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01.
arXiv (CS.AI) 2026-06-18

From Specification to Execution: AI Assisted Scientific Workflow Management

arXiv:2606.18425v1 Announce Type: cross Abstract: Scientific workflow management systems (WMS) support scalable and reproducible execution of complex pipelines, but workflow design, implementation, and debugging remain largely manual and require significant expertise. Recent approaches using large language models (LLMs) show promise for workflow generation from natural language, but often rely on direct code synthesis, which limits transparency, reproducibility, and integration with workflow systems. We present an AI-assisted approach to scientific workflow management that combines specification-driven workflow generation, automated debugging, and distributed execution. The method introduces a structured specification phase that separates workflow intent, design, and implementation, allowing validation prior to code generation. We also develop an LLM-based debugging agent that diagnoses and resolves failures across multiple system layers. To support distributed execution and user interaction, we integrate Pegasus, a widely used WMS, with a Model Context Protocol (MCP) layer, providing a unified interface for workflow submission, monitoring, and control. We evaluate the approach using a federated learning workflow for medical imaging, chosen for its parallel, iterative, and dependency-intensive structure. The system generated and executed large-scale workflows with thousands of jobs, reduced debugging effort, and allowed non-expert users to construct workflows with expert-level design patterns. These results indicate that end-to-end AI-assisted workflow generation and execution is feasible, and point toward AI-driven platforms for managing the scientific workflow lifecycle.

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

Rift: A Conflict Signature for Deception in Language Models

Authors:

A model that lies while knowing the truth is the central case ELK cannot handle with behavioral evaluation alone. We ask whether such deception leaves an internal signature distinguishing it from honest error. Our key move is a control for wrongness: we contrast a sleeper agent (knows the truth, lies on trigger) against a naive liar (fine-tuned to emit the same wrong answers with no honest training). Both produce identical wrong outputs; any difference is about knowledge conflict, not incorrectness. We find deceptive forward passes carry a conflict signature - 2.1-2.3x higher residual rank than naive-liar passes on the same wrong answer - strong enough to identify which of two responses is the lie with 100% accuracy and no labels, across GPT-2 small/medium (three seeds) and three instruct models. Across Qwen2.5-1.5B/7B and Phi-3-mini, instructed deception raises residual rank on every tested fact (18/18, 40/40, 34/34); on Phi-3, lies separate perfectly from both honest answers and hallucinations (AUC 1.0, Wilcoxon p~6e-11). The signature survives strategic self-constructed deception (model invents its own lie, AUC 1.0), active concealment attempts (AUC 1.0), and length-controlled replication (20/20, AUC 1.0, p~1e-6). Using basis-free relative representations, a probe trained on one model family detects deception in two other families zero-shot (mean AUC 0.933), surviving simultaneous architecture and format change (AUC 0.821), and transfers across five languages (AUC 1.000, length-controlled). The signature is read-only: detectable but not injectable (0/8 both directions). Honest limitations and six negative experiments are documented in full.

03.
arXiv (CS.AI) 2026-06-19

DataMagic: Transforming Tabular Data into Data Insight Video

arXiv:2606.20388v1 Announce Type: cross Abstract: Data videos integrate dynamic charts, voice narration, and synchronized animations to communicate data insights as temporal narratives, making them an effective medium for improving data consumption efficiency in the data management lifecycle. However, producing high-quality data videos requires expertise spanning data analysis, narrative design, and video production. Existing approaches fall short: static visualization tools (e.g., BI dashboards) lack narrative logic and animation; authoring tools require users to pre-prepare visualizations rather than working from raw data; pixel-level video generation models cannot guarantee data fidelity or provenance. We demonstrate DataMagic, an end-to-end interactive system that transforms raw tabular data and natural language queries into narrative data-insight videos. To ensure data fidelity, DataMagic introduces the declarative specification DVSpec, which binds visual and animation elements to underlying data fields through data-driven semantic references. To address the combinatorial explosion of the design space, DataMagic adopts a Generate-then-Orchestrate multi-agent architecture that generates candidate scenes in parallel and then optimizes narrative coherence through global orchestration. Leveraging DVSpec's decoupling of logic and rendering, the system further supports three interaction modes and structured provenance-based data Q&A, transforming one-way videos into explorable interactive data interfaces. Evaluation on 109 real-world samples validates the effectiveness of the DataMagic. Homepage: https://datamagic-home.github.io/

