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01.
arXiv (CS.LG) 2026-06-11

A Riemannian Approach to Low-Rank Optimal Transport

arXiv:2606.12120v1 Announce Type: new Abstract: Low-rank optimal transport (OT) mitigates the quadratic scaling of classical solvers, yet existing approaches rely heavily on first-order mirror-descent updates that require careful hyperparameter tuning and ignore the optimization landscape's curvature. To address these limitations, we propose a unified Riemannian geometric framework for low-rank OT, modeling balanced and unbalanced rank-$r$ positive factored couplings as novel smooth embedded submanifolds of the positive orthant. By equipping these manifolds with the Fisher-Rao product metric, we derive tractable formulations for Riemannian projectors, retractions, and Hessian-vector products. Our cost-agnostic framework seamlessly extends to linear OT, Gromov-Wasserstein (GW), fused GW, and their unbalanced counterparts. For balanced OT, our geometric ingredients are computed via efficient conjugate-gradient and iterative Bregman updates. For the unbalanced OT, our operations elegantly reduce to closed-form scalings, completely eliminating inner iterative loops. In both regimes, per-iteration complexity scales linearly with dataset size, and we provide a rank-sufficiency certificate for global optimality verification. Extensive experiments across a range of problem sizes demonstrate that our regularization-free first- and second-order solvers achieve faster convergence and superior performance over existing state-of-the-art low-rank OT solvers.

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

CoreMem: Riemannian Retrieval and Fisher-Guided Distillation for Long-Term Memory in Dialogue Agents

Personalized dialogue agents require continuous long-term memory to maintain coherent interactions across multiple sessions. However, deploying these capabilities on consumer-grade hardware (e.g., 8 GB VRAM edge devices) introduces severe memory and compute bottlenecks. Existing systems typically rely on isotropic cosine similarity for retrieval and heuristic rules for context compression. These approaches lack a unified theoretical foundation, frequently suffering from the hubness problem in high-dimensional retrieval and syntactic fragmentation during compression. To overcome these limitations, we propose CoreMem, a resource-efficient edge-cloud memory architecture fundamentally unified by information geometry. First, Riemannian retrieval replaces cosine matching with a locally adaptive Fisher-Rao metric, effectively penalizing hub memories via Mahalanobis distance with O(Ndr) Woodbury acceleration for real-time search. Second, Fisher-guided discrete token distillation (FDTD) introduces a hierarchical sentence-to-token compression mechanism. It derives sensitivity scores from Fisher information traces, providing a principled compression-KL tradeoff augmented with explicit structural syntax protection. Evaluated on the LOCOMO and LongMemEval-S benchmarks, CoreMem achieves strong accuracy improvements, yielding substantial gains in Open-domain (+4.51 pp) and Temporal (+4.17 pp) reasoning. Extensive profiling confirms that CoreMem operates seamlessly within a strict 8 GB VRAM budget, successfully bridging the gap between resource-constrained edge devices and the demand for theoretically grounded, lifelong memory agents.

03.
arXiv (CS.LG) 2026-06-17

A fairness-aware extension of Stochastic Multicriteria Acceptability Analysis for ranking

arXiv:2606.17756v1 Announce Type: new Abstract: Fairness has become a central concern in ranking problems involving individuals or social groups, particularly under the Responsible Artificial Intelligence agenda. In Multi-Criteria Decision Analysis, Stochastic Multicriteria Acceptability Analysis (SMAA) provides a robust framework for handling uncertainty and incomplete preference information, but it does not explicitly address fairness in the resulting rankings. This paper proposes SMAA-Fair, a fairness-aware extension of SMAA for ranking problems. The approach reweights the simulated rankings generated by SMAA according to their level of group fairness, so that fairer rankings contribute more strongly to the acceptability indices and central weights vector. The framework is independent of the aggregation model and can incorporate different fairness metrics. In this study, Statistical Parity, normalized discounted Kullback–Leibler divergence (rKL) and normalized discounted cumulative Kullback–Leibler divergence (nDKL) are adopted. Rankings are derived from the fairness-adjusted acceptability matrix using expected ranking and maximum acceptability ranking. We also derive the central weight according to the degree of fairness in the obtained rankings. Numerical experiments with synthetic and real data show that SMAA-Fair improves the representation of protected groups among favourable ranking positions, while preserving robustness to preference uncertainty.

