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01.
arXiv (CS.CL) 2026-06-12

HyPE: Category-Aware Hypergraph Encoding with Persistent Edge Embeddings for Persona-Grounded Dialogue

Persona-grounded dialogue systems aim to produce responses consistent with a speaker's persona, yet existing methods treat personas as a flat set of sentences and fail to model the high-order relations among persona attributes-e.g., that several persona sentences share a topical category. We propose HyPE (Hypergraph Persona Encoder), a framework that (i) analyzes each persona-bearing text as a (Core, Expression, Sentiment, Category) quadruple, and (ii) organizes persona elements into a hypergraph whose hyperedges are induced by shared category labels. An HyperGCN hypergraph neural network propagates this structure into a persona summary vector and a soft-memory bank that condition the response generator. We further propose Persistent Edge Embeddings (PEE), lightweight per-category learnable priors fused into the HyperGCN message-passing step. On PersonaChat under greedy decoding, HyPE consistently outperforms sentence-level pooling baselines across GPT-2, LLaMA-3.2-3B, and Qwen2.5-3B backbones by demonstrating that structured hyperedge-level persona encoding provides a transferable advantage across model scales.

02.
arXiv (CS.AI) 2026-06-15

Federated Causal Inference from Multi-Site Observational Data via Propensity Score Aggregation

arXiv:2505.17961v4 Announce Type: replace-cross Abstract: Causal inference typically assumes centralized access to individual-level data. Yet, in practice, data are often decentralized across multiple sites, making centralization infeasible due to privacy, logistical, or legal constraints. We address this problem by estimating the Average Treatment Effect (ATE) from decentralized observational data via a Federated Learning (FL) approach, allowing inference through the exchange of aggregate statistics rather than individual-level data. We propose a novel method to estimate propensity scores via a federated weighted average of local scores using Membership Weights (MW), defined as probabilities of site membership conditional on covariates. MW can be flexibly estimated with parametric or non-parametric classification models using standard FL algorithms. The resulting propensity scores are used to construct Federated Inverse Propensity Weighting (Fed-IPW) and Augmented IPW (Fed-AIPW) estimators. In contrast to meta-analysis methods, which fail when any site violates positivity, our approach exploits heterogeneity in treatment assignment across sites to improve overlap. We show that Fed-IPW and Fed-AIPW perform well under site-level heterogeneity in sample sizes, treatment mechanisms, and covariate distributions. Theoretical analysis and experiments on simulated and real-world data demonstrate clear advantages over meta-analysis and related approaches.

03.
arXiv (CS.AI) 2026-06-12

From Digital to Physical: Digital Agents as Autonomous Coaches for Physical Intelligence

arXiv:2601.21570v2 Announce Type: replace Abstract: The field of Embodied AI is witnessing a rapid evolution toward general-purpose robotic systems, fueled by high-fidelity simulation and large-scale data collection. However, this scaling capability remains severely bottlenecked by a reliance on labor-intensive manual oversight from intricate reward shaping to hyperparameter tuning across heterogeneous backends. Inspired by LLMs' success in software automation and science discovery, we introduce \textsc{EmboCoach-Bench}, a benchmark evaluating the capacity of LLM agents to autonomously engineer embodied policies. Spanning 32 expert-curated RL and IL tasks, our framework posits executable code as the universal interface. We move beyond static generation to assess a dynamic closed-loop workflow, where agents leverage environment feedback to iteratively draft, debug, and optimize solutions, spanning improvements from physics-informed reward design to policy architectures such as diffusion policies. Extensive evaluations yield three critical insights: (1) autonomous agents can qualitatively surpass human-engineered baselines by 26.5\% in average success rate; (2) agentic workflow with environment feedback effectively strengthens policy development and substantially narrows the performance gap between open-source and proprietary models; and (3) agents exhibit self-correction capabilities for pathological engineering cases, successfully resurrecting task performance from near-total failures through iterative simulation-in-the-loop debugging. Ultimately, this work establishes a foundation for self-evolving embodied intelligence, accelerating the paradigm shift from labor-intensive manual tuning to scalable, autonomous engineering in embodied AI field.

