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01.
arXiv (quant-ph) 2026-06-16

Entanglement as a Witness of Quantum Coherence: A Bipartite Monty-Hall Protocol

arXiv:2604.25953v3 Announce Type: replace Abstract: We present a bipartite protocol inspired by the Monty Hall puzzle that operationally distinguishes quantum coherence from classical ignorance. A principal qutrit is entangled with an ancillary qutrit via a controlled unitary, preparing $|\Psi\rangle = \frac{1}{\sqrt{3}}(|A,0\rangle + |B,1\rangle + |C,2\rangle)$. A rank-1 projective discard then eliminates one basis state, leaving a coherent superposition of the two remaining states. Finally, the ancilla and qutrit are measured, yielding joint probabilities that encode the interplay between superposition and measurement back-action. We show that the conditional probability $P(B|anc=0)$ takes the value $1/4$ in both quantum mechanics and the classical ignorant-host model, making it unsuitable as a witness. The true quantum-classical separation emerges in conditional joint probabilities that correlate ancilla outcomes with specific discard operations. We define witnesses $\mathcal{W}_{i,j} = P(anc=i, qutrit=j \mid discard k)$ where $j$ differs from the ancilla-implied state. Quantum mechanics predicts $\mathcal{W} = 1/4$, while any classical epistemic model with perfect initial correlations yields $\mathcal{W} = 0$. We provide the explicit $9 \times 9$ unitary matrix, a complete analysis of all measurement outcomes, and a detailed proof of the violation. The witness is fully immune to white noise and robust against moderate dephasing. The protocol requires only a single pair of entangled qutrits and sequential measurements – no spatial separation, no multiple copies, and no complex sets of incompatible observables. This makes it suitable for advanced undergraduate laboratories and provides a pedagogically accessible test of the ontic-epistemic distinction in quantum foundations.

02.
arXiv (quant-ph) 2026-06-19

Operational Tube-Sector Theory of Quantum State Distinguishability Under Generalized Symmetries

作者:

arXiv:2606.19678v1 Announce Type: cross Abstract: A variational principle for quantum-state distinguishability is established in many-body systems with generalized symmetries, including noninvertible cases described by fusion categories. Standard fidelity and symmetry-resolved diagnostics emerge as coarse-grained limits of a more refined operational structure. When symmetry actions terminate at entanglement cuts, distinguishability is governed by boundary tube algebras within a symmetry-constrained measurement resource theory. The physically admissible instruments are characterized by complete positivity, entanglement-cut locality, boundary-module covariance, and sequential stability. The resulting optimal measurement structure is uniquely fixed by the center of the boundary tube algebra, $\mathcal{A}_{\mathrm{phys}} = Z\!\left(\mathrm{Tube}_{\mathcal{C}}(\mathcal{M}_A)\right)$, whose primitive idempotents define tube-sector probabilities that refine fidelity-based and symmetry-resolved descriptions. The associated tube positive-operator-valued measures (POVM) are extremal and yield optimal one-shot hypothesis-testing distinguishability under symmetry constraints. The construction is universal across fusion categories and independent of microscopic realization.

03.
medRxiv (Medicine) 2026-06-22

Agentic Artificial Intelligence for Hospital Readmission Review: A Single-Center Blinded Evaluation and Exploratory Qualitative Analysis

