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

Using Cognitive Models to Improve Language Model Simulation of Human Persuasion Games

arXiv:2606.17657v1 Announce Type: new Abstract: People make decisions differently in strategic interactions. Some update beliefs like a Bayesian; others exhibit biases like motivated reasoning. Although creators of large language models use simulated humans for safety evaluations and training, they often fail to cover this breadth of human behavior. We argue that cognitive science and economics provide a convenient tool for doing so, making use of mathematical models of human decision-making. We propose an approach that we call Equation-to-Behavior Prompting for guiding large language models to match cognitive models, and evaluate this approach on persuasion games based on legal decision-making. We find that large models can approximate equation-based specifications – Bayesian updating, affine distortion, motivated updating, and Grether's $\alpha$-$\beta$ model – using prompting, but small models fail to do so. However, training small models with reinforcement learning to adhere to mathematical rules, Equation-to-Behavior RL, reduces belief error by 26.5% in out-of-distribution parameterizations. We show that these simulations can help create diverse training environments; training small models to consider different kinds of decision-makers improves average belief change by 2.5%–12% over Bayesian-only training, even when persuading GPT-5-mini. Our work could improve human simulations for training and evaluation in increasingly realistic settings, and could also enable novel research into more complicated mathematical models of human decision-making.

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

A Stationarity-and-Coupling Criterion for Training-Free Time-Lagged Spectral Embeddings of Multivariate Time Series

arXiv:2606.13823v1 Announce Type: new Abstract: We study training-free fixed-length descriptors for multivariate time series and ask not merely whether such a descriptor performs well, but when it can be expected to work at all. Our object of study is $D(\tau)$, built from a time-lagged correlation matrix truncated at the Marchenko-Pastur edge so that only signal-bearing eigenvalues survive and classified by cosine similarity to class centroids with zero learned parameters. The central contribution is not the descriptor but a falsifiable applicability criterion for it. Working from a stationary Gaussian VAR(1) model, we argue that $D(\tau)$ separates two classes when the signals are approximately stationary and the class information lives in their cross-channel temporal coupling rather than in marginal per-channel power. We derive, semi-formally, three consequences: a distinguishability condition, why the static ($\tau=0$) covariance collapses to chance, and why a stationary but power-discriminated paradigm defeats the descriptor. The criterion is operational: a two-part pre-flight test – an augmented Dickey-Fuller stationarity check and a power-baseline saturation check – predicts applicability before any training. We validate both halves on a mixed assortment. On four paradigms that satisfy the criterion (Sleep-EDF, BCI-IV-2a, MIT-BIH, ESC-50) the descriptor is competitive with strong baselines at a fraction of their cost, reaching $88.5\pm4.5\%$ under 20-subject leave-one-subject-out on Sleep-EDF on a single CPU thread. On three that violate it – non-stationary ERPs, and financial-volatility and wearable-stress regimes that are power-discriminated – it fails exactly as the pre-flight predicts, and these negatives are the more informative half. We are explicit that $D(\tau)$ is not the most accurate representation; its value is a compact, training-free embedding whose domain of validity is known in advance.

03.
PLOS Computational Biology 2026-06-22

Adhesion and polarity-driven morphogenesis: Mechanisms and constraints in tissue formation

by Yoshiyuki T. Nakamura, Chikara Furusawa, Kunihiko Kaneko Embryonic development in multicellular organisms exhibits diverse morphogenetic patterns, which can generally be categorized into fundamental types such as monolayer and multilayer spheres, as well as cell masses. Furthermore, we identify two distinct processes for the formation of spherical structures. These basic patterns are thought to be governed by the microscopic properties of intercellular adhesion. However, the specific mechanisms linking the microscopic factors to the emergence of distinct macroscopic morphogenetic patterns remain poorly understood. In this study, we explore how different morphogenetic patterns arise by employing a computational model that incorporates intercellular adhesion and polarity. Our results demonstrate that all fundamental morphogenetic patterns can be generated through the interplay of two key parameters: the polarity strength of the cell and the regulation of polarity via mechanical signals. Furthermore, analytical considerations reveal key mechanisms underlying the formation of these patterns. These findings highlight the critical role of physical constraints in morphogenesis and suggest potential applications to the design of artificial tissues and organoids.

