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01.
medRxiv (Medicine) 2026-06-23

Unscreenable: The Burden, Structure, and Analytic Consequences of "Unable to Assess" Delirium Documentation in the Intensive Care Unit

Objective: To quantify the burden, structure, and downstream analytic consequences of "Unable to Assess" (UTA) delirium documentation in the intensive care unit (ICU). Design: Retrospective cross-sectional and repeated-measures study. Setting: A single US academic medical center (Medical Information Mart for Intensive Care IV [MIMIC-IV], 2008-2019). Patients: 72,944 adult ICU stays with at least 1 delirium screen. Interventions: None. Measurements and Main Results: Among 610,632 screens, 130,455 (21.4%; 95% CI, 21.0%-21.8%) were recorded as UTA, exceeding the 119,052 (19.5%) scored positive. The UTA fraction rose from 2.0% at a Richmond Agitation-Sedation Scale (RASS) score of 0 to 97.8% at RASS -4; 22.0% of UTA screens occurred in arousable patients, where UTA was associated with mechanical ventilation (odds ratio [OR], 3.43; 95% CI, 3.17-3.71) and non-English primary language (OR, 3.74; 95% CI, 3.43-4.08). Building the delirium label three ways from the same patients shifted prevalence modestly (32.1% to 30.8%) and prediction (area under the curve, 0.737 to 0.719) but most affected the delirium-mortality association: in a baseline-adjusted model the OR was 4.12 (95% CI, 3.88-4.36) under complete-case handling and fell to 2.16 (95% CI, 2.06-2.27) when UTA was recoded as negative. UTA was recoverable from the observed clinical state (area under the curve, 0.95). Conclusions: In this ICU cohort, Unable to Assess was the most common recorded delirium result other than Negative, exceeding positive screens; recoding it as negative roughly halved the apparent delirium-mortality association by relabeling deeply sedated, high-mortality patients. Delirium datasets should preserve and report UTA, whose concentration among arousable non-English-speaking patients is a measurable equity target.

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

Extracting Semantics: LLM-Guided Automatic Population of Robot Ontology from URDF

arXiv:2606.17073v1 Announce Type: cross Abstract: While commonsense knowledge may suffice for virtual agents, embodied robots interacting with humans require grounded and semantically rich representations of both their environment and their own physical embodiment. In cognitive robotics, ontologies are effective for integrating such heterogeneous knowledge to enable explainable reasoning, even during continuous knowledge updates. Yet, their manual construction remains a bottleneck. We present a preliminary approach for the automatic generation of robot semantic abstractions by transforming Unified Robot Description Format (URDF) models into populated ontologies. Although URDF files provide structural and kinematic descriptions, their identifiers often require commonsense interpretation to recover meaningful semantics, a task at which Large Language Models (LLMs) excel. Our pipeline leverages LLMs to infer semantic relationships by prompting them with concepts from an existing ontology, ensuring the final classification remains aligned with the formal model. To improve reliability, the pipeline combines majority voting across multiple LLM queries along with syntactic and schema-level validation to ensure that generated outputs conform to the expected representation format and ontology constraints. We evaluate the approach on multiple robot descriptions and discuss the generated abstractions. Initial results indicate that the proposed method can effectively bridge the gap between low-level robot descriptions and the structured, grounded knowledge representations required for human-robot interaction.

03.
medRxiv (Medicine) 2026-06-18

Multicluster measles outbreak with a substantial proportion of modified cases in Tokyo, Japan, January-May 2026

Tokyo experienced a measles outbreak (260 cases) in early 2026 despite elimination status. Adults aged 20-39 years were most affected, and 38% of cases were modified measles, increasing with prior vaccination. Although incidence rose until April, the effective reproduction number; R(t) fell below 1, consistent with outbreak control. Multiple clusters were identified, but many cases lacked epidemiological links, suggesting that modified measles is less likely to be considered in differential diagnosis. Intensive contact tracing and surveillance contributed to limiting transmission.

