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

All Smoke, No Alarm: Oracle Signals in Agent-Authored Test Code

arXiv:2606.18168v1 Announce Type: cross Abstract: Software practitioners increasingly use AI coding agents that generate test code alongside production code in open source pull requests (PRs). Recent studies report more than 932,000 agent-authored PRs across more than 116,000 repositories, yet whether their test files contain meaningful verification logic remains underexplored. Test files lacking explicit assertions execute code without verifying behavior, so quality gates based on test-file presence overestimate verification strength. The goal of this paper is to help practitioners assess the verification strength of agent-authored patches by characterizing oracle signals and their link to merge outcomes and review effort. We conduct an empirical study of 86,156 test-file patches from 33,596 agent-authored PRs across 2,807 GitHub repositories produced by five coding agents: OpenAI Codex, GitHub Copilot, Devin, Cursor, and Claude Code. A qualitative analysis of 384 stratified patches informs a syntactic taxonomy of eight oracle signal categories. Applied at scale, 80.2% of test patches contain weak or no explicit oracle signals. While raw merge rates are lower for strong-oracle PRs, a regression analysis adjusting for agent, PR size, repository popularity, task type, and language shows strong oracles significantly improve merge likelihood (OR = 1.28, p < 0.001). Our findings suggest that test file counts substantially overestimate verification strength and that practitioners can adopt oracle-aware quality checks to more accurately evaluate agent-authored contributions.

02.
arXiv (CS.CL) 2026-06-17

Smarter edits? Post-editing with error highlights and translation suggestions

As MT quality increases, interest in enhanced post-editing features such as QE-derived error highlights is growing, yet evidence for their usefulness remains limited. In this work, we explore the usefulness of LLM-derived error highlights and correction suggestions based on automatic post-editing (APE). We conduct a study where professional translators (En-Nl) post-edit translations using APE error highlights and correction suggestions and compare productivity, quality and user experience to regular PE and PE with QE-derived highlights. While no condition yielded productivity or quality gains compared to regular PE, APE highlights were better received than QE-derived highlights, and correction suggestions improved overall user experience.

03.
arXiv (quant-ph) 2026-06-11

A Pfaffian quantum Hall state of ultracold bosons

arXiv:2606.12409v1 Announce Type: cross Abstract: Fractional quantum Hall states are a cornerstone of topological physics, hosting fractionally charged quasiparticles with exotic statistics that promise to enable topologically protected quantum information processing. Among these, the Pfaffian state introduced by Moore and Read implements a p-wave pairing structure that supports excitations with non-Abelian exchange statistics. Despite extensive study in electronic systems, direct access to its pairing structure has remained limited. Here we realize a three-particle bosonic Pfaffian state of ultracold $^{87}\mathrm{Rb}$ atoms in an optical lattice subject to a Floquet-engineered synthetic magnetic field. Using a Bayesian-optimized adiabatic protocol, we prepare a state exhibiting Pfaffian pairing correlations. Site-resolved measurements of multi-point density correlations reveal a pronounced suppression of short-range three-body coincidences, reflecting the underlying pairing structure. We further probe the state's transport response through Hall drift measurements. Our results establish a bottom-up approach to engineering non-Abelian topological order and lay the groundwork for future explorations of anyonic braiding in synthetic matter.

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

PerceptionDLM: Parallel Region Perception with Multimodal Diffusion Language Models

Multimodal large language models (MLLMs) have achieved remarkable progress in visual understanding tasks. However, most existing MLLMs rely on autoregressive generation, which limits their efficiency for perception tasks that require captioning multiple regions. In this work, we propose PerceptionDLM, a multimodal diffusion language model optimized for efficient parallel region perception. Built upon PerceptionDLM-Base, a strong foundational baseline that achieves state-of-the-art performance among open-source diffusion MLLMs, our architecture fully leverages the parallel decoding nature of DLMs. Specifically, we introduce efficient prompting and structured attention masking to enable simultaneous perception of multiple masked regions, allowing the model to generate region descriptions in parallel at both the sequence and token levels. This design significantly improves inference efficiency compared with existing approaches that process regions sequentially. To systematically evaluate the parallelism property of visual perception capability for DLMs, we construct a new Parallel Detailed Localized Captioning Benchmark (ParaDLC-Bench) by scaling the DLC-Bench to include multiple region masks per image, enabling joint evaluation of both caption quality and inference efficiency. Experiments demonstrate that PerceptionDLM maintains competitive performance in region captioning while achieving substantial speed improvements for multi-region perception tasks. Our results highlight the potential of multimodal diffusion language models for efficient, parallel visual perception. To the best of our knowledge, we are the first to achieve parallel region caption and perception by leveraging the advantages of diffusion language models. Code, models, and datasets are released.

