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02.
arXiv (quant-ph) 2026-06-24

Resource theory of interactive quantum instruments

作者:
Chung-Yun Hsieh↗Armin Tavakoli↗Huan-Yu Ku↗Paul Skrzypczyk↗

arXiv:2603.27676v2 Announce Type: replace Abstract: Quantum instruments describe both the classical outcome and the updated quantum state in a measurement process. To do this in a non-trivial way, instruments must have the capability to interact coherently with the state that they measure. Here, we develop a resource theory for instruments. We consider a relevant quantifier of the separation between interactive and non-interactive instruments and show that it admits three distinct operational interpretations in terms of quantum information tasks. These concern (i) the preservation of maximally entangled states after a local measurement, (ii) the average ability to preserve random states after measurement, and (iii) the ability to recover the classical information generated from measuring half of a maximally entangled state. We also introduce a natural set of allowed operations and show that the third task fully characterises the resource content of instruments. Our general framework reproduces as special cases established resource theories for channels and measurements.

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

A Study of Belief Revision Postulates in Multi-Agent Systems (Extended Version)

作者:
Michael Thielscher↗Tran Cao Son↗

arXiv:2605.02249v2 Announce Type: replace Abstract: We investigate the belief revision problem in epistemic planning, i.e., what will be the beliefs of all agents in a multi-agent system after an agent gains the belief in some state property. Based on the standard representation in epistemic planning of agents' beliefs via a single multi-agent Kripke model, we generalize the classical AGM belief revision postulates to the multi-agent setting, with the aim to provide a formal framework for evaluating dynamic epistemic reasoning frameworks in which the beliefs of all agents as the result of actions are computed. As an example of a simple operator that satisfies all of the generalized AGM postulates, we present generalized full-meet multi-agent belief revision. We moreover define a generalization of the standard postulates for iterated revision, present a more sophisticated, event model based revision operator, and discuss the potential issues in defining an epistemic operator on Kripke models that can satisfy all of the generalized postulates for iterated multi-agent belief revision.

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04.
arXiv (CS.AI) 2026-06-17

LongWebBench: Evaluating Structural and Functional Webpage Generation in Long-Horizon Settings

作者:
Yi Zhao↗Zhen Yang↗Mengpan Chen↗Mingde Xu↗Shanghui Gong↗Xijun Liu↗Jibing Gong↗Jie Tang↗

arXiv:2606.17727v1 Announce Type: new Abstract: Recent vision-language models (VLMs) have shown promising progress in generating webpages from visual inputs, yet existing evaluations mainly focus on short, single-screen, and largely static webpages. We introduce LongWebBench, a benchmark for evaluating long-horizon webpage generation from both structural and functional perspectives. LongWebBench contains 490 real-world long webpages for structural fidelity evaluation and 507 goal-oriented interaction tasks over 129 webpages for functional evaluation. It employs two complementary protocols: a multi-dimensional VLM-based metric for assessing long-range structural coherence, and a DOM-augmented agent-based pipeline for end-to-end functional verification. We further examine the automatic evaluation protocols through human agreement analysis. Experiments with state-of-the-art open-source and proprietary VLMs under single-image and multi-image settings reveal that structural fidelity degrades as webpage length increases, while visually plausible generations often fail to support executable multi-step interactions. These results highlight the need to evaluate long webpage generation beyond visual similarity, with executable interaction as a core criterion. Our code and data are available at https://github.com/zheny2751-dotcom/LongWebBench.

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05.
arXiv (CS.CV) 2026-06-18

Confidence is Not Reliability: Rethinking MC Dropout in Brain Tumour Segmentation

作者:
Xin Ci Wong↗Duygu Sarikaya↗Kieran Zucker↗Marc De Kamps↗Nishant Ravikumar↗

Glioma segmentation in multiparametric MRI is a critical component of treatment planning. A segmentation model that fails silently on treatment-critical sub-regions represents a patient safety risk that overlap-based metrics such as Dice scores cannot expose. We ask whether voxel-level uncertainty estimation via Monte Carlo (MC) Dropout can reliably identify segmentation errors in clinically critical sub-regions, and whether calibration failure modes are detectable from standard reporting metrics alone. In an empirical two-model case study on 126 BraTS21 patients, we evaluate a high-performance pretrained SegResNet and a locally trained UNet with residual units (UNet-Res). MC dropout preserved segmentation accuracy ($|\Delta Dice|$ $

