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01.
medRxiv (Medicine) 2026-06-19

Grey- and white-matter resilience to tau, cognition and sex in Alzheimer's disease

作者:
Boutin↗Houze↗Bedetti↗Pichet Binette↗Brambati↗S. M↗Alzheimer's Disease Neuroimaging Initiative↗

INTRODUCTION: Brain resilience to tau has been mainly studied in relation to grey matter, while its role in white matter remains unclear in Alzheimer's disease (AD). Sex may moderate associations between brain resilience and cognition. METHODS: We analyzed medial temporal lobe tau PET SUVR, entorhinal cortical thickness, cingulum-hippocampal mean diffusivity, and cognition in 205 amyloid-positive individuals from ADNI. Associations between grey- and white-matter resilience to tau and cognitive performance or decline were examined using linear and mixed-effects models, including sex interactions and stratified analyses. RESULTS: Higher grey-matter resilience to tau related to better cross-sectional memory and language performance (p

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02.
arXiv (quant-ph) 2026-06-19

Entanglement Scaling and Problem Structure in Quantum Approximate and Adiabatic Optimization Algorithms

作者:
Georgios Arapantonis↗Paraj Titum↗Gregory Quiroz↗

arXiv:2606.19502v1 Announce Type: new Abstract: Entanglement is widely regarded as a key resource underlying the power of quantum algorithms and their potential to achieve quantum advantage. With the emergence of variational quantum algorithms, however, questions have arisen regarding how entanglement relates to problem structure and algorithmic performance in near-term quantum applications. Here, we examine this relationship through the Quantum Approximate Optimization Algorithm (QAOA), a specific class of variational algorithms, applied to the MaxCut problem. We show that suboptimal variational parameter training can significantly modify the observed entanglement profile, obscuring its scaling behavior. By employing a high-performance optimizer, we find empirical evidence that QAOA exhibits entanglement scaling consistent with that of fermionic Gaussian states (up to a scaling factor) across a broad range of MaxCut instances. We further compare these results with adiabatic quantum computation, observing annealing-schedule-dependent entanglement profiles whose scaling behavior differs markedly from that of QAOA. Together, these findings provide new insight into how entanglement manifests in and distinguishes these two algorithmic paradigms, highlighting its connection to both computational performance and application structure.

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03.
arXiv (CS.CV) 2026-06-16

Hierarchical GRU with Input-Conditioned Slot Queries for Ball Action Anticipation

作者:
Parthsarthi Rawat↗

We present a hierarchical model for ball action anticipation in football broadcast video. Given a 30-second observation window, the system predicts actions occurring in the subsequent 5-second window across 10 classes. A shared local Transformer encodes clip-level features within each 5-second sub-window; a GRU then aggregates temporal context across all sub-windows; finally, a Transformer decoder with K input-conditioned event slots decodes the anticipation target via three decoupled heads (objectness, class, temporal offset). We introduce frequency-reweighted Hungarian matching that systematically favours rare action classes, and Gaussian soft targets for temporal bin supervision. On the SoccerNet Ball Action Anticipation benchmark, our method achieves 17.91% mAP on the test server.

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04.
arXiv (CS.CV) 2026-06-16

OneFocus: Enabling Real-World X-ray Security Screening with a Unified Vision-Language Model

作者:
Jiali Wen↗Hongxia Gao↗Litao Li↗Yixin Chen↗Kaijie Zhang↗Qianyun Liu↗Xiaoqin Wen↗

X-ray contraband detection is critical for security in large-scale logistics and transportation, yet conventional detectors struggle to adapt to emerging contraband types and lack fundamental visual understanding. Vision-language models (VLMs) offer strong generalization but are hindered by the scarcity of high-quality X-ray image-caption data. To bridge this critical gap, we present MMXray, a meticulously curated benchmark of 52,124 image-caption pairs spanning 28 fine-grained classes of X-ray contraband. To enrich MMXray with realistic occlusion patterns, we further introduce CleanDET, a dedicated synthesis dataset containing clean foreground contraband images from 28 categories and background images with diverse density levels, together with AnyContraSyn, a controllable synthesis method designed to operate on CleanDET. We also develop OnePipe, an extensible pipeline for systematic data curation. Built on MMXray, we propose OneFocus, a unified VLM that supports four core tasks: visual question answering, contraband localization, classification, and image understanding. OneFocus achieves state-of-the-art performance in X-ray contraband understanding and demonstrates robust cross-domain generalization, establishing a strong vision-language baseline for security screening.

