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

Learning task-specific subspaces via interventional post-training of speech foundation models

Speech foundation models, pre-trained on large corpora of unlabelled speech data, produce general-purpose representations which are useful across tasks. However, these representations encode information about salient speech variables in a distributed manner, while downstream speech tasks rely on only some of this variability. In this work, we propose a post-training refinement approach using interventional contrastive learning. By leveraging an interventional dataset and multi-part contrastive loss, we learn a transformation from the entangled representation space of speech foundation models into separate content and speaker subspaces. We evaluate the learnt representations on speaker verification and keyword spotting tasks, showing improved out-of-domain speaker verification performance and evidence that speaker and content information are separated across the learned subspaces.

02.
medRxiv (Medicine) 2026-06-10

Longitudinal brain structural changes during clozapine treatment: associations with neuroreceptor architecture and clinical response

In treatment-resistant schizophrenia, clozapine treatment has been associated with longitudinal reductions in subcortical volumes, ventricular enlargement, and widespread cortical thinning. However, it is unknown how these structural changes relate to clozapines pharmacological profile and clinical efficacy. We combined five longitudinal datasets with MRI acquired before and on average 5 months after clozapine initiation in 143 individuals to quantify brain structural changes and their association with normative maps relating to neuroreceptor architecture and physiological systems, and improvement in symptom severity. Clozapine treatment was associated with grey matter volume reductions across multiple subcortical regions (including the amygdala, hippocampus, thalamus, caudate, putamen and nucleus accumbens), increases in pallidal volume, ventricular enlargement, and widespread cortical thinning. Cortical regions showing the greatest magnitude of thinning corresponded to areas with higher normative densities of serotonergic 5-HT1A, 5-HT2A and 5-HT4 receptors. Changes in subcortical volume or cortical thickness during clozapine treatment were not associated with changes in total or positive symptom severity. In addition, baseline subcortical volume, cortical thickness, or gyrification prior to starting clozapine did not predict subsequent symptom improvement. Cortical thinning may partly reflect clozapines activity at serotonergic receptors, which have been implicated in cortical network stabilisation and neuroplasticity, however structural remodelling during clozapine treatment may reflect a process independent from its clinical efficacy in improving core symptoms of psychosis.

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

Complex Layout Classification in the Wild: A Low-Resource Approach with Layout-Preserving Augmentations

Many digitized corpora suffer from low resources because annotations may be scarce, page scans are noisy and of poor resolution, or layouts are structurally complex in ways that negatively affect the quality of automatic transcription. Developing robust classification models for low-resource languages is inhibited by the lack of large-scale annotated data and by the frequent semantic complexity of page layouts. To this end, we have curated a complex-layout dataset, manually classified into eight distinct layout types based on their separator regions. To overcome data scarcity, we propose a novel training strategy in the form of a CNN-based classifier that employs strong, domain-aware augmentations to improve generalization. We utilize narrow anisotropic Gaussian masking to suppress incidental textual details while preserving essential separations, compelling the model to learn global geometric arrangements. Additionally, we implement reflection-induced label transformations to enrich the training distribution while maintaining label consistency across asymmetric categories. The results demonstrate that layout-specific augmentations can substantially improve page-level layout classification under severe annotation scarcity.

04.
arXiv (CS.CV) 2026-06-19

Language-Instructed Vision Embeddings for Controllable and Generalizable Perception

Vision foundation models are typically trained as static feature extractors, placing the burden of task adaptation onto large downstream models. We propose an alternative paradigm: instead of solely feeding visual features into language models, we use language itself to dynamically guide the vision encoder. Our method, Language-Instructed Vision Embeddings (LIVE), leverages language as high-level guidance to produce task-centric embeddings at inference time, removing the need for task-specific retraining. This enables the encoder to focus on contextually relevant aspects of the input, yielding more controllable and generalizable representations. Empirically, LIVE reduces visual hallucinations (+34 points on MMVP), surpasses vision-language models with orders of magnitude more parameters on visual question answering, and generalizes to unseen instructions and tasks – offering a direct path toward adaptive, instruction-driven visual intelligence.

