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01.
arXiv (CS.CV) 2026-06-15

Hierarchical Consistency Learning for Test-time Adaptation in Camouflage Perception

Camouflaged object detection (COD) aims to localize targets that exhibit minimal perceptual differences from backgrounds through physical attributes. Existing methods, constrained by the static train-then-freeze paradigm, suffer from domain rigidity and annotation dependency, limiting their adaptability to scene variations and unseen camouflage patterns. To overcome these, we propose the hierarchical consistency learning (HCL) framework, which integrates test-time adaptation for dynamic representation recalibration. Specifically, we design the hierarchical representation reconstruction (HRR) to alleviate feature entanglement by synergizing spatial reconstruction with dual-stream frequency-domain decomposition, enhancing robustness against appearance homogenization. The pixel and spectrum inference provide structural and contextual priors. We further introduce task affinity guidance (TAG) to propagate knowledge across branches via channel-wise affinity, aligning local discriminative cues and mitigating semantic drift. To ensure semantic invariance, we formulate the prototype consistency calibration (PCC), which aggregates region features into compact prototypes and establishes prototype-feature similarity. This imposes implicit and hierarchical constraints that bridge task and representation gaps. Extensive experiments across four camouflaged and four underwater object benchmarks, under three degradation settings, demonstrate that our method consistently outperforms state-of-the-art approaches, highlighting its robustness and generalization under distribution shifts.

02.
arXiv (CS.LG) 2026-06-12

ShapeBench: A Scalable Benchmark and Diagnostic Suite for Standardized Evaluation in Aerodynamic Shape Optimization

arXiv:2605.20763v2 Announce Type: replace Abstract: Rapid progress in aerodynamic shape optimization (ASO) has outpaced currently-available standardized evaluation frameworks. Fair comparison requires a unified benchmark spanning diverse shape classes, objective formulations, and matched-budget state-of-the-art baselines. We introduce ShapeBench, an open-source ASO benchmark with a unified API spanning 103 tasks across eight shape categories and multiple optimization regimes. Each ShapeBench task includes a validated surrogate for fast search; when feasible, a high-fidelity Computational Fluid Dynamics (CFD) pipeline for final verification is available, enabling systematic fidelity-gap analysis. ShapeBench provides a reproducible protocol with well-configured baselines to compare fairly using a consistent budget metric, allowing for comparison among both classical and LLM-driven methods, including general-purpose optimizers and a new domain-specialized evolutionary LLM baseline, ShapeEvolve. Results on ShapeBench demonstrate substantial variance in optimizer rankings across shape categories and problem formulations, with mean pairwise Spearman $\rho = 0.013$, so single-task conclusions do not reliably generalize across problem classes. The benchmark is also far from saturation; classical methods are rarely applicable across all shape categories and tasks, further highlighting the need for more general-purpose approaches.

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

GrowthHacker: Automated Off-Policy Evaluation Optimization Using Code-Modifying LLM Agents

With data-driven development now widely adopted, online A/B testing is an established method for measuring the effects of new technologies. However, deploying online experiments demands resources for design, implementation, and deployment, and may negatively impact users (e.g., unsafe or unethical outcomes) while requiring weeks of data collection. To address this, the growing research area of off-policy evaluation (OPE), or offline A/B testing, assesses new technologies offline using previously collected logged data. OPE is also a fundamental problem in reinforcement learning and is important where online testing is expensive or risky, such as healthcare, recommender systems, education, and robotics. Despite advances in code-generation large language models (LLMs) and agentic workflows, little is known about whether and how LLMs and LLM-based agents can automatically optimize OPE implementations. We propose GrowthHacker, a benchmark that evaluates baseline LLMs and LLM-based agents on large-scale public datasets. GrowthHacker autonomously and iteratively modifies code, runs OPE, and uses the metrics to guide subsequent optimization. We evaluate methods on Open Bandit Pipeline (OBP) and Scope-RL, and develop a two_agent framework that addresses limitations of existing frameworks while reducing complexity. Across both libraries, two_agent shows the highest reliability (98.1%-100% success rate) and positive-outcome rate (78%), with a median improvement of 4.4% among positive outcomes; CrewAI achieves the highest average improvement (37.9%) and is the only framework with zero extreme-value failures. AutoGen and Default each reach 65% positive-outcome rates. These results establish the feasibility of using LLM-based agents as automated "growth hackers" to continuously improve OPE systems, with implications for scaling data-driven decision-making where manual optimization is expensive.

