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01.
arXiv (CS.CV) 2026-06-12

SalArt-VQA: Diagnosing Whether VLMs Understand Salient Artifacts in Generated Images

Vision-language models (VLMs) are increasingly used to detect whether AI-generated images contain visible artifacts, yet their ability to analyze such artifacts remains poorly understood. A correct image-level decision can still hide important failures: a model may correctly flag an artifact while relying on the wrong visual cue, selecting the wrong region, or describing a defect that the image does not support. To evaluate these behaviors directly, we introduce SalArt-VQA, a diagnostic benchmark for fine-grained SALient ARTifact understanding in AI-generated images. SalArt-VQA contains 950 images and 3,681 human-authored multiple-choice questions spanning artifact images, matched real reference images, and paired generated reference images. Four aligned question types evaluate presence detection, semantic localization, spatial grounding, and evidence-grounded defect identification, while the reference splits test calibration and abstention when the annotated defect is absent. Across 20 VLMs, SalArt-VQA reveals failures that image-level detection accuracy hides: the strongest model reaches 99.37% detection recall on artifact images but answers all four artifact-side questions correctly on only 53.26% of images. Comparing artifact images with artifact-free references reveals a sensitivity-calibration tradeoff: sensitive models often make unsupported artifact claims, while conservative models avoid false alarms largely by missing real artifacts. These results show that high artifact detection accuracy alone does not imply grounded artifact understanding. SalArt-VQA exposes these hidden failure modes and provides a fine-grained evaluation of whether VLM artifact claims are supported by local visual evidence.

02.
arXiv (quant-ph) 2026-06-11

Logical error estimation from syndrome data of surface-code experiments

arXiv:2606.11496v1 Announce Type: new Abstract: Decoders for quantum error correction (QEC) experiments rely on detector error models (DEMs), which encode, for each error, its probability and the detectors and logical observables it flips. Here we show that estimating DEM event probabilities from experimental syndromes is feasible, avoids independent device benchmarking, and produces useful decoder priors for estimating and reducing decoded logical error probabilities. We evaluate our methods using open-source data from surface-code memory experiments performed on Google's Willow chip, and we carry out analogous surface-code experiments on IBM's \texttt{ibm\_miami} processor. Despite the different physical error scales of the Google and IBM devices, in both cases our estimated DEMs improve logical error probabilities relative to baseline device-informed DEMs, typically at the $5\%-10\%$ level and with larger gains in some IBM cases, without additional calibration circuits, decoder fine-tuning, or supervised fitting to logical outcomes.

03.
arXiv (CS.LG) 2026-06-24

Machine Learning and Deep Learning for Exoplanet Detection and Atmospheric Characterization with JWST and the Upcoming Ariel Mission

arXiv:2606.23766v1 Announce Type: cross Abstract: The detection and atmospheric characterization of exoplanets have entered a new data-intensive era driven by the James Webb Space Telescope and the upcoming Ariel mission. Modern surveys produce millions of light curves and high-resolution spectra that overwhelm traditional pipelines, motivating the rapid integration of Machine Learning and Deep Learning methods into the exoplanet workflow. This review synthesizes the latest progress in applying ML/DL techniques to exoplanet detection (transit identification, candidate vetting, false-positive rejection) and atmospheric characterization (retrieval, detrending, cross-correlation, surrogate modelling) in the context of JWST and Ariel. We start with classical algorithms such as Random Forests and Convolutional Neural Networks, move through Transformers and Recurrent architectures, then survey modern simulation-based inference using Neural Posterior Estimation and Flow Matching Posterior Estimation with normalizing or continuous normalizing flows. We discuss benchmark efforts, including the Ariel Machine Learning Data Challenges (2019 to 2025) hosted with NeurIPS, and key JWST case studies such as the WASP-39b Early Release Science programme. Results indicate that DL approaches consistently match or exceed traditional pipelines in both speed and accuracy, while ML-driven retrievals reduce inference time from CPU-hours to seconds and can accelerate nested-sampling retrievals by factors of 3-8 without compromising Bayesian evidence. We identify outstanding challenges interpretability, calibration of uncertainties under noisy data, hybrid modelling, and the generalization of models across instruments and planet populations and outline a research roadmap spanning the JWST era and beyond into Ariel's launch in 2029.