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

A unified complexity bound for logconcave sampling

arXiv:2606.12694v1 Announce Type: cross Abstract: We give a simple, unified, and nearly tight bound for sampling arbitrary logconcave distributions from a warm start using the In-and-Out algorithm along with exponential lifting. The main new ingredient in the analysis is an improved bound on the Poincaré constant of a lifted distribution. As a consequence, the resulting convergence rate is nearly tight for both constrained settings (e.g., Gaussian restricted to a convex body) and well-conditioned settings (e.g., strongly logconcave and smooth densities).

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

TLA-Prover: Verifiable TLA+ Specification Synthesis via Preference-Optimized Low-Rank Adaptation

arXiv:2606.06133v2 Announce Type: replace-cross Abstract: TLA+ is a formal specification language for verifying distributed systems and safety-critical protocols. Large language models (LLMs) frequently produce TLA+ specifications that fail the TLC model checker for semantic reasons. Across 25 LLMs, the best public baseline is 26.6% syntactic parse and 8.6% semantic model-check. We present TLA-Prover, a 20-billion-parameter model for TLA+ specification synthesis. Training combines supervised fine-tuning (SFT) on verified examples with repair-based group-relative policy optimization (GRPO). In the GRPO stage, the model learns to fix its own rejected specifications. We also train a direct preference optimization (DPO) variant from the same SFT checkpoint as an ablation. TLC provides the reward signal directly, with no learned reward model. Four tiers grade each output: Bronze (parses), Silver (no warnings), Gold (passes TLC), and Diamond. To reach Diamond, the model's correctness property is automatically altered in a small way; TLC must then detect a violation. If TLC still passes, the property was always-true and contributes nothing; the output fails Diamond. TLA-Prover reaches 9/30 (i.e. pass@1 = 30%) at both Gold and Diamond on a held-out 30-problem benchmark. This is roughly 3.5x the 8.6% untuned baseline. The DPO variant reaches 20% at Diamond. Gold and Diamond coincide at every checkpoint; this prevents the trivial-property failure mode.

07.
arXiv (CS.CL) 2026-06-11

When More Documents Hurt RAG: Mitigating Vector Search Dilution with Domain-Scoped, Model-Agnostic Retrieval

Retrieval-augmented generation degrades when scaled to large, heterogeneous document collections, where dense similarity loses discriminative power, and top-k retrieval increasingly returns semantically similar but contextually incorrect chunks. We refer to this failure mode as vector search dilution. Even when using hybrid dense+sparse retrieval, we observed this firsthand in a deployed Wyoming Department of Transportation corpus, where scaling from 54 to 1,128 documents (88,907 chunks) reduced accuracy from 75% to below 40%. To address this dilution, we propose MASDR-RAG ( Multi-Agent Scoped Domain Retrieval for RAG) and evaluate it on 200 expert-validated queries across five LLM backbones, six corpora, and two index stacks. Our results indicate that domain scoping using organizational metadata is the key fix, significantly improving P@10 from 0.77 to 0.86 ($p < 0.05$). Furthermore, our investigation of multi-agent orchestration revealed that a high degree of configuration dependence results –creating what we call the precision-faithfulness paradox. Based on these varied outcomes, our practical recommendation is simple: scope first, then perform a single synthesis call, reserving full multi-agent orchestration for genuinely multi-domain corpora paired with native-tool-call backbones. Code and Data will be made public upon acceptance.

08.
arXiv (math.PR) 2026-06-16

Balanced affine Motzkin paths: Pearson geometry and global endpoint asymptotics

arXiv:2601.17634v2 Announce Type: replace Abstract: We study endpoint distributions of balanced affine weighted Motzkin paths. In the balanced case, the generating-function equation has Pearson-type characteristic geometry. We show that this geometry controls the terminal-height law globally: the characteristic escape time determines the limiting cumulant generating function, the large-deviation rate function, and the ray-scale asymptotics. Thus the usual Gaussian window is only the local quadratic approximation to a global Pearson-driven profile. For finite sizes, we prove a uniform Daniels saddlepoint approximation in the one-dominant-singularity regimes and identify the exceptional antipodal case requiring a lattice/interference correction.

