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01.
bioRxiv (Bioinfo) 2026-06-11

HalluDesign-NA: Extending HalluDesign for De Novo Nucleic Acid Design

AlphaFold3 has revolutionized the prediction of biomolecular structures and interactions, including atomic-level modeling of nucleic acids. However, the de novo design of structured and functional nucleic acids remains a significant challenge. Here, we extend our HalluDesign framework to nucleic acid design by integrating NA-MPNN for nucleic acid sequence optimization and design. This new framework, HalluDesign-NA, enables iterative sequence-structure co-optimization, facilitating the de novo design of nucleic acids. Computational benchmarking across ssDNA, ssRNA, and aptamer design tasks demonstrates consistent improvements in confidence scores (pLDDT, ipTM), supporting the feasibility of de novo nucleic acid design under various constraints, such as sequence length, symmetry, and protein structure context. We anticipate that HalluDesign-NA will accelerate the de novo design of functional nucleic acids for applications in biotechnology and medicine. The source code for HalluDesign-NA is available at https://github.com/MinchaoFang/HalluDesign_NA.

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

Not Just How Much, But Where: Decomposing Epistemic Uncertainty into Per-Class Contributions

arXiv:2602.21160v3 Announce Type: replace-cross Abstract: In safety-critical classification, the cost of failure is often asymmetric, yet Bayesian deep learning summarises epistemic uncertainty with a single scalar, mutual information (MI), that cannot distinguish whether a model's ignorance involves a benign or safety-critical class. We decompose MI into a per-class vector $C_k(x)=\sigma_k^{2}/(2\mu_k)$, with $\mu_k{=}\mathbb{E}[p_k]$ and $\sigma_k^2{=}\mathrm{Var}[p_k]$ across posterior samples. The decomposition follows from a second-order Taylor expansion of the entropy; the $1/\mu_k$ weighting corrects boundary suppression and makes $C_k$ comparable across rare and common classes. By construction $\sum_k C_k \approx \mathrm{MI}$, and a companion skewness diagnostic flags inputs where the approximation degrades. After characterising the axiomatic properties of $C_k$, we validate it on three tasks: (i) selective prediction for diabetic retinopathy, where critical-class $C_k$ reduces selective risk by 34.7\% over MI and 56.2\% over variance baselines; (ii) out-of-distribution detection on clinical and image benchmarks, where $\sum_k C_k$ achieves the highest AUROC and the per-class view exposes asymmetric shifts invisible to MI; and (iii) a controlled label-noise study in which $\sum_k C_k$ shows less sensitivity to injected aleatoric noise than MI under end-to-end Bayesian training, while both metrics degrade under transfer learning. Across all tasks, the quality of the posterior approximation shapes uncertainty at least as strongly as the choice of metric, suggesting that how uncertainty is propagated through the network matters as much as how it is measured.

03.
arXiv (CS.CV) 2026-06-17

Future Dynamic 3D Reconstruction: A 3D World Model with Disentangled Ego-Motion

Forecasting the evolution of dynamic environments is crucial for autonomous agents. While generative world models have recently achieved high photorealism in 2D video synthesis by mixing ego-motion and environmental dynamics within the image plane, they exhibit physical inconsistencies, such as morphing or vanishing objects, especially over long time horizons. In this paper, we propose FR3D, a world model that predicts a persistent 3D latent representation for future dynamic 3D reconstruction. Unlike prior works that treat the world as a sequence of image-based features, FR3D explicitly decouples the 3D evolution of the scene from the agent's trajectory, treating the inferred ego-motion as a latent proxy for action. This disentanglement resolves the ambiguities between self-motion and world-motion, ensuring geometric consistency into the future. Furthermore, we introduce a teacher-student distillation strategy that leverages the spatial "common sense" of off-the-shelf foundation models, leading to robust zero-shot generalization. Extensive experiments demonstrate FR3D's strong performance for future dynamic 3D reconstruction from monocular observations across multiple datasets, even 2 seconds into the future. Project page: https://fr3d-wm.github.io.

