics analyses. Users can input genes, novel cDNA sequences, peptides, or alternative splicing results to pinpoint peptides of interest and identify their associations with target genes or isoforms. We demonstrate the straightforward application of IsoPepTracker in proteogenomics through case studies. IsoPepTracker not only provides informative peptide signatures to understand the protein-level consequences of alternative splicing but also supplies peptide candidates for validation in shotgun proteomics.

15.
arXiv (CS.LG) 2026-06-18

Fair Online Resource Allocation

arXiv:2606.18679v1 Announce Type: cross Abstract: We study the problem of fair online resource allocation, motivated by applications such as refugee resettlement and airline scheduling, where agents arrive sequentially and must be assigned to facilities with limited capacities. We introduce a model that maximizes the overall welfare subject to resource constraints and a Lipschitz fairness requirement, which ensures that similar agents arriving in the same batch receive similar expected outcomes. We first analyze the offline problem, proving that the value of the optimal fair allocation is at least an $\Omega(1/\gamma)$ fraction of the optimal unfair allocation, where $\gamma$ is the fairness coefficient, thereby bounding the price of fairness. For the online setting, we propose an algorithm based on dual mirror descent that enforces fairness constraints within batches while estimating optimal dual variables. We prove that this algorithm achieves sublinear regret relative to the optimal offline fluid benchmark. Finally, we validate our theoretical results using real-world data from the Refugee Economies Programme, demonstrating the algorithm's performance and examining the trade-offs between welfare maximization and fairness enforcement.

16.
arXiv (math.PR) 2026-06-16

Phase Transition in Convex Relaxations for Graph Alignment

arXiv:2606.15581v1 Announce Type: cross Abstract: We study the graph alignment problem for correlated Gaussian Orthogonal Ensemble (GOE) matrices, where the goal is to recover a hidden vertex permutation given two correlated symmetric Gaussian matrices $(A, B)$ with correlation $1/\sqrt{1+\sigma^2}$. While the maximum likelihood estimator is information-theoretically optimal, its computation, which reduces to a quadratic assignment problem, is intractable. Motivated by this, we analyze convex relaxations based on minimizing $\|AX - XB\|_F$ over the set of doubly stochastic matrices and the unit hypercube. We show that when the correlation parameter satisfies $\sigma = o(n^{-1/2}/\log^4 n)$, the solution of either relaxation $(X^\star)$ concentrates around the ground-truth permutation matrix $(\Pi^\star)$, i.e., $\|X^\star-\Pi^\star\|_F^2 = o(n)$, implying recovery of all but a vanishing fraction of vertices after simple post-processing. Combined with existing lower bounds, our results precisely characterize that $\|X^\star-\Pi^\star\|_F^2$ transitions from $o(n)$ for $\sigma = \tilde{o}(n^{-1/2})$ to $\Omega(n)$ for $\sigma = \tilde{\Omega}(n^{-1/2})$. In doing so, our analysis significantly tightens prior results and extends them beyond doubly stochastic relaxations.

17.
arXiv (CS.LG) 2026-06-17

Learning in Matching Games with Bandit Feedback

arXiv:2506.03802v2 Announce Type: replace Abstract: We introduce a learning problem in a generalized two-sided matching market, where agents select actions to interact with their match. Specifically, we consider a setting in which matched agents engage in zero-sum games with initially unknown payoff matrices, and we investigate whether a centralized procedure can learn an equilibrium from bandit feedback. We adopt the solution concept of a matching equilibrium, where a matching \( \mathfrak{m} \) and a set of agent strategies \( X \) form an equilibrium if no agent has an incentive to deviate from \( (\mathfrak{m}, X) \). To quantify deviations of a candidate solution \( (\mathfrak{m}, X) \) from the equilibrium \( (\mathfrak{m}^\star, X^\star) \), we introduce the notion of matching instability, which serves as a regret measure for the learning problem. We propose a UCB-based algorithm in which agents form preferences and select actions according to optimistic estimates of the payoffs. Our analysis establishes a sublinear, instance-independent regret upper bound, further supported by empirical evidence.