09.
medRxiv (Medicine) 2026-06-23

Linking mpox wastewater surveillance with reported clinical cases in three countries in Sub-Saharan Africa

The emergence of the novel monkeypox virus (MPXV) clade Ib in the Democratic Republic of the Congo (DRC) and neighboring countries in late 2023 highlighted the need for rapid, scalable surveillance approaches to support outbreak detection and response. As part of the ODIN-Mpox project, wastewater surveillance (WWS) systems were established as an emergency public health measure in three Sub-Saharan African countries (DRC, Tanzania, and Burkina Faso) to evaluate the feasibility of wastewater-based monitoring for mpox and strengthen local surveillance capacity. Between January 2025 and April 2026, 117 wastewater samples were collected from selected sites and analyzed for MPXV DNA using targeted qPCR assays. Clinical mpox data were obtained from national surveillance systems and WHO reports to assess epidemiological linkages between wastewater detections and reported infections. Six wastewater samples tested positive for MPXV DNA. During the study period, DRC experienced the highest disease burden, with weekly reported cases peaking at about 3,000 in January 2025, while Tanzania reported a peak of 20 weekly cases in March 2025. No confirmed clinical cases were reported in Burkina Faso. No clear relationship was observed between reported case numbers and qPCR Ct values in positive wastewater samples. Despite the low detection frequency, the project demonstrated the operational feasibility of implementing MPXV wastewater surveillance in resource-limited settings and established laboratory capacity for environmental monitoring of emerging infectious diseases. Given the early stage of WWS implementation in the region, the study identified opportunities for further system strengthening, including optimization of sample processing and reporting workflows, improved access to laboratory supplies, and enhanced integration of environmental and clinical surveillance data streams. These findings highlight the value of WWS as a complementary component of integrated public health surveillance systems and emphasize the need for continued investment in laboratory capacity, harmonized methodologies, governance frameworks, and knowledge exchange to enhance outbreak preparedness and response in low-resource settings.

10.
arXiv (CS.LG) 2026-06-15

Machine Learning for Biomedical Raman Spectroscopy: From Spectral Acquisition to Clinical Translation

arXiv:2606.14169v1 Announce Type: new Abstract: Raman spectroscopy provides label-free, chemically specific characterization of biological systems and has become an important tool for cancer diagnosis, molecular subtyping, microbiological identification, and intraoperative decision support. Biomedical Raman spectra are, however, high-dimensional, noisy, and affected by fluorescence background, acquisition variability, and biological heterogeneity, making robust computational analysis essential. This review examines the role of machine learning across the biomedical Raman spectroscopy pipeline, from preprocessing and signal correction to unsupervised structure discovery, supervised diagnosis and molecular stratification, representation and transfer learning, explainability, biomarker discovery, and multimodal integration with imaging, pathology, and molecular profiling. Emphasis is placed on the use of machine learning not only for diagnostic classification, but also for biologically interpretable and clinically actionable analysis. We also discuss the main barriers to clinical translation, including limited dataset sizes, inter-instrument variability, inconsistent preprocessing, insufficient external validation, reproducibility concerns, and limited sharing of software, data, and metadata. We argue that progress will require methodological advances together with standardization, robust validation, explainability, and deployment-ready analytical frameworks. By integrating methodological, biomedical, and translational perspectives, this review outlines key directions for developing reliable and clinically deployable Raman-AI systems.

11.
bioRxiv (Bioinfo) 2026-06-17

Posterior-calibrated multimodal motor states reveal longitudinal and imaging-associated heterogeneity in Parkinson's disease

