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01.
bioRxiv (Bioinfo) 2026-06-08

TRACEY: an updated resource for SNARE protein domain annotation with improved HMMs and expanded sequence coverage

Authors:
Pulido-Quetglas↗Fasshauer↗

Motivation: SNARE proteins catalyse membrane fusion across the eukaryotic endomembrane system, from synaptic vesicle exocytosis to intracellular trafficking, endosomal and vacuolar transport, and autophagy, and their accurate domain annotation depends on the quality of profile models and the sequence diversity behind them. The original SNARE domain classification predates the recent expansion of eukaryotic sequence data, leaving its HMM profiles and subgroup coverage unable to resolve divergent and lineage-specific paralogs. Results: We present an updated release of TRACEY built on a resynchronized, non-redundant collection of 18,915 curated SNARE proteins spanning 1,188 species, together with a consolidated set of 83 HMM profiles, including 43 models for newly defined subgroups, reconstructed through an iterative, mixture-model-driven procedure. In direct comparison with the legacy models, at least ~75% of sequences in every overlapping group scored better with the new HMMs, indicating systematic gains in domain detection. A redesigned web interface adds multiparameter querying, FASTA download, and direct scanning of user-submitted sequences against the curated profiles. Availability and implementation: TRACEY is freely available at https://tracey.unil.ch.

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02.
arXiv (CS.CV) 2026-06-11

DeceptionX: Explainable Deception Detection with Multimodal Large Language Models

Authors:
Jiayu Zhang↗Shuo Ye↗Jiajian Huang↗Yawen Cui↗Taorui Wang↗Wei Xia↗Zeheng Wang↗Haowen Tang↗Hui Ma↗Zitong Yu↗

Deception detection is a critical and highly challenging task within affective computing and behavioral analysis. Existing deep learning methods typically treat this task as a straightforward classification problem; however, this black-box approach lacks interpretability and fails to capture the complex logical deduction processes utilized by human experts when identifying lies. While Multimodal Large Language Models (MLLMs) have shown potential, applying them effectively requires a bridge between low-level audiovisual cues and high-level logical reasoning. In this paper, we propose DeceptionX, a novel MLLM framework that shifts the paradigm of deception detection from black-box classification to an interpretable Observe-Think-Summarize reasoning process. To address the scarcity of high-quality reasoning data, we first constructed DeceptChain, a high-quality dataset developed through a human-in-the-loop process. This dataset synthesizes fine-grained visual and auditory evidence (such as micro-expressions and vocal tremors) into structured chain-of-thought reasoning data. Furthermore, we propose a three-stage training pipeline and a Discrepancy-Aware Redundancy Elimination~(DARE) strategy for DeceptionX to further enhance the model's generalization capabilities. Extensive experiments demonstrate that DeceptionX not only outperforms existing MLLM baselines and state-of-the-art methods on standard real-world benchmarks but also provides transparent, expert-level reasoning paths, bridging the critical gap between accuracy and interpretability in multimodal deception detection.

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03.
arXiv (CS.AI) 2026-06-11

WeaveBench: A Long-Horizon, Real-World Benchmark for Computer-Use Agents with Hybrid Interfaces

Authors:
Wanli Li↗Bowen Zhou↗Yunyao Yu↗Zhou Xu↗Yifan Yang↗Dongsheng Li↗Caihua Shan↗

arXiv:2606.09426v2 Announce Type: replace Abstract: Computer-use agents (CUAs) increasingly operate in runtimes that combine visual desktop control, command-line execution, code editing, browsers, and external tools. Existing benchmarks, however, often evaluate these interfaces as separable capabilities, leaving long-horizon cross-interface orchestration under-tested. Thus, we introduce WeaveBench, a long-horizon hybrid-interface benchmark with 114 tasks across 8 real-world work domains, grounded in real user requests and publicly verifiable artifacts. Each task requires agents to combine GUI observations/actions with CLI/code operations within a single trajectory. We evaluate these tasks on a real Ubuntu desktop inside deployed CLI-agent runtimes, augmented with a minimal desktop-control plugin. We also propose a companion trajectory-aware judge that inspects deliverables, files, screenshots, logs, and action traces, while detecting shortcut behaviors such as fabricated visual evidence or hard-coded metrics. Across frontier model-runtime pairings, the best PassRate reaches only 41.2%, showing the benchmark remains far from saturated. The trajectory-aware judge further reveals that outcome-only grading substantially overestimates agent performance. Overall, WeaveBench exposes a critical gap in CUA evaluation and provides an effective testbed to measure whether agents can orchestrate GUI, CLI, and code operations across long-horizon real-world tasks.

