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01.
arXiv (CS.LG) 2026-06-17

Softmax as Linear Attention in the Large-Prompt Regime: a Measure-based Perspective

arXiv:2512.11784v2 Announce Type: replace Abstract: Softmax attention is a central component of transformer architectures, yet its nonlinear structure poses significant challenges for theoretical analysis. We develop a unified, measure-based framework for studying single-layer softmax attention under both finite and infinite prompts. For i.i.d. Gaussian inputs, we lean on the fact that the softmax operator converges in the infinite-prompt limit to a linear operator acting on the underlying input-token measure. Building on this insight, we establish non-asymptotic concentration bounds for the output and gradient of softmax attention, quantifying how rapidly the finite-prompt model approaches its infinite-prompt counterpart, and prove that this concentration remains stable along the entire training trajectory in general in-context learning settings with sub-Gaussian tokens. In the case of in-context linear regression, we use the tractable infinite-prompt dynamics to analyze training at finite prompt length. Our results allow optimization analyses developed for linear attention to transfer directly to softmax attention when prompts are sufficiently long, showing that large-prompt softmax attention inherits the analytical structure of its linear counterpart. This, in turn, provides a principled and broadly applicable toolkit for studying the training dynamics and statistical behavior of softmax attention layers in large prompt regimes.

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

PACT: Preserving Anchored Cores in Task-vectors for Model Merging

arXiv:2606.18627v1 Announce Type: new Abstract: Model merging has emerged as a training-free alternative to multi-task learning, aiming to combine multiple task-specific fine-tuned models into a single multi-task model. Most existing model merging approaches follow the Task Arithmetic paradigm, which decomposes fine-tuned weights into pre-trained parameters and task vectors, and performs merging exclusively in the task-vector space. The effectiveness of this paradigm implicitly relies on the assumption that task-specific knowledge is encoded solely within task vectors. We argue that this assumption generally does not hold due to the intrinsic task preferences of pre-trained models. Specifically, we identify Load-Bearing Wall (LBW) dimensions, namely some task-critical knowledge that remains embedded in the pre-trained weights rather than being fully transferred into task vectors. We characterize LBW dimensions from both scalar-weight and subspace perspectives, thereby covering the major paradigms of existing model merging methods. Our analysis reveals that, by ignoring LBW dimensions, task-vector-based approaches fail to fully resolve task conflicts and may inadvertently damage task-specific knowledge encoded in the pre-trained model, leading to degradation. To address this issue, we propose PACT, which preserves the anchored task-specific cores (i.e., LBW dimensions) within task vectors by aligning their orthogonal complements with the subspace of the pre-trained weights. These aligned subspace components are then removed from the task vectors before applying existing model merging algorithms. Furthermore, we develop an efficient variant based on randomized SVD to improve scalability. PACT can be seamlessly integrated with existing methods. Extensive experiments across multiple benchmarks demonstrate that PACT consistently enhances mainstream model merging approaches and establishes new state-of-the-art performance.

03.
arXiv (quant-ph) 2026-06-16

Quantum Illumination with Symmetry-Constrained Random Unitaries

arXiv:2606.15586v1 Announce Type: new Abstract: Quantum illumination provides a quantum advantage in detecting weakly reflecting objects embedded in a noisy environment, even when environmental noise destroys most of the initial entanglement. We investigate this advantage using Haar-random probe states constrained to symmetry-resolved subspaces. Employing tools from quantum channel discrimination and asymptotic hypothesis testing, we derive the discrimination exponents associated with Haar-random probe ensembles and identify the role of symmetry in determining their performance. We show that typical states drawn from fixed-charge sectors achieve the same asymptotic quantum-illumination advantage as maximally entangled probes. In particular, we show that the effective thermal-noise suppression and the corresponding Chernoff exponent are governed by the dimension of the accessible symmetry sector. Our results reveal that the operational resource underlying quantum illumination can be generalized from fine-tuned structure of a specific probe state to the existence of a large symmetry-protected correlation subspace. These findings establish a direct connection between quantum illumination, symmetry-resolved typicality, and quantum channel discrimination, and demonstrate that near-optimal quantum hypothesis testing resources can emerge naturally from generic many-body quantum states constrained by conservation laws.