04.
arXiv (CS.CV) 2026-06-15

Diffusion-Refined Segmentation and Vision-Language Interpretation for Pediatric Brain Tumor MRI

Accurate pediatric brain tumor segmentation remains challenging due to limited annotated data, heterogeneous imaging phenotypes, diffuse tumor boundaries, and class imbalance across tumor subregions. Here, we present a two-stage deep learning framework for improving multi-modal pediatric brain MRI segmentation and clinical interpretation. First, we evaluate 3D Res U-Net and Swin-UNETR baselines on BraTS-PEDs MRI scans, using four co-registered modalities to predict tumor core, whole tumor, and enhancing tumor regions. Second, we introduce diffusion-based refinement models conditioned on coarse Swin-UNETR predictions, including a 3D DDPM refiner and MedSegDiff. Conditioning substantially improves diffusion stability and performance, particularly for enhancing tumor boundary segmentation. Conditioned MedSegDiff achieves the strongest boundary agreement with the lowest HD95. Finally, predicted tumor volumes and representative segmentation overlays are integrated with a multimodal language model to generate structured radiology-style reports. Together, our results suggest that coarse-to-refined diffusion segmentation can improve pediatric tumor boundary delineation and support end-to-end interpretable AI-assisted neuro-oncology workflows.

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

PointDiffusion: Diffusion-Based Scene Completion in the Point Cloud Domain

Reconstructing dense 3D scenes from sparse LiDAR point clouds is a fundamental challenge in autonomous driving, where latent diffusion models offer a promising solution. However, existing approaches rely on object-level autoencoders that collapse into unstable global representations at outdoor scale and suffer from ground truth data corrupted by odometry drift that systematically degrades supervision quality. Furthermore, multi-step diffusion inference incurs prohibitive latency for real-time deployment. We propose a novel multi-token Gaussian VAE with cross-attention pooling for stable scene-scale LiDAR compression, combined with an anchor-based ICP ground truth refinement pipeline that eliminates drift-induced noise from training supervision. Together, these components enable a scaffold-free single-step diffusion completion model that achieves an approximately 16x reduction in squared Chamfer distance on SemanticKITTI seq. 08 (0.396 m^2 to 0.024 m^2), surpasses LiDiff and ScoreLiDAR by 17-19% and 10-11%, respectively, and operates at 25-143x lower inference latency. Our results demonstrate that data quality dominates model design in this regime and that multi-token latent spaces provide a stable first stage for latent diffusion-based scene completion.

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

Learning Variable-Length Tokenization for Generative Recommendation

arXiv:2605.17779v2 Announce Type: replace Abstract: Generative recommendation reformulates recommendation as next-token prediction over discrete semantic identifiers (IDs). A fundamental yet unexplored design choice is that existing methods employ fixed-length tokenization for all items, implicitly assuming uniform encoding capacity regardless of item characteristics. Through systematic experiments across four datasets, we discover the Popularity-Length Paradox: popular items achieve optimal performance with short IDs, while tail items require substantially longer codes to capture discriminative semantics. This reveals a critical mismatch where popular items benefit from abundant collaborative signals and require minimal semantic detail, whereas tail items must rely on fine-grained content features due to sparse interaction data. To address this, we propose VarLenRec, a framework for learning variable-length tokenization. We develop Popularity-Weighted Information Budget Allocation (PIBA), an information-theoretic framework proving that optimal ID length should scale as a negative power of popularity. Directly implementing variable-length allocation faces two technical challenges: standard Euclidean residual quantization lacks geometric capacity to support diverse code lengths without distortion, and discrete length decisions are non-differentiable. We address these through Hyperbolic Residual Quantization, which leverages the exponential volume growth of the Poincaré ball to naturally stratify encoding capacity, and a Soft Length Controller, which enables differentiable length prediction via continuous layer retention probabilities regularized by PIBA-derived priors. Extensive experiments demonstrate that VarLenRec achieves significant improvements over state-of-the-art methods in recommendation accuracy and training/inference efficiency, revealing the importance of adaptive encoding capacity in generative recommendation.