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

Lightweight Distillation of SAM 3 and DINOv3 for Edge-Deployable Individual-Level Livestock Monitoring and Longitudinal Visual Analytics

作者:
Haiyu Yang↗Miel Hostens↗

Foundation-model pipelines for individual-level livestock monitoring – combining open-vocabulary detection, promptable video segmentation, and self-supervised visual embeddings – have raised the accuracy ceiling of precision livestock farming (PLF), but their GPU memory budgets exceed the envelope of commodity edge accelerators. To close this gap, the 446M-parameter Perception Encoder (PE-ViT-L+) backbone of SAM 3 is distilled into a 40.66M-parameter multi-scale student through three mechanisms: a Feature Pyramid Network student encoder built on TinyViT-21M-512, a four-term direction-then-scale distillation loss, and backbone-substitution inference with sliding-window session pruning that bounds streaming GPU memory growth. The DINOv3 family includes a pre-distilled ViT-S/16 variant (21.6M parameters) released alongside a 6716M-parameter ViT-7B teacher; the ViT-S (21M) variant is adopted as the per-individual embedder. On the Edinburgh Pig dataset, the compressed pipeline reaches 92.29% MOTA and 96.15% IDF1 against the SAM 3 teacher (1.68- and 0.84-percentage-point losses), achieves a 7.77-fold reduction in system-level parameters and a 3.01-fold reduction in peak VRAM (19.52GB -> 6.49GB), and reaches 97.34% top-1 accuracy with 91.67% macro-F1 on nine-class pig behaviour classification. The pipeline fits inside an NVIDIA Jetson Orin NX 16GB envelope with 4.9GB of headroom, supporting a proposed – but not yet empirically validated – on-device embedding-pool re-identification mechanism whose per-individual footprint of approximately 94MB per animal per year produces a longitudinal visual record amenable to retrospective association with disease, lameness, reproductive, and growth outcome labels.

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

The Geometry of Phase Transitions in Generative Dynamics via Projection Caustics

作者:
Ryosuke Sakamoto↗Kotaro Sakamoto↗

arXiv:2606.13191v1 Announce Type: new Abstract: Continuous-state generative samplers, including diffusion and flow-matching models, evolve through continuous reverse-time dynamics, yet their samples often undergo abrupt qualitative changes: trajectories commit to modes, semantic alternatives collapse, and small perturbations in narrow time windows can produce large downstream effects. This paper develops a geometric account of such phase-transition-like behaviour. We view denoising as gradient descent on a free energy landscape and show that sharp transitions arise near projection caustics, where the nearest-point projection onto the data support ceases to be unique. Motivated by this perspective, we introduce the Critical Boundary Detector (CBD), as practical diagnostics for score-direction instability. Across toy models, standard diffusion models, and latent text-to-image diffusion models, CBD localises mode commitment, predicts intervention-sensitive windows, and supports targeted control in geometrically sensitive regions. Our results connect geometry of data and dynamics of diffusion generation.

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07.
arXiv (CS.AI) 2026-06-12

Reasoning for Mobile User Experience with Multimodal LLMs: Task, Benchmark, and Approach

作者:
Ruichao Mao↗Zhou Fang↗Teng Guo↗Hao Yang↗Yaping Li↗Shaohua Peng↗Maji Huang↗Xiaoyu Lin↗Shuoyang Liu↗Xuepeng Li↗Yuyu Zhang↗Hai Rao↗…

arXiv:2606.13192v1 Announce Type: new Abstract: User experience (UX) centered on usability, perceived consistency, and functional clarity is fundamental to real-world user interfaces (UI). The application of multimodal large language models (MLLMs) in the field of user interfaces is evolving rapidly, such as visual element grounding, graphical user interface (GUI) agents, and design-to-code generation. However, research efforts on evaluating UX based on UI screenshots are still immature. To address this, we propose UXBench, a novel multimodal benchmark consisting of 2,000 VQA data samples designed to assess MLLMs' ability to perform UI-based reasoning. UXBench includes 8 tasks based on real-world UI screenshots that require fine-grained diagnosis of UX issues across layout relationships, visual hierarchy, and content consistency. Our extensive evaluation of mainstream MLLMs shows that they remain fundamentally limited in their capacity for UI-based reasoning. The results underscore the need for further advancements in this area. To bridge this gap, we propose UI-UX, an MLLM based on Qwen3-VL-4B-Thinking foundation model and enhanced via reinforcement learning with two key innovations: a reward routing mechanism that dynamically balances perceptual understanding and logical reasoning during inference, and an asymmetric transition reward that suppresses redundant or insufficient reasoning steps. Experiments demonstrate that UI-UX achieves state-of-the-art (SOTA) performance on UXBench, attaining an accuracy of 0.7963 – surpassing Claude-4.5-Sonnet's 0.6550 – while exhibiting strong generalization across diverse UI tasks and maintaining low inference latency.