18.
arXiv (CS.AI) 2026-06-15

SkillAudit: Ground-Truth-Free Skill Evolution via Paired Trajectory Auditing

arXiv:2606.14239v1 Announce Type: new Abstract: Agent skills are structured procedural packages that guide frozen LLM agents in specialized workflows. Skills rarely remain sufficient after deployment: edge cases, API changes, and deployment constraints become visible only through use, making skill evolution a practical necessity. Existing methods depend on privileged feedback such as held-out validation scores, hidden test outcomes, or environment rewards – signals often unavailable when a practitioner has only a task description and workspace data. We introduce SkillAudit, a framework for evolving agent skills without ground-truth feedback. The key idea is paired trajectory auditing: at each iteration, the same task is executed with and without the candidate skill, isolating how the skill changes agent behavior without external labels. To turn behavioral differences into edit guidance, SkillAudit uses Process-Aligned Contrastive Evaluation (PACE), a cluster of evaluators that maps trajectory divergences to diagnostic signals linked to specific passages in the skill document. A structural verifier, compiled once from the task specification and then fixed, checks task constraints and rolls back harmful updates. SkillAudit routes edits through two pipelines: Refine removes noisy or irrelevant guidance from broadly useful skills, while Repair replaces passages that conflict with the task. Across 89 containerized tasks spanning 8 professional domains, SkillAudit achieves 73.9% average task reward, outperforming an agent without skills (40.9%) and the static expert skill (56.7%). These gains are obtained without accessing hidden tests, reference solutions, or external scoring functions during evolution.

19.
arXiv (CS.LG) 2026-06-24

Stabilizing Black-Box Prompt Optimization with Textual Regularization and Signal Aggregation

arXiv:2507.09839v2 Announce Type: replace Abstract: An increasing number of NLP applications interact with large language models (LLMs) through black-box APIs, making prompt engineering critical for controlling model behavior. Recent Automatic Prompt Optimization (APO) methods iteratively refine prompts using model-generated critiques (often called textual gradients), but they predominantly optimize from failures and underutilize information contained in correct predictions, leading to instability and semantic drift. We propose TRAS (Textual Regularization with Aggregated Signals), a feedback-centric framework that is plug-and-play with existing APO search backbones. It retains the standard textual gradient signal from prior work for error correction and introduces a complementary textual regularizer derived from successful predictions to preserve beneficial prompt components. Because both signals are stochastic and can be noisy, we further introduce Monte Carlo Signal Aggregation (MCSA), which samples multiple gradients or regularizers and aggregates them into a single actionable directive, emphasizing consistent, actionable advice while filtering out outliers. Motivated by rapid model churn, we also formalize Automatic Prompt Migration (APM), the practical problem of adapting an expert prompt across model versions or API providers without losing critical instructions. Across standard APO and APM scenarios, our approach consistently outperforms strong baselines, yielding higher accuracy, faster convergence, and lower query cost, while substantially reducing the degradation observed under naive prompt migration.

20.
arXiv (CS.CV) 2026-06-11

Moving Beyond Diffusion: Hierarchy-to-Hierarchy Autoregression for fMRI-to-Image Reconstruction

Reconstructing visual stimuli from fMRI signals is a central challenge bridging machine learning and neuroscience. Recent diffusion-based methods typically map fMRI activity to a single neural embedding, using it as static guidance throughout the entire generation process. However, this fixed guidance collapses hierarchical neural information and is misaligned with the stage-dependent demands of image reconstruction. In response, we propose MindHier, a coarse-to-fine fMRI-to-image reconstruction framework built on scale-wise autoregressive modeling. MindHier introduces three components: a Hierarchical fMRI Encoder to extract multi-level neural embeddings, a Hierarchy-to-Hierarchy Alignment scheme to enforce layer-wise correspondence with CLIP features, and a Scale-Aware Coarse-to-Fine Neural Guidance strategy to inject these embeddings into autoregression at matching scales. These designs make MindHier an efficient and cognitively aligned alternative to diffusion-based methods by enabling a hierarchical reconstruction process that synthesizes global semantics before refining local details, akin to human visual perception. Extensive experiments on the NSD dataset show that MindHier achieves superior semantic fidelity, 4.67$\times$ faster inference, and more deterministic results than the diffusion-based baselines.

21.
arXiv (CS.AI) 2026-06-16

MiroBench: Benchmarking Realism in Agentic Simulation of Real-world Discussions

arXiv:2606.14715v1 Announce Type: cross Abstract: LLM agents are increasingly used to simulate real world interactions, but it remains unclear whether simulated behaviors preserve the content patterns and interaction dynamics of real human behaviors. Existing evaluations remain fragmented, which makes it difficult to compare systems or measure progress. In this paper, we focus on Reddit discussions as a concrete first step toward evaluating real-world social simulation. Reddit threads provide public, topic-grounded, multi-party interactions where people share experiences, debate, seek advice, express emotion, and collectively respond to products, events, and social issues. These discussions offer an observable window into broader social behavior, making them a useful setting for testing whether LLM agents can reproduce not only fluent text, but also the distributional patterns and interaction dynamics of real online communities. We introduce MiroBench, a benchmark for Reddit discussion simulation built from 4,292 real Reddit threads. MiroBench uses statistical tests to compare generated and real discussions across four major aspects: repetition and semantic uniformity, narrative content, toxicity and aggression, and structural complexity. Experiments across five domains and five models show that current simulators remain distributionally mismatched with real Reddit threads, while a lightweight prompt-based improvement procedure provides only limited gains. MiroBench offers a concrete benchmark for measuring, diagnosing, and improving realism in LLM-based social simulation.