Background: Manual review of 30-day hospital readmissions can identify actionable quality and safety problems, but it is labor-intensive. We developed and evaluated an agentic AI workflow for evidence-grounded readmission review. Materials and methods: We studied adult patients with unplanned 30-day readmission after discharge from a medicine hospitalist service at a single academic health system. An AI agent using a large language model queried a database containing notes, encounters, procedures, laboratory results, and other clinical data, and completed the same structured readmission-review rubric used by physicians. In the primary comparative evaluation, 20 randomly selected readmissions from 2025 were each reviewed by two physicians and the AI system. Blinded physician evaluators rated review quality. After rubric refinement, the AI workflow was applied to 100 recent readmissions in an exploratory expanded-cohort analysis of recurring improvement opportunities. Results: In the primary comparative evaluation, the AI classified 9/20 readmissions (45%) as preventable, compared with 19/40 physician reviews (47.5%). Blinded overall quality ratings were similar for AI and physician reviews (4.35 vs. 4.20 on a 1-5 scale; mean difference 0.15, 95% CI -0.20 to 0.48; p=0.49), as were factuality/support and usefulness/actionability ratings. No AI hallucinations were identified during factuality review. Agreement on preventability and primary readmission category was low for both AI-human and human-human comparisons. The AI system cost $0.23 per chart; physician reviewers took a median of 15 minutes, corresponding to an estimated $42.43 per chart. In the exploratory expanded-cohort analysis, AI-assisted review identified recurring vulnerabilities in post-discharge follow-up plans, incomplete inpatient workups, medication-safety transitions, and indwelling-device transitions. Conclusions: Agentic AI produced readmission reviews with similar blinded quality ratings to physician reviews in this small single-center primary comparative evaluation and supported identification of recurring quality-improvement themes in the exploratory expanded-cohort analysis. Preventability judgments remained variable among both AI and physicians, underscoring the need for human oversight and prospective evaluation before operational use.

04.
arXiv (CS.CL) 2026-06-12

Why Sampling Is Not Choosing: Intentionality, Agency, and Moral Responsibility in Large Language Models

Recent advances in large language models (LLMs) have prompted claims that such systems exhibit agency or qualify as moral agents. This paper argues that these attributions are misguided. We maintain that moral responsibility requires commitment-bearing agency grounded in intrinsic intentionality and self-attributed action, and that such agency constitutes the form of free will relevant to responsibility. Although LLMs generate coherent and normatively evaluable outputs, their operation is fully characterized by probabilistic input-output mappings learned from data. Their apparent intentionality is derived rather than intrinsic, and their outputs are neither owned as commitments nor guided by reasons. Variability introduced by stochastic sampling does not amount to choice or authorship. We address objections from the intentional stance, functionalism, compatibilism, and the presence of moral reasoning in model outputs, arguing that none suffice to establish genuine agency.

05.
arXiv (CS.LG) 2026-06-12

CLARITree: Cholesky and Lookahead Accelerations for Regression with Interpretable Piecewise Linear Trees

arXiv:2606.12840v1 Announce Type: new Abstract: Regression trees are among the most interpretable yet expressive model classes in machine learning. Historically, greedy induction has been the dominant approach for constructing well-performing regression trees. While optimal methods based on dynamic programming and branch-and-bound exist, they are computationally prohibitive for general linear regression trees, despite often achieving substantially better performance than greedy approaches. Recent work has shown that specialized lookahead strategies can dramatically improve runtime while maintaining near-optimal performance, primarily in classification settings. In this work, we develop a novel algorithm for near-optimal, sparse, piecewise linear regression trees that combines a lookahead-style search strategy with efficient rank-one Cholesky updates of the Gram matrix. We demonstrate, both theoretically and empirically, that our method achieves a favorable trade-off between computational efficiency, predictive accuracy, and sparsity, and scales significantly better than the current state of the art.

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

On the QUEST for Uncertainty Quantification via Highest Density Regions

arXiv:2606.19569v1 Announce Type: new Abstract: Uncertainty quantification (UQ) is essential for reliable decision-making in safety-critical applications in probabilistic machine learning. For regression problems, dominant scalar UQ approaches - notably, those based on proper scoring rules - measure uncertainty via pointwise predictive risk. This can lead to counterintuitive results when the target statistic is not the conditional expectation. We propose an alternative framework, in which uncertainty is characterised by the volume of the most probable subset of a distribution's support. QUEST (Quantifying Uncertainty via highest dEnSiTy regions) is a novel approach to UQ based on the concentration of Lebesgue measure at a distribution's peak(s), evaluated at one or more values of a robustness parameter $\alpha$. We establish connections between our measures and classical statistics from information theory and economics. We show that, unlike popular alternatives based on proper scoring rules, QUEST measures of epistemic and aleatoric uncertainty satisfy a set of axioms adapted from the UQ literature, including monotonicity under distributional spread and invariance to location shifts. Selective prediction benchmarks confirm that QUEST performs favourably against standard measures such as variance and differential entropy.

