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01.
arXiv (CS.CL) 2026-06-25

Graph-Based Phonetic Error Correction of Noisy ASR

Automatic speech recognition (ASR) systems, despite low overall word error rates, produce residual lexical errors that disproportionately affect semantically critical tokens such as named entities, negations, and sentiment-bearing words. These errors are often structured, arising from phonetic similarity rather than random noise, making naive token-level correction insufficient. We propose a structured ASR correction framework, that we call G-SPIN, that combines phonetic graph modeling with contextual language understanding. A graph neural network (GNN) first constructs acoustically plausible candidate neighborhoods for flagged tokens, explicitly restricting the correction search space to phonetic alternatives. A masked language model (MLM) then provides local contextual scoring, and an instruction-tuned large language model (LLM) performs final context-aware re-ranking over this compact candidate set. By decoupling structured phonetic reasoning from contextual semantic selection, our method avoids unconstrained generation while improving correction accuracy. The framework is lightweight, modular, and operates entirely at inference time.

02.
arXiv (CS.CV) 2026-06-19

HumanScale: Egocentric Human Video Can Outperform Real-Robot Data for Embodied Pretraining

Embodied foundation models are expected to benefit from data scaling like large language models, but face a much tighter data bottleneck. Teleoperated real-robot trajectories remain the dominant pretraining source due to their precise action supervision and embodiment alignment, yet their scalability is limited by high collection cost, acquisition difficulty, and low behavioral and environmental diversity. These limitations have sparked interest in egocentric human video as a scalable, substantially lower-cost, and more diverse alternative for embodied model pretraining. However, its effectiveness compared to teleoperated real-robot data remains underexplored. To address this question, we conduct a systematic study comparing egocentric human video and teleoperated real-robot trajectories as pretraining data sources for embodied foundation models, under fixed post-training and validation protocols. Surprisingly, we find that egocentric data, when processed through a carefully designed filtering and labeling pipeline, is not merely a viable substitute for model pretraining but can lead to superior performance. With the same amount of pretraining data, models pretrained on egocentric data achieve a 24% lower validation loss on real-robot action prediction, as well as 52.5% and 90% higher success rates on in-distribution and out-of-distribution real-robot task execution, respectively. This finding verifies a scalable paradigm for embodied foundation models: pretrain on egocentric human video to learn diverse world representations, then adapt with a small amount of labeled real-robot data for action-space alignment. We hope this study encourages broader exploration of egocentric data and offers guidance for data quality assessment before costly robot data collection.

03.
medRxiv (Medicine) 2026-06-16

Higher Population Coverage with Typhoid Conjugate Vaccine is Needed to Induce Herd Protection: Evidence from a Cluster-Randomized Trial in Urban Bangladesh

Introduction: A cluster randomized trial (CRT) in Bangladesh found that Vi-tetanus toxoid (Vi-TT) vaccine conferred 85% protection to vaccinees at 18 months of follow-up; however, it failed to confer significant herd protection to non-vaccinees. Methods: In the CRT, children aged 9 months to

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

A Systematic Evaluation of Black-Box Uncertainty Estimation Methods for Large Language Models

arXiv:2606.19868v1 Announce Type: new Abstract: Although large language models (LLMs) have shown strong capabilities across a wide range of tasks, their outputs often remain unreliable and may contain hallucinations, making uncertainty estimation (UE) essential for building trustworthy LLMs. In practice, many mainstream LLMs are only accessible through restricted APIs, where internal signals such as logits and hidden states are unavailable, making black-box UE especially important. However, existing work on black-box UE for LLMs remains fragmented in methodology and lacks a unified empirical comparison. To address this gap, we present a systematic review of black-box UE methods and organize them into five categories: verbalization-based, sampling-based, explanation-based, multi-agent, and hybrid methods. We further build a unified evaluation framework and benchmark 24 representative methods across 4 models and 4 dataset settings. Our results show that no single method consistently dominates across all settings. Nevertheless, methods that reason over and compare candidates in the answer space are generally effective, and hybrid methods that combine multiple uncertainty signals perform well under most conditions. By releasing the benchmark data and a unified evaluation framework, we aim to facilitate reproducible comparisons and support future research, while our empirical findings provide practical guidance for developing future black-box UE methods for LLMs.