04.
bioRxiv (Bioinfo) 2026-06-14

Systematic AI-Driven Drug Repurposing via Clinical Trial Data Mining: A Framework and Six Cross-Therapeutic Case Studies.

Authors:

Drug repurposing, the application of approved or shelved compounds to new therapeutic indications, offers a cost- and time-efficient alternative to de novo drug discovery. However, the systematic identification of repurposing candidates from the rapidly expanding body of clinical trial data remains a significant challenge. Here we present a publicly accessible AI-powered tool that mines the ClinicalTrials.gov registry to identify approved drugs with under-explored therapeutic potential in high-value disease areas. The tool integrates natural language processing, mechanism-of-action pathway analysis, and trial density scoring to surface candidates where biological plausibility is high and clinical trial coverage is sparse. We demonstrate the tool's utility across six cross-therapeutic case studies spanning oncology, cardiology, neurology, rare diseases, immunology, and infectious disease. Key findings include: the identification of Zonisamide as an under-explored combination candidate for obesity alongside GLP-1 receptor agonists; mechanistic validation of SGLT2 inhibitors in heart failure with preserved ejection fraction (HFpEF); and a novel cross-domain mapping of anti-TNF biologics to early-stage neurodegeneration via shared neuroinflammatory pathways. The tool is freely accessible and designed to lower the barrier for academic and industry researchers to systematically pursue repurposing opportunities.

05.
arXiv (quant-ph) 2026-06-24

Enhancing quantum-classical configuration interaction methods using a neural-network classifier

arXiv:2606.24332v1 Announce Type: cross Abstract: Selected configuration interaction methods achieve near-exact electronic structure calculations by iteratively constructing compact variational spaces, but their efficiency depends critically on the heuristics used to identify important determinants. Here, we introduce a data-driven selection framework that recasts determinant importance as a binary classification task and integrates a neural-network classifier into the iterative CI workflow through an active-learning loop. At each iteration, a random subset of candidate determinants is labelled via temporary diagonalisation, and the trained classifier guides selection of the remaining configurations. We demonstrate the utility of this framework for both classical and quantum CI methods by calculating the ground-state energy of a diatomic molecule. Our method achieves result parity with traditional configuration interaction methods at substantially lower computational cost: roughly a $\times 5$ reduction in memory and per-iteration cost for the classical cHCI variant, and convergence in markedly fewer iterations for the quantum-classical cSQD variant. These results establish classifier-assisted determinant selection as a lightweight, method-agnostic tool for compressing variational spaces and accelerating both classical and hybrid quantum-classical configuration interaction algorithms.

06.
arXiv (CS.CV) 2026-06-16

DYNA-PRUNER: Input-Adaptive Data-Model Co-Pruning for Efficient and Scalable Spatio-Temporal Media Prediction

Spatio-temporal prediction supports radar/satellite nowcasting and city-scale traffic monitoring, but modern models are often too expensive for real-time deployment. This stems from a mismatch between dense computation and strong input-dependent redundancy (e.g., calm seas or clear skies). To enable automated, resource-aware architecture optimization in scalable media analysis, we propose Dyna-Pruner, an end-to-end framework for input-dependent co-pruning of data and model structure. A shared-importance synchronization mechanism generates coupled masks that prune redundant regions and their corresponding computational units (e.g., convolutional filters), yielding per-sample sparse sub-networks at inference time. Experiments on WeatherBench, SEVIR, and TaxiBJ show seamless integration with CNN, RNN, and Transformer backbones, reducing FLOPs by up to $70\%$ and achieving a $2.5\times$ speedup on NVIDIA Jetson AGX Orin with negligible accuracy loss ($

07.
arXiv (CS.CV) 2026-06-24

LoT-Pass: Long-term-robust Image Watermarking for Image to Video Generation

The rapid progress of image-guided video generation (I2V) has raised concerns about its potential misuse in misinformation and fraud, underscoring the urgent need for effective digital watermarking. While existing watermarking methods demonstrate robustness within a single modality, they fail to trace source images in I2V settings. To address this gap, we introduce the concept of Robust Diffusion Distance, which measures the temporal persistence of watermark signals in generated videos. Building on this, we propose I2VWM, a cross-modal watermarking framework designed to enhance watermark robustness across time. I2VWM leverages a video-simulation noise layer during training and employs an optical-flow-based alignment module during inference. Experiments on both open-source and commercial I2V models demonstrate that I2VWM significantly improves robustness while maintaining imperceptibility, establishing a new paradigm for cross-modal watermarking in the era of generative video. \href{https://github.com/MrCrims/I2VWM-Robust-Watermarking-for-Image-to-Video-Generation}{Code Released.}