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08.
arXiv (CS.CL) 2026-06-15

Implicit Reasoning for Large Language Model-based Generative Recommendation

作者:
Yinhan He↗Liam Collins↗Bhuvesh Kumar↗Jundong Li↗Neil Shah↗Donald Loveland↗

Large Language Models (LLMs) are increasingly adopted as backbones for Generative Recommendation (GR), promising access to pretrained world knowledge. Yet reliably invoking this knowledge for GR remains poorly understood. A key obstacle is that LLM-based GR typically represents items with Semantic IDs (SIDs), disrupting LLMs' natural-language reasoning interface because these tokens are unseen by the LLM during pretraining. Existing approaches address this with expensive multi-stage pipelines that ground SIDs and elicit explicit rationales, but offer limited insight into when and why each stage is necessary. In this work, we systematically decompose explicit reasoning training pipelines for LLM-based GR, revealing three key limitations: weakened world-knowledge verbalization, misalignment between SID and natural-language token embedding spaces, and sensitivity to rationale quality, all of which hurt explicit reasoning performance. To circumvent these issues, we propose PauseRec, a lightweight implicit reasoning paradigm tailored for GR. PauseRec is exceptionally practical, avoiding costly reasoning trace acquisition and reasoning alignment training, leading to a multitude of benefits: (1) it outperforms standard explicit CoT methods by up to 6.22%, (2) it reduces training cost by up to 65% GPU hours, and (3) it speeds up inference by up to 71.3%. These results position PauseRec as a lightweight alternative to explicit rationale generation, enabling more effective and efficient LLM-based GR.

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

Holding the FP8 Quality Ceiling at 8-Bit Weights and Activations: INT8 and GGUF Post-Training Quantization of Ideogram 4.0 for Consumer GPUs

作者:
Deep Gandhi↗Ali Asaria↗Tony Salomone↗

arXiv:2606.12280v1 Announce Type: new Abstract: Post-training quantization lets large text-to-image diffusion transformers run on consumer GPUs, yet the hardware-specific trade-offs are seldom measured directly. We quantize Ideogram 4.0 - a 9.3B flow-matching diffusion transformer (DiT), shipped as two separate-weight copies of a single-stream 34-layer backbone for classifier-free guidance and conditioned by a Qwen3-VL-8B encoder - for Ampere RTX 3090 GPUs, which lack FP8 tensor cores. Our INT8 W8A8 recipe (per-channel weights, per-token dynamic activations, SmoothQuant, and mixed-precision protection of a small high-fragility layer set) holds the FP8 quality ceiling: on a 200-prompt benchmark the paired same-seed bootstrap CI for INT8-FP8 includes zero on both Pick and CLIP, while INT8 improves on NF4 by $+1.9$ CLIP (95% CI $[+1.21,+2.64]$, excluding zero). A per-category OCR analysis, to our knowledge unreported for this model class, confirms text legibility is preserved, and an ablation isolates protection of the FFN down-projections as the dominant quality lever. Our GGUF Q4_K quantization beats NF4 at equal on-disk size and is the Pareto winner on the quality-memory frontier, with paired confidence intervals excluding zero (Q8_0 is quality neutral). Finally, we characterize where 8-bit quantization helps and where it does not: INT8's weights match FP8's footprint rather than shrink it, so a speed gain on Ampere awaits a fused INT8 kernel.