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

GRACE-DS: a Guarded Reward-guided Agent Correction Environment in Data Science

We introduce GRACE-DS, a Guarded Reward-guided Agent Correction Environment in Data Science for pre-deployment evaluation of LLM-powered AutoML agents. GRACE-DS is a set of evaluation metrics in an isolated environment that can be applied to tabular ML tasks specific to a particular organization. It exposes agents to realistic workflow stages, from planning and data inspection through feature engineering, model development, validation, and code repair to final submission, while hidden executable validators measure not only final predictive performance but also leakage avoidance, reproducibility, protocol validity, correction behavior, and reward alignment. The strongest structured regime, flexible iterative interaction (our approach), achieves higher end-to-end normalized hidden-test quality than single-shot generation, unstructured interaction, and restart-based baselines, while also improving protocol-valid completion. Validated across more than 7,000 episodes, these results establish GRACE-DS as a robust platform for assessing the capacity of LLM-based AutoML agents to execute machine learning workflows under production-like conditions and in accordance with organization-specific requirements.

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

Robin-Neumann Coupling of PINN and FEM Solvers: A Steklov-Poincaré View, with Application to Fluid-Structure Interaction with Contact

arXiv:2606.14181v1 Announce Type: cross Abstract: Physics-informed neural networks (PINNs) are meshless and carry moving geometry and topology change through resampling of collocation points; the finite-element method (FEM) is the workhorse for boundary-fitted discretisations. Coupling the two across a shared interface promises the best of both, yet existing PINN-FEM schemes are validated only empirically. We put the coupling on a domain-decomposition footing: viewing each solver as a Steklov-Poincaré (trace-to-flux) operator, we transfer the classical Dirichlet-Neumann (DN) divergence diagnosis and its Robin-Neumann (RN) cure, including a closed-form, sweep-free interface impedance, and prove a PINN-specific contraction theorem: a trained network realises only a perturbed Steklov operator with a per-step training residual, and RN still contracts, with no shared-eigenbasis hypothesis, to a floor set by the achieved training loss. Because a PINN has no stiffness matrix, we introduce a Fourier-mode interface probe that recovers the network's resolvable Steklov eigenvalues to within 0.5% and doubles as a diagnostic of the network's spectral cap. The theory predicts measured PINN-FEM contraction rates to within 7% on 1D and 2D Poisson couplings, and a two-slab analogue of the large-added-mass regime shows RN's per-mode impedance matching winning decisively where tuned scalar relaxation saturates. We demonstrate the framework on a Stokes/rigid-disc problem with Alart-Curnier contact: the meshless PINN fluid absorbs the topology change at contact by collocation exclusion alone, no remeshing and no cut cells, and the static-equilibrium contact reaction matches the submerged weight to 0.4% under mesh refinement. We quantify remaining limitations: the warm-started PINN drifts off the Stokes manifold over long horizons, and matched FEM-FEM benchmarks attribute pre-impact squeeze-film signatures to PINN under-resolution.