Parkinson's disease (PD) motor heterogeneity is commonly summarized by hard subtype labels, although clinical states vary longitudinally, severity can dominate unsupervised structure, and model uncertainty is rarely calibrated. We developed a posterior and refit-stability calibrated multimodal motor state framework that assigns probabilistic MDS-UPDRS-III motor states, aggregates them at the patient level, separates global burden from residual tremor-axial profile, and tests whether imaging can recover the resulting posterior distribution. In 29,366 aligned PPMI motor-posterior visits spanning 4,773 participant identifiers, patient-level state families were stable on average (modal-family fraction 0.925; 95% CI 0.921 - 0.930), but 25.5% of patients transitioned state over follow-up (95% CI 24.1 - 26.7%). PD-only cohort definitions produced smaller denominators and are reported as sensitivity cohorts with rerun calibration and imaging-posterior checks. Severity and covariates explained substantial motor-domain variance, especially bradykinesia (rsecond=0.850), but residual profile modeling retained five active components across total-severity, principal-component, leave-one-domain, non-target-burden, and clinical-only severity axes. Refit-stability calibration with 250 patient-blocked bootstrap refits showed high nominal posterior confidence (0.989) but lower empirical label consistency (0.849), quantifying overconfidence rather than hiding it. Patient-held-out temporal modeling predicted future axial burden (best XGBoost rsecond=0.605) and future state transition (XGBoost AUC=0.830; 95% CI 0.822 - 0.837). DaTSCAN plus FreeSurfer ROI features predicted patient-level soft motor posterior vectors (RF jsd=0.209; 95% CI 0.199 - 0.220; macro-AUROC=0.692), while severity/demographic-adjusted imaging features further improved soft posterior recovery (jsd=0.188). BioFIND transfer reproduced clinically meaningful endpoint gradients after state assignment in 225 external patients, supporting external face validity rather than definitive transportability. These results support PD motor phenotypic states as calibrated, dynamic, clinically interpretable profiles with convergent imaging associations, not as definitive biological subtypes.

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

GLARE: A Natural Language Interface for Querying Global Explanations

arXiv:2606.19735v1 Announce Type: new Abstract: While global explanations are crucial for understanding vision models across datasets, classes, and decision contexts, their complex and monolithic nature often hinders practical exploration. Because users typically seek targeted answers to specific questions rather than static artifacts, we present an LLM-based interactive interface that provides natural language access to global explanations for black-box image classifiers. The system's core LLM acts as a mediator, translating natural language questions into structured SQL queries over local explanation data. This enables flexible aggregation without exposing users to low-level representations. For each query, the interface outputs statistics-augmented natural language responses, supporting local explanations, and intent-aligned visualizations. We evaluate the system on intent interpretation, query mapping accuracy, generalization to novel queries and datasets, and robustness to linguistic errors. Our results demonstrate that LLM-mediated querying substantially improves the accessibility and usability of global explanations for human-centered XAI.

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

LaQual: An Automated Framework for LLM App Quality Evaluation

arXiv:2508.18636v2 Announce Type: replace-cross Abstract: Representing a new paradigm in software distribution, LLM app stores are rapidly emerging, offering users diverse choices for content generation, coding assistance, education, and more. However, current ranking and recommendation mechanisms in LLM app stores predominantly rely on static metrics, such as user interactions and favorites, making it challenging for users to efficiently identify high-quality apps. At the same time, current academic research focuses on specific vertical fields and lacks a general, automated evaluation framework applicable to the diverse LLM app ecosystem. To address the above challenges, we present LaQual, an automated framework for LLM app quality evaluation. LaQual integrates three key stages: (1) LLM app labeling and hierarchical classification for precise scenario mapping; (2) static indicator evaluation using time-weighted user engagement and functional capability indicators to filter low-quality apps; and (3) dynamic scenario-adapted evaluation, where an LLM generates scenario-specific evaluation metrics, scoring criteria, and tasks for comprehensive quality evaluation. Experiments on a mainstream LLM app store demonstrate the effectiveness of LaQual. Its automated scores show high consistency with human judgments. Through effective screening, LaQual can reduce the candidate LLM app pool by 66.7% to 81.3%. User studies further validate its significant outperformance over baseline systems, particularly in comparison efficiency (mean 5.45 vs. 3.30) and value of explanatory information (4.75 vs. 2.25). These results demonstrate that LaQual provides a scalable, objective, and user-centric solution for high-quality discovery and recommendation of LLM apps in real-world scenarios.

