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01.
arXiv (CS.AI) 2026-06-15

VISTA: View-Consistent Self-Verified Training for GUI Grounding

arXiv:2606.14579v1 Announce Type: new Abstract: When applying Group Relative Policy Optimization (GRPO) for GUI Grounding, rollouts are sampled from a single screenshot view; groups often become either all failures on difficult instances or all successes on easy ones, yielding no useful relative advantage. We propose VISTA (View-Consistent Self-Verified Training), a GRPO-based training framework that constructs each comparison group from multiple target-preserving views of the same GUI instance.Each view is generated by a crop that keeps the target element visible and remaps its box exactly, so model rollouts are compared across semantically equivalent but geometrically different inputs. To stabilize short coordinate generation without turning reinforcement learning into unconditional imitation, VISTA further adds a self-verified cross-view anchor: an oracle answer optimized with an advantage-weighted loss, excluded from the group baseline and activated only when the model has produced a maximum-reward rollout. Across five GUI-grounding benchmarks and multiple Qwen backbones, VISTA consistently improves grounding accuracy.On ScreenSpot-Pro, it raises Qwen3-VL 4B/8B/30B-A3B from 55.5/52.7/53.7 to 63.4/65.8/67.0. Robustness analyses further show higher worst-view accuracy and lower prediction flip rates.

02.
arXiv (CS.LG) 2026-06-18

Data-driven sparse identification of governing PDEs via knockoff filters and multi-criteria trade-offs

arXiv:2605.26631v2 Announce Type: replace-cross Abstract: We propose KO-PDE-IDENT, a data-driven framework for identifying parsimonious partial differential equations (PDEs) with false discovery rate (FDR) control. PDE discovery from noisy observations is often hindered by extreme multicollinearity among candidate terms, which causes typical sparse-regression methods to select spurious terms. To address this problem, KO-PDE-IDENT initially mines a support set of potential candidate terms via model-X knockoff filters with finite-sample FDR control, then refines and ranks the surviving PDE alternatives. The framework integrates three components. First, knockoff feature statistics are constructed by coupling $\ell_{0}$-constrained adaptive best-subset selection with SHapley Additive exPlanations (SHAP), yielding an effective and computationally efficient difference statistic. Second, a recursive feature elimination (RFE) procedure removes terms whose marginal contributions are dispensable and assesses statistical necessity through knockoff-perturbed hypothesis testing. Third, the final model selection is formulated as a multi-criteria decision-making (MCDM) problem, where the optimal governing equation is the alternative that best balances a wide range of criteria such as predictive accuracy, model complexity and coefficient uncertainty. We evaluate KO-PDE-IDENT on five canonical PDEs under severe noise corruption. Empirical results show that our framework can exactly recover the true PDE structure, eliminating false discoveries while retaining all true underlying terms, with low coefficient estimation error.

03.
PLOS Computational Biology 2026-06-04

Cell differentiation can underpin the reproducibility of morphogenesis

by Dominic K. Devlin, Austen R. D. Ganley, Nobuto Takeuchi Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we ask how this reproducibility is achieved by evolving complex morphologies in a multi-scale, computational model. Each morphology consists of a population of cells on a two-dimensional grid using the Cellular Potts Model framework. Each cell contains a genome that encodes a gene regulatory network, morphogens for cell-cell signalling, and proteins that determine cell behaviours. By repeatedly simulating our model with different initial conditions under selection for shape complexity, we obtained a “zoo” of evolved morphologies. We find that these evolved, complex morphologies are reproducible in a sizeable fraction of simulations, despite no direct selection for reproducibility. We show that high reproducibility is caused by spatially segregating moving cells that “shape” morphologies from stationary cells that “maintain” morphologies during morphogenesis. Strikingly, most highly reproducible morphologies also evolved cell differentiation, where proliferative, moving progenitor cells irreversibly differentiate into non-dividing, stationary differentiated cells at tissue boundaries. These results suggest that cell differentiation observed in natural development plays a fundamental role in morphogenesis in addition to the production of specialised cell types. This previously unrecognised role of cell differentiation has major implications for our understanding of how morphologies are generated and regenerated.

