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01.
arXiv (math.PR) 2026-06-11

Delta-Epsilon-Common Knowledge and Quantitative Agreement Theorems

arXiv:2606.11902v1 Announce Type: cross Abstract: Aumann defined common knowledge mathematically and established his now famous Agreement Theorem. We present a novel approach to quantifying how close individuals are to commonly knowing events, $(\delta,\epsilon)$-common knowledge, which is defined for any (and not just countable) probability spaces, and provide quantitative versions of the key results in this field. Specifically, we do this for Aumann's Agreement Theorem and Nielsen's extension thereof to random variables, as well as for the setting in which posteriors are communicated back and forth between individuals. Our results apply in particular to noisy communication settings.

02.
arXiv (CS.LG) 2026-06-11

PCS-UQ: Uncertainty Quantification via the Predictability-Computability-Stability Framework

arXiv:2505.08784v2 Announce Type: replace-cross Abstract: As machine learning (ML) enters high-stakes domains, trustworthy uncertainty quantification (UQ) is essential for safety. In this paper we introduce PCS-UQ, a framework based on the Predictability, Computability, and Stability (PCS) principles for veridical data science. Starting with a candidate set of models or algorithms, PCS-UQ integrates a rigorous prediction-check to screen out unsuitable models in the set and utilizes bootstrap samples, in order to capture both inter-sample variability and algorithmic instability for the prediction-checked algorithms. We then introduce a novel multiplicative calibration scheme to enhance local adaptivity, which basically corresponds to a new score in conformal prediction. Moreover, we produce a compilation of 17 real-world regression datasets with manually-constructed subgroups. On this benchmark, PCS-UQ maintains the target coverage while outperforming or matching conformal methods equipped with oracle-selected algorithms in interval width. PCS-UQ achieves consistent subgroup coverage, outperforming these oracle-selected conformal methods. Notably, PCS-UQ stands out in achieving both competitive interval widths and consistent subgroup coverage.Across 6 classification datasets, PCS-UQ reduces prediction set sizes by 20\%. To scale the framework for deep learning, we propose computationally efficient variants that bypass expensive retraining. On three computer vision benchmarks, these variants reduce prediction set sizes by 20\% over conformal baselines. Finally, we provide theoretical proof that a modified PCS-UQ algorithm preserves valid coverage under exchangeability as a form of split conformal inference.

03.
Nature Medicine 2026-06-10

Dual-target gene therapy in Parkinson’s disease: a multicenter phase 1 trial

Authors:

Restoring striatal dopamine synthesis is a promising gene therapy strategy for Parkinson’s disease. Previous adeno-associated virus-mediated aromatic L-amino acid decarboxylase (AADC) monotherapies remain dependent on exogenous levodopa, whereas multigene delivery is constrained by strict adeno-associated virus packaging limits. A ‘dual approach’ targeting the two rate-limiting enzymes, tyrosine hydroxylase (TH) and AADC, offers the potential for autonomous dopamine synthesis. We report the 12-month primary safety and tolerability outcomes of a multicenter, open-label, dose-escalation, phase 1 trial evaluating BBM-P002, a new adeno-associated virus vector—AAVT42—codelivering constitutively active TH and AADC. Ten participants with moderate-to-advanced Parkinson’s disease were enrolled and received bilateral intraputaminal infusions across doses of 4.0 × 1011 vg (Cohort 1; n = 1), 6.0 × 1011 vg (Cohort 2; n = 2), 1.0 × 1012 vg (Cohort 3; n = 2) and 1.2 × 1012 vg (Cohort 4; n = 5). The trial achieved its primary outcome, as BBM-P002 demonstrated a favorable safety and tolerability profile within 12 months post-treatment. No dose-limiting toxicities or drug-related serious adverse events occurred. A total of 23 adverse events were reported, all judged unrelated to BBM-P002 and primarily mild and transient. Systemic toxicity and clinically meaningful immunogenicity were absent. In conclusion, intraputaminal delivery of BBM-P002 was safe and well tolerated in this phase 1 trial, supporting continued clinical development. ClinicalTrials.gov registration: NCT05822739 . Phase 1 results reveal that BBM-P002, a dual-target gene therapy co-delivering TH and DDC, is safe and well tolerated in Parkinson’s disease, with 12-month motor improvements signaling therapeutic potential.