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

Least-Action-Guided Diffusion for Physical Extrapolation

arXiv:2606.11277v1 Announce Type: new Abstract: Reliable extrapolation remains a central challenge for generative models in computational physics, because models trained over finite ranges of time, parameters, or geometries may produce physically inconsistent predictions outside the training distribution. We introduce a least-action-principle-guided diffusion, LAPG, a framework that promotes physical consistency during inference rather than relying solely on constraints imposed during training. The method combines a conditional score-based diffusion model with an action-derived physical guidance score. In the first stage, the learned score model generates an in-distribution proposal; in the second, an action-based variational prior refines this proposal toward the target out-of-distribution condition. This formulation turns the principle of least action into a differentiable inference-time correction mechanism and provides an alternative to pointwise residual penalties that often require empirical loss balancing. We evaluate LAPG on representative ordinary- and partial-differential-equation systems, including free fall, conservative and dissipative spring-mass dynamics, interacting point vortices, and potential flow over parameterized airfoils. In temporal, parameter, and geometric extrapolation tests, LAPG reduces phase drift, preserves dissipative decay, captures vortex motion, and improves the lift response of airfoil flows compared with training-time physics-informed baselines.

05.
arXiv (CS.LG) 2026-06-16

Conformal Candidate Certification for Offline Model-Based Optimization

arXiv:2606.15217v1 Announce Type: cross Abstract: Offline model-based optimization (MBO) proposes candidates by optimizing a surrogate trained on a fixed historical dataset. Because candidates are deliberately out-of-distribution, surrogate rankings are least reliable exactly where the optimizer is most aggressive, yet existing methods provide no per-candidate statistical certificate that a design meets a target threshold. We propose Conformal Candidate Certification (CCC), a post-hoc wrapper that attaches a calibrated one-sided lower bound to each candidate and advances only those whose bound exceeds the target. We show that entropy-regularized surrogate maximization induces a Gibbs-tilted proposal, so the same surrogate supplies importance weights for weighted conformal prediction without a separate density-ratio estimation step. In a controlled synthetic study, CCC certifies $16.7\%$ of an aggressive proposal pool with empirical coverage 0.990 at nominal 0.90, while standard conformal prediction ignoring the covariate shift collapses to 0.416 coverage.

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

RubricsTree: Scalable and Evolving Open-Ended Evaluation of Personal Health Agents across Health Memory and Medical Skills

The LLM-empowered personal health agents with user health (sensor) metrics have offered a promising pathway to alleviate global disparities in healthcare access. However, large-scale clinical deployment remains constrained by an open-ended evaluation bottleneck: physician annotation is reliable but costly and unscalable, while LLM-as-a-judge evaluators are scalable but subjective, inconsistent, and sometimes clinically misaligned. We introduce RubricsTree, a scalable evaluation framework with an expert-aligned hierarchical taxonomy of over 100 atomic, clinically-verifiable Boolean rubrics, evolving from the insights of 4,000 real user queries through an iterative human-in-the-loop curation protocol with an expertise panel led by an experienced physician. A context-aware adaptive router activates only the relevant auto-weighted rubric subset per query, providing the throughput needed for scalable evaluation with expert-aligned quality. Through a systematic meta-evaluation, we show that RubricsTree (i) substantially exceeds a strong large-scale evaluation baseline in expert alignment on challenging open-ended queries; (ii) reliably penalizes contextually degraded responses; and (iii) when used as structured instructions, text feedback, or training rewards for performance optimization, yields up to ~66% relative gains on HealthBench for Gemini, GPT, and Qwen model families. RubricsTree thus provides a scalable, auditable, and evolving evaluation infrastructure required for the continuous optimization of product-level personal healthcare AI.