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

Sub-Token Routing for KV Cache Compression

Transformer inference often requires a large KV cache, especially for long-context language modeling and multimodal generation. Existing compression methods usually reduce cache cost by selecting, evicting, quantizing, or compressing cached tokens, or by reducing the visual-token sequence before language-model inference. We introduce sub-token routing, a KV-compression method that adds a finer control axis inside retained tokens. It splits each retained value vector into groups and keeps only selected groups, while leaving query and key states unchanged. The method is designed to work after token-level reduction. First, a token-reduction method determines which tokens are retained. Then, sub-token routing compresses the value states inside those retained tokens. Experiments under matched KV budgets show that adding sub-token routing improves token-level reduction performance in both LLM and VLM settings, including Quest on LLaMA-2-7B and Qwen2.5-7B, and FastV/VisionZip across LLaVA and Qwen-VL models. The gains are larger at smaller KV budgets, suggesting that value-group routing is especially useful when further token removal becomes costly. Overall, token-level reduction and sub-token routing provide complementary ways to reduce KV cost.

08.
bioRxiv (Bioinfo) 2026-06-11

Integrating Spatially Adjusted Protein Summaries for Survival Prediction in Spatial Proteomics

Recent advances in spatial proteomics, particularly imaging mass cytometry, enable the measurement of protein expression at the single-cell level while preserving a spatial context. Conventional survival analyses, however, typically rely on patient-level averages of protein intensities and therefore overlook spatial heterogeneity and tissue architecture. To address this limitation, we introduce a framework that incorporates spatial information into survival modeling by generating spatially adjusted protein summaries (SAPS). In this approach, cell-level protein intensities within each patient are modeled using spatial spline regression to capture spatial trends. From these models, we extract two complementary features: a spatially adjusted mean expression and a residual variance that reflects cell-to-cell variability unexplained by spatial effects. These summaries are then incorporated into Cox proportional hazards models in combination with clinical covariates. In simulation studies, our proposed framework achieved improved predictive performance compared to other alternative methods. The application of the method to breast cancer imaging mass cytometry data indicate that spatially adjusted summaries may enhance survival prediction and reveal biologically interpretable spatial protein patterns, suggesting high translational potential. This methodology offers an efficient means of translating complex spatial proteomics data into patient-level features, providing both improved survival prediction and new insights into the role of spatial heterogeneity in cancer outcomes.

09.
arXiv (math.PR) 2026-06-16

Geometry of critical discrete structures: long-range percolation on the hierarchical lattice and the discrete torus

arXiv:2509.09589v2 Announce Type: replace Abstract: Consider (a) balls $\Lambda_n$ of growing volumes in the $d$-dimensional hierarchical lattice, and (b) the $d$-dimensional discrete torus $\mathbb{T}_n^d$ on $n^d$ vertices. Place edges independently between each pair of vertices $x\neq y\in\Lambda_n$ or $\mathbb{T}_n^d$ with probability $1-\exp(-\beta J(x, y) )$ where $J(x, y) \asymp \| x-y \|^{-\alpha}$ for some $0

10.
arXiv (CS.CV) 2026-06-11

From Simulation to Real-World: An In-Field 6D Pose Dataset and Baseline for Robotic Strawberry Harvesting

Robotic strawberry harvesting requires precise 6D pose estimation; however, collecting 6D pose ground truth in real agricultural fields is inherently challenging. Existing 6D pose estimation methods have therefore relied solely on synthetic data that lacks scene-level realism, leaving their performance under real agricultural field conditions unquantified. In this work, we present, to the best of our knowledge, the first real-world 6D pose ground truth dataset of strawberries collected in actual agricultural fields (12,040 images). We also introduce a synthetic dataset rendered in NVIDIA Isaac Sim, featuring scene-level realism and domain randomization. Nevertheless, our experiments reveal that a significant sim-to-real gap persists, underscoring the necessity of real agricultural field data for reliable evaluation. We further quantify the sim-to-real gap through baseline 6D pose estimation results across backbone encoders, serving as a reference for future work. The real-world dataset will be made available upon acceptance.