04.
arXiv (CS.CV) 2026-06-11

Mitigating Content Shift and Hallucination in GenAI Image Editing via Structural Refinement

Generative AI (GenAI) image editors, such as Nano Banana, produce visually compelling results for retouching tasks, enabling non-experts to edit images through text prompts alone. However, the generative nature of these models often introduces spatial misalignment, texture distortion, and content hallucination, all of which are detrimental to downstream workflows that require pixel-level fidelity. We identify a problem setting we call "structure-preserving GenAI fusion" for black-box GenAI image retouching: retain the perceptual enhancements of a GenAI output while enforcing structural faithfulness to the original input image. To address this problem, we propose a post-processing framework that fuses an input image with its GenAI-enhanced counterpart by first establishing coarse spatial and photometric correspondences, then performing a fusion stage that transfers desired enhancements while suppressing hallucinated content. In the absence of direct prior work in this setting, we evaluate our framework against representative methods from photorealistic style transfer and image fusion. Our experiments demonstrate that our method better preserves aesthetic quality while maintaining pixel-level structural consistency and the input resolution.

05.
arXiv (CS.CL) 2026-06-25

BitNet Text Embeddings

LLM-based text embedders have substantially improved retrieval and semantic representation quality, but their deployment remains costly: large backbone models slow down embedding inference, while high-dimensional full-precision embeddings impose substantial storage and bandwidth overhead on large-scale indexes. In this paper, we present BITEMBED, an extreme low-bit framework for LLM-based text embedding that jointly targets encoding efficiency and vector storage. BITEMBED converts pretrained LLM backbones into BitNet-style embedding encoders with ternary weights, quantized activations, and lightweight normalization refinement. The converted model is adapted to representation learning through continual contrastive pre-training, followed by supervised contrastive fine-tuning with both similarity-distribution distillation and attention-relation distillation from a full-precision teacher. Beyond quantizing the backbone, BITEMBED further trains output embeddings to support multiple storage precisions meeting different storage needs in various scenarios. Experiments on MMTEB (eng, v2) with Qwen3-0.6B and Gemma3-270M show that BITEMBED is largely comparable to full precision teacher embedders. Moreover, BITEMBED flexibly obtains text embeddings of various precisions, achieving a trade-off between performance and storage cost.

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

Helping Figures Tell their Story! Paper-Grounded Video Generation Explaining Complex Scientific Figures

Scientific figures compress complex pipelines into a single canvas, yet understanding them requires paper-grounded, step-by-step narration aligned with visual highlights a capability missing from current video generation systems and benchmarks. To address this, we introduce paper-grounded figure-to-video generation: generating narrated, region-grounded walkthrough videos from a figure and its paper. We propose MINARD (Multimodal Interpretation of Narrated Architecture via Region Decomposition), a pipeline that generates paper-grounded narrations and sequentially grounds them to figure regions. We also release FigTalk, a benchmark with new sequential and component-level grounding metrics derived. On FigTalk, MINARD generates humanlike, paper-faithful narrations and outperforms narration-conditioned figure spatial grounding compared to existing approaches in both automatic and human evaluation

07.
arXiv (math.PR) 2026-06-15

The 1/4-phenomenon of placement probabilities of tilings in the Aztec diamond

arXiv:2512.08377v2 Announce Type: replace-cross Abstract: We consider domino tilings of the Aztec diamond. Using the Domino Shuffling algorithm introduced by Elkies, Kuperberg, Larsen, and Propp in arXiv:math/9201305, we are able to generate domino tilings uniformly at random. In this paper, we investigate the probability of finding a domino at a specific position in such a random tiling. We prove that this placement probability is always equal to $1/4$ plus a rational function, whose shape depends on the location of the domino, multiplied by a position-independent factor that involves only the size of the diamond. This result leads to significantly more compact explicit counting formulas compared to previous findings. As a direct application, we derive explicit counting formulas for the domino tilings of Aztec diamonds with $2\times 2$-square holes at arbitrary positions.