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10.
arXiv (CS.AI) 2026-06-19

Exploring Feature Extraction Technique Parameters for Acoustic Gunshot Classification

作者:
Sinclair Gurny↗Ryan Quinn↗

arXiv:2606.19568v1 Announce Type: cross Abstract: Acoustic gunshot detection is a problem with applications across civilian public safety, military operations, and wildlife conservation, yet the field lacks a rigorous exploration of feature extraction techniques with a focus on generalization to realistic data. The mixed effectiveness of commercial gunshot detection and classification systems indicates an open problem that is not adequately addressed by the current literature. In this paper, we present a systematic investigation of common feature extraction techniques using a dataset of 23,000 gunshot recordings across 85 firearms and 21 calibers. We benchmark three feature extraction techniques with 12 total unique parameter sets using ResNet-18. Our results demonstrate that using the correct feature extraction technique can improve top-1 accuracy by up to 20%, and utilizing the correct parameters for a given feature extraction technique can improve that value by up to 4.7%.

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11.
arXiv (math.PR) 2026-06-16

Malliavin Calculus for the stochastic Cahn-Hilliard equation driven by fractional noise

作者:
Dimitrios Dimitriou↗Dimitris Farazakis↗Georgia Karali↗

arXiv:2601.10490v2 Announce Type: replace Abstract: The stochastic partial differential equation analyzed in this work is the Cahn-Hilliard equation perturbed by an additive fractional white noise (fractional in time and white in space). We work in the case of one spatial dimension and apply Malliavin calculus to investigate the existence of a density for the stochastic solution $u$. In particular, we show that $u$ admits continuous paths almost surely and construct a localizing sequence through which we prove that its Malliavin derivative exists locally, and that its law is absolutely continuous with respect to the Lebesgue measure on $\bf R$, establishing thus that a density exists. A key contribution of this work is the analysis of the stochastic integral appearing in the mild formulation: we derive sharp estimates for the expectation of the $p$-th power ($p \geq 2$) of the $L^{\infty}(D)$-norm of this stochastic integral as well as for the integral involving the $L^{\infty}(D)$-norm of the operator associated with the kernel appearing in the integral representation of the fractional noise, all of which are essential for this study.

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

Vines-DB: An RGB image dataset for multi-species ornamental vine segmentation

作者:
Saroj Burlakoti↗Utsav Bhandari↗Aaron Etienne↗Shital Poudyal↗

The Vines-DB dataset contains 1,218 original high-resolution RGB images of seven ornamental vine species collected under field conditions at the Utah Agricultural Experiment Station's Greenville Research Farm in Logan, Utah, USA. The dataset was generated from 168 individual vine plants that were transplanted in 2022 and photographed repeatedly across multiple months during the 2023 and 2024 growing seasons (July-October). Images were captured with an iPhone 16 Pro equipped with a 48 MP camera between 10:00 AM and 12:00 PM under daylight. Vines were grown on 1.2m x 2.4m trellises and photographed from a distance of 1m against black or white Styrofoam backdrops to improve contrast and reduce background noise. The dataset includes Akebia quinata, Campsis radicans, Hydrangea anomala petiolaris, Lonicera x heckrottii, Campsis x tagliabuana 'Madame Galen', Parthenocissus quinquefolia, and Wisteria floribunda. All original images were manually annotated in Roboflow by trained annotators to produce polygon-based instance segmentation masks for eight classes, including seven species and background. After preprocessing and data augmentation, the working dataset was expanded to 2,307 images for model development and evaluation. The augmented dataset was divided into 2,019 training images, 192 validation images, and 96 test images using stratified sampling to maintain balanced representation. Vines-DB supports the development and evaluation of deep learning models for multi-class instance segmentation in precision horticulture and urban ecology. The dataset enables applications such as automated canopy cover estimation, species identification, and scalable field phenotyping. In addition, repeated monthly imaging of the plants captures temporal variation in canopy development and plant appearance, increasing the dataset's utility for segmentation benchmarking under realistic field conditions.

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13.
arXiv (CS.CV) 2026-06-16

Double-Helix Vision (DH-V2): A Geometry-Based Visual Sampler for Bandwidth-Constrained Perception

作者:
Jinwen Wen↗

We present Double-Helix Vision (DH), a geometry-based visual sampler that compresses 2D images into compact 1D signals using paired golden-ratio-inspired spiral trajectories. Rather than processing every pixel uniformly, DH employs two phase-shifted helices (Alpha and Beta, offset by 180 degrees) to sample the image with biologically-inspired foveation: high density at the center, sparse coverage at the periphery. At 4K resolution, DH achieves a 1,433x compression ratio (99.93% reduction) while preserving the geometric structure of the scene. The full perception pipeline – including spatial mapping, temporal collision detection, and intra-frame structural disparity estimation – runs in 0.52 ms at 1080p on CPU-only hardware, with no neural network dependencies. On CIFAR-10 at extreme sampling budgets (K=128 points per helix), DH achieves a +6.03% accuracy gain over uniform random sampling. A JSON-serializable Robotics API is provided, delivering sub-millisecond spatial perception reports in 2.7 KB packets. Code and benchmarks are available under the MIT License.