07.
arXiv (quant-ph) 2026-06-19

Subsystem Quantum Error Correction for Noisy Quantum Metrology

arXiv:2606.19628v1 Announce Type: new Abstract: Quantum error correction has been successfully applied to enhance the precision of parameter estimation in the presence of noise. Nonetheless, existing methods require a number of noiseless, controllable ancillae and lack efficient encoding and decoding procedures. In this Letter, we demonstrate that subsystem error correction provides a new direction that can substantially simplify the metrological protocol. We derive general conditions under which subsystem stabilizer codes achieve the Heisenberg limit and show that, for broad classes of noise, this can be realized by syndrome-free protocols using at most a single ancilla qubit. Furthermore, we extend this framework to dynamical error correction and show that Floquet codes can protect time-dependent metrological signals in reaching the Heisenberg limit.

08.
medRxiv (Medicine) 2026-06-23

A pharmacometric grey zone reconciles high metronidazole resistance rates with bismuth quadruple therapy efficacy in Helicobacter pylori

Summary Background Metronidazole (MET) resistance in Helicobacter pylori (H. pylori) exceeds 50-60% globally, yet MET-containing bismuth quadruple therapy (BQT) achieves &gt90% eradication in MET-resistant infections. We hypothesise this discordance stems from a structural limitation of two-fold dilution: a pharmacometric grey zone between the 128 and 256 &microg/mL breakpoints where treatable isolates are systematically misclassified as high-level resistance. Methods In a real-world cohort of 4610 treatment-na&iumlve children (2019-2024), checkerboard assays determined the bismuth-MET synergy factor (SF). Population PK/PD modelling simulated gastric MET exposure (AUC

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

SAGE: Scalable AI Governance & Evaluation

arXiv:2602.07840v4 Announce Type: replace-cross Abstract: Evaluating relevance in large-scale search systems is fundamentally constrained by the governance gap between nuanced, resource-constrained human oversight and the high-throughput requirements of production systems. While traditional approaches rely on engagement proxies or sparse manual review, these methods often fail to capture the full scope of high-impact relevance failures. We present SAGE (Scalable AI Governance \& Evaluation), a framework that operationalizes high-quality human product judgment as a scalable evaluation signal. At the core of SAGE is a bidirectional calibration loop where natural-language Policy, curated Precedent, and an LLM Surrogate Judge co-evolve. SAGE systematically resolves semantic ambiguities and misalignments, transforming subjective relevance judgment into an executable, multi-dimensional rubric with near human-level agreement. To bridge the gap between frontier model reasoning and industrial-scale inference, we apply teacher-student distillation to transfer high-fidelity judgments into compact student surrogates at 92$\times$ lower cost. Deployed within LinkedIn Search ecosystems, SAGE guided model iteration through simulation-driven development, distilling policy-aligned models for online serving and enabling rapid offline evaluation. In production, it powered policy oversight that measured ramped model variants and detected regressions invisible to engagement metrics. Collectively, these drove a 0.25\% lift in LinkedIn daily active users.