11.
arXiv (CS.AI) 2026-06-18

SciRisk-Bench: A Risk-Dimension-Aware Benchmark for AI4Science Safety

arXiv:2606.18936v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly embedded in AI for Science (AI4Science) workflows, from scientific question answering and literature analysis to laboratory planning and autonomous discovery. This progress creates an urgent need for safety benchmarks that evaluate not only scientific competence, but also whether models recognize and avoid risks in high-stakes scientific contexts. Existing AI4Science safety datasets cover several disciplines and task formats, leaving the underlying risk dimensions underspecified. We introduce SciRisk-Bench, a benchmark designed to evaluate AI4Science safety from two complementary perspectives: explicit risk dimensions and scientific disciplines. SciRisk-Bench covers 7 disciplines, 31 subdisciplines and 10 risk dimensions. In the experimental section, we evaluate both mainstream LLMs and science-oriented LLMs across risk dimensions, disciplines, and sub-disciplines, enabling fine-grained diagnosis of where scientific models remain unsafe.

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

Multiscale Hypersonic Boundary Layer Reconstruction via Spectral Binning and Subdomain-wise Conditional Diffusion

arXiv:2606.15023v1 Announce Type: cross Abstract: We propose a multiscale probabilistic reconstruction framework for hypersonic Couette flow, where near-wall states are inferred from limited top-wall observations using conditional diffusion model. The boundary layer is divided into overlapping wall-normal subdomains, and a single height- and Mach-conditioned Elucidating Diffusion Model (EDM) is trained jointly for M=6,7,8 to sample velocity, density, pressure, and temperature fields conditioned on a top-wall boundary slice. A soft overlap inpainting strategy assembles subdomain predictions into full-volume reconstructions while maintaining inter-subdomain continuity and small-scale variability. To improve the spectral fidelity of the generated fields, we introduce a novel bounded binned spectral power (BSP) loss that preserves high-wavenumber content while remaining numerically stable across the diffusion noise schedule. Validation against direct numerical simulation data shows that the model recovers instantaneous structures, spectra, statistical profiles, correlations, and wall quantities across all training Mach numbers, while providing spatially structured uncertainty estimates. The reconstructed Mach-conditioned profiles also collapse under the Trettel-Larsson transformation, indicating consistency with compressibility scaling. These results establish the domain decomposed conditional diffusion model with a bounded binned spectral loss as an effective probabilistic surrogate for near-wall reconstruction in hypersonic wall-bounded turbulence.

13.
arXiv (CS.CV) 2026-06-15

Generation of Maximal Snake Polyominoes Using a Deep Neural Network

Maximal snake polyominoes are difficult to study numerically in large rectangles, as computing them requires the complete enumeration of all snakes for a specific rectangle size, which corresponds to a brute force algorithm. This hinders the study of maximal snakes in larger rectangles. Moreover, most enumerable snakes lie in small rectangles, obscuring large-scale patterns. In this paper, we investigate the contribution of a deep neural network to the generation of maximal snake polyominoes from a data-driven training, where the maximality and adjacency constraints are not encoded explicitly, but learned. To this extent, we experiment with a denoising diffusion model, which we referred as Structured Pixel Space Diffusion (SPS Diffusion). We find that SPS Diffusion generalizes from small rectangles to larger ones, generating valid snakes up to 28x28 squares and producing maximal snake candidates on squares close to the current computational limit. The model is, however, prone to errors such as branching, cycles, or multiple snake components. Overall, the diffusion model is promising and suggests that complex combinatorial objects can be understood by deep neural networks, which is useful in their investigation.

14.
arXiv (CS.CV) 2026-06-12

Surflo: Consistent 3D Surface Flow Model with Global State

Geometry is invariant to viewpoint, which makes any collection of images a redundant encoding of a single 3D state. Existing feed-forward reconstruction models fail to exploit this: per-view methods emit overlapping, unaligned pointmaps that grow linearly with input count, while global-latent methods commit to a fixed, low-resolution output. We introduce Surflo, which compresses a variable number of unposed RGB views into K latent tokens-one global state-and decodes oriented 3D surface points by independently transporting them from noise onto the surface via flow matching. This frees the output from any fixed grid or token budget: the same latent yields from a few thousand to a million points in a single forward pass. To suppress the local inconsistencies inherent to independent per-point decoding, an inference-time guidance term correlates nearby points by injecting a photometric gradient during ODE integration. Surflo matches or surpasses feed-forward baselines on surface metrics, runs an order of magnitude faster than optimization-based methods that require hundreds of views, and is the only feed-forward approach to combine a global latent with arbitrary-resolution decoding.