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

HMR-Net: Hierarchical Modular Routing for Cross-Domain Object Detection in Aerial Images

作者:
Pourya Shamsolmoali↗Masoumeh Zareapoor↗Michael Felsberg↗Nick Pears↗Huiyu Zhou↗Yue Lu↗

Despite advances in object detection, aerial imagery remains a challenging domain, as models often fail to generalize across variations in spatial resolution, scene composition, and semantic label coverage. Differences in geographic context, sensor characteristics, and object distributions across datasets limit the capacity of conventional models to learn consistent and transferable representations. Shared methods trained on such data tend to impose a unified representation across fundamentally different domains, resulting in poor performance on region-specific content and less flexibility when dealing with novel object categories. To address this, we propose a novel modular learning framework that enables structured specialization in aerial detection. Our method introduces a hierarchical routing mechanism with two levels of modularity: a domain routing layer that uses latent geographic embeddings to assign inputs to domain-specialized expert modules, and a scene routing mechanism that allocates image subregions to scene-specific expert modules. This allows our method to specialize across datasets and within complex scenes. Additionally, the framework contains a conditional expert module that uses external semantic information (e.g., category names or textual descriptions) to enable detection of novel object categories during inference, without the need for retraining or fine-tuning. By moving beyond monolithic representations, our method provides an adaptive framework for remote sensing object detection. Comprehensive evaluations on four datasets highlight improvements in multi-dataset generalization, region-level specialization, and open-category detection.

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15.
arXiv (CS.CL) 2026-06-11

WorldReasoner: Evaluating Whether Language Model Agents Forecast Events with Valid Reasoning

作者:
Yizhou Chi↗Eric Chamoun↗Zifeng Ding↗Andreas Vlachos↗

Forecasting real-world events requires language-model agents to reason under uncertainty from incomplete, time-bounded information. Yet evaluating whether agents genuinely forecast requires more than final-answer accuracy: a model may be correct by recalling memorized training facts, citing fabricated evidence, or producing an unsupported causal story. We present WorldReasoner, an evaluation framework for temporally valid event forecasting. Each task gives an agent a resolved forecasting question, a simulated forecast date, and access only to evidence available before that date; after resolution, the framework scores the submitted probability, cited evidence, and optional causal event graph. WorldReasoner reports three complementary axes: outcome quality against resolved answers, evidence quality over cited sources, and reasoning quality against post-resolution hindsight graphs. The benchmark is built by an agentic construction pipeline that generates forecasting questions, collects time-stamped evidence, and builds hindsight reference graphs at scale, yielding 345 resolved tasks derived from 14,141 articles with graphs covering 8,087 extracted events. Across six controlled agent settings, temporally valid retrieval is the strongest driver of outcome accuracy; causal graph construction improves key-event recovery; and correct graph-enabled forecasts are more strongly grounded in key events and relevant sources, yet agents still struggle to convert grounded evidence into calibrated probabilities.

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16.
arXiv (CS.AI) 2026-06-18

DeepInflation: an AI agent for research and model discovery of inflation

作者:
Ze-Yu Peng↗Hao-Shi Yuan↗Qi Lai↗Jun-Qian Jiang↗Gen Ye↗Jun Zhang↗Yun-Song Piao↗

arXiv:2601.14288v2 Announce Type: replace-cross Abstract: We present DeepInflation, an AI agent designed for research and model discovery in inflationary cosmology. Built upon a multi-agent architecture, DeepInflation integrates Large Language Models (LLMs) with a symbolic regression (SR) engine and a retrieval-augmented generation (RAG) knowledge base. This framework enables the agent to automatically explore and verify the vast landscape of inflationary potentials while grounding its outputs in established theoretical literature. We demonstrate that DeepInflation can successfully discover simple and viable single-field slow-roll inflationary potentials consistent with the latest observations (with the ACT DR6 results taken as an example) or any given $n_s$ and $r$, and provide accurate theoretical context for obscure inflationary scenarios. DeepInflation serves as a prototype for a new generation of autonomous scientific discovery engines in cosmology, which enables researchers and non-experts alike to explore the inflationary landscape using natural language. This agent is available at https://github.com/pengzy-cosmo/DeepInflation.