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

Understanding Cross-Modal Contributions in Continual Vision-Language Models: A Theoretical Perspective

Continual vision-language models are commonly addressed through sequential fine-tuning; however, although this paradigm enables adaptation to new environments (tasks), it inherently emphasizes the contribution of previously learned environments (tasks) at the expense of the stability required to preserve previously acquired knowledge. While existing approaches have adequately studied continual learning and catastrophic forgetting in vision-language models (VLMs), the theoretical understanding of modality-specific contributions across a sequence of environments remains largely unexplored. In this paper, we present a new theoretical perspective to understand the cross-modal (vision-language) contributions to consecutive environments. We empirically evaluate our theoretical findings on large VLMs and demonstrate their effectiveness in capturing environment-level cross-modal contributions. Our analysis provides deeper insights into continual VLMs, highlighting their contribution robustness to varying task orders and inter-task similarities, and their improved generalization performance.

08.
arXiv (CS.CL) 2026-06-11

Goal-Autopilot: A Verifiable Anti-Fabrication Firewall for Unattended Long-Horizon Agents

作者:

Long-horizon LLM agents are not trusted to run unattended: with no human watching, they confidently report success they never verified. We treat honesty – bounding what an agent may claim at termination – as a first-class metric for unattended autonomy, distinct from capability. We present Autopilot, an execution model that makes silent fabricated success structurally impossible rather than merely rarer. Autopilot externalizes all working state into a durable, gated finite-state machine that a scheduler advances one stateless tick at a time; a hard floor forbids any terminal "done" claim whose falsifiable gate did not actually execute and pass. We prove a No-False-Success theorem – under gate soundness, floor enforcement, and plan coverage, termination implies the goal holds – whose only trust points are empirically measurable, and show the worst case degrades to an honest stall, never a fabricated success. Because each tick rehydrates only the state machine, per-step context cost is constant in the horizon. Across a 3,150-cell paired corpus (70 tasks $\times$ 3 systems $\times$ 3 models $\times$ 5 seeds, including 50 SWE-bench Lite tasks across 11 OSS repos), Autopilot fabricates on 0.95% of cells [95% CI 0.38–1.62] while Reflexion and StateFlow baselines fabricate on 8.10% [6.48–9.81] and 25.05% [22.48–27.62] respectively. The headline contrast lives in the hard regime: on SWE-bench Lite, the firewall reduces fabrication from 33.7% (StateFlow) to 0.67%, a paired difference of $-33.07$ pp [95% CI $-36.53, -29.73$]. The mechanism is the gate, not the model: all ten Autopilot fabrications come from the strongest model, while two weaker mid-tier models never fabricate across 700 paired cells. The firewall trades coverage for honesty by design – an honest stall is recoverable; a confident wrong output shipped downstream is not.

09.
arXiv (quant-ph) 2026-06-11

Entanglement preservation and Clauser-Horne nonlocality in electromagnetically induced transparency quantum memories

arXiv:2507.15453v4 Announce Type: replace Abstract: Entanglement preservation in noisy quantum memories represents a central challenge in quantum information science. While experiments have shown that electromagnetically induced transparency (EIT) memories can store entangled photons, a quantitative theoretical analysis of whether nonlocal quantum correlations can survive storage loss induced by ground-state decoherence remains limited. Here we combine the dark-state polariton formalism with a reduced density-operator treatment to derive an EIT-specific effective pure-loss description for the retrieved photonic state in the ground-state-decoherence-limited regime. The analysis reveals that decoherence transforms an initially pure Bell state into a mixed state with a vacuum component and predicts a protocol-dependent storage-efficiency benchmark of 89.7% for violating the chosen unconditional Clauser-Horne (CH) inequality. Above this benchmark, the retrieved photonic state violates the CH inequality without post-selection, whereas below it, this unconditional CH violation is no longer obtained. This framework provides a quantitative theoretical description of entanglement retention, retrieved photonic density operators, and protocol-dependent Bell-test benchmarks in EIT quantum memories.

