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

Rethinking Air-Ground Collaboration: A Progressive Cross-Task Benchmark and Socialized Learning Framework

Air-ground collaborative perception is crucial for robust visual understanding in real-world dynamic environments. However, existing studies typically formulate collaboration as single-task cross-view fusion, overlooking the functional dependencies among localization, target association, and fine-grained parsing. In addition, the heterogeneous nature of aerial and ground views introduces substantial geometric, scale, and occlusion discrepancies, making uniform feature sharing vulnerable to negative transfer. To tackle these issues, we model air-ground perception as a progressive cross-task collaboration task and construct the Air-Ground Progressive Collaboration (AGPC) benchmark, a spatio-temporally aligned benchmark comprising more than 745K raw video frames. Built upon this benchmark, we propose Socialized Co-Perception (SCP), a coarse-to-fine framework that organizes collaboration progressively from aerial global localization to ground target association and identity-aware parsing. Its core module, the Dual-Layer Router (DLR), decouples input-side multi-scale expert selection from output-side task-conditioned modulation, enabling selective cross-view and cross-task interaction while suppressing harmful interference. Extensive experiments demonstrate the effectiveness of SCP. It achieves a 3.73\% coevolutionary gain and a 7.86\% improvement in average downstream performance. These results show that task-conditioned collaboration is more effective than uniform fusion for heterogeneous air-ground perception. The code is available at https://github.com/g1136639260-spec/AGSCP.

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

Memory-Efficient Meta-Reinforcement Learning for Adaptive Safety-Critical Control in Adversarial Spacecraft Proximity Operations

arXiv:2606.17414v1 Announce Type: new Abstract: Autonomous spacecraft rendezvous and proximity operations (RPO) require controllers that guarantee safety under thrust constraints while minimizing fuel expenditure. Input-constrained control barrier functions (ICCBFs) provide a control method for nonlinear systems with actuation constraints that construct a forward-invariant safe set. Previous work has shown that learning class-$\mathcal{K}$ functions defining the ICCBF recursion via meta reinforcement learning (meta-RL) yields a robust, non-greedy approach to safety-critical control in RPO. This paper extends that framework further by investigating the performance of three recurrent network architectures (Long Short Term Memory (LSTM), Gated Recurrent Unit (GRU), Selective State Space Model (Mamba)) and two training algorithms (Proximal Policy Optimization (PPO) and Soft Actor Critic (SAC)) to identify the best setup for tuning ICCBF class-K functions via meta-RL. In addition to cooperative test cases, performance is evaluated in the presence of adversarial behavior where the target spacecraft behaves in a way that worsens the safety of the chaser spacecraft. Results indicate that state space models such as Mamba when used with PPO achieve superior task completion, safety, and fuel-savings compared to other architectures, across all cooperative and uncooperative scenarios tested.

03.
medRxiv (Medicine) 2026-06-17

Perceptions of aging well among older adults with heart failure: insights from a qualitative study

Background: Heart failure (HF) is a prevalent and often debilitating cardiovascular condition among older adults, frequently accompanied by multimorbidity, functional limitations, and the need to age in place. Traditional models of successful aging emphasize disease absence and preserved function, yet most individuals with HF live with ongoing symptoms and chronic health challenges. How older adults with HF define aging well, particularly across different socioeconomic contexts, remains underexplored. Objectives: To explore how older adults with HF conceptualize aging well and to identify perceived facilitators and barriers across more and less resourced New York City neighborhoods. Methods: We conducted semi-structured interviews with 20 adults diagnosed with HF residing in Manhattan and Brooklyn neighborhoods classified by 2019 United States Census data. Interviews were guided by Rowe and Kahn's model. Transcripts were analyzed using an inductive-deductive thematic approach and interpreted in alignment with the Healthy People 2030 framework. Results: Participants had a mean age of 69 years; 50% identified as Black and 50% were women. Despite functional limitations, 65% reported aging well. Five themes emerged: maintaining physical function, maintaining cognitive function, sustaining social relationships, avoiding pain, and promoting overall well-being. Avoiding pain and promoting well-being extended beyond traditional models. Neighborhood context shaped priorities, with financial stability emphasized in more affluent areas and social cohesion prioritized in less affluent communities. Conclusions: Older adults with HF frequently perceive themselves as aging well despite chronic illness, reframing successful aging beyond disease avoidance. These findings support a patient-centered, place-informed model of aging well with implications for healthcare delivery and policy.