07.
arXiv (CS.AI) 2026-06-15

CADET: Physics-Grounded Causal Auditing and Training-Free Deconfounding of End-to-End Driving Planners

作者:

arXiv:2606.14438v1 Announce Type: cross Abstract: End-to-end (E2E) autonomous-driving planners trained by imitation are prone to statistical shortcuts: they associate scene elements that merely co-occur with expert actions (a roadside object, a building facade) with driving decisions, rather than the variables that causally determine them. Such causal confusion silently compromises reliability in long-tail scenarios, and it is difficult to detect, because prevailing open-loop metrics (L2 displacement and collision rate) are dominated by ego status and do not indicate whether a planner depends on spurious cues. Existing remedies based on causal-intervention training require retraining large models and cannot audit a planner that is already deployed. We present CADET, a training-free framework that audits, benchmarks, and repairs spurious reliance in pretrained E2E planners without any parameter update.

08.
arXiv (quant-ph) 2026-06-17

Quantum mechanics in configuration space in context

arXiv:2606.17622v1 Announce Type: new Abstract: To enhance the way in which wave-particle duality is implemented in the modelling of quantum mechanical systems, Bukhari et al. [New J. Phys. 27, 084501 (2025)] recently introduced an alternative approach to quantum mechanics, namely quantum mechanics in configuration space. This formalism is based on a physically motivated quantisation of Newtonian mechanics and promotes the classical position-velocity states (x,v) to pairwise distinguishable quantum states. The resulting |x,v> states form the basis of the Hilbert space of individual quantum mechanical particles and evolve along classical trajectories. In this paper, we consider the modelling of a mechanical particle in free space and put quantum mechanics in configuration space into context. It is shown that this formalism increases the continuity between quantum and classical mechanics by avoiding a conceptual inconsistency associated with the definition of momentum in canonical quantisation. In addition, we emphasise that standard quantum mechanics and quantum mechanics in configuration space are based on two distinct formulations of classical mechanics.

09.
arXiv (CS.CV) 2026-06-15

RT-VLA: Real-Time Vision-Language-Action Models via Knowledge Distillation

Vision-Language-Action (VLA) models have shown strong potential for end-to-end autonomous driving by jointly modeling visual perception, language reasoning, explainability and action prediction. However, their large vision-language backbones and reasoning modules introduce substantial inference latency and thereby prevent their deployment in the unforgiving reality of the road networks. We propose RT-VLA, a lightweight, distilled VLA model that transfers the driving and reasoning capabilities of the state-of-the-art SimLingo model into a compact student through multi-level supervised distillation. RT-VLA preserves language-based reasoning and supports post-hoc explanation through offline language analysis of safety-critical driving moments without adding latency to real-time control. Compared to the SimLingo teacher, RT-VLA maintains competitive closed-loop driving and language reasoning performance while reducing inference time by 44.8X in vision-only mode and 7.9X in vision+language mode. These results suggest that supervised distillation is a practical approach for building real-time, explainable VLA-style autonomous driving models.

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

Impact of Hand Impairment and Occlusions on Hand Pose Estimation Accuracy in Augmented Reality Applications

Mixed reality applications can be designed for hand rehabilitation. Augmented reality (AR) head mounted displays (HMDs) specifically allow for ecologically valid tasks because individuals can see their real environment and interact with real objects while receiving additional cues on the HMD. While these applications rely on accurate hand pose estimation, there is a gap in investigating the influence of hand impairment or occlusion from real-object interactions on pose estimation accuracy. Further, comparisons between AR HMD predictions and state-of-the-art pose estimation methods have not been established. The current study assessed pose estimation accuracy of the HoloLens 2 HMD and state-of-the-art pose estimation algorithms (WiLoR, HaMeR, WildHands, and MediaPipe) while individuals with cervical spinal cord injury (cSCI; n = 13, Neurological Level of Injury: C3-C6; American Spinal Injury Association Impairment Scale: A-D) and 15 uninjured controls interacted with clear and opaque objects. Ground truth estimates of 3D joint positions were generated via triangulation from a multi-camera setup. Pose estimation accuracy did not differ between the cSCI and uninjured control groups suggesting that 3D joint predictions from the HoloLens 2 and pose estimation algorithms can generalize to populations with hand impairment. Further, clear objects provided a small accuracy advantage over opaque objects (0.1 mm) and predictions from both WiLoR and HaMeR were slightly more accurate than the HoloLens 2 (2 mm). Overall, these results suggest that the HoloLens 2 may be viable for hand rehabilitation applications and the dataset generated can be used to refine pose estimation methods for hand-impaired populations.