04.
arXiv (CS.AI) 2026-06-19

A Deep Generative Model for Resting-State EEG Synthesis and Transferable Representation Learning

arXiv:2503.02636v5 Announce Type: replace-cross Abstract: Resting-state EEG provides a non-invasive view of spontaneous brain activity, but extracting meaningful patterns is often limited by scarce high-quality data and reliance on manually engineered features. Generative adversarial networks (GANs) can synthesize neural signals and learn transferable representations directly from raw data, a dual capability that remains underexplored in EEG research. Here, we introduce REST-GAN, a GAN-based framework for resting-state EEG that combines adversarial training with an auxiliary self-supervised reconstruction objective to support signal synthesis and unsupervised feature extraction. Although trained only on raw time-domain signals, without explicit frequency-domain or sensor-topographic supervision, the generated time series reproduced key temporal, spectral, and connectivity properties of real EEG. In band-power feature space, generated samples showed high precision and recall across eyes-open and eyes-closed conditions (EO: 0.91/0.67; EC: 0.87/0.65), while group-average spectral coherence matrices showed low mean absolute differences from real data across frequency bands (~0.01-0.03). The representations learned by the model's critic transferred to independent resting-state demographic classification tasks, outperforming models trained directly on raw EEG and showing competitive performance relative to a recent EEG foundation model, while requiring substantially less training data and computational resources. These findings highlight a computationally efficient, architecture-driven strategy in which generative models serve not only as EEG signal generators, but also as unsupervised feature extractors. This approach may support more data-efficient EEG analysis while reducing reliance on manual feature engineering. The implementation code for REST-GAN is available at: https://github.com/Yeganehfrh/REST-GAN.

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

Surpassing Scale by Efficiency: A Compact 135M Parameter Foundational LLM Natively Adapted for the Bangla Language

While the NLP landscape is dominated by multi-billion parameter architectures, their deployment in low-resource, non-Latin scripts remains computationally prohibitive for edge configurations, mobile systems, and decentralized local hardware. This paper presents bangla-smollm-135m, a highly compact 135-million parameter decoder-only foundational model engineered explicitly for high-efficiency language modeling in the Bangla script. By leveraging a deterministic intersect-and-append token merging strategy between TituLLMs and SmolLM2-135M, the model overcomes subword script fragmentation without destabilizing early pretrained parameter states. In zero-shot multi-task benchmark evaluations (PIQA_bn, OpenBookQA_bn, CommonsenseQA_bn, and Bangla_MMLU), bangla-smollm-135m matches or outperforms models twice its size (Gemma-3-270m) and achieves parity with models in the 1B parameter tier. The model is available at rnnandi/bangla-smollm-135m

06.
arXiv (quant-ph) 2026-06-12

Multiple Topological Haldane Phases for Symmetry-Protected Quantum Information Processing

arXiv:2606.12685v1 Announce Type: new Abstract: Symmetry-protected topological phases have attracted significant interest at the fundamental level and as a potential platform for quantum information processing, owing to their protected edge states and resilience to perturbations. Applying these features for practical and efficient quantum computation is highly desirable, but remains an open challenge. Here, we demonstrate the partitioning into multiple independent Haldane phase subsystems of a single spin-1/2 ladder system and propose this as a scalable architecture for gate-based quantum computation, which takes advantage of the symmetry-protected topological order. We encode qubits in the two topological states of the $S^{z}=0$ sector of each subsystem. Finite-size effects, typically viewed as detrimental, instead provide a controllable energy splitting that enables single-qubit rotations using only local magnetic fields. An Ising-type interaction between neighboring subsystem edges generates entangling gates, enabling universal quantum computation driven by two control parameters that are easily accessible experimentally. Our results demonstrate how symmetry-protected topological phases can be directly harnessed for circuit-model quantum computation in realistic systems.

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

CRAG: Can 3D Generative Models Help 3D Assembly?