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04.
arXiv (CS.CL) 2026-06-12

AI SciBrief as a Gateway to Research: A Framework for Onboarding Students into New Research Areas

Authors:
Andrei Lazarev↗Dmitrii Sedov↗

Students at all levels of higher education face a significant barrier in the form of information overload, which often paralyzes the initial stages of the research process and suppresses motivation. In response, this article introduces a pedagogical framework that leverages AI SciBrief, a platform powered by a Large Language Model (LLM) designed to automatically generate digests of scientific trends. We describe how this multidisciplinary tool - with initial coverage in finance, medicine, and education - can be integrated into the curriculum to overcome this "entry barrier." The framework provides concrete methodologies for utilizing these digests to facilitate topic selection for term papers, accelerate literature reviews for dissertations, and enable postgraduate students to continuously monitor emerging trends. We conclude that AI SciBrief functions as a "gateway to research" effectively reducing students' cognitive load and empowering them to transition more rapidly from information searching to knowledge creation.

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05.
arXiv (CS.AI) 2026-06-11

CredibleDFGO: Differentiable Factor Graph Optimization with Credibility Supervision

Authors:
Liang Qian↗Penggao Yan↗Penghui Xu↗Li-Ta Hsu↗

arXiv:2605.06100v2 Announce Type: replace-cross Abstract: Global navigation satellite system (GNSS) positioning is widely used for urban navigation, but the covariance reported by the GNSS solver is often unreliable in urban canyons. Existing differentiable factor graph optimization (DFGO) methods learn measurement weighting through the solver, but they still use position-only objectives. As a result, the position estimate may improve while the reported covariance remains too small, too large, or incorrectly oriented. We propose CredibleDFGO (CDFGO), a differentiable GNSS factor graph framework that makes covariance credibility an explicit training target. A Weighting Generation Network (WGN) predicts per-satellite reliability weights, and a differentiable Gauss-Newton solver maps these weights to a position estimate and a Hessian-derived posterior covariance. We use proper scoring rules to supervise the East-North predictive distribution end to end. We study negative log-likelihood (NLL), the energy score (ES), and their combination. Results on three UrbanNav test scenes show consistent gains in covariance credibility. Positioning accuracy also improves on the medium-urban and harsh-urban scenes; on the deep-urban scene, both the mean horizontal error and the 95th-percentile error improve. On the harsh-urban Mong Kok (MK) scene, CDFGO-Combined reduces the mean horizontal error from 13.77 m to 11.68 m, reduces NLL from 40.63 to 6.59, and reduces ES from 12.31 to 9.05 relative to DFGO (MAE). Case studies link the MK improvement to better axis-wise consistency, more credible local covariance ellipses, and satellite-level reweighting.

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

TERMS-Bench: Diagnosing LLM Negotiation Agents Beyond Deal Rate

Authors:
Erica Zhang↗Fangzhao Zhang↗Aneesh Pappu↗Batu El↗Jose Blanchet↗Susan Athey↗Jiashuo Liu↗James Zou↗

arXiv:2605.13909v2 Announce Type: replace-cross Abstract: Negotiation is a central mechanism of economic exchange, shaping markets, procurement, labor agreements, and resource allocation. It is also a canonical testbed for agentic language models, requiring multi-turn interaction under hidden preferences, strategic communication, and binding constraints. These properties make negotiation hard to evaluate: unlike math or code, it has no intrinsic verifier. Existing LLM negotiation evaluations rely on LLM-vs.-LLM interaction or aggregate outcomes such as deal rate, leaving failures opaque. We introduce Terms-Bench, short for Testbed for Economic Reasoning in Multi-turn Strategy, a Bayesian-game framework that makes the environment itself the verifier by specifying the counterpart's latent type, policy, and payoff structure. We instantiate it in bilateral price negotiation, where the counterpart's private state and simulator policy are hidden from the agent but observable to the evaluator. This turns the counterpart from a black-box opponent into a diagnostic instrument, enabling agent-attributable failure analysis and oracle-reference optimality gaps. Evaluating 13 LLM agents spanning frontier systems from major providers, Terms-Bench turns negotiation evaluation from aggregate ranking into actionable diagnosis: where agents fail, why they fail, and what to strengthen. Empirically, frontier models saturate deal rate yet diverge in surplus extraction, cue use, belief calibration, and compliance, revealing agent-specific bargaining bottlenecks masked by prior benchmarks.