05.
arXiv (CS.AI) 2026-06-12

"Is This Not Enough?": Asymmetries in Institutional Accountability and Collective Sensemaking in the Case of Canada's Algorithmic Visa Triage System

arXiv:2606.13071v1 Announce Type: cross Abstract: This paper examines how algorithmic accountability in Canada's visa system is articulated institutionally and experienced by applicants across borders. We analyzed Immigration, Refugees and Citizenship Canada (IRCC)'s Algorithmic Impact Assessment (AIA) for the temporary resident visa (TRV) triage system using the algorithmic decision-making adapted for the public sector (ADMAPS) framework and analyzed Reddit discussions among applicants using a mixed-methods approach. We show that while institutional artifacts emphasize transparency, procedural safeguards, and bounded impacts, applicants engage in collective sensemaking to interpret opaque decisions, often relying on peer knowledge amid uncertainty. We identify three asymmetries between how institutional accountability is structured and how people perceive the process: epistemic asymmetry in access to decision logic, jurisdictional asymmetry in exposure shaped by geopolitical positioning, and temporal–relational asymmetry in how waiting and uncertainty are experienced. We emphasize why it is important to shift attention from institutional design to the uneven distribution of experiences with public-sector algorithmic governance. Together, these contributions demonstrate how algorithmic governance systems in the context of transnational migration produce structured asymmetries not captured by institutional disclosure frameworks, and how extending ADMAPS can account for those uneven translations of accountability.

06.
bioRxiv (Bioinfo) 2026-06-19

Perturbation Curve models continuous transcriptional response trajectories and improves prediction of genetic modulations

Single-cell CRISPR screens, Perturb-seq, have revolutionized functional genomics by revealing biological causality. However, although perturbation assignments are typically represented as discrete labels, the cell-level effective strength of perturbations is often continuous and diverse. Current analytical frameworks struggle to decouple the variability in perturbation strength from the diversity of downstream responses. Here, we present Perturbation Curve (PertCurve), a nonlinear, curve-based computational framework that models the trajectories of transcriptomic responses by explicitly incorporating diverse perturbation magnitudes and strengths. By ordering cells by perturbation strength, we demonstrate that PertCurve accurately recapitulates the response magnitudes and reveals the distinct modularity and asynchrony patterns of downstream gene behaviors. These patterns are categorized into archetypes, including proportional, sensitive, and threshold responses. By applying this framework across CRISPRi/a modalities, we identify universal response patterns in viral infection, apoptosis, and proliferation genes, and reveal previously overlooked context-specific regulatory features in cell differentiation. Finally, incorporating PertCurve into perturbation prediction models and evaluation metrics enhances predictive performance, delivering actionable insights for refining established models.

07.
arXiv (quant-ph) 2026-06-25

A Candidate Framework for Free-Space Quantum Key Distribution based on Geometrical-Configuration Modulation

arXiv:2606.25807v1 Announce Type: new Abstract: This paper proposes a candidate framework for free-space quantum key distribution (QKD) based on geometrical-configuration modulation (GM). In the minimal implementation considered here, Alice coherently splits a single photon emitted from one source into two spatial output modes with a tunable separation, and uses the source separation $R$ as the GM variable that defines the prepared single-photon spatial superposition state. Bob records the single-photon detection coordinate in the far field or Fourier plane, providing the correlated data used for soft-input information reconciliation. Based on this physical mechanism, we first establish an $R-x$ protocol model in which the source separation $R$ and the single-photon detection coordinate $x$ are random variables, and further propose an $R-\Delta x$ extension based on the difference variable $\Delta x$ between adjacent accepted detection events to mitigate slowly varying center drift in free-space links. The framework specifies state preparation, far-field conditional probabilities, soft-input information generation, parameter estimation, reconciliation, and asymptotic candidate key-rate formulas. A complete composable security analysis further requires derive an explicit computable upper bound on Eve's information from experimentally observed parameters, together with finite-key analysis and experimental validation under free-space conditions. The proposed candidate framework (GM-QKD) provides a modulation approach based on spatial degrees of freedom in which the source geometry serves as the modulation variable.