Most existing 3D assembly methods treat the problem as pure pose estimation, rearranging observed parts via rigid transformations. In contrast, human assembly naturally couples structural reasoning with holistic shape inference. Inspired by this intuition, we reformulate 3D assembly as a joint problem of assembly and generation. We show that these two processes are mutually reinforcing: assembly provides part-level structural priors for generation, while generation injects holistic shape context that resolves ambiguities in assembly. Unlike prior methods that cannot synthesize missing geometry, we propose CRAG, which simultaneously generates plausible complete shapes and predicts poses for input parts. Extensive experiments demonstrate state-of-the-art performance across in-the-wild objects with diverse geometries, varying part counts, and missing pieces. Project Page: https://ai4ce.github.io/CRAG/

08.
medRxiv (Medicine) 2026-06-15

Diabetes and the Life-Course: Evidence from Panel Data and Electronic Health Records

Incidence of type 2 diabetes is increasing at ages when education, work, family, and financial transitions are taking place, yet we lack robust evidence of whether earlier treatment changes life-course outcomes and over which time span this takes place. This paper uses the medical cutoff for diabetes diagnosis (HbA1c of 6.5 percent) as a natural experiment to study the effects of diabetes treatment using electronic health records (EHR) and panel data. This paper has three main findings. First, using EHR data, we find that there is a sharp increase in the probability of both diagnosis of diabetes and prescription when the HbA1c equals 6.5 percent. Second, we find that treating diabetes reduces HbA1c levels, weight, BMI, and blood pressure and increases the amount of care received, proxied by the number of HbA1c tests. Both the diagnosis and a prescription are independently able to produce positive changes in metabolic health, although a prescription is more effective in this regard. Third, we conclude that treating diabetes does not have a significant effect on life-course outcomes for a cohort of young Americans aged 24-32, although it does result in a reduction in HbA1c levels that are seen even eight years after the intervention. Taken together, these findings suggest that receiving a diagnosis and prescription are both effective treatments for diabetes, but they do not translate to significant alterations in the lives of young adults in the medium-term.

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

MolSight: Molecular Property Prediction with Images

Every molecule ever synthesised can be drawn as a 2D skeletal diagram, yet in modern property prediction this universally available representation has received less focus in favour of molecular graphs, 3D conformers, or billion-parameter language models, each imposing its own computational and data-engineering overhead. We present $MolSight$, the first systematic large-scale study of vision-based Molecular Property Prediction (MPP). Using 10 vision architectures, 7 pre-training strategies, and $2\,M$ molecule images, we evaluate performance across 10 downstream tasks spanning physical-property regression, drug-discovery classification, and quantum-chemistry prediction. To account for the wide variation in structural complexity across pre-training molecules, we further propose a $chemistry-informed curriculum$: five structural complexity descriptors partition the corpus into five tiers of increasing chemical difficulty, consistently outperforming non-curriculum baselines. We show that a single rendered bond-line image, processed by a vision encoder, is sufficient for competitive molecular property prediction, i.e. $chemical insight from sight alone$. The best curriculum-trained configuration achieves the top result on $5 of 10$ benchmarks and top two on $all 10$, at $$80$\times$ lower$$ FLOPs than the nearest multi-modal competitor.

10.
arXiv (CS.CV) 2026-06-17

Divide, Deliberate, Decide: A Multi-Agent Framework for Fine-Grained Egocentric Action Recognition

Fine-grained action recognition in egocentric video is challenging for Vision-Language Models (VLMs): actions often differ only in small visual cues, and a single model tends to be biased toward a subset of these cues. We propose Divide, Deliberate, Decide, a fully-local, zero-shot multi-agent framework in which (i) a VLM orchestrator chunks the video and proposes a top-k candidate label list per segment, (ii) an ensemble of heterogeneous VLM specialists, drawn from different open model families, engages in a structured deliberation that includes a peer-consultation round of questions, and (iii) agent rankings are aggregated with a Borda count and the orchestrator re-ranks its own prediction in light of the specialists' evidence. The entire pipeline runs locally with no fine-tuning. Experiments show that our method positively improves zero-shot action recognition performance over the baseline, highlighting the influence of a heterogeneous deliberation step, showing that the gain stems from decorrelated model priors rather than from additional compute.