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07.
arXiv (quant-ph) 2026-06-12

The Pound-Drever-Hall Method for Superconducting-Qubit Readout

Authors:
Ibukunoluwa Adisa↗Won Chan Lee↗Kevin C. Cox↗Alicia J. Koll\'ar↗

arXiv:2512.03138v3 Announce Type: replace Abstract: Scaling quantum computers to large sizes requires the implementation of many parallel qubit readouts. Here we present an ultrastable superconducting-qubit readout method using the multi-tone self-phase-referenced Pound-Drever-Hall (PDH) technique, originally developed for use with optical cavities. In this work, we benchmark PDH readout of a single transmon qubit, using room-temperature heterodyne detection of all tones to reconstruct the PDH signal. We demonstrate that PDH qubit readout is insensitive to microwave phase drift, displaying $0.73^\circ$ phase stability over 2 hours, and capable of single-shot readout in the presence of phase errors exceeding the phase shift induced by the qubit state. We show that the PDH sideband tones do not cause unwanted measurement-induced state transitions for a transmon qubit, leading to a potential signal enhancement of at least $14$~dB.

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

ArFake: A Robust Framework for Multi-Dialect Arabic Speech Spoofing Detection Benchmark

Authors:
Mohamed Elsetohy↗Alhassan Ehab↗Ali Mekky↗Besher Hassan↗Shady Shehata↗

With the rise of generative text-to-speech models, distinguishing between real and synthetic speech has become challenging, especially for Arabic that have received limited research attention. Most spoof detection efforts have focused on English, leaving a significant gap for Arabic and its many dialects. In this work, we introduce the first multi-dialect Arabic spoofed speech dataset. To evaluate the difficulty of the synthesized audio from each model and determine which produces the most challenging samples, we aimed to guide the construction of our final dataset either by merging audios from multiple models or by selecting the best-performing model, we conducted an evaluation pipeline that included training classifiers using two approaches: modern embedding-based methods combined with classifier heads; classical machine learning algorithms applied to MFCC features; and the RawNet2 architecture. The pipeline further incorporated the calculation of Mean Opinion Score based on human ratings, as well as processing both original and synthesized datasets through an Automatic Speech Recognition model to measure the Word Error Rate. Our results demonstrate that FishSpeech outperforms other TTS models in Arabic voice cloning on the Casablanca corpus, producing more realistic and challenging synthetic speech samples. However, relying on a single TTS for dataset creation may limit generalizability.

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09.
arXiv (CS.CV) 2026-06-19

Distill Once, Adapt Life-Long: Exploring Dataset Distillation for Continual Test-Time Adaptation

Authors:
Hyun-Kurl Jang↗Jihun Kim↗Hyeokjun Kweon↗Kuk-Jin Yoon↗

Continual Test-Time Adaptation (CTTA) aims to maintain model performance under evolving target domains by adapting online without labeled data. However, practical deployments often cannot retain the source dataset due to privacy or licensing constraints, and purely source-free CTTA methods tend to become unstable under long-term distribution shift, suffering from compounding self-training errors and catastrophic forgetting. We introduce DO-ALL (Distill Once, Adapt Life-Long), a plug-and-play framework that revisits source information in a compact and privacy-conscious form via Dataset Distillation (DD). Before deployment, DO-ALL performs DD to produce a small set of synthetic distilled anchors that summarize the source distribution. During adaptation, each target sample is matched with its most semantically aligned anchor, which provides a stable reference for various CTTA via source replay, representation alignment, and manifold-smoothing regularization. DO-ALL can be seamlessly integrated into existing CTTA algorithms, consistently improving long-term robustness across CIFAR100-C, ImageNet-C, and the CCC benchmark. This demonstrates the potential of leveraging DD to enable stable and continuous adaptation without retaining raw source data. The code is available at https://github.com/blue-531/DOALL.