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

Shift-and-Sum Quantization for Visual Autoregressive Models

作者:
Jaehyeon Moon↗Bumsub Ham↗

Post-training quantization (PTQ) enables efficient deployment of deep networks using a small set of data. Its application to visual autoregressive models (VAR), however, remains relatively unexplored. We identify two key challenges for applying PTQ to VAR: (i) large reconstruction errors in attention-value products, especially at coarse scales where high attention scores occur more frequently; and (ii) a discrepancy between the sampling frequencies of codebook entries and their predicted probabilities due to limited calibration data. To address these challenges, we propose a PTQ framework tailored for VAR. First, we introduce a shift-and-sum quantization method that reduces reconstruction errors by aggregating quantized results from symmetrically shifted duplicates of value tokens. Second, we present a resampling strategy for calibration data that aligns sampling frequencies of codebook entries with their predicted probabilities. Experiments on class-conditional image generation, inpainting, outpainting, and class-conditional editing show consistent improvements across VAR architectures, establishing a new state of the art in PTQ for VAR.

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

Descriptive versus Regulatory Uncertainty in Bounded Predictive Systems

作者:
Ahmed Gamal Eldin↗

arXiv:2605.18909v2 Announce Type: replace Abstract: Any system that models the world under finite representational capacity must compress; any compression entails a prior; and the prior is the system's bias. What has not been established is whether uncertainty participates in the dynamics governing future behavior, or merely describes the output distribution without consequence. We introduce a structural distinction between descriptive uncertainty, which does not recursively modulate the system's policy, and regulatory uncertainty, which directly enters the optimization landscape and drives persistent adaptive restructuring. We prove formally that current transformer architectures are confined to descriptive uncertainty at inference. We ground this in thermodynamics via Landauer's principle: for uncertainty to be regulatory, epistemic error must cost real energy; in a decoupled system, hallucinations and correct derivations dissipate identical energy. We test this empirically across three locally-deployed language models (3B, 8B, 70B parameters). Token-level Shannon entropy is statistically invariant across tasks spanning pattern retrieval, causal operator application, and out-of-distribution causal generalization in all three models (all pairwise p >= 0.568; within-model ranges 0.011-0.028 nats), while task accuracy varies substantially across the same conditions (0%-100%). Entropy and accuracy are orthogonal. The decoupling is scale-invariant: larger models achieve higher accuracy but identical entropy flatness. This structural incapacity is not resolvable by additional parameters or training data. Genuine epistemic grounding requires physical coupling between thermodynamic substrate state and information processing cost.

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08.
arXiv (CS.AI) 2026-06-24

OrbitForge: Text-to-3D Scene Generation via Reconstruction-Anchored Video Synthesis

作者:
Chenrui Fan↗Paolo Favaro↗

arXiv:2606.24799v1 Announce Type: cross Abstract: Generic text-to-video models can be used as rich open-world scene priors. Despite the high quality of today's generated videos, they do not directly yield reliable 3D assets: camera motion is difficult to control, view coverage is partial, and frames often contain inconsistencies across time. We introduce OrbitForge, an adapter built from frozen video priors and per-prompt Gaussian Splatting reconstruction optimization that converts a single text-generated video into a canonical closed-orbit 3D Gaussian Splatting scene. We use 3D reconstruction as an anchor to improve the 3D consistency of the generated video. We obtain a preliminary 3D reconstruction from a first generated video via Deformable Gaussian Splatting with a robust MedianGS proxy. We render views from a prescribed orbit to detect missing viewpoints. OrbitForge uses the text-to-video model to complete only the missing views, and reconstructs the completed orbit into a final Gaussian Splatting scene. This design requires no task-specific video or multiview fine-tuning, avoids per-prompt score-distillation optimization, and does not progressively generate views one step at a time. We further argue that this setting demands coverage-aware evaluation: local smoothness alone rewards methods that never attempt a full orbit. On a frozen 300-prompt T3Bench-derived audit, OrbitForge reconstruction attains a 359.0-degree measured median span, raises originally unsupported-bin Q10 ImageReward from 8.07 to 16.36 relative to MedianGS-only reconstruction, while remaining competitive with VideoMV on the coverage-quality.