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

A Three-Layer Framework for AI in Scientific Discovery

Authors:

arXiv:2606.13566v1 Announce Type: new Abstract: Current discussions of AI in scientific discovery are often dominated by two visible capabilities: search over existing knowledge and execution through optimization, simulation, and automation. Both are important, but neither fully captures the central act of discovery: the formation and evolution of models. This paper proposes a three-layer view of AI in discovery. Layer 1 is search and retrieval by large language models. Layer 2, as the main innovation of this paper, is model formation through qualitative reasoning: the capacity to recognize when a current framework is structurally inadequate and to understand the problem within a broader representational space, not through trial and error, but through structural insight into what is missing and where it can be found. Layer 3 is execution, optimization, and refinement. The main claim is that Layer 2 is both the most important and the least developed. Search without model formation remains confined to inherited frameworks, while execution without conceptual revision only amplifies an existing formulation. We illustrate Layer 2 reasoning through three case studies: S. S. Chern's intrinsic proof of the Gauss-Bonnet theorem, the resolution of the Nesterov Accelerated Gradient convergence problem via Lyapunov functions, and the autonomous disproof of the Erdos unit distance conjecture by OpenAI in 2026. Each case exhibits the same structural signature: a framework that had become inadequate, a missing conceptual object, and a resolution found in an unexpected neighboring field.

09.
medRxiv (Medicine) 2026-06-18

Plasma proteomics reveals clinical and mechanistic heterogeneity among individuals who develop coronary artery disease

BACKGROUND: Individuals who develop coronary artery disease (CAD) are clinically and mechanistically heterogeneous, and understanding this variation is crucial for precise risk stratification and tailored interventions. However, the molecular mechanisms that connect these two kinds of heterogeneity remain unclear, limiting progress toward biologically grounded risk stratification and targeted interventions. Here, we investigated the heterogeneity of individuals who develop CAD by leveraging plasma proteomic signatures, placed individuals along continuous metabolic gradients and revealed the molecular programs underlying these patterns, thereby linking mechanistic variation to clinical heterogeneity. METHODS AND RESULTS: From 42,803 UK Biobank participants, including 3,713 individuals who developed CAD within 10 years (incident CAD), we first identified a 320-protein panel from 2,923 baseline proteins that improved prediction of incident CAD beyond clinical risk scores. Using reverse graph embedding, we reduced the proteomic data to two dimensions and mapped each incident case onto the resulting two-dimensional latent proteomic space. These proteomic dimensions show significant associations with cardiometabolic and kidney-related clinical markers. The patterns were replicated in the EPIC-Norfolk study. Phenome-wide Cox regression analyses further linked these proteomic dimensions to 10-year incidence rates for various diseases, including type 2 diabetes, obesity, and chronic kidney disease (CKD). Furthermore, adding the proteomic dimensions to clinical variable-based Cox regression model improved prediction of 10-year incidence of CKD and other diseases, demonstrating the value of proteomic dimensions beyond conventional clinical risk factors. Moreover, individuals with prevalent CAD (diagnosed before proteomic sampling) exhibited high, metabolically adverse dimension values, indicating that these axes capture cumulative metabolic burden. Pathway enrichment analyses implicated altered extracellular matrix organization and immune programs among the proteins contributing to the proteomic dimensions. CONCLUSIONS: Our findings demonstrate that plasma proteomic signatures can dissect the heterogeneity of individuals who develop CAD in continuous phenotypic gradients, improve prediction of CAD and comorbidities, and map underlying biological mechanisms.

10.
arXiv (CS.AI) 2026-06-18

Searching for Synergy in Shared Workspace Human-AI Collaboration

arXiv:2606.18413v1 Announce Type: new Abstract: Automated AI agents are increasingly capable, yet many scientific and professional tasks require human judgment and contextual expertise. We study shared-workspace human-AI teams, where AI agents and human collaborators must coordinate responsibilities before submitting a final answer. Using the Collaborative Gym environment with DiscoveryBench tasks, we examine when adding simulated human collaborators improves performance and when process loss turns additional collaborators into coordination overhead. Across 1,482 sessions, adding relevant collaborators can lower performance when teams lack structure to coordinate their contributions. We then evaluate scaffolding that combines shared group memory with simulated human-in-the-loop (HITL) gates, where selected actions require approval from a designated simulated participant. This scaffolding yields higher mean performance, most clearly in three-person teams, with clearer responsibility signals and stronger routing of expertise to team actions. Overall, how human-AI teams coordinate and integrate expertise matters as much as the capability available to them.