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10.
arXiv (CS.AI) 2026-06-16

Few-shot Class-variable Incremental Audio Classification via Prototype Adaptation and Pseudo Class-variable Training

Authors:
Yanxiong Li↗Guoqing Chen↗Qianqian Li↗Sen Huang↗

arXiv:2606.08898v2 Announce Type: replace-cross Abstract: In the task of few-shot class-incremental audio classification, the number of classes is assumed to always increase without considering the possibility of decrease. However, the number of classes generally increases or decreases in practice. In this paper, we investigate a problem of Few-shot Class-variable Incremental Audio Classification (FCIAC), in which the number of classes increases or decreases. We propose a FCIAC method using prototype adaptation and pseudo class-variable training. The model in our method consists of an encoder and a classifier. The classifier is initialized by a class-variable prototype adaptation network, whose structure dynamically changes with the change of classes. In addition, we design a pseudo class-variable training strategy to enhance the model's adaptability to changing classes. Experiments on three public datasets show that our method exceeds previous methods in average accuracy. The code is at: https://github.com/cgq2971-afk/FCIAC.

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11.
arXiv (CS.CV) 2026-06-18

BindEdit: Taming Attention Leakage for Precise Multi-Object Image Editing

Authors:
Chaewon Park↗Soyoon Lee↗Naeun Lee↗Minjung Shin↗Seogkyu Jeon↗Kibeom Hong↗

Real image editing enables precise manipulation of visual content, yet existing methods often fail in complex multi-object scenarios, causing semantic blending, object duplication, or incomplete edits. We attribute these failures to attention leakage, where signals across spatial regions and text tokens become entangled during the denoising process. Specifically, we identify two distinct forms of leakage: Edit-Token Leakage, where ambiguous token-region alignment leads to object blending, and Source Dominance Leakage, where tokens of unchanged source objects overwhelm the attention intended for target entities. To resolve these leakages, we propose BindEdit, which enforces attention-level constraints within a single diffusion trajectory. To suppress Edit-Token Leakage, BindEdit jointly regularizes cross- and self-attention so that each target token group is bound to its corresponding spatial region while maintaining instance-level separation. To suppress Source Dominance Leakage, a cross-attention re-balancing mechanism amplifies target token influence and attenuates residual source semantics within editable regions. Moreover, a region fidelity term ensures that each target concept is expressed coherently across the entire editing mask. Additionally, we propose a comprehensive multi-object benchmark encompassing diverse object counts and categories. Extensive experiments demonstrate that BindEdit consistently outperforms existing methods within a single diffusion trajectory, maintaining robust performance across both single- and multi-object editing scenarios.

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

Federated Learning for Feature Generalization with Convex Constraints

Authors:
Dongwon Kim↗Donghee Kim↗Sung Kuk Shyn↗Kwangsu Kim↗

arXiv:2606.14416v1 Announce Type: new Abstract: Federated learning (FL) often struggles with generalization due to heterogeneous client data. Local models are prone to overfitting their local data distributions, and even transferable features can be distorted during aggregation. To address these challenges, we propose FedCONST, an approach that adaptively modulates update magnitudes based on the parameter strength of the global model. This prevents over-emphasizing well-learned parameters while reinforcing underdeveloped ones. Specifically, FedCONST employs linear convex constraints to ensure training stability and preserve locally learned generalization capabilities during aggregation. A Gradient Signal to Noise Ratio (GSNR) analysis further validates the effectiveness of FedCONST in enhancing feature transferability and robustness. As a result, FedCONST effectively aligns local and global objectives, mitigating overfitting and promoting stronger generalization across diverse FL environments, achieving state-of-the-art performance.

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

Intelligent Automation for Embodied Benchmark Construction: Pipelines, Embodiments, Simulators, and Trends

Authors:
Jinshan Lai↗Jianwei Hu↗Baoyang Jiang↗Fengchun Zhang↗Leyuan Wang↗Haotian Li↗Yida Wang↗Tingxuan Huang↗Xi Ren↗Qiang Ma↗

arXiv:2606.12207v1 Announce Type: cross Abstract: Embodied intelligence now spans navigation, household assistance, manipulation, autonomous driving, aerial agents, and multimodal large-model control. This expansion has made benchmark construction a central bottleneck for reliable evaluation. Unlike static datasets, embodied benchmarks combine task specifications, environments, robot data, demonstrations, annotations, metrics, evaluation scripts, and release policies into a single evaluation system. This survey reviews the literature through a five-stage construction pipeline: requirement and task construction, data acquisition, data cleaning and annotation, benchmark suite generation and metric definition, and evaluation execution with diagnostic feedback. For each stage, the survey analyzes the transition from manual curation to traditional automation, foundation-model assistance, and agentic closed-loop workflows. It also compares qualitative construction costs across human labor, data and asset acquisition, compute and simulation, validation and debugging, governance and maintenance, and rework risk. The main conclusion is that automation does not simply reduce benchmark cost. Instead, it often shifts cost toward validation, auditability, version control, and long-term governance. Progress in embodied evaluation will therefore depend not only on larger benchmark suites, but also on construction pipelines that are diagnosable, auditable, and responsibly refreshable.