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

4DP-QA: Scalable QA for 4D Perception in Vision Language Models

Despite recent advances, Vision Language Models (VLMs) still struggle to grasp the dynamics of the world. We note that the ability to reason about a 4D scene, challenging in itself, is further complicated by two factors. First, VLMs observe motion indirectly via its projection onto 2D images. Second, existing datasets fail to disentangle object and camera motion. To address these challenges, we present a QA generation pipeline that focuses on motion-related scene understanding. We take particular care of the entanglement of camera and object motion by casting tracking in both the traditional way and in a novel, fixed reference system, dubbed True-Motion Tracking, which provides an intuitive description of motion. From this pipeline, we generate a large-scale training dataset of 400K samples, 4DP-QA (4D Perception QA), and a 2.2K-sample benchmark, 4DP-QA-Bench. Training existing models on our dataset yields performance improvements on an external benchmark, validating the effectiveness of our method.

12.
arXiv (CS.CL) 2026-06-16

VeriGraph: Towards Verifiable Data-Analytic Agents

LLM-based agents have demonstrated strong capabilities in data-intensive analytical tasks, yet their outputs are rarely verifiable: a reliance on linear text trajectories makes their reasoning difficult to audit. In particular, deterministic computations over raw data and semantic deductions over natural-language claims are often entangled in an unstructured stream, leaving numerical conclusions hard to reproduce and qualitative judgments hard to inspect. To address this, we propose VeriGraph, a traceable neuro-symbolic reasoning framework that enables agents to construct an explicit heterogeneous evidence directed acyclic graph (DAG) during execution. VeriGraph introduces three evidence-expansion primitives, namely computational, grounding, and derivational expansion, to connect raw data, interpreter variables, computed results, and natural-language claims in a unified graph. Under this formulation, structural traceability is reduced to graph reachability from raw data sources to terminal claims, while semantic support is measured by claim-level evidence evaluation. To improve graph construction, we further design a graph-based policy optimization strategy with a composite reward that jointly supervises answer correctness, computational integrity, and derivational coherence. Experiments on four benchmarks show that VeriGraph-8B achieves the highest overall score among all baselines. More importantly, VeriGraph produces auditable evidence graphs with substantially stronger claim grounding, achieving a 87.61\% Grounding Rate under our claim-level evidence support evaluation. These results suggest that explicit evidence-graph construction is a promising path toward verifiable data-analytic agents. Our code is available at https://github.com/ignorejjj/VeriGraph.

13.
arXiv (CS.AI) 2026-06-11

From Uniform to Learned Graph Priors: Diffusion for Structure Discovery

arXiv:2606.11831v1 Announce Type: cross Abstract: Neural relational inference (NRI) methods discover interaction graphs from trajectories through variational reasoning on discrete potential edges. However, these methods typically rely on oversimplified, factorized graph priors. Such priors, typically nearing uniform distributions, treat edges as independent entities. This systemic misalignment does not match the real-world systems and yields diffuse and indecisive edge posteriors limiting the reliability of structural discovery. To address this, we propose Diff-prior, a diffusion-parameterized adaptive prior used to calibrate latent graph distribution rather than generate graphs. Our core insight is to reframe prior integration as a learnable denoising-style calibration that organizes scattered, uncertain edge posteriors into a more reliable overall structure which can be trained by the diffusion model. Diff-prior learns an adaptive structure prior that performs structured calibration on the edge posteriors during inference, guiding it towards a distribution closer to the underlying structure. The diff-prior operates before structural sampling and acts as a denoising calibrator directly on the encoder edge distribution, which provides a generic training paradigm over structured variables. Experiments on standard benchmarks validated our framework, and the results indicate that Diff-prior improves the performance of structure inference and generates more decisive edge posteriors across multiple NRI-family architectures. The code is available on https://github.com/Hardy158118/Diffprior.