04.
medRxiv (Medicine) 2026-06-10

A risk-of-contagion index using a Bayesian based model for the COVID-19 epidemic in Mexico

During the COVID-19 pandemic, limited testing capacity and reporting delays complicated epidemic surveillance and decision-making in Mexico. We calibrated textit{covidestim}, a Bayesian nowcasting model, to estimate the total SARS-CoV-2 infections from reported cases and deaths using Mexican surveillance data. Disease-progression distribution priors were calibrated using Mexico City records and validated through comparisons with national seroprevalence surveys, hospitalization data, and annual reported severe-case rates across all states. Using the reconstructed estimates of active infections, we implemented an event-based risk framework that quantifies the probability of encountering at least one infectious individual in gatherings of different sizes. This probability was subsequently translated into a four-level epidemiological traffic-light indicator and computed at both state and municipality levels. The resulting estimates revealed substantial spatial heterogeneity that is obscured by state-level aggregation, particularly in states with marked differences between urban and rural municipalities. To evaluate consistency with public-health indicators, we compared the proposed risk classification with the official Mexican epidemiological traffic-light system, considering interpretable gathering sizes relevant to public-health decision making. Weekly reports derived from this framework were delivered to policymakers in the State of Queretaro in Mexico, as an anticipation tool for school reopening and public-space management. This demonstrates that this Bayesian reconstruction of infections combined with event-based risk metrics can provide an interpretable and generalizable municipality-level complement to routine surveillance systems, particularly in regions with limited testing capacity and heterogeneous local transmission dynamics.

05.
arXiv (CS.CL) 2026-06-17

Smarter edits? Post-editing with error highlights and translation suggestions

As MT quality increases, interest in enhanced post-editing features such as QE-derived error highlights is growing, yet evidence for their usefulness remains limited. In this work, we explore the usefulness of LLM-derived error highlights and correction suggestions based on automatic post-editing (APE). We conduct a study where professional translators (En-Nl) post-edit translations using APE error highlights and correction suggestions and compare productivity, quality and user experience to regular PE and PE with QE-derived highlights. While no condition yielded productivity or quality gains compared to regular PE, APE highlights were better received than QE-derived highlights, and correction suggestions improved overall user experience.

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

HeteRo-Select: Informativeness as the Participation Driver in Heterogeneous Federated Learning

arXiv:2508.06692v2 Announce Type: replace Abstract: Federated learning systems typically allocate gradient compression by link speed. This is sensible when bandwidth and data informativeness align. However, under non-IID data, these signals often decorrelate or invert. A bandwidth-driven allocator then risks compressing the most informative gradients hardest. We propose HeteRo-Select, a framework that replaces bandwidth with a per-client informativeness score as the primary driver of compression. The score jointly governs three decisions per round: client selection, compression ratio, and server aggregation weight, with bandwidth retained only as a hard ceiling. Score-proportional selection provably reduces the effective heterogeneity of the chosen subset; score-proportional compression provably lowers aggregate top-$k$ error at fixed traffic. Under the exact FedCG simulation protocol, HeteRo-Select delivers a $1.78\times$ speedup and an $18.2\%$ reduction in traffic on CIFAR-10. The same configuration, unchanged, scales from a $7{,}850$-parameter logistic regression to an $11.27$M-parameter ResNet-18, hitting the accuracy target on three of four benchmarks. When bandwidth and informativeness are deliberately anti-correlated, the method still achieves the target accuracy with less traffic than the normal-bandwidth run.

07.
arXiv (CS.LG) 2026-06-15

LapidaryEngine: Fully Conversational Crystal Generation

arXiv:2606.14215v1 Announce Type: new Abstract: The emergence of Large Language Models (LLMs) has inspired the vision of generating bespoke crystal materials directly from natural-language instructions, enabling users to design materials through intuitive, conversational interaction. Existing text-to-crystal generative models represent important early steps toward this goal, but they suffer from two critical limitations: (i) restricted input formats that require highly structured descriptions (e.g., chemical formulas), and (ii) one-directional generation, where models can map text to crystal but cannot perform the inverse. These limitations prevent fully conversational workflows and hinder alignment with users' inherently ambiguous and evolving desiderata. We address these challenges with LapidaryEngine, the first model to support fully conversational crystal generation. LapidaryEngine accepts free-form natural-language requests and performs iterative refinement and editing in a dialogue-like manner. The key innovation is a pivot representation, a third, intermediate form that enables bidirectional translation between text and crystal structures despite the absence of direct paired datasets. Leveraging this pivot allows robust interpretation of user feedback and precise structural control. We demonstrate LapidaryEngine across diverse tasks, including insulator discovery, stability optimization, compositional modification, and structural editing, showcasing its ability to align generated materials with user intent in an interactive manner.