04.
bioRxiv (Bioinfo) 2026-06-12

Computational Design of Optimal Sequences for Targeted Hypermutagenesis Using Recombination-Coupled Diversity-Generating Retroelements

Diversity-generating retroelements (DGRs) are natural systems that accelerate evolution via targeted hypermutation at adenines. We previously developed DGRec, a system combining DGRs and recombineering for programmable mutagenesis in Escherichia coli. We here address two important issues with DGRec: the dependence of mutagenesis efficiency on the dgrRNA secondary structure and the variability of the reverse-transcription biases with sequence context and position. First, we introduce and validate a method to recode non-functional templates, i.e. with low mutagenesis efficiency, into highly functional ones through synonymous mutations. Second, we develop a Long Short-Term Memory (LSTM) model to predict DGRec mutational profiles for any given template sequence. By integrating this LSTM model with our recoding method, we establish a comprehensive workflow for customized directed evolution, enabling researchers to precisely fine-tune DGRec in vivo mutagenesis to their engineering needs.

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

ResidualPlanner+: a scalable matrix mechanism for marginals and beyond

arXiv:2305.08175v5 Announce Type: replace-cross Abstract: Noisy marginals are a common form of confidentiality protecting data release and are useful for many downstream tasks such as contingency table analysis, construction of Bayesian networks, and even synthetic data generation. Privacy mechanisms that provide unbiased noisy answers to linear queries (such as marginals) are known as matrix mechanisms. We propose ResidualPlanner and ResidualPlanner+, two highly scalable matrix mechanisms. ResidualPlanner is both optimal and scalable for answering marginal queries with Gaussian noise, while ResidualPlanner+ provides support for more general workloads, such as combinations of marginals and range queries or prefix-sum queries. ResidualPlanner can optimize for many loss functions that can be written as a convex function of marginal variances (prior work was restricted to just one predefined objective function). ResidualPlanner can optimize the accuracy of marginals in large scale settings in seconds, even when the previous state of the art (HDMM) runs out of memory. It even runs on datasets with 100 attributes in a couple of minutes. Furthermore, ResidualPlanner can efficiently compute variance/covariance values for each marginal (prior methods quickly run out of memory, even for relatively small datasets). ResidualPlanner+ provides support for more complex workloads that combine marginal and range/prefix-sum queries (e.g., a marginal on race, a range query on age, and a combined race/age tabulation that answers age range queries for each race). It even supports custom user-defined workloads on different attributes. With this added flexibility, ResidualPlanner+ is not necessarily optimal, however it is still extremely scalable and outperforms the prior state-of-the-art (HDMM) on prefix-sum queries both in terms of accuracy and speed.

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

Order Is Not Control

AI alignment, interpretability, steering, and neural perturbation studies identify order-inducing objects. We argue that order is not control. Control requires a receiver-gated response law: a denominator-indexed operator mapping material state, action/drive, bath, and receiver state to response displacement, sinks, effort, and basin projection. We identify it across biological, LLM, adapter, and stochastic-operator panels. The laws are local: an intervention can be admitted, saturated, sign-changing, leaky, or overdriven depending on medium, bath, receiver state, action port, and comparator. Control is assigned when finite effort moves a target or outcome-readout class under the same denominator while damage, null/evasive, invalid format, overdrive, and unnecessary effort stay bounded. Mouse ALM, C. elegans, and zebrafish panels provide physical response-operator evidence while excluding coordinate identity and controller conclusions. LLM panels show generated-output response laws: across four material conditions, response vectors are predictable at 72.8-73.7% component-sign accuracy, rising to 84.3-84.8% on nonzero components; held-out observers predict system-effect and target/oracle families at 93.6% and 91.7% accuracy. Constitution-conditioned adapters reshape susceptibility as prepared media, and stochastic-operator panels separate measured opportunity from deployable action policies. This gives a driven-dissipative response-system account at the mesoscopic control level: drives act through prepared media, baths, and receivers, producing admitted movement, impedance, sinks, or overdrive. The evidence supports local admitted control and measurable stochastic response operators, while leaving deployable pre-generation control, hidden/logit causal sufficiency, biological-to-LLM coordinate identity, and literal thermodynamic quantities outside scope.