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17.
arXiv (quant-ph) 2026-06-11

Towards the implementation of a quantum classifier

作者:
Lorenzo Confalonieri↗

arXiv:2606.10150v2 Announce Type: replace Abstract: In this work, we investigate the use of a quantum circuit as a binary classification model in the context of quantum machine learning. We call this model, binary quantum classifier. First, we describe fundamental concepts of quantum computing and introduce the computational tool used: Qibo, an open-source framework for efficient quantum simulations and quantum hardware control. Then, we describe how to design a binary quantum classifier for the classification of images and small arrays of variables by showing how to input data in the circuit, defining a quantum circuit model Ansatz with trainable parameters and a loss function, and implementing multiple minimizers. We test our quantum classifier with two data sets. The first one is the MNIST data set which is composed of handwritten digits (reduced to only handwritten zeros and handwritten ones for binary classification). We study the behavior of different minimizers by increasing the number of layers of the Ansatz. The second data set represents two different high energy collisions that can occur at colliders such as LHC (CERN). Due to in-time proton-proton interactions known as pile-up, we distinguish two different data sets: "without pile-up" and "with pile-up". These collisions can be represented by images of size 32x32 or by six high-level variables that we call features. By increasing the size of the training data set and the number of layers of the Ansatz, we search for the best minimizer. Splitting the data set in training set and test set, we compute: ROC curve, AUC score, confusion matrices and test set accuracy. For "with pile-up" images, we compare the results obtained with the quantum classifier with a small convolutional neural network. We conclude that is possible to build a binary quantum classifier with a quantum circuit and we highlight its performances and limitations in comparison with classical technologies.

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18.
arXiv (CS.LG) 2026-06-19

Doeblin Curves

作者:
Dongmin Lee↗William Lu↗Anuran Makur↗Japneet Singh↗

arXiv:2606.19859v1 Announce Type: cross Abstract: Recent research on Doeblin coefficients has shed light on their usefulness as a multi-way generalization of the Dobrushin contraction coefficient for TV distance, in a separate vein from their classic role in the theory of Markov chain ergodicity. However, strong conditions, such as being bounded away from 0, are typically necessary for Doeblin coefficients to establish the existence of information contraction. Building on recently formulated concepts of nonlinear information contraction, we aim to propose a finer-grained Doeblin-based characterization of multi-way contraction behavior which yields non-vacuous contraction guarantees even for channels whose Doeblin coefficient is 0. To this end, we introduce the notion of a Doeblin curve – a nonlinear function which quantifies the contraction behavior of a Markov kernel on collections of input distributions at specific levels of divergence and power. Through the course of our analysis, we develop a new variational characterization of Doeblin coefficients, present several properties of Doeblin curves, define several versions of power-constrained Doeblin curves, and derive upper and lower bounds using our aforementioned variational characterization. We then utilize these results in diverse areas, including generalization bounds for noisy iterative optimization, error bounds for reliable computation with noisy circuits, and differential privacy guarantees for online iterative algorithms. In particular, we extend results in these areas to broader domains or group settings, leveraging Doeblin curves to reveal finer-grained contraction phenomena than Doeblin coefficients.

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20.
bioRxiv (Bioinfo) 2026-06-19

Perturbation Curve models continuous transcriptional response trajectories and improves prediction of genetic modulations

作者:
Zhong↗wang↗Yang↗Yu↗Qi↗Jiang↗

Single-cell CRISPR screens, Perturb-seq, have revolutionized functional genomics by revealing biological causality. However, although perturbation assignments are typically represented as discrete labels, the cell-level effective strength of perturbations is often continuous and diverse. Current analytical frameworks struggle to decouple the variability in perturbation strength from the diversity of downstream responses. Here, we present Perturbation Curve (PertCurve), a nonlinear, curve-based computational framework that models the trajectories of transcriptomic responses by explicitly incorporating diverse perturbation magnitudes and strengths. By ordering cells by perturbation strength, we demonstrate that PertCurve accurately recapitulates the response magnitudes and reveals the distinct modularity and asynchrony patterns of downstream gene behaviors. These patterns are categorized into archetypes, including proportional, sensitive, and threshold responses. By applying this framework across CRISPRi/a modalities, we identify universal response patterns in viral infection, apoptosis, and proliferation genes, and reveal previously overlooked context-specific regulatory features in cell differentiation. Finally, incorporating PertCurve into perturbation prediction models and evaluation metrics enhances predictive performance, delivering actionable insights for refining established models.