08.
arXiv (CS.CV) 2026-06-24

Towards Fast and Effective Long Video Understanding of Multimodal Large Language Models via Adaptive Quasi-Gaussian Sampling

Long video understanding remains a daunting challenge for Multimodal Large Language Models (MLLMs) due to the excessive computation and memory footprint. Thus, keyframe selection is often adopted to mitigate this shortcoming, which however still suffers from low flexibility and high noise due to its hard sampling principle. In this paper, we define video frame selection as a problem of Quasi-Gaussian Sampling, and propose an adaptive and training-free approach termed AdaQ. Inspired by the $3$-$\sigma$ rule of Gaussian distribution, the objective of AdaQ is to achieve the optimal $3$-$\sigma$ interval for different examples, i.e., a smaller $3$-$\sigma$ interval for the local query and a larger one for the global query, thereby facilitating robust and adaptive frame sampling. To validate AdaQ, we apply it to four MLLMs with three embedding models. The extensive experimental results not only show its obvious performance gains over the default MLLMs and the SOTA keyframe selection methods, e.g., helping Qwen3-VL-8B outperform GPT4o by 15.8\% on average by using only 64 frames, but also confirm its superior robustness and high efficiency for long-video understanding, e.g., only 1 hyper-parameter needs to be set. Our code project is given at \href{https://github.com/Zkayovo-xmu/AdaQ}{https://github.com/Zkayovo-xmu/AdaQ}.

09.
arXiv (CS.LG) 2026-06-18

INDEQS: Informed Neural controlled Differential EQuationS

arXiv:2606.19138v1 Announce Type: new Abstract: Neural Controlled Differential Equations (NCDE) provide a powerful continuous-time framework for forecasting time series, but standard graph-based extensions typically learn spatial structure purely from data, even in settings where a directed graph structure is known a priori. We introduce Informed Neural controlled Differential EQuationS (INDEQS), a graph-based NCDE forecasting method that incorporates prior knowledge of a directed graph at distinct architectural positions. INDEQS separates inner mixing of hidden states across graph nodes from outer mixing between vector field and control, and offers both a lightweight graph-constrained variant and a more expressive variant, learning additional graph connections from data via adaptive graph convolutions. To systematically study when graph informedness is beneficial in forecasting, we devise a continuous advection simulation on directed graphs, yielding synthetic spatio-temporal datasets with known ground-truth flow structure. We then evaluate INDEQS on two real-world tasks: river discharge forecasting on a hydrological network and traffic flow prediction on PeMS08. Across these synthetic and real-world benchmarks, outer informedness consistently improves mean absolute error over an uninformed NCDE with comparable parameter count, particularly on larger graphs, while inner informedness offers a more parameter-efficient alternative when strict adherence to a known adjacency is desired. A comparison of discrete convolutional and continuous-time decoders further shows that continuous decoders yield better accuracy and greater temporal flexibility on real-world tasks. An implementation of INDEQS and the advection simulation is available at https://github.com/Mitchi1/indeqs.

10.
arXiv (CS.AI) 2026-06-24

Legal Reasoning Is Not Lawyering: Rethinking Legal Benchmarks for Pro Se Access to Justice

arXiv:2606.23716v1 Announce Type: cross Abstract: Legal AI benchmark research frequently invokes the assumption that large language models can improve access to justice, including for people who cannot access lawyers in order to understand and exercise their legal rights. We argue that current benchmarks are not equipped to support this assumption because they evaluate legal reasoning over inputs that have already been preprocessed by legal experts, which measures the upper bound of model performance. Access to justice depends on a lower bound: how models perform when inputs come from pro se litigants, whose prompts may contain noisy narratives, buried facts, omissions, folk-legal assumptions, and surface-level errors. These degradations are comparable to conditions under which LLMs are known to degrade in the general machine learning literature, including long-context sensitivity, underspecification, hallucination, and typographical perturbations. We connect evidence from pro se literature with this body of machine learning research and present a small perturbation experiment on LEXam, a legal benchmark, to illustrate the gap between these two bounds. If model development continues to focus on benchmarks that measure only the upper bound, this gap may remain hidden or even widen. We conclude by calling for legal benchmarks that directly measure robustness under pro se-like inputs so that access-to-justice claims about legal AI can become empirically testable.