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

Phase-Aware Guidance Injection for Recurrent MAPPO in Assembly-Line Disruption Recovery

arXiv:2606.16330v1 Announce Type: new Abstract: Disruption recovery in industrial assembly lines requires timely decisions under machine faults, worker absence, and emergency orders. Existing methods either rely on rigid handcrafted recovery logic or learn adaptive policies that do not readily exploit heterogeneous external recovery knowledge at decision time to reduce abnormal recovery time (ART) and preserve on-time delivery (OTD). To address this gap, we propose a phase-aware guidance injection framework that augments a trained recurrent MAPPO (RMAPPO) scheduling policy through logit-level action bias during evaluation. The framework provides a unified decision-time interface for rule-based, replay-based, and online LLM-based guidance, while activating intervention only during abnormal and recovery phases. Experiments on a custom AssemblyLineEnv show that high-quality rule guidance yields the strongest gains, replay-based guidance degrades smoothly under imperfect availability, and online LLM guidance still provides useful intermediate improvements. These results show that decision-time guidance injection can exploit heterogeneous recovery hints without redesigning the actor.

16.
medRxiv (Medicine) 2026-06-10

Healthy Heart Actions Right Time (HHART): Co-design priorities to connect Aboriginal and Torres Strait Islander community and clinic activities for healthy hearts

Aim: Healthy Heart Actions Right Time (HHART) is a multi-phased research project that seeks to identify, implement and evaluate strategies to connect community and clinical activities to reduce the burden of heart disease for Aboriginal and Torres Strait Islander people. The aim in Phase One was to identify priority activities for two participating services. Background: The ongoing effects of colonisation drive a disproportionate burden of heart disease for Aboriginal and Torres Strait Islander people. Clinical and community groups both have established strengths in reducing the risk of heart disease, but these are not always well connected. Methods: Using a case study methodology in two locations we partnered in a 12-month co-design process to identify priority activities to connect clinical and community activities. Findings: Three priorities emerged from the Phase One co-design process: (i) community-led gardening as a strategy to promote heart health through connection and healthy lifestyles; (ii) community days to increase engagement in heart checks and strengthen community-clinic relationship; and (iii) clinic-led development of culturally relevant education resources to promote clinician confidence and community heart health knowledge.

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

Efficient Temporal Modeling for Mobile Sleep Staging via Lightweight Random Attention

arXiv:2606.13694v1 Announce Type: cross Abstract: Mobile sleep staging serves as a foundational infrastructure for in-home sleep monitoring and closed-loop modulation. But existing sequential models such as RNNs and Transformers are computationally expensive for mobile deployment. In this paper, we propose Random Attention (RA), a lightweight temporal modeling module based on fixed random projections, which replaces learnable sequence modeling with similarity-based aggregation. RA introduces little additional parameters beyond the epoch encoder while enabling effective temporal smoothing. We further provide a theoretical interpretation via the Random Attention Prior Kernel (RAPK), which decomposes RA into a global smoothing term and a feature similarity term, offering an interpretable view of temporal sleep structure. Experiments on Sleep-EDF-20 and Sleep-EDF-78 show that RA consistently improves epoch-wise baselines by 1-3\% in accuracy and F1 score, while achieving competitive performance compared with LSTM, GRU, and Transformer models. RA also demonstrates strong generalization across different backbone encoders and improved robustness over conventional temporal smoothing methods. These results indicate that efficient sleep staging can be achieved through lightweight similarity-based temporal aggregation, making RA suitable for real-time wearable applications.