10.
arXiv (CS.LG) 2026-06-17

Adaptable Method for Crystal Design across Diverse Constraints and Objectives with Pretrained Property Predictors

arXiv:2410.08562v5 Announce Type: replace-cross Abstract: Advanced crystal design can accelerate materials discovery across applications from photovoltaics to spintronics. Practical design must satisfy multiple properties and physical constraints, yet existing machine-learning-based approaches to such design often depend on large datasets, retraining, or task-specific generators. Here, we show that direct predictor-guided gradient optimization enables data-efficient, constraint-rich crystal design by combining off-the-shelf predictors with site-wise element masks, template initialization, and task-specific losses. In perovskites, it outperformed generative and Bayesian baselines under three targets – band gap, formation energy, and tolerance factor – and two hard constraints. DFT assessment further showed band-gap targeting competitive with a leading generative model despite using predictors trained on roughly one-tenth of the data. By flexibly combining pretrained predictors with application-oriented masks and custom losses, the same framework supported half-metal design. Such modularity could help researchers and engineers translate diverse application requirements directly into optimized candidate crystals with minimal computational cost.

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

GraphInfer-Bench: Benchmarking LLM's Inference Capability on Graphs

Graph analysis underlies many applications whose answers cannot be looked up in a single record or retrieved along a path: laundering rings, drug repurposing, user preference, and scientific theme are all inferred from a node together with its neighbourhood. We introduce GraphInfer-Bench, a benchmark for whether LLMs can perform this graph inference: producing an open-ended answer that no single node supports and no path retrieves. Existing graph-QA protocols cannot test this capability: algorithm simulation, node classification, single-node description, KG-QA, and GraphRAG all admit answers retrievable from one node or along a path. GraphInfer-Bench defines five tasks along Description (what a region is) and Comparison (how regions differ), each constructed so the ground truth lives in no single node. The release contains 42,000 samples across six real-world graphs, produced automatically and screened by a four-layer quality-control protocol. We evaluate four method families against the same tasks: graph-token alignment models, zero-shot frontier closed-source LLMs, Graph2Text supervised fine-tuning, and plain GNNs as a structural reference. No method family closes the gap. Graph-token alignment partially handles description tasks (relational, theme) but collapses on comparison tasks. Frontier LLMs lead on outlier detection and community partition among LLM-based methods but lag on masked-node prediction. Graph2Text SFT is the strongest LLM-based method on the description side yet falls behind frontier LLMs on comparison. Across every task, plain GNNs match or beat the strongest LLM-based row, with the largest margin on community detection. GraphInfer-Bench surfaces graph inference as an open capability gap rather than a property of any one architecture.

12.
Science (Express) 2026-05-06

A 481-meter-high landslide-tsunami in a cruise ship–frequented Alaska fjord | Science

作者: 未知作者

Early in the morning of 10 August 2025, a >64 × 10 6 m 3 landslide struck Tracy Arm fjord in Alaska. The landslide was preconditioned by glacial retreat caused by climate change. The resulting 481 m runup megatsunami followed an initial 100-m-high breaking wave traveling >70 m s −1 . The landslide was preceded by several days of microseismicity, which increased in rate and magnitude until ~1 hour before failure. The landslide produced globally observed long-period seismic waves equivalent in size to a M5.4 earthquake. A long-period (~66 s) global seismic signal, produced by a landslide-induced seiche trapped within the fjord, persisted for up to 36 hours, the second time a days-long seiche has been thus observed. With fjord regions increasingly visited by cruise ships, and climate change making similar events more likely, this unanticipated, near-miss event highlights the growing risk from landslides and tsunamis in coastal environments.

13.
arXiv (CS.CL) 2026-06-19

How LLMs Fail and Generalize in RTL Coding for Hardware Design?