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

Generating Input Distributions for Explaining Portfolio Optimization Pipelines

arXiv:2606.25808v1 Announce Type: cross Abstract: We propose a predict-optimize-explain framework that uses gradient-based sample generation to interpret various portfolio models by identifying macroeconomic conditions that induce specified portfolio outcomes. Unlike traditional feature-importance methods, this approach directly probes decision pipelines (predictive models coupled with portfolio optimization) by constructing economically meaningful what-if questions. We focus on four such questions: under what macroeconomic conditions a predict-then-optimize pipeline closes or reverses its return gap with a predict-and-optimize pipeline; what conditions lead a pipeline to diversify rather than concentrate its allocation; when a pipeline trained on calm markets overtakes one trained through crises; and what conditions would let a pipeline match a benchmark return. These examples illustrate how our framework uncovers key behavioral differences between various decision pipelines. Beyond these cases, the proposed framework is flexible and can support a wide range of probing questions tailored to specific portfolio objectives. Our findings highlight the value of integrating prediction, optimization, and explanation to produce more robust and transparent portfolio strategies.

12.
arXiv (CS.CL) 2026-06-11

Causal Emotion Recognition in Conversation: Context Saturation and Discourse-Marker Evidence

We address two persistent gaps in Emotion Recognition in Conversation: which modeling choices materially affect performance, and how recognition findings connect to interpretable discourse-level patterns. We study both through a systematic investigation on IEMOCAP with cross-dataset validation on MELD. For recognition, we run controlled ablations with 10 random seeds and paired significance tests with multiple-comparisons correction, yielding three findings. First, conversational context is the dominant factor, but performance saturates quickly: roughly 90% of the gain is captured within the most recent 10-30 preceding turns, depending on the label set. Second, hierarchical sentence representations help most in utterance-only settings and show a clear advantage on MELD, but their benefit disappears once turn-level context is available, suggesting that conversational history subsumes much of the intra-utterance structure. Third, integrating an external affective lexicon does not improve results, consistent with pretrained encoders already capturing most of the affective signal needed for ERC. Under a strictly causal setting, our simple models achieve strong performance (82.69% 4-way; 67.07% 6-way weighted F1), showing that competitive accuracy is achievable without future turns. For linguistic analysis, we examine 5,286 discourse-marker occurrences and find a reliable association between emotion and marker position (p < .0001). Sad utterances show reduced left-periphery marker usage (21.9%) relative to other emotions (28-32%), consistent with accounts linking left-periphery markers to active discourse management. This aligns with our recognition results, where Sad benefits most from conversational context (+22 percentage points), suggesting sadness may be more context-dependent than emotions with stronger local pragmatic cues.

13.
arXiv (CS.AI) 2026-06-18

SWE-Future: Forecast-Conditioned Data Synthesis for Future-Oriented Software Engineering Agents

arXiv:2606.18733v1 Announce Type: cross Abstract: Realistic coding-agent benchmarks often replay public GitHub issues and pull requests, making them vulnerable to overlap with model pretraining, fine-tuning, synthetic-data generation, or benchmark-driven model selection. Fully synthetic tasks avoid direct historical replay, but can drift away from real repository needs. We propose SWE-Future, a forecast-conditioned data synthesis method for future-oriented coding tasks. Given a forecast snapshot at time $T_0$, the method uses only pre-$T_0$ repository evidence to forecast future feature implementation/enhancement, bugfix, and refactor task families. We first validate this forecasting step retrospectively: after forecasts are fixed, later pull requests are used only to measure whether the predicted task families match future repository work. In an 80-repository study, the forecaster achieves 58.1\% future-work relevance under the main semantic matching metric. We then use validated forecast families as conditioning signals to synthesize a 200-task coding-agent dataset across 61 repositories from a task-generation snapshot, rather than replaying the later pull requests used for validation. SWE-Future shows that repository-evolution forecasts can guide realistic, future-oriented coding-task synthesis while reducing direct dependence on historical pull-request replay.