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

FacProcessTwin: An LLM-Based System for Process Twin Development

arXiv:2606.17666v1 Announce Type: cross Abstract: Process twins provide real-time representations of entire production processes. By capturing how process steps interact, rather than monitoring a single machine in isolation as an asset-based digital twin does, they have the potential to drive efficiency gains across the whole process. However, developing a process twin is costly. It requires accurately modelling the entire production process: its process steps, the equipment and product-specific settings each step uses, and its process variations. The resulting model must then be bound to live operational data. We present FacProcessTwin, a system that leverages a large language model (LLM) to reduce this development time, building a process twin from a plant's process documentation and natural-language input from an operator. FacProcessTwin generates this complete process model and then automatically binds its process steps to live operational data. The generated model and its data bindings are rendered as an interactive process diagram through which manufacturing personnel can monitor and correct the system's autonomous decisions, such as resolving uncertainty at safety-critical binding steps. We evaluate FacProcessTwin through a real-world case study of an Australian food manufacturer, covering 16 production process flows that span chilled, frozen, and aseptic shelf-stable product categories and include process variations within the same product. The results show that FacProcessTwin generates these process models accurately (a mean F1 of 95.2% against ground truth) and builds each twin in roughly a sixth of the manual time. Its human-in-the-loop governance then keeps the safety-critical bindings correct: at ambiguous tags where a single-pass baseline silently mis-binds 75.0% of the time, FacProcessTwin defers to the operator and mis-binds none.

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

Trimodal Glioma Representation Alignment via Volumetric Contrastive Learning

Glioma grading and survival prediction require the integration of heterogeneous information collected at different spatial and biological scales. Histopathology describes tissue morphology, mRNA expression captures molecular activity, and magnetic resonance imaging provides a non-invasive view of tumor extent and radiological heterogeneity. Existing glioma prognosis models often combine only two of these sources, while their alignment objectives remain mostly pairwise. This paper introduces GLORIA, a novel trimodal framework for GLioma Omics - Radiology - hIstopathology Alignment. GLORIA processes whole-slide image regions, gene-expression profiles, and 3D MRI volumes through modality-specific encoders, projects them into a shared latent space, and aligns them with a Gramian contrastive loss that measures the volume spanned by the three modality embeddings. The aligned representations are fused through a cross-modal gating module and optimized jointly for three-class glioma grading and overall survival prediction. We evaluate GLORIA on a matched TCGA-GBM/LGG and BraTS21 cohort, comprising 132 patients with all three modalities. On the shared trimodal test set, GLORIA improves over the bimodal WSI-mRNA baseline in all the metrics considered.

16.
bioRxiv (Bioinfo) 2026-06-11

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

Single-cell multi-omics technologies have recently advanced to enable the profiling of epigenomic, transcriptomic, and proteomic layers within individual cells, offering new opportunities to characterize cellular states as integrated biological systems. However, developing a unified framework that can seamlessly integrate diverse omics modalities and remain robust to heterogeneous modality missingness remains challenging. Here we present HoloCell, to our knowledge the first generative foundation model for joint representation learning and generative modeling across all three major single-cell omics modalities, i.e., epigenomics, transcriptomics, and proteomics. HoloCell contains over 860 million parameters and is pretrained on the Human-Multi-Omics-Corpus, which comprises approximately 468 million single-cell profiles across these three omics layers, corresponding to over 425 billion tokens. HoloCell introduces a simple yet biologically grounded hierarchical tokenization strategy that encodes cis-regulatory elements, genes, and proteins as structured tokens within a shared modeling framework. We evaluated HoloCell across single-omics representation learning, paired multi-omics integration, unpaired multi-omics alignment, and cross-modal generation via iterative diffusion and remasking, demonstrating its superior performance and flexibility across diverse omics tasks. From a representation perspective, HoloCell provides a unified digital mapping of cellular states across multiple omics layers, capturing cell heterogeneity as an integrated system. From a generation perspective, its iterative diffusion and remasking framework accounts for the inherently unordered nature of biological features, enabling in silico simulation of multi-omics information flow. Together, these capabilities position HoloCell as a versatile foundation model toward the emerging concept of a virtual cell, offering both systematic characterization and generative simulation of cellular systems within a unified framework.