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09.
arXiv (CS.LG) 2026-06-16

Brownian Kernel Ladders

作者:
Mahdi Mohammadigohari↗Giuseppe Di Fatta↗Giuseppe Nicosia↗Panos M Pardalos↗

arXiv:2606.15812v1 Announce Type: new Abstract: Constructing mathematically tractable function spaces that capture hierarchical compositional representations remains a central challenge in statistical learning theory. We introduce Brownian kernel ladders (BKLs), a recursively defined hierarchy of integral reproducing kernel Hilbert spaces generated through Brownian-kernel integral constructions. Starting from linear functionals, each layer is obtained by integrating Brownian kernels over probability measures supported on subsets of the previous layer, yielding a recursive function-space model in which depth is encoded directly through the hierarchy. Based on this framework, we define canonical BKL spaces together with an associated complexity functional. We establish several analytical and statistical properties of these spaces. In particular, we show that BKL spaces form quasi-Banach spaces, satisfy depth-dependent Hölder regularity estimates, and exhibit strict monotonicity with respect to depth. We further prove existence results for regularized empirical risk minimization and derive Gaussian complexity bounds that remain uniformly controlled with respect to both the ambient dimension and the hierarchy depth. A key ingredient of the analysis is a combinatorial proof technique based on recursive subset decompositions and Brownian-kernel threshold representations. These estimates yield excess-risk guarantees of near-parametric order for regularized empirical risk minimization over BKL spaces. Our results provide a mathematically tractable hierarchical function-space framework for studying compositional representations in deep learning.

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10.
arXiv (quant-ph) 2026-06-24

Rotational Vacuum Friction of Nonabsorbing Particles

作者:
F. Javier Garc\'ia de Abajo↗Alejandro Manjavacas↗

arXiv:2606.24723v1 Announce Type: new Abstract: A nonabsorbing particle rotating in vacuum can lose angular momentum only by converting mechanical energy into electromagnetic radiation. Here, we develop a quantum theory of rotational vacuum friction for small lossless particles and show that axial symmetry qualitatively changes the leading dissipation channel. At zero temperature, the frictional torque scales as $M\propto\Omega^7$ with rotation frequency $\ Omega$ in anisotropic particles due to the emission of correlated photon pairs whose frequencies sum to $2\Omega$, while a contribution to the torque linear in $\ Omega$ is found at finite temperature. In contrast, axisymmetric particles are protected against photon-assisted friction regardless of temperature.

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

PhysDrift: Bridging the Embodiment Gap in Humanoid Co-Speech Motion Generation

作者:
Zhangzhao Liang↗Xiaofen Xing↗Mingyue Yang↗Wenlve Zhou↗Xiangmin Xu↗

arXiv:2606.19935v1 Announce Type: new Abstract: Humanoid robots require co-speech motions that are not only expressive and speech-aligned, but also physically executable under embodiment constraints. Existing co-speech generation pipelines are predominantly human-centric: motions are first generated in human-body representations such as SMPL-X and subsequently retargeted to humanoid robots. In this work, we identify a fundamental embodiment gap in this paradigm, where the mismatch between human motion manifolds and humanoid embodiment constraints disrupts embodiment consistency during motion transfer and physical execution. Through extensive analysis, we show that although retargeting can preserve coarse motion semantics, it significantly compresses motion diversity and weakens prosody-motion synchronization, limiting expressive humanoid behaviors. To address this problem, we first propose IK-EER, a prosody-preserving humanoid motion curation framework that jointly optimizes kinematic feasibility and speech-motion temporal alignment during retargeting. Building upon the curated robot-native motion dataset, we further introduce PhysDrift, an embodiment-aware co-speech motion generation framework that directly predicts executable humanoid joint trajectories from speech without relying on intermediate human-body representations. Unlike conventional human-centric pipelines, PhysDrift maintains embodiment consistency throughout both training and inference while incorporating physical regularization to stabilize robot motion dynamics. Extensive experiments and real-world humanoid deployment demonstrate that embodiment-aware robot-native generation substantially improves speech-motion alignment, physical plausibility, motion smoothness, inference efficiency, and real-time interaction capability.