14.
arXiv (CS.LG) 2026-06-16

Representation Costs in Data Science: Foundations and the Quasi-Banach Spaces of Deep Neural Networks

arXiv:2606.14954v1 Announce Type: cross Abstract: We develop a general framework for analyzing representation costs of parametric data-fitting methods through their parameter-space regularizers. From this abstract perspective, we define representation costs for arbitrary parametric models and reveal their induced (native) function spaces. This unifies recent function-space views of data-fitting methods. We also prove that many natural results hold in this abstract setting, including representer theorems for parametric methods on their native spaces. The framework also rigorously connects parametric methods with their equivalent nonparametric descriptions under sufficient overparameterization. Classical methods and their native spaces, such as kernel methods / reproducing kernel Hilbert spaces, wavelets / Besov spaces, and shallow neural networks / variation spaces emerge as special cases of our abstract framework. A byproduct of "axiomatizing" the study of representation costs is that we also immediately obtain new results for deep neural networks: For depth-$L$ feedforward ReLU networks, their induced native spaces are $p$-normable quasi-Banach spaces with $p = 2/L$. This reveals that the inductive bias of deep neural networks (as given by the representation cost) cannot be captured by norms for depths $L > 2$.

15.
arXiv (CS.AI) 2026-06-19

AURA: Adaptive Uncertainty-aware Refinement for LLM-as-a-Judge Auditing

arXiv:2606.19714v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used as judges for open-ended generation, as large-scale human evaluation is often expensive and difficult to scale, yet their preferences remain imperfect proxies for human judgment. Existing auditing pipelines often assume that a reliable subset of examples or clean supervision signals are available beforehand, for example from human annotation, heuristic filtering, or the outputs of strong judges. In LLM evaluation, this assumption is fragile: the initial split may inherit judge bias, while human verification is typically too scarce to define stable groups at scale. We propose AURA, an adaptive uncertainty–aware refinement framework for auditing pairwise LLM–as–a–judge decisions under selected human verification. AURA iteratively learns a human-consistency signal, propagates reliable evidence, and prioritizes uncertain comparisons for human review. The key idea is to treat trust in a judge as a latent quantity that is progressively refined as evidence accumulates. We provide a compact formulation, a stable refinement procedure, and a comprehensive evaluation on both synthetic and real pairwise LLM-answer data.

16.
PLOS Computational Biology 2026-06-02

A comparative study of simulation-based inference methods for epidemic models with identifiability considerations

Authors:

by Geunsoo Jang, K. Selçuk Candan, Gerardo Chowell Epidemic models play a critical role in understanding transmission dynamics, generating forecasts, and informing public health interventions when they are properly calibrated to epidemiological data. Traditional Bayesian inference methods rely on the likelihood function to update prior knowledge using observed data. However, for realistic epidemic models, likelihood functions are often analytically intractable or computationally prohibitive, which can limit the applicability of these methods. Simulation-based inference provides a promising alternative by approximating posterior distributions through forward simulations rather than an explicit likelihood evaluation. In this study, we present a systematic comparison of four approaches: Approximate Bayesian Computation (ABC), Neural Posterior Estimation (NPE), a neural method with temporal embedding, and Preconditioned Neural Posterior Estimation (PNPE), which integrates elements of both classical and neural techniques. These methods are evaluated across epidemic models of increasing complexity under fixed simulation budgets and varying levels of observational noise, with explicit attention to both structural and practical identifiability. Our results show that neural methods generally improve posterior fidelity and predictive accuracy compared with ABC under constrained simulation budgets. PNPE achieved strong performance in several simulation settings, whereas temporal embeddings improved inference in models with complex epidemic dynamics by capturing sequential dependencies. These gains come with important trade-offs: PNPE required substantially greater computational resources and, unlike fully amortized NPE-based methods, may require reconditioning for each new observation. In contrast, ABC remained computationally efficient and provided reasonable, though often more conservative, posterior estimates. Overall, our findings highlight trade-offs among computational efficiency, posterior accuracy, uncertainty calibration, and inference reusability, suggesting that method selection should depend on model complexity, data quality, identifiability, and available computational resources.