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

JetParticle-JEPA: An Efficient Self-Supervised Representation Learning method for Jet Tagging in High-Energy Physics

arXiv:2606.14813v1 Announce Type: cross Abstract: Jet tagging at the Large Hadron Collider increasingly relies on deep learning models trained on massive simulated datasets, leading to high computational costs and limited robustness to detector mismodeling. We introduce JetParticle-JEPA (JP-JEPA), a self-supervised Joint-Embedding Predictive Architecture that learns physically meaningful jet representations directly from continuous particle clouds without tokenization or reconstruction of raw inputs. Built on a Particle Transformer backbone, JP-JEPA predicts latent representations of masked particles while preserving fine-grained kinematic correlations. On the JetClass benchmark, JP-JEPA achieves performance comparable to fully supervised state-of-the-art methods on the full dataset, surpasses supervised baselines in low-label regimes, and significantly outperforms existing SSL approaches. On Top Quark and Quark-Gluon Tagging benchmarks, it remains on par with supervised methods. The learned representations also exhibit strong robustness to missing detector information and improved uncertainty behavior, highlighting JP-JEPA as a promising foundation-model framework for robust and data-efficient jet physics at the LHC.

09.
arXiv (CS.AI) 2026-06-24

Cryptographic certificates of validity for trustworthy AI

arXiv:2606.23768v1 Announce Type: cross Abstract: We propose cryptographic certificates of validity for agentic AI systems. The core idea is to formally specify a correctness or policy condition as a logical predicate, compile this predicate to a witness-checking problem over polynomial constraints, and use a succinct cryptographic proof system (and optionally zero-knowledge) to certify that the condition holds. This offers a middle ground between formal verification of source code, and cryptographic authentication. An agent's action can be accompanied by an independently checkable proof that it satisfies an agreed formal policy, without requiring the verifier to trust the agent or to re-execute computation. We outline the approach at a high level, give the core mathematical translation, relate the proposal to proof-carrying code, zkVMs, formal methods, and agent governance, and note the specification, auditing, and deployment questions that a full implementation must answer.

10.
arXiv (CS.CL) 2026-06-11

Pre-AF 13: An Interpretable Atrial Fibrillation Risk Score Mined from Discharge Reports

Background. Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia and a major determinant of prognosis. Established AF risk scores rely on factors (older age, hypertension) nearly ubiquitous among patients with cardiovascular disease (CVD), offering limited stratification in this high-risk group. Most target long-term (5-10 year) rather than medium-term prediction. We developed interpretable ML models predicting AF risk over a 24-month and entire follow-up horizon in CVD patients using routinely collected hospital data. Methods. Single-center retrospective study of electronic health records from the National Research Cardiology Center (Russia) for patients aged >=18 with CVD but without pre-existing AF, hospitalized more than once between January 2012 and May 2019. A custom NLP pipeline transformed unstructured discharge reports into 73 structured features, combining a rule-based parser with transformer-based NER. Using LightAutoML we built a full model (73 features), a simple model (reduced subset), and a linear model for a bedside risk score. Performance was assessed by ROC AUC, compared with CHARGE-AF, C2HEST, MHS, and HAVOC, and interpreted via SHAP. Results. Of 80,576 records from 45,000 patients, 17,562 met inclusion criteria; 1,438 (8.19%) developed AF. The full model reached ROC AUC 0.735 (24-month) and 0.696 (entire follow-up); the simple model was nearly identical (0.725, 0.696). All non-linear models outperformed the four clinical risk scores (ROC AUC 0.53-0.64). The simple model uses 13 features and is named Pre-AF 13. SHAP identified age and left atrial volume as dominant predictors. A linear risk score (Pre-AF 9) stratified observed 24-month AF incidence from ~7% to 36%. Conclusion. Interpretable ML models built from routinely collected EHR data identify high-AF-risk CVD patients, outperforming established clinical risk scores.