18.
arXiv (math.PR) 2026-06-16

Stein's method for the matrix normal distribution

arXiv:2601.11422v2 Announce Type: replace-cross Abstract: This work presents the first systematic development of Stein's method for matrix distributions. We establish the basic essential ingredients of Stein's method for matrix normal approximation: we derive an extended-generator-based Stein identity from a matrix Ornstein-Uhlenbeck diffusion with two-sided scales, provide an explicit semigroup representation for the solution of the Stein equation, and obtain regularity estimates for the solution. The new methodology is demonstrated in three examples: (i) smooth Wasserstein distance bounds to quantify the matrix central limit theorem (a didactic example), (ii) a Wasserstein distance bound for the matrix normal approximation of the centered matrix $T$ distribution, and (iii) a Stein's method-of-moments approach to estimating the row and column covariance factors of the matrix normal, yielding a flexible class of weighted flip-flop Stein estimators that generalize Dutilleul's classical flip-flop algorithm and naturally accommodate row/column importance weights, systematic missingness, and projection onto structured covariance families. The latter two examples are intrinsically matrix-valued and cannot be treated using naive vectorization.

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

The Range Shrinks, the Threat Remains: Re-evaluating LLM Package Hallucinations on the 2026 Frontier-Model Cohort

arXiv:2605.17062v2 Announce Type: replace-cross Abstract: Spracklen et al. (USENIX Security '25) showed that code-generating large language models hallucinate package names that do not exist on PyPI or npm at rates ranging from 5.2% on commercial models to 21.7% on open-source models, creating an attack surface for slopsquatting – the registration of malicious packages under hallucinated names. We replicate their methodology on five frontier code-capable LLMs released between October 2025 and March 2026: Claude Sonnet 4.6, Claude Haiku 4.5, GPT-5.4-mini, Gemini 2.5 Pro, and DeepSeek V3.2. Across 199,845 paired Python and JavaScript prompts validated against PyPI and npm master lists, we measure overall hallucination rates between 4.62% (Claude Haiku 4.5) and 6.10% (GPT-5.4-mini) – an order-of-magnitude compression of the inter-model spread observed by Spracklen, but not a retirement of the threat. Beyond replication, we identify a set of 127 package names (109 on PyPI, 18 on npm) that all five evaluated models invent identically; following coordinated disclosure with PyPI Security and Socket.dev, 53 of these (41 on PyPI, 12 on npm) remain registrable by an attacker after each registry's existing defenses, constituting a model-agnostic supply-chain attack surface that no single-model study can reveal. We further document a Python-over-JavaScript hallucination asymmetry that inverts Spracklen's 2024 finding, identify a Haiku-below-Sonnet inversion within the Anthropic family, and observe a Jaccard-similarity peak between DeepSeek V3.2 and GPT-5.4-mini (J = 0.343) suggestive of shared training-data origins.

20.
arXiv (CS.LG) 2026-06-18

The Road to Artificial SuperIntelligence: A Comprehensive Survey of Superalignment

arXiv:2412.16468v4 Announce Type: replace Abstract: The emergence of large language models (LLMs) has sparked discussion on Artificial Superintelligence (ASI), a hypothetical AI system that surpasses human intelligence. Although ASI remains hypothetical and far beyond current AI capabilities, discussing its potential and exploring its feasibility and potential risks is critical for the development of future AI systems. The idea of superalignment originates from scalable oversight, which studies how to supervise increasingly capable AI systems when direct human supervision becomes insufficient. In this paper, we focus on the superalignment problem: "The process of supervising, controlling, and governing artificial superintelligence." We first review scalable oversight paradigms-Sandwiching, Self-Enhancement, and Weak-to-Strong Generalization – then analyze the limitations of current paradigms through the lens of possibility and impossibility, discuss key challenges, and propose pathways for the safe and continual improvement of future AI systems.

21.
arXiv (CS.LG) 2026-06-16

Repeated Bilateral Trade: The Quest for Fairness

arXiv:2606.15369v1 Announce Type: new Abstract: We study repeated bilateral trade from a fairness perspective. At each round, a fresh seller-buyer pair arrives, and the platform posts a price before observing the traders' valuations. Trade occurs only if both agents accept the price. Rather than maximizing only the gain from trade, we consider platforms that seek balanced divisions of the generated surplus. We show that natural fairness desiderata lead to a one-parameter Rawls-to-Nash family of fair-gain objectives, obtained by aggregating the seller's and buyer's net gains through nonpositive Hölder means. Unlike the standard gain-from-trade objective and the Rawlsian fair-gain objective studied in prior work, our proposed objectives induce a new statistical structure in which expected rewards are recovered from threshold feedback through a two-dimensional singular-kernel integral identity. This leads to a nonstandard pure-exploration problem whose natural estimators are rectangular double sums with row-column dependence and singular weights. Assuming independent i.i.d. seller and buyer valuation sequences with arbitrary unknown marginals, we characterize the optimal learning rates for the whole Rawls-to-Nash family of fair-gain objectives, giving matching fixed-confidence sample-complexity and regret bounds up to polylogarithmic factors.