17.
arXiv (CS.LG) 2026-06-12

Is Spurious Correlation Removal Always Learnable?

arXiv:2606.12930v1 Announce Type: new Abstract: Invariant learning can fail even when the invariant structure is statistically identifiable. We show a conditional computational barrier: under a black-box samplable supervised sparse recovery primitive motivated by average-case sparse-recovery reductions, there exist samplable multi-environment instances with a one-dimensional predictive invariant subspace ($k=1$) that are learnable with polynomial samples by exhaustive search, while any polynomial-time constant-accuracy recovery algorithm would contradict the primitive. We further quantify environment diversity by a separation parameter $\gamma$, which controls identifiability and the curvature of invariance objectives. Under sufficient diversity and local Gaussian regularity, the minimax risk is $\mathbb{E}[\dist(\hat{V},V_{\mathrm{inv}})^2]=\Theta(k(d-k)/(n|\mathcal{E}|))$, and under label-induced shifts a phase transition occurs at $n^*\propto k(d-k)/(|\mathcal{E}|\gamma^2)$ with refined estimation error scaling proportional to $1/\gamma^2$. Synthetic and real datasets illustrate the predicted gaps and transitions and motivate simple diversity diagnostics.

18.
arXiv (CS.AI) 2026-06-19

Calibration Without Comprehension: Diagnosing the Limits of Fine-Tuning LLMs for Vulnerability Detection in Systems Software

arXiv:2606.20502v1 Announce Type: cross Abstract: Whether LLMs scoring well on vulnerability benchmarks genuinely reason about security or merely pattern-match on contaminated data remains unresolved. We present CWE-Trace, a framework for LLM vulnerability detection built from 834 manually curated Linux kernel samples spanning 74 CWEs. The framework enforces a strict temporal split (pre-2025 historical set / post-cutoff leakage-free set), preserves context-aware vulnerable–patched pairs, and introduces two diagnostic metrics: the Directional Failure Index (DFI) and Hierarchical Distance and Direction (HDD). We evaluate eight vanilla LLMs and 15 LoRA fine-tuned variants across non-targeted detection, targeted detection, and CWE classification. Our analysis yields two key results. First, data contamination provides no measurable advantage. Function-level analysis shows that 84% of nominally contaminated samples carry no usable memorization signal: vulnerable functions are absent or cross-mapped across datasets, and ~31% of contaminated samples carry CWE misclassification. Second, backbone directional priors dominate fine-tuning. Models exhibit stable, systematic failure modes (DFI ranging from -85.5 to +94.8 pp) that persist from historical to post-cutoff data and resist correction. Fine-tuning shifts the output threshold without changing the decision policy. This is calibration without comprehension: output distributions adapt to training data while the underlying security reasoning remains absent. The weakest backbone at binary detection (DeepSeek-R1) gains the most in coarse CWE classification, revealing that detection and understanding are decoupled capabilities. The best detection score reaches only 52.1% (+2.1 pp above chance); exact CWE ranking remains below 1.3% Top-1 accuracy, confirming that current LLMs lack reliable security reasoning for systems software, regardless of fine-tuning strategy.

19.
arXiv (CS.AI) 2026-06-11

Towards a Bridge Layer Between Bibliographic and Formalized Mathematical Knowledge

Authors:

arXiv:2606.11430v1 Announce Type: cross Abstract: Mathematical knowledge is split between bibliographic databases (e.g., MathSciNet, zbMATH Open) and formal proof libraries (e.g., Lean mathlib), preventing unified access between published results and their formalizations. We propose a relational bridge-database that aligns publication metadata with formal artifacts, providing an interoperability layer between mathematical literature and machine-verifiable proofs. We introduce a paper-level formalization score that measures how much of a publication is covered in formal systems. As a feasibility study, we show how such scores can be estimated via cross-document alignment between informal texts and Lean formalizations, enabling large-scale analysis of formalization coverage. This framework is a first step toward integrating bibliographic and formal mathematical ecosystems into scalable, machine-actionable knowledge graphs linking publications to formal proof objects.