04.
arXiv (quant-ph) 2026-06-16

Generalized Kerr-Cat Qubit Codes

arXiv:2606.14901v1 Announce Type: new Abstract: We present a systematic study of Schrödinger cat codes constructed from Kerr-type coherent states, including displaced Kerr coherent states and Barut–Girardello Kerr coherent states, each admitting two distinct families determined by the sign of the Kerr nonlinearity. By tuning the Kerr parameter and coherent-state amplitude, these states interpolate between $\mathfrak{su}(2)$, $\mathfrak{su}(1,1)$ coherent states, providing a unified and versatile foundation for this type of bosonic quantum error correction. Unlike standard two-component Schrödinger cat codes, where a single photon-loss event induces an uncorrectable bit-flip, the nonlinear phase-space structure of Kerr cat states enables simultaneous detection and correction of both photon-loss and dephasing errors within a unified recovery framework, with optimal recovery operations determined via convex optimization. We demonstrate that Kerr cat encodings significantly outperform conventional cat codes under combined loss and dephasing noise, and that judicious parameter optimization can suppress both error channels to a level that reduces the overhead of additional error correction layers. We further show that Kerr-deformed coherent-state manifolds under engineered two-photon driving emerge as effective steady states of driven-dissipative dynamics, with single-photon decoherence strongly suppressed and leakage outside the protected manifold appearing only as higher-order corrections in the deformation strength. Our extended formalism identifies generalized Kerr Schrödinger cat codes as promising candidates for fault-tolerant bosonic quantum computation in experimental platforms such as nonlinear photonics.

05.
Nature (Science) 2026-06-22

C-glycoside synthesis via radical cross-coupling of glycohydrazides

Authors:

Carbohydrates are among the most abundant and structurally diverse biomolecules in nature, playing central roles in energy storage, molecular recognition, and cell signaling. Within this domain, C-glycosides1-3, in which the oxygen atom of the glycosidic bond in O-glycosides is replaced by carbon, have emerged as valuable motifs in medicinal chemistry due to their resistance to enzymatic hydrolysis2,4. Of particular importance are C-aryl glycosides, exemplified by the SGLT2 inhibitors dapagliflozin, canagliflozin, and empagliflozin, which are frontline therapies for type 2 diabetes5-7. However, scalable syntheses of C-aryl glycosides have traditionally relied on protected sugar derivatives, lengthy sequences, or conventional cross-couplings that often suffer from poor selectivity, limited scope, and extensive protecting-group manipulation6. Herein, we report a practical approach to C-aryl glycosides using glycosyl sulfonyl hydrazides as redox-neutral radical precursors for cross-coupling. Prepared directly from unprotected native sugars, these reagents generate glycosyl radicals under mild conditions and enable efficient access to diverse C-aryl glycosides, including all approved SGLT2 inhibitors, natural products such as salmochelins and neopetrosins, and medicinally relevant probes. Beyond anomeric functionalization, this platform enables C–C bond formation at multiple positions on carbohydrate scaffolds and supports stereoretentive radical coupling that can override inherent stereochemical biases, expanding practical access to carbohydrate-derived therapeutics and chemical tools.

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

Achieving High-Quality Portfolio Optimization with the Variational Quantum Eigensolver

arXiv:2508.18625v2 Announce Type: replace Abstract: Portfolio optimization lies at the core of quantitative finance and aims to determine how assets should be allocated to balance expected returns against risk. It can be formulated as a Quadratic Unconstrained Binary Optimization (QUBO) problem, which is NP-hard. Quantum computing offers the potential to solve such problems more efficiently than classical methods. In this work, we employ the Variational Quantum Eigensolver (VQE) to address the portfolio optimization problem. To increase the likelihood of converging to high-quality solutions, we propose using the Weighted Conditional Value-at-Risk (WCVaR) as the cost function and the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) as the optimizer. Our experiments are conducted using both classical simulations and quantum hardware on the Wuyue QuantumAI platform. Together, these results demonstrate that the combination of WCVaR and CMA-ES improves the performance of VQE for portfolio optimization and provides a practical route for applications on NISQ devices.