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

Bridging Day and Night: Unsupervised Cross-Domain Re-Identification with Synergistic Prompt and Prototype Learning

Cross-domain day-night re-identification (ReID) is fundamentally challenged by the substantial visual appearance discrepancies between daytime and nighttime scenes. Existing fully supervised methods rely heavily on labor-intensive annotations, which are costly and exhibit limited generalization across domains. In this work, we investigate unsupervised day-night ReID and propose a novel framework that synergistically combines prompt learning and prototype-based representation learning to associate identities across domains without requiring manual labels. Our approach follows a progressive two-stage training strategy. In the first stage, we exploit the vision-language model to generate instance-specific textual prompts in an annotation-free manner. We employ an instance-level alignment mechanism to embed visual features and textual prompts into a unified semantic space, aligning unlabeled day/night images with learnable prompts via instance-aware dynamic-bias adaptation. In the second stage, we construct domain-specific prototype memory banks and introduce two complementary modules: i) an intra-domain identity association module to enhance feature discriminability within each domain, and ii) a cross-domain prototype matching module to reliably identify positive and negative prototype pairs, thereby establishing robust identity correspondences across day and night. Extensive experiments on public benchmarks validate the effectiveness of our method. Under the unsupervised setting, our framework attains Rank-1 accuracy comparable to state-of-the-art fully supervised methods.

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

Enhancing LLM Safety Through a Theoretical Minimax Game Lens

The rapid advancement of large language models (LLMs) necessitates effective mechanisms to ensure their responsible deployment by accurately distinguishing unsafe content from benign content. While substantial safety datasets are available in English, multilingual safety modeling remains underexplored due to limited open-source safety datasets in other languages. Even within English datasets, safe yet sensitive corner-case content is scarce, leading to shortcut learning by models and non-trivial false-positive rates. To mitigate these issues, we introduce a novel minimax reinforcement learning (RL) framework wherein a data generator and a classifier model co-evolve, facilitating the production of high-quality synthetic multilingual safety data. We theoretically formalize this interaction as a minimax game and rigorously demonstrate convergence to a Nash equilibrium. Empirical evaluations confirm that our synthetic data generation method significantly enhances the classifier model performance, enabling a substantially smaller model to surpass the state-of-the-art by nearly 10% on English benchmarks while achieving 4.5x faster inference speed. These results establish a scalable and efficient methodology for synthetic data generation, advancing the development of safer and more robust multilingual LLM deployments.

13.
Nature (Science) 2026-06-17

Reimagining machine vision with optical computing

作者: 未知作者

A general-purpose artificial-intelligence vision system for use in image-sensing devices has been developed by embedding fundamentals of core computer-vision operations into a light-manipulating planar material called an optical metasurface. A prototype enables accurate, real-time perception and processing across diverse tasks, suggesting that this could be a solution for rapid, low-energy, on-device vision intelligence. A specialized ‘metasurface’ can preprocess incoming scene information on image-generating devices.

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

Efficient Real-World Dehazing via Physics-Inspired Global-Local Decoupling

Real-world single image dehazing is highly ill-posed due to spatially and spectrally varying scattering, while practical deployment demands lightweight and low-latency models. Existing approaches either rely on fragile physical inversion under simplified assumptions or adopt heavy blind architectures unsuitable for edge deployment. To overcome these limitations, we propose PGL-Net (Physics-Inspired Global-Local Decoupling Network), a lightweight framework that incorporates physical inductive biases via operator-level emulation, avoiding explicit parameter estimation. It decouples dehazing into global distribution rectification and local structural refinement. A Physics-Inspired Affine Fusion (PAF) module performs globally conditioned alignment across hierarchical skip connections to compensate for haze-induced bias, while a compact Degradation-Aware Modulation (DAM) block adaptively restores spatially and spectrally variant details through dynamic feature modulation. Extensive experiments on multiple real-world benchmarks demonstrate that PGL-Net achieves state-of-the-art restoration quality with significantly reduced complexity. Compared with the recent SOTA SGDN, the Tiny variant (PGL-Net-T) improves PSNR by up to 2.6dB and consistently enhances downstream object detection accuracy, while achieving over a 10x reduction in inference latency. Code is publicly available at: https://github.com/sc-30-bit/PGL-Net.