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

ANCHOR: Error-Controlled Adaptive Numerical Correction for Neural Operator Time Marching

arXiv:2512.19643v2 Announce Type: replace Abstract: Numerical simulation of time-dependent partial differential equations (PDEs) is central to scientific and engineering applications, but high-fidelity solvers are often prohibitively expensive for long-horizon or time-critical settings. Neural operator (NO) surrogates offer fast inference across parametric and functional inputs; however, most autoregressive NO frameworks remain vulnerable to compounding errors, and ensemble-averaged metrics provide limited guarantees for individual inference trajectories. In practice, error accumulation can become unacceptable beyond the training horizon, and existing methods lack mechanisms for online monitoring or correction. To address this gap, we propose ANCHOR (Adaptive Numerical Correction for High-fidelity Operator Rollouts), an online, instance-aware hybrid inference framework for stable long-horizon prediction of nonlinear, time-dependent PDEs. ANCHOR treats a pretrained NO as the primary inference engine and adaptively couples it with a classical numerical solver using a physics-informed, residual-based error estimator. Inspired by adaptive time-stepping in numerical analysis, ANCHOR monitors an exponential moving average (EMA) of the normalized PDE residual to detect accumulating error and trigger corrective solver interventions without requiring access to ground-truth solutions. We show that the EMA-based estimator correlates strongly with the true relative L2 error, enabling data-free, instance-aware error control during inference. Evaluations on six canonical PDEs: 1D and 2D Burgers', 2D Allen-Cahn, 2D Cahn-Hilliard, 2D Navier-Stokes, and 3D heat conduction, demonstrate that ANCHOR reliably bounds long-horizon error growth, stabilizes extrapolative rollouts, and significantly improves robustness over standalone neural operators, while remaining substantially more efficient than high-fidelity numerical solvers.

15.
arXiv (CS.CV) 2026-06-16

Domain-Guided Prompting of the Segment Anything Model for Seismic Interpretation: The Role of Attributes, Visualization, and Hybrid Prompts

The advent of large pretrained foundation models for computer vision has significantly improved the efficiency of visual data interpretation. The Segment Anything Model (SAM), in particular, offers powerful zero shot segmentation capabilities through prompt based interaction, thus making it a promising tool for seismic interpretation. However, most existing applications of SAM rely on fine tuning for specific geological targets, which requires extensive labeled data, incurs high computational cost, and often compromises the model's generalization capability. In this study, we introduce a principled framework for zero shot adaptation of foundation models to seismic data. The framework is built on two key components: (1) aligning seismic attributes and visualization choices (e.g., colormaps) with the geological target of interest, and (2) employing a hybrid prompting strategy that combines sparse user defined point prompts with dense mask prompts derived from SAM's internal feature activations. We systematically evaluate this framework across multiple geological targets, datasets, prompt configurations, and seismic attribute representations. Our results demonstrate that geologic target aware selection of seismic attributes and colormaps, combined with hybrid prompting, enhances the separability of geological features and improves boundary delineation and segmentation accuracy relative to point based prompting alone. Our findings show that, when these components are jointly applied, SAM can achieve competitive segmentation performance in a fully zero shot setting, thereby eliminating the need to retrain SAM for each geologic feature. This work establishes a practical and scalable pathway to leverage foundation models in seismic interpretation, reducing reliance on labeled data while preserving model generality.

16.
PLOS Computational Biology 2026-06-15

Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery

by Daniel S. Berman, Libby M. Lewis, Tom D. Curtis, Olivia N. Tiburzi, Daniel F. Q. Smith, Arturo Casadevall, Laura J. Dunphy Emerging fungal pathogens represent a concerning threat to both global health and food security. In this study, we aimed to address our rising vulnerability to fungal pathogens through the development of the Fung-AI pipeline: an AI/ML-driven approach for antifungal discovery. A generative adversarial network (GAN) was trained to generate novel candidate antifungal peptide sequences. Next, in silico antifungal and hemolytic classifiers were built to further prioritize AI-generated peptides for experimental validation. From a pool of ~10,000 candidates, thirteen peptides were selected for testing over two-stages of experimentation. Five peptides were found to display mild antifungal activity against the wheat pathogen, Fusarium graminearum, with minimal inhibitory concentrations (MICs) ranging from 250 µg/mL to 500 µg/mL. Four of the five peptides also showed activity against the human pathogen, Candida albicans (MIC: 500 µg/mL). Two of our AI-generated antifungal peptides additionally demonstrated low cytotoxicity in HepG2 human liver carcinoma cells (LC50 > 704.2 µg/mL) indicating that they may be useful as scaffolds for future optimization for therapeutic applications. None of our peptides were found to considerably inhibit the emerging pathogen C. auris, suggesting the need for pathogen-specific down-selection of candidate peptides. Overall, we present a proof-of-principle, generative-AI-based approach for the rapid design of de novo antifungal peptides.