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

A nonparametric two-sample test using a parametric integral probability metric

arXiv:2606.16941v1 Announce Type: cross Abstract: Detecting distributional differences between two independent samples is a fundamental problem in statistics and machine learning. Nonparametric two-sample testing provides a principled framework for determining whether two samples are drawn from the same underlying distribution, without assuming any specific parametric form for the distribution. In this study, we propose a new two-sample test statistic based on a newly introduced integral probability metric (IPM), using a specially designed parametric discriminator class with a single node of a neural network. We show that the resulting test statistic, called PReLU-IPM, is nonparametric and establish theoretical guarantees for the associated two-sample testing procedure, PReLU-TST, including its consistency and asymptotical equivalence to nonparametric IPM-based tests under regularity conditions. By analyzing multiple simulated and real benchmark datasets, we demonstrate that PReLU-TST achieves higher power across a range of alternatives or performs comparably to its competitors, for finite samples.

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

Gaussian DP for Reporting Differential Privacy Guarantees in Machine Learning

arXiv:2503.10945v3 Announce Type: replace-cross Abstract: Current practices for reporting differential privacy (DP) guarantees for machine learning (ML) algorithms such as DP-SGD provide an incomplete and potentially misleading picture. For instance, if only a single $(\varepsilon, \delta)$ is known about a mechanism, standard analyses show that there could exist highly accurate inference attacks against training data records, when, upon a more careful analysis, such accurate attacks do not exist for most practical mechanisms. In this position paper, we argue that using _non-asymptotic_ Gaussian Differential Privacy (GDP) as the primary means of communicating DP guarantees in ML avoids these potential downsides. Using two recent developments in the DP literature: (i) open-source numerical accountants capable of computing the privacy profile and $f$-DP curves of DP-SGD to arbitrary accuracy, and (ii) a decision-theoretic metric over DP representations, we show how to provide non-asymptotic bounds on GDP using numerical accountants, and show that GDP can capture the entire privacy profile of DP-SGD and related algorithms with virtually no error, as quantified by the metric. To support our claims, we investigate the privacy profiles of state-of-the-art DP large-scale image classification, and the TopDown algorithm for the U.S. Decennial Census, observing that GDP fits their profiles remarkably well in all cases. We conclude with a discussion on the strengths and weaknesses of this approach, and discuss which other privacy mechanisms could benefit from GDP.

13.
arXiv (CS.LG) 2026-06-12

Disparate Impact in Synthetic Data Generation

arXiv:2606.13105v1 Announce Type: new Abstract: We revisit the fairness notion of disparate impact for synthetic data generation (SDG), that assesses whether the utility of generated records is the same across sensitive groups. Our approach departs from existing work on fair SDG, that address the problem of correcting for undue biases in the observed distribution, hence redefining SDG as learning a distribution that is not that of the real data. By contrast, non-disparate impact is notably achieved when the synthetic and real distributions are the same. We expose reasons why SDG may fail to reach that solution and discuss why approximation and estimation errors occur and can be disparate across groups. We notably look into the expressive power of SDG methods relative to distribution complexity, sampling errors due to group proportions, and estimation errors induced by differential privacy mechanisms. We illustrate cases of disparate impact on both artificial and real-world data, focusing on SDG methods that rely on probabilistic graphical models. We also introduce a strategy of learning group-wise SDG models and illustrate how it can improve both the overall utility and its parity in many settings.