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14.
arXiv (CS.LG) 2026-06-15

A Low-Rank Subspace Analysis of LLM Interventions

Authors:
Angira Sharma↗Christian Schroeder de Witt↗Philip Torr↗Anisoara Calinescu↗Jialin Yu↗

arXiv:2606.14388v1 Announce Type: new Abstract: Interventions designed to modify a particular behavior in LLMs, such as refusal or sycophancy, often produce unintended changes in other behaviors. This lack of targeted control makes it difficult to design and implement reliable safety controls. To understand these side-effects, we introduce a diagnostic framework for analyzing interacting behaviors in LLMs. We model behaviors as low-rank subspaces in activation space, and study how interventions influence across behaviors. Across multiple instruction-tuned models (7B-70B) and across refusal, jailbreak, and sycophancy settings, we find that different behaviors share internal representations, and intervening on one behavior alters others in asymmetric ways. Some behaviors act as upstream control points whose interventions propagate broadly across other behaviors, while others remain more isolated. We relate these effects to two geometric quantities: (i) the overlap between behavior subspaces, measured as the average squared cosine of principal angles, and (ii) the angle between each behavior subspace and the decision subspace (capturing the model's final decision e.g., refuse vs. comply). Empirically, intervention effects on other behaviors tend to be larger for behavior pairs with higher subspace overlap, and for source behaviors whose subspaces lie closer (smaller angle) to the decision subspace. These findings highlight a challenge for targeted behavior control: behaviors are difficult to modify independently, as interventions can propagate through shared representations and asymmetric interactions.

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

Cross-Modal Masked Compositional Concept Modeling for Enhancing Visio-Linguistic Compositionality

Authors:
Wei Li↗Zhen Huang↗Xinmei Tian↗

Contrastively trained vision-language models like CLIP, have made remarkable progress in learning joint image-text representations, but still face challenges in compositional understanding. They often exhibit a "bag-of-words" behavior–struggling to capture the object relations, attribute-object bindings, and word order dependencies. This limitation arises not only from the reliance on global, single-vector representations for optimization, but also from the insufficient exploitation and modeling of the rich compositional information inherently present in paired image text data. In this work, we propose MACCO (MAsked Compositional Concept MOdeling), a framework that masks compositional concepts in one modality and reconstructs them conditioned on the full contextual information from the other, enabling the model to capture and align cross-modal compositional structures more effectively. To facilitate this process, we introduce two auxiliary objectives that jointly align and regularize masked features both inter-modally and intra-modally. Extensive experiments on five compositional benchmarks, along with in-depth analyses, demonstrate that our approach not only significantly enhances compositionality in VLMs but also improves their ability to capture syntactic structure and linguistic information. Additionally, the improved compositionality also benefits text-to-image generation and multimodal large language model. Code is available at https://github.com/hiker-lw/MACCO.

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

One Step Closer to Ground Truth: A Multi-Scale Residual-Aware Representation Learning Pipeline for Predicting Time Series Data

Authors:
Amrijit Biswas↗Mustafa Kamal↗Robin Krambroeckers↗M. M. Lutfe Elahi↗Sifat Momen↗Nabeel Mohammed↗Shafin Rahman↗

arXiv:2606.10678v2 Announce Type: replace Abstract: Transformer-based models have emerged as leading paradigms in time-series forecasting in recent years, employing self-attention mechanisms to capture long-range dependencies. Despite their success, these single-stage forecasting architectures exhibit persistent systematic residual biases arising from structural discrepancies, unmodeled stochastic components, or inadequate multi-scale temporal representations. This limitation persists when residuals are treated as irreducible noise, precluding adaptive correction of structured error patterns. To address this limitation, we introduce a two-stage, model-agnostic framework that explicitly decouples forecasting and residual learning into distinct stages of representation learning. A base transformer first generates the initial predictions. Subsequently, a dedicated meta-corrector dynamically models structured error patterns across multivariate channels, preserves cross-variable dependencies, and iteratively refines the residual bias of the base transformer. By formalizing this pipeline as a hypothesis space expansion, our framework addresses approximation limitations inherent in single-stage architectures, removes reliance on restrictive assumptions, and enables end-to-end learning of complex error dynamics. Evaluated on eight popular benchmark datasets using established protocols, our approach achieves state-of-the-art performance, with significant improvements in standard metrics (MSE, MAE). The results demonstrate the framework's ability to mitigate systematic biases and enhance robustness to complex temporal dynamics, advancing the practical applicability of transformer-based forecasting models.