11.
arXiv (quant-ph) 2026-06-19

Electrical Noise Produced by Micron-Sized Particles above a Surface Paul Trap

arXiv:2606.19585v1 Announce Type: new Abstract: Electric field noise produced by the surface of ion trap electrodes reduces the fidelity of quantum computing operations. Despite decades of investigation its microscopic origins remain unclear. Here, we measure electric field noise at trapping locations along the symmetry axis of a linear surface Paul trap. We find that noise levels vary by three orders-of-magnitude in one 600$\,\mu$m section of the trap. Optical and scanning electron microscope images show micron-sized particles close to the trapping locations with the highest noise levels. We find that modeling the particles as a lossy dielectric with a effective loss tangent $\tan\theta=0.33(0.06)$ describes the magnitude of the noise, as well as its spatial and frequency dependence. Our observations may explain the large variation of reported noise levels in literature.

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

Cross-Layer Discrete Concept Discovery for Interpreting Language Models

Interpreting language models remains challenging due to the existence of residual stream, which linearly mixes and duplicates features across adjacent layers, causing single-layer analyses to miss this cross-layer structure. Cross-layer sparse autoencoders (SAEs) address layer mixing but operate in continuous space, where concepts split across many neurons without clear boundaries. We introduce Cross-Layer Vector Quantized-Variational Autoencoder (CLVQ-VAE), a novel framework which maps representations from a lower layer to a higher layer through a discrete vector-quantization bottleneck, collapsing duplicated residual-stream features into compact, interpretable concept vectors. Our approach combines top-k temperature-based sampling with exponential moving average (EMA) codebook updates, providing controlled exploration of the discrete latent space while maintaining codebook diversity. Across both encoder- and decoder-based models on ERASER-Movie, Jigsaw, and AGNews, CLVQ-VAE outperforms clustering, single-layer vector quantized-variational autoencoder (VQ-VAE), and sparse autoencoder (SAE) baselines across three evaluation axes: removing identified concepts drops model accuracy by up to 93%, LLM judges rank our concepts first in 66.7% of comparisons, and human annotators recover model predictions from our visualizations with 78% accuracy versus 54% for clustering.

13.
arXiv (CS.CV) 2026-06-18

Hand-4DGS: Feed-Forward 3D Gaussian Splatting for 4D Hand Reconstruction from Egocentric Videos

Dynamic 3D hand reconstruction from egocentric videos is essential for next-generation computing platforms such as AR/VR and AI glasses. Despite its importance, most prior works focus either on multi-view 3D hand reconstruction or on 4D human body reconstruction. Egocentric 4D hand reconstruction remains challenging due to fast head motion, rapid hand dynamics, severe occlusions, and inherent ambiguity from single-view observations. To address these challenges, we introduce Hand-4DGS, the first feed-forward framework for reconstructing dynamic 4D hands directly from egocentric videos, enabling both fast (~60 FPS) inference and strong generalization. Our approach incorporates a mesh-guided representation for structural priors and temporal convolutions to model dynamic motion. We evaluate our framework on two challenging egocentric datasets, H2O and ARCTIC, and demonstrate significant improvements over baselines. Our method benefits from the generalization capability of feed-forward networks and effective 2D image supervision through Gaussian splatting, without requiring expensive 3D hand pose ground-truth annotations.

14.
arXiv (CS.AI) 2026-06-25

How Small Can 6G Reason? Scaling Tiny-to-Small Language Models for AI-Native Networks

arXiv:2603.02156v2 Announce Type: replace-cross Abstract: Emerging 6G visions, reflected in ongoing standardization efforts within 3GPP, IETF, ETSI, ITU-T, and the O-RAN Alliance, increasingly characterize networks as AI-native systems in which high-level semantic reasoning layers operate above standardized control and data-plane functions. Although frontier-scale large language models (LLMs) such as Qwen2.5-7B and Olmo-3-7B demonstrate strong reasoning capability, their computational footprint limits deployment in latency-sensitive, edge-native infrastructures. This paper presents a systematic empirical study of the scaling behavior and deployment efficiency of compact language models for network-level semantic reasoning in AI-native 6G systems. Using 6G-Bench, a standardization-aligned benchmark comprising 30 decision-making tasks across five capability domains, we evaluate models ranging from 135M (SmolLM2-135M) to 7B parameters (Qwen2.5-7B), including mid-scale architectures such as Llama-3.2-1B, Granite-1B, and Qwen2.5-3B. Deterministic accuracy (pass@1) increases from 0.224 at 135M to 0.707 at 7B, but scaling gains are highly non-uniform. A pronounced stability transition occurs in the 1 to 1.5B range, where accuracy rises from 0.373 (Llama-3.2-1B) to 0.531 (Qwen2.5-1.5B) and the instability gap Delta_5 contracts from 0.356 to 0.138. Beyond 3B parameters, improvements diminish (+0.064 from 3B to 7B). Through single-query inference profiling and an Edge Score metric that normalizes accuracy by latency and memory footprint, we show that semantic reliability per unit edge resource does not scale monotonically with parameter count. Instead, mid-scale models (approximately 1.5 to 3B) achieve the most favorable balance between deterministic stability and computational efficiency, providing deployment-relevant guidance for AI-native 6G architectures. All scripts and results are publicly available at https://github.com/maferrag/6G-Bench