14.
PLOS Computational Biology 2026-06-22

A lactylation- and autophagy-associated prognostic signature reveals LSEC-derived CLEC3B as a novel mediator of hepatocellular carcinoma suppression

作者:

by Youai Song, Yinkuan Ning, Meihui Li, Jianwei Lan, Liangchen Lei, Yufei Han, Zhuo Meng, Binjie Li, Pengpeng Liu, Quanyan Liu The crosstalk between lactylation and autophagy within the hepatocellular carcinoma (HCC) microenvironment is a burgeoning field with profound implications. By integrating multi-omics data from public cohorts, we delineated two molecular subtypes of HCC with divergent clinical outcomes and established a lactylation-autophagy-related prognostic signature. This signature highlighted CLEC3B as a pivotal gene. Subsequent single-cell RNA sequencing and experimental validation unequivocally pinpointed liver sinusoidal endothelial cells (LSECs) as the principal cellular source of CLEC3B, which was significantly downregulated in HCC tissues. Functionally, conditioned media derived from CLEC3B-overexpressing LSECs potently inhibited HCC cell proliferation. Mechanistic investigations revealed that this tumor-suppressive effect was orchestrated through the concurrent suppression of autophagy and diminution of lactylation levels. Our findings position LSEC-secreted CLEC3B as a novel metabolic mediator in HCC, bridging two key pathways in tumor suppression, and endorse its clinical value both as a prognostic indicator and a promising therapeutic target.

15.
bioRxiv (Bioinfo) 2026-06-18

Bayesian modeling of longitudinal metatranscriptomes of broiler meat spoilage microbiomes shows shared predictive signature associated with spoilage at refrigerated temperatures

Microbial spoilage of packaged meat is driven by complex microbial succession and related metabolic activity, yet conventional shelf-life assessment is mainly based on shelf-life studies relying on culturing and sensory analysis. In routine quality assurance, results are obtained retrospectively, and they are only indirectly linked to the metabolic activity related to sensory deterioration. Functional, time informative approaches that capture the active metabolic state of the spoilage microbiome and predict the rate of spoilage are lacking. We developed a censoring-aware Gaussian process (CAGP) framework to model longitudinal pathway expression profiles from broiler meat metatranscriptomes collected over consecutive storage days at 4 or 6{degrees}C. Samples were annotated using odor-based sensory scores defining fresh, early-spoilage, and late-spoilage phases. Because observed zeros in pathway-level data may reflect non-detection rather than true absence, the model treats low values as left-censored observations below a detection threshold while estimating smooth temporal trajectories with uncertainty. In leave-one-out prediction within the 4{degrees}C time series, predicted sampling days differed from the true days by an average of 0.43 days, and predicted spoilage phases agreed with the sensory classification. Trajectories learned at 4{degrees}C also transferred to an independent 6{degrees}C time series at the spoilage-phase level, suggesting that shared functional spoilage programs are preserved despite temperature-dependent changes in spoilage rate. Cross-entropy ranking further identified pathway modules carrying time- and phase-informative signals across temperatures. Overall, this framework provides a probabilistic approach for linking metatranscriptomic functional dynamics to sensory spoilage progression, supporting shelf-life assessment beyond retrospective microbial enumeration.

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

SpikF-GO: Spiking Fourier Graph Operators for Multivariate Time Series Forecasting