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13.
arXiv (math.PR) 2026-06-17

Time-dependent averages of a critical long-range stochastic heat equation

作者:
Sefika Kuzgun↗Ran Tao↗

arXiv:2411.09058v2 Announce Type: replace Abstract: We study the time-dependent spatial averages of a critical stochastic partial differential equation, namely the stochastic heat equation in dimension $d\geq 3$ with noise white in time and colored in space with covariance kernel $\|\cdot\|^{-2}$. The solution to this SPDE is a singular measure and was constructed by Mueller and Tribe in [MT04]. We show that the time-dependent spatial averages of this SPDE over a ball of radius $R$ at time $t$ have different limits under different space-time scales. In particular, when $t\ll R^2$, the central limit theorem holds; when $t=R^2$, the spatial average is a non-Gaussian random variable; when $t\gg R^2$, the spatial average becomes extinct.

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

When the Past Matters: FlashBack Memory for Precipitation Nowcasting

作者:
Yuhao Du↗Boxiao Huang↗Chengrong Wu↗Jiankai Zhang↗

Accurate precipitation nowcasting is crucial for disaster mitigation and socio-economic planning, yet existing methods often struggle with false alarms, missed events, and long range dependency modeling at high spatiotemporal resolution. To address these challenges, we propose FlashBack Memory (FB), a module that dynamically retrieves key historical states and integrates them via an adaptive fusion gate, enhancing the spatiotemporal representation capability of recurrent-based models. We incorporate FB into PredRNN, PredRNNpp, MIM, MotionRNN, and PredRNN-V2, and evaluate on CIKM2017, Shanghai2020, and SEVIR datasets. Experimental results demonstrate that FB significantly improves MSE, MAE, SSIM, and CSI metrics, particularly for high-intensity rainfall and long-sequence predictions, while reducing false alarms and missed events and enhancing temporal consistency and spatial localization. The proposed method provides a general and efficient memory enhancement mechanism, improving the overall performance of recurrent-based precipitation nowcasting models.

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

RLPR: Radar-to-LiDAR Place Recognition via Two-Stage Asymmetric Cross-Modal Alignment for Autonomous Driving

作者:
Zhangshuo Qi↗Jingyi Xu↗Luqi Cheng↗Shichen Wen↗Guangming Xiong↗

All-weather autonomy is critical for autonomous driving, which necessitates reliable localization across diverse scenarios. While LiDAR place recognition is widely deployed for this task, its performance degrades in adverse weather. Conversely, radar-based methods, though weather-resilient, are hindered by the general unavailability of radar maps. To bridge this gap, radar-to-LiDAR place recognition, which localizes radar scans within existing LiDAR maps, has garnered increasing interest. However, extracting discriminative and generalizable features shared between modalities remains challenging, compounded by the scarcity of large-scale paired training data and the signal heterogeneity across radar types. In this work, we propose RLPR, a robust radar-to-LiDAR place recognition framework compatible with single-chip, scanning, and 4D radars. We first design a dual-stream network to extract structural features that abstract away from sensor-specific signal properties (e.g., Doppler or RCS). Subsequently, motivated by our task-specific asymmetry observation between radar and LiDAR, we introduce a two-stage asymmetric cross-modal alignment (TACMA) strategy, which leverages the pre-trained radar branch as a discriminative anchor to guide the alignment process. Experiments on four datasets demonstrate that RLPR achieves state-of-the-art recognition accuracy with strong zero-shot generalization capabilities.

