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01.
arXiv (CS.AI) 2026-06-16

RECTOR: Masked Region-Channel-Temporal Modeling for Affective and Cognitive Representation Learning

arXiv:2606.15278v1 Announce Type: cross Abstract: Affective and cognitive disorders manifest as distributed, time-varying brain network dynamics across regions, channels, and time, challenging robust representation learning from EEG/sEEG for clinical diagnosis. We propose RECTOR (Masked Region-Channel-Temporal Modeling), an end-to-end self-supervised framework that unifies joint region-channel-temporal representation learning beyond fixed anatomical priors. At its core, RECTOR-SA is a hierarchical, block-sparse self-attention induced by Adaptive Functional Partitioning that evolves region structures from static anatomical definitions to adaptive functional regions. The self-supervision is driven by Masked Topology and Representation Learning, which jointly optimizes three complementary objectives: Masked Predictive Modeling, Topological Structure Modeling, and Cross-View Consistency. Across diverse benchmarks, RECTOR sets a new state-of-the-art in EEG emotion recognition and sEEG task-engagement classification. Crucially, its strong robustness to missing channels and cross-montage generalization underscores its potential for large-scale pre-training on heterogeneous EEG/sEEG, providing interpretable insights at both region and channel levels.

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

Engineering Robustness into Personal Agents with the AI Workflow Store

arXiv:2605.10907v3 Announce Type: replace-cross Abstract: The dominant paradigm for AI agents is an "on-the-fly" loop in which agents synthesize plans and execute actions within seconds or minutes in response to user prompts. We argue that this paradigm short-circuits disciplined software engineering (SE) processes – iterative design, rigorous testing, adversarial evaluation, staged deployment, and more – that have delivered the (relatively) reliable and secure systems we use today. By focusing on rapid, real-time synthesis, are AI agents effectively delivering users improvised prototypes rather than systems fit for high-stakes scenarios in which users may unwittingly apply them? This paper argues for the need to integrate rigorous SE processes into the agentic loop to produce production-grade, hardened, and deterministically-constrained agent *workflows* that substantially outperform the potentially brittle and vulnerable results of on-the-fly synthesis. Doing so may require extra compute and time, and if so, we must amortize the cost of rigor through reuse across a broad user community. We envision an *AI Workflow Store* that consists of hardened and reusable workflows that agents can invoke with far greater reliability and security than improvised tool chains. We outline the research challenges of this vision, which stem from a broader flexibility-robustness tension that we argue requires moving beyond the ``on-the-fly'' paradigm to navigate effectively.

03.
arXiv (quant-ph) 2026-06-16

Scalable generation of heralded single photons via active feed-forward switching of a fiber delay line

arXiv:2606.16741v1 Announce Type: new Abstract: Quasi-deterministic single-photon generation is a key requirement for many photonic quantum technologies. Photon sources based on spontaneous parametric down-conversion (SPDC) are widely used for producing high-quality photons; however, the probabilistic nature of the process limits the generation of synchronized multi-photon states. Here, we demonstrate temporal synchronization of multiple photon-generation events using a free-space-fiber hybrid delay line with feed-forward control, enabling fast and efficient switching and scalable operation. Narrow-band, telecom-wavelength photons compatible for fiber transmission are heralded from a monolithic cavity SPDC source and synchronized across 20 time bins. This yields a sixfold enhancement in synchronized rates and enables multi-photon synchronization, with only a marginal increase of higher-order photon-number contributions.

04.
medRxiv (Medicine) 2026-06-18

AlphaGenome identifies a deep intronic variant in a family with PLA2G6-associated neurodegeneration: Closing the diagnostic gap in rare genetic diseases

A molecular diagnosis remains out of reach for a substantial subset of patients with clinically recognizable Mendelian disorders, even after comprehensive next-generation sequencing. Causal variants in non-coding regions are difficult to detect and interpret using standard pipelines. Deep intronic variants that disrupt splicing are a known but underexplored source of pathogenic alleles, and systematic tools to evaluate them at scale have only recently emerged. We aimed to resolve an incomplete genetic diagnosis in two siblings with early-onset parkinsonism, prominent neuropsychiatric features, and autonomic dysfunction consistent with PLA2G6-associated neurodegeneration (PLAN), an autosomal recessive condition. Prior clinical exome sequencing, genome sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA), and long-read sequencing had identified only a single heterozygous PLA2G6 missense variant, c.2132C>G (p.Pro711Arg). We used AlphaGenome to score 91 non-coding variants shared among the affected siblings and their father within 1 megabase of the PLA2G6 locus. The deep-learning model identified an intronic variant (c.2034+355G>A) that was predicted to create a cryptic splice acceptor site that could result in inclusion of a 160-bp cryptic exon. Tissue-specific predictions indicated the aberrant splicing would be detectable in blood, confirmed by junction-spanning RNA-seq reads from an unrelated carrier. This analysis completed a compound heterozygous PLAN diagnosis nearly two decades after symptom onset and demonstrates the utility of sequence-to-function models. Systematic integration of tools like AlphaGenome into rare disease workflows offers a practical, low-barrier route to closing the diagnostic gap for patients with compelling Mendelian phenotypes and incomplete genetic diagnoses.