15.
arXiv (quant-ph) 2026-06-19

Faking entanglement with imperceptible measurement deviations

arXiv:2606.20396v1 Announce Type: new Abstract: Quantum entanglement is a central resource underpinning emerging quantum technologies, enabling capabilities beyond those of classical systems. Accurate verification of entanglement is therefore crucial. However, experimental schemes usually rely on the assumption that quantum measurements can be realized exactly. As the complexity of a quantum system grows, this assumption typically becomes increasingly unrealistic, therefore leading to a widening mismatch between theoretical models and experimental implementations. Here we demonstrate that arbitrarily small measurement errors, when adversarially encoded in the measurement apparatus, can lead to the false certification of high-dimensional entanglement in systems that are, in fact, separable. This is achieved by introducing explicit hacking attacks to measurement devices in well-established entanglement verification tests. We further experimentally demonstrate this effect using classical photonic states encoded in the spatial degree of freedom, spanning up to 61 dimensions with measurement fidelity errors as low as 0.23%. Our results uncover a fundamental vulnerability in current methods for high-dimensional entanglement detection, highlighting the susceptibility of complex quantum devices to small adversarial perturbations. The findings underscore the need for developing secure verification of quantum information that is robust to bounded discrepancies between theory and experiment.

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

FacProcessTwin: An LLM-Based System for Process Twin Development

arXiv:2606.17666v1 Announce Type: cross Abstract: Process twins provide real-time representations of entire production processes. By capturing how process steps interact, rather than monitoring a single machine in isolation as an asset-based digital twin does, they have the potential to drive efficiency gains across the whole process. However, developing a process twin is costly. It requires accurately modelling the entire production process: its process steps, the equipment and product-specific settings each step uses, and its process variations. The resulting model must then be bound to live operational data. We present FacProcessTwin, a system that leverages a large language model (LLM) to reduce this development time, building a process twin from a plant's process documentation and natural-language input from an operator. FacProcessTwin generates this complete process model and then automatically binds its process steps to live operational data. The generated model and its data bindings are rendered as an interactive process diagram through which manufacturing personnel can monitor and correct the system's autonomous decisions, such as resolving uncertainty at safety-critical binding steps. We evaluate FacProcessTwin through a real-world case study of an Australian food manufacturer, covering 16 production process flows that span chilled, frozen, and aseptic shelf-stable product categories and include process variations within the same product. The results show that FacProcessTwin generates these process models accurately (a mean F1 of 95.2% against ground truth) and builds each twin in roughly a sixth of the manual time. Its human-in-the-loop governance then keeps the safety-critical bindings correct: at ambiguous tags where a single-pass baseline silently mis-binds 75.0% of the time, FacProcessTwin defers to the operator and mis-binds none.

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

Qwen-RobotNav Technical Report: A Scalable Navigation Model Designed for an Agentic Navigation System

Agentic navigation systems require a base navigation model whose observation strategy can be externally reconfigured at inference time, because instruction following, object search, target tracking, and autonomous driving share the same perception-planning backbone yet demand fundamentally different strategies for consuming the visual stream. We present Qwen-RobotNav, a scalable navigation model built on Qwen-RobotNav that addresses it through a parameterised interface with two complementary dimensions: multiple task modes that select the navigation behaviour, and controllable observation parameters (e.g., token budget, per-camera weights) that govern how visual history is encoded. With training-time randomization over all parameters, Qwen-RobotNav is robust to any inference-time configuration requiring zero architectural modification to the Qwen-RobotNav backbone. We train Qwen-RobotNav on 15.6M samples; co-training with vision-language data prevents the collapse into reactive action-sequence mappers observed in trajectory-only training. The parameterised interface also makes Qwen-RobotNav a natural building block for agentic systems: for long-horizon scenarios, an upper-level planner decomposes goals into sub-tasks and dynamically switches Qwen-RobotNav's task mode and context strategy mid-episode, composing complex behaviours from repeated calls to the same model. Extensive experiments show that Qwen-RobotNav sets new state-of-the-art results across major navigation benchmarks. The model exhibits favourable scaling from 2B to 8B parameters, with joint multi-task training developing a shared spatial-planning substrate that transfers across task families, and demonstrates strong zero-shot generalisation to real-world robots across diverse environments.