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21.
arXiv (CS.LG) 2026-06-15

Code Correctness Signals in LLM Hidden States: Pre-Generation Probing and Repair Geometry

作者:
Carlo Di Cicco↗

arXiv:2606.14530v1 Announce Type: new Abstract: Large language models encode rich information in their hidden states. This work asks whether code correctness is legible in the hidden states of Qwen3-4B-Instruct-2507, before it generates and as it repairs a failed attempt, studied on 444 LiveCodeBench tasks. It reports two findings connected by a single confound-control tool: residualization. First, the correctness of the model's first-attempt code is linearly decodable from the prompt-final hidden state, with a leakage-free held-out AUC of 0.931 +/- 0.008 across 50 outer splits. After the linear effect of prompt length is removed from each hidden state dimension, the probe still reaches 0.911 +/- 0.010, well above a prompt-length baseline of 0.754 +/- 0.014. Second, on 236 cleaned cases where the model attempts to repair a failed first attempt, the hidden state shift from the failing attempt to its repair carries a statistically detectable contrastive direction, significant on both a magnitude and a split-half test against label-shuffled nulls. This direction does not survive a conditional residualization against repair-context covariates that differ between successful and failed repairs, marking it as a correlate of repair success driven by the repair context rather than an isolated repair-comprehension feature. The probe layer is selected by nested cross-validation, and the same residualization approach that upholds the pre-generation correctness result overturns the repair-direction interpretation. The contribution is as much methodological as empirical: a diagnostic honest enough to report a negative result alongside a positive one.

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22.
arXiv (CS.CL) 2026-06-16

State-Grounded Multi-Agent Synthetic Data Generation for Tool-Augmented LLMs

作者:
Rahul Khedar↗Eshita↗Sneha Teja Sree Reddy Thondapu↗Mayank Malhotra↗Arup Das↗Jitesh Chandra↗Yun-Shiuan Chuang↗Chaitanya Kulkarni↗Arun Menon↗Linsey Pang↗Avinash Karn↗Mouli V↗…

Training tool-augmented LLM agents requires large corpora of multi-turn, tool-grounded conversational data that is expensive to annotate, privacy-constrained in production settings, and largely absent from public datasets. We present StateGen, a synthetic data generation platform that produces scored, reasoning-trace-rich training conversations by orchestrating a four-role LLM loop: a persona-conditioned user simulator, an agent under test, a state-grounded tool simulator, and a multi-axis LLM judge. The key architectural contribution is an authoritative state manager that maintains a structured world-state object across turns, enforcing a backend-is-truth invariant that eliminates the dominant class of tool-call hallucinations by construction. StateGen extends naturally to hierarchical multi-agent settings by declaring sub-agents as tools, all sharing a single state object. We report results on 64,698 evaluated conversations across three production corpora: tool-call hallucination scores reach 9.66/10, the system supports persona-driven variation via a 23-dimensional trait vector, and a cleanly separated train and golden evaluation set split confirms the data is not memorization bait (per-criterion gap analysis). Comparison with eight external systems shows that no single publicly available platform combines multi-turn generation, state-grounded tool simulation, hierarchical multi-agent support, and built-in judge scoring.

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23.
medRxiv (Medicine) 2026-06-22

Substantia Nigra and Subthalamic Nucleus Deep Brain Stimulation Exert Opposing Effects on Novelty Recognition in Parkinson's Disease