05.
arXiv (CS.CL) 2026-06-18

Dango: A Strictly L1-Only Large Language Model for Studying Second Language Acquisition

We introduce Dango, a 1.8B-parameter large language model designed for controlled studies of L1-to-L2 (Japanese-to-English) transfer in second language acquisition (SLA). While previous studies have explored SLA in language models, they have predominantly relied on smaller or non-decoder models, limiting their ability to generate open-ended text and reducing their suitability as practical L2 simulators. We identify a key challenge when scaling models to this size: L2 contamination within the "monolingual" pretraining corpus used for L1 acquisition. To address this, we propose a filtering method to reduce premature exposure to English while preserving realistic, minimal exposure. We then fine-tune the model on LLM-generated L2-learning lessons to simulate the L2 acquisition process. Our evaluations confirm that Dango develops human-like L2 production patterns, outperforming both unfiltered and standard multilingual baselines. We release the model, data, and code to facilitate reproducible computational SLA research and learner-facing applications.

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

Library-Aware Doubles and Iterative Repair for Large Language Model-Generated Unit Tests in OpenSIL Firmware

arXiv:2606.19725v1 Announce Type: cross Abstract: Validating changes in low-level C firmware is expensive because unit tests (UTs) are fragile under strict build constraints, where missing headers, unresolved symbols, and dependency mismatches frequently prevent compilation and linking. This study introduces an automated UT authoring workflow for the Open-Source Silicon Initialization Library (openSIL) firmware codebase maintained by Advanced Micro Devices (AMD) that reduces manual effort through a large language model (LLM) guided multi-agent pipeline. The workflow combines automated generation of test scaffolds, library-aware creation or reuse of stubs, mocks, and fakes, and an iterative compile-dispatch repair loop driven by build logs and line-coverage feedback. We evaluate the approach using compilation success, repair iterations, dispatch success, and line coverage, with time, cost, and token usage as secondary measures. Across 76 functions under test, the workflow generated compilable UTs for 73 functions. In a configuration without line coverage guidance or retrieval augmentation, mean line coverage reached 73.9%. On a 48-function subset evaluated under both configurations, mean line coverage reached 98.8% with line-coverage guidance alone and reached 94.7% when combined with vector-database retrieval. Results show that automated generation-and-repair pipelines can substantially improve UT creation efficiency and coverage for constrained firmware environments while reducing manual debugging effort.

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

Metriplectic Conditional Flow Matching for Dissipative Dynamics

arXiv:2509.19526v2 Announce Type: replace Abstract: Metriplectic conditional flow matching (MCFM) learns dissipative dynamics without violating first principles. Neural surrogates often inject energy and destabilize long-horizon rollouts; MCFM instead builds the conservative-dissipative split into both the vector field and a structure preserving sampler. MCFM trains via conditional flow matching on short transitions, avoiding long rollout adjoints. In inference, a Strang-prox scheme alternates a symplectic update with a proximal metric step, ensuring discrete energy decay; an optional projection enforces strict decay when a trusted energy is available. We provide continuous and discrete time guarantees linking this parameterization and sampler to conservation, monotonic dissipation, and stable rollouts. On a controlled mechanical benchmark, MCFM yields phase portraits closer to ground truth and markedly fewer energy-increase and positive energy rate events than an equally expressive unconstrained neural flow, while matching terminal distributional fit.

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

Persona-Pruner: Sculpting Lightweight Models for Role-Playing

Language Models (LMs) have shown remarkable potential as role-playing chatbots, delivering consistent, stylized interactions when given a specification of a character or user persona. However, applying these capabilities to real-world applications (e.g., ecosystems with numerous NPCs interacting simultaneously) exposes a critical inefficiency due to the excessive computational cost. In this paper, we question the necessity of dedicating a full, generalist model to a single persona, hypothesizing that a specific character identity relies on only a fraction of the model's total capacity. We observe that naively pruning LMs often severely degrades the role-playing performance for a specific persona; it does not distinguish between redundant knowledge and essential character traits. We propose Persona-Pruner, a framework that sculpts a lightweight role-playing model by isolating persona-specific sub-networks from a single description. Our experiments consistently show that Persona-Pruner preserves role-playing performance substantially more effectively than existing state-of-the-art LLM pruning techniques, reducing the performance drop from the dense model by up to 93.8% over the strongest baseline on RoleBench in LLM-as-a-judge score, while still maintaining general LLM capabilities. Code is available at https://github.com/jsu-kim/Persona-Pruner.