04.
arXiv (CS.CL) 2026-06-11

Unstable Features, Reproducible Subspaces: Understanding Seed Dependence in Sparse Autoencoders

Sparse autoencoders (SAEs) are widely used to interpret neural network representations, but their utility depends on whether the learned features are reproducible across training runs. We study this question through feature stability: for each SAE feature, we estimate the probability that a similar feature reappears in an independently trained SAE. This yields a scalable per-feature signal that separates stable from unstable features. In a large-scale study across seeds, models, layers, dictionary sizes, and SAE variants, we find a pronounced functional asymmetry: stable features carry most of the reconstruction- and prediction-relevant signal, while unstable features have weak marginal impact and are dominated by low-frequency surface-form triggers in both activation statistics and automatic explanations. Geometrically, unstable features are individually non-reproducible but concentrate in reproducible lower-rank subspaces, suggesting that seed dependence often reflects basis ambiguity within a shared region of activation space rather than pure noise. A controlled synthetic model makes this mechanism explicit, showing that low-rank ground-truth features can be recovered at the subspace level while remaining non-identifiable as individual SAE latents across seeds. Finally, by pooling unique cross-seed features, we construct more stable SAEs while preserving explained variance in this setting. Together, these results show that unstable features are not merely failed or noisy latents: they have weak individual functional impact, but reflect reproducible low-dimensional structure that standard SAEs resolve differently across seeds.

05.
medRxiv (Medicine) 2026-06-16

Non-invasive Detection of Fasciculation Using Surface EMG with a Wavelet-Based Analytical Method (DEWCS)

Objective: Needle electromyography (nEMG) is essential for diagnosing neuromuscular disorders but is invasive and often painful. We employed single-channel bipolar surface EMG (sEMG) analyzed with a novel wavelet-based analytical approach, Detecting and Extracting Elemental Wave Components based on a Wavelet Coefficient Set (DEWCS) and investigated whether fasciculation-related activity could be identified. Methods: In this prospective study, 28 patients undergoing nEMG for suspected neuromuscular disorders and 13 healthy controls were included. Resting-state sEMG was recorded from selected muscles using single-channel bipolar active electrodes at a high sampling rate. DEWCS was used to extract indices reflecting fast- and slow-type motor unit (MU)-related activity. These standardized indices were evaluated against nEMG-detected fasciculation potentials using generalized estimating equation logistic regression to account for within-subject clustering. Diagnostic performance was assessed by receiver operating characteristic analysis. Results: A total of 67 muscles from 38 participants were analyzed. Indices of fast- and slow-type MU-related activity were significantly associated with fasciculation potentials (slow: OR 5.10, p = 0.0041; fast: OR 2.38, p = 0.0162). The combined model showed excellent discrimination (area under the curve = 0.97), outperforming either index alone. Muscle region had no significant effect. Conclusions: A single-channel bipolar sEMG setup combined with DEWCS detected fasciculation-related activity with promising accuracy. This method may serve as a non-invasive surrogate marker of lower motor neuron involvement. Further validation in larger cohorts is warranted. Significance: This non-invasive sEMG approach may help detect fasciculation-related activity and complement nEMG in neuromuscular diagnostics.

06.
Nature (Science) 2026-06-17

Towards Conversational AI for Disease Management

While large language models (LLMs) have shown promise in diagnostic dialogue1, their capabilities for effective management reasoning—including disease progression, therapeutic response, and safe medication prescription—remain under-explored. We advance the previously demonstrated diagnostic capabilities of the Articulate Medical Intelligence Explorer (AMIE)1−3 through a new LLM-based agentic system optimized for multi-visit clinical management and dialogue. To ground its reasoning in authoritative clinical knowledge, AMIE leverages Gemini’s long-context capabilities4, combining in-context retrieval with structured reasoning to align its output with up-to-date clinical practice guidelines and drug formularies. In a randomized, blinded virtual Objective Structured Clinical Examination (OSCE) study, AMIE was compared to 21 primary care physicians (PCPs) across 100 multi-visit case scenarios designed to reflect UK NICE Guidance and BMJ Best Practice guidelines. AMIE was non-inferior to PCPs in management reasoning as assessed by specialists and scored better in both preciseness of treatments and investigations, and in its alignment with and grounding in clinical guidelines. To benchmark medication reasoning, we developed RxQA, a multiple-choice question benchmark derived from two national drug formularies (US, UK) and validated by board-certified pharmacists. Though AMIE and PCPs both benefited from the ability to access external drug information, AMIE outperformed PCPs on higher difficulty questions. While further research would be needed before real-world translation, AMIE’s strong performance across evaluations marks a significant step towards conversational AI as a tool in disease management.