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

FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction

arXiv:2602.22822v3 Announce Type: replace Abstract: Tandem mass spectrometry (MS/MS) is central to small molecule identification, but current deep learning systems for spectrum prediction still remain difficult to evaluate and deploy in practice. While novel architectures constantly claim state-of-the-art performance, inconsistent metadata conditioning and entangled preprocessing pipelines hinder fair architectural comparisons. Besides, existing evaluations are often restricted to curated datasets, failing to capture the heterogeneity and cross-domain shifts of real-world metabolomics. Furthermore, current benchmarks lack difficulty-aware diagnostics and leave blind to how models behave under specific compute or data constraints. To address this, we present FlexMS, a modular public-data benchmark framework that standardizes MS/MS prediction across public resources while keeping molecular encoders, metadata conditioning, predictor heads, and downstream retrieval under one protocol. FlexMS establishes a fair evaluation playground which significantly lowers the barrier for integrating new predictive tools. Rather than solely optimizing for average scores, FlexMS augments aggregate accuracy with difficulty-aware diagnostics, providing actionable guidance on model selection across different compute constraints, data scales, and downstream retrieval objectives. Ultimately, FlexMS provides the community with a reproducible standard to identify which algorithmic conclusions are stable and which operating points are most viable in practice.

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

Stochastic Signed Distance Processes

Multi-view surface reconstruction is a core problem in computer vision. One prominent line of work represents the surface implicitly as a signed distance field (SDF), optimizing it based on the photometric loss between rendered and observed pixel colors. These approaches typically employ SDF-based volume rendering to obtain a differentiable relaxation of discontinuous visibility along rays, thereby reducing reliance on silhouette supervision. In this paper, we reformulate SDF-based volume rendering as probabilistic surface rendering, where each pixel color is modeled as a mixture distribution induced by the random first ray-surface intersection. To this end, we introduce Stochastic Signed Distance Processes (SSDP), which model the SDF along each ray as a stochastic process, inducing a first-passage-time distribution for each ray. We then derive the first-passage probability for each sampling interval based on Bayesian filtering, together with its practical approximation for parallel rendering. We further show that NeuS, an existing SDF-based volume rendering method, arises as a special case of our formulation. Experiments on the DTU and MobileBrick datasets demonstrate that our method outperforms baselines in both surface reconstruction and uncertainty quantification, supporting the effectiveness of our first-passage formulation. Our code is available at https://github.com/skmhrk1209/SSDP.

20.
bioRxiv (Bioinfo) 2026-06-16

MetaPilot: genome-aware adaptive search-space refinement for unified DDA and DIA metaproteomics

Metaproteomic peptide identification is constrained by the structure and size of the protein search space. Pooled gene catalogues provide coverage but obscure genome-level evidence, and current workflows for data-dependent (DDA) and data-independent (DIA) acquisition diverge in their database strategies. We present MetaPilot, a genome-aware workflow that uses conserved marker-protein evidence to rank candidate genomes from MGnify catalogues and construct adaptive, sample-specific search spaces. Applied to paired DDA/DIA datasets of defined mixtures and fecal samples, MetaPilot adapted genome selection to community complexity and reproduced published peptide evidence while expanding the detectable peptide space. In DDA-independent reanalysis of Orbitrap human gut DIA data, MetaPilot identified 24.4% more peptides than the published DDA-derived library and 2.06-fold more than the matched DDA-assisted DIA search. On timsTOF DIA-PASEF mouse intestinal data, it outperformed uMetaP by 41.8~119.7%, enabling genome-resolved functional interpretation without DDA-PASEF input.