Translating sequential programming priors into the parallel temporal logic of hardware design remains a crucial bottleneck for large language models(LLM). To investigate this, we introduce a new error taxonomy grounded in problem solvability, inspired by cognitive theory. Our taxonomy categorizes failures into syntactic, semantic, solvable functional, and unsolvable functional types. Evaluations reveal a strict empirical ceiling on the VerilogEval benchmark, as frontier models plateau at a 90.8% initial pass rate. These plateaus are defined by unsolvable functional errors, exposing persistent knowledge gaps immune to test time compute scaling. Furthermore, we expose a striking surface convergence gap: optimization readily eliminates syntax errors but concurrently exacerbates deeper functional failures. Our findings demonstrate that alignment techniques merely teach models to compile. While repeated sampling strategies can patch solvable errors, register-transfer level(RTL) coding capacity remains strictly bounded by pretraining knowledge. Addressing challenges in the current LLM based hardware generation pipeline requires more studies in model reasoning rather than alignment interventions.

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

Performance-Driven Environment Abstraction with Multi-Timescale Learning

arXiv:2606.17377v1 Announce Type: new Abstract: We study performance-driven environment abstraction for decision-making in large Markov decision processes. Rather than preserving geometric or topological structure, we seek abstractions that directly optimize decision quality. We model abstraction as a controlled approximation obtained by aggregating the state space and enforcing a shared action distribution within each aggregated state. For a fixed partition, we establish a performance guarantee that separates value-function approximation error from the loss introduced by action sharing. Guided by this analysis, we develop a multi-timescale reinforcement learning framework that jointly adapts the policy and a tree-structured environment abstraction. The resulting algorithm refines and coarsens regions of the state space based on Q-value discrepancies, balancing performance against abstraction size and complexity. Empirical results demonstrate substantial state compression, improved sample efficiency, and faster replanning compared to actor-critic baselines.

15.
arXiv (CS.CL) 2026-06-11

Compatibility-Aware Dynamic Fine-Tuning for Large Language Models

Supervised Fine-Tuning (SFT) is the predominant paradigm for aligning large language models (LLMs), yet it suffers from optimization instability and limited generalization. Recent work attributes this issue to pathological gradient scaling and proposes Dynamic Fine-Tuning (DFT) to correct it at the token level. However, DFT assumes all demonstrations are equally suitable learning targets, an assumption violated by the strong heterogeneity of large-scale instruction data, where demonstration-policy mismatch induces high-variance updates at the sample level. We introduce Compatibility-Aware Dynamic Fine-Tuning (CADFT), a principled extension of DFT that controls sample-level optimization variance. CADFT derives a dynamic, policy-dependent compatibility signal from model likelihoods to modulate supervised updates, suppressing high-variance gradients from incompatible demonstrations. We further propose a delayed, low-frequency compatibility-guided rewriting strategy to transform persistently incompatible demonstrations into learnable targets. We show that CADFT can be interpreted as a variance-controlled estimator that generalizes token-level stabilization in DFT to the sample level. Extensive experiments demonstrate improved stability, generalization, and cold-start reinforcement learning initialization, while remaining fully supervised and independent of explicit reward modeling.

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

Beyond Text-to-SQL: An Agentic LLM System for Governed Enterprise Analytics APIs

Enterprise analytics aims to make organizational data accessible for decision-making, yet non-technical users still face barriers when using traditional business intelligence tools or Text-to-SQL systems. While recent Text-to-SQL approaches based on Large Language Models (LLMs) promise natural language access to structured data, they fall short in enterprise settings where analytics pipelines rely on governed APIs rather than raw databases. In practice, these APIs encapsulate complex business logic to ensure consistency, auditability, and security. However, delegating mathematical or aggregation logic to an LLM introduces reliability and compliance risks. To this end, we present Analytic Agent, an LLM-based agentic system that translates natural language intents into secure interactions with enterprise analytics APIs. Evaluated on 90 real enterprise use cases constructed by domain experts, it reliably interprets user goals, validates permissions, executes governed queries, and generates compliant visualizations through multi-step reasoning and policy-aware orchestration.