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

When Cognitive Graphs Meet LLMs: BDEI Cognitive Pathways for Panic Emotional Arousal Prediction

Predicting individual panic emotional arousal timing before manifestation is essential for proactive emergency intervention. Existing methods incorporate cognitive elements but none explicitly model the emotional arousal process, making them ill-suited for emotional arousal timing prediction. We argue that grounding prediction in appraisal emotion theory is necessary because it explicitly models this process, but three problems must be solved. (1) Appraisal theory posits that emotion arises from simultaneous evaluation across multiple threat dimensions, yet no prior work fuses these inputs into risk perception. (2) Existing cognitive models lack an Emotion node, decoupling threat appraisal from emotional arousal and forcing emotions to be inferred indirectly from behaviors. (3) Given their generalizable cognitive reasoning, current approaches adopt LLMs as the primary decision-maker, yet overlook the fragility and hallucination-proneness of their outputs. To address these issues, we introduce PanicCognitivePath (PCP), a framework that addresses all three. A Psychological Safety Distance (PSD) model, grounded in psychological distance theory, maps four-domain signals into a unified risk metric as the entry condition for subsequent cognitive reasoning. An explicit Emotion node grounded in appraisal emotion theory is introduced into BDI, forming a Belief-Desire-Emotion-Intention (BDEI) pathway. Agents whose risk metric exceeds the PSD threshold enter this pathway, coupling threat appraisal directly to emotional arousal. The BDEI pathway governs all state transitions while the LLM is confined to parameter estimation for the Belief-to-Desire transition, confining hallucinations to a single step and preventing error propagation. Experiments on Hurricane Sandy show PCP improves arousal timing accuracy by 10.68% over baselines, reduces peak count error to 7.07%.

08.
arXiv (quant-ph) 2026-06-16

Exactly Solvable Quantum Model with Spin-Dependent Coulomb Interaction

arXiv:2501.05103v5 Announce Type: replace Abstract: In this work, we report an exactly solvable quantum model featuring a spin-dependent Coulomb interaction, described by the spin vector potential \(\vec{\mathcal{A}} = k (\vec{r} \times \vec{S}) / r^2\) together with a Coulomb-type scalar potential \(\varphi = \kappa / r\) . The model is governed by the Schrödinger-type Hamiltonian \(\mathcal{H}_S = \vec{\Pi}^2 / (2M) + q \varphi\) in nonrelativistic quantum mechanics and by the Dirac-type Hamiltonian \(\mathcal{H}_D = c \vec{\alpha} \cdot \vec{\Pi} + \beta M c^2 + q \varphi\) in relativistic quantum mechanics, where \(\vec{\Pi} = \vec{p} - (q/c)\vec{\mathcal{A}}\) is the canonical momentum. We demonstrate two main results: (i) Just as the Coulomb-type scalar potential \(\mathcal{S}_Maxwell = \{\vec{\mathcal{A}} = 0,\ \varphi = \kappa / r\}\) is a local exact solution of Maxwell's equations on $r\neq0$, the gauge potential \(\mathcal{S}_YM = \{\vec{\mathcal{A}} = k (\vec{r} \times \vec{S}) / r^2,\ \varphi = \kappa / r\}\) constitutes a local exact solution of the Yang–Mills equations on the punctured region $r\neq0$. (ii) Both Hamiltonians \(\mathcal{H}_S\) and \(\mathcal{H}_D\) can be solved exactly in the presence of this spin-dependent Coulomb interaction. The resulting energy spectra are derived, and they naturally reduce to those of the ordinary hydrogen atom when the spin-dependent terms are neglected. Finally, we clarify the quantization conditions and the fixed-background interpretation of the model.

09.
arXiv (CS.CL) 2026-06-11

AI Coding Agents in Social Science: Methodologically Diverse, Empirically Consistent, Interpretively Vulnerable

The deployment of LLM-based agents in scientific analysis raises opposing concerns: that agents may reduce methodological diversity, or that they may amplify the analytic flexibility through which researchers reach motivated conclusions. We argue these worries target two empirically separable layers: a design layer of methodological choices, and a verdict layer in which a decision rule maps estimates to a substantive claim. We test both by running 20 independent executions of Claude Code and Codex on a prominent immigration and social-policy against a many-analysts human baseline. At the design layer, Codex matches human methodological diversity and Claude Code produces nearly three times as many specifications; both agents' effect estimates remain broadly aligned with the human consensus, and no agent model exactly matches any human model. A prompt-induced anti-immigration researcher prior reorganizes each agent's methodological decisions but, unlike for biased human analysts in the same data, does not shift aggregate estimates or final verdicts; nor do agents reroute along the methodological axes humans use to bias their estimates. At the verdict layer, an explicit confirmatory prompt flips Claude Code's verdicts from 10% to 90% support while leaving its coefficient distribution essentially unchanged, operating through rule omission rather than rule softening. AI agents can rival or exceed human methodological diversity at the design layer while remaining vulnerable at the verdict layer. In our setting, the locus of AI bias is not estimation but interpretation.