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

HLS-GPT: A Generative Pretrained Transformer (GPT) for Continental-Scale NASA Harmonized Landsat and Sentinel-2 (HLS) Reflectance Reconstruction Across All Bands on Arbitrary Dates

Recent deep learning methods for Landsat and Sentinel-2 reflectance time series reconstruction remain limited by restricted spectral coverage, limited geographic scalability, or patch-based designs with short temporal contexts. We present HLS-GPT, a large-scale generative pretrained Transformer model for reconstructing NASA Harmonized Landsat Sentinel-2 30 m surface reflectance for all bands, any date, and any pixel location. HLS-GPT uses a hierarchical Transformer architecture to handle the different spectral band configurations of Landsat and Sentinel-2 and operates on single-pixel 12-month time series. To capture geographic and seasonal variability, the model was trained with nine years of HLS time series from more than 0.25 million training pixels across the conterminous United States. A random cropping and masking strategy extracts 12-month periods with varying start dates across epochs, masks 50% of valid observations, and trains the model to reconstruct the masked reflectance values from the remaining observations. Evaluation using more than 62,000 independent test pixels shows robust reconstruction under diverse land surface conditions, including complex crop phenology and sparse, irregular observations. Leave-one-observation-out evaluation achieved reconstruction RMSE below 0.026 for all HLS spectral bands, with relative RMSE below 35% for visible bands and below 13% for other bands. Red-edge band errors were comparable to red and near-infrared errors despite the absence of red-edge bands on Landsat. Sensitivity analyses that randomly masked 10% to 90% of test observations showed only modest degradation when 10% to 50% of observations were masked, with all-band RMSE below 0.028. Image reconstruction over nine independent 109 by 109 km CONUS HLS tiles further demonstrates that HLS-GPT outperforms two conventional methods and the NASA-IBM Prithvi model.

05.
arXiv (quant-ph) 2026-06-24

Quantum Adaptive Self-Attention for Quantum Transformer Models

arXiv:2504.05336v4 Announce Type: replace Abstract: A recurring weakness in quantum machine learning (QML) is that reported ``quantum advantages'' are seldom tested against a capacity-matched classical control, leaving it unclear whether a gain comes from the quantum substrate or from the architectural change that accompanies it. Our primary contribution is methodological: a protocol for attributing such gains honestly – a capacity-matched classical bottleneck of identical parameter budget, transparent reporting of where quantum does not help, and validation on real quantum hardware – which we develop and apply through a concrete case study. That case study is Quantum Adaptive Self-Attention (QASA), a hybrid Transformer that replaces the value projection of a single encoder layer with a 36-parameter parameterized quantum circuit (PQC), keeping all other layers classical. Across nine synthetic benchmarks and the real-world ETTh1 dataset, QASA improves on a full-capacity classical Transformer for chaotic and trend-dominated signals. To ask whether this is a genuinely quantum effect, we introduce a control rarely applied in quantum machine learning – a capacity-matched classical bottleneck with the same parameter budget – and find that it matches the PQC on the error metrics. The gain is therefore attributable to the low-rank value-projection bottleneck (an architectural parsimony principle), not to quantumness; adding further quantum layers only degrades performance and trainability. We accordingly position the quantum layer not as a source of accuracy advantage but as a competitive instantiation of this principle: its low-rank compression onto the signal's intrinsic dimensionality is matched by a classical bottleneck, so the gain is architectural rather than quantum.

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

Utility-Constrained Policy Optimization

arXiv:2606.14029v1 Announce Type: new Abstract: Constrained MDPs (CMDPs) are a widely adopted framework for incorporating safety into RL agents; however, the framework does not support risk-sensitive constraints. This can be problematic: For example, CMDPs allow for optimal solutions that, in order to satisfy the risk-neutral constraints, mix infrequent catastrophic behaviors and frequent, overly conservative ones. Moreover, prior empirical results suggest that enforcing stricter, risk-sensitive constraints can improve performance even under risk-neutral evaluation. The natural framework to incorporate risk-sensitive constraints is utility-constrained MDPs (UCMDPs), but no practical solutions for this problem existed. In this work, we introduce a simple yet powerful methodology for UCMDPs and constrained RL. Besides allowing for risk-sensitive constraints, our framework does not require us to fix constraint limits in advance of training the agent, provided that a sensible range is known. This increases policy flexibility and, in practice, allows for adjustments to these limits at no extra training cost. Besides benefiting from the generality of the framework, our agent shows strong performance in practice, consistently matching or outperforming existing baselines in several Safety Gymnasium benchmark tasks.