21.
arXiv (CS.CV) 2026-06-16

MNet++: Extended 2D/3D Networks for Anisotropic Medical Image Segmentation

This work demonstrates a full reproduction and extension of MNet, a hybrid 2D/3D convolutional network designed for anisotropic medical image segmentation. The original architecture was re-implemented within the nnU-Net framework to verify its reported performance and robustness to variable voxel spacing, known as anisotropy. Experiments were conducted on PROMISE prostate MRI and a controlled subset of LiTS liver CT under matched preprocessing and compute constraints. The reproduced MNet achieved a Dice similarity coefficient (DSC) of 89.0 +/- 0.9% on PROMISE, within 0.8% of the published result, and 94.3 +/- 1.9% / 54.6 +/- 3.1% for liver and tumor segmentation on LiTS, respectively. Two lightweight extensions were further introduced: (1) a learned Fusion Gating mechanism enabling adaptive 2D-3D feature blending, and (2) a VMamba state-space module for efficient long-range depth modelling. The Spatial Gating variant improved DSC by +0.8% with less than 3% inference overhead, while VMamba improved performance consistency, reducing PROMISE Dice variation to +/- 0.7% and achieving the strongest LiTS liver performance at 95.8% Dice. Both extensions preserved MNet robustness to anisotropy, with delta Dice = 1.5% across 1-4 mm voxel spacing. Overall, the study confirms MNet reproducibility and demonstrates that adaptive fusion and state-space modelling have the potential to further strengthen segmentation reliability under anisotropic conditions. However, further tests are required to provide definitive conclusions.

22.
arXiv (CS.AI) 2026-06-25

Reasonable Motion: A General ASP Foundation for Environment Constrained Movement Trajectory Computation

arXiv:2606.25626v1 Announce Type: new Abstract: We present a general answer set programming based hybrid quantitative-qualitative method for computing constrained branching trajectory modes for moving objects in real-world settings. The method performs constrained traversal of an environment graph, enumerating geometrically admissible motion behaviours as stable models, each constituting a distinct trajectory mode characterised by both domain-dependent and independent factors such as derived event sequence, map topology, and domain norms. The hybrid trajectory computation method is generally applicable across motion characteristics typically encountered in diverse dynamic domains with moving objects, e.g., autonomous driving. We demonstrate applicability and highlight how computed trajectories are traceable to their underlying stable model, thereby affording verifiable interpretability that purely learned approaches cannot provide. We also perform an empirical evaluation with Argoverse 2, a large-scale real-world autonomous driving benchmark representative of the class of dynamic domains within the scope of the proposed method.

23.
arXiv (CS.AI) 2026-06-25

ECM Contracts: Contract-Aware, Versioned, and Governable Capability Interfaces for Embodied Agents

arXiv:2604.13097v2 Announce Type: replace-cross Abstract: Embodied agents increasingly rely on modular capabilities that are installed, upgraded, composed, and governed at runtime, yet the interfaces between these modules are specified only at the level of message types, so integration failures surface only during execution. We present ECM Contracts, a contract-based interface model for embodied capability modules. Unlike conventional interfaces that specify only input and output types, ECM Contracts encode six dimensions of embodied execution: functional signature, behavioral assumptions, resource requirements, permission boundaries, recovery semantics, and version compatibility. On this model we build a compatibility framework that checks installation, composition, and upgrade before deployment, and a release discipline of version-aware compatibility classes and upgrade gates. We evaluate the prototype by predicting real, independently documented integration failures in the ROS ecosystem: contracts are reconstructed blind from each module's published interface, scored by a checker frozen before reconstruction against bugs from third-party datasets, and confirmed in live runtime execution. Contract checking predicts 56% and 72% of these documented failures across two substrates, against at most 17% for the strongest type and quality-of-service baselines, with the advantage statistically significant and zero false positives on matched-good controls. The resource and version dimensions carry most of this margin; the behavioral dimension adds little beyond the middleware's quality-of-service check, and we report the permission and recovery dimensions as forward-looking. Stable embodied software ecosystems require not just modular packaging but explicit contracts connecting composition, governance, and evolution.