08.
arXiv (CS.AI) 2026-06-17

EvolveNav: Proactive Preflection and Self-Evolving Memory for Zero-Shot Object Goal Navigation

arXiv:2606.18235v1 Announce Type: new Abstract: Zero-Shot Object-Goal Navigation (ZS-OGN) requires embodied agents to explore and locate target objects without any prior training. To this end, recent methods leverage foundation models. But they typically rely on static priors and lack adaptation, which leads to repeated errors and costly trial and error. In this paper, we propose a self-evolving ZS-OGN framework that enables continuous test-time improvement. Specifically, we build an agentic rule memory by extracting actionable knowledge from past trajectories. Then, we propose a retrieval strategy based on upper confidence bound, selecting effective rules by balancing semantic relevance and historical success. In addition, we introduce a memory-guided preflection module that forecasts potential outcomes before action, reducing inefficient exploration. Extensive experiments show that our method outperforms existing zero-shot baselines, achieving a 10.1\% improvement in success rate with fewer unnecessary steps.

09.
medRxiv (Medicine) 2026-06-15

Active commuting, anxiety symptoms and mental wellbeing: a dose-response study

Climate change draws attention to the planetary health perspective in sport and exercise sciences, that is, to physical activity that supports both human wellbeing and environmental sustainability. Active commuting is a sustainable form of physical activity with well-established somatic health benefits. However, more knowledge is needed on its relationship with mental health. We examined dose-response associations between active commuting, anxiety symptoms, and mental wellbeing among Finnish adults, and whether green commuting environment moderates these relationships. We used data from the cross-sectional Environment and Health Survey collected in June-September 2023 in the ten largest cities in Finland. Employed participants with data on anxiety symptoms (Generalized Anxiety Disorder-7, GAD-7), mental wellbeing (World Health Organization-Five Well-Being Index, WHO-5), commuting profile over a year (mode, frequency, distance, and perceived greenness along the commute route), and sociodemographic and lifestyle factors were included (n=1,672; mean age 45.3 years; 53.8% women). Active commuting was defined as travelling the entire commute by walking or cycling (including e-biking) that was converted into approximated annual km/week and MET-h/week. We used linear and logistic regression with restricted cubic splines to evaluate dose-response associations, adjusted for key covariates. The role of perceived greenness was tested using an active commuting x commute greenness interaction term. We found no dose-response relationships between active commuting and anxiety symptoms or mental wellbeing in any of the models. No effect modification by commute greenness was observed. More research on how active commuting may support planetary health from a mental health perspective is needed.

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

TIMI: Training-Free Image-to-3D Multi-Instance Generation with Spatial Fidelity

Precise spatial fidelity in Image-to-3D multi-instance generation is critical for downstream real-world applications. Recent work attempts to address this by fine-tuning pre-trained Image-to-3D (I23D) models on multi-instance datasets, which incurs substantial training overhead and struggles to guarantee spatial fidelity. In fact, we observe that pre-trained I23D models already possess meaningful spatial priors, which remain underutilized as evidenced by instance entanglement issues. Motivated by this, we propose TIMI, a novel Training-free framework for Image-to-3D Multi-Instance generation that achieves high spatial fidelity. Specifically, we first introduce an Instance-aware Separation Guidance (ISG) module, which facilitates instance disentanglement during the early denoising stage. Next, to stabilize the guidance introduced by ISG, we devise a Spatial-stabilized Geometry-adaptive Update (SGU) module that promotes the preservation of the geometric characteristics of instances while maintaining their relative relationships. Extensive experiments demonstrate that our method yields better performance in terms of both global layout and distinct local instances compared to existing multi-instance methods, without requiring additional training and with faster inference speed.

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

PermDoRA – Understanding Adapter Interference in Language Models: Limits of Parameter-Space Geometry

arXiv:2606.11262v1 Announce Type: cross Abstract: Access control in large language models (LLMs) requires modular mechanisms to enable domain-specific behavior without retraining or cross-domain interference. A common hypothesis is that interference during adapter composition arises from overlap in linear parameter updates, suggesting that enforcing orthogonality or directional independence should improve multi-domain performance. We test this hypothesis using DoRA-RBAC, a hierarchical adapter composition framework based on weight-decomposed low-rank adaptation. We compare conventional Euclidean merging with a geometry-aware Riemannian-inspired merging strategy that approximates the Frechet mean via normalized directional averaging across multiple QA benchmarks (GPQA, PubMedQA, SimpleQA, WMDP) on LLaMA-3.1-8B and Mistral-7B. Our results show that while single-domain performance matches LoRA, geometry-aware merging provides no consistent advantage over standard averaging in multi-domain settings.Diagnostic analysis further reveals that angular alignment and orthogonality of adapter updates are weak predictors of composition performance. These findings suggest that adapter interference is not governed primarily by parameter-space geometry, but is instead consistent with interactions in shared nonlinear representations.