17.
arXiv (CS.CV) 2026-06-11

From Correspondence to Actions: Human-Like Multi-Image Spatial Reasoning in Multi-modal Large Language Models

While multimodal large language models (MLLMs) have made substantial progress in single-image spatial reasoning, multi-image spatial reasoning, which requires integration of information from multiple viewpoints, remains challenging. Cognitive studies suggest that humans address such tasks through two mechanisms: cross-view correspondence, which identifies regions across different views that correspond to the same physical locations, and stepwise viewpoint transformation, which composes relative viewpoint changes sequentially. However, existing studies incorporate these mechanisms only partially and often implicitly, without explicit supervision for both. We propose Human-Aware Training for Cross-view correspondence and viewpoint cHange (HATCH), a training framework with two complementary objectives: (1) Patch-Level Spatial Alignment, which encourages patch representations to align across views for spatially corresponding regions, and (2) Action-then-Answer Reasoning, which requires the model to generate explicit viewpoint transition actions before predicting the final answer. Experiments on three benchmarks demonstrate that HATCH consistently outperforms baselines of comparable size by a clear margin and achieves competitive results against much larger models, while preserving single-image reasoning capabilities.

18.
bioRxiv (Bioinfo) 2026-06-11

SPARK: A Systems-level Computational Framework for Reconstructing Transcriptomic State Organisation in Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) exhibits substantial molecular heterogeneity, which complicates tumour stratification and limits the ability of mutation-centric models to capture tumour behaviour and predict patient outcomes. This study investigates whether coordinated transcriptomic programs can provide a systems-level representation of tumour states. Bulk RNA-sequencing data from the TCGA-LUAD cohort were analysed to reconstruct pathway-level transcriptomic organisation using a stability-optimised network framework (SPARK). This analysis identified eight transcriptomic modules representing coordinated biological processes active across tumours. Module activity scores were subsequently used to derive a composite Transcriptomic Risk Score through elastic-net Cox proportional hazards modelling. The resulting risk score showed a significant association with overall survival in the discovery cohort and improved prognostic discrimination beyond clinical variables. An independent evaluation in the CPTAC-LUAD cohort confirmed the prognostic signal and preserved risk stratification across patient groups. Unsupervised clustering of module activity further revealed three transcriptomic patient groups characterised by distinct biological programs, genomic alteration patterns, and survival outcomes. Single-cell analysis also demonstrated that the identified transcriptomic modules reflect coordinated organisation of the tumour-immune-stromal ecosystem across cellular compartments. Together, these findings suggest that LUAD heterogeneity can be organised into coordinated transcriptomic programs with measurable clinical relevance, providing a systems-level framework for representing tumour molecular states.

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

Token Factory: Efficiently Integrating Diverse Signals into Large Recommendation Models

arXiv:2606.19635v1 Announce Type: cross Abstract: Large Recommendation Models (LRMs) have demonstrated promising capabilities in industry-scale recommendation tasks. However, holistically integrating traditional signals into these transformer-based architectures effectively and efficiently remains a major challenge. Conventional approaches that "textualize" these signals directly or create discrete item representations often lead to excessively long prompts, substantial memory footprints, and high computational overhead. To overcome these limitations, we propose "Token Factory", a framework designed to transform traditional signals into "soft tokens" that can be directly processed by LRMs. This approach enables efficient integration and compression of heterogeneous input features, preventing prompt length explosion while enhancing model performance. We detail the architecture of Token Factory and present experimental results validating its effectiveness in a production-scale recommendation environment.