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

Exact Schur-Sylvester Dimensionality Reductions for Non-Smooth Stochastic Complexity and Manifold Sampling

作者:
Trenton Lau↗Gary P. T. Choi↗

arXiv:2606.23867v1 Announce Type: new Abstract: The exact computation of the Normalized Maximum Likelihood (NML) codelength for regular non-smooth estimators (e.g., Lasso) has been historically limited by the cubic scaling walls of manifold-constrained projection and volume integration. At each step of the geometric Propose-and-Project Metropolis–Hastings (PPMH) sampler, evaluating the projection operator requires inverting an $(N+k) \times (N+k)$ generalized KKT matrix, while calculating the volume factor requires the determinant of an $(N-k) \times (N-k)$ Gram matrix. This paper presents an exact, mathematically equivalent formulation that bypasses both bottlenecks by utilizing the block Schur complement and Sylvester's determinant identity. We prove that the computational complexity of both operations collapses from $\mathcal{O}(N^3)$ to $\mathcal{O}(k^3 + N^2 k)$ per step. We generalize this reduction to Sparse Support Vector Machines (SVMs), Elastic Net, and Group Lasso. Finally, we provide a rigorous numerical stability analysis and evaluate the sampler's efficiency using the Effective Sample Size (ESS) per second. Our empirical benchmarks on high-dimensional datasets confirm a constant speedup exceeding $14{,}100\times$ while maintaining double-precision numerical equivalence, rendering exact non-smooth NML estimation highly tractable for large-scale statistical inference.

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17.
arXiv (CS.CV) 2026-06-24

DivRL: Disentangled Self-Similarity Rewards for Diverse Subject-Driven Generation

作者:
Qian Wang↗Zhenyu Li↗Abdelrahman Eldesokey↗Peter Wonka↗

Subject-driven image generation faces an "Identity-Diversity Paradox", where strong identity preservation often leads to rigid and low-diversity outputs. We propose a post-training framework called DivRL that jointly optimizes identity consistency and structural diversity simultaneously by leveraging disentangled visual features from a robust similarity model. Specifically, we introduce a Negative Self-Similarity Measure (nSSM) to quantify structural diversity, and Visual Semantic Matching (VSM) to evaluate identity consistency. We propose an "Explore-and-Suppress" strategy that treats VSM as a gated constraint: the model freely explores structurally diverse configurations, and only samples that violate the identity threshold are penalized via a quadratic hinge loss. This converts identity preservation from a competing objective into a feasibility constraint, allowing nSSM and VSM to improve jointly. Experiments demonstrate that our method effectively pushes the model to generate both consistent and diverse images and improves structural diversity while maintaining comparable identity consistency through a gated optimization formulation.

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

Non-Parametric Machine Text Detection via Multi-View Gaussian Processes

作者:
Aleem Khan↗Nicholas Andrews↗

Adversarial conditions such as paraphrasing and targeted style transfer sharply degrade the accuracy of machine text detectors. A document, however, carries multiple complementary signals (e.g., stylistic features, likelihood and rank-order features, and structural features), and an attack that suppresses one may leave others intact. While a parametric classifier can learn to combine these features given sufficient supervision, classifiers are prone to making confidently incorrect predictions when the distribution shifts (e.g., novel attacks or unseen language models). To address this, we propose a multi-view, non-parametric detection framework that extracts complementary feature views from the same document and aggregates per-view evidence through a Gaussian process ensemble. By aggregating evidence across views, an adversary must simultaneously defeat multiple independent axes of detection, substantially raising the cost of evasion. The Gaussian process formulation additionally provides calibrated probabilities and principled abstention on out-of-distribution inputs, supporting reliable deployment in high-stakes settings. We evaluate on three benchmarks spanning diverse generators and attacks: the DetectRL and RAID benchmarks, and the PAN2025 shared task and demonstrate that our multi-view detector maintains strong performance under the considered attacks, outperforming existing approaches against held out attacks.

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19.
arXiv (math.PR) 2026-06-16

Well-posedness of stochastic parabolic equations with gradient nonlinearities and applications to phase-field models

作者:
Amjad Saef↗

arXiv:2606.15425v1 Announce Type: new Abstract: We study well-posedness of stochastic parabolic equations with gradient nonlinearities. Our analysis is based on recent maximal-regularity frameworks for nonlinear stochastic parabolic equations in critical spaces. We extend the existing results by controlling drift and noise coefficient separately. This way we can allow for less regular driving noise in case of subcritical dispersion coefficients. Our approach, based on gluings of local solutions, moreover implies new continuation criteria. We then apply our existence result and the continuation criteria to show global well-posedness of phase-field models of moving boundary problems.