15.
arXiv (CS.AI) 2026-06-12

Mental-R1: Aligning LLM Reasoning for Mental Health Assessment

arXiv:2606.13176v1 Announce Type: new Abstract: Mental health problems such as anxiety, depression, and suicide remain urgent global challenges, where timely and accurate assessment is critical for effective intervention. Recently, large language models have been explored for mental health assessment. However, existing general-purpose post-training methods do not align with the cognitive processes of human assessment, which may lead to unreliable reasoning outcomes. To bridge this gap, we propose Cognitive Relative Policy Optimization (CRPO), a reinforcement learning framework tailored for the mental health domain. CRPO extends group relative policy optimization by integrating stage-dependent uncertainty modeling into the policy optimization process. Specifically, we introduce a stage-wise entropy regularization mechanism that encourages broad exploration in early reasoning phases and progressively enforces confident decision-making in later stages, mimicking the human cognitive shift from uncertainty to certainty. In addition, inspired by cognitive appraisal theory, we formalize cognitive reasoning stages, thereby guiding theory-grounded interpretable inference. Experiments on 8 mental health datasets show that CRPO achieves an average improvement of 10.4 percentage points in weighted F1-score over the best reinforcement learning baseline. Furthermore, the CRPO-trained model Mental-R1 demonstrates clear advantages compared with existing large language models on reasoning-intensive cases, suggesting that CRPO enhances reasoning capabilities for mental health assessment.

16.
arXiv (CS.CV) 2026-06-24

Full-resolution MLPs Empower Medical Dense Prediction

Dense prediction is a fundamental requirement for many medical vision tasks such as medical image restoration, registration, and segmentation. The most popular vision model, Convolutional Neural Networks (CNNs), has reached bottlenecks due to the intrinsic locality of convolution operations. Recently, transformers have been widely adopted for dense prediction for their capability to capture long-range visual dependence. However, due to the high computational complexity and large memory consumption of self-attention operations, transformers are usually used at downsampled feature resolutions. Such usage cannot effectively leverage the tissue-level textural information available only at the full image resolution. This textural information is crucial for medical dense prediction as it can differentiate the subtle human anatomy in medical images. In this study, we hypothesize that Multi-layer Perceptrons (MLPs) are superior alternatives to transformers in medical dense prediction where tissue-level details dominate the performance, as MLPs enable long-range dependence at the full image resolution. To validate our hypothesis, we develop a full-resolution hierarchical MLP framework that uses MLPs beginning from the full image resolution. We evaluate this framework with various MLP blocks on a wide range of medical dense prediction tasks including restoration, registration, and segmentation. Extensive experiments on six public well-benchmarked datasets show that, by simply using MLPs at full resolution, our framework outperforms its CNN and transformer counterparts and achieves state-of-the-art performance on various medical dense prediction tasks.

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

When AI Says "I have been in similar situations": Synthetic Lived Experience in Peer-Like Caregiver Support

Caregivers often turn to online communities for informational and emotional support. In these spaces, peer supporters frequently draw on personal narratives to respond to emotionally complex caregiving situations. As LLMs are increasingly designed as peer-like sources of support, they introduce a critical tension: AI can provide immediate, private, and nonjudgmental support, but it cannot authentically possess the lived experiences that make human peer support meaningful. Yet, when prompted to sound peer-like, LLMs may generate language that implies lived experience. This creates a synthetic lived experience paradox: the same experiential language that may make AI support feel warm, relatable, and peer-like can also falsely position the system as someone with lived experience. We examine this paradox in the context of family caregivers of people living with Alzheimer's Disease and Related Dementias (ADRD). Drawing on caregiver support exchanges from online communities and prompted peer-like responses from three LLMs – LLaMA, GPT-4o-mini, and MedGemma – we analyze how human peers use personal narratives and how AI incorporates similar narrative forms. Psycholinguistic analysis shows that peer responses used significantly more first-person and past-focused language than peer-like AI responses. Qualitatively, we identify seven types of personal narratives in human peer support and show that AI often captures their emotional work, but can fabricate experiential grounding. These findings reveal a narrative authenticity gap: peer-like AI can generate synthetic lived experience without the real experience that makes peer support meaningful. We argue that caregiver-support AI systems need mechanisms to distinguish supportive peer-like framing from fabricated lived experience, ensuring that models can offer warmth and validation without falsely positioning themselves as experiential peers.