07.
PLOS Computational Biology 2026-06-15

A multilevel hierarchical framework for quantification of experimental heterogeneity in population snapshot data

by David J. Warne, Xiangrun Zhu, Thomas P. Steele, Stuart T. Johnston, Scott A. Sisson, Matthew Faria, Ryan J. Murphy, Alexander P. Browning Biological systems exhibit substantial heterogeneity: that is, variation in specific characteristics of individuals within a population. As a result, it is of critical importance to appropriately account for biological heterogeneity when calibrating mathematical models to infer cellular processes and predict behaviour. Recent approaches consider ordinary differential equations with random parameters to quantify heterogeneity in dynamical processes of cells. In this setting, statistical inference is performed to characterise the distribution of these random parameters within a cell population. One significant limitation of this approach is the tacit assumption that there are no substantial deviations in these distributions across experimental replicates. In this work, we propose a flexible Bayesian hierarchical differential equation modelling framework that quantifies and distinguishes both inter-experimental heterogeneity (heterogeneity between experimental replicates) and intra-experimental heterogeneity (biological heterogeneity within replicate populations). We consider two recent studies that employ mathematical models to interpret flow cytometry snap-shot data and quantify heterogeneity in nano-particle cell interactions and cell internalisation processes. Using simulation data, we demonstrate that substantial inaccuracy in the inferred dynamics can arise when experimental heterogeneity is not accounted for. By contrast, our hierarchical approach is robust to variability in inter-experimental and intra-experimental heterogeneity and our method simplifies to previous methods when inter-experimental heterogeneity is negligible. Our approach is flexible and widely applicable to applications involving replicate populations and snapshot data. We provide open-source implementations of our methods on GitHub.

08.
arXiv (CS.LG) 2026-06-16

Next-Latent Prediction Transformers Learn Compact World Models

arXiv:2511.05963v4 Announce Type: replace Abstract: Transformers replace recurrence with a memory that grows with sequence length and self-attention that enables ad-hoc lookups over past tokens. Consequently, they lack an inherent incentive to compress history into compact latent states with consistent transition rules. This often leads to learning solutions that generalize poorly. We introduce Next-Latent Prediction (NextLat), which extends standard next-token training with self-supervised predictions in the latent space. Specifically, NextLat trains a transformer to learn latent representations that are predictive of its next latent state given the next token. Theoretically, we show that these latents provably converge towards belief states, compressed information about the history necessary to predict the future. This simple auxiliary objective injects a recurrent inductive bias into transformers while leaving their architecture, parallel training efficiency, and inference unchanged. NextLat effectively encourages transformers to form compact internal world models with coherent belief states and transition dynamics – crucial properties not guaranteed by standard next-token prediction alone. Empirically, across benchmarks in world modeling, reasoning, planning, and language modeling, NextLat demonstrates significant gains over standard next-token prediction and other baselines in downstream accuracy, representation compression, and lookahead planning. Furthermore, NextLat enables variable-length self-speculative decoding, accelerating inference by up to 3.3x in language modeling. NextLat offers a simple yet effective paradigm for learning compact, predictive representations in transformers that generalize better. Our code is available at https://github.com/JaydenTeoh/NextLat.

09.
arXiv (CS.CV) 2026-06-12

Contrast-Informed Augmentation and Domain-Adversarial Training for Adult-to-Neonatal MR Reconstruction Generalization

Purpose: To investigate whether contrast-informed data augmentation and domain-adversarial training improve the adult-to-neonatal generalization of the E2E-VarNet. Methods: Three training regimes were investigated: (1) adult-only training with unaugmented adult data, (2) mixed training with paired unaugmented and neonatal-informed augmented adult data, and (3) mixed training with a domain-adversarial objective. Models were trained on retrospectively undersampled multi-coil adult T2-weighted brain MR data and evaluated on neonatal and adult test data at acceleration factors $R=4$ and $R=8$ using quantitative metrics and qualitative evaluation. Feature analyses assessed whether domain-adversarial training altered the latent representations of unaugmented adult, augmented adult, and neonatal test samples. Results: Mixed training (Mixed) and mixed domain-adversarial training (Mixed-DAT) outperformed unaugmented adult-only training (Unaug-Only) when evaluated on neonatal data. At R=4, Mixed-DAT achieved the best performance (SSIM = 0.924 +/- 0.027, PSNR = 33.98 +/- 1.15 dB). At R=8, Mixed-DAT performed best when measured using SSIM (0.848 +/- 0.031 vs. 0.766 +/- 0.037 for Unaug-Only and 0.814 +/- 0.035 for Mixed) and Mixed performed best when measured using PSNR (29.56 +/- 0.83 dB vs. 26.26 +/- 0.78 dB for Unaug-Only and 29.43 +/- 0.83 dB for Mixed-DAT). Qualitative assessment of t-SNE plots suggested that Mixed-DAT increased the overlap among the latent representations of the unaugmented adult, augmented adult, and neonatal test data. Conclusion: Contrast-informed augmentation and domain-adversarial training improved adult-to-neonatal generalization of deep learning-based MR reconstruction. These findings suggest that contrast-informed data augmentation combined with adversarial training may improve robustness to domain shift in undersampled neonatal MR reconstruction.