arXiv:2606.13901v1 Announce Type: new Abstract: Spiking Neural Networks (SNNs) have emerged as an energy-efficient alternative to conventional neural networks, demonstrating strong performance in computer vision and robotics. More recently, SNNs have been applied to time series forecasting (TSF), with methods exploring spiking temporal backbones, spike-compatible positional encodings, Fourier-domain processing, and redesigned neuron dynamics. However, existing SNN forecasting approaches process variables independently, lacking explicit mechanisms for modeling inter-variable dependencies. This is a critical limitation in multivariate settings, where cross-variable correlations carry substantial predictive information. We propose Spiking Fourier Graph Operators (SpikF-GO), which addresses this gap by combining a hypervariate graph formulation in which every scalar observation becomes a graph node with spike-driven spectral processing. SpikF-GO introduces a Hard Concrete frequency gate for learnable sparse frequency selection and a Complex LIF gate that applies independent spiking neurons to real and imaginary Fourier components, preserving binary, event-driven computation throughout the spectral domain. We further present a variant incorporating Central Pattern Generator-based positional encodings for stronger long-range temporal modeling. Evaluated on eight benchmarks under a unified experimental protocol, SpikF-GO achieves the best average rank among all SNN methods and outperforms its ANN counterpart, FourierGNN, at reduced energy cost. SpikF-GO maintains competitive accuracy even at substantially smaller embedding dimensions, thereby achieving significant energy reductions. To our knowledge, this is among the first works to bring graph-based multivariate modeling into the spiking domain for TSF and the first to provide a unified comparison across SNN forecasting architectures under a common experimental protocol.

17.
arXiv (quant-ph) 2026-06-19

Battery-Explicit Thermodynamic Witnesses of Bell Post-Quantumness

arXiv:2605.09149v3 Announce Type: replace Abstract: We introduce a battery-explicit thermodynamic witness of post-quantum Bell correlations. In each round, a single supplied excitation is routed into an explicit two-level battery if and only if a Bell-game condition is satisfied. The routing operation is implemented by an energy-preserving controlled SWAP, with all logical control registers taken to be degenerate. Thus the correlation resource does not create energy; it only determines the probability that the supplied excitation reaches the battery. The construction is first formulated for finite two-player XOR games. For any such game, the mean battery charge is exactly the game success probability multiplied by the battery gap. Optimizing over local, quantum, or nonsignalling behaviours therefore turns the corresponding game values into local, quantum, or nonsignalling thermodynamic ceilings. For the CHSH game, Tsirelson's bound becomes a strict quantum ceiling on the mean battery charge, while a PR-box behaviour reaches the single-excitation cap. The witness is trusted-module rather than device-independent: it assumes calibrated Hamiltonians, correct classical wiring, and a trusted energy-preserving battery module. We also discuss a reversible-controller implementation, finite-statistics certification from work data, robustness to imperfect battery readout, and cyclic bookkeeping showing that no positive net work is obtained once fuel restoration and memory erasure are included.

18.
arXiv (quant-ph) 2026-06-12

Effective Geometry and Position-Dependent Mass in Dual-$q$ Quantum Mechanics

arXiv:2606.12444v1 Announce Type: new Abstract: This work investigates the deformed-derivative formalism introduced by Borges, with emphasis on the relation between the linear operator $D_{(q)}$ and its nonlinear dual counterpart $D^{(q)}$. Directly inserting the dual derivative into the kinetic term leads to a nonlinear Schrödinger equation and obscures the usual interpretation of superposition and probability. We show that this nonlinearity can be removed by a simultaneous transformation of the coordinate and of the wave function. The transformed problem is an ordinary linear Schrödinger equation in a deformed coordinate, and its representation in the physical coordinate is equivalent to a Hermitian position-dependent-mass (PDM) Hamiltonian. In this formulation, the deformation parameter $q$ determines both the effective mass profile and the associated metric. The formalism is applied to the free particle, the infinite square well, the rectangular barrier, and the harmonic oscillator in the weak-deformation regime. Comparison with the nonadditive-translation approach of Costa Filho et al. shows that the Borges dual-$q$ framework provides an alternative route to the same effective geometric structure. For $q1$, the effective length is increased, which lowers the spectrum and suppresses tunneling relative to the undeformed limit $q=1$.