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

Stealthy World Model Manipulation via Data Poisoning

Authors:
Yibin Hu↗Xiaolin Sun↗Zizhan Zheng↗

arXiv:2606.18697v1 Announce Type: new Abstract: Model-based learning agents use learned world models to predict future states, plan actions, and adapt to new environments. However, the process of updating world models from collected experience creates a training-time attack surface: adversarially poisoned fine-tuning trajectories can manipulate the learned dynamics and thereby corrupt downstream planning. In this paper, we propose SWAAP, the first two-stage data poisoning framework for learned world models. In the first stage, SWAAP identifies a harmful target world model that induces low-return behavior under planning while remaining close to clean dynamics, using first-order bilevel optimization enabled by a transition-gradient theorem. In the second stage, SWAAP realizes this target through stealth-constrained gradient matching, modifying only a limited fraction of fine-tuning transition targets so that the induced training gradients steer the victim model toward the adversarial target, while a prediction-error regularizer encourages the poisoned targets to remain close to the world model's natural approximation error. To assess attack stealthiness, we evaluate defenses and detectability across three stages of the poisoning pipeline: pre-training detection of poisoned transitions, robust training during fine-tuning, and test-time monitoring of the resulting world model. Across diverse continuous-control tasks, SWAAP causes substantial performance degradation while keeping poisoned transitions close to clean data and evading the evaluated non-adaptive residual/CUSUM/TRIM-style defenses. These results reveal a practical vulnerability in world-model adaptation pipelines and highlight the need for robustness methods that protect both world-model training data and learned dynamics.

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

Physics-Informed Attention Mechanism and Generalization Capability of Deep Learning-Based Grain Growth Evolution Prediction

Authors:
Pungponhavoan Tep↗Marc Bernacki↗

arXiv:2606.17235v1 Announce Type: cross Abstract: Machine Learning (ML) models for grain growth prediction are typically trained on idealized synthetic data, yet practical applications require generalization to conditions outside the training distribution. This study evaluated the Out-Of-Distribution (OOD) generalization capability of the trained model from our previous study across three test cases, including experimental microstructures, microstructures characterized by a bimodal grain size distribution, and abnormal grain growth. To further probe whether physics-informed architectural design could improve robustness under these different conditions, a boundary-masked attention mechanism was proposed specifically for grain growth, constraining attention to grain boundary pixels. Both the baseline and the proposed physics-informed attention model were evaluated without retraining or fine-tuning on the OOD data. Both models successfully generalized to all three test cases, yet the boundary-masked attention mechanism provided substantial improvements, with the most notable gains for microstructures characterized by a bimodal grain size distribution, where Structural Similarity Index Measure (SSIM) improved from \num{0.6221} to \num{0.7609} and mean grain size ($\overline{R}$) error decreased from \operatorname{SI}{8.75}{\percent} to \operatorname{SI}{3.57}{\percent}. The attention heatmap analysis revealed that the boundary-masked attention model learned to concentrate attention on large grain boundaries in a manner consistent with curvature-driven grain growth physics, emerging from training without being explicitly encoded into the architecture. These results indicate that models trained on synthetic data can generalize to diverse OOD conditions without retraining, and that physics-informed attention may improve accuracy when the boundary morphology matches the training domain.

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19.
bioRxiv (Bioinfo) 2026-06-11

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

Authors:
Fang↗Wang↗Cao↗

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.

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20.
arXiv (CS.CL) 2026-06-16

MAWARITH: A Dataset and Benchmark for Legal Inheritance Reasoning with LLMs

Authors:
Abdessalam Bouchekif↗Shahd Gaben↗Samer Rashwani↗Somaya Eltanbouly↗Mutaz Al-Khatib↗Heba Sbahi↗Mohammed Ghaly↗Emad Mohamed↗