07.
arXiv (quant-ph) 2026-06-24

Crystalline Spectral Form Factors

arXiv:2512.11054v3 Announce Type: replace Abstract: We investigate crystalline-like behavior of the spectral form factor in unitary quantum systems with extremely strong eigenvalue repulsion. Using a low-temperature Coulomb gas as a model of repulsive eigenvalues, we derive the Debye-Waller factor suppressing periodic oscillations of the spectral form factor and estimate the order of its singularities at multiples of the Heisenberg time. We also reproduce this crystalline-like behavior using perturbed permutation circuits and random matrix ensembles associated with Lax matrices. Our results lay a foundation for future studies of quantum systems that exhibit intermediate level statistics between standard random matrix ensembles and permutation circuits.

08.
arXiv (CS.AI) 2026-06-15

Closing the Reflection Gap: A Free Calibration Bonus for Agentic RL

Authors:

arXiv:2606.14211v1 Announce Type: new Abstract: LLMs are increasingly deployed as agents that interact with external environments and observe feedback such as execution results, error messages, and tool outputs. A well-functioning agent should be able to leverage this feedback to accurately assess its own performance. Yet we find a persistent reflection gap: LLM agents tend to mis-assess their own outputs after observing concrete environment feedback – even for questions they correctly answered – and standard RL barely helps due to a credit-assignment mismatch. To close this gap, we propose RefGRPO, a simple yet effective fix that augments standard RL algorithms with two key ingredients: a free calibration bonus computed by contrasting the agent's own reflection with the actual outcome (requiring no additional reward model, LLM judge, or external annotation), and a dynamic schedule on its coefficient. Compared to standard RL baselines, our method simultaneously improves reflection calibration (e.g., reduces underconfidence rate $44.4\% \to 7.7\%$) and task accuracy (e.g., $75.1\% \to 76.5\%$) on text-to-SQL across five benchmarks. The resulting calibrated reflection turns the agent into its own verifier grounded in environment feedback, which further enables (i) better self-improvement that uses reflections as pseudo-rewards without outcome supervision, and (ii) more effective test-time selective prediction by committing only to rollouts flagged as correct.

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

Data-Driven Decoding of Russell's Circumplex Model of Affect

Affective computing increasingly relies on deep learning to represent emotions, yet latent spaces often remain opaque, high-dimensional black boxes. This paper investigates whether Transformers' embeddings recover the geometric regularities of Russell's circumplex model. We unify two complementary experiments testing the hypothesis that, after training models on text and speech, their resulting latent spaces encode a topology consistent with valence-arousal and reproduce human-like neighborhood relations. Specifically, we evaluate deep representations extracted from Transformer-based text (RoBERTa) and speech (wav2vec 2.0) encoders, along with a multimodal Transformer fusion architecture, across naturalistic datasets like MSP-Podcast and controlled LLM-generated stimuli. Our analysis reveals that multimodal fusion of text and audio yields perfect topological alignment with Russell's primary emotion ordering. Furthermore, in a zero-shot setting using generic text embeddings, projected fine-grained emotion terms fall close to their established human-mapped coordinates. Our contribution is a novel, data-driven framework for validating emotion models, demonstrating that Russell's circumplex structure is intrinsically encoded in the embeddings of these modalities rather than being solely an artifact of human labeling, thereby bridging the gap between psychological theory and representation learning.

10.
arXiv (quant-ph) 2026-06-11

Compressed minimum-purity time evolution for late-time quantum dynamics

arXiv:2606.11392v1 Announce Type: cross Abstract: Unitary time evolution of initially simple quantum many-body states rapidly generates entanglement and complex correlations, which limits direct numerical simulations. The late-time dynamics of physical observables, however, typically exhibits an effective simplicity in the form of hydrodynamics or kinetic theory. This leads to the question whether microscopic equations of motion can remain accurate and tractable up to long time scales by discarding irrelevant information in a controlled manner. Here, we introduce compressed minimum-purity time evolution (CoMPuTE) as an approach to keep track of a consistent set of reduced local density matrices, closing the hierarchical equations of motion using a minimum-purity principle. In benchmark applications we demonstrate (i) accurate description of energy diffusion in the one-dimensional mixed-field Ising model, (ii) the applicability to genuinely out-of-equilibrium Floquet dynamics starting from a pure state, and (iii) the limitations of the local reduced density matrix approximation when describing transport in the XXZ chain at $\Delta=1$ that is governed by increasingly non-local integrals of motion. The CoMPuTE method enhances computational efficiency in comparison to the closely related local-information time evolution algorithm, opening a possible route towards an extension to systems in higher spatial dimensions.