20.
arXiv (CS.AI) 2026-06-25

SycoEval-EM: Sycophancy Evaluation of Large Language Models in Simulated Clinical Encounters for Emergency Care

arXiv:2601.16529v3 Announce Type: replace Abstract: Large language models (LLMs) deployed in clinical decision support may acquiesce to patient requests for care that conflicts with evidence-based guidelines. We developed SycoEval-EM, a multi-agent simulation framework to evaluate LLM robustness to adversarial patient persuasion in emergency medicine. Across 19 contemporary LLMs and 1,425 simulated clinical encounters spanning three Choosing Wisely scenarios, acquiescence rates ranged from 0% to 100%, revealing a bimodal distribution. Seven models maintained near-perfect guideline adherence, while six acquiesced in the majority of encounters. Vulnerability varied substantially across clinical scenarios. Acquiescence was highest for CT imaging requests, intermediate for antibiotic prescriptions for sinusitis, and lowest for opioid prescriptions for acute back pain. Model scale, recency, and performance on static medical benchmarks did not consistently predict robustness. All five persuasion tactics produced similar acquiescence rates, with no statistically significant differences after correction for multiple comparisons, suggesting a generalized susceptibility rather than tactic-specific weaknesses. LLM-as-judge evaluation was validated against two independent physician raters across 95 matched conversations and demonstrated near-perfect agreement for the primary outcome of acquiescence (Cohens kappa = 0.957). These findings indicate that static medical benchmarks are insufficient to predict safety performance under sustained social pressure and support incorporating multi-turn adversarial testing into clinical AI evaluation. Notably, two models achieved perfect guideline adherence across all encounters, demonstrating that robustness to patient pressure is attainable without sacrificing effective clinical communication.

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

MUZZLE: Adaptive Agentic Red-Teaming of Web Agents Against Indirect Prompt Injection Attacks

arXiv:2602.09222v2 Announce Type: replace-cross Abstract: Large language model (LLM) based web agents are increasingly deployed to automate complex online tasks by directly interacting with web sites and performing actions on users' behalf. While these agents offer powerful capabilities, their design exposes them to indirect prompt injection attacks embedded in untrusted web content, enabling adversaries to hijack agent behavior and violate user intent. Despite growing awareness of this threat, existing evaluations rely on fixed attack templates, manually selected injection surfaces, or narrowly scoped scenarios, limiting their ability to capture realistic, adaptive attacks encountered in practice. We present MUZZLE, an automated agentic framework for evaluating the security of web agents against indirect prompt injection attacks. MUZZLE utilizes the agent's trajectories to automatically identify high-salience injection surfaces, and adaptively generate context-aware malicious instructions that target violations of confidentiality, integrity, and availability. Unlike prior approaches, MUZZLE adapts its attack strategy based on the agent's observed execution trajectory and iteratively refines attacks using feedback from failed executions. We evaluate MUZZLE across diverse web applications, user tasks, and agent configurations, demonstrating its ability to automatically and adaptively assess the security of web agents with minimal human intervention. Our results show that MUZZLE effectively discovers 44 new attacks on 4 web applications with 10 adversarial objectives that violate confidentiality, availability, or privacy properties across different LLMs and agent scaffolds. MUZZLE also identifies novel attack strategies, including 3 cross-application prompt injection attacks and an agent-tailored phishing scenario.

22.
medRxiv (Medicine) 2026-06-24

Study partner profile effects on CDR-SB change in anti-amyloid therapy evaluation

INTRODUCTION: The Clinical Dementia Rating Sum of Boxes (CDR-SB), a primary outcome in anti-amyloid therapy (AAT) trials, integrates information from participants and study partners. CDR-SB scores may vary by study partner characteristics, but their impact on 18-month change interpretation remains unclear. METHODS: Using the NACC Uniform Data Set, we fitted linear mixed-effects calibration models in an Alzheimer's disease (AD)-primary early symptomatic cohort and propagated study partner-associated coefficients through Monte Carlo simulations. We estimated components of 18-month CDR-SB change under observed profile changes, simulated follow-up imbalance in a common female living-with profile, and tipping-point scenarios. Analyses were repeated in amyloid-positive and trial-like cohorts. RESULTS: The AD-primary cohort included 15,061 participants and 7,683 baseline-to-18-month pairs. Observed profile changes generated a negligible cohort-level component (mean 0.0014 points, 95% simulation interval 0.0006 to 0.0022). Simulated follow-up imbalance generated differences of 0.014 to 0.071 points across 10% to 50% reassignment. Under the primary calibration model, generating a 0.45-point difference, equal to the reported Clarity AD CDR-SB group difference, required median net imbalance >100% and was feasible in 48% of iterations. Amyloid-positive and trial-like cohorts had lower median tipping points but wider intervals, reflecting coefficient imprecision. DISCUSSION: In the large AD-primary cohort, observed study partner profile changes and simulated follow-up imbalance generated CDR-SB differences that were small relative to the 0.45-point Clarity AD benchmark. Biomarker-confirmed estimates were less stable because of coefficient imprecision. These findings suggest limited impact under typical AD-primary conditions but support systematic study partner profile collection and sensitivity analyses in observational and external-comparator CDR-SB studies for AAT evaluation.