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

AI-Driven Framework for Adaptive Water Network Management with Proof-of-Concept Implementation: Addressing Non-Revenue Water in Jordan

arXiv:2606.15709v1 Announce Type: new Abstract: Jordan faces severe water scarcity with 50\% of water produced is lost to leakage, theft and metering issues also known as non-revenue water (NRW). Traditional reactive approaches have proven insufficient for sustained NRW reduction. This paper proposes an intelligent framework integrating EPANET hydraulic modeling, digital twin technology, SCADA systems, and large language model (LLM)-based AI agents for continuous network monitoring and adaptive decision-making. The system combines real-time data streams with physics-based simulation to detect anomalies, employing retrieval-augmented generation (RAG) for policy interpretation and function calling for network control. A proof-of-concept implementation validates technical feasibility using EPYT with offline LLMs (llama3.1:8b via Ollama) on a 1,164-junction Amman district network. The system demonstrates automated hydraulic simulation, flow-based anomaly detection aligned with water distribution zone (DZ) practice, and AI-generated health reports with response times under 2 minutes and zero API costs. Burst detection relies on local flow anomaly analysis: a 30.1~L/s simulated leak produces measurable flow redistribution in 15 pipes, flagging a 15-junction cluster that localises the burst – confirming alignment with water distribution zone (DZ) monitoring practice. The framework accommodates Jordan's intermittent supply patterns and limited automation through phased implementation, offering a scalable pathway for water-scarce regions to leverage intelligent automation for NRW reduction and operational efficiency.

08.
arXiv (CS.AI) 2026-06-16

WorkflowPerturb: Calibrated Stress Tests for Evaluating Multi-Agent Workflow Metrics

arXiv:2602.17990v2 Announce Type: replace Abstract: Multi-agent LLM systems that generate structured workflows from natural-language requests are now deployed in production across cloud automation, DevOps, and enterprise process orchestration. Operating such systems exposes a recurring change-management problem. Routine updates, such as re-running the same input, swapping the underlying LLM, or refactoring an agent's prompt or orchestration code, frequently produce workflows that differ substantially from previously validated references. Engineers are then left without a principled way to decide whether a change is safe to ship. Automatic workflow evaluation is the natural tool for answering this question. In practice, however, metric scores are poorly calibrated, and a numeric change rarely communicates the severity of the underlying degradation. We introduce WorkflowPerturb, a controlled benchmark for studying workflow evaluation metrics by applying realistic, graded perturbations to golden workflows. WorkflowPerturb contains 4,973 golden workflows and 44,757 perturbed variants across three perturbation types (Missing Steps, Compressed Steps, and Description Changes), each applied at severity levels of 10%, 30%, and 50%. We benchmark multiple metric families and analyze their sensitivity and calibration using expected score trajectories and residuals. Our results characterize systematic differences across metric families and support severity-aware interpretation of workflow evaluation scores in change-management settings. Our dataset will be released upon acceptance.

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

Signed Compression Progress on a Sealed Audit is Goodhart-Resistant

arXiv:2606.11417v1 Announce Type: cross Abstract: Compression progress is a long-standing proposal for intrinsic motivation: reward an agent when its world model becomes better at predicting or compressing experience. The folk claim is that this reward is "credible" because it is paid only for learning. We make this precise and prove it. If intrinsic reward is the signed decrease of a fixed sealed-audit loss, r_t = E(theta_{t-1}) - E(theta_t), then cumulative reward telescopes exactly to endpoint audit improvement, so no policy can push reward up indefinitely while true audit performance stagnates or degrades. For finite audit panels the same result holds with a sharp false-positive budget: cumulative empirical reward is at most true audit improvement plus 2 Delta_n(F, delta), the uniform audit deviation of the model class. This is horizon-free: adaptivity over time costs nothing once the sealed panel uniformly controls the class. The theorem also identifies the failure modes: the guarantee disappears if progress is clipped, scored on the agent's own stream, exposed to a high-capacity model on a reusable panel, or applied to a neural class that makes Delta_n vacuous. We give a Lean 4 mechanization of the structural core (telescoping, the finite-audit bound, finite Gibbs, and the entropy floor) and an experiment suite on ARC-TGI grid-transformation generators with adaptive holdout attacks. Experiments confirm the theory: finite-audit deviation scales as n^{-0.527}; signed progress resists clip-farming, stream leakage, and noisy-TV curiosity; naive reusable audits are exploitable by black-box scalar feedback, while standard release defenses keep the attack below the 2 Delta_n threshold. Signed compression progress on a sealed audit is an accounting signal of genuine improvement.