11.
arXiv (quant-ph) 2026-06-15

Spin counting via projection noise measurement of mesoscopic solid-state spin ensemble

arXiv:2606.14437v1 Announce Type: new Abstract: Quantum projection noise is the fundamental noise source for the population measurement of spin ensembles. While projection-noise-limited measurements have been extensively studied in atomic systems, corresponding experiments on solid-state spin ensembles remain challenging due to dominant classical readout noise. Here, we report direct measurement of the quantum projection noise of mesoscopic ensembles of nitrogen-vacancy (NV) spin defects at room temperature. Our experiment is enabled by a high optically-detected magnetic resonance (ODMR) contrast of over 20% for a single crystallographic orientation of the defect spins, obtained by combining polarization-selective optical excitation with spin-to-charge conversion. We use our protocol to demonstrate projection noise measurements and spin counting from nanoscale NV ensembles of up to 43 spins. We further demonstrate that the protocol allows for significant gains in sensitivity for magnetometry applications without need for cryogenic operation or high bias magnetic fields.

12.
bioRxiv (Bioinfo) 2026-06-14

Transposable elements as evolutionary substrates of proteindisorder in the human proteome

Intrinsically disordered regions (IDRs) are central contributors to protein function, evolution and human disease, yet the evolutionary routes that seed new disordered segments within pre-existing proteins are still poorly understood. Sequence insertions provide a powerful mechanism for disorder expansion, but the genomic donors of inserted IDR and its long-term conformational fate remain largely unknown. Transposable elements (TEs), abundant mobile genetic elements with distinctive compositional biases, represent compelling candidates for generating disorder within proteins. Here, we systematically mapped TE-derived segments across human proteins and isoforms, and we found that these insertions are strongly enriched in intrinsic disorder. The structural consequences of their insertion are shaped by TE class and family, reflecting the sequence biases of the elements from which they originate. Recent, Primate specific insertions preferentially generate disordered segments, whereas older insertions more frequently occupy ordered structural contexts, revealing an age-dependent transition in the conformational state of TE-derived sequences. TE-containing isoforms are expressed at lower levels than TE-free isoforms, particularly when insertions are young and disorder-rich, suggesting that intrinsic disorder may constrain the cellular tolerance of newly exonized sequences. These findings identify TEs as a major evolutionary mechanism linking genome mobility to the emergence of new disordered conformational ensembles in the human proteome.

13.
arXiv (CS.LG) 2026-06-16

Semi-Supervised Noise Adaptation: Transferring Knowledge from Noise Domain

arXiv:2606.00558v2 Announce Type: replace Abstract: Transfer learning aims to facilitate the learning of a target domain by transferring knowledge from a source domain. The source domain typically contains semantically meaningful samples (*e.g.*, images) to facilitate effective knowledge transfer. However, a recent study observes that the noise domain constructed from simple distributions (*e.g.*, Gaussian distributions) can serve as a surrogate source domain in the semi-supervised setting, where only a small proportion of target samples are labeled while most remain unlabeled. Based on this surprising observation, we formulate a novel problem termed *Semi-Supervised Noise Adaptation* (SSNA), which aims to leverage a synthetic noise domain to improve the generalization of the target domain. To address this problem, we first establish a generalization bound characterizing the effect of the noise domain on generalization, based on which we propose a Noise Adaptation Framework (NAF). Extensive experiments demonstrate that NAF effectively leverages the noise domain to tighten the generalization bound of the target domain, leading to improved performance. The codes are available at https://github.com/AIResearch-Group/SSNA.

14.
arXiv (math.PR) 2026-06-16

The Winner Takes It All

arXiv:2606.16885v1 Announce Type: cross Abstract: The winner-takes-all (WTA) process takes place on an arbitrary graph. There is an agent on each vertex of the graph, and active agents at neighboring vertices play games. In each game, a randomly chosen agent wins, while the loser is eliminated from subsequent games. The games are played at random times; each game finishes instantaneously, and the games cease when each active agent has only losers among its neighbors. On the one-dimensional lattice, the fraction of winners in the final state is $e^{-1}$, and we also determine the fractions $w_j$ of winners who won $j=0, 1, 2$ games. For the WTA process on a segment, we determine statistics of the total number of winners (the average, the variance, and all higher cumulants), the probabilities of reaching the final state with the minimum or maximum number of winners, and establish the behavior near the boundaries. For infinite regular trees with vertices of degree $d$, i.e., Bethe lattices with coordination number $d$, the fraction of winners is $(2/d)^{d/(d-2)}$.