09.
arXiv (CS.AI) 2026-06-15

Applicability Condition Extraction for Therapeutic Drug-Disease Relations

arXiv:2606.14031v1 Announce Type: new Abstract: Identifying conditions that a certain drug takes therapeutic effect on a target disease is crucial for clinical decision-making support. However, most existing biomedical information extraction methods have focused on identifying only relations between drugs and diseases, while largely overlooking the context-specific conditions where such relations can apply. To address this problem, we introduce the task of applicability condition extraction for therapeutic drug–disease relations from biomedical research literature. We create the first dataset that has manually annotated triples of drugs, diseases, and applicability conditions on biomedical paper abstracts with 1,119 drug-disease pairs. Using this dataset, we systematically evaluate the performance of a range of existing methods. In addition, we propose a new method that enhances LoRA to consider relations between drugs and diseases. Our method consistently outperforms strong baselines across different evaluation settings. The source code and dataset of this paper can be obtained from: https://github.com/guantingluo98/Drug-ACE

10.
arXiv (CS.LG) 2026-06-15

AGORA: Can Deliberation and Governance Gates Absorb Participation Bias in Transit Planning?

arXiv:2606.13696v1 Announce Type: cross Abstract: Transit network design depends not only on the optimization algorithm but also on who shows up to the public hearing. Current practice often collects one-directional comments from self-selected attendees, leaving participant mix as an uncontrolled source of outcome variation. We present AGORA, a framework that holds the network, demand, and solver fixed while systematically varying meeting composition through stakeholder agents, structured deliberation, and governance gates. Across two standard benchmark networks at different scales, we find that (i) aggregate outcomes vary little across compositions, but on tail risk and fairness disparity, representative sampling still tends to outperform skewed compositions; (ii) without deliberation, composition produces no variation at all, showing that deliberation is the mechanism through which who attends affects outcomes; and (iii) governance gates compress cross-profile variance without shifting the average outcome on Mandl, but low acceptance on Mumford0 shows thresholds require instance-specific calibration. These findings reframe participation bias from an uncontrollable input to a process-design problem: even without guaranteed representative attendance, well-structured deliberation and governance criteria can substantially reduce how much outcomes depend on who is in the room.

11.
arXiv (CS.CV) 2026-06-12

Revisiting Vehicle Color Recognition in Long-Tailed Surveillance Scenarios

Vehicle color recognition is an important cue for vehicle identification in surveillance systems, especially when license plates are illegible due to low resolution, occlusion, motion blur, or poor illumination. However, real-world vehicle color distributions are highly imbalanced, making overall accuracy insufficient to assess performance on rare but operationally relevant colors. This paper presents a comprehensive study of vehicle color recognition under severe class imbalance using UFPR-VeSV, a challenging real-world surveillance dataset. We investigate synthetic minority-class augmentation through two off-the-shelf generative strategies: text-conditioned image generation with RunDiffusion/JuggernautXL and image-conditioned color editing with Gemini 2.0 Flash. The curated synthetic data are combined with modern visual representations, loss reweighting, learning-rate scheduling, color-safe augmentation, foreground-aware preprocessing, and ensemble fusion. The bestperforming approach achieves 94.6% micro accuracy and 79.7% macro accuracy, improving macro accuracy by 8.2 percentage points over recent literature. A manual error analysis further shows that many remaining failures are visually ambiguous even for human annotators, highlighting the practical limits of color-based vehicle identification in unconstrained surveillance imagery. The generated images and source code are publicly available at https://github.com/viniciusorru/vcr-synthetic