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

Cordyceps: Covert Control Attacks on LLMs via Data Poisoning

arXiv:2605.26595v2 Announce Type: replace-cross Abstract: Large language models (LLMs) are often fine-tuned on uncurated text datasets that adversaries can poison. Existing poisoning attacks primarily rely on fixed trigger phrases that defenses such as outlier detection, clean-data regularization, or online monitoring can neutralize. In this paper, we propose a data poisoning method that teaches an LLM an information hiding scheme reliably and stealthily through semantic associations between shared knowledge such as facts or concepts and attacker-chosen phrases. The induced hiding scheme can encode and decode arbitrary malicious instructions, thus revealing a new and subtle poisoning-induced vulnerability: covert control attacks. We precisely characterize covert control attacks and evaluate them across $5$ LLMs, $3$ backdoor defenses, and $4$ prompt injection defenses. With a small poisoned fraction, covert control attacks outperform heuristic-based prompt injection attacks in average attack success rate by about $40\%$ relative to clean fine-tuned models. They also circumvent defenses based on detection and fine-tuning, maintaining up to $93\%$ attack success rate after backdoor defenses and up to $98\%$ after prompt injection defenses.

11.
bioRxiv (Bioinfo) 2026-06-15

Multi-platform reassessment of human mitochondrial DNA methylation reveals signals consistent with technical artifacts

The existence and functional relevance of mitochondrial DNA methylation remain controversial. Here, we systematically profiled cytosine methylation and hydroxymethylation across human brain and blood tissues spanning healthy and malignant states using orthogonal sequencing approaches that avoid chemical conversion during library preparation. While nuclear DNA exhibited canonical methylation patterns, mitochondrial DNA consistently showed negligible signal, indistinguishable from background technical noise. By mapping cytosine-guanine sites between mitochondrial DNA and nuclear-embedded mitochondrial sequences, we demonstrate the potential of these nuclear counterparts to confound not only cytosine methylation but also hydroxymethylation measurements, corroborating and extending prior findings implicating nuclear contamination as a potential source of apparent mitochondrial epigenetic signals. Additional technical factors that inflate apparent mtDNA methylation signals were identified, including sequence context biases, flow cell chemistries, and coverage-dependent discrepancies between the heavy and light strands. Collectively, these results provide convergent evidence against the presence of biologically meaningful cytosine methylation or hydroxymethylation in mitochondrial DNA. These findings caution against interpreting apparent mtDNA methylation signals in human adult tissues as meaningful without rigorous orthogonal validation and comprehensive consideration of technical and analytical confounding factors.

12.
arXiv (CS.CL) 2026-06-18

SproutRAG: Attention-Guided Tree Search with Progressive Embeddings for Long-Document RAG

Retrieval-augmented generation (RAG) systems must balance retrieval granularity with contextual coherence, a challenge that existing methods address through LLM-guided chunking, single-level context expansion, or hierarchical summarization. These approaches variously depend on costly LLM calls during indexing or retrieval, limit context aggregation to a single granularity level, or introduce information loss through summarization. We present SproutRAG, an attention-guided hierarchical RAG framework that addresses this trade-off by organizing sentence-level chunks into progressively larger but semantically coherent units, using learned inter-sentence attention to construct a binary chunking tree. Unlike prior approaches that rely on external LLMs, fixed context expansion, or lossy summarization, SproutRAG learns which attention heads and layers best capture semantic document structure, enabling multi-granularity retrieval without additional LLM calls or compressed summaries. At retrieval time, SproutRAG uses hierarchical beam search to retrieve candidates at multiple granularities, capturing multi-sentence relevance beyond flat retrieval. The framework is trained end-to-end with a joint objective that improves both embeddings and tree structure. Experiments across four benchmarks spanning scientific, legal, and open-domain settings demonstrate that SproutRAG improves information efficiency (IE) by 6.1% on average over the strongest baseline. Code is available on https://github.com/AmirAbaskohi/SproutRAG.