15.
arXiv (quant-ph) 2026-06-16

Communication Complexity of Distributed Unitary Synthesis

arXiv:2511.04250v2 Announce Type: replace Abstract: We study space-bounded communication complexity for unitary implementation in distributed quantum processors, where we restrict the number of qubits per processor to ensure practical relevance and technical non-triviality. We model distributed quantum processors using distributed quantum circuits with nonlocal two-qubit gates, defining the distributed communication complexity of a unitary as the minimum number of such nonlocal gates required for its realization, up to permutations of data qubit positions. Our contributions are twofold. First, for general $n$-qubit unitaries, we improve upon the trivial $O(4^n)$ communication bound. Considering $k$ pairwise-connected processors (each with $n/k$ data qubits and $m$ ancillas), we prove the communication complexity satisfies $O\left(\max\{4^{(1-1/k)n - m}, n\}\right)$ – for example, $O(2^n)$ when $m=0$ and $k=2$ – and establish the tightness of this upper bound. We further extend the analysis to approximation models and general network topologies. Second, for special unitaries, we show that both the Quantum Fourier Transform (QFT) and Clifford circuits admit linear upper bounds on communication complexity in the exact model, outperforming the trivial quadratic bounds applicable to these cases. In the approximation model, QFT's communication complexity reduces drastically from linear to logarithmic, while Clifford circuits retain a linear lower bound. These results offer fundamental insights for optimizing communication in distributed quantum unitary implementation, advancing the feasibility of large-scale DQC systems.

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

High-Fidelity Two-Step Image Generation via Teacher-Aligned End-to-End Distillation

Few-step diffusion distillation has become increasingly mature for 4-8-step generation, yet pushing further to 2 steps remains challenging. In this work, we introduce Z-Image Turbo++, a high-quality 2-step image generation model distilled from the 8-step Z-Image Turbo teacher. Our method addresses the central bottlenecks of increased task difficulty and limited model capacity in 2-step generation through three simple but effective design choices tailored to this regime. First, we propose Distribution-Aligned Adversarial Learning, which uses teacher-generated images rather than external real images as real samples for GAN training, providing a more attainable and informative adversarial target. Second, we adopt Step-Decoupled Parameterization, assigning independent model parameters to the two denoising steps to better match their distinct capacity demands. Third, we perform End-to-End Training with Iterative Regularization, allowing the first step to receive gradients from final image quality while preserving a meaningful intermediate generation through an explicit step-1 loss. Together, these designs substantially narrow the quality gap between 2-step and 8-step generation in both qualitative and quantitative evaluations, highlighting the potential of carefully tailored distillation strategies for improving the quality-efficiency trade-off in few-step generation.

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

A Red-Team Study of Anthropic Fable 5 & Opus 4.8 Models

Authors:

We evaluate the adversarial robustness of two frontier large language models (LLMs) developed by Anthropic, Fable 5 and Opus 4.8, against four families of automated jailbreak attack across 7 826 harmful intents spanning a ten-category harm taxonomy. Using the HackAgent red-teaming framework, hundreds of thousands of adversarial attempts were generated and every apparent success was independently re-adjudicated by a panel of three judge models (majority vote). Both models resist the majority of attacks, but the residual surface is larger than aggregate framing suggests: it is dominated by adaptive iterative attacks, while static obfuscation is near-fully neutralised. The strongest adaptive search (tree-of-attacks) breaks Opus 4.8 on 11.5% of intents overall, whereas Fable 5 stays in the single digits (6.1% worst-case). Aggregate rates therefore should not be read as reassurance. Even in these hardened configurations, the two models produced 1 620 (Opus 4.8) and 702 (Fable 5) panel-confirmed harmful completions spanning every harm category, located automatically, cheaply, and within the first one or two refinement steps by an attacker model with no human expert in the loop. The reasonable conclusion is that even the best, most-tested frontier models remain reliably breakable under sustained automated pressure.