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

Beyond the Blood Draw: Explainable Machine Learning for Non-Invasive Dysglycemia Risk Screening

arXiv:2606.16056v1 Announce Type: new Abstract: Dysglycemia, encompassing both prediabetes and diabetes, affects huge numbers of adults worldwide, yet many of them remain undiagnosed. We developed and validated machine-learning (ML) models for non-invasive screening of dysglycemia risk that require no laboratory tests. Pooling data from the National Health and Nutrition Examination Survey (NHANES) 2017–2023 (n=14,352), we trained six ML models with stratified 5-fold cross-validation and compared them with two established clinical risk scores. LightGBM achieved the highest area under the receiver operating characteristic curve (AUC=0.820, 95% CI: 0.806–0.835), outperforming the Finnish Diabetes Risk Score (0.745) and American Diabetes Association Risk Test (0.783). SHAP analysis identified age, race/ethnicity, and waist-to-height ratio as the most influential predictors. Subgroup analyses confirmed consistent performance across demographic strata (AUC: 0.735–0.832). These results demonstrate the feasibility of explainable, laboratory-free dysglycemia screening for deployment in community settings and self-tracking health applications.

11.
medRxiv (Medicine) 2026-06-16

Fidelity-Derived Quantum Dissimilarity-Enhanced k-Nearest Neighbor Algorithm for Arterial Hypertension Prediction

We present a quantum-enhanced version of the classic k-Nearest Neighbors (kNN) classification algorithm, applied to the prediction of arterial hypertension. The traditional Euclidean distance metric of the kNN algorithm is replaced with a Fidelity-derived quantum dissimilarity measure to evaluate the similarity between data samples. We map classical real-world clinical and ECG-derived data features into quantum states via the Dense-Angle Encoding, which efficiently utilizes parameterized rotation gates to pack multiple features into minimal qubits while maintaining pure states. We evaluate the performance of the dissimilarity measure using both the noiseless state vector Simulator and the IBM Qiskit Estimator primitives. The quantum circuit demonstrates robust predictive capabilities comparable to the classical model. While it does not claim computational supremacy over the classical baseline, the framework proves that fidelity-based similarity is a physically meaningful and efficient approach for hybrid quantum classical classification.

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

Out-of-Distribution (OOD) Detectors for Open-Set RF Fingerprinting

arXiv:2606.12718v1 Announce Type: new Abstract: Radio-frequency (RF) fingerprinting systems must operate in open-world environments where signals from unknown transmitters and temporal drift introduce distribution shift at test time. Out-of-distribution (OOD) detection provides a natural framework for this problem, yet its application to RF fingerprinting (RFF) remains limited. A key barrier to their adoption is that most OOD detectors require auxiliary OOD data for parameter tuning, an assumption that is difficult to satisfy in RF environments where representative OOD data is impractical to collect. In this work, we introduce a promising set of OOD detection methods from the machine learning literature to open-set RFF domain. We present these methods within a unified mathematical framework based on information theory, which is a natural framework for communication systems. Our framework allows for the systematic analysis of methods and development of new methods. We further demonstrate the applicability of recent work on tuning OOD detectors without given OOD tuning data for open-set RFF. We evaluate on the POWDER RF fingerprinting dataset, showing that detectors tuned without any given OOD data achieve performance comparable to baselines with access to true OOD tuning data and greatly out-perform baseline approaches without access to true OOD tuning data, showcasing the practical viability for the RFF problem.

13.
arXiv (quant-ph) 2026-06-16

Intermodal entanglement in a quantum optical model of HHG due to the back-action on the driving field

arXiv:2603.01315v2 Announce Type: replace Abstract: Preparation of nonclassical light with special quantum properties is essential for quantum technologies. High-harmonic generation (HHG) is a process which not only enables the creation of attosecond pulses but also has the potential to generate light with intricate quantum properties. In a recent experiment [1], nonclassical inter-harmonic correlations have been measured from a HHG source. In this work, we theoretically investigate entanglement between different harmonics within an effective quantum optical model. This model implements a signifcant degree of simplifcation regarding the processes within the target material, treating the material through susceptibilities, as it is usual in quantum optics. Such an approach yields a general description of HHG, permitting the implications that can be derived within it to hold broadly. We find that entanglement is produced as a result of the often neglected back-action. We can qualitatively reproduce experimentally measured nonclassicalities, which suggests that intermodal entanglement can, to an extent, be considered a universal phenomenon associated with HHG, rather than a result of using specific material targets.