13.
arXiv (CS.LG) 2026-06-11

Quantum Occam Learning: Sample-Supported Expressibility for Circuit-Based Quantum Learning

arXiv:2606.12211v1 Announce Type: cross Abstract: A central principle in quantum machine learning is that an ansatz should be expressive enough to represent the quantum data of interest. Yet, the expressibility is statistically meaningful only insofar as it can be learned from finitely many copies of an unknown quantum state. In this work, we develop an information-theoretic Occam theory for quantum data generated by finite-size quantum circuits. For the class $S_{n,G}$ of $n$-qubit pure states preparable with at most $G$ two-qubit gates, a metric-entropy argument gives the realizable sample law $\widetilde{\Theta}(G/\epsilon^2)$ in the circuit-limited regime. For an arbitrary source $\hat{\rho}$, we introduce the best $G$-gate approximation error $d_G(\hat{\rho})$ and the approximate circuit complexity $C_\eta(\hat{\rho})$. We prove an agnostic quantum Occam theorem: with $M$ copies, one can learn up to the best $G$-gate approximation error plus a statistical penalty $\widetilde{O}(\sqrt{G/M})$. We then remove the need to know $G$ in advance through an adaptive model-selection theorem whose oracle inequality selects the circuit complexity justified by the data. Matching lower bounds yield a sample-supported expressibility law: at trace-distance accuracy $\epsilon$, $M$ samples can support only $G_supported \simeq M\epsilon^2$ gates, up to logarithmic factors and tomography saturation at $2^n$. Thus, the circuit complexity becomes an adaptive statistical resource rather than a static promise. Our framework turns bounded circuit complexity into a model-selection principle for quantum machine learning.

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

Spokes: Optimizing for Diverse Pretraining Data Selection

Diversity plays a critical role in data selection, improving performance under fixed data budgets by reducing redundancy and repetition. However, optimizing for diversity is inherently challenging, as it is a set-level property that depends on interactions between data points rather than individual examples. As a result, existing approaches typically rely on proxies or approximations, which often fail to ensure sufficiently diverse subsets. In this work, we directly optimize diversity by introducing a probabilistic diversification framework based on the G-Vendi score, optimized via exponentiated gradient descent. Our method produces subsets that are substantially more diverse than those obtained via random sampling, achieving a +489 increase in G-Vendi score on a 500k-sample subset. We evaluate our approach on FineWeb and DCLM, where it consistently outperforms existing methods. Notably, SPOKES (diversity-only) improves average downstream performance by +0.4 and +0.5 points over random sampling on DCLM and FineWeb, respectively. More importantly, jointly optimizing for both quality and diversity yields the strongest results: SPOKES achieves gains of +1.5 and +1.4 points on DCLM and FineWeb, outperforming all baselines, including semantic deduplication and quality filtering.

15.
medRxiv (Medicine) 2026-06-22

Use of the Pharmacy First service in England in the first 12 months: geographic variation and health system context

Objectives: The Pharmacy First (PF) service was introduced across England from 31 January 2024 to expand the clinical role of community pharmacies and improve access to primary care. This paper describes use of PF in its first 12 months, in terms of uptake, access routes, consultation outcomes, geographic variations, service costs and antimicrobial supply. Methods: A descriptive analysis of all PF consultations submitted for payment to NHS Business Services Authority in England between 31 January 2024 and 31 January 2025. Pharmacy-level consultation data were linked to national data on population, location and pharmacy characteristics. PF use was examined using population-standardised consultation rates and consultations per pharmacy. Results: During the first year of implementation, 2,205,731 PF consultations were recorded as delivered across 11,349 pharmacies, with payment of GBP123 million to pharmacies. Uptake increased steadily over time. Most consultations were for acute sore throat (33%) and uncomplicated urinary tract infection (27%), with corresponding antibiotics, phenoxymethylpenicillin and nitrofurantoin being the most supplied. Most people self-referred (74%) into the service, with 95% of consultations managed without onward referral. Substantial geographic variation was observed. Northern regions had higher use based on the eligible population. The South East and Midlands had higher activity per pharmacy. London showed a distinct pattern, with higher self-referral into the service, lower medication supply and higher referral to other healthcare services. Higher consultation volume was weakly associated with pharmacy characteristics, including opening hours, pharmacy type and retail setting, and local context, in terms of socio-economic and geographic factors. Conclusions: PF had immediate uptake and is operating primarily as a direct-access model for common acute conditions. Findings suggest that PF is contributing to improved access to care and may shift demand away from general practice. However, the service uptake appears to be shaped by geographic location, proximity to other healthcare services and pharmacy characteristics.