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

When Rules Learn: A Self-Evolving Agent for Legal Case Retrieval

arXiv:2606.17220v1 Announce Type: new Abstract: Legal case retrieval remains challenging due to the complexity of legal language and the need for precise lexical alignment between queries and relevant cases. Although dense retrieval models have achieved notable progress, empirical studies show that BM25 continues to serve as a strong baseline in this domain. It motivates us to propose a self-evolving framework for rule-driven query rewriting that enhances BM25 without any parameter training. The framework equips an LLM-based agent with an automatic evaluation environment, enabling it to iteratively create rewriting rules, plan validation experiments over rule combinations, and eliminate ineffective rules based on historical feedbacks. We evaluate our method on the Chinese legal case retrieval benchmark LeCaRD-v2. Experimental results demonstrate that the proposed framework outperforms non-evolutionary baselines, including human-designed rules and greedy rule selection, particularly when powered by a highcapacity core LLM. We also conduct detailed analyses to investigate the mechanisms underlying self-evolution. Our findings reveal that LLM's capabilities to leverage previous experimental results and its intrinsic knowledge of rule elimination play critical roles in refining the rule set via self-evolution.

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

Biarchetype analysis for univariate functional data. An application to macroeconomic financial time series

arXiv:2606.15881v1 Announce Type: cross Abstract: We introduce biarchetype analysis for the first time in the context of univariate functional data. This unsupervised methodology extends archetype analysis by simultaneously identifying archetypal structures across both the cases (countries, in our application) and the temporal argument. Both cases and time points are expressed as mixtures of biarchetypes, yielding a concise and highly interpretable representation of complex functional observations. Although biarchetype analysis is not intended as a clustering technique, it offers superior interpretability compared with biclustering approaches, as it is based on extreme, representative patterns rather than average centroids, thereby enhancing human comprehension. We apply the proposed method to 10-year government bond yields of European countries over the period 2001-2025. The results identify three distinct time regimes (the pre-crisis period, the euro-area sovereign debt crisis, and the post-crisis period), and reveal Germany, Greece, and Hungary as country archetypes.

07.
arXiv (math.PR) 2026-06-11

Capital Asset Pricing Model with Size Factor and Normalizing by Volatility Index

arXiv:2411.19444v5 Announce Type: replace-cross Abstract: The Capital Asset Pricing Model (CAPM) relates a well-diversified stock portfolio to a benchmark portfolio. We insert size effect in CAPM, capturing the observation that small stocks have higher risk and return than large stocks, on average. For some size-based stock portfolios, dividing their returns by the Volatility Index makes them closer to independent and normal. In this article, we combine these ideas to create a new discrete-time model, which includes volatility, relative size, and CAPM. We fit this model using real-world data, prove the long-term stability, and connect this research to Stochastic Portfolio Theory. We fill important gaps in our previous article on CAPM with the size factor.

08.
arXiv (CS.CL) 2026-06-11

On The Effectiveness-Fluency Trade-Off In LLM Conditioning: A Systematic Study

Controlling the output of Large Language Models (LLMs) is a central challenge for their reliable deployment, yet a clear understanding of the involved trade-offs remains elusive. Current approaches to conditioning are often evaluated with a narrow focus on their effectiveness at injecting or removing a target concept, neglecting generation quality. We systematically investigate a range of conditioning methods in both injection and removal scenarios. We find that efficient steering methods frequently achieve conditioning at a steep cost to fluency. Furthermore, we identify a critical yet previously overlooked interaction with the training paradigm: activation steering methods are far less effective on instruction-tuned models than on their base counterparts. Simple prompting and full-fledged supervised fine-tuning, on the other hand, are viable options for concept injection, but are not as good at concept removal. Finally, cheaply computed textual metrics highly correlate to costly LLM-as-judge scores, and provide insights on the behavior of conditioning methods.