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

Telenor Nordics Customer Service self-help corpus

Authors:

This paper presents a multilingual customer service self-help corpus comprising 1,122 manually validated documents in Finnish, Danish, Norwegian, and Swedish, totaling 274,599 words and 1,884,833 characters. The documents have been sourced from the public self-help pages of four Nordic telecommunications operators and subsequently filtered for person-identifiable information and relevance through a combined LLM and human annotation pipeline. Domain-specific datasets for Nordic languages remain scarce, particularly in customer service: a domain of growing importance for retrieval-augmented generation, cross-lingual transfer learning, and emerging agent-based service architectures. An analysis of the corpus reveals substantial variation in document length and structure across operators, reflecting distinct editorial strategies, as well as broad topical coverage spanning network hardware, mobile services, TV and streaming, billing, and account management. The dataset is publicly available under a CC-BY-NC-SA-4.0 license at https://zenodo.org/records/20732652, intended to support reproducible research in Nordic NLP and information retrieval.

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

Structure preserving properties of higher order moment closures for TASEP

arXiv:2604.15925v2 Announce Type: replace-cross Abstract: The totally asymmetric simple exclusion process (TASEP) is a stochastic model for the unidirectional flow of interacting particles on a 1D-lattice that is much used in systems biology and statistical physics. Its master equation describes the evolution of the probability distribution on the configuration space. The size of the master equation grows exponentially with the length of the lattice. It is known that the complexity of the system may be reduced using mean-field approximations. We provide a rigorous definition of a family of such models using moments of any order and an extension to the pair approximation for obtaining closures for the system. The dimension of these models grows linearly with the lattice size and exponentially in the order of the approximation. Moreover, we show that the states of these models still have a probabilistic interpretation and that basic structural properties of the master equation are preserved. This extends known results on the Ribosome Flow Model which can be viewed as the first order approximation for TASEP.

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

Emergence of Hierarchical Emotion Organization in Large Language Models

As large language models (LLMs) increasingly power conversational agents, understanding how they model users' emotional states is critical for ethical deployment. Inspired by emotion wheels, i.e., a psychological framework that argues emotions organize hierarchically, we analyze probabilistic dependencies between emotional states in model outputs. We find that LLMs naturally form hierarchical emotion trees that align with human psychological models, and larger models develop more complex hierarchies. We also uncover systematic biases in emotion recognition across socioeconomic personas, with compounding misclassifications for intersectional, underrepresented groups. Human studies reveal striking parallels, suggesting that LLMs internalize aspects of social perception. Beyond highlighting emergent emotional reasoning in LLMs, our results hint at the potential of using cognitively-grounded theories for developing better model evaluations.

13.
medRxiv (Medicine) 2026-06-17

Characterizing the genetic basis of Cardio-Renal-Metabolic multimorbidity using multivariate genomic modelling

Cardio-renal-metabolic multimorbidity (CRMM) encompasses interrelated conditions affecting the heart, kidneys, and metabolic systems. Although the genetics of individual components are well studied, their shared architecture remains unclear. Here, we performed the largest multi-ancestry multivariate GWAS of CRMM across seven biobanks, including individuals of European (EUR; neff = 353,130), African (AFR; neff = 75,436), and East Asian (EAS; neff = 164,373) ancestry. We identified 287 lead loci in EUR, 30 in AFR, and 202 in EAS. Cross-ancestry analyses revealed ancestry-specific signals and 24 shared loci mapping to FTO and TCF7L2. Drug-repurposing highlighted candidates used for type 2 diabetes and hypertension. Mendelian randomization supported causal links with diverse diseases, while polygenic risk scores showed improved prediction across ancestries. Collectively, these findings advance understanding of CRMM genetics and inform precision medicine.