16.
arXiv (CS.CV) 2026-06-12

VISTA: Video Interaction Spatio-Temporal Analysis Benchmark

Existing benchmarks for Vision-Language Models (VLMs) primarily evaluate spatio-temporal understanding on simple single-action videos, closed attribute sets and restricted entity types, failing to capture the freeform, multi-action interactions between diverse entities which characterize real-world video understanding. Furthermore, the lack of a systematic framework for analyzing model failures across complementary spatio-temporal axes hinders comprehensive evaluation. To address these gaps, we introduce VISTA, a Video Interaction Spatio-Temporal Analysis benchmark designed for open-set, multi-entity and multi-action spatio-temporal understanding in VLMs. VISTA decomposes videos into interpretable entities, their associated actions, and relational dynamics, enabling multi-axis diagnostics and unified assessment of relational, spatial, and temporal understanding. Our benchmark integrates multiple datasets into a single interaction-aware taxonomy and comprises ~12K curated video-query pairs spanning diverse scenes and complexities. We systematically evaluate 11 state-of-the-art VLMs on VISTA, and break down aggregate performance across our taxonomy to reveal shortcomings and pronounced spatio-temporal biases obscured by traditional metrics. By providing detailed, taxonomy-driven diagnostics on a challenging dataset, VISTA offers a nuanced framework to guide advances in model design, pretraining strategies, and evaluation protocols. Overall, VISTA is the first, large-scale, interaction-aware diagnostic benchmark for spatio-temporal understanding in VLMs.

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

Visual enhancement and 3D representation for underwater scenes: a review

Underwater visual enhancement (UVE) and underwater 3D reconstruction pose significant challenges in computer vision and AI-based tasks due to complex imaging conditions in aquatic environments. Despite the development of numerous enhancement algorithms, a comprehensive and systematic review covering both UVE and underwater 3D reconstruction remains absent. To advance research in these areas, we present an in-depth review from multiple perspectives. First, we introduce the fundamental physical models, highlighting the peculiarities that challenge conventional techniques. We survey advanced methods for visual enhancement and 3D reconstruction specifically designed for underwater scenarios. The paper assesses various approaches from non-learning methods to advanced data-driven techniques, including Neural Radiance Fields and 3D Gaussian Splatting, discussing their effectiveness in handling underwater distortions. Finally, we conduct both quantitative and qualitative evaluations of state-of-the-art UVE and underwater 3D reconstruction algorithms across multiple benchmark datasets. Finally, we highlight key research directions for future advancements in underwater vision.

18.
arXiv (quant-ph) 2026-06-11

Mixed-State Topological Order under Coherent Noise

arXiv:2411.03441v2 Announce Type: replace Abstract: Mixed-state phases of matter under local decoherence have recently garnered significant attention due to the ubiquitous presence of noise in current quantum processors. One of the key issues is understanding how topological quantum memory is affected by realistic coherent noise, such as random rotation noise and amplitude-damping noise. In this work, we investigate the intrinsic error threshold of the two-dimensional toric code (TC), a paradigmatic topological quantum memory, under these types of coherent noise by employing both analytical and numerical methods based on the doubled-Hilbert-space formalism. A connection between the mixed-state phase of the decohered TC and a non-Hermitian Ashkin-Teller-type statistical-mechanics model is established, and the mixed-state phase diagrams under the coherent noise are obtained. We find remarkable stability of mixed-state topological order under random rotation noise with axes near the $Y$-axis of qubits. We also identify intriguing extended critical regions at the phase boundaries, highlighting a connection with non-Hermitian physics. We argue that these phase boundaries provide upper bounds for the intrinsic error threshold, beyond which quantum error correction becomes impossible. We complement these findings by estimating the error thresholds for random rotation noise under standard quantum error correction, thereby providing lower bounds on the intrinsic error threshold.