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20.
bioRxiv (Bioinfo) 2026-06-20

The recount3 Python package for programmatic access to uniformly processed RNA-seq data

作者:
Alsalihi↗Flight↗R. M↗Moseley↗H. N. B↗

The recount3 online resource provides tens of thousands of uniformly processed RNA-seq samples across human and mouse from major sequencing repositories like the Sequence Read Archive. While access to these datasets has traditionally been centered in the R/Bioconductor ecosystem, the growing prominence of Python in bioinformatics and machine learning necessitates native, efficient tooling for Python users. Therefore, we present the recount3 Python package with robust application programming interface (API) and command-line interface (CLI) for discovering, downloading, and materializing recount3 resources. The software orchestrates uniform resource locator (URL) resolution, persistent on-disk caching, and the automatic parsing of data into analysis-ready data structures, including Pandas DataFrames and BiocPy RangedSummarizedExperiment objects. The recount3 Python package drastically lowers the barrier to entry for large-scale utilization of RNA-seq data in Python-based computational pipelines, bridging the gap between massive public transcriptomic data and modern machine learning ecosystems.

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

Reinforcing Dual-Path Reasoning in Spatial Vision Language Models

作者:
Yatai Ji↗An-Chieh Cheng↗Yang Fu↗Yukang Chen↗Han Zhang↗Zhaojing Yang↗Wei Huang↗Ka Chun Cheung↗Song Han↗Vidya Nariyambut Murali↗Pavlo Molchanov↗Jan Kautz↗…

Spatial VLMs have made substantial progress in geometric perception, yet complex spatial reasoning requiring multi-step inference over depth, distance, and scene relations remains challenging. Moreover, different spatial queries call for fundamentally different strategies: some are best addressed through purely linguistic, step-by-step deduction, while others require explicit 3D grounding before quantitative inference. We present Dual-Path Spatial Reasoning via Reinforcement Learning for Spatial VLMs (SR-REAL), a unified framework that equips a spatial VLM with two complementary reasoning paths: Language-Only Reasoning (LOR), which performs step-by-step linguistic deduction, and Detect-Then-Reason (DTR), which detects 3D geometric cues (e.g., centers or bounding boxes) via region tokens before explicit geometric inference. SR-REAL begins with a cold-start supervised fine-tuning stage that constructs LOR and DTR chain-of-thought supervision and exposes a region-to-3D interface, followed by RL that optimizes the policy model with accuracy and format rewards; for DTR, a discrete center-based detection reward further refines geometric alignment. Across diverse spatial benchmarks, SR-REAL significantly outperforms spatial VLM baselines: (i) a single RL-trained model supports both reasoning paths, with DTR excelling in region-aware tasks through precise 3D localization and LOR enhancing general spatial reasoning; (ii) jointly training both paths fosters mutual reinforcement; (iii) high-quality, blended cold-start data is crucial for stable RL optimization; and (iv) the model generalizes across datasets and domains without per-task tuning, demonstrating positive transfer between LOR and DTR.

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22.
arXiv (math.PR) 2026-06-11

Mean-field limits for stochastic particle systems on dense graphs

作者:
Angeliki Koutsimpela↗Elena Magnanini↗

arXiv:2606.11369v1 Announce Type: new Abstract: We study stochastic interacting particle systems whose interaction structure is described by dense weighted directed graphs converging to a graphon. In the thermodynamic limit, we prove a law of large numbers for the empirical measure process and derive a deterministic nonlinear master equation describing the macroscopic evolution. The limiting equation retains the heterogeneous interaction structure of the microscopic system through the limiting graphon, allowing for spatially non-homogeneous behaviors such as localized or community-type interactions.