14.
arXiv (CS.LG) 2026-06-11

Few-Shot Resampling for Scalable Statistically-Sound Data Mining

arXiv:2606.11235v1 Announce Type: new Abstract: A key step in knowledge discovery is the evaluation of data mining results. In several applications, including pattern mining, graph analysis, and others, this step includes the evaluation of the statistical significance of the results, to avoid spurious discoveries due only to noise or random fluctuations in the data. While specialized procedures have been developed for some specific applications, resampling-based approaches are widely used, in particular for complex analyses where analytical results cannot be derived. However, current resampling-based approaches require the generation and analysis of thousands of resampled datasets, and are therefore impractical for large datasets or computationally intensive analyses. In this paper, we introduce FewRS, a simple and effective resampling-based approach to assess the statistical significance of data mining results with rigorous guarantees on the probability of false discoveries. Our approach can be used in every situation where resampling-based approaches are applied. FewRS builds on our derivation of a novel bound to the supremum deviation of test statistics representing the quality of data mining results. We prove that FewRS needs to generate and analyze an extremely small number of resampled datasets, leading to a highly scalable approach with wide applicability. We test our approach on common tasks such as pattern mining and network analysis. In all cases, our approach results in a reduction of up to two orders of magnitude in running time compared to the state of the art, while preserving high statistical power, enabling the statistical validation of data mining results on large-scale real-world datasets.

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

Application of integrated gradients explainability to sociopsychological semantic markers

Classification of textual data in terms of sentiment, or more nuanced sociopsychological markers (e.g., agency), is now a popular approach commonly applied at the sentence level. In this paper, we exploit the integrated gradient (IG) method to capture the classification output at the word level, revealing which words actually contribute to the classification process. This approach improves explainability and provides in-depth insights into the text. We focus on sociopsychological markers beyond sentiment and investigate how to effectively train IG in agency, one of the very few markers for which a verified deep learning classifier, BERTAgent, is currently available. Performance and system parameters are carefully tested, alternatives to the IG approach are evaluated, and the usefulness of the result is verified in a relevant application scenario. The method is also applied in a scenario where only a small labeled dataset is available, with the aim of exploiting IG to identify the salient words that contribute to building the different classes that relate to relevant sociopsychological markers. To achieve this, an uncommon training procedure that encourages overfitting is employed to enhance the distinctiveness of each class. The results are analyzed through the lens of social psychology, offering valuable insights.

16.
arXiv (CS.CV) 2026-06-11

VOID: Defeating Unauthorized Mimicry in Latent Diffusion Models

While Latent Diffusion Models (LDMs) have revolutionized visual synthesis, they are increasingly exploited for unauthorized mimicry of individuals. Existing defenses inject deceptive perturbations to steer the generated images toward irrelevant targets. However, this approach hinges on an ungrounded assumption: subtle perturbations can maintain their deceptive efficacy throughout an LDM's extensive generation process. In reality, the model's innate restoration mechanism will remove such perturbations and cause individual identities to re-emerge in the images generated. We propose VOID, a defense framework that overcomes this conundrum by manipulating an LDM's intrinsic stochasticity. VOID perturbs the diffusion pipeline in two novel ways: 1) amplifying the latent encoding errors to shatter an image's semantic structure, and 2) counteracting the target guidance signals to suppress the model's restoration capabilities. This results in a semantic corruption that thwarts any unauthorized mimicry. Notably, the security gain does not come at the price of visual utility, as VOID simultaneously manages to confine perturbations to human-imperceptible regions of protected images. Our comprehensive evaluation of 24 state-of-the-art defenses against 10 mimicry attacks on 5 datasets demonstrates VOID's unprecedented protection power: it increases the average Frechet Inception Distance (FID) from 113 to 365, a 223% improvement over the strongest defense to date.