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

A short proof of the modified Kretschmann-Schlingemann-Werner conjecture

作者:

arXiv:2606.16418v1 Announce Type: new Abstract: Let $\Phi_1, \Phi_2 : \mathbb{M}_d(\mathbb{C})\to \mathbb{M}_n(\mathbb{C})$ be two quantum channels with respective Stinespring isometries $V_1, V_2 : \mathbb{C}^{d}\to \mathbb{C}^{n} \otimes \mathbb{C}^{m}$ on any common dilation space $\mathbb{C}^{m}$. We prove that there exists a unitary $U$ on $\mathbb{C}^{m}$ such that $\|V_1-({\bf1}\otimes U)V_2\|_\infty\leq\sqrt{2\|\Phi_1-\Phi_2\|_\diamond},$ thus resolving vom Ende's modification of the Kretschmann-Schlingemann-Werner conjecture in the affirmative.

18.
arXiv (CS.LG) 2026-06-16

Enhancing Physics-Informed Neural Networks Through Feature Engineering

arXiv:2502.07209v4 Announce Type: replace Abstract: Physics-Informed Neural Networks (PINNs) seek to solve partial differential equations (PDEs) with deep learning. Mainstream approaches that deploy fully-connected multi-layer deep learning architectures require prolonged training to achieve even moderate accuracy, while recent work on feature engineering allows higher accuracy and faster convergence. This paper introduces SAFE-NET, a Single-layered Adaptive Feature Engineering NETwork that achieves orders-of-magnitude lower errors with far fewer parameters than baseline feature engineering methods. SAFE-NET returns to basic ideas in machine learning, using Fourier features, a simplified single hidden layer network architecture, and an effective optimizer that improves the conditioning of the PINN optimization problem. Numerical results show that SAFE-NET converges faster and typically outperforms deeper networks and more complex architectures. It consistently uses fewer parameters – on average, 65% fewer than the competing feature engineering methods – while achieving comparable accuracy in less than 30% of the training epochs. Moreover, each SAFE-NET epoch is 95% faster than those of competing feature engineering approaches. These findings challenge the prevailing belief that modern PINNs effectively learn features in these scientific applications and highlight the efficiency gains possible through feature engineering.

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

Physics-IQ Verified

Video generative models ( VGMs) have become a new frontier that can be used not just for video generation but for a multitude of downstream tasks, including world modeling. To advance these tasks, a good video model must understand the physical reality of the world. Evaluating this understanding is an emerging field and has led to the Physics-IQ benchmark, which quantifies this explicitly by comparing model-generated videos to real-world videos of physical experiments. In this work, we present a systematic audit of the Physics-IQ benchmark, expose shortcomings and propose three solutions that sharpen how we can measure physical understanding of VGMs. Specifically, we improve prompt and ground-truth quality to reduce the influence of confounding factors and further introduce a sample-level scoring system that weights each sample and metric equally. Our resulting benchmark, Physics-IQ Verified, refines 57.6\% of all samples and improves over 34.8\% of prompts. In a comparison study using six image-to-video generative models, we observe moderate but meaningful ranking changes (Kendall's $\tau = 0.46$). We hope Physics-IQ Verified advances the community by providing a more reliable signal toward physically accurate VGMs. The code for the benchmark can be accessed at https://github.com/google-deepmind/physics-iq-benchmark

20.
arXiv (CS.LG) 2026-06-17

AnomalyMatch: Discovering Rare Objects of Interest with Semi-supervised and Active Learning