20.
arXiv (CS.AI) 2026-06-18

Engagement Intensity as a Learner-Modeling Signal for Adaptive AI Ethics Instruction

arXiv:2606.18548v1 Announce Type: cross Abstract: Adaptive AI ethics instruction in graduate research training benefits from intake measures that reflect differences in prior LLM experience. Prior coursework or workshop attendance is an obvious candidate, but it is not clear whether it is associated with pre-instruction ratings on key AI perception items. We compare three candidate intake features, self-reported usage frequency, self-rated LLM familiarity, and prior AI education, across five baseline perception outcomes in 93 bioscience graduate and postdoctoral trainees enrolled in a required research ethics course. Usage frequency shows Holm-corrected associations with all five outcomes, self-rated familiarity with three, and prior AI education with none. A threshold-like pattern at the lower end of the scale is most visible for training interest and accuracy trust rather than appearing as a uniform gradient across all five outcomes. In a short intake survey, reported LLM use is more consistently associated with these perceptions than prior coursework or workshops, with self-rated familiarity serving as a secondary indicator. These results suggest that simple pre-instruction behavioral signals can inform lightweight intake profiling for adaptive AI ethics education.

21.
arXiv (CS.CL) 2026-06-11

Factions Within, Uncertain Across: Within-Document Reader Sub-Groups in Social Highlighting

When many people highlight the same document, is the crowd a single consensus, or is it internally structured into reader sub-groups that mark different things – and is that structure a stable property of a reader or of the document? Building on prior work showing an individual's within-document highlighting signal is a whisper while individuality lives in selection, we ask the group-level question on a co-readership platform using a margin-preserving curveball null. Experiment 1: within a document, readers form strong sub-groups – pairs agree far beyond what shared salience, mark density, and sentence popularity predict (nearest-neighbour agreement z=+6.3, significant in 88% of documents). Under an eight-block region-preserving null, shared engagement with the same coarse regions of the document accounts for about 40% of this excess; the majority survives as finer reader-specific agreement (z=+3.6, 77% significant). So the within-document crowd is, in a descriptive sense, factional. Experiment 2: is that grouping a stable reader trait? Here we are honest about power. The cross-document split-half reproducibility of a pair's agreement is near zero pooled (+0.078 and 0.000 in two separately drawn samples), and a power calibration shows the test is informative only for pairs that co-read many documents. In the only informative high-overlap subset (k>=4), point estimates are positive but small-sample, imprecise across the separately drawn samples, never significant, and attenuate under the region-preserving null. We therefore leave cross-document stability unresolved: the data is consistent with anything from situational grouping to a weak-to-moderate stable reader trait. The crowd is factional within a document; whether its factions follow the reader across documents is, honestly, beyond our reach.

22.
medRxiv (Medicine) 2026-06-22

Rare loss-of-function variants in POLD1, PMS1 and FAN1 modify age at onset of motor symptoms in Huntington's disease

Huntington's disease is a rare neurodegenerative disease whose primary risk factors are inherited expansions of a CAG repeat tract in the HTT gene. Somatic expansion of these tracts leads to neuronal toxicity, neuronal death and clinical disease progression. To identify genetic factors with a major impact on disease onset and progression, we genome sequenced 18,825 individuals for the ENROLL-HD study. Our results show rare inactivating mutations in three genes, all involved in DNA damage repair, are major determinants of age of onset for motor symptoms (n=10,610) and other clinical manifestations. Heterozygote carriers of predicted loss-of-function (pLoF) variants in POLD1 and PMS1 developed motor symptoms an average 20 years (n=3; P=1x10-5) and 7 years (n=6; P=2x10-3) later than non-carriers, respectively. Conversely, heterozygote carriers of pLoF variants in FAN1 (n=30) developed symptoms 10 years earlier (P=2x10-10). Our findings highlight therapeutic strategies and help predict age of onset for at-risk individuals.