14.
arXiv (CS.CV) 2026-06-15

Representation Forcing for Bottleneck-Free Unified Multimodal Models

Unified multimodal models (UMMs) aim to handle perception and generation in a single model. Yet existing UMMs still rely on a frozen, separately pretrained VAE for image generation, imposing a structural bottleneck. Naively removing it introduces a quality gap, as the model must learn both high-level structure and low-level details from raw pixels. In this paper, we propose Representation Forcing (RF), a technique that closes this gap by making representation prediction a native capability of the model. Concretely, RF forces the decoder to autoregressively predict visual representations as intermediate tokens before pixels; these tokens then stay in context to guide pixel diffusion within the same backbone. By turning representations from perception outputs into generation targets, RF eliminates the need for any external generative latent space. We find that RF benefits both understanding and generation. On image generation, our pixel-space model with RF matches state-of-the-art VAE-based unified models. On image understanding, pixel-space RF generally outperforms its VAE-based variant. Together, these results offer an effective step toward end-to-end, bottleneck-free UMMs.

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

Semantic Robustness Certification for Vision-Language Models

Vision-language models (VLMs) are now widely used in downstream tasks. However, real-world applications often expose VLMs to distribution shifts induced by semantic variation (e.g., shape, size, and style). Robustness certification determines if a model's prediction changes when transformations are applied to its input. While most certification frameworks study geometric or pixel-level transformations over inputs, this work proposes a novel framework that enables certifying VLM robustness under semantic-level transformations. Leveraging the open-vocabulary capability of VLMs, we use text prompts as semantic proxies to construct transformations parameterized by an extent that controls the degree of semantic variation. By characterizing the VLM decision boundary in closed form, our framework quantitatively certifies extent intervals for which the predicted class remains unchanged under the semantic transformation. Our framework is the first to certify VLM robustness under semantic-level variations without requiring additional data for each variation, making it practical to apply. Experiments on both synthetic and real-world data show that our framework enables certifying robustness under diverse semantic variations across scenarios.

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

Semantic-Anchored Evidential Fusion for Domain-Robust Whole-Slide Survival Analysis

arXiv:2606.19966v1 Announce Type: cross Abstract: Whole-slide images (WSIs) are widely used for computational cancer prognosis. However, most existing methods primarily focus on in-domain performance and fail to generalize across clinical centers. This limitation stems from their reliance on pixel-derived representations that are highly susceptible to domain-specific artifacts caused by staining protocols and scanner hardware. We hypothesize that high-level pathology semantics, such as tumor grade and micro-environmental architecture, provide a domain-invariant semantic representation that mirrors the robust diagnostic logic of human pathologists. Therefore, we propose a Semantic-Anchored Evidential Fusion Survival (SAEFS) framework, where SAEFS derives semantic anchors from WSIs via Visual Question Answering (VQA), employs a dual-stream WSI evidence extraction architecture, uses Dirichlet-based Subjective Logic to model uncertainty, and fuses semantic and visual evidence through a cautious conjunction rule to avoid overconfident fusion from correlated sources. Trained exclusively on one source domain and evaluated zero-shot across four unseen domains, SAEFS consistently outperforms state-of-the-art models both in prediction accuracy and reliability, improving the average C-index by 10.2%. Quantitative analyses further show that VQA-derived semantic features exhibit significantly lower cross-center divergence than pixel-derived features, highlighting their robustness for cross-center clinical applications.