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

Escaping the Self-Confirmation Trap: An Execute-Distill-Verify Paradigm for Agentic Experience Learning

Experience-driven self-evolution is critical for large language model (LLM) agents to improve through open-world interaction. However, existing experience learning methods mostly rely on single-agent loops, where the same agent executes tasks, summarizes outcomes, and determines memory content. This setup makes agents vulnerable to the Self-Confirmation Trap: wrong-but-self-consistent trajectories are misidentified as successful experience, leading to cumulative errors during retrieval and reuse. To address this issue, we propose EDV, an Execute-Distill-Verify framework for reliable experience learning. In the Execute stage, multiple heterogeneous agents explore the same task space in parallel to generate diverse candidate trajectories. In the Distill stage, a dedicated third-party agent comparatively analyzes these trajectories to produce candidate experiences, reducing executor-centric summarization bias. In the Verify stage, the execution group validates candidates via a consensus mechanism, and only approved experiences are written into shared or private memory. By decoupling the three stages, EDV transforms experience learning from isolated self-reflection into collaborative construction, filtering erroneous and noisy content before memory insertion. We evaluate EDV on three challenging long-horizon benchmarks: tau2-bench, Mind2Web and MMTB. Results show EDV consistently outperforms strong baselines, validating that reliable experience construction is essential for robust agent self-evolution. Our code is available at https://github.com/shidingz/EDV.

10.
Nature (Science) 2026-06-10

A vast whale necropolis has been found

In the Indian Ocean, a deep-sea area roughly 1,200 kilometres long and 7 kilometres deep was found to harbour an ecological landmark site of whale remains. In the Indian Ocean, a deep-sea area roughly 1,200 kilometres long and 7 kilometres deep was found to harbour an ecological landmark site of whale remains.

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

Cordyceps: Covert Control Attacks on LLMs via Data Poisoning

arXiv:2605.26595v2 Announce Type: replace-cross Abstract: Large language models (LLMs) are often fine-tuned on uncurated text datasets that adversaries can poison. Existing poisoning attacks primarily rely on fixed trigger phrases that defenses such as outlier detection, clean-data regularization, or online monitoring can neutralize. In this paper, we propose a data poisoning method that teaches an LLM an information hiding scheme reliably and stealthily through semantic associations between shared knowledge such as facts or concepts and attacker-chosen phrases. The induced hiding scheme can encode and decode arbitrary malicious instructions, thus revealing a new and subtle poisoning-induced vulnerability: covert control attacks. We precisely characterize covert control attacks and evaluate them across $5$ LLMs, $3$ backdoor defenses, and $4$ prompt injection defenses. With a small poisoned fraction, covert control attacks outperform heuristic-based prompt injection attacks in average attack success rate by about $40\%$ relative to clean fine-tuned models. They also circumvent defenses based on detection and fine-tuning, maintaining up to $93\%$ attack success rate after backdoor defenses and up to $98\%$ after prompt injection defenses.

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

PHINN: Persistent Homology Inspired Neural Network for Rare-Event Time Series Generation

arXiv:2606.15452v1 Announce Type: new Abstract: Rare events in time series are critical to model but hard to learn due to data scarcity. Current generative models struggle with extreme values. We observe that rare events leave distinct topological fingerprints - transitions in Betti numbers from point-cloud embeddings - that are more stable and discriminative than statistical moments. We introduce PHINN, a flow-matching framework using dynamic Betti curves as conditioning signals and a persistence landscape loss for homology consistency. It scales to multivariate data, includes a natural-language interface to set Betti targets, supports cross-domain meta-learning and few-shot generation, and provides certified adversarial robustness. On financial, epidemiological, and multi-modal benchmarks, PHINN outperforms statistical and diffusion baselines in topological fidelity (beta-RMSE down 41-63%, transition accuracy up 84%) and matches jump-diffusion models in tail coverage while exceeding them in shape fidelity. All results have 95% confidence intervals.

13.
medRxiv (Medicine) 2026-06-22

A Randomized, Controlled, Double Blind Clinical Study to Evaluate Use of Hydron Alkaline Ionised Water (HAIW) in Healthy Participants