17.
arXiv (CS.LG) 2026-06-15

Implicit Variational Rejection Sampling

arXiv:2606.14235v1 Announce Type: new Abstract: Variational Inference (VI) is a fundamental inference technique in Bayesian machine learning for approximating complex posterior distributions. Traditional VI often relies on the mean-field factorization, which can inadequately capture true posterior complexity. Recent advancements have leveraged neural networks to model implicit distributions, offering increased flexibility. However, the practical constraints of neural network architectures still produces inaccuracies. In this paper, we propose a method called Implicit Variational Rejection Sampling (IVRS), which integrates implicit distributions with rejection sampling to improve the posterior approximation. Our method uses neural networks to construct implicit proposal distributions, and rejection sampling with a discriminator network that estimates the density ratio between the implicit proposal and the true posterior for refining the approximation. Towards this end, we introduce the Implicit Resampling Evidence Lower Bound (IR-ELBO) as a metric to characterize the resampled distribution's quality and derive a tighter variational lower bound. Experimental results demonstrate that our method outperforms traditional variational inference techniques.

18.
arXiv (CS.LG) 2026-06-15

Machine-learned particle flow as a foundation model for collider physics

arXiv:2606.14373v1 Announce Type: cross Abstract: The workflow from particle collision to physics analysis passes through a series of reconstruction steps that are traditionally modular and disconnected, with no shared representation linking low-level detector data to high-level analysis tasks. We show that casting event reconstruction as a machine learning problem naturally produces such a shared representation. We repurpose a machine learning model trained for particle-flow reconstruction (MLPF) to perform three distinct analysis tasks: jet flavor identification, jet energy regression, and missing momentum regression. By appending the per-particle latent representations learned during reconstruction as additional input features, we substantially improve over baselines that use kinematic features alone. We further demonstrate that a single linear layer trained using only the latent representations achieves competitive performance against state-of-the-art baseline architectures, and outperforms the baseline for missing momentum regression with approximately 35 times fewer parameters. These results demonstrate that the latent representations learned during reconstruction encode essential physics information needed for downstream analysis, establishing MLPF as a foundation model and offering a concrete step toward an end-to-end pipeline from detector data to physics analysis.

19.
arXiv (CS.LG) 2026-06-16

Diversity-Driven Offline Multi-Objective Optimization via Nested Pareto Set Learning

arXiv:2606.15115v1 Announce Type: new Abstract: Multi-objective optimization (MOO) has emerged as a powerful approach to solving complex optimization problems involving multiple objectives. In many practical scenarios, function evaluations are unavailable or prohibitively expensive, necessitating optimization solely based on a fixed offline dataset. In this setting, known as offline MOO, the goal is to find out the Pareto set without access to the true objective functions. This setting suffers from the out-of-distribution (OOD) issue, where the surrogate model is not accurate for unseen designs. Due to the OOD issue, surrogate errors may cause the optimizer to select solutions that do not lie on the true Pareto front and are biased toward its extremes. To address this, this paper proposes Diversity-driven Offline Multi-Objective Optimization (DOMOO), which aims to find out a diverse and high-quality set of solutions. First, DOMOO incorporates an accumulative risk control module that estimates the potential risk of candidate solutions and alleviates the OOD issue between the training data and the generated solutions. In addition, a nested Pareto set learning (PSL) strategy is proposed to jointly learn preference and PSL parameters, then optimize them, enabling adaptation to diverse Pareto front geometries. To further enhance solution quality, we design a diversity-driven selection strategy that extracts a representative and well-distributed set of final solutions. To achieve this diversity-driven selection strategy, we propose $IGD_offline$, a tailored indicator for the offline setting that considers both diversity and convergence, and avoids the bias of hypervolume indicator. Extensive experiments on synthetic and real-world benchmarks show that DOMOO achieves the best average rank across tasks in both convergence and diversity among the compared methods.