10.
arXiv (CS.CV) 2026-06-16

PhyloSDF: Phylogenetically-Conditioned Neural Generation of 3D Skull Morphology via Residual Flow Matching

Generating novel, biologically plausible three-dimensional morphological structures is a fundamental challenge in computational evolutionary biology, hampered by extreme data scarcity and the requirement that generated shapes respect phylogenetic relationships among species. In this work, we present PhyloSDF, a phylogenetically-conditioned neural generative model for 3D biological morphology that integrates two innovations: (1) a DeepSDF auto-decoder regularized by a novel Phylogenetic Consistency Loss that structures the latent space to correlate with evolutionary distances (Pearson r=0.993); (2) a Residual Conditional Flow Matching (Residual CFM) architecture that factorizes generation into analytic species-centroid lookup and learned residual prediction, enabling generation from as few as ~4 specimens per species. We evaluate PhyloSDF on 100 micro-CT-scanned skulls of Darwin's Finches and their relatives across 24 species. The model generates novel meshes achieving 88-129% of real intra-species variation at the code level, with all 180 generated meshes verified as non-memorized. Residual CFM surpasses denoising diffusion (which fails entirely at this scale), standard flow matching (which mode-collapses to 3-6% variation), and a Gaussian mixture baseline in both fidelity (Chamfer Distance 0.00181 vs. 0.00190) and morphometric Fr\'{e}chet distance (10,641 vs. 13,322). Leave-one-species-out experiments across 18 species demonstrate phylogenetic extrapolation capability, and smooth latent interpolations produce biologically plausible ancestral skull reconstructions.

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

PhysGuard: Fisher-Guided Gradient Projection for Sim-to-Real Neural PDE Surrogates

arXiv:2606.16602v1 Announce Type: new Abstract: Neural operator models trained on simulation data often lose accuracy when applied to experimental measurements due to the sim-to-real gap. Standard fine-tuning with limited real data can reduce this gap, but it may also damage the core physics-relevant representations learned during pretraining. Although knowledge-preserving adaptation has been widely investigated in vision or language tasks, it remains unclear whether these methods are suitable for neural operators whose architectures and protected knowledge are fundamentally different. Neural operators need to preserve core-scale physical structures rather than semantic or visual features. We propose PhysGuard, a physics-preserving framework for accurate sim-to-real adaptation of neural operators. Specifically, PhysGuard uses the empirical Fisher Information Matrix computed on simulation data to identify physics-critical parameter directions, then restricts fine-tuning updates to directions that do not interfere with them. A layer-wise Gram-matrix formulation makes this efficient for models with millions of parameters, while an adaptive threshold automatically determines the protected subspace size. A spectral probe experiment shows that the dominant Fisher directions are strongly associated with low-frequency output structures. Experiments on benchmark across four neural operator architectures and different physical systems show that PhysGuard performs strongly on most evaluation metrics compared to baselines. The benefits are most evident under severe domain shift, where it reduces low-frequency error by up to 32\% compared to standard fine-tuning while maintaining adaptability. Our code is available at https://github.com/ZhouChaunge/PhysGuard.

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

Visual Verification Enables Inference-time Steering and Autonomous Policy Improvement

arXiv:2606.18247v1 Announce Type: cross Abstract: Robots deployed in the real world should learn from their experience and improve over time. This requires a mechanism of practicing and learning from feedback. In this paper, we propose VERITAS, a generator-verifier framework for generalist robot policies for inference-time policy steering and self-improvement. We use a pre-trained generalist robot policy as a ``generator'' and pair it with a gradient-free ``visual verifier'' that evaluates actions at inference time. This framework enables inference-time steering that improves policy performance without additional training. We demonstrate that inference-time verification consistently outperforms vanilla generalists without training on additional demonstration data. Additionally, we demonstrate that the verified rollouts provide effective supervision for offline policy improvement: policies fine-tuned on verified self-generated trajectories achieve consistent performance gains. Notably, we find that post-training with verified rollouts achieves comparable efficiency to expert demonstrations, while requiring no human interventions. Our results highlight inference-time verification as a practical and scalable mechanism for improving robotic policies during deployment.