19.
arXiv (quant-ph) 2026-06-16

Magic transfer in quantum spin chains

arXiv:2606.14855v1 Announce Type: new Abstract: Quantum communication protocols based on spin chains have been extensively studied, yet their ability to transmit nonstabilizer resources has not been systematically addressed. We investigate the transport of quantum magic in spin chains through the natural dynamics of systems initialized in nonstabilizer states, and quantify the transported resource via the stabilizer norm. We analyze three experimentally feasible state-transfer protocols, ranging from noisy to (quasi-)perfect transfer, including one realizable in trapped-ion platforms. We find that the geometry of the injected state strongly influences transport: states in the lower Bloch hemisphere achieve higher transfer quality, whereas states in the upper hemisphere give rise to an efficient magic transport only beyond a threshold value of the parameter controlling the tendency towards perfect transfer. These features are robust across all protocols and identify the Hamiltonian and state properties that favor high-quality transfer. Moreover, we identify a parameter region, relevant to the initial state preparation, in which the transported magic exceeds the initial encoding, indicating that such spin systems can act as magic-amplification channels. Our results establish the conditions for efficient transport of nonstabilizer resources and demonstrate quantum magic as a sensitive probe of quantum transport beyond population dynamics.

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

A Controlled Study of Decoding-Time Truthfulness Methods on Instruction-Tuned LLMs

作者:

In this work, we introduce CHAIR (Classifier of Hallucination As ImproveR), a supervised framework for detecting hallucinations by analyzing internal logits from each layer of every token. Our method extracts a compact set of features such as maximum, minimum, mean, standard deviation, and slope-from the token logits across all layers, enabling effective hallucination detection without overfitting. Experiments on TruthfulQA and MMLU datasets demonstrate that CHAIR significantly improves detection accuracy, particularly in zero-shot scenarios, showcasing its robustness and generalizability. Beyond hallucination detection, CHAIR highlights the potential of using internal representations for designing advanced decoding strategies. By leveraging patterns in logits, we suggest that more sophisticated models and adaptive decoding methods could further reduce hallucinations and enhance text completion quality. CHAIR not only offers a practical solution for detecting hallucinations but also lays the groundwork for exploring richer representations in LLMs to improve their factuality and coherence.

21.
bioRxiv (Bioinfo) 2026-06-11

Machine Learning-Guided Discovery of Bacterial-Selective Membrane-Active Compounds Reveals Mechanistic Bias in Antibiotic Training Datasets

The rise of antibiotic resistance necessitates the discovery of antibacterial compounds with novel mechanisms of action (MoAs). Recent machine learning approaches have shown promise in antibacterial compound discovery, but often identify derivatives of known antibiotic classes rather than mechanistically novel compounds. Previous approaches applied Tanimoto similarity filters at the end of screening pipelines, but this method has substantial drawbacks: Tanimoto similarity can be misleading in chemical space, and post-hoc filtering does not influence what activity models learn to prioritize. Here, we present a machine learning pipeline that addresses chemical novelty upfront by employing an XGBoost-based MoA classifier to explicitly prioritize compounds predicted to have mechanisms distinct from known antibiotic classes, combined with graph neural networks for antibacterial activity and toxicity prediction. Applied to the Zinc20 database, our approach successfully identified non-toxic antibacterial compounds structurally distinct from known antibiotics. Notably, the majority of these hits exhibited membrane-targeting activity with selectivity for bacterial cells over mammalian cells, suggesting potential for next-generation membrane-active antibiotics. However, we did not identify compounds with novel protein targets. Systematic analysis revealed that this limitation stems from mechanistic bias in training data rather than model architecture. Specifically, our activity model learned to preferentially score compounds similar to specific groups in the training data, thus overrepresenting certain MoA classes including membrane-active compounds. Even substantial model architecture and training data enhancements did not overcome this constraint. Our findings demonstrate that the primary bottleneck for discovering mechanistically novel antibiotics is the scarcity of diverse, mechanistically-annotated training data. This work provides both a methodological framework for mechanism-aware screening and critical insights into data requirements for genuinely novel antibiotic discovery.