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

Deployment-Centered Evaluation: Predicting Query-Level Rejection Risk in a Clinical LLM System

arXiv:2606.12702v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly integrated into clinical systems, making it essential to evaluate the real-world utility of these systems. However, static benchmarks tend to measure correctness rather than user acceptance, aggregate performance across queries, and require densely annotated datasets – leading to major blind spots for evaluating clinical systems. In this work, we perform a deployment-centered evaluation of an LLM system embedded within electronic health records at an academic medical center, where user feedback is sparse but closely reflects the deployment conditions. Specifically, we train a pre-response classifier that estimates the risk that a future interaction will result in the user rejecting the LLM response, based on query content and deployment-specific context available before generation. We conduct a prospective analysis of our model over 4.5 months of user feedback, finding that our prediction model achieves an AUROC of 0.719. Further, we estimate the benefit of such predictions in two downstream use cases (guardrail triggering and abstention). Our key conceptual insight is that making use of deployment-specific context (i.e., the provider type, department name, language model used for response), as opposed to only query content, improves the ability to predict whether the user will reject the system output. Altogether, our empirical case study demonstrates the feasibility of predicting user rejection using deployment-specific context, opening the door to targeted guardrails.

20.
PLOS Computational Biology 2026-06-01

Supervised deep learning with gene functional annotation for cell classification

作者:

by Zhexiao Lin, Yuanyuan Gao, Wei Sun Gene-by-gene differential expression analysis is a widely used supervised approach for interpreting single-cell RNA-sequencing (scRNA-seq) data. However, modern scRNA-seq datasets often contain large numbers of cells, leading to the identification of many differentially expressed genes with extremely small p-values but negligible effect sizes, thus making biological interpretation difficult. To overcome this challenge, we developed Supervised Deep learning with gene functional ANnotation (SDAN), a method that integrates gene functional annotation information (e.g., protein-protein interaction) with gene-expression profiles through a graph neural network. SDAN identifies functionally coherent gene sets that optimally classify cells, and the resulting cell-level classification scores can be aggregated to make individual-level predictions. We evaluated SDAN alongside three representative existing methods in three real-data applications aimed at identifying gene sets associated with severe COVID-19, dementia, and cancer immunotherapy response. Across all applications, SDAN consistently outperformed the alternative approaches by achieving two objectives simultaneously: accurate outcome classification and clear assignment of genes to functionally related gene sets.

21.
arXiv (CS.AI) 2026-06-17

Learning to Decide with AI Assistance under Human-Alignment

arXiv:2605.12646v2 Announce Type: replace-cross Abstract: It is widely agreed that when AI models assist decision-makers in high-stakes domains by predicting an outcome of interest, they should communicate the confidence of their predictions. However, empirical evidence suggests that decision-makers often struggle to determine when to trust a prediction based solely on this communicated confidence. In this context, recent theoretical and empirical work suggests a positive correlation between the utility of AI-assisted decision-making and the degree of alignment between the AI confidence and the decision-makers' confidence in their own predictions. Crucially, these findings do not yet elucidate the extent to which this alignment influences the complexity of learning to make optimal decisions through repeated interactions. In this paper, we address this question in the canonical case of binary predictions and binary decisions. We first show that this problem is equivalent to a two-armed online contextual learning problem with full feedback, and establish a lower bound of $\Omega (\sqrt{|H| \cdot |B| \cdot T} )$ on the expected regret any learner can attain, where $H$ and $B$ denote the sets of human and AI confidence values. We then demonstrate that, under perfect alignment between AI and human confidence, a learner can attain an expected regret of $O(\sqrt{|H| \cdot T\log T})$ and, when $\sqrt{|H|} = O(\log T)$ and $B$ is countable, a non-trivial generalization of the Dvoretzky-Kiefer-Wolfowitz inequality improves the regret bound to $O(\sqrt{T\log T})$. Taken together, these results reveal that alignment can reduce the complexity of learning to make decisions with AI assistance. Experiments on real data from two different human-subject studies where participants solve simple decision-making tasks assisted by AI models show that our theoretical results are robust to violations of perfect alignment.

22.
arXiv (quant-ph) 2026-06-17

Intrinsic Pointer Basis and Irreversible Classicality from Coherence Contraction

arXiv:2604.23304v4 Announce Type: replace Abstract: This work analyzes an operational route to classical behavior for reduced quantum states using the intrinsic reference basis (IRB). Relative to a fixed physical conjugation, the IRB separates intrinsic populations from a real antisymmetric cohesion sector. A globally bounded cohesion index is defined and its exponential contraction is proved for phase-free dephasing dynamics aligned with the IRB; for general aligned dephasing, the corresponding modulus-based coherence functional contracts at the same computable rates. The results provide distance bounds to the IRB-diagonal description and a logarithmic upper bound on the time required to reach a prescribed experimental tolerance. The IRB projectors constitute state-derived candidate pointer sectors, and they become dynamically stable pointer sectors when the effective dephasing generator is aligned with them and damps the relevant inter-sector coherences. Degenerate population sectors lead naturally to block-classicality and protected intra-block coherence. In a two-level active sector, the cohesion index equals fringe visibility, giving a direct interferometric test of the contraction law. The construction is independent of any spacetime- or unification-emergence hypothesis and is intended as a channel-level complement to environment-induced einselection.