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

FlowMaps: Modeling Long-Term Multimodal Object Dynamics with Flow Matching

arXiv:2606.20209v1 Announce Type: cross Abstract: Joint spatial and temporal understanding of 3D scenes is a crucial requirement for robots deployed in everyday household environments. Such agents must not only comprehend and navigate spatial layouts, but also reason about how these spaces evolve over time. In particular, humans interact with objects daily, causing them to change position throughout the environment and making it difficult for robots to reliably associate current observations with previously seen objects. However, these interactions are not random: human habits and routines induce spatio-temporally consistent patterns in object locations, which robotic agents can potentially learn and then exploit for downstream tasks such as navigation. To this end, we introduce FlowMaps, a latent flow matching model for estimating multimodal distributions over the future locations of dynamic objects in a continuous 3D space. By learning the implicit dependencies among objects and their temporal evolution, FlowMaps predicts likely changes in object locations conditioned on past human interactions, while supporting generalization across previously unseen environments that share similar object routines. To demonstrate the utility of this method, we deploy FlowMaps in a downstream dynamic Object Navigation task in both simulated and real-world environments. Across more than 600 episodes, FlowMaps outperforms state-of-the-art approaches, showing that modeling object dynamics through continuous, multimodal spatio-temporal distributions improves robotic search and navigation in changing household environments. Code and additional material is available at https://fra-tsuna.github.io/flowmaps/.

13.
arXiv (quant-ph) 2026-06-12

Quantum Reference Fields Transformations in Linearized Quantum Gravity

arXiv:2606.09344v1 Announce Type: cross Abstract: Diffeomorphism invariance is a central feature of general relativity. Without external reference structures, matter and geometry must be specified relationally, with respect to internal subsystems serving as reference frames. In quantum gravity, these reference systems must themselves be treated as quantum, motivating the use of quantum reference frames. In this work, we address how such a relational description could be formulated within linearized quantum gravity. To this purpose, we introduce quantum reference fields, i.e. sets of four dynamical scalar fields whose stress-energy tensors enter the gravitational constraints. These fields extend the notion of quantum reference frames to local field-theoretic reference systems, allowing matter and gravitational degrees of freedom to be described relationally with respect to physical quantum systems. By generalizing the perspective-neutral construction of quantum reference frames, we show that relational, gauge invariant observables admit reduced descriptions in the perspective of each quantum reference field, and we derive the unitary transformations relating them. The resulting unitary maps implement local quantum coordinate changes between different internal perspectives, and act on the linearized gravitational field with an analogous structure to a linearized diffeomorphism, but with the classical gauge parameter replaced by a physical quantum field. Finally, we construct a relational von Neumann-type measurement scheme, showing how the corresponding reduced observables can be accessed operationally from the perspective of a quantum reference field.

14.
arXiv (CS.CL) 2026-06-19

NEST: Narrative Event Structures in Time for Long Video Understanding

Recent progress in vision-language models has enabled the processing of increasingly long video sequences, but the ability to handle extended token streams does not translate to understanding of narrative structure in long videos. Existing long video benchmarks focus on needle-in-a-haystack retrieval rather than evaluating how low-level actions form events, how events interact across time, and how narratives progress, for example, whether a model can connect an early setback, such as a job loss to a later relationship breakup, despite long gaps, intervening scenes, or flashbacks that reframe what occurred. We introduce NEST (Narrative Event Structures in Time for Long Video Understanding), a dataset of 1005 full-length movies (avg. 98 minutes), each annotated with 102 multimodal narrative events grounded in visual content, dialogue, and audio. NEST captures multimodal narrative events with structured annotations grounded in visual content, dialogue, and audio, and links them through relations that reflect narrative structure, including temporal ordering, hierarchical composition, and long-range dependencies. We introduce baselines for event trigger detection (ETD), event localization (EL), event argument extraction (EAE), and event relation extraction (ERE). The benchmark is highly challenging for grounded event discovery, with ETD below 8%, EL under 6%, and EAE below 11%. In contrast, ERE is more tractable once events are given, reaching 35.45% F1 zero-shot and 44.42% F1 after fine-tuning.

15.
arXiv (CS.CL) 2026-06-11

Verifiable Environments Are LEGO Bricks: Recursive Composition for Reasoning Generalization

Reinforcement Learning (RL) with verifiable environments has emerged as a powerful approach for enhancing the reasoning capabilities of Large Language Models (LLMs). While prior research demonstrates that scaling environment quantity improves RL performance, existing manual or individual construction methods suffer from linear scaling limits, thereby hindering scalable reasoning generalization. This paper introduces RACES (Recursive Automated Composition for Environment Scaling), a framework that conceptualizes verifiable environments as composable building blocks that can be recursively assembled. The key insight is that when the codomain (output type) of one environment matches the domain (input type) of another, they can be automatically fused into a new verifiable environment, enabling recursive composition. RACES is implemented with 300 individual environments and defines a set of composition operators (\textsc{SEQUENTIAL}, \textsc{PARALLEL}, \textsc{SORT}, and \textsc{SELECT}) that induce diverse reasoning patterns. Extensive experiments show that RL training on these composite environments consistently enhances reasoning generalization. Specifically, RACES improves DeepSeek-R1-Distill-Qwen-14B by an average of 3.1 points (from 48.2 to 51.3) and boosts Qwen3-14B performance from 58.8 to 61.1 on six benchmarks, which are unseen during the construction of training environments. Moreover, RACES achieves performance comparable to training on 300 individual environments using only 50 base environments, demonstrating significant efficiency in environment utilization.