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

Another Look at Log-PCA for Probability Measures: A Dynamical Formulation and Statistical Convergence

arXiv:2606.17196v1 Announce Type: cross Abstract: This paper is concerned with learning principal variations of random probability measures on $\mathbb{R}^m$ under the Wasserstein geometry. We introduce a new dynamical formulation to interpret the log-PCA, a linearized principal geodesic analysis, as a variational approach. Our differentiable version, termed as the Wasserstein Tangential PCA (WT-PCA), captures the local principal modes of geodesic variations of a (weighted) probability measure on the Wasserstein space via its covariance operator at barycenter. Based on the dynamical perspective and leveraging parallel transport structure of the optimal transport problems, we derive a general statistical convergence rate of the empirical WT-PCA when estimated from data in terms of the 2-Wasserstein distance between the population and empirical barycenter reference measures.

05.
arXiv (CS.CL) 2026-06-11

Measuring Epistemic Resilience of LLMs Under Misleading Medical Context

Large language models (LLMs) now reach expert-level scores on medical licensing exams, encouraging the assumption that high scores imply safe medical judgment while patients increasingly use them for health advice. We show this assumption is fragile: when misleading context is injected into questions that LLMs originally answer correctly, they abandon the correct answer. We call the ability to maintain correct judgment under adversarial context epistemic resilience, and introduce MedMisBench to measure it. MedMisBench contains 10,932 medical question items and 48,889 misleading context-option pairs spanning medical reasoning, agentic capability, and patient-journey evaluation. Across 11 model configurations, mean accuracy falls from 71.1% on original questions to 38.0% under focused misleading context, with 51.5% attack success. The most damaging injections are formal, rule-like fabrications: authority-framed falsehoods reach 69.5% attack success and exception-poisoning claims reach 64.1%. A 14-member clinical panel from 7 countries identified serious potential harm in 38.2% of reviewed cases. MedMisBench exposes a structural blind spot in LLM evaluation in medical settings: existing benchmarks measure what models know, but not whether they preserve correct medical judgment under misleading context.

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

When in Doubt, Plan It Out: Committed Small Language Model Deliberation for Reactive Reinforcement Learning

arXiv:2606.16995v1 Announce Type: new Abstract: Reinforcement Learning (RL) policies often degrade in unfamiliar environments because they lack explicit deliberation. We propose Plan, Align, Commit, Think (PACT), a hybrid architecture that combines a fast, reactive RL policy with a slow, deliberative Small Language Model (SLM) planner. PACT invokes the SLM asynchronously to generate and validate candidate action plans. Once a plan is verified through simulation as safe, feasible, and complete, it is executed directly, bypassing the RL policy without retraining or modifying it. Evaluated on three FrozenLake configurations of increasing difficulty, PACT outperforms all baselines while relying on a 2B-parameter SLM backbone, suggesting that deliberative planning and reactive execution are more powerful in concert than either is alone in these settings.

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

Stability of the $k$-Plane Transform on Measures and Hölder-Type Comparisons of Wasserstein Metrics

arXiv:2605.00375v2 Announce Type: replace-cross Abstract: We establish stability estimates for the $k$-plane transform on finite positive Radon measures, with emphasis on Fourier and Wasserstein metrics. We first introduce a metric on $k$-plane transform data and prove a bi-Lipschitz stability estimate showing that this metric is equivalent to a generalized Fourier metric obtained by augmenting the Fourier distance between centered normalized measures with separate barycenter and total mass difference terms. Building on a Hölder-type comparison between Fourier and Wasserstein metrics due to Carrillo and Toscani, we extend this comparison to positive Radon measures under uniform bounds on centered moments of order slightly larger than $2$. This yields Hölder-type stability for the $k$-plane transform in a generalized $2$-Wasserstein metric and, in particular, a $W_2$-stability estimate for centered probability measures. We also compare the $2$-Wasserstein distance with its max-sliced analogue. For centered probability measures with uniformly bounded moments of order slightly larger than $2$, we prove a two-sided Hölder-type comparison between these distances. We then extend the result to positive Radon measures by applying it to centered normalized measures and adding separate barycenter and mass terms. Finally, for absolutely continuous compactly supported probability measures with bounded densities, we prove a strong equivalence between the $2$-Wasserstein distance of the measures and the $(k/2-1)$-order Sobolev norm of the $k$-plane transform data of the difference of their densities.