18.
arXiv (CS.CV) 2026-06-17

ActWorld: From Explorable to Interactive World Model via Action-Aware Memory

Interactive world models aim to simulate environment dynamics under real-time user actions. However, their action vocabulary is largely confined to navigation: most actions correspond to motion (e.g., walk, turn, look around), while interaction with objects in the scene (e.g., pick up plates, open doors, or trigger physical responses) is either absent, restricted to game domains, or relegated to prompt-to-full-video scenarios. The resulting worlds are visually explorable but not truly actionable. In this work, we present ActWorld, an interactive world model that extends prior navigation-centric generators to support mid-rollout object interaction within a chunk-autoregressive framework. We argue that the navigation-interaction gap stems from two bottlenecks. First, a data bottleneck: the lack of human-object interaction data with accurate, dense labels. Second, a memory bottleneck: recency-biased history compression in existing world models discards the event-transition frames that causally determine subsequent object states, leading to an action-forgetting pathology. On the data side, we construct a 100K interaction video dataset, each annotated with per-chunk captions via chain-of-thought reasoning. On the model side, we introduce a hierarchical action-aware memory design that routes history compression by interaction importance, complemented by a persistent memory bank that maintains event-update and object-identity tokens across long rollouts. Experiments show that ActWorld supports both flexible navigation and rich object interaction within a single model, substantially improving interaction fidelity over navigation-only baselines without sacrificing viewpoint control. Project page is available at https://interactwm.github.io/ActWorld.

19.
arXiv (CS.LG) 2026-06-11

Fourier Features Let Agents Learn High Precision Policies with Imitation Learning

arXiv:2606.12334v1 Announce Type: new Abstract: High-precision robotic manipulation requires fine-grained spatial reasoning that is often difficult to achieve with RGB-only policies due to depth ambiguity and perspective scale issues. Policies that leverage 3D information directly, such as those based on point clouds, offer a stronger geometric prior over purely image-based ones, yet their performance remains highly task-dependent. We hypothesize that this discrepancy may be due to the spectral bias of neural networks towards learning low frequency functions, which especially affects architectures conditioned on slow-moving Cartesian features. We thus propose to map point clouds from Cartesian space into high-dimensional Fourier space, effectively equipping the point cloud encoder with direct access to high-frequency features. We experimentally validate the use of Fourier features on challenging manipulation tasks from the RoboCasa and ManiSkill3 benchmarks and on a real robot setup. Despite their simplicity, we find that Fourier features provide significant benefits across diverse encoder architectures and benchmarks and are robust across hyperparameters. Our results indicate that Fourier features let policies leverage geometric details more effectively than Cartesian features, showing their potential as a general-purpose tool for point cloud-based imitation learning. We provide source code and videos on our project page: https://fourier-il.github.io/fourier-il

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

Direct Fisher Score Estimation for Likelihood Maximization

arXiv:2506.06542v2 Announce Type: replace-cross Abstract: We study the problem of likelihood maximization when the likelihood function is intractable but model simulations are readily available. We propose a sequential, gradient-based optimization method that directly models the Fisher score based on a local score matching technique which uses simulations from a localized region around each parameter iterate. By employing a linear parameterization to the surrogate score model, our technique admits a closed-form, least-squares solution. This approach yields a fast, flexible, and efficient approximation to the Fisher score, effectively smoothing the likelihood objective and mitigating the challenges posed by complex likelihood landscapes. We provide theoretical guarantees for our score estimator, including bounds on the bias introduced by the smoothing. Empirical results on a range of synthetic and real-world problems demonstrate the superior performance of our method compared to existing benchmarks.

21.
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.