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

A Lightweight Fiducial-Based Pipeline for 3D Hyperspectral Mapping of ex-vivo Lumpectomy Specimens

Hyperspectral Imaging (HSI) is a promising modality for intraoperative assessment of resection margins in Breast-Conserving Surgery (BCS), but its clinical translation requires aligning the inherently 2D spectral information onto the 3D shape of the excised tissue so that suspicious regions can be precisely localized for targeted follow-up. We present a fully automated, calibration-free pipeline that produces a 3D hyperspectral point cloud of an ex-vivo lumpectomy specimen from a set of consumer-camera RGB images and a single top-down HSI acquisition. The 3D geometry is reconstructed with a deep-learning Structure-from-Motion backbone, stabilized in a metric reference frame by a custom bundle adjustment that enforces consistency on the corners of four ArUco markers placed around the specimen. The HSI cube is then registered to the reconstruction without recovering the HSI camera pose: the markers, visible in both modalities, define 16 corner correspondences that drive a planar homography, and 3D coordinates are recovered by lookup on an orthographically rendered depth map. Evaluated on two ex-vivo lumpectomy specimens, the pipeline achieves a median 3D registration error below 1~mm and a 2D reprojection error below 0.02 mm, with a total per-specimen processing time under 4 minutes on accelerated hardware. These results support the feasibility of integrating HSI-guided spatial localization into intraoperative margin assessment workflows for breast-conserving surgery.

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

SAFformer:Improving Spiking Transformer via Active Predictive Filtering

Spiking Neural Networks (SNNs) offer notable advantages in biological plausibility and energy efficiency, making them promising candidates for building low-power Transformers. However, existing Spiking Transformers largely adhere to a passive reactive paradigm, which struggles to focus on task-relevant information and incurs substantial computational overhead when processing redundant visual data. To overcome this fundamental yet underexplored limitation, we propose SAFformer, a novel Spiking Transformer architecture based on an active predictive filtering paradigm. Inspired by the brain's predictive coding mechanism, SAFformer actively suppresses predictable signals and focuses on salient visual features. Extensive experiments show that SAFformer establishes new state-of-the-art performance on CIFAR-10/100 and CIFAR10-DVS. Remarkably, on ImageNet-1K, it achieves 80.44% Top-1 accuracy with only 26.58M parameters and an energy consumption of 5.88 mJ, demonstrating an exceptional balance between accuracy and efficiency.

19.
medRxiv (Medicine) 2026-06-16

Adverse Childhood Experiences and Growth Outcomes in Childhood: A Longitudinal EHR-Based Study

Question Are adverse childhood experiences (ACEs) associated with altered growth trajectories in childhood? Findings In this cohort study of 412,549 children and adolescents, ACEs were associated with lower height throughout childhood, earlier pubertal timing, and shorter final stature. Height differences emerged approximately 2 years before ACE documentation and were greatest among those with earlier documentation. Meaning These findings suggest that early adversity affects physical growth in children and may serve as a measurable indicator of the biological consequences of early-life stress, especially in those with documentation of ACEs prior to the onset of typical pubertal growth. Importance Adverse childhood experiences (ACEs) are among the strongest risk factors for long-term mental and physical health complications, yet their impact on physical growth in childhood remains incompletely understood. Objective To determine the association of ACEs on childhood growth trajectories and growth dynamics. Design, Setting and Participants Retrospective cohort study using longitudinal electronic health record data. Data was collected from participants between February 1999 and August 2025. A large academic medical center biobank linked to deidentified electronic health records in the southeastern United States. A total of 412,549 individuals with at least 2 recorded height measurements between the ages of 2 and 20 were included in the primary analysis. Growth curve analyses were performed in a subset of 199,844 individuals with at least 3 height measurements spanning at least 2 years. Genetic analyses were performed in a subset of 10,114 individuals of primarily European ancestry. Exposure(s) Documented exposure to adverse childhood experiences before age 18 years identified through a natural language processing algorithm. Main Outcome(s) and Measure(s) Height-for-age z-scores across childhood, final attained height, and growth curve parameters estimated using SuperImposition by Translation and Rotation (SITAR) modeling. Results Among 412,549 participants, 18,502 (4.5%) had clinically documented ACEs during childhood. ACE documentation was associated with lower height-for-age z-scores throughout childhood and adolescence. Final attained height was significantly lower among ACE-documented individuals, with mean differences of -3.0 cm among males (174.0 cm vs 177.0 cm, p < 0.001) and -1.3 cm among females (161.8 cm vs 163.1 cm, p < 0.001). Height differences emerged approximately 2 years before clinical ACE documentation. Earlier age at first ACE documentation was associated with progressively shorter final attained height, with each year decrease in age at ACE documentation associated with a decrease in final height of -0.20 cm in females and -0.35 cm in males. Those with first ACE documented prior to pubertal age also showed the most pronounced growth dynamic differences, with males demonstrating a mean reduction in size of 5.25 cm (95% CI, -6.79 cm to -3.70 cm) and 1.26-year earlier pubertal timing (95% CI, -1.50 to -1.03 years), and females demonstrating a reduction in growth curve size of 3.62 cm (95% CI, -4.83 to -2.41 cm) and 1.14-year earlier pubertal timing (95% CI, -1.29 to -0.99 years). Conclusions and Relevance In this large clinical cohort, clinically documented ACEs were associated with time-dependent reductions in stature, earlier pubertal timing, and short final attained height. These findings suggest that early childhood adversity may have lasting effects on physical development and highlight growth trajectories as a potential marker of the biological consequences of early-life stress.