Background and Objectives: Alkaline Ionized Water (AIW) is considered among the highest quality healthy drinking water worldwide and is widely discussed for its various health benefits. Hydron Alkaline Ionized Water (HAIW) is produced through electrolysis, resulting in a stable pH of approximately 9.5 with a negative Oxidation Reduction Potential (ORP), making it an antioxidant beverage. The objective of this study was to evaluate the safety of HAIW and its effects on digestion, sleep, energy, and overall quality of life in healthy participants compared to Packaged Drinking Water (PDW). Materials and Methods: A randomized, controlled, double blind, prospective clinical study was conducted in which a total of 24 healthy participants between the age group of 21 to 40 years were randomized in a 1:1 ratio to either HAIW Group or Packaged Drinking Water Group with equal gender distribution. Participants were hospitalized for 7 days and asked to consume at least 3 litres of the assigned water daily. Primary outcomes were safety-related laboratory parameters and adverse event monitoring. Secondary outcomes included assessment of digestion (appetite, digestion, bowel habits), urine parameters, sleep quality, freshness after waking, fatigue, energy/stamina/strength, quality of life, and global assessment Results: All 24 participants completed the study with no dropouts. Baseline demographics were comparable between the two groups. Assessment of primary safety-related laboratory parameters including Complete Blood count, liver function tests, renal function tests, blood sugar, Electrocardiogram and serum electrolytes showed non-significant change from baseline to 7 days and remained within normal limits in both groups, with non-significant difference between groups (p>0.05). HAIW showed significantly better improvement in appetite, digestion, and bowel habits from Day 2 onwards compared to Packaged drinking water. Sleep quality and freshness after waking up showed significant improvement from Day 3 and Day 2 respectively in the HAIW and PDW group, with significantly better improvement in HAIW group. Fatigue scores showed significant reduction at Day 6 and 7 in both groups with non-significant difference between groups. A total of 5 adverse events were reported (3 in HAIW, 2 in PDW), all unrelated to study products and were mild in nature. Global assessment showed excellent to good overall safety and tolerability in both groups. Conclusion: HAIW was well tolerated by all participants without any adverse effects. All laboratory safety parameters remained within normal range. HAIW demonstrated significant improvements in digestive function (appetite, digestion, bowel habits), sleep quality, and freshness after waking as compared to PDW. The study concludes that HAIW can be safely consumed. HAIW improves digestive and sleep-related functions.

14.
arXiv (CS.AI) 2026-06-12

PI-Hunter: Automated Red-Teaming for Exposing and Localizing Prompt Injections

arXiv:2606.12737v1 Announce Type: cross Abstract: Large Language Models (LLMs) are rapidly evolving into agentic systems that interact with external tools and environments, introducing new security risks such as indirect prompt injection attacks through untrusted external sources. Existing defenses mainly focus on blocking malicious content at inference time, and current red-teaming methods primarily optimize attack success. As a result, developers have limited visibility into how latent prompt injections emerge and propagate through agents. We propose PI-Hunter, an automated agentic auditing framework for proactive vulnerability exposure in LLM agents. PI-Hunter constructs realistic source-aware test cases and iteratively evolves them through feedback-driven exploration to induce agents to retrieve and reveal latent malicious instructions embedded within external environments. Extensive experiments across multiple benchmarks, agent architectures, attacks, and defenses demonstrate that PI-Hunter substantially improves vulnerability exposure and attack-surface coverage over strong automated red-teaming baselines, while remaining effective under existing prompt injection defenses.

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

MVAD: A Benchmark Dataset for Multimodal AI-Generated Video-Audio Detection

The rapid advancement of AI-generated multimodal video-audio content has raised significant concerns regarding information security and content authenticity. Existing synthetic video datasets predominantly focus on the visual modality alone, while the few incorporating audio are largely confined to facial deepfakes–a limitation that fails to address the expanding landscape of general multimodal AI-generated content and substantially impedes the development of trustworthy detection systems. To bridge this critical gap, we introduce the Multimodal Video-Audio Dataset (MVAD), the first comprehensive dataset specifically designed for detecting AI-generated multimodal video-audio content. Our dataset exhibits three key characteristics: (1) genuine multimodality with samples generated according to three realistic video-audio forgery patterns; (2) high perceptual quality achieved through diverse state-of-the-art generative models; and (3) comprehensive diversity spanning realistic and anime visual styles, four content categories (humans, animals, objects, and scenes), and four video-audio multimodal data types. Our dataset will be available at https://github.com/HuMengXue0104/MVAD.