20.
arXiv (CS.CL) 2026-06-19

Quantifying Aleatoric Uncertainty of In-Context Learning for Robust Measure of LLM Prediction Confidence

In-Context Learning (ICL) allows LLMs to adapt to new tasks from a few demonstrations, but its reliability remains a concern: predictions are highly sensitive to both prompt design and the model's ability to understand the context, obscuring whether failures arise from data properties or model limitations. Uncertainty decomposition-separating aleatoric from epistemic sources-is particularly crucial in this setting, yet existing methods, designed for standard generation tasks, fail to capture the unique dynamics of ICL. To address this, we introduce a concept of self-function vectors, built upon Bayesian views and the mechanistic interpretability of ICL. These vectors leverage internal model representations to model the latent concept learned during in-context prompting, thereby enabling a direct estimation of aleatoric uncertainty within a Bayesian framework and circumventing the reliance on brittle input or decoding manipulations. Given the lack of established benchmarks and suitable evaluation protocols, we also propose the first and rigorous evaluation protocol, in which data is manipulated in controlled ways so as to quantify aleatoric uncertainty precisely and separately from epistemic uncertainty. With this new evaluation framework, initially grounded in synthetic tasks for conceptual development and subsequently extended to real-world datasets, we show that our proposed methodology can measure uncertainty of LLM predictions made under ICL more reliably than existing alternative methods. Moreover, we show it can be used as a practical tool for trustworthy-related applications, such as hallucination detection. Our findings pave a new direction for connecting the quantitative view of uncertainty with the mechanistic understanding of model behavior.

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

Detecting Functional Memorization in Code Language Models

Large language models (LLMs) are increasingly used to generate code at scale. Meanwhile, prior work has investigated whether training data may be recoverable from model outputs, by auditing the textual overlap between training examples and model generations. Code, however, can be functionally equivalent while textually dissimilar. In this work, we study functional memorization: extraction of functional logic beyond what verbatim metrics detect. We construct a counterfactual setup for Olmo-3-32B, comparing a midtrained model (exposed to target code) against a pretrained reference (not exposed). We prompt both models with Python function signatures and measure both textual and functional similarity (i.e., LLM-as-a-judge, execution-based). Our results show clear evidence of functional memorization, highlighting the need for auditing metrics that go beyond textual overlap.

22.
arXiv (quant-ph) 2026-06-19

Fidelity bounds for adiabatic gates and other quantum operations with time-dependent dissipation

arXiv:2606.20501v1 Announce Type: new Abstract: As quantum-computing platforms are susceptible to noise, the fidelity of quantum operations is limited by decoherence. Understanding this limitation is crucial for building utility-scale quantum processors. In previous works [Phys. Rev. Lett. 129, 150504 (2022); Quantum 9, 1684 (2025)], we presented analytical formulae for the average gate fidelity of multi-qubit operations under static Markovian noise processes, including operations that temporarily leave the computational subspace. However, some quantum-computing architectures dynamically modulate qubit or coupler frequencies to implement two-qubit gates, e.g., baseband flux gates; such modulation can lead to dissipation rates varying in time. In this Letter, we therefore generalize the fidelity-reduction formulae to encompass time-dependent dissipation. Applying our generalized formula, we obtain a fidelity bound for adiabatic operations and demonstrate that flux-dependent noise sensitivity, combined with qubit-coupler hybridization, significantly reduces the fidelity of adiabatic controlled-Z (CZ) gates in superconducting quantum computers. Our work thus provides essential theoretical tools for evaluating error budgets and optimizing the design of quantum operations in tunable quantum-computing architectures, and may also find applications in quantum-sensing and quantum-communication protocols that are affected by time-dependent dissipation.