20.
arXiv (CS.AI) 2026-06-19

ELVA: Exploring Ranking-Driven Universal Multimodal Retrieval

arXiv:2606.20280v1 Announce Type: cross Abstract: Leveraging Multimodal Large Language Models (MLLMs) via contrastive learning has become a mainstream paradigm for improving the performance of Universal Multimodal Retrieval (UMR). However, previous works have ignored the grain blindness when adapting the contrastive paradigm into retrieval tasks. Grain blindness refers to the tendency of the model to overlook grain-level information contained in the query, which is crucial for effectively handling complex queries. This stems from contrastive learning treating samples as a binary classification (positive/negative), while ignoring the different information carried by each negative sample. To address this, we argue that negatives should be treated differently according to their similarity to the positive sample, enabling the model to learn distinct grain information from each negative. In this paper, we introduce a simple but effective framework, called ELVA, a novel rule-based RL framework that mitigates grain blindness through ranking-driven MLLMs. 1) Instead of relying on reward models, we extend Reinforcement Learning with Verifiable Rewards (RLVR) to retrieval tasks, allowing the model to explore new ranking behaviors without explicit ranking labels. 2) By utilizing rule-based rewards, our approach jointly optimizes the ranking of negative samples while enlarging the similarity gap between positive and negative. To more precisely measure grain blindness, we further introduce MRBench, a new benchmark specifically designed for multi-grain query scenarios. ELVA achieves state-of-the-art results across standard retrieval benchmarks, and its notable 13.1% improvement on MRBench further demonstrates its effectiveness in alleviating grain blindness.

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

The Discrete-Log Clock: How a Transformer Learns Modular Multiplication

arXiv:2606.17399v1 Announce Type: cross Abstract: When small transformers grok modular multiplication, prior work reports that the learned embedding has a "dense" Fourier spectrum requiring all frequencies. This contrasts with modular addition, where only a sparse set of key frequencies suffices. We show this density is an artifact of analyzing in the wrong basis. The natural Fourier transform for multiplication is not the standard additive DFT but the multiplicative character transform, which decomposes functions on the multiplicative group $(\mathbb{Z}/p\mathbb{Z})^*$ into its irreducible representations. Applying this transform to a grokked transformer trained on $a \cdot b \bmod 113$, we find the embedding spectrum becomes highly sparse (Gini coefficient 0.58 vs. 0.07 in the additive basis) with only 4 key frequencies carrying significant energy. Furthermore, 96.9% of MLP neurons are cleanly tuned to a single multiplicative frequency, and neuron activation heatmaps reveal 2D-periodic structure when reordered by the discrete logarithm. These results demonstrate the transformer reduces multiplication to addition in discrete-log space, implementing a "Discrete-Log Clock" algorithm analogous to Nanda et al.'s Clock algorithm for addition. The methodology generalizes: matching the analysis basis to the algebraic structure of the task reveals interpretable structure where standard tools see noise.