12.
bioRxiv (Bioinfo) 2026-06-13

PertDiffBench: Benchmarking Diffusion Models for Single-Cell Perturbation Response Prediction

Diffusion models are increasingly used to predict transcriptional responses to perturbations, but whether they improve on simpler generative and representation-based baselines remains unclear. Existing evaluations often do not separate the effects of model architecture, input representation, biological context and metric choice, making it difficult to determine where diffusion-based methods are useful. Here we introduce PertDiffBench, a standardized benchmark for diffusion-based transcriptomic perturbation prediction across single-cell and bulk RNA-seq datasets. PertDiffBench evaluates diffusion-based models across three complementary evaluation settings: standard prediction in known single-cell contexts and bulk perturbation conditions, generalization to unseen cell types, species, drugs and intermediate time points, and stress tests of feature dimensionality, input representation, noise type and gene ordering. Across these settings, diffusion models did not show a consistent advantage. scGen remained a strong baseline in common prediction tasks, whereas scDiffusion was the most competitive diffusion-based method in several generalization settings. Temporal imputation showed a different pattern, with a simple DDPM operating directly in expression space outperforming more specialized models. Stress tests showed that performance was model dependent and sensitive to feature dimensionality, encoder choice, noise type and gene ordering. Pretrained encoders did not consistently improve performance, with the classical scVI representation slightly exceeding STATE in seen-condition and unseen-cell-type settings. These results indicate that diffusion-model performance in perturbation response prediction depends strongly on task design and representation choice. PertDiffBench provides a practical framework for evaluating these models under biologically varied and stress-tested conditions.

13.
arXiv (CS.AI) 2026-06-24

OpenThoughts-Agent: Data Recipes for Agentic Models

arXiv:2606.24855v1 Announce Type: new Abstract: Agentic language models dramatically expand the applications of AI yet little is publicly known about how to curate training data for broadly capable agents. Existing open efforts such as SWE-Smith, SERA, and Nemotron-Terminal typically target a single benchmark, leaving open the question of how to train models that generalize across diverse agentic tasks. The OpenThoughts-Agent (OT-Agent) project addresses this gap with a fully open data curation pipeline for training agentic models. We conduct more than 100 controlled ablation experiments to systematically investigate each stage of the pipeline, yielding insights on the importance of task sources and diversity. We then assemble a training set of 100K examples from our pipeline and fine-tune Qwen3-32B on this dataset, which yields an average accuracy of 44.8% across seven agentic benchmarks and a 3.9 percentage point improvement over the strongest existing open data agentic model (Nemotron-Terminal-32B, 40.9%). Moreover, our training data exhibits strong scaling properties, outperforming alternative open datasets at every training set size in compute-controlled comparisons. We publicly release our training sets, data pipeline, experimental data, and models at openthoughts.ai to support future open research on agentic model training.

14.
arXiv (quant-ph) 2026-06-17

Probing PbTe-Pb nanowire devices with radio-frequency reflectometry

arXiv:2606.04544v2 Announce Type: replace-cross Abstract: We report the implementation of radio-frequency (rf) reflectometry on selective-area-grown PbTe-Pb nanowire devices on a CdTe substrate. These nanowires are predicted to host Majorana zero modes. We demonstrate the compatibility of the rf technique, including both resistive and capacitive sensing, with these nanowires. The effect of dielectric loss from the CdTe substrate is quantitatively characterized. Furthermore, the feasibility of rf reflectometry is verified under finite magnetic fields where zero-energy modes can emerge. Our results establish the fast control of PbTe quantum devices, paving the way for their applications in topological quantum computation.