23.
bioRxiv (Bioinfo) 2026-06-11

PhyloZoo: a unified framework for phylogenetic network analysis in Python

作者:

Reticulate evolutionary processes (events in which lineages merge, such as hybridization, recombination, and horizontal gene transfer) are widespread across nature but cannot be represented by phylogenetic trees alone. Phylogenetic networks have therefore become an important modelling tool, yet existing software is typically tied to specific inference paradigms and provides limited support for working with multiple network representations in a unified and programmable environment. PhyloZoo is an open-source Python framework that lowers the barrier to developing practical, easy-to-use software for phylogenetic network analysis. It provides data structures and algorithms covering the main representations used in the field, together with dedicated visualization tools and robust I/O for all major phylogenetic file formats. A particular emphasis lies on semi-directed phylogenetic networks, which explicitly represent root uncertainty and have so far received limited support in existing software. By offering a shared foundation for developing interoperable tools and a combinatorial layer that supports computational proofs and theoretical exploration, PhyloZoo enables reproducible workflows for applied, methodological, and theoretical studies of reticulate evolution. Availability and implementation: PhyloZoo is implemented in Python and installable from PyPI, with source code, documentation, and examples available at https://github.com/nholtgrefe/phylozoo.

24.
arXiv (CS.AI) 2026-06-11

Physics-informed generative AI for semiconductor manufacturing: Enforcing hard physical constraints in generative models by construction

arXiv:2606.11247v1 Announce Type: cross Abstract: Generative models are increasingly used to propose designs, data, and control actions for physical systems, yet many such systems are governed by hard physical constraints rather than by perceptual plausibility. Semiconductor manufacturing provides a demanding test case: generated masks, layouts, synthetic defect data, and process recipes must obey lithography, transport, reaction, and device-physics constraints, because physically invalid samples are not merely low quality but unusable. This Perspective argues that semiconductor manufacturing exposes a broader computational-science challenge, namely that generative AI for constrained physical domains must be physics-informed by construction, not corrected only through post-hoc filtering. We survey the emerging architectural toolkit, including physics-informed diffusion, PDE-constrained variational models, neural-operator priors, and conservation-law-respecting generative networks, and show how it connects to differentiable lithography, TCAD, process simulation, and autonomous experimentation. We identify four integration patterns between generative models and physics-based simulators, and we propose a research agenda centered on physics-fidelity benchmarks, differentiable simulator infrastructure, and multimodal foundation models for physical design and manufacturing. The central claim is analytical rather than rhetorical: where physical validity is the binding criterion of success, architectures that enforce it by construction should be expected to outperform those that filter for it after the fact, and the fab is the setting where this distinction is sharpest.

25.
arXiv (CS.CV) 2026-06-16

SACE: Concept Erasure at the Semantic Singularity in Visual Autoregressive Models

The rapid progress of visual autoregressive (VAR) models has unlocked a transformative frontier for high-fidelity text-to-image synthesis, while heightening concerns over the safety alignment of generated content. Naive application of existing erasure techniques to VAR models causes catastrophic semantic collapse and visual artifacts, since they are predominantly designed for the homogeneous denoising steps of diffusion models. To address this foundational challenge, we first propose the Semantic Singularity Axiom, which posits that any target semantic concept embedded within a prompt is definitively locked at Scale-0. Then rigorously validate this axiom through our proposed Incremental Semantic Saliency Analysis (ISSA),which also enable the community to transparently inspect the coarse-to-fine semantic injection process. Guided by this insight, we introduce the first scale-aware concept erasure framework (SACE) for VAR models. By strictly confining interventions to the first scale, our approach couples an Entropy-Regularized Erasure Objective to prevent high-entropy sampling degeneration, alongside a restorative preservation loss to safely anchor the integrity of entangled benign priors. Extensive experiments demonstrate that our method achieves surgical concept erasure performance across various domains with minimal training overhead, timely and elegently resolute the critical safety vulnerabilities inherent in emerging VAR architectures. Code is available at: https://github.com/limerenceysy/SACE}{https://github.com/limerenceysy/SACE.