13.
bioRxiv (Bioinfo) 2026-06-18

Trajectory inference of epithelial-centered neighborhood profiles reconstructs a pseudo-temporal continuum in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is characterized by complex lung architecture and spatially heterogeneous remodeling, which have hindered integrated analysis of cell-intrinsic activity and intercellular communication during disease progression. Here we profiled six IPF lung specimens comprising more than 630,000 cells using the Xenium 5k panel and developed an epithelial-centered neighborhood profiling framework based on the local cellular composition around each epithelial cell. This approach captured fibrosis-associated variation in epithelial niches without requiring predefined histological regions. Pseudo-temporal continuum inference of these profiles reconstructed a continuous axis that reflected the spatial progression of fibrotic remodeling from relatively preserved alveolar regions to fibrotic and airway-like remodeled regions. Within this spatial dataset, we mapped coordinated changes in epithelial states, local microenvironments, epithelial intracellular pathway activities, and directional interactions with neighboring cell types along the same axis. Our findings provide a spatial framework that generates testable hypotheses for progressive epithelial niche remodeling in IPF.

14.
arXiv (CS.AI) 2026-06-17

LLM-Powered Multi-Agent System for Automated Crypto Portfolio Management

arXiv:2501.00826v3 Announce Type: replace-cross Abstract: Cryptocurrency portfolio management requires the fusion of heterogeneous multi-modal signals, including structured price and on-chain time series, unstructured news text, and technical indicators, under high-volatility and real-time constraints. While deep learning approaches show predictive capability, their opacity limits practical adoption, and single large language model (LLM) agents struggle to process the breadth of modality-specific inputs needed for robust decision-making. We propose a multi-agent system (MAS) framework in which three modality-specialised agents, a Crypto Agent for market dynamics, a News Agent for weekly news sentiment, and a Trading Agent for signal fusion and portfolio execution, decompose the task across three communication architectures: hierarchical, collaborative, and debate. We evaluate four capability configurations: zero-shot, chain-of-thought (CoT), retrieval-augmented generation (RAG), and skill-augmented. In a 52-week backtest over calendar year 2025 across the top 15 L1 blockchain native cryptocurrencies by market capitalisation as of January 2025, the best configuration, Hierarchical (Skill), achieves a cumulative return of 133.52% and a Sharpe ratio of 1.502, outperforming single-agent variants, passive benchmarks, and deep learning baselines. An ablation study identifies the Crypto Agent as the most critical component, with its removal reducing cumulative return by 42.57 percentage points. A cross-model comparison further shows that MAS outperforms the single-agent baseline under GPT-4o, GPT-5, and Claude Sonnet 4.5, suggesting that the benefit of multi-agent coordination is model-agnostic. Unlike black-box deep learning models, every portfolio decision is traceable to explicit agent reasoning, offering an interpretable and effective approach to multi-modal cryptocurrency portfolio management.

15.
arXiv (CS.CL) 2026-06-16

Islamic Large Language Models: From Knowledge Acquisition to Trustworthy and Hallucination-Resistant AI

Large language models (LLMs) are increasingly used for knowledge-intensive question answering, including religious and legal questions. Islamic knowledge is a particularly demanding setting: answers are expected to be grounded in authoritative sources, citations must be exact, Arabic varieties differ substantially from the language of classical sources, and legitimate jurisprudential disagreement must be represented rather than collapsed into a single answer. This survey reviews the emerging field of Islamic LLMs and trustworthy Islamic AI. We organize the literature around Arabic NLP and Arabic-centric LLMs, Islamic NLP resources, Qur'anic question answering, Islamic knowledge benchmarks, retrieval-augmented generation, Islamic legal reasoning, inheritance reasoning, hallucination evaluation, and trustworthiness. We argue that fluency in Arabic is not sufficient for Islamic AI. Reliable systems require curated sources, retrieval and verification modules, citation-aware generation, madhhab-aware reasoning, human expert evaluation, and benchmarks that measure not only answer accuracy but also faithfulness, source validity, and reasoning quality. The survey concludes with a research agenda for hallucination-resistant Islamic AI systems.