18.
arXiv (CS.AI) 2026-06-12

Modern analog computing for solving differential and matrix equations

arXiv:2606.13179v1 Announce Type: cross Abstract: In recent years, driven by the computational demands of data-intensive applications such as artificial intelligence and scientific computing, analog computing has gained renewed interest. Given the diversity of computational tasks and recent advancements in analog CMOS circuits and resistive memory technologies, we refer to the evolving landscape as modern analog computing. In this context, we identify three core computational primitives: solving differential equations, solving matrix equations, and performing matrix-vector multiplications, and we explore the connections among them. We also examine various hardware implementations of these analog computing operators, including those built with discrete components, integrated circuits, and resistive memory devices. Among these, resistive memory arrays emerge as particularly promising due to their implementation efficiency. The paper then surveys recent progress in leveraging modern analog computing to solve differential and matrix equations using both advanced analog CMOS circuits and resistive memory arrays. Finally, we discuss the applications of these circuits, the precision and scalability issues and their potential solutions, the relationship with in-memory computing, and the unique computational complexity of analog computing. This paper provides a unified perspective on analog computing, highlighting its strengths, current developments, and challenges, and positioning it as a pivotal enabler of next-generation computational frontiers.

19.
medRxiv (Medicine) 2026-06-24

Structural ethnic inequities in maternal mortality between Indigenous and non-Indigenous women in Paraguay, 2014-2023: a national analysis of territorial, institutional, and preventable factors.

Background: Indigenous women in Paraguay continue to experience disproportionately high maternal mortality despite national efforts to improve maternal health. Evidence on the structural factors underlying these disparities remains limited. Objectives: To analyze structural ethnic inequities in maternal mortality between Indigenous and non-Indigenous women in Paraguay, focusing on territorial patterns, institutional access, and potentially preventable causes of death. Design: National population-based study using maternal mortality records registered in Paraguay between 2014 and 2023. Maternal mortality ratios (MMRs), incidence rate ratios (IRRs), and absolute differences were estimated according to Indigenous status. Logistic regression models were used to assess associations with deaths occurring outside healthcare institutions and specific preventable causes of death. Results: A total of 907 maternal deaths were identified, including 112 among Indigenous women (12.3%). Indigenous women were overrepresented by a factor of 4.8 relative to their population share. Maternal mortality remained consistently higher among Indigenous women throughout the study period, with mortality ratios ranging from 317.7 to 773.6 per 100,000 live births, compared with 58.7 to 145.1 among non-Indigenous women. Absolute inequalities remained persistently high over time. Overall, 24.3% of maternal deaths occurred outside healthcare institutions, with a substantially higher proportion among Indigenous women (44.6% versus 21.5%). After adjustment for age and educational level, Indigenous women had more than three times greater odds of dying outside healthcare institutions (aOR = 3.41; 95% CI: 2.20-5.29). Potentially preventable causes accounted for 42.4% of maternal deaths. Obstetric hemorrhage was strongly associated with Indigenous status (aOR = 3.83; 95% CI: 2.31-6.37). Conclusion: Indigenous women in Paraguay experience a disproportionate burden of maternal mortality characterized by persistent ethnic disparities, higher occurrence of deaths outside healthcare institutions, and a substantial burden of preventable causes of death. These findings suggest the presence of enduring territorial, institutional, and healthcare access barriers that contribute to structural ethnic inequities in maternal health.

20.
bioRxiv (Bioinfo) 2026-06-11

EditorForge: An Active-Site-Aware Framework for Inverse-Folding-Based Protein Redesign

Inverse-folding models can rapidly generate protein sequences compatible with a supplied backbone, but unconstrained redesign is poorly suited to enzyme and genome-editor-associated domains, where catalytic, substrate-proximal, and conserved structural regions must remain protected. In this paper, we present EditorForge, a modular constraint-and-audit suite for editor-domain protein redesign that wraps fixed-backbone inverse folding with explicit design masks, fixed-position enforcement, active-site-proximity auditing, active-site-shielded regeneration, and downstream structural quality control. Using full-length Moloney murine leukemia virus reverse transcriptase structure 4MH8 (MMLV RT 4MH8) as a demonstration target, EditorForge first restricted redesign to a bounded 25-position envelope while fixing 428 residues. An initial audit detected active-site-proximal failure modes despite fixed-position integrity. Later, the Active Site Shield module then removed five unsafe design positions, replaced them with lower-contact alternatives, and regenerated candidates under stricter constraints. Post Shield Audit evaluated 24 regenerated candidates, all of which satisfied the hard sequence/mask and active-site-shield constraints. For the eight candidates that were selected or returned for structure-prediction/refolding quality control. Enhanced RefoldQC found that all 8 evaluated predicted structures passed the computational structure-QC screen. That said, the selected 8 candidates passed the computational structure-QC screen, with global C RMSD values of 1.2061–1.5555~[A], active-site C RMSD values of 0.4098–1.8397~[A], mutation-neighborhood C RMSD values of 1.3155-1.6848~[A], and average pLDDT-like confidence values of 94.87-95.11. In short, EditorForge provides a reproducible triage layer that converts general inverse-folding output into constrained and editor-specific candidate sets for downstream structural and biological review on top of existing structural prediction tools.