Islamic inheritance law is challenging for large language models because solving inheritance cases requires complex, structured, multi-step reasoning and the correct application of juristic rules to compute heirs' shares. We introduce MAWARITH, a large-scale annotated dataset of 12,500 Arabic inheritance cases for training and evaluating models on the full reasoning chain: (i) identifying eligible heirs, (ii) applying blocking (\d{hajb}) and allocation rules, and (iii) computing exact inheritance shares. To the best of our knowledge, MAWARITH is the first Arabic corpus and benchmark designed for end-to-end Islamic inheritance reasoning. Unlike prior datasets that restrict inheritance case solving to multiple-choice questions, MAWARITH supports the full reasoning chain and provides step-by-step solutions with justifications grounded in classical juristic sources and established inheritance rules, as well as exact share calculations. This enables models to learn how to generate detailed, step-by-step responses to user queries that reflect real-world Islamic inheritance cases. To evaluate models beyond final-answer accuracy, we propose MIR-E (Mawarith Inheritance Reasoning Evaluation), a weighted multi-stage metric that scores key reasoning stages and captures error propagation across the pipeline. We evaluate six large language models in a zero-shot setting. A commercial model achieves about 90\%, whereas all evaluated open-source models remain below 50\%. Our error analysis identifies recurring failure patterns, including scenario misinterpretation, errors in heir identification, errors in share allocation, and missing or incorrect application of key inheritance rules such as \textquotesingle awl and radd. The MAWARITH dataset is publicly available at https://gitlab.com/nlpresearcher/mawarith.

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21.
arXiv (CS.AI) 2026-06-19

PSCT-Net: Geometry-Aware Pediatric Skull CT Reconstruction via Differentiable Back-Projection and Attention-Guided Refinement

Authors:
Dong Yeong Kim↗Jaewon Choi↗Youmin Shin↗Jungyu Lee↗Myeongseop Kim↗Jinwook Choi↗Joo Whan Kim↗Young-Gon Kim↗

arXiv:2606.19867v1 Announce Type: cross Abstract: Computed Tomography (CT) is essential for diagnosing pediatric craniofacial abnormalities, yet poses radiation risks to developing anatomies. Reconstructing 3D CT from sparse bi-planar X-rays offers a low-dose alternative but is severely ill-posed. Existing methods employ geometry-agnostic feature lifting, naively projecting 2D features into 3D without explicit spatial modeling, causing depth ambiguity and degraded osseous boundaries. We present PSCT-Net, a geometry-aware framework with differentiable back-projection. Differentiable back-projection establishes a spatially faithful volumetric prior, alleviating depth ambiguity. An Attention-Guided Projection (AGP-3D) module then learns non-linear voxel-wise correspondences between 2D regions and 3D locations. A Bidirectional Mamba (BiM-3D) module captures long-range volumetric dependencies with linear complexity. We further curate a private institutional pediatric skull CT cohort, PedSkull-CT, comprising normal and pathological cases for internal evaluation, addressing the gap in adult-centric, trunk-focused datasets.

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22.
medRxiv (Medicine) 2026-06-17

Efficacy of a Gamified Digital Platform for Substance Use Education and Overdose Prevention Among College Students: a Pilot and Feasibility Study

Authors:
Hilliard↗M. E↗Foreman↗Khan↗Zona↗Mishra↗Howse↗S. J↗

Background: For US young adults aged 18-25 in the 2018-2024 period, fentanyl was involved in 78.2% of the 44,020 unintentional or undetermined-intent overdose deaths, most often co-involving stimulants and other non-opioid substances. While fatal overdose rates in this age group have fallen to their lowest recorded level, emergency medical services-attended non-fatal overdose events have reached record highs, shifting the decisive variable toward bystander recognition and response. College students report near-universal alcohol education but minimal education on the substances actually driving overdose mortality. Methods: We conducted a single-group pre-post evaluation of the DopaGE Portal, a gamified, mastery-based digital platform covering cocaine, MDMA, benzodiazepines, and opioid overdose response, deployed at a public university (UNL) and a multi-campus volunteer network (TACO). Paired pre/post surveys (N=42) measured self-efficacy (7 items; primary), behavioral intentions, risk perception, and knowledge/attitudes on 5-point scales, plus four factual knowledge questions. Paired t-tests, exact McNemar tests, and Benjamini-Hochberg correction across eight primary tests were applied. Institutional naloxone distribution at UNL was tracked as an ecological behavioral outcome. A mandated high-school cohort (N=94) provided supplementary acceptability data. Results: Self-efficacy increased from 2.82 to 4.46 (d=2.00, 95% CI 1.46-2.55; adjusted p

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23.
arXiv (CS.CV) 2026-06-16

Variational Network with Wavelet-based UNET in Accelerated MRI Reconstruction from Under Sampled K-space Data