16.
arXiv (CS.CV) 2026-06-18

Benchmarking Physics-Informed Time-Series Models for Operational Global Station Weather Forecasting

The development of Time-Series Forecasting (TSF) models is often constrained by the lack of comprehensive datasets, especially in Global Station Weather Forecasting (GSWF), where existing datasets are small, temporally short, and spatially sparse. To address this, we introduce WEATHER-5K, a large-scale observational weather dataset that better reflects real-world conditions, supporting improved model training and evaluation. While recent TSF methods perform well on benchmarks, they lag behind operational Numerical Weather Prediction systems in capturing complex weather dynamics and extreme events. We propose PhysicsFormer, a physics-informed forecasting model combining a dynamic core with a Transformer residual to predict future weather states. Physical consistency is enforced via pressure-wind alignment and energy-aware smoothness losses, ensuring plausible dynamics while capturing complex temporal patterns. We benchmark PhysicsFormer and other TSF models against operational systems across several weather variables, extreme event prediction, and model complexity, providing a comprehensive assessment of the gap between academic TSF models and operational forecasting. The dataset and benchmark implementation are available at: https://github.com/taohan10200/WEATHER-5K.

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

Non-Autoregressive Minimum Bayes' Risk Decoding for Fast Speech Recognition

Non-autoregressive (NAR) decoding generates output tokens in parallel, making speech recognition faster than autoregressive decoding, which generates them sequentially from left to right. However, the recognition performance is degraded because NAR decoding cannot resolve uncertainty by conditioning on previously generated tokens. To address this issue, we propose a novel NAR decoding framework based on minimum Bayes' risk (MBR) decoding, termed NAR-MBR decoding, that maximizes the expected utility calculated from samples drawn from the output probability of an NAR model rather than maximizing the output probability. Notably, by leveraging the nature of NAR models, multiple samples are obtained efficiently with a single forward computation. Our experiments across LibriSpeech, Switchboard, AMI, and web presentation corpus demonstrated that our NAR-MBR decoding outperformed previous NAR decoding and ran faster than AR decoding.

18.
arXiv (CS.CL) 2026-06-24

AGORA: An Archive-Grounded Benchmark for Agentic Workplace Document Reasoning

Large language models are increasingly deployed as agents that reason over documents rather than answer from parametric knowledge. We study archive-grounded reasoning: locating sparse evidence across a large, messy collection of workplace files, reconciling inconsistent terminology, units, and time conventions, and computing an answer. Existing benchmarks address only parts of this setting and none jointly stresses archive-groundedness, agentic exploration, and cross-domain coverage. We introduce Agora, a benchmark pairing 362 questions with eight domain collections of 9,664 authentic documents and 372M tokens, far exceeding any model's context window, so agents must explore deliberately rather than scan exhaustively. Agora is built by an agentic pipeline combining cross-document task synthesis, leakage-preventing obfuscation, and difficulty filtering. Evaluating eight models, we find the task far from solved: even the strongest reaches only 59.4% accuracy, with notable variation across domains.

19.
arXiv (CS.AI) 2026-06-12

CRAFTIIF: Cross-Resolution Analytic Four-Type Interpretable Isolation Forest for Multivariate Time Series Anomaly Detection

Authors:

arXiv:2606.13486v1 Announce Type: cross Abstract: Anomaly detection in multivariate time series is challenged by four structurally distinct anomaly types – point (isolated spikes), distributional (level shifts), temporal (rhythm changes), and collective (inter-sensor correlation breakdowns) – each requiring different feature representations. Most unsupervised methods target only one or two types and provide limited interpretability. We present CRAFTIIF (Cross-Resolution Analytic Four-Type Interpretable Isolation Forest), a fully unsupervised framework targeting all four types without dataset-specific tuning. CRAFTIIF generates K=500 random analytic wavelet feature draws across four families (Morlet, DOG, Haar, Coiflet), each targeting a specific anomaly type, feeding five structured Isolation Forests – one per type plus a meta-IF for compound anomalies. An adaptive Otsu/MAD threshold calibrates detection automatically across anomaly rates from 0.1% to 69.2%. Because each IF is trained exclusively on type-specific features, branch firing provides direct anomaly-type attribution by construction, without post-hoc explanation. Evaluated on all 19 datasets of the mTSBench benchmark (Zhou et al., TMLR 2026), CRAFTIIF achieves mean F1=0.228 (all 19 datasets) and F1=0.322 (13 detectable datasets), ranking first among all 25 evaluated methods on VUS-PR (0.463 vs. previous best 0.329, +40.7%). A diagnostic framework – oracle F1, detectability limits, and branch separation ratios – identifies 6 of 19 datasets as fundamentally undetectable by any unsupervised method. Ablation over 11 conditions confirms adaptive thresholding (+38% F1), four-branch structure (+20%), and meta-IF (+23%) are each essential. Code: https://github.com/smitswil/craftiif