08.
arXiv (math.PR) 2026-06-16

BBP Phase Transition for a Doubly Sparse Deformed Model

arXiv:2603.04832v3 Announce Type: replace Abstract: We prove the equivalent of the Baik, Ben Arous, Péché (2004) phenomenon for a novel, doubly sparse model where both the Wigner noise matrix and signal vector(s) are sparse. Specifically, we consider a deformed sub-Gaussian sparse Wigner ensemble with a fixed number of sub-Gaussian spike vectors of the same-order sparsity added. We show that spike vectors with signals greater than one are correlated with the top eigenvectors of the deformed ensemble and that each spike vector of signal greater than one induces an outlier eigenvalue. Notably, our results hold in the supercritical sparsity regime for the Wigner matrix ($q \gg \frac{\log n}{n}$) and for any sparse spike vector with an unbounded number of entries ($np\to \infty$). No further relationship between the sparsities of the noise matrix ($q$) and spike vectors ($p$) is necessary. This generalizes the work of Benaych-Georges and Nadakuditi (2010) and Péché (2005).

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

CoCoGEC: Counterfactual Generation for Robust Grammatical Error Correction

Grammatical error correction (GEC) systems are usually trained and evaluated on GEC benchmarks, but their performance often drops sharply once the surrounding context is slightly perturbed or extended. This indicates that the existing GEC models usually fail to understand the error patterns in the varying contexts. In this paper, we thoroughly investigate the counterfactuals for GEC tasks, where the subtle changes to the contexts could lead to the label flipping issue. We propose CoCoGEC, a counterfactual generation framework that creates copies of training instances with error-irrelevant contexts altered. Our framework systematically generates counterfactuals by (1) generating intra- and inter-sentence counterfactuals that maintain the error patterns as well as syntax of the original instances by altering the word-level and sentence-level contexts; (2) revising the generated counterfactuals by selecting the instances with flipped labels and high GEC Mutual Information (MI) coefficient. Extensive experiments show that our method substantially improves the stability of GEC models, outperforming a set of data augmentation baselines. Particularly, it could achieve absolute F0.5 gains of +9.9, +11.3, and +20.8 points on the perturbed BEA-19*,CoNLL-14*, and TEM-8* data set.Our code is released at https://github.com/Quinnok/CoCoGEC

10.
arXiv (quant-ph) 2026-06-15

Interpreting Bohm-like quantum potentials in "Computing quantum waves exactly from classical action"

arXiv:2605.20443v3 Announce Type: replace Abstract: The recent posting arXiv:2605.02621 [14], commenting on the article rspa.2025.0413 [7], argues that the proof of Lemma 3.1 in [7] is missing the spatial derivative of the density, which would lead to a Bohm-like quantum potential. This technical note shows why the propagated density is independent of space in the Feynman propagator construction of Lemma 3.1. This is done by extending the proof of Lemma 3.1 explicitly with Bohm-like quantum potential terms along the stationary action paths, and then showing that these terms are exactly zero. In [7], this property can also be verified directly on most examples (double slit, Aharonov-Bohm, potential well, harmonic oscillator, tunneling, EPR, QED), as well as in the derivations of the Pauli, Dirac, and Maxwell equations. For more general nonlinear actions, a time rescaling may be required to guarantee this space independence along stationary paths. In the hydrogen atom example, this time rescaling can be computed in closed form. In contrast to the general wave of the Madelung solution [9] Lemma 3.1 of [7] is defined first for a propagator, and a general wave is then constructed in a second step. Recall that a propagator is a specific quantum wave, which is initialized at $t=0$ with a Dirac impulse at a given initial position or momentum. In turn, a general wave is constructed in a second step by superposing a distribution of initial conditions using the propagator. This key difference is why the Bohm-like quantum potential terms disappear in the construction [7] (specifically, in the first step) while the Bohm potential in the Madelung analysis does not. This fundamental difference is also consistent with the fact that the wave construction in [7] extends naturally to relativistic contexts, while Bohmian non-locality notoriously prevents such extensions. Keywords - Response to arXiv:2605.02621, in relation to rspa.2025.0413