23.
Nature Biotechnology 2026-06-19

Optimized R2 retroelement complexes for DNA insertion into plant genomes

Traditional approaches for DNA insertion into plant genomes using Agrobacterium tumefaciens result in random integration. Newer genetic engineering methods based on nucleases, prime editors, transposases and recombinases extend capabilities but remain constrained with low efficiencies, off-target integration or limited payload size. Here we adapt the avian Taeniopygia guttata R2 protein (R2Tg) for targeted DNA insertion into plant genomes by engineering R2Tg expression cassettes and RNA payloads carrying intron-disrupted reporters, with optimized ribosomal DNA homology arms and untranslated regions. In Arabidopsis thaliana protoplasts, Nicotiana benthamiana leaves and Solanum lycopersicum seedlings, our R2Tg editor system achieves targeted insertion of full-length payloads ranging from 2.2 kb to 5 kb. In Nicotiana benthamiana leaves, integration occurs, on average, at 1 copy per genome, which is 30 times more efficient than that achieved by Cas9 homology-directed repair. This work establishes an R2Tg ribonucleoprotein platform for targeted DNA insertion into plant genomes, using a multicopy genomic safe-harbor site to enable efficient addition of multikilobase genes. R2 retrotransposons are used to integrate DNA into plant and crop 25S ribosomal DNA sites.

24.
arXiv (CS.AI) 2026-06-16

Medical Heuristic Learning: An LLM-Driven Framework for Interpretable and Auditable Clinical Decision Rules

arXiv:2606.16337v1 Announce Type: new Abstract: Predictive modeling for clinical tabular data is central to clinical decision support and therefore requires not only strong predictive performance but also transparent decision logic. Although deep learning and tree-based ensemble methods can achieve high accuracy, their black-box nature remains a major obstacle to clinical deployment. This challenge is further compounded by common characteristics of medical data, including limited sample sizes, severe class imbalance, and feature evolution arising from changes in diagnostic criteria and clinical documentation. To address these issues, we propose Medical Heuristic Learning (MHL), an instantiation of the learning-beyond-gradients paradigm for clinical tabular prediction. Instead of relying on neural network weight updates, MHL uses a large language model (LLM)-driven workflow that integrates statistical probes, medical knowledge probes, rule synthesis, and code-level iterative refinement to optimize a deterministic and executable decision system. The resulting model is expressed not as opaque parameters, but as versioned pure-Python decision rules that are explicitly interpretable, fully auditable, and clinically grounded. MHL also supports continual learning by starting from previously validated rules and iteratively revising them using updated feature information under data drift or feature evolution. Comprehensive experiments on medical datasets show that MHL achieves performance comparable to state-of-the-art methods while maintaining strong behavior in small-sample and highly imbalanced settings. The results further indicate that this explicit rule update mechanism can help alleviate catastrophic forgetting under feature evolution. Overall, these findings suggest that non-gradient-based heuristic systems offer a transparent and adaptable alternative for high-stakes clinical decision support.

25.
bioRxiv (Bioinfo) 2026-06-16

Expanding gene regulatory networks from transcriptome data through graphical modeling with heterogeneous priors

Gene regulatory network inference is widely used to reconstruct large-scale networks and identify functional genes from transcriptome data. Meanwhile, in many biological fields, core regulatory genes have been extensively studied, leading to the establishment of small-scale gene regulatory networks, and novel genes connected to these networks remain to be identified. However, methods for expanding existing gene networks by identifying novel regulatory interactions, rather than reconstructing the entire network, are not well established. Here, we propose a method for gene network expansion that incorporates known regulatory relationships and evaluates each candidate gene individually to infer its regulatory connections to the existing network. Using simulated datasets from the DREAM4 benchmark and the PRECISE-1K experimental dataset, our method outperformed conventional methods by incorporating prior knowledge. In particular, it improved the ability to distinguish true regulatory interactions from indirect associations arising from strong correlations among genes in the existing network. The method also showed strong performance for interactions involving genes with high outdegree or centrality. Furthermore, it maintained stable performance as the size of the existing network increased and was robust to noise in prior information. These results demonstrate that our method provides an effective framework for expanding existing gene regulatory networks by leveraging prior knowledge.