23.
arXiv (quant-ph) 2026-06-11

Logical error estimation from syndrome data of surface-code experiments

arXiv:2606.11496v1 Announce Type: new Abstract: Decoders for quantum error correction (QEC) experiments rely on detector error models (DEMs), which encode, for each error, its probability and the detectors and logical observables it flips. Here we show that estimating DEM event probabilities from experimental syndromes is feasible, avoids independent device benchmarking, and produces useful decoder priors for estimating and reducing decoded logical error probabilities. We evaluate our methods using open-source data from surface-code memory experiments performed on Google's Willow chip, and we carry out analogous surface-code experiments on IBM's \texttt{ibm\_miami} processor. Despite the different physical error scales of the Google and IBM devices, in both cases our estimated DEMs improve logical error probabilities relative to baseline device-informed DEMs, typically at the $5\%-10\%$ level and with larger gains in some IBM cases, without additional calibration circuits, decoder fine-tuning, or supervised fitting to logical outcomes.

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

SSH-Net: A Deep Neural Network for Predicting Failure Time Distribution Functions under Competing Risks with Application to GPU Data

arXiv:2606.20451v1 Announce Type: cross Abstract: Competing risks are commonly observed in engineering fields and can bring challenges to time-to-event data modeling when the application scenarios are complicated. Recently, deep neural networks have received great attention for prediction with competing risks, due to their flexibility and high learning capability. However, the complexity of neural network structure brings extra difficulty in hyperparameter tuning based on different data inputs. Additionally, when an engineered system has complex physical structures with multiple hierarchical levels, treating all structural levels as a single group of inputs may fail to capture critical information. To address the issues, we propose a Structured Segmented Hazard Deep Neural Network (SSH-Net) for failure time prediction under cause-specific competing risks framework. Our approach associates neural network structure with data structures, and allows different covariate groups to impact the failure prediction through separate sub-networks. The neural network is constructed based on a cause-specific competing risks model. The SSH-Net outputs cause-specific hazard functions, and utilizes the penalized log-likelihood as the loss function. The prediction accuracy of SSH-Net is validated through simulation studies by evaluating the Brier score, the area under receiver operating characteristic curves (AUC), and the root mean square error (RMSE) of the predicted cause-specific cumulative incident function. We further demonstrate the model's ability to predict failure time distribution functions using the Titan GPU failure time data.

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

Visual-Redundancy-Controlled Parallel Decoding for Diffusion-Based Multimodal Large Language Models

arXiv:2605.25820v2 Announce Type: replace Abstract: Diffusion-based multimodal large language models (dMLLMs) decode by iteratively predicting tokens at multiple masked positions in parallel. This turns each decoding step into a position-selection problem: the model must choose not only which predictions are reliable in isolation, but also which positions should be committed together as context for later decoding steps. Existing confidence-based decoding ranks masked positions independently and commits the top-K positions, largely ignoring whether the committed tokens provide complementary visual grounding. We identify a step-level limitation of this strategy in multimodal settings: high-confidence tokens selected in the same step can rely on overlapping visual grounding, introducing visual redundancy among the committed tokens and leaving less complementary visual grounding available for later decoding. To quantify this effect, we introduce the Visual Redundancy Index (VRI), which measures visual grounding overlap among tokens committed in parallel. To control this redundancy during decoding, we propose Visual-Redundancy-Controlled Decoding (VRCD), a training-free inference-time decoding method that uses token-to-image attention to prioritize visually complementary positions. Across diverse multimodal benchmarks, VRCD reduces visual redundancy and remaining-position entropy with modest runtime overhead. In longer decoding experiments, it also achieves relative accuracy gains of up to 18.8% on M^3CoT and 6.9% on MMBench over confidence-based decoding. Code is available at https://github.com/infiniteYuanyl/VRCD.