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

Gefen: Optimized Stochastic Optimizer

AdamW is a default optimizer for modern deep learning, but its first and second moment states add roughly two parameter-sized buffers to training memory. We propose Gefen, a memory-efficient optimizer that automatically shares second-moment estimates across parameter blocks and quantizes the first moment using a learned codebook, thereby reducing AdamW's memory footprint by ~8x while maintaining the same performance, corresponding to a reduction of 6.5 GiB per billion parameters. The method is motivated by a theoretical result showing that large mixed Hessian entries constrain the ratio of squared gradients toward one, suggesting that Hessian-aligned parameters are natural candidates for sharing second-moment statistics. Since computing Hessians is impractical at scale, Gefen infers block structure from the initial squared gradients, requiring no architecture-specific metadata or hyperparameters beyond AdamW defaults. Gefen learns an exact histogram-based dynamic-programming quantization codebook and reuses the same blocks for first-moment scaling. Across diverse experiments, Gefen achieves the lowest peak optimizer memory among the compared AdamW-like methods while maintaining AdamW-level performance. In FSDP and DDP training, the reduced memory footprint enables larger microbatches and improves throughput significantly over AdamW, providing a practical drop-in replacement with lower memory usage that can increase throughput and enable training larger models or using larger batch sizes. We provide the complete Python implementation, including fused CUDA kernels at https://github.com/ndvbd/Gefen

17.
bioRxiv (Bioinfo) 2026-06-19

Evaluation of analysis modes for RNA coexpression in single-cell and bulk tissue

Coexpression of transcripts presents the most common means of computational inference of transcription factor regulation, and is often combined with other data types to infer regulatory networks. With the growing popularity of single-cell approaches, there are questions about how best to extract coexpression information from the data. Recently we reported a simulation study that explored the differences among coexpression performed at different levels: across single cells (xCell, per cell type), across subjects from pseudobulked single-cell data (xSubject, per cell type), or across subjects using bulk tissue samples (xBulk). Here we test predictions made by those models using real data. We consider both preservation (consistency of coexpression findings across different levels of analysis of the same data) and replicability across independent studies, as well as biological interpretability. We find that preservation across levels is limited, indicating the choice of analysis level will affect outcomes. We show that xCell coexpression is more replicable across studies compared to xSubject. xBulk coexpression is dominated by patterns driven by variability in cellular composition and fails to capture much coexpression that is reliably detected at finer resolutions. While all modes of analysis exhibit some enrichment for known regulatory relationships, it was highest with the xCell mode. Finally, we present a case study of the effect of analysis modes on a schizophrenia-associated pattern, reinforcing the importance of analytic choices in the interpretation and replicability of coexpression analyses. Together with our modeling study, this work emphasizes the importance of understanding sources of expression covariation as they relate to the goals of the analysis, and recommend single-cell-based data with biological replicates should be the focus of attempts to infer dynamic regulatory interactions that are more likely to be replicable by others.

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

On the Limits of LLM-as-Judge for Scientific Novelty Assessment

arXiv:2606.12071v1 Announce Type: cross Abstract: LLMs are increasingly used to generate and judge scientific ideas. This makes novelty evaluation a central problem. Full idea evaluation is difficult because it often requires judging a method, its feasibility, and its empirical promise. We therefore study a cleaner upstream object: the research question (RQ). RQ generation is a prerequisite for scientific ideation, and RQs can be compared against questions pursued in real papers. We introduce RQ-Bench, a benchmark built from recent arXiv papers. For each paper, we reconstruct author-anchored RQs from its cited background, gaps, and contributions. These RQs are not the only valid questions for the same background. They are author-anchored reference points for testing novelty judgments. We evaluate model-generated RQs with standalone LLM judging, comparative LLM judging, and human expert evaluation. LLM judges consistently rate model-generated RQs as highly novel, producing a novelty mirage; in comparative evaluations, this preference becomes even stronger. Domain experts, however, reach the opposite conclusion and prefer the author-anchored reference questions. We further find that many generated RQs are narrow or source-bound, a dimension that LLM judges often miss unless explicitly tested. Overall, the contradictory novelty evaluations between LLM judges and human experts raise a serious concern about the reliability of using LLMs to assess the scientific novelty of research questions.

19.
arXiv (CS.CL) 2026-06-24

Exploring Academic Influence of Algorithms by Co-occurrence Network Based on Full-text of Academic Papers

Algorithms have become central to scientific research in the era of artificial intelligence (AI). Although algorithm mentions in papers are often used to indicate popularity and influence, existing studies usually evaluate individual algorithms in isolation and pay limited attention to the collective influence formed through their interconnections. This study constructs large-scale algorithm co-occurrence networks in natural language processing (NLP) based on the full text of academic papers and investigates algorithm influence from a network perspective. Using deep learning models, we extract algorithm entities and build overall, cumulative, and annual co-occurrence networks. We analyze their structural characteristics and apply multiple centrality measures to assess the group influence of algorithms across the whole field and over time. The results show that algorithm networks display typical features of complex networks, with increasingly dense connections developing over approximately two decades. Classic, high-performing algorithms and those located at the intersections of different research periods tend to have high popularity, control, centrality, and balanced influence. When the influence of an algorithm declines, it usually loses its core network position first, followed by weaker associations with other algorithms. This study is the first large-scale analysis of algorithm co-occurrence networks. Covering more than four decades of academic publications, it provides a temporal and structural view of algorithm influence and offers a foundation for future research on networks linking algorithms, scholars, and tasks.