17.
bioRxiv (Bioinfo) 2026-06-12

Systematic functional annotation of thousands of BAHD acyltransferases in plant genomes using Protein Language Model and phylogenomic tools

The functional annotation of plant genes lags significantly behind their genomic annotation. Closing this gap requires thorough cataloging of reported protein activities alongside predictive methods that scale beyond sequence-similarity inference. Focusing on the BAHD acyltransferase enzyme family as a model, we assembled FuncZymeDB-BAHD, a large database of 2,705 LLM-retrieved and curated enzyme-acceptor-donor activities covering 336 BAHDs from 156 plant species, a 2-to-6-fold expansion over Swiss-Prot and prior compilations. We further developed FuncPred-OG, which maps queries to orthologous groups and previously characterized enzymes in FuncZymeDB-BAHD, returning hits with high evidence provenance. FuncPred-OG enabled functional prediction of over half of BAHDs across 85 plant proteomes, of which five novel predictions were validated via in vitro assays and recent studies. For the remaining BAHDs without FuncPred-OG annotation, we developed FuncPred-AI, where logistic-regression classifiers trained on protein language model embeddings achieved high Area-Under-the-Precision-Recall-curve (AUPR) scores and correct-hit rates up to 93%. FuncPred-AI yielded >1 probable donor/acceptor annotation for 99.9% (8894/8897) of BAHDs in our pan-plant dataset. Finally, the FuncPred workflow and datasets were deployed on a web portal for broader utilization, potentially reducing experimentalist efforts for selecting candidates from days to minutes. Overall, this framework provides a generalizable template for functional annotation of entire enzyme families.

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

PaLMR: Towards Faithful Visual Reasoning via Multimodal Process Alignment

Reinforcement learning has recently improved the reasoning ability of Large Language Models and Multimodal LLMs, yet prevailing reward designs emphasise final-answer correctness and consequently tolerate process hallucinations–cases where models reach the right answer while misperceiving visual evidence. We address this process-level misalignment with PaLMR, a framework that aligns not only outcomes but also the reasoning process itself. PaLMR comprises two complementary components: a perception-aligned data layer that constructs process-aware reasoning data with structured pseudo-ground-truths and verifiable visual facts, and a process-aligned optimisation layer that constructs a hierarchical reward fusion scheme with a process-aware scoring function to encourage visually faithful chains-of-thought and improve training stability. Experiments on Qwen2.5-VL-7B show that our approach substantially reduces reasoning hallucinations and improves visual reasoning fidelity, achieving state-of-the-art results on HallusionBench while maintaining strong performance on MMMU, MathVista, and MathVerse. These findings indicate that PaLMR offers a principled and practical route to process-aligned multimodal reasoning, advancing the reliability and interpretability of MLLMs.

19.
arXiv (quant-ph) 2026-06-12

Toward quantum-noise-limited interferometric measurements of optical nonlinearity in vacuum

arXiv:2602.10896v2 Announce Type: replace-cross Abstract: Quantum Electrodynamics predicts that the vacuum must behave as a nonlinear optical medium: the vacuum optical index should increase when it is stressed by intense electromagnetic fields. The DeLLight (Deflection of Light by Light) project aims to measure it by using intense and ultra-short laser pulses. The experiment uses a Sagnac interferometer to amplify the tiny deflection signal of a low-intensity probe pulse crossing the vacuum refractive-index gradient produced by an external high-intensity pump pulse. The measurement of the amplified signal by a CCD camera requires a high spatial resolution, which is limited by the ultimate quantum noise of the CCD. However, interferometric phase noise induced by the mechanical vibrations of the interferometer is also amplified and degrades spatial resolution. To overcome this, we propose a new method named High-Frequency Phase Noise Suppression (HFPNS), based on the addition of a delayed replica (5 ns) of the probe pulse. The delayed pulse, which is not affected by the pump but is subject to the same vibration noise, enables offline subtraction of correlated phase noise. In this work, we present an experimental proof-of-concept on a prototype interferometer operating with a limited amplification factor ($\mathcal{A}\simeq25$), about 10 times smaller than the required value of the final experiment. We have succeeded in reducing phase noise by a factor of 40, resulting in a residual noise level 2.3 times higher than the expected quantum noise. The residual noise is linked to delay-line instabilities and incident beam pointing fluctuations present during these tests. This result validates HFPNS as a robust method for future quantum-noise-limited interferometric measurements of vacuum optical nonlinearity, though additional stabilization and higher interferometric amplification are still needed.