16.
arXiv (math.PR) 2026-06-15

Longest weakly increasing subsequences of discrete random walks on the integers with heavy tailed distribution of increments

arXiv:2603.29047v2 Announce Type: replace-cross Abstract: We investigate the behavior of the length of the longest weakly increasing subsequences (weak LIS) of $n$-step random walks with nonzero integer increments $k = \pm 1, \pm 2, \dots$ given by a symmetric heavy tailed mass distribution proportional to $|k|^{-1-\alpha}$ for several values of the real parameter $\alpha > 0$ together with that of the simple random walk ($k=\pm 1$), to which the $n$-step heavy tailed walks reduce when $\alpha$ grows large enough that step jumps beyond $\pm 1$ become essentially absent on the scale of $n$. By means of exploratory fits, weighted nonlinear least squares, and nested-model comparisons, we found that the sample average length $\langle{L_{n}}\rangle$ scales like $\langle{L_{n}}\rangle \sim \sqrt{n}\log{n}$ when the distribution of increments has finite variance ($\alpha > 2$) and $\langle{L_{n}}\rangle \sim n^{\theta}$ with a varying exponent $\theta > 0.5$ when the variance is infinite ($\alpha \leq 2$). Distributional diagnostics indicate that the bulk of the $L_{n}$ distribution is very well-approximated by a lognormal model, though systematic deviations are observed in the tails. Our results corroborate and expand upon previous results for the LIS of other types of heavy-tailed random walks and raise a conjecture as to whether the distribution of $L_{n}$ is given, or can be effectively described, by a lognormal distribution.

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

On the Memorization Behavior of LLMs in Generative Recommendation: Observations, Implications, and Training Strategies

arXiv:2606.17276v1 Announce Type: cross Abstract: Generative recommendation (GR) has emerged as a promising direction for recommender systems. Recently, large language models (LLMs) have been increasingly adopted for GR, as their rich pretrained knowledge is expected to help them generalize beyond common user behavior patterns that traditional memorization-oriented baselines can capture. However, existing LLM-based GR works largely ignore LLMs' well-known tendency to memorize, which, if present in LLMs fine-tuned for GR, would restrict their utilization of pretrained knowledge. In this work, we investigate this concern by examining one-hop memorization, where a model recommends items that are direct successors of items in the training data. We show that LLMs do this more than non-LLM-based GR models-in fact, the vast majority of their gains over GR baselines are actually on users whose target items can be predicted through one-hop memorization. We intuit that improving performance on the remaining users requires LLMs to learn richer item-item relations beyond one-hop transitions. To achieve this, we propose IIRG, a novel training strategy that teaches LLMs to capture: (1) collaborative relations derived from item co-occurrences across multiple hops in user sequences, and (2) semantic relations among items with similar themes, both of which can serve as useful recommendation signals. We show that IIRG significantly improves over LLMs trained solely with standard next-item prediction, with especially large gains for users whose test items are not covered by train-time one-hop transitions.

18.
arXiv (CS.AI) 2026-06-17

Unlocking LLM Code Correction with Iterative Feedback Loops

arXiv:2606.17514v1 Announce Type: cross Abstract: Large Language Models have shown remarkable capabilities in code generation. However, most existing evaluations focus only on single-attempt accuracy and overlook the iterative refinement process that is central to real-world programming. This study presents a systematic investigation of LLMs' ability to rectify their own code through execution feedback. Using real-world programming problems across four models and two major programming languages, this study evaluates performance using iterative refinement framework where LLMs receive compiler error messages and testcase feedback after each attempt. This study introduces metrics to evaluate code failures, analyze rectification patterns, and compare the effectiveness of reasoning and non-reasoning models, offering actionable insights into both the understanding and practical application of feedback loops in LLM-driven code generation systems. Results show that reasoning models consistently improve over iterations, substantially outperforming non-reasoning models in leveraging feedback, while syntactic and runtime errors are far more tractable than logical or algorithmic failures.

19.
arXiv (quant-ph) 2026-06-12

Representation-Induced Symmetry Trapping in Adaptive Variational Quantum Simulations of Multi-Reference Topologies

arXiv:2606.13387v1 Announce Type: new Abstract: Evaluating the trainability of adaptive quantum chemistry algorithms under multi-reference static correlation requires understanding how representation topologies intertwine with molecular geometry. We systematically expose a deep physical dependence on point-group symmetry by evaluating a spin-conserved SUSD operator pool across highly stretched configurations (2 x Re) of asymmetric LiH, symmetric BeH2, and asymmetric H2O. Under asymmetric distortions, the non-local mapping constraints of the Bravyi-Kitaev transformation create an optimization trapping effect–an encodement-locked manifestation of the broader barren plateau crisis. Crucially, by comparing these to the symmetrical stretching baseline of BeH2, we demonstrate that the preservation of point-group symmetry structurally protects the optimization landscape, proving that ansatz symmetry restrictions are necessary but insufficient without accounting for the underlying fermion-to-qubit representation. While current methods rely on numerical pruning to throttle pool sizes, our structural approach establishes that the mapping representation remains a critical factor in maintaining landscape trainability. Furthermore, exploiting structural overlap within our pool, we introduce a covariance-driven, adaptive shot-allocation filter. Diverging from static energy-variance minimization frameworks, our allocation engine operates as a dynamic runtime diagnostic tool. By continuously monitoring the gradient precision threshold epsilon, it aggressively prunes dead symmetry channels and triggers an automated circuit-termination sequence upon detecting representation-induced flat-lined states (dE/dtheta approx 0). This integration of algebraic measurement reuse with topology-aware statistical filtering provides a promising, resource-efficient strategy for executing deep variational algorithms on early fault-tolerant architectures.