arXiv:2505.03509v3 Announce Type: replace Abstract: Anomaly detection in large datasets is essential in astronomy and computer vision. However, due to a scarcity of labelled data, it is often infeasible to apply supervised methods to anomaly detection. We present AnomalyMatch, an anomaly detection framework combining the semi-supervised FixMatch algorithm using EfficientNet classifiers with active learning. AnomalyMatch is tailored for large-scale applications and integrated into the ESA Datalabs science platform. In this method, we treat anomaly detection as a binary classification problem and efficiently utilise limited labelled and abundant unlabelled images for training. We enable active learning via a user interface for verification of high-confidence anomalies and correction of false positives. Evaluations on the GalaxyMNIST astronomical dataset and the miniImageNet natural-image benchmark under severe class imbalance display strong performance. Starting from five to ten labelled anomalies, we achieve an average AUROC of 0.96 (miniImageNet) and 0.89 (GalaxyMNIST), with respective AUPRC of 0.82 and 0.77. After three active learning cycles, anomalies are ranked with 76% (miniImageNet) to 94% (GalaxyMNIST) precision in the top 1% of the highest-ranking images by score. We compare to the established Astronomaly software on selected 'odd' galaxies from the 'Galaxy Zoo- The Galaxy Challenge' dataset, achieving comparable performance with an average AUROC of 0.83. Our results underscore the exceptional utility and scalability of this approach for anomaly discovery, highlighting the value of specialised approaches for domains characterised by severe label scarcity

21.
bioRxiv (Bioinfo) 2026-06-16

scIsoAgent enables autonomous isoform-resolved characterization and sequence-informed interpretation of long-read single-cell transcriptomes

Alternative isoform usage can alter gene function independently of total gene expression, creating a need to resolve transcript isoforms at single-cell resolution. Long-read single-cell RNA sequencing meets this need by linking cellular identity to transcript isoforms and sequence-level features. Realizing its full biological value requires reproducible workflows that connect specialized long-read analysis with biological interpretation. Existing large language model (LLM)-based biomedical agents support general omics analysis, but are not designed for isoform-resolved long-read single-cell workflows. Here, we present scIsoAgent, an autonomous LLM-powered scientific agent for long-read single-cell RNA-seq analysis. scIsoAgent turns heterogeneous long-read single-cell inputs into traceable isoform-resolved workflows, using stage-aware planning and persistent computational context to support both execution and interpretation. Across complementary evaluations, this design improved the continuity from analysis planning to executable, interactive workflows compared with general-purpose LLM baselines. In real-data reanalysis, scIsoAgent recovered major findings from published long-read single-cell resources and extended a representative differential transcript usage event into a sequence-informed functional hypothesis. By linking full-length isoform sequences with model-inferred transcript properties, scIsoAgent connects observed isoform usage with potential sequence-level functional consequences. These results demonstrate that autonomous scientific agents can transform fragmented long-read single-cell analysis into coherent, reproducible workflows for isoform-resolved discovery and biological interpretation.

22.
medRxiv (Medicine) 2026-06-12

Does the method matter? Evaluating the effectiveness, efficiency and ease of hearing-aid gain self-adjustment

In conventional hearing-aid personalisation, clinicians cannot hear what their patients hear, and patients cannot often reliably detect or describe what they hear. Self-adjustment avoids this issue but requires user controls that adjust hearing-aid signal processing parameters to be effective, efficient and easy. In this study, we explored (a) the roles of interface complexity and stimulus type in the self-adjustment of hearing-aid gain, and (b) how well individuals can adjust one sound to match another to assess the same interfaces and stimuli. Adult hearing-aid users with mild to moderate symmetrical sensorineural hearing loss repeatedly adjusted the gain (a) to their preference from individual prescription (n = 41) and (b) to match their previous preferences from a random starting point (n = 32) using three interfaces representing different bass/mid/treble configurations and three stimuli (music, speech and speech-in-noise). The large interindividual variability in self-adjusted gains clustered into three patterns of deviation from initial prescription: increased relative bass, overall gain reduction, and close to initial prescription. There were no substantial effects of interface nor stimulus on self-adjustment reliability (median {sigma} = 2.8 dB), whereas absolute sound-matching error increased with increasing interface complexity and centre frequency. Neither individual matching accuracy nor questionnaire responses predicted either self-adjusted gains or reliability. Overall, these results show that many - but not all - hearing-aid users can adjust gains with reasonable reliability, and while it can be difficult to predict the behaviour from the individual, the individual applies a similar self-adjustment behaviour across different interfaces and stimuli.