22.
Nature (Science) 2026-06-24

Daily briefing: Sperm whales have different dialects

作者:

Whales in different areas of the Mediterranean use varying patterns of clicks and pauses. Plus, a technique to make protein samples one billion times bigger and the science of grief. Whales in different areas of the Mediterranean use varying patterns of clicks and pauses. Plus, a technique to make protein samples one billion times bigger and the science of grief.

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

Multifidelity-Augmented Gaussian Process Inputs for Surrogate Modeling from Scarce Data

arXiv:2603.22050v2 Announce Type: replace-cross Abstract: Supervised machine learning describes the practice of fitting a parameterized model to labeled input-output data. Supervised machine learning methods have demonstrated promise in learning efficient surrogate models that can (partially) replace expensive high-fidelity models, making many-query analyses, such as optimization, uncertainty quantification, and inference, tractable. However, when training data must be obtained through the evaluation of an expensive model or experiment, the amount of training data that can be obtained is often limited, which can make learned surrogate models unreliable. In many engineering and scientific settings, cheaper low-fidelity models may be available, for example arising from simplified physics modeling or coarse grids. These models may be used to generate additional low-fidelity training data. The goal of multifidelity machine learning is to use both high- and low-fidelity training data to learn a surrogate model which is cheaper to evaluate than the high-fidelity model, but more accurate than any available low-fidelity model. This work proposes a new multifidelity training approach for Gaussian process regression which uses low-fidelity data to define additional features that augment the input space of the learned model. Similarly to cokriging estimators, the proposed approach conditions the high-fidelity surrogate model on the predictions of all available low-fidelity surrogate models, while benefiting from the computational efficiency of autoregressive estimators. Numerical experiments on several test problems demonstrate both increased predictive accuracy and reduced computational cost relative to the state of the art.

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

Latent Space Analysis for Interpretable Uncertainty in Melanoma Classification

Melanoma is a highly aggressive skin cancer, making early and accurate diagnosis critical. While deep learning excels in skin lesion classification, standard ``black-box" models struggle to explain diagnostic uncertainty, limiting clinical trust. This work introduces a hybrid framework combining a class-aware adversarial Variational Autoencoder and an XGBoost classifier, transcending simple binary classification by leveraging a generative latent space for interpretable decision support. Guided by adversarial training, the model learns the visual characteristics of skin lesions and projects them into a continuous latent space, ensuring that similar images are grouped closely together. Trained on this latent space, the XGBoost classifier achieves a robust AUC of 0.868, competing closely with state-of-the-art models. For borderline cases, the framework enables clinicians to leverage the latent topology through Content-Based Image Retrieval. This provides a dual benefit: it allows the clinician to visually compare an ambiguous lesion against biopsy-confirmed precedents and acts as an early warning sign since a borderline classification can indicate that a lesion shares features of both nevi and melanomas, potentially requiring close monitoring. Our approach translates algorithmic hesitation into transparent, evidence-based visual support, bridging the gap between predictive performance and clinical trust.

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

Advanced Machine Learning and Deep Learning Techniques for Enhanced Cattle Identification and Detection: A Comprehensive Review

arXiv:2606.15655v1 Announce Type: new Abstract: The need for effective cattle identification technology is now more acutely felt than ever in maintaining biosecurity, food safety, and supply chain efficacy in livestock management. This paper presents a systematic review of recent research in cattle identification using machine learning and deep learning techniques. The present systematic review measures the effectiveness of traditional and modern cattle identification techniques using studies from major academic databases, where articles were subjected to full-text review. Among these techniques, classical Machine Learning Techniques such as K-Nearest Neighbors and Support Vector Machines have demonstrated good results in cattle identification; however, Deep Learning Techniques, such as Convolutional Neural Networks, Residual Networks, and You Only Look Once, are better in cognition, detection, and identification tasks. Feature extraction relies on common techniques like Local Binary Pattern (LBP), Speeded-Up Robust Features (SURF), and Scale-Invariant Feature Transform (SIFT), while key features commonly used in these studies include muzzle prints and coat patterns. The review highlights key hurdles involving cattle identification, such as the limited number of publicly accessible datasets, issues with data quality susceptible to environmental changes and animal mobility, and high demand for real-time processing ability. The paper aims to inform researchers, policymakers, and stakeholders about implementing scalable, humane, and effective cattle identification systems to achieve sustainable livestock management.