20.
arXiv (CS.CV) 2026-06-12

Ex-Omni: Enabling 3D Facial Animation Generation for Omni-modal Large Language Models

Omni-modal large language models (OLLMs) aim to unify multimodal understanding and generation, yet extending them to jointly produce speech and 3D facial animation remains largely unexplored despite its importance for natural human-computer interaction. A key challenge is the mismatch between the discrete semantic reasoning of LLMs and the dense temporal dynamics required for 3D facial motion. We propose Expressive Omni (Ex-Omni), an open-source model that augments OLLMs with native speech-accompanied 3D facial animation. Ex-Omni decouples semantic reasoning from temporal generation through a blendshape-aware speech unit generator and a blendshape decoder, where speech units provide temporal scaffolding and hidden speech representations carry facially relevant cues. We further introduce a unified token-as-query gated fusion (TQGF) mechanism for controlled semantic injection, as well as InstructS2SF-1200K, a dataset consisting of 1200K samples for pre-training. Extensive experiments show that Ex-Omni maintains competitive speech understanding and generation ability while achieving better audio-visual synchronization and lower face-generation latency than cascaded pipelines.

21.
medRxiv (Medicine) 2026-06-23

Shared Polygenic Architecture Across Arteriopathies: An Integrative Cross-Trait Analysis

Background: Non-monogenic arteriopathies are often classified as distinct entities according to the arterial territory involved, yet they share clinical features and may co-occur in the same individual. This pattern suggests shared susceptibility across anatomically distinct arteriopathies, potentially driven by common biological and genetic mechanisms. Methods: We investigated the shared genetic architecture of five arteriopathies (cervical artery dissection (CeAD), intracranial aneurysm (IA), spontaneous coronary artery dissection (SCAD), aortic aneurysm and dissection (AAD), and fibromuscular dysplasia (FMD)) using LD score regression, Association analysis based on SubSETs (ASSET), pairwise Multi-Trait Analysis of Genome-wide association summary statistics (MTAG), pleiotropy mapping and Mendelian randomization (MR) to identify shared loci and prioritise candidate causal genes. Results: LD score regression identified significant positive genetic correlations between CeAD-SCAD (rg = 0.64), IA-AAD (rg = 0.33), IA-SCAD (rg = 0.37), CeAD-AAD (rg = 0.56) and SCAD-AAD (rg = 0.20). ASSET identified 37 shared independent loci, and in MTAG analyses, one novel locus was identified for CeAD and SCAD (SLC39A8) and one for IA (FGF5). 13 loci showed strong cross-trait colocalization, including PHACTR1, LRP1, and CDKN2B-AS1. Using the Genotype-Phenotype Map, we found that arteriopathy-associated variants colocalized with blood pressure- and migraine-related traits, while many showed effect directions opposite to those observed for coronary artery disease. Proteome-wide MR identified 67 circulating proteins associated with at least one trait, including ECM1 and SHISA5 for CeAD and FGF5 for IA, with 17 supported by colocalization. Transcriptome-wide MR identified 204 colocalized tissue?specific signals, of which, 14 were shared across multiple traits. Enrichment analyses implicated pathways related to vascular development, smooth muscle cell function, extracellular matrix organization, and TGF-? signaling. Conclusions: These findings support shared genetic architecture across anatomically distinct arteriopathies, implicating pathways involved in vascular structure and prioritising therapeutic targets for future mechanistic investigation.

22.
arXiv (CS.LG) 2026-06-12

Geometry of Lightning Self-Attention: Identifiability and Dimension

arXiv:2408.17221v3 Announce Type: replace Abstract: We consider function spaces defined by self-attention networks without normalization, and theoretically analyze their geometry. Since these networks are polynomial, we rely on tools from algebraic geometry. In particular, we study the identifiability of deep attention by providing a description of the generic fibers of the parametrization for an arbitrary number of layers and, as a consequence, compute the dimension of the function space. Additionally, for a single-layer model, we characterize the singular and boundary points. Finally, we formulate a conjectural extension of our results to normalized self-attention networks, prove it for a single layer, and numerically verify it in the deep case.