作者:
Li↗Jiang↗Liu↗Yang↗Yao↗Zhang↗Xie↗Hollunder↗Strange↗Meng↗Wang↗Shi↗…

Episodic memory plays a critical role in supporting adaptive behavior; however, whether it can be causally regulated in humans via deep subcortical stimulation remains unclear. In the present study, we investigated the differential effects of substantia nigra (SN) and subthalamic nucleus (STN) stimulation on episodic memory, as well as the underlying mechanisms of its associated brain networks, using a recognition memory task combined with concurrent functional magnetic resonance imaging in patients with Parkinson's disease. SN-DBS increased recognition sensitivity and reduced false alarms at both frequencies, whereas 10 Hz STN-DBS reduced sensitivity and increased false alarms. Functional connectivity analyses in the absence of DBS stimulation identified a false recognition-related network linking nigral, pallidal, subthalamic, medial temporal, frontal, and occipital regions. SN-DBS-related false alarm reduction tracked modulation of this circuit and was marked by its baseline vulnerability state. These behavioral effects mapped onto target-dependent parieto-occipital and SN-visual retrieval pathways, supporting a model in which DBS bidirectionally regulates recognition memory through target- and frequency-dependent subcortical-cortical circuits.

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24.
Nature Biotechnology 2026-06-19

Efficient site-specific gene addition using R2 retrotransposons in tobacco and rice

作者:
Zahir Ali↗

Precise integration of multikilobase DNA fragments remains a major technical barrier in plants. Here we introduce non-long terminal repeat (non-LTR) R2 retrotransposons as a versatile system for targeted gene integration in plants. We reconstituted R2 activity in Nicotiana benthamiana and benchmarked insertion efficiency and fidelity using a TMV-based episomal reporter system. We demonstrate site-specific integration of GFP (2.2 kb) and recombinase-compatible landing pads (0.6 kb) into 28S rDNA arrays, with intact cassette insertion frequencies up to 75% and 53%, respectively. To temporally constrain donor availability and avoid DNA intermediates, we combined in planta effector expression with recombinant RNA virus-mediated donor delivery. We apply R2 retrotransposons for targeted insertion of resistance cassettes within the rDNA of rice callus, achieving integration efficiencies up to 17%. These results position R2 retrotransposons as a double-strand break-free system for RNA-templated insertion of multikilobase gene cassettes at rDNA loci, for safe-harbor trait stacking in plants with potential applications in crop improvement and synthetic biology. Retrotransposons are applied in plants for safe-harbor transgene integration.

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25.
medRxiv (Medicine) 2026-06-16

The Target48 Neurodegeneration Panel: A Novel Tool for Profiling Protein Signatures in Neurodegenerative Disorders

作者:
Hok-A-Hin↗Y. S↗Vermunt↗de Jong↗del Campo↗Vijverberg↗Lemstra↗A. W↗Pijnenburg↗Y. A. L↗Van Harten↗A. C↗…

Introduction: Novel tools for absolute quantification of established and emerging fluid neuro-biomarkers are required to advance diagnostic studies and improve biological insights. Methods: We conducted an extensive analytical and clinical validation of the Olink Target 48 Neurodegeneration panel (T48 Neuropanel) in 352 paired CSF and plasma samples from cognitively unimpaired controls (CU), Alzheimer dementia (AD), frontotemporal dementia (FTD), and dementia with Lewy bodies (DLB), n=44 per group. Comparisons with benchmark assays were performed. Results: Good detectability (CSF: 31 out of 42 assays; plasma: 38 out of 42 assays) and technical performance was observed. Benchmark assays showed good correlations, supporting method transformation formulas. Next to emerging biomarkers (MMP10, ITGB2), discriminative performance was excellent in AD: CSF pTau217: AUC=1; FTD: plasma NfL: AUC=0.952; and DLB: CSF DDC: AUC=0.901. Discussion: This analytical and clinical validation of the T48 Neuropanel highlights initial cut-offs and emerging biomarkers to aid clinical studies for the diagnosis, prognosis, and monitoring of neurodegenerative diseases. Highlights: The T48 Neuropanel shows robust analytical performance, with high detectability across both plasma and CSF matrices. The T48 Neuropanel validates established (i.e., pTau217, Abeta42, NfL, and GFAP) and emerging biomarkers (i.e., DDC, MMP10, ITGB2, ITGAM, NPTX2, NPTXR, SMOC1, sTREM1, and sTREM2) in CSF and plasma. CSF NfL, GFAP, ITGB2, and ITGAM and plasma GFAP were dysregulated across AD, FTD, and DLB dementias. -The multiplex design of the T48 Neuropanel enables rich biological interpretation by simultaneously quantifying established and emerging neurodegeneration biomarkers. Importantly, the inclusion of absolute quantification facilitates the establishment of cut-offs, supporting its potential for clinical translation.

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