24.
medRxiv (Medicine) 2026-06-15

Comparative Analysis of Machine Learning Models vs. Traditional Clinical Calculators for Cardiovascular Risk Prediction

Background: Cardiovascular diseases (CVD) remain the leading global cause of mortality, responsible for approximately 31% of all deaths worldwide in 2021. Traditional risk calculators, including Framingham, ASCVD, SCORE, and SCORE2, have long constituted the cornerstone of primary prevention strategies; however, they were derived predominantly from high-income European and North American populations, thereby limiting their predictive accuracy in diverse epidemiological contexts, particularly among Hispanic/Latino communities. Machine learning (ML) offers an alternative to capture the non-linear interactions inherent in biomedical data. Objective: The present study develops and validates ML-based models for cardiovascular mortality prediction using the National Health and Nutrition Examination Survey (NHANES) 1999-2018 dataset, and systematically compares their discriminative performance against eleven conventional clinical CVD risk calculators. Materials and Methods: A dedicated software platform, "CardioPrediQ," was designed to integrate multiple CVD calculators with ML-based risk assessment. A cohort of 12,847 participants with 16 predictor variables was derived from NHANES. Six algorithms (Logistic Regression, Cox Proportional Hazards, Gradient Boosting, AdaBoost, Random Forest, and Extra Trees) were trained in combination with six class-balancing strategies, yielding 36 model configurations. All models were trained on a stratified 70/30 split and calibrated using the Saerens prior probability adjustment method. Performance was evaluated using AUC-ROC, sensitivity, specificity, F1-score, and a weighted composite score. DeLong's test was employed to assess the statistical significance of AUC differences between the best-performing ML model and each conventional calculator. Results: Gradient Boosting with 2:1 oversampling and Saerens calibration achieved the best overall performance (AUC = 0.8934; composite score = 0.7904), outperforming all traditional calculators in composite ranking. The top six positions were occupied exclusively by ML and statistical models. The mean age of cardiovascular decedents was 67.43 years compared with 47.74 years among survivors. DeLong's test confirmed statistical superiority over six traditional CVD calculators (p < 0.05), whereas the difference against the top-performing calculators (ASCVD, HEARTS Caribbean, ASCVD Colombia, SCORE2, HEARTS North America) did not reach statistical significance. Age dominated feature importance at 41.2% relative weight, followed by systolic blood pressure (18.7%). Saerens calibration reduced the Brier score from 0.1286 to 0.1158, substantially improving probability calibration. Conclusions: ML models demonstrated superior composite performance over traditional calculators. The statistical equivalence with the highest-performing conventional calculators in the NHANES cohort is context-dependent and validates the methodological pipeline. The CardioPrediQ platform addresses the critical need for integrated, scalable CVD risk assessment tools, which is particularly relevant for Latin American populations where calculator validation remains limited. These findings support the integration of calibrated ML-based risk prediction into clinical practice while underscoring the importance of probability calibration for informed clinical decision-making.

25.
bioRxiv (Bioinfo) 2026-06-16

Better data, better trees: GenBank-GISAID deduplication and source-specific artifact masking in viral genomics

GenBank and GISAID are the primary repositories for viral genomic data, but integrating records across them remains a challenge. The same sequence could be made available in both databases without any cross-reference linking the two entries. Consequently, there is no systematic way to identify this redundancy, which compromises the compilation of representative, non-redundant large-scale datasets. In parallel, the growth of viral genomic data has increased the risk of systematic technical artifacts introduced during sequencing or assembly. These artifacts can inflate substitution rate estimates and degrade temporal signal, biasing evolutionary rate estimates. To address both challenges, here we present a formal, reproducible workflow integrating two newly developed complementary tools: G2G matcher for cross-repository harmonization and Lab-Specific Bias FILTer (LSBFILT) for masking of laboratory-specific artifacts. Using the Eastern/Central/South African (ECSA) chikungunya virus lineage as a proof-of-concept, we demonstrate that our integrated workflow restores temporal signal and provides a robust, curated dataset for downstream phylodynamic analyses. Critically, restricting masking of homoplastic sites to specific sequences reduces the substitution rate estimate from an inflated 8.517 x 10e-4; to 5.078 x 10e-4; substitutions/site/year and increases the coefficient of determination (R2) of the root-to-tip regression analysis from 0.353 to 0.677. By enabling systematic cross-repository harmonization and source-specific artifact masking, we provide the molecular epidemiological community with scalable tools to reconcile fragmented genomic data and reduce technical biases, fostering more accurate and reproducible phylogenetic analysis. G2G matcher is available at https://github.com/andrezaleite/G2G-Matcher, and LSBFILT at https://github.com/khourious/LSBFILT.