23.
arXiv (math.PR) 2026-06-11

Stochastic Reaction Networks Within Interacting Compartments with Content-Dependent Fragmentation

arXiv:2511.10223v4 Announce Type: replace Abstract: Stochastic reaction networks with mass-action kinetics provide a useful framework for understanding processes – biochemical and otherwise – in homogeneous environments. However, cellular reactions are often compartmentalized, either at the cell level or within cells, and hence non-homogeneous. We investigate a model of compartmentalization in which the rate of fragmentation of a compartment depends on the abundance of some designated species inside that compartment. The particular model of study is part of a general framework for compartmentalized chemistry with dynamic compartments that was proposed in (Duso and Zechner, PNAS, 2020). This paper builds on (Anderson and Howells, Bull. Math. Biol., 2023) where the special case where the compartment dynamics do not depend on their contents was studied mathematically. In particular, we demonstrate that the explosivity characterization from (Anderson and Howells, Bull. Math. Biol., 2023) fails in this setting and provide new sufficient conditions for non-explosivity and positive recurrence, under the assumption that the underlying CRN admits a linear Lyapunov function. These results extend the theoretical foundation for modeling content-mediated compartment dynamics, with implications for systems such as cell division and intracellular transport.

24.
arXiv (quant-ph) 2026-06-11

Tensor-Network-Based Distributed Quantum Dynamics on Independent Quantum Computers

arXiv:2606.11579v1 Announce Type: new Abstract: We present an approach based on tensor networks for distributed quantum computing simulation of chemical wavepacket dynamics in a continuous variable representation. The central idea is that the tensor-network representation of the multidimensional time-evolution operator naturally induces an elevated Hilbert space where the dynamics decomposes into a set of independent lower-dimensional propagations. This transformation converts an entangled quantum evolution into a set of parallel computational tasks that can be executed asynchronously across heterogeneous quantum and classical computing architectures. The resulting formalism establishes a direct connection between tensor-network decompositions, uniformly controlled quantum circuits, and asynchronous distributed quantum computing. The approach is developed with a goal towards hybrid quantum/classical implementation, and is appropriate for a general heterogeneous mixture of quantum hardware systems. The experimental realization of the asynchronously distributed quantum processes that arise from the tensor-network decomposition are carried out on the Sandia National Laboratories' trapped-ion quantum computer, where the circuits are compiled using native partial-entangling $XX(\theta)$ gates, reducing the expected two-qubit gate infidelity by more than 30\% relative to conventional fully entangling decompositions. We demonstrate the methodology by quantum computing the vibrational spectra of a small protonated water cluster that shows critical quantum nuclear behavior. Such water cluster systems have been found to be challenging for experimental action spectroscopy and for theory, and here, for the first time, we provide results for vibrational spectroscopy that are in agreement with the respective classical results to within 4cm$^{-1}$, thus allowing for the potential for spectroscopic accuracy from quantum computations.

25.
arXiv (CS.CL) 2026-06-24

Quantifying Prior Dominance in RAG Systems

作者:

Retrieval-Augmented Generation (RAG) grounds Large Language Models in external knowledge, yet current evaluations rely on discrete heuristics that suffer from ''epistemic blindness'' - failing to distinguish genuine contextual information extraction from parametric memory recall. To address this, we introduce the Normalized Context Utilization (NCU) metric, leveraging continuous token log-probabilities across zero-shot, oracle, and adversarial conditions to strictly quantify contextual information gain. Evaluating architectures ranging from 1.5B to 72B parameters alongside a proprietary commercial API reveals that for strict factual extraction (without Chain-of-Thought reasoning), traditional scaling laws exhibit extreme diminishing returns: highly efficient Small Language Models (SLMs) match or outperform high-capacity architectures. Furthermore, we demonstrate that ``Prior Dominance'' correlates with model scale and proprietary alignments. The evaluated commercial API not only overrode explicit external evidence in nearly half of adversarial conflicts, but also frequently suffered from systemic confidence collapse (Negative Transfer) when its parametric priors were contradicted. Our findings highlight the structural epistemic advantage and superior contextual adherence of SLMs in strict extraction workflows.