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

Soft-Prompt Tuning for Fair and Efficient LLM Benchmark Evaluation

Benchmark scores often misrepresent a large language model's (LLM's) knowledge, because they rely, e.g., on the model's ability to follow specific formatting requirements. This especially penalizes base models that may know the correct answers but lack the ability – typically introduced in post-training – to structure them as instructed. To overcome this, we propose soft-prompt tuning, an efficient, fair, and architecture-agnostic model evaluation. By optimizing only 10 soft-prompt vectors (roughly 0.0006% parameters for a 7B model) over a short tuning period, we adapt models to specific benchmark formats, closing gaps in format-following and ensuring that underlying knowledge is accurately reflected in benchmark scores. This allows one to fairly compare different base models – trained with various pre-training recipes – on benchmarks without the need for full post-training. We evaluated soft-prompt tuning across 7 models and 7 datasets. The results show that (a) soft-prompt tuning saturates format-following within 80 steps (~640 samples) making it highly efficient, (b) soft-prompt tuning significantly outperforms zero- and few-shot prompting, surfacing base model knowledge that standard prompting misses, that (c) even post-trained models can benefit from soft-prompts to maximize format compliance, and that (d) soft-prompted base model performance predicts post-trained model rankings more reliably than zero- and few-shot baselines, offering a low-cost proxy for downstream model quality. Our contributions include (1) metrics which disentangle format-following and knowledge accuracy, (2) a fairer benchmarking protocol of LLM knowledge, and (3) a cost- and memory-effective recipe to identify optimal pre-training strategies early in LLM development.

12.
arXiv (CS.LG) 2026-06-11

A Data-Centric Framework for Detecting and Correcting Corrupted Labels

arXiv:2606.11699v1 Announce Type: new Abstract: The performance of machine learning and deep learning models largely depends on the quality of the training data. However, the quality of the real-world datasets is often compromised by noisy labels, which can substantially degrade model accuracy and reliability. To address this challenge, we propose Relabeler, an end-to-end data-centric framework for detecting and correcting corrupted labels. For corrupted label detection, Relabeler jointly leverages both local and global relationships among data instances to identify potentially noisy samples. After detecting suspicious instances, Relabeler further performs label correction by estimating the most probable clean label for each instance based on both its input features and observed noisy label. Extensive experiments across multiple datasets, noise types, and noise rates demonstrate that Relabeler consistently outperforms state-of-the-art baselines, achieving up to 58% improvement in label correction precision and 6% improvement in downstream task performance.

13.
arXiv (quant-ph) 2026-06-17

SPICE-Q and Large-Scale Quantum Chip Production

arXiv:2606.17907v1 Announce Type: new Abstract: We propose SPICE-Q, a SPICE-inspired design-technology co-optimization framework for superconducting quantum processors. Rather than replacing tools such as HFSS, Qiskit Metal, pyEPR, SQcircuit, SQuADDS, scqubits, or QuTiP, SPICE-Q aims to connect them through a unified, traceable data chain spanning process rules, layout, electromagnetic simulation, energy-participation-ratio and circuit quantization, Hamiltonian extraction, noise analysis, cryogenic test, and manufacturing feedback. The central mapping is from process and PDK constraints to layout geometry, electromagnetic modes, equivalent circuit parameters, effective Hamiltonians, and finally metrics such as frequency, coupling, anharmonicity, decoherence, readout performance, and yield. This flow must capture Josephson-junction variability, transmon frequency allocation, resonator and Purcell constraints, coupler crosstalk, microwave routing, 3D interconnects, material/interface loss, package modes, and wafer-scale process statistics. By introducing standardized model interfaces, statistical parameter models, model cards, version governance, and closed-loop calibration from cryogenic and fabrication data, SPICE-Q frames superconducting quantum-chip design as an engineering workflow rather than a collection of isolated simulations. We argue that scalable and fault-tolerant quantum processors will require such a continuous model chain from device physics and electromagnetic fields to quantum dynamics, noise, manufacturability, and system-level yield.

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

The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models

High-grade gliomas integrate into neural circuits through functional synapses with neurons, raising the question of which noncoding elements shape synaptogenic gene expression in tumor cells. The regulatory program written across the dark genome, what we call the $dark regulome$, is the natural substrate to probe, and sequence foundation models offer a zero-shot route through in-silico mutagenesis (ISM); yet likelihood-based scoring is tautologically coupled to local sequence predictability, leaving the regulatory interpretation underdetermined. Across three architecturally distinct foundation models (Caduceus-Ph, HyenaDNA, Enformer) and 30,448 dark genome elements at 92 glioma-relevant loci, we introduce a residualization-and-permutation diagnostic that separates predictability-driven from regulation-driven RIS variance. A sharp 10kb proximal-regulatory horizon survives every control we apply, but the LM-derived element-class hierarchy does not: a six-feature linear baseline matches Caduceus top-decile membership at AUC $= 0.985$. Cross-architecture decomposition cleanly separates a sequence-predictability layer (the two language models co-rank long well-predicted transposable elements) from a regulatory-output layer (Enformer alone retains residual cCRE-discriminative signal), with literally zero overlap between the two top-100 lists. Conservation, brain cis-eQTL, and STRING-PPI cross-checks then anchor what biology survives: top-100 elements across all three models are $3.3\times$ enriched per model for matching brain eQTLs ($p_\mathrm{emp} < 5\times 10^{-3}$), while a tempting transposable-element regulatory layer and a striking NRXN1+NLGN1 protein-pair convergence both fail proper permutation tests once those tests are constructed. We deliver the diagnostic as a general methodological tool for any ISM-based regulatory study.