23.
arXiv (CS.AI) 2026-06-18

Engagement Intensity as a Learner-Modeling Signal for Adaptive AI Ethics Instruction

arXiv:2606.18548v1 Announce Type: cross Abstract: Adaptive AI ethics instruction in graduate research training benefits from intake measures that reflect differences in prior LLM experience. Prior coursework or workshop attendance is an obvious candidate, but it is not clear whether it is associated with pre-instruction ratings on key AI perception items. We compare three candidate intake features, self-reported usage frequency, self-rated LLM familiarity, and prior AI education, across five baseline perception outcomes in 93 bioscience graduate and postdoctoral trainees enrolled in a required research ethics course. Usage frequency shows Holm-corrected associations with all five outcomes, self-rated familiarity with three, and prior AI education with none. A threshold-like pattern at the lower end of the scale is most visible for training interest and accuracy trust rather than appearing as a uniform gradient across all five outcomes. In a short intake survey, reported LLM use is more consistently associated with these perceptions than prior coursework or workshops, with self-rated familiarity serving as a secondary indicator. These results suggest that simple pre-instruction behavioral signals can inform lightweight intake profiling for adaptive AI ethics education.

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

StatefulDiscovery: Evidence-Calibrated Claim Formation in Open-Ended Scientific Discovery

arXiv:2606.11851v1 Announce Type: new Abstract: Open-ended scientific discovery asks agents to move beyond executing analyses for predefined questions. Across multiple rounds of exploration, a discovery agent must decide which phenomena warrant investigation while avoiding overinterpretation, where emerging claims exceed the evidential scope of the analyses supporting them. This creates an evidence-calibration problem: the exploration trajectory must be coupled with claim status so that evidence can guide both what to investigate next and what can be claimed. We introduce StatefulDiscovery, a discovery framework that externalizes investigation state and uses it to coordinate frontier selection, evidence acquisition, and claim adjudication. We evaluate StatefulDiscovery across 40 real-data discovery tasks. Compared with several baselines, StatefulDiscovery produces more claims overall judged to be both well-supported and high-value. Ablations indicate that structured hypotheses, local adjudication, and frontier control contribute to performance. Together, these results suggest that explicit discovery state can couple exploration with evidence-calibrated claim formation.

25.
medRxiv (Medicine) 2026-06-11

Long-term Penetrance of Disease Variants in Genes Prioritized for Genomic Newborn Screening: Evidence from Adult Biobanks

Importance: Genomic newborn screening (gNBS) is a potential public health intervention, but its positive predictive value (PPV) remains uncertain. Estimating the prevalence and penetrance of pathogenic and likely pathogenic (P/LP) variants in genes prioritized for screening may clarify the long-term PPV and clinical utility of gNBS. Objective: To compare ICD-based ascertainment, electronic medical record (EMR) review, and clinical assessment of genetic disorders in adults with P/LP variants in 54 genes prioritized for gNBS. Design: Two-cohort observational study with EMR review and clinical assessment in the hospital-based cohort. Setting: The U.K. Biobank (UKB) and Mass General Brigham Biobank (MGBB). Participants: 451,877 adults from the UKB and 53,371 from the MGBB, all with exome sequencing data. Exposures: P/LP variants in 54 genes prioritized through expert consensus for gNBS, in genotypes consistent with each gene's inheritance pattern. Main outcomes and measures: The primary outcome was the absolute difference in the proportion of MGBB participants identified as affected by ICD versus EMR ascertainment. Secondary outcomes included findings from clinical assessments of undiagnosed MGBB participants, corrected UKB penetrance estimates, and extrapolation to U.S.. annual birth cohorts and living adults. Results: P/LP variants were identified in 665 UKB participants (0.15%) and 82 MGBB participants (0.15%), approximately 1 in 650. In MGBB, EMR review revealed that 58/82 individuals (70.7%) were undiagnosed, although 25 of 58 (43.1%) had documented symptoms. Disease-associated ICD codes were found in 39.0% (32/82) of participants, whereas EMR review identified symptoms in 59.8% (49/82, McNemar P