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

Frames2LoRA: Parametric Video Internalization for Vision-Language Models

Processing video in vision-language models is expensive: each frame occupies hundreds of tokens, and inference cost scales with every frame and every repeated query. We introduce Frames2LoRA, a method for parametric video internalization. A perceiver hypernetwork reads the intermediate representations produced layer-by-layer as a frozen VLM encodes a video, and generates a Low-Rank Adaptation (LoRA) adapter in a single forward pass. Unlike standard LoRA fine-tuning, which requires iterative gradient updates, Frames2LoRA predicts these weights directly from the video. Trained for SmolVLM2 500M and 2.2B on video summarization and captioning, Frames2LoRA enables the same frozen VLM to answer queries from the adapter alone, with zero visual tokens in its context at query time. Frames2LoRA is statistically non-inferior and equivalent to direct video-in-context inference across all five captioning benchmarks at both model scales, and across seven of eight video question answering benchmark-scale pairings. Although trained only on 12 frames at 384px, it remains stable up to 1,024 frames and 1024px, where direct video-in-context inference often degenerates. Across this sweep, it reduces answer-time visual-token load by up to 1,500x and query TTFT by 6-80x, while preserving video-faithful outputs. We also find that independently generated adapters for non-overlapping video segments can compose in rank space, suggesting a path toward chunked long-video internalization.

24.
medRxiv (Medicine) 2026-06-15

CDH13 is associated with cellular viability after exposure to ionizing radiation using genome-wide screening

Background: It is well known that genetic variants contribute to cellular sensitivity to chemotherapeutic agents and ionizing radiation (IR). The aim of this study was to identify single nucleotide polymorphisms (SNPs) and genes associated with the spectrum of normal cellular sensitivity of lymphoblastoid cell lines (LCLs) towards ionizing radiation and mitomycin C (MMC). Methods: In a first step, we determined the viability of LCLs established from male participants of the Berlin Aging Study II (BASE-II) aged >=62 years following treatments with increasing doses of IR (n=137 cell lines) or MMC (n=140 cell lines) using the alamarBlue assay. Results from intra-experimental triplicates and three independent experiments for each cell line and treatment were used to calculate the area under the curves (AUCs) representing the specific sensitivity to IR and MMC of each LCL. The data from these experiments were subsequently used as outcomes in genome-wide association studies (GWASs). In addition, we calculated polygenic risk scores (PGS) from UK Biobank GWAS results for four cancer-related phenotypes and assessed the extent to which the variance in the IR and MMC sensitivity is explained by these PGS. Results: The GWAS analyses revealed one variant, rs74728080, located in CDH13 on chromosome 16, to show genome-wide significant (p < 5 x 10-8, beta = 2.81) association with cellular viability after treatment with IR. In the GWAS on MMC sensitivity the most interesting signal was elicited by SNP rs113978558 in an intron of the PLD5 gene on chromosome 1 (p = 9.232 x 10-8; beta = 1.44). Several other SNPs with statistically suggestive (i.e., p < 1 x 10-5) evidence of association with IR or MMC sensitivity were identified. PGSs calculations from GWAS of four cancer-related traits in UKB explained ~5% and ~3% of phenotypic variance in IR- and MMC-induced cell viability, respectively. Conclusion: The genome-wide significant association of rs74728080 with IR sensitivity and the location of this variant in CDH13 is interesting and functionally highly plausible given its known involvement in oxidative-stress response and function as tumor suppressor. Taken together, our novel data suggest that CDH13 may be genuinely involved in regulating cellular IR sensitivity.

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

DrivingAgent: Design and Scheduling Agents for Autonomous Driving Systems

Many autonomous driving systems are increasingly incorporating foundation models to improve generalization and handle long-tail scenarios. However, this trend introduces two key challenges: (i) the manual and labor-intensive process of designing and integrating new models, and (ii) the lack of intelligent, dynamic scheduling mechanisms to meet strict real-time constraints. While Large Language Model (LLM)-based agents offer a promising avenue for automation, existing frameworks are ill-suited for autonomous driving. Specifically, they fail to distinguish between the fundamentally different requirements of system design and real-time scheduling, treat modules as opaque black boxes, and are not designed for continuous operation. To address these limitations, we propose DrivingAgent, a novel agent framework tailored to the dual challenges of autonomous driving system design and scheduling. In the design phase, DrivingAgent automates module development by interpreting system architecture, generating code, and validating modules via super-network training. In the scheduling phase, it employs a lightweight LLM trained with reinforcement learning to dynamically orchestrate system modules in real time, supported by a structured memory that integrates long-term storage with timestamped short-term context. Experimental results demonstrate that DrivingAgent achieves a superior speed–accuracy trade-off on both the nuScenes and Bench2Drive benchmarks.