15.
medRxiv (Medicine) 2026-06-17

Adverse Childhood Experiences Reorganise the Brain-Personality Network Across the Psychosis Spectrum

Exposure to adverse childhood experiences is a pervasive risk factor for psychosis, exhibiting a linear relationship across the psychosis spectrum from subclinical schizotypal traits to schizophrenia spectrum disorders. While this association is often conceptualised within the vulnerability-stress framework, the systemic mechanisms through which childhood trauma reconfigures the brain-personality interactome remain poorly understood. We examined clinical, neuropsychological, and neuroimaging data from a sample of low- and high-schizotypy individuals, and patients with a diagnosis of schizophrenia spectrum disorder (N=120). Our aim was to map how trauma reconfigures interactions between neurobiology and schizotypal phenomenology. We adopted a mixed graphical model approach to jointly estimate conditional dependencies between childhood trauma, regional brain morphometry, and schizotypal traits across the psychosis spectrum. Our results show that childhood trauma reconfigures the brain-personality network, shifting it from a state driven by cognitive processes to one anchored in emotional (limbic) reactivity. This transition is marked by the increased influence of impulsive traits and a significant strengthening of connections within the salience network. These changes converge with a reduced thickness of the frontal executive regions, the brain's control centres, identified in our models. Collectively, our results suggest a structural phenomenological decoupling, where trauma conditioned affective circuits may bypass weakened top-down regulatory controls. These findings highlight the necessity of using integrative frameworks to capture how trauma fundamentally reshapes the relationship between the brain and schizotypal personality.

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

A Comprehensive Survey of Medical Image Segmentation: Challenges, Benchmarks, and Beyond

Medical image segmentation plays a critical role in clinical diagnostics, treatment planning, disease monitoring, and neurological disorder identification. This article presents a comprehensive review of its systematic development, covering widely used public datasets, representative methods built on the U-Net, Transformer, and SAM architectures, and key evaluation metrics with their differences, followed by an analysis of major challenges from multiple perspectives. Unlike surveys that focus on a single model family or a specific clinical application, this review organizes U-Net-, Transformer-, and SAM-based methods within a unified analytical framework, with a particular focus on their effectiveness in improving segmentation accuracy and efficiency. This work aims to guide future research and support clinical translation of medical image segmentation, with all related resources publicly available in our GitHub repository: https://github.com/andrew-pengyu/Awsome_MedSeg/tree/main.

17.
arXiv (CS.CL) 2026-06-16

Are Online Skill and Memory Modules Always Worth Their Tokens? A Budget-Constrained Study of Web Agents

Online web agents often augment a base actor with memory, workflow, or skill modules. These modules can improve performance, but they also consume test-time tokens, a cost rarely reported alongside the actor's inference cost. We study online augmentation, where this overhead is paid on every task, and re-evaluate its benefits under a fixed total inference budget. We compare AWM, ASI, and ReasoningBank with a token-matched vanilla baseline that uses the same budget for additional actor steps. Across three WebArena domains and three models, Gemini 3 Flash, GPT-5.4-mini, and Qwen 3.6-27B, the vanilla baseline matches or surpasses all three augmentation methods in aggregate success rate while often using fewer total tokens. We observe a similar trend on WorkArena-L1 with Qwen 3.6-27B, indicating that the effect extends to enterprise knowledge-work tasks. Our results suggest that skills and workflow memory can be useful in specific domains, but their apparent gains often vanish against a budget-matched actor. We further show that run-to-run variance materially affects outcomes and should be reported as a core evaluation criterion for online web agents.