20.
arXiv (CS.CV) 2026-06-15

Rethinking Global Average Pooling: Your Classifier Is Secretly a Multi-Instance Learner

Authors:

Modern image classifiers widely adopt global average pooling (GAP) followed by a linear classification head. This linearity ensures that the image-level logits equal the average of logits obtained by applying the classification head pointwise to the feature grid prior to GAP. Consequently, standard classifiers may inherently retain spatial class evidence that remains recoverable even when the image-level prediction is incorrect. This structure naturally suggests a multiple-instance learning (MIL) interpretation, where an image is viewed as a bag of spatial instances. Within this formulation, we demonstrate that standard classifiers trained with a single label per image can still learn the intended classification task in multi-object scenes. We further exploit this property to decompose image-level logits into a prediction grid, providing a post-hoc diagnostic to extract spatial class evidence that GAP otherwise obscures. Our systematic evaluation reveals that off-the-shelf models consistently recover the ground-truth class within foreground regions. The MIL interpretation further suggests that common classifier failures reflect known limitations of mean aggregation.

21.
arXiv (quant-ph) 2026-06-16

Neural network inverse design of nanophotonic scintillators

arXiv:2606.16309v1 Announce Type: cross Abstract: Scintillators are materials converting high-energy radiation into optical light, essential in a range of technologies such as medical imaging systems and security scanners. Scintillator development and optimization have remained limited by the complexity of their underlying physics, involving stochastic cascades of electron-electron, electron-phonon, and electron-photon interactions. Such processes are typically modeled by non-differentiable Monte Carlo simulations, limiting the applicability of machine learning for scintillator development. Here we present a physics-informed neural network that learns the scintillation cascade process from the incident high-energy particle to photon emission, substantially accelerating scintillator design and optimization. Combining this neural network with photonic simulations enables end-to-end differentiable optimization of the scintillator geometry. This allows us to optimize for arbitrary figures of merit, such as specific target emission patterns.. We demonstrate the concept and characterize it relative to previous approaches by inverse design of nanophotonic scintillators for X-ray imaging.

22.
arXiv (quant-ph) 2026-06-19

Benchmark of quantum algorithms for ground state preparation in the presence of noise

arXiv:2606.20551v1 Announce Type: new Abstract: We compare the performance of representative cooling, adiabatic, and optimization algorithms for ground-state preparation in the presence of noise. Using an exactly solvable family of quadratic fermionic Hamiltonians subject to depolarizing noise, we derive the scaling of the achievable relative energy as a function of the noise rate and support these results with numerical simulations. The Hamiltonian exhibits two phases, separated by a quantum phase transition. As expected, the performance of the different algorithms depends on the phase: adiabatic evolution is favorable in the trivial phase, while a multi-frequency cooling algorithm, as proposed in [1], becomes competitive or superior in the topological phase, where gap-closing limits adiabatic protocols. We further present numerical results for the quantum approximate optimization algorithm [2], showing that it performs competitively with cooling in the trivial phase but is typically outperformed in the topological regime. Finally, we show that for this model the cooling protocol exhibits enhanced robustness to parameter imperfections, highlighting its potential advantage for realistic implementations of noisy quantum state preparation. The analytical approach developed here, in conjunction with numerical validation, establishes an extendable approach to benchmarking ground-state preparation algorithms.