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

Permutation-Invariant N-body gates via Tavis-Cummings Hamiltonian

作者:
Plato Deliyannis↗Iman Marvian↗

arXiv:2506.03453v3 Announce Type: replace Abstract: Global control provides a promising route to implementing multi-qubit gates without individual qubit addressing. This is especially appealing for permutation-invariant (PI) gates, whose symmetry is often broken when they are compiled into individually addressed one- and two-qubit gates. Important examples include SWAP, $\sqrt{iSWAP}$, and the n-qubit controlled-Z gate, which is equivalent, up to two single-qubit Hadamard gates, to the multi-qubit Toffoli gate. Motivated by this global-control perspective, we show that all PI unitaries on an arbitrary number of qubits can be realized using the Tavis-Cummings (TC) interaction, the multi-qubit version of the Jaynes-Cummings interaction, together with global uniform z and x fields. Here, the $n$ qubits are identically coupled to a single bosonic mode (oscillator), which is initialized in and returned to its vacuum state. A corollary is that all PI states, including GHZ and Dicke states, can be prepared using the same global control. For the case n=2 qubits, which is particularly important in quantum computing, we also find explicit pulse sequences for implementing all PI qubit unitaries that conserve angular momentum in the z direction, using only the TC interaction and global z fields. This includes controlled-Z, SWAP, and $\sqrt{iSWAP}$.

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24.
bioRxiv (Bioinfo) 2026-06-12

From Proteome Mining to Structural Validation: Phosphopyruvate Hydratase as a Structurally Tractable Drug Target in Kinetoplastid Parasites

作者:
Goyzueta Mamani↗L. D↗Barazorda Ccahuana↗H. L↗G Ng↗Pineda R↗Medina Franco↗J. L↗Florin Christensen↗Ferraz Coelho↗E. A↗Spadafora↗…

Chagas disease, caused by Trypanosoma cruzi, demands novel therapeutic strategies that overcome the toxicity and limited efficacy of current treatments. To address this need, herein we report an integrative, target-centric strategy that combines parasite proteome mining, structural modeling, and experimental validation. Functional enrichment and druggability analyses identified phosphopyruvate hydratase (PPH) as a promising candidate due to its essential metabolic role and limited similarity to human homologs. Notably, proteome mining revealed the presence and conservation of PPH across kinetoplastid parasites, including Leishmania donovani, supporting its evaluation beyond T. cruzi. For the selected PPH sequences, AlphaFold-derived three-dimensional models underwent extensive molecular dynamics refinement, yielding stable conformational ensembles suitable for structure-based studies. Using this validated model, virtual screening of the Latin American Natural Products Database - LANaPDB - identified aptosimon as a top-ranked compound candidate. Molecular dynamics simulations further showed ligand-dependent binding behavior, suggesting alternative binding modes distinct from the canonical substrate configuration. In vitro assays demonstrated consistent antiparasitic activity against intracellular T. cruzi amastigotes (IC50 = 3.52 ug/mL) and Leishmania donovani promastigotes (IC50 = 13.06 ug/mL), supporting the biological relevance of the aptosimon-related lignan chemotype, hinokinin, across two kinetoplastid parasite models. Together, these results support PPH as a structurally tractable and biologically relevant candidate target, while identifying an aptosimon-related lignan chemotype, represented experimentally by hinokinin, as a cross-species antiparasitic scaffold that warrants further biochemical target-validation studies.

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25.
PLOS Computational Biology 2026-06-09

Evolution of phenocopying in a dynamical model of developmental trajectories

作者:
Yuuki Matsushita↗

by Yuuki Matsushita, Archishman Raju Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside the range of conditions to which they are robust, they often produce phenotypes similar to known mutants, called phenocopies. This correspondence between the effects of environmental and genetic perturbations has received little theoretical attention. Here, we study an abstract regulatory model that is evolved to follow a specific trajectory. We then study the effects of small and large perturbations to the trajectory, both by changing parameters and by perturbing the state at specific times. We find that the phenomenon of phenocopying emerges in evolved trajectories and is not present in a null model of randomly sampled trajectories. Our results suggest that, in this class of dynamic models, evolution can allow high-dimensional phenotypic landscapes to simultaneously exhibit robustness and phenocopying.

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