18.
arXiv (quant-ph) 2026-06-16

Instrument-based quantum resources: quantification, hierarchies and towards constructing resource theories

arXiv:2508.09134v3 Announce Type: replace Abstract: Quantum resources are certain features of the quantum world that provide advantages in certain information-theoretic, thermodynamic, or other useful operational tasks that are outside the realm of what classical theories can achieve. Quantum resource theories provide us with an elegant framework for studying these resources quantitatively and rigorously. While numerous state-based quantum resource theories have already been investigated, and to some extent, measurement-based resource theories have also been explored, instrument-based resource theories remain largely unexplored, with only a few notable exceptions. As quantum instruments are devices that provide both the classical outcomes of induced measurements and the post-measurement quantum states, they are quite important, especially for scenarios where multiple parties sequentially act on a quantum system. In this work, we study several instrument-based resource theories, namely (1) the resource theory of information preservability, (2) the resource theory of (strong) entanglement preservability, (3) the resource theory of (strong) incompatibility preservability, (4) the resource theory of traditional incompatibility, and (5) the resource theory of parallel incompatibility. Furthermore, we outline the hierarchies of these instrument-based resources and provide measures to quantify them. We then also established a relationship between our resource measure and the advantage in an information-theoretic task. In short, we provide a detailed framework for a wide variety of instrument-based quantum resource theories.

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

Multi-Class Brain Tumor Classification Using Advanced Deep Learning Models: A Comparative Study

Despite recent advancements in deep learning, accurately classifying brain tumors from MRI images continues to pose challenges. In this research, we present a comprehensive evaluation of five different convolutional neural networks (CNN) architectures, including a customized baseline model and four pre-trained models - for use in classifying multi-class brain tumors using a clinically-sourced dataset of approximately 10,000 MRI images. We have utilized five different architectures; VGG16, VGG19, DenseNet121, and EfficientNetB0, which were all tested and trained within an identical experimental framework. Performance was measured by both overall accuracy and tumor-wise recall as a means to measure the clinically-relevant performance of each architecture. We found that EfficientNetB0 had the best overall classification accuracy at 95%, when compared to the other architectures tested; specifically VGG16 (94.37%), VGG19 (92.29%), DenseNet121 (90.91%) and the customized CNN (78.00%). An especially important finding of our research was the considerable improvement in detecting meningiomas; specifically, while simple CNNs could detect meningiomas with a recall rate of approximately 20%, EfficientNetB0 was able to detect meningiomas with a recall rate of 89%. Meningiomas are often difficult to detect because they can appear very subtly on MRI images. Additionally, an interesting finding was that the deeper VGG19 performed worse than the shallower VGG16. This indicates that in many cases the architectural efficiency of a CNN model may be more important than its depth when working with medical images. Overall, EfficientNetB0 appears to provide the optimal trade-off between classification accuracy, number of parameters used in the model and clinically meaningful performance.

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

Poster: EdgeCitadel – Hybrid NATS-MQTT Orchestration for Edge Multi-Agent Systems

arXiv:2606.14710v1 Announce Type: cross Abstract: Edge-resident AI agents increasingly span home servers, IoT hubs, laptops, and phones, yet their coordination stacks still assume cloud-style transports or a central relay. We present EdgeCitadel, an edge multi-agent orchestration platform built around a single NATS 2.10 server with the built-in MQTT adapter. The design combines MQTT connectivity for heterogeneous agents, JetStream-backed persistence and replay for backend services, direct peer delegation over a shared subject namespace, and a passive aggregator that visualizes and stores traffic without sitting on the delivery path. Our poster highlights the migration from MQTT relay prototypes (common in IoT communication) to the current hybrid architecture and demonstrates a working cross-device testbed spanning ARM64, x64, and Android clients.