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

HSQ-VLM: A Novel Spatially-Constrained Quadrant Segmentation VLM Model for Explainability in Diabetic Retinopathy

Authors:

Diabetic Retinopathy (DR) is an aggressive retinal disease and a leading cause of global blindness, yet its clinical management is currently hindered by the black-box nature of diagnostic AI. While deep learning models achieve high classification accuracy, there is a critical lack of explainability methods capable of detailing the exact anatomical landmarks and lesion distributions that lead to a clinical decision for DR. Therefore, we propose HSQ-VLM, a novel quadrant segmentation pipeline on fundus images that utilizes a Landmark-Anchored Cartesian Cross-Attention mechanism to unify visual feature extraction with structured clinical reasoning. Unlike traditional methods that rely on arbitrary image partitioning, our pipeline implements 4-quadrant Topological Latent Partitioning (TLP) to dynamically align retinal features with a fovea-centered coordinate system. This allows the Vision-Language Model to generate natural language reports that quantify pathology with anatomical precision. On a dataset of 3,500 high-resolution fundus images, this innovative methodology achieved a lesion detection sensitivity of 99.6% for hemorrhages and 96.4% for microaneurysms, while demonstrating a significant reduction in boundary-ambiguity errors compared to standard segmentation baselines.

23.
PLOS Computational Biology 2026-06-22

Cell-type resolved transcriptional network analysis of <i>in vivo</i> cellular senescence following injury

Authors:

by Alda Sabalic, Victoria Moiseeva, Andres Cisneros, Oleg Deryagin, Eusebio Perdiguero, Pura Muñoz-Cánoves, Jordi Garcia-Ojalvo Identifying the genetic correlates of complex phenotypes is a challenging task. Methods coming from the field of complex networks can help finding such molecular patterns, by revealing statistical associations among groups of genes that correlate with the phenotype. Here we study cellular senescence, a complex cell state whose molecular underpinnings are still under active investigation. We analyze cell type–resolved RNA sequencing data obtained from injured muscle tissue in mice, with a network-based approach that merges eigenvector centrality feature selection and community detection. Our analysis identifies genetic markers that had not been associated with senescence so far, which are validated with existing single-cell RNA sequencing data in a different type of tissue. The identified key genes belong to transcriptional pathways associated with established hallmarks of senescence, and thus can be interpreted as molecular correlates of such hallmarks. The method proposed here could be applied to any complex cellular phenotype even when only bulk RNA sequencing is available, provided the data is resolved by cell type.

24.
arXiv (CS.AI) 2026-06-15

AdaTKG: Adaptive Memory for Temporal Knowledge Graph Reasoning

arXiv:2605.07121v2 Announce Type: replace Abstract: Temporal knowledge graphs (TKGs) represent time-stamped relational facts and support a wide range of reasoning tasks over evolving events. However, existing methods produce entity representations that are static at the entity level, in that each representation is a function of learned parameters only and retains no trace of the interactions in which the entity has participated. In this paper, we depart from this static view and propose that each entity be modeled as an adaptive process whose representation is refined every time the entity participates in a fact. To this end, we propose AdaTKG, which maintains a per-entity memory that is updated with every observed interaction, with the memory accumulating online and predictions improving as more interactions arrive. Specifically, we instantiate the memory update as a learnable exponential moving average governed by a single shared scalar instead of using learnable parameters for each entity, enabling AdaTKG to handle entities unseen during training. Extensive experiments confirm consistent gains over TKG baselines, demonstrating the effectiveness of adaptive memory. Code is available at: https://github.com/seunghan96/AdaTKG

25.
Science (Express) 2026-05-07

Induction of broadly neutralizing HIV antibodies by a two-step mechanism informs vaccine design | Science

Authors: Unknown Author

A major obstacle confronting HIV-1 vaccine and cure research is the lack of an outbred animal model for rapid and consistent induction of broadly neutralizing antibodies (bNAbs). We designed an epitope-focused simian-human immunodeficiency virus (SHIV.5MUT) that elicited broad and potent V3-glycan-targeted antibodies within a year of infection in 14 of 22 macaques compared with 0 of 14 control animals. SHIV.5MUT elicited bNAbs by a two-step mechanism, inducing an initial wave of V1-directed antibodies that selected for Envs with shortened, hypoglycosylated V1 loops, which in turn primed V3-glycan bNAb precursors. Rhesus bNAbs were immunogenetically and structurally diverse, closely resembling human V3-glycan bNAbs. Env-bNAb coevolution revealed a diverse repertoire of bNAb precursors and the Env variants that matured them, yielding a molecular blueprint for vaccine design.