20.
PLOS Computational Biology 2026-06-08

Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings

by Julia Pilarski, Tanja Stadler, Sophie Seidel Multicellular organisms develop from a single cell by repeated rounds of cell division, differentiation, and death, which can be represented as a single-cell phylogenetic tree. Genetic lineage tracing allows us to investigate this development by tracking the ancestry of individual cells as populations grow and change over time. However, accurate reconstruction of the cell phylogeny and quantification of the corresponding phylodynamic parameters – cell division, differentiation, and death rates – from this tracking data remains challenging and needs to be systematically evaluated. We perform simulations and assess, using the Bayesian framework, the joint inference of time-scaled cell phylogenies and phylodynamic parameters from CRISPR lineage recordings with random or sequential edits. Principally, we characterize the inference improvements as the recorder capacity increases. We observe more accurate phylogenetic reconstruction from sequential compared to random recordings, but no substantial improvement in phylodynamic inference when using the additional information contained in the order of edits. Overall, we find that CRISPR lineage recordings carry a strong signal on the rates of cell division when appropriate models are used. However, we detect biases in the inferred rates of cell division and death under phylodynamic model misspecification, i.e., when fitting classic memoryless birth-death processes to synchronous cell divisions. Moreover, for scenarios when cells differentiate into distinct types, we demonstrate that Bayesian phylodynamic analysis of sparse end-point measurements can resolve these cell differentiation trajectories by lineage and time. Under prototypical dynamics, we recover cell type-specific division and death rates, and cell type transition rates in over 80% of simulations. Overall, this simulation study explores how much information on cellular development can be extracted from state-of-the-art genetic lineage tracing data using phylogenetic and phylodynamic methodology.

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

A Mathematical Theory of Value: a synthesis on goal-directed agency under resource constraints

Authors:

arXiv:2606.12502v1 Announce Type: cross Abstract: We propose that value – the quantity goal-directed agents create, destroy, and exchange – is a lawful structural quantity in the same category as information. Following Shannon's method, we make one ruthless abstraction: value is the rate at which an agent converts a resource into goal-progress, relative to a frame fixed by its goal. A scale-invariance axiom forces a logarithmic measure, $V=\sum_i k_i \ln e_i$; compounding of a reinvested resource forces the same form via the ergodicity argument of Peters (2019). The two routes are kin rather than independent; their agreement is a consistency check, not an over-determination. We derive a coding theorem of value: $\Delta G \le I(X;Y)$, achieved by Bayes-proportional allocation; realized value decomposes as $G=D(q\|r)-D(q\|p)$, identifying misalignment with measurable waste. For populations, value is frame-relative while price is frame-independent; a fleet that pools its resource and fuses its perception inherits the ceiling $G_{\mathrm{fleet}} \le I(X;Y_{1:m}) \le H(X)$ (a corollary; an earlier sum-form claim was wrong and is corrected in v5). A dynamical layer yields an is/ought asymmetry from which alignment emerges as a control-stability condition with a closed-form residual. We test the single-frame laws on live language models in a pre-registered scale-up: perception mutual information tracks realized capability rather than parameter count (Spearman $\rho = 0.977$ pooled over 30 model$\times$domain points), out-of-sample $\Delta G$ tracks $I(X;Y)$, and over-confidence is measurable dissipation; a further pre-registered test shows the bridge is shape-invariant across four task shapes ($n=42$, slope 0.953). None of the mechanisms is individually new – generalized Kelly, Armstrong & Mindermann (2018), classical control; the contribution is their unification and the governance mapping (incentive design over oversight) that follows.