22.
arXiv (CS.CL) 2026-06-19

Characterizing Narrative Content in Web-scale LLM Pretraining Data

The narrative composition of web-scale LLM pretraining corpora remains largely unexplored even though narrative is a fundamental mode of human communication. We present the first fine-grained study of narrative features in Dolma, a 3-trillion-token open pretraining corpus. Drawing on narrative theory, we design a framework spanning three core narrative elements (agency, setting, and events) operationalized as 11 interpretable dimensions. After sampling and annotating a diverse set of 400 passages, we finetune and validate NarraBERT, a RoBERTa-based model for fine-grained narrative prediction. We apply NarraBERT to 3M passages, resulting in a new dataset, NarraDolma. We find (i) narrative structure is measurable at scale across extremely heterogeneous data, (ii) we uncover a continuous, multidimensional narrative structure underlying web text, and (iii) narrative qualities are unequally distributed across pretraining sources and topics in ways that current curation practices neither measure nor account for. Our framework, dataset, and analyses provide a foundation for understanding how narrative qualities are distributed in LLM pretraining data and for studying how data composition affects narrative reasoning tasks. We publicly release NarraDolma and NarraBERT.

23.
arXiv (CS.LG) 2026-06-19

How to sketch a learning algorithm

作者:

arXiv:2604.07328v3 Announce Type: replace Abstract: How does the choice of training data influence an AI model? This broad question is of central importance to interpretability, privacy, and basic science. At its technical core is the data deletion problem: after a reasonable amount of precomputation, quickly predict how the model would behave in a given situation if a given subset of training data had been excluded from the learning algorithm. We present a data deletion scheme capable of predicting model outputs with vanishing error $\varepsilon$ and failure probability $\delta$ in the deep learning setting. Our precomputation and prediction algorithms are only $\tilde{O}(\log(1/\delta)/\varepsilon^2)$ factors slower than regular training and inference, respectively. The storage requirements are those of $\tilde{O}(\log(1/\delta)/\varepsilon^2)$ models. Our proof is based on an assumption that we call stability. In contrast to the assumptions made by prior work, stability appears to be fully compatible with learning powerful AI models. In support of this, we show that stability is satisfied in a minimal set of experiments with microgpt. Our code is available at https://github.com/SamSpo1/microgpt-sketch. At a technical level, our work is based on a new method for locally sketching an arithmetic circuit by computing higher-order derivatives in random complex directions. Forward-mode automatic differentiation allows cheap computation of these derivatives.

24.
arXiv (CS.CL) 2026-06-11

Augmenting Molecular Language Models with Local $n$-gram Memory

Transformer-based language models for SMILES strings suffer from a locality gap: standard character-level tokenization fragments chemically meaningful motifs, forcing models to repeatedly learn local syntax at the expense of long-range dependencies. To address this without disrupting standard tokenizers, we propose MolGram, which integrates a conditional $n$-gram memory module into molecular language models. MolGram maps local string patterns to learned embeddings via scalable hash lookups and dynamically injects this regional context into hidden states. Evaluations across three tasks, including unconditional molecule generation, forward reaction prediction, and single-step retrosynthesis, show that MolGram consistently improves performance. Crucially, our analyses demonstrate that MolGram outperforms baselines with 3$\times$ more parameters, establishing explicit local pattern memory as a highly efficient inductive bias.

25.
arXiv (CS.AI) 2026-06-11

Runtime Skill Audit: Targeted Runtime Probing for Agent Skill Security

arXiv:2606.11671v1 Announce Type: cross Abstract: Agent skills let LLM agents reuse instructions, resources, tools, and workflows, but they also create a new place for malicious behavior to hide. A skill may look benign in its documentation or code while becoming harmful only when it is invoked with particular user requests, local assets, persistent state, or multi-step tool interactions. This makes purely static vetting brittle. We present Runtime Skill Audit (RSA), a dynamic analysis method that audits skills by asking what the skill-mediated agent actually does under targeted runtime conditions. Instead of testing every skill with the same generic tasks, RSA profiles risk-relevant interfaces, prepares the execution context needed to exercise them, and assigns security labels from the resulting trace evidence. We instantiate RSA on OpenClaw and evaluate it on 100 skills against representative static baselines. RSA achieves 90.0\% accuracy with an 88.0\% true positive rate and an 8.0\% false positive rate, improving accuracy by 13.0 percentage points over the best static baseline. Under self-evolving attacks, static detectors collapse after one or two rounds, while RSA continues to detect 19–20 out of 20 malicious skills across rounds.