21.
bioRxiv (Bioinfo) 2026-06-11

TMO: ASYMMETRIC CROSS-MODAL ATTENTION FOR LEARNINGCELL-STATE-DEPENDENT REGULATORY LAGS FROM SINGLE-CELL MULTIOMIC DATA

Abstract Background: Single-cell multi-omics technologies simultaneously measure chromatin accessibility (ATAC) and gene expression (RNA), providing a unique window into the temporal ordering of regulatory events during differentiation. However, most computational models treat the two modalities symmetrically, ignoring the directional relationship between chromatin and transcription, and existing lag-aware methods estimate a single global lag per gene, failing to capture cell-state-dependent dynamics. Methods and Results: We introduce Temporal Multi-Omics (TMO), a deep learning framework that learns signed, cell-state-conditional regulatory lags ({Delta}{tau}) using asymmetric cross-modal attention. TMO projects RNA and ATAC into 50 latent components each, tokenises each cell as a sequence of 100 tokens, and uses a two-pass transformer in which a data-driven lag prior - derived from a sliding-window cross-correlation function - directly biases attention asymmetrically. On four independent 10x Multiome datasets (mouse brain, human brain, mouse kidney, human PBMC), the asymmetric model achieves Lag Concordance Scores (LCS) of 0.988-0.999, compared to 0.048-0.108 for an architecturally identical symmetric baseline. A stratified 80/20 held-out experiment confirms that the learned component-lag ordering generalises to unseen cells (held-out LCS 0.85-0.99). Clustered {Delta}{tau} heatmaps show positive {Delta}{tau} (ATAC-led priming) in early pseudotime and negative {Delta}{tau} (RNA-led, activity-dependent regulation) in late pseudotime; the ATAC-RNA correlation heatmap exhibits a U-shaped pattern indicative of developmental decoupling. Components with the most positive {Delta}{tau} are enriched for chromatin organization and stem cell differentiation (FDR < 0.05), while those with the most negative {Delta}{tau} are enriched for synaptic signalling and immune activation. Ablating the cell-state information from the lag predictor reduces the LCS and collapses per-component temporal dynamics (KS p [&le;] 0.039 in all four tissues), proving that TMOs dynamic lag patterns depend on cell-state conditioning. Independent ChIP-seq validation for four transcription factors (PAX5, Pax6, ASCL1, Hnf4) confirms highly significant separation between target genes and expression-matched background (p < 10-4 in all cases). Two Multiome Perturb-seq screens provide causal validation: SMARCB1 knockout shows a directional trend (1.5-fold target shift, p = 0.056, n = 147 perturbed cells), and SMARCE1 knockout reaches statistical significance (p = 0.0089, n = 3,394 perturbed cells). Gene-level cross-correlation independently validates that the regulatory lag signal is present in the raw data, and TMO further identifies rare, statistically significant biphasic gene programs where the regulatory direction reverses across pseudotime. Conclusions: TMO is the first method to make regulatory lag a learnable, cell-state-conditional, and architecturally encoded parameter. It is scalable, interpretable, and open-source, providing a powerful tool for studying regulatory timing in development, disease, and perturbation screens.

22.
medRxiv (Medicine) 2026-06-15

Evaluation of AI-Generated Synthetic Data for Clinical Research in Secondary Cardiovascular Prevention among Dyslipidemia Patients

Background: Access to high-quality clinical data is essential for advancing medical research and developing effective medical statistical and Artificial Intelligence models. However, privacy regulations and logistical barriers often hinder timely access to real-world data. Synthetic data offer a promising solution, preserving the statistical characteristics of original datasets while protecting patient privacy. Objectives: This study investigates the use of synthetic data for secondary cardiovascular prevention in patients with dyslipidemia, using two real-world datasets from Centro Cardiologico Monzino. Methods: Given the high dimensionality and limited sample size of the datasets, we employed a custom generative framework based on Large Language Models (LLMs). Pre-trained LLMs were fine-tuned on original clinical records to synthesize tabular data replicating source-data distributions. Fine-tuning was performed within the Centro Cardiologico Monzino's secure infrastructure to ensure data sovereignty. We evaluate clinical utility and privacy using fidelity and privacy metrics, identifying the optimal generative model and benchmarking against traditional anonymization methods. Results: Synthetic data achieved a superior trade-off than classically anonymized datasets. Real and synthetic datasets showed strong agreement, with significant distributional differences limited to few variables. Models trained on synthetic data replicated key associations from the original dataset, including therapy modification and creatine phosphokinase as predictors of SAMS, and pharmacological intensity as the main driver of LDL-C reduction. Conclusions: Results support the feasibility of using synthetic data as a proxy for real-world datasets in exploratory analyses and model development. Despite slight attenuation of some effect sizes, preserved clinical relationships reinforce the validity of synthetic data in medical research.