21.
PLOS Computational Biology 2026-06-01

BeetleAtlas 2: An enhanced <i>Tribolium castaneum</i> web resource for tissue and developmental transcriptomics allowing refinement of gene predictions

by David P. Leader, Muhammad T. Naseem, Janina L. Rinke, Kenneth Veland Halberg BeetleAtlas is an online resource for tissue- and stage-specific transcriptomics in the red flour beetle, Tribolium castaneum. On updating from the original Tcas5.2 genome assembly to the more recent improved icTriCast1.1 genome assembly it became evident that there were major discrepancies between the gene models of the two genome annotations in use: the OGS3 and the NCBI gene sets. As neither was clearly superior we implemented a new design in BeetleAtlas 2 (beetleatlas.org) comprising two parallel ‘modes’ — one incorporating results using the NCBI gene models and a second incorporating those using the OGS3 gene models. This allows direct comparison where equivalent gene models exist: 50–57% of cases. To aid resolution of discrepancies between the two gene model sets and verification of results, gene models are linked to a custom visualization of RNA-seq read coverage of the genome in the UCSC Genome Browser. This displays reads from 22 tissues and life stages superimposed on the icTriCast1.1 genome assembly. Reference tracks show the NCBI gene models, the OGS3 gene models after translation of their coordinates from the Tcas5.2 assembly, and 1050 discontinued NCBI gene models from the previous assembly after a similar transfer of coordinates. We document various situations in which distinct patterns of expression of the tissues can be used to confirm and extend correlations between the two gene sets, resolve discrepancies between them, make corrections and identify putative genes or exons absent from the current gene sets. BeetleAtlas 2 allows those involved in Tribolium research to avoid the pitfalls inherent in incorrect gene models when planning experiments on specific genes and interpreting the results. It also demonstrates how BeetleAtlas 2 might play an important role in establishing a revised gene set for Tribolium castaneum in the future.

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

Towards Data-Efficient Cross-Device Generalization of Grad-Shafranov Equilibria via Transfer Learning Neural Operator

arXiv:2606.15512v1 Announce Type: new Abstract: Real-time reconstruction of magnetohydrodynamic equilibria is essential for plasma shaping, stability assessment and feedback control in magnetic confinement fusion. However, Grad-Shafranov equilibrium calculations remain largely device-specific and iterative, limiting their use in latency-constrained control settings. Existing neural approaches can accelerate individual equilibrium predictions, but they do not generally provide reusable models across changing plasma boundaries or tokamak geometries. Here we show that equilibrium reconstruction can be recast as a cross-device operator learning problem. We develop a domain-specific neural operator framework that maps geometry and profile parameters directly to the poloidal flux field, replacing repeated solve-on-demand computation with amortized operator inference. Using the analytically tractable Solov'ev family as a controlled Grad-Shafranov testbed, we generate equilibria across eight geometrically distinct tokamak-like configurations and benchmark five neural operator architectures under four transfer-learning strategies. Single-geometry pretraining gives poor transfer to unseen devices, whereas multi-geometry pretraining enables data-efficient adaptation. The Wavelet Neural Operator gives the strongest cross-geometry performance, reaching mean relative L2 errors below 4% with 100 labelled target equilibria and below 2% with full fine-tuning. The predicted magnetic fields satisfy the divergence-free constraint to numerical precision, and four architectures achieve millisecond or sub-millisecond inference. These results identify neural operator pretraining as a route towards reusable, real-time equilibrium inference across fusion device configurations.