20.
arXiv (CS.AI) 2026-06-16

Where Did It Go Wrong? Process-Level Evaluation of Web Agents with Semantic State Tracking

arXiv:2606.15673v1 Announce Type: new Abstract: Web agents act through long interaction sequences, yet existing benchmarks evaluate only terminal success, discarding all process information and offering little guidance on improvement. In this work, we conduct a process-level analysis of web agents. We introduce WebStep, a benchmark of 1,800 task instances with controlled difficulty and automatic semantic state tracking. Each website exposes a deterministic semantic MDP alongside the GUI: the agent operates on the interface, while the environment records high-level states and transitions in the background, enabling fine-grained analysis without manual annotation. Based on the semantic trajectory, we first show that process metrics reveal differences invisible to outcome evaluation: three agents whose success rates cluster within 31-33% diverge in exploration reach versus execution accuracy. Then, decomposing by skill characterizes the nature of these differences, exposing opposite per-skill rankings hidden within the same website: e.g., on Housing, OpenAI CUA outperforms Qwen3.5 by 23.7% on commit actions yet underperforms it by 15.6% on filtering, pinpointing a concrete skill to improve even within a domain. Bifurcation analysis further localizes the decisive error that loses the task and shows that this error is agent-specific rather than shared. Finally, these differences widen as tasks grow harder: success rate is similar on easy tasks but separates sharply as exploration becomes more demanding. Our process-level analysis opens a new avenue in web agent evaluation, providing fine-grained and actionable insight into where and how each agent should be improved.

21.
bioRxiv (Bioinfo) 2026-06-11

STITCH links cellular morphology and gene expression in spatial transcriptomics

In situ spatial (ISS) sequencing can uncover co-variation between cellular morphology and gene expression in vivo. However, a principled and interpretable mathematical representation of morphology has not yet been applied in this context. In particular, current deep learning-based representations of cell images confound a cell's shape with its size. We present an interpretable representation of cellular boundary contours, based on tangent principal component analysis (TPCA) in a Kendall shape manifold, that captures size-independent contour shape features. This approach successfully recovers shape-perturbing genes in an RNAi screen than a previous metric geometry-based approach. We build on TPCA to develop STITCH (Shape-TranscriptomIc Correlation and Harmonization), an approach to reveal covariation between cell morphology with gene expression in ISS datasets. In a Xenium dataset, STITCH outperforms a deep learning-based approach in both recovering the layered organization of keratinocytes and a spatial gradient in nuclear eccentricity. Across samples in a melanoma CosMx dataset, STITCH reproducibly associates elongated and triangular fibroblasts with proximity to malignant cells and myofibroblast-like transcriptional program. Finally, STITCH independently recovers a known link between mesenchymal-like malignant cell states and increased cell area in two melanoma cohorts. STITCH can thus yield interpretable morphology-transcriptome relationships across cell types, patients, and spatial transcriptomics platforms.