Authors:
Yasir Arafat Prodhan↗Shaikh Anowarul Fattah↗

Fully sampled MRI requires dense k-space acquisition, leading to long scan times, reduced clinical throughput, and increased sensitivity to patient motion. Accelerated MRI addresses this by acquiring undersampled k-space data and reconstructing the missing information computationally. However, reconstruction from undersampled measurements is highly ill-posed and can introduce aliasing artifacts, noise amplification, and loss of anatomical detail. Although conventional parallel imaging and compressed sensing methods mitigate these issues, and deep learning methods have further improved reconstruction quality, preserving high-frequency structures under aggressive undersampling remains challenging. In this work, we propose a Variational Network with a Wavelet-based U-Net (W-UNet) for accelerated MRI reconstruction. The framework combines physics-guided iterative reconstruction with learnable multi-scale frequency representations. Standard pooling operations are replaced with Discrete Wavelet Transform and Inverse Wavelet Transform modules, enabling lossless downsampling while preserving low-frequency structure and high-frequency edge details. Integrated into the refinement and sensitivity map estimation stages, the proposed design improves artifact suppression, feature preservation, and reconstruction fidelity in both single-coil and multi-coil settings. Experiments on fastMRI knee and M4Raw brain datasets show state-of-the-art performance. Ablation studies further confirm the effectiveness of wavelet-based feature decomposition for accelerated MRI reconstruction.

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

Photon: Federated LLM Pre-Training

Authors:
Lorenzo Sani↗Alex Iacob↗Zeyu Cao↗Royson Lee↗Bill Marino↗Yan Gao↗Dongqi Cai↗Zexi Li↗Wanru Zhao↗Xinchi Qiu↗Nicholas D. Lane↗

arXiv:2411.02908v2 Announce Type: replace Abstract: Scaling large language models (LLMs) demands extensive data and computing resources, which are traditionally constrained to data centers by the high-bandwidth requirements of distributed training. Low-bandwidth methods like federated learning (FL) could enable collaborative training of larger models across weakly-connected GPUs if they can effectively be used for pre-training. To achieve this, we introduce Photon, the first complete system for federated end-to-end LLM training, leveraging cross-silo FL for global-scale training with minimal communication overheads. Using Photon, we train the first federated family of decoder-only LLMs from scratch. We show that: (1) Photon can train model sizes up to 7B in a federated fashion while reaching an even better perplexity than centralized pre-training; (2) Photon model training time decreases with available compute, achieving a similar compute-time trade-off to centralized; and (3) Photon outperforms the wall-time of baseline distributed training methods by 35% via communicating 64x-512xless. Our proposal is robust to data heterogeneity and converges twice as fast as previous methods like DiLoCo. This surprising data efficiency stems from a unique approach combining small client batch sizes with extremely high learning rates, enabled by federated averaging's robustness to hyperparameters. Photon thus represents the first economical system for global internet-wide LLM pre-training.

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25.
arXiv (CS.CV) 2026-06-18

Hierarchical Multi-Modal Retrieval for Knowledge-Grounded News Image Captioning

Authors:
Minh-Loi Nguyen↗Xuan-Vu Le↗Long-Bao Nguyen↗Hoang-Bach Ngo↗Trung-Nghia Le↗

Traditional image captioning methods often struggle to generate comprehensive, context-rich descriptions, especially for details not directly observable from visual cues. To overcome this, we propose a novel retrieval-augmented image captioning framework that generates captions with deeper insights, such as object attributes, event context, and underlying significance, by leveraging external knowledge. Our approach features a hierarchical multi-modal article retrieval mechanism that moves beyond monolithic text entities. This retrieval considers article structure-aware features, including weighted textual components (e.g., headlines, body sections) and visual placement patterns, alongside multi-faceted similarity computations (content–visual, visual–visual, and discourse positioning). A subsequent contextual relevance refinement stage further enhances the retrieved information. The retrieved articles then serve as the knowledge base for caption generation: first, a VLM generates a concise image description; second, we segment relevant information from the retrieved articles based on this description; and finally, an LLM utilizes both the description and extracted knowledge to generate a comprehensive, contextually detailed caption. We participated in the ACM Multimedia EVENTA 2025 Challenge and achieved 5th place with an overall score of 0.2824 on the private test set of the OpenEvent-V1 dataset. Source code is publicly released at https://github.com/mf0212/EVENTA-Challange.

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