22.
arXiv (CS.AI) 2026-06-18

Pareto Q-Learning with Reward Machines

arXiv:2606.19134v1 Announce Type: cross Abstract: We present Pareto Q-Learning with Reward Machines (PQLRM), a multi-objective reinforcement learning algorithm for tasks whose reward structure is specified by a set of reward machines (RMs). PQLRM combines Pareto Q-Learning (PQL), which maintains sets of vector-valued Q-estimates to approximate the Pareto front, with enhancements from Q-Learning with Reward Machines (QRM), which exploits the factored automaton structure of the reward signal. This yields a multi-policy algorithm that remains sample-efficient under non-Markovian, RM-encoded rewards. Experimental trials show that PQLRM converges faster than a naive PQL baseline applied to the cross-product MDP and can synthesize Pareto-optimal policies that QRM cannot.

23.
arXiv (CS.CV) 2026-06-12

Where, What, Why, and Importance: Structured Defect Grounding for Text-to-Image Feedback

Despite generating increasingly photorealistic images, text-to-image (T2I) models still exhibit localized, subtle, and structurally complex failures. Diagnosing these failures requires instance-level feedback that answers where a defect occurs, what type it is, why it is defective, and its importance to overall image quality. While recent dense-feedback methods move beyond scalar supervision, their heatmap-centric representations still formulate diagnosis as pixel-field regression, making it difficult to localize variable-cardinality defects and bind semantic reasons to individual failures. To address this representation bottleneck, we propose Structured Defect Grounding (SDG), which casts T2I diagnosis as structured set prediction by modeling each defect as a (location, type, reason, importance) tuple. To make this formulation trainable and measurable, we introduce SDG-30K, a 30K-image dataset with box-grounded annotations across four modern T2I generators, together with a dedicated evaluation protocol, SDG-Eval. Building on this structured representation, we further present a diagnosis-to-alignment framework in which a Vision-Language Model (VLM) serves as the SDG detector, and BoxFlow-GRPO converts predicted defect sets into box-derived, importance-weighted spatial rewards for diffusion model alignment. Extensive experiments show that our SDG detector outperforms leading proprietary VLMs on structured defect grounding, while SDG-guided rewards consistently improve T2I alignment and support localized image refinement. These results establish SDG as a unified, instance-level interface for diagnosing, evaluating, and enhancing modern generative models.

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

The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models

High-grade gliomas integrate into neural circuits through functional synapses with neurons, raising the question of which noncoding elements shape synaptogenic gene expression in tumor cells. The regulatory program written across the dark genome, what we call the $dark regulome$, is the natural substrate to probe, and sequence foundation models offer a zero-shot route through in-silico mutagenesis (ISM); yet likelihood-based scoring is tautologically coupled to local sequence predictability, leaving the regulatory interpretation underdetermined. Across three architecturally distinct foundation models (Caduceus-Ph, HyenaDNA, Enformer) and 30,448 dark genome elements at 92 glioma-relevant loci, we introduce a residualization-and-permutation diagnostic that separates predictability-driven from regulation-driven RIS variance. A sharp 10kb proximal-regulatory horizon survives every control we apply, but the LM-derived element-class hierarchy does not: a six-feature linear baseline matches Caduceus top-decile membership at AUC $= 0.985$. Cross-architecture decomposition cleanly separates a sequence-predictability layer (the two language models co-rank long well-predicted transposable elements) from a regulatory-output layer (Enformer alone retains residual cCRE-discriminative signal), with literally zero overlap between the two top-100 lists. Conservation, brain cis-eQTL, and STRING-PPI cross-checks then anchor what biology survives: top-100 elements across all three models are $3.3\times$ enriched per model for matching brain eQTLs ($p_\mathrm{emp} < 5\times 10^{-3}$), while a tempting transposable-element regulatory layer and a striking NRXN1+NLGN1 protein-pair convergence both fail proper permutation tests once those tests are constructed. We deliver the diagnostic as a general methodological tool for any ISM-based regulatory study.