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

Hilbert-Geo: Solving Solid Geometric Problems by Neural-Symbolic Reasoning

Geometric problem solving, as a typical multimodal reasoning problem, has attracted much attention and made great progress recently, however most of works focus on plane geometry while usually fail in solid geometry due to 3D spatial diagrams and complex reasoning. To bridge this gap, we introduce Hilbert-Geo, the first unified formal language framework for solid geometry, including an extensive predicate library and a dedicated theorem bank. Based on this framework, we propose a Parse2Reason method containing two steps of first parsing then reasoning. In the parsing step, we utilize conditional description language (CDL), a formalized language composed of predicates specifically designed to construct geometric conditions, to represent both problem description (natural text) and solid diagrams (visual image). In the reasoning step, we leverage those formal CDL and the theorem bank to perform relational inference and algebraic computation, generating strictly correct, verifiable, and human-readable reasoning processes. Notably, our proposed Hilbert-Geo is also applicable to plane geometry. To advance geometric reasoning, we curate two expert-annotated dataset SolidFGeo2k and PlaneFGeo3k, which are furnished with geometric formal language annotations, solutions and answers. Extensive experiments show that our proposed method achieves the state-of-the-art (SOTA) performance 77.3% in SolidFGeo2k and 84.1% in MathVerse-Solid (one small subset in MathVerse dedicated to solid geometry), substantially outperforming leading MLLMs, such as Gemini-2.5-pro (54.2% on SolidFGeo2k) and GPT-5 (62.9% on MathVerse-Solid). In addition, our method achieves the SOTA accuracy 80.2% in PlaneFGeo3k, demonstrating the generality of the Hilbert-Geo in geometric reasoning. Our code and datasets are released at https://github.com/PremiLab-Math/Hilbert-Geo.

23.
arXiv (CS.CV) 2026-06-17

R1-SyntheticVL: Is Synthetic Data from Generative Models Ready for Multimodal Large Language Model?

In this work, we aim to develop effective data synthesis techniques that autonomously synthesize multimodal training data for enhancing MLLMs in solving complex real-world tasks. To this end, we propose Collective Adversarial Data Synthesis (CADS), a novel and general approach to synthesize high-quality, diverse and challenging multimodal data for MLLMs. The core idea of CADS is to leverage collective intelligence to ensure high-quality and diverse generation, while exploring adversarial learning to synthesize challenging samples for effectively driving model improvement. Specifically, CADS operates with two cyclic phases, i.e., Collective Adversarial Data Generation (CAD-Generate) and Collective Adversarial Data Judgment (CAD-Judge). CAD-Generate leverages collective knowledge to jointly generate new and diverse multimodal data, while CAD-Judge collaboratively assesses the quality of synthesized data. In addition, CADS introduces an Adversarial Context Optimization mechanism to optimize the generation context to encourage challenging and high-value data generation. With CADS, we construct MMSynthetic-20K and train our model R1-SyntheticVL, which demonstrates superior performance on various benchmarks.

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

Honeypot Protocol

作者:

arXiv:2604.13301v1 Announce Type: cross Abstract: Trusted monitoring, the standard defense in AI control, is vulnerable to adaptive attacks, collusion, and strategic attack selection. All of these exploit the fact that monitoring is passive: it observes model behavior but never probes whether the model would behave differently under different perceived conditions. We introduce the honeypot protocol, which tests for context-dependent behavior by varying only the system prompt across three conditions (evaluation, synthetic deployment, explicit no-monitoring) while holding the task, environment, and scoring identical. We evaluate Claude Opus 4.6 in BashArena across all three conditions in both honest and attack modes. The model achieved 100% main task success and triggered zero side tasks uniformly across conditions, providing a baseline for future comparisons with stronger attack policies and additional models.

25.
arXiv (CS.LG) 2026-06-15

Zero-shot generalization of transformer neural operators to larger domains

arXiv:2606.14597v1 Announce Type: new Abstract: Transformer-based neural operators have shown remarkable performance for approximating solution operators of partial differential equations on complex geometries. However, existing approaches implicitly assume a fixed domain size, which limits their ability to generalize at inference. In this work, we investigate domain extension, namely zero-shot inference on spatial domains that are significantly larger than those encountered during training. We argue that this setting fundamentally requires spatial locality and translation equivariance. We propose to implement this locality via a decomposable bias in the attention logits computation, enabling finely controllable locality while remaining fully decomposable into query-key inner products and directly compatible with optimized attention kernels. Combined with rotary positional embeddings, it enables expressive embeddings with controllable spatial support without altering the transformer architecture. We empirically show that our approach substantially improves zero-shot generalization to larger domains across two PDE benchmarks and a 3D industrial atmospheric flow application. Our code and datasets are available at https://github.com/cerea-daml/domain-extension.