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

Configurable Clinical Information Extraction with Agentic RAG: What Works, What Breaks, and Why

arXiv:2606.19602v1 Announce Type: new Abstract: Patient contexts span hundreds of heterogeneous documents and thousands of structured data points, yet the document-level metadata that AI systems need for retrieval and triage is absent or incomplete. Standard retrieval-augmented generation fails on this data, mishandling temporal reasoning, cross-document dependencies, and missing metadata. We deploy ACIE (Agentic Clinical Information Extraction) at University Medicine Essen: an on-premise agentic RAG pipeline that reasons over complete patient contexts and grounds every answer in source passages for clinician verification. We quantify the metadata gap, trace the architectural decisions it shaped, and evaluate extraction alongside an independent retrospective lymphoma registry study, in which nuclear-medicine physicians verify every extracted value against its cited sources. Across 7,326 judgments, clinicians accepted 96.5\% of extractions, with per-type acceptance ranging from 80\% to 99\%.

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

OmniLoc: A Geometry-Aware Foundation Model for Anchor-Free UE Localization Across Diverse Indoor Environments

arXiv:2606.11490v1 Announce Type: new Abstract: Indoor localization from wireless measurements remains challenging in large-scale deployments due to substantial variation in building geometry, the set of detectable access points (APs), and the heterogeneity of received signals. Existing learning-based methods often perform well only in limited settings and degrade under environmental shifts, making robust anchor-free localization across diverse indoor environments notoriously difficult. In this paper, we present OmniLoc, an environment-interactive foundation model for anchor-free user equipment localization across diverse indoor environments. To the best of our knowledge, OmniLoc is the first foundation-model-based approach built directly on wireless measurements for this task. OmniLoc is built on three key designs. First, a unified input tokenization module converts heterogeneous wireless measurements into a common representation that is more amenable to learning. Second, a geometry-aware Transformer performs AP-aware feature extraction by emphasizing dominant APs while aggregating complementary evidence from supporting APs. Third, a geometry-aware location estimation module conditions regression on geometric embeddings to produce geometrically consistent location predictions. We evaluate OmniLoc on both a large-scale in-house dataset and a public benchmark dataset. Results show that OmniLoc significantly outperforms existing methods, consistently improves existing backbones when its design components are integrated, and demonstrates strong generalization in cross-environment evaluations.

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

SACE: Concept Erasure at the Semantic Singularity in Visual Autoregressive Models

The rapid progress of visual autoregressive (VAR) models has unlocked a transformative frontier for high-fidelity text-to-image synthesis, while heightening concerns over the safety alignment of generated content. Naive application of existing erasure techniques to VAR models causes catastrophic semantic collapse and visual artifacts, since they are predominantly designed for the homogeneous denoising steps of diffusion models. To address this foundational challenge, we first propose the Semantic Singularity Axiom, which posits that any target semantic concept embedded within a prompt is definitively locked at Scale-0. Then rigorously validate this axiom through our proposed Incremental Semantic Saliency Analysis (ISSA),which also enable the community to transparently inspect the coarse-to-fine semantic injection process. Guided by this insight, we introduce the first scale-aware concept erasure framework (SACE) for VAR models. By strictly confining interventions to the first scale, our approach couples an Entropy-Regularized Erasure Objective to prevent high-entropy sampling degeneration, alongside a restorative preservation loss to safely anchor the integrity of entangled benign priors. Extensive experiments demonstrate that our method achieves surgical concept erasure performance across various domains with minimal training overhead, timely and elegently resolute the critical safety vulnerabilities inherent in emerging VAR architectures. Code is available at: https://github.com/limerenceysy/SACE}{https://github.com/limerenceysy/SACE.

25.
arXiv (quant-ph) 2026-06-16

Comparative Performance Analysis of NIST PQC Standards: From STM32 Software Limitations to FPGA-SoC Acceleration

arXiv:2606.15744v1 Announce Type: new Abstract: The rapid advancement of quantum computing poses a significant threat to classical public-key cryptographic systems, necessitating the transition to Post-Quantum Cryptography (PQC). This study investigates the implementation challenges of NISTstandardized signature schemes on resource-constrained embedded hardware. We present a comparative analysis of SPHINCS+ and CRYSTALS-Dilithium on an ARM Cortex-M4 (STM32F407G) microcontroller. Our findings reveal that SPHINCS+ is practically unusable in this software-only environment, with impractical execution times. Furthermore, the reference Dilithium implementation failed to execute entirely on the MCU due to severe RAM and timing constraints. To overcome these hardware limitations, we integrated a hardware-accelerated Dilithium core onto a Xilinx Zynq-7000 ZedBoard SoC. By implementing a specialized Number Theoretic Transform (NTT) accelerator in the FPGA fabric, we achieved successful execution with performance rates for key generation and signature generation at millisecond levels. These results demonstrate that while pure software PQC is non-viable for standard microcontrollers, a hardware-software codesign approach provides the necessary efficiency for quantumresistant embedded systems.