23.
PLOS Computational Biology 2026-06-09

Evolution of phenocopying in a dynamical model of developmental trajectories

by Yuuki Matsushita, Archishman Raju Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside the range of conditions to which they are robust, they often produce phenotypes similar to known mutants, called phenocopies. This correspondence between the effects of environmental and genetic perturbations has received little theoretical attention. Here, we study an abstract regulatory model that is evolved to follow a specific trajectory. We then study the effects of small and large perturbations to the trajectory, both by changing parameters and by perturbing the state at specific times. We find that the phenomenon of phenocopying emerges in evolved trajectories and is not present in a null model of randomly sampled trajectories. Our results suggest that, in this class of dynamic models, evolution can allow high-dimensional phenotypic landscapes to simultaneously exhibit robustness and phenocopying.

24.
medRxiv (Medicine) 2026-06-16

Development and reliability and validity test of the Questionnaire on Knowledge, Attitude and Practice of ICU Nurses on Blood Oxygen Saturation Management in Mechanically Ventilated Patients

Objective: A questionnaire on the knowledge, attitude and practice of ICU nurses regarding the management of blood oxygen saturation in patients with mechanical ventilation was compiled, and its reliability and validity were tested. Method: Drawing upon the knowledge-attitude-practice theory, the initial questionnaire draft was developed through literature review and consultation with Delphi experts. Employing convenience sampling, 32 nurses from the General ICU of Wuxi Second People's Hospital were surveyed between 1 August 2025 and 27 September 2025, enabling item screening and assessment of reliability and validity.The full version of the developed questionnaire is provided as Supporting Information (S1 File). All items are published under a CC BY 4.0 license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Result: A questionnaire on the knowledge, attitude and practice of ICU nurses regarding the management of blood oxygen saturation in mechanically ventilated patients was finalised, comprising 26 items: 11 in the knowledge dimension, 6 in the attitude dimension and 9 in the behaviour dimension. The overall Cronbach's coefficient for the questionnaire was 0.88, with dimension-specific coefficients of 0.787, 0.722, and 0.781 respectively. The Spearman-Brown coefficient for the entire questionnaire was 0.967, while dimension-specific coefficients were 0.796, 0.666, and 0.728 respectively. The content validity index at the questionnaire level (S-CVI) was 0.886, and the item-level content validity index (I-CVI) ranged from 0.913 to 0.967. 0.728. The questionnaire's level content validity index (S-CVI) was 0.886, and the item level content validity index (I-CVI) ranged from 0.913 to 1.00. Conclusion: The questionnaire on knowledge, attitude and practice of blood oxygen saturation management in mechanically ventilated patients demonstrates good reliability and validity. It may serve as an assessment tool for intensive care unit nurses regarding their knowledge, attitude, and practices concerning blood oxygen saturation management in mechanically ventilated patients, thereby establishing a foundation for developing targeted intervention strategies in future practice.

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

Depth-Attention: Cross-Layer Value Mixing for Language Models

Self-attention selects information freely across the sequence, but across depth, Transformers merely add each layer's output to the residual stream, so later layers cannot selectively reuse earlier-layer representations. Recent cross-layer methods improve this flow but operate on hidden states outside attention, adding state beyond the key-value cache at inference–a cost that becomes increasingly salient as modern LLMs compress the cache with grouped-query and multi-head latent attention. We introduce Depth-Attention, which performs this selection inside the attention module itself: before a layer attends over the sequence, its query attends over the keys of earlier layers at the same token position and mixes their values into the value that self-attention then reads. Because Depth-Attention reuses the standard attention queries, keys, and value-cache slots, storing depth-mixed values in place of the original values, it adds no parameters and introduces no persistent inference state beyond the standard key-value cache–the same cache size as a vanilla decoder and less than hidden-state-based cross-layer methods. On Qwen3-style decoders at 1.5B and 3B parameters, Depth-Attention attains the lowest perplexity and the highest average downstream accuracy, improving over the vanilla Transformer by up to 2.3 accuracy points and surpassing strong cross-layer baselines in perplexity and average accuracy, while adding under 0.01% extra arithmetic FLOPs and no additional persistent inference state. The gains hold from 360M to 3B parameters and extend to looped Transformers.