23.
arXiv (CS.AI) 2026-06-11

AI4Land: Scalable Deep Learning for Global High-Resolution Land Use Reconstruction

arXiv:2606.11793v1 Announce Type: cross Abstract: Uncertainty in the terrestrial carbon cycle remains a major constraint in climate projections, partly driven by the uncertainties affecting the land surface representation and variability in Earth system models. To address this limitation, we present a data-driven framework AI4Land, for generating high-resolution historical reconstructions and future projections of key land surface variables. The framework follows a two-phase approach using a U-Net architecture. In the first phase, which is the focus of this work, it reconstructs annual land use and land cover by integrating coarse-resolution scenario data with static geophysical features. In a planned second phase, the resulting high-resolution maps will be used to predict dynamic biophysical variables, particularly leaf area index, at finer temporal scales. Trained on Earth observation data, the models learn to reproduce spatially explicit and physically consistent land surface patterns, extending temporal coverage to periods lacking direct observations. AI4Land was developed and trained on MareNostrum5, demonstrating how GPU-accelerated HPC infrastructure enables global-scale climate AI pipelines. The final product is a suite of open-source emulators designed for real-time coupling with digital twin platforms, such as those developed under the Destination Earth initiative. By delivering realistic and evolving land surface conditions on demand, this work aims to reduce critical uncertainties and improve the predictive power of next-generation climate simulations.

24.
medRxiv (Medicine) 2026-06-18

Plasma proteomics reveals clinical and mechanistic heterogeneity among individuals who develop coronary artery disease

BACKGROUND: Individuals who develop coronary artery disease (CAD) are clinically and mechanistically heterogeneous, and understanding this variation is crucial for precise risk stratification and tailored interventions. However, the molecular mechanisms that connect these two kinds of heterogeneity remain unclear, limiting progress toward biologically grounded risk stratification and targeted interventions. Here, we investigated the heterogeneity of individuals who develop CAD by leveraging plasma proteomic signatures, placed individuals along continuous metabolic gradients and revealed the molecular programs underlying these patterns, thereby linking mechanistic variation to clinical heterogeneity. METHODS AND RESULTS: From 42,803 UK Biobank participants, including 3,713 individuals who developed CAD within 10 years (incident CAD), we first identified a 320-protein panel from 2,923 baseline proteins that improved prediction of incident CAD beyond clinical risk scores. Using reverse graph embedding, we reduced the proteomic data to two dimensions and mapped each incident case onto the resulting two-dimensional latent proteomic space. These proteomic dimensions show significant associations with cardiometabolic and kidney-related clinical markers. The patterns were replicated in the EPIC-Norfolk study. Phenome-wide Cox regression analyses further linked these proteomic dimensions to 10-year incidence rates for various diseases, including type 2 diabetes, obesity, and chronic kidney disease (CKD). Furthermore, adding the proteomic dimensions to clinical variable-based Cox regression model improved prediction of 10-year incidence of CKD and other diseases, demonstrating the value of proteomic dimensions beyond conventional clinical risk factors. Moreover, individuals with prevalent CAD (diagnosed before proteomic sampling) exhibited high, metabolically adverse dimension values, indicating that these axes capture cumulative metabolic burden. Pathway enrichment analyses implicated altered extracellular matrix organization and immune programs among the proteins contributing to the proteomic dimensions. CONCLUSIONS: Our findings demonstrate that plasma proteomic signatures can dissect the heterogeneity of individuals who develop CAD in continuous phenotypic gradients, improve prediction of CAD and comorbidities, and map underlying biological mechanisms.

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arXiv (CS.CV) 2026-06-16

Assessing Reliability of Symbol Detection in Concept Bottleneck Models

Concept Bottleneck Models (CBMs) are a relevant tool for explainable Artificial Intelligence because they make their predictions through human-interpretable symbols. However, high task accuracy does not guarantee that these symbols are detected faithfully: jointly trained CBMs may encode task-specific shortcuts in the bottleneck, making their explanations unreliable. In this paper, we study concept-detection reliability by swapping independently trained concept detectors and classification heads that share the same symbolic vocabulary. We use the resulting performance degradation, concept-level metrics, and symbol-wise uncertainty estimates to identify concepts that are especially prone to spurious firing. Finally, we propose a reliability-aware training strategy in which a shared concept detector is optimized with multiple classification heads and penalized for relying on globally or instance-wise unreliable symbols. On CUB-200-2011 with full concept supervision, detectors and heads are almost freely interchangeable (swap drop below one accuracy point, relative retention above $99\%$, and no concept detected below chance), whereas on a controlled synthetic task we show that, as the concept-supervision weight is reduced, models keep near-perfect task accuracy while swapped accuracy and agreement with the ground-truth concepts collapse to chance. Our reliability-aware training substantially mitigates this leakage, roughly doubling swap accuracy in the leaky regime.