23.
arXiv (CS.LG) 2026-06-19

Weibull Weight-Scale Parameter Evolution under AdamW Training Dynamics

Authors:

arXiv:2606.19367v1 Announce Type: new Abstract: Building on a two-parameter Weibull framework for diagnosing transformer weight distributions, we study why the Weibull weight-scale parameter $\lambda$ grows, overshoots, and then relaxes during AdamW training. We derive a leading-order three-force decomposition of the squared weight norm from the AdamW update: an alignment force measuring the correlation between weights and the adaptive update direction, an injection force from adaptive step magnitude, and a decay force from decoupled weight decay. On self-trained Pythia-70M models with ground-truth optimizer moments, alignment dominates the rise phase, contributing 88-94% of the absolute force budget across four random seeds and remaining robust to super-weight removal. Near saturation, alignment and decay approach balance, explaining the transition from weight-scale growth to relaxation. These force dynamics directly govern the squared-norm component underlying $\lambda(t)$; the remaining RMS-to-Weibull reconstruction offset is measurable and decomposes into bridge and integration components, totaling approximately 5-6% in densely sampled regions. To extend the analysis to real models where optimizer moments are unavailable, we introduce a spline displacement method that recovers the alignment force from sparse checkpoints with approximately 92-94% accuracy, about twice the naive two-point baseline. We further observe that the peak value of $\lambda(t)$ varies with training-data coherence in our experiments, suggesting a data-dependent component of weight-scale growth that we leave to a controlled follow-up study. Code and data are available at https://github.com/tiexinding/NPM-Weibull-public.

24.
arXiv (CS.AI) 2026-06-25

Silent Failures in Physics-Informed Neural Networks: Parameter Poisoning and the Limits of Loss-Based Validation

arXiv:2606.25151v1 Announce Type: cross Abstract: Physics-informed neural networks (PINNs) embed governing equations in their loss function, enabling mesh-free solutions to partial differential equations. Low training loss is treated as evidence that the learned solution is physically correct. This paper shows that assumption breaks down when encoded physics are incorrect. By perturbing PDE parameters before training, a setting we describe as physics parameter poisoning or parameter misspecification, we produce models that train to low loss but give incorrect answers; we treat the perturbation schedule as sensitivity analysis rather than only as a security threat, and none of our claims requires an adversary. Achieving low residual loss does not discriminate accurate from inaccurate solutions: poisoned models reach losses at or below the clean baseline yet differ by large margins, so driving the residual down is not evidence of physical accuracy. Across three PDE systems (Burgers equation, Navier-Stokes cavity, and convection-diffusion), poisoned models match or beat the clean-model training loss while their solutions differ by up to 71% in the fixed sweep and up to 128% under adversarial search; at Cavity Re=400 the poisoned loss falls below the clean baseline. We define a detection difficulty ratio R (solution error divided by training loss) to summarize how invisible the corruption is, though cross-PDE comparison is complicated by differences in loss scale. We test six candidate defenses, none of which reliably detects corruption across all regimes. We propose a post-hoc defense: sweeping the PDE residual loss across parameter values without retraining. The loss minimum recovers the true training parameter without external data, and generalizes across all three PDE systems. The effect holds across five network architectures (8.7K to 133K parameters), is bidirectional, and is confirmed across multiple random seeds.

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arXiv (CS.CV) 2026-06-19

EventVLA: Event-Driven Visual Evidence Memory for Long-Horizon Vision-Language-Action Policies

Memory remains a critical bottleneck for long-horizon robotic manipulation, as standard Vision-Language-Action (VLA) policies often fail when task-relevant cues become occluded or unobservable over time. While existing memory-augmented methods utilize historical context, they either suffer from severe information bottlenecks, incur high latency via decoupled dual systems, or rely on unselective buffers that accumulate massive visual redundancies. To address these limitations, we introduce EventVLA, an end-to-end framework founded on the concept of sparse visual evidence memory that comprises two core components: foundational visual anchors to retain initial and short-term contexts, and a dynamic Keyframe Evidence Memory (KEM) module. Specifically, KEM directly predicts future keyframe probabilities from the VLA's latent embeddings to autonomously capture and store sparse, task-critical visual events. This foresight-driven mechanism empowers the policy to dynamically evaluate the future causal utility of current observations, preserving transient visual evidence before it becomes unobservable. Furthermore, we propose RoboTwin-MeM, a diagnostic benchmark specifically designed to evaluate non-Markovian manipulation tasks with interactive visual evidence. Extensive evaluations show that across 17 memory-requiring simulation tasks and 4 real-world bimanual tasks, EventVLA achieves an average success rate improvement of +40% over state-of-the-art memory-augmented VLAs.