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

VOiLA: Vectorized Online Planning with Learned Diffusion Model for POMDP Agents

arXiv:2606.19729v1 Announce Type: cross Abstract: Planning under uncertainty is an essential capability for autonomous robots. The Partially Observable Markov Decision Process (POMDP) provides a powerful framework for such a capability. Although POMDP-based planning has advanced significantly, its application to real-world problems is often limited by the difficulty of obtaining faithful POMDP models. We present Vectorized Online planning wIth Learned diffusion model for POMDP Agents (VOiLA), a framework that learns task-agnostic POMDP models for online planning under uncertainty. VOiLA learns transition and observation samplers using conditional diffusion models and learns observation-likelihood models for particle-based belief updates. To enable efficient online planning, the diffusion samplers are distilled into compact feedforward generators and integrated with Vectorized Online POMDP Planner (VOPP), an online POMDP planner designed to leverage GPU parallelization. Experimental results indicate the distillation strategy reduces sampling cost by up to nearly three orders of magnitude, making learned generative POMDP models practical for online planning. Evaluation of VOiLA on three benchmark problems indicate that VOiLA achieves equal or better performance than Recurrent Soft Actor Critic while using less than 10% training data, and generalizes much better to unseen environment configurations. Physical robot evaluation indicates VOiLA uses the models learned using only simulated data and generates a policy that successfully accomplish the task in 10 of 10 runs.

23.
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.

24.
arXiv (CS.LG) 2026-06-18

KEPLA: A Knowledge-Enhanced Deep Learning Framework for Accurate Protein-Ligand Binding Affinity Prediction

arXiv:2506.13196v5 Announce Type: replace Abstract: Accurate prediction of protein-ligand binding affinity is critical for drug discovery. While recent deep learning approaches have demonstrated promising results, they often rely solely on structural features of proteins and ligands, overlooking their valuable biochemical knowledge associated with binding affinity. To address this limitation, we propose KEPLA, a novel deep learning framework that explicitly integrates prior knowledge from Gene Ontology and ligand properties to enhance prediction performance. KEPLA takes protein sequences and ligand molecular graphs as input and optimizes two complementary objectives: (1) aligning global representations with knowledge graph relations to capture domain-specific biochemical insights, and (2) leveraging cross attention between local representations to construct fine-grained joint embeddings for prediction. Experiments on two benchmark datasets across both in-domain and cross-domain scenarios demonstrate that KEPLA consistently outperforms state-of-the-art baselines. Furthermore, interpretability analyses based on knowledge graph relations and cross attention maps provide valuable insights into the underlying predictive mechanisms.

25.
arXiv (CS.CV) 2026-06-12

DuET: Dual Expert Trajectories for Diffusion Image Editing

Recent diffusion editors perform diverse instruction-based edits while conditioning on the source image at every denoising step. Yet persistent source-image conditioning can limit how fully an edit is executed and how natural the result appears, especially when the target scene diverges substantially from the input. We introduce DuET (Dual Expert Trajectories), a training-free inference method that temporarily relaxes source-image conditioning by transitioning through a text-to-image phase before returning to edit mode, allowing the denoising trajectory to move toward the target distribution while retaining the structural benefits of image-conditioned editing. Without modifying model weights or increasing sampling cost, DuET consistently improves instruction relevance, semantic fidelity, and perceptual quality across diverse models and benchmarks. In some cases, these gains come with a modest reduction in source-image preservation, revealing a predictable trade-off between source preservation and edit fidelity.