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

Seeing Roads Through Words: A Language-Guided Framework for RGB-T Driving Scene Segmentation

Robust semantic segmentation of road scenes under adverse illumination, lighting, and shadow conditions remain a core challenge for autonomous driving applications. RGB-Thermal fusion is a standard approach, yet existing methods apply static fusion strategies uniformly across all conditions, allowing modality-specific noise to propagate throughout the network. Hence, we propose CLARITY that dynamically adapts its fusion strategy to the detected scene condition. Guided by vision-language model (VLM) priors, the network learns to modulate each modality's contribution based on the illumination state while leveraging object embeddings for segmentation, rather than applying a fixed fusion policy. We further introduce two mechanisms - one which preserves valid dark-object semantics that prior noise-suppression methods incorrectly discard, and a hierarchical decoder that enforces structural consistency across scales to sharpen boundaries on thin objects. Experiments on the MFNet dataset demonstrate that CLARITY establishes a new state-of-the-art (SOTA), achieving 62.3% mIoU and 77.5% mAcc.

17.
arXiv (CS.LG) 2026-06-16

Inference-Time Decision Calibration for Temporal Classification

arXiv:2606.16034v1 Announce Type: new Abstract: Temporal classification errors are often treated as representation failures, but they can also arise from how available evidence is converted into decisions. This paper proposes a representation–calibration decomposition for temporal classification. We keep a trained native classifier frozen and separate two inference-time interventions: a conservative residual multi-scale branch that adds auxiliary logits to the native prediction, and a post-hoc branch-aware calibrator that recombines native and residual evidence at decision time. This design distinguishes missing temporal evidence from underused decision-level evidence without retraining the backbone. Across FI-2010, PTB-XL, UCI-HAR, MHEALTH, and HARTH, we find that gains are strongly regime-dependent. Residual multi-scale evidence is most useful in noisy or representation-limited settings, especially short-horizon FI-2010 and weaker recurrent backbones, while branch-aware calibration helps when native and auxiliary logits contain complementary evidence not fully exploited by the raw decision rule. Near-saturated settings show limited gains from either intervention. These results suggest that temporal classification should be understood not only as representation learning, but also as the problem of trusting, combining, and calibrating evidence from multiple views.

18.
medRxiv (Medicine) 2026-06-16

Presurgical immune biomarkers associated with pain intensity and pain interference recovery after total knee arthroplasty: findings from the PRIME-KNEE study

Chronic postsurgical pain (CPSP) prevalence after total knee arthroplasty (TKA) is >20%. Circulating immune biomarkers are known factors of musculoskeletal pain but poorly understood as CPSP predictors. This prospective, longitudinal study of 203 patients s/p TKA tested presurgical plasma biomarkers associated with 6-month CPSP, using promising approaches from geriatrics biomarker research: expected recovery differential (ERD; resilience outcome) and penalized, machine-learning regularization modeling (elastic net and LASSO regression). Forty-nine presurgical candidate biomarkers were considered. CPSP was operationalized using ERDs built around PROMIS pain intensity and pain interference, which quantified the difference between observed and expected recovery after accounting for demographic, comorbidity, reserve, and perioperative factors. Plasma/ERDs from ~130 patients revealed 13 biomarkers with the highest selection stability criteria, and either positive or negative (+/-) associations with ERDs. Interleukin (IL) 5 (-) and Lipopolysaccharide-Binding Protein (LBP; +) were associated with both ERDs. Unique associations with pain intensity ERD included Cytomegalovirus-Specific IgG Negative (CMV IGg-; -), Macrophage Inflammatory Protein-1 Beta (MIP1b; -), IL12p70 (-, Cluster of Differentiation 30 (sCD30;-), Interferon alpha 2a (IFN2a;+), and Leukemia Inhibitory Factor (LIF;+). Unique associations with pain interference ERD included Lipopolysaccharide (LPS;-), Activin A (-), IL8 (-), Serum Amyloid A (SAA;-), and IL7 (+). Protein-protein interaction analyses and topology motifs suggest a centralized network with higher-than-expected connectivity, involving IL5, IL7, IL8, MIP1{beta}, and IFN2a, among others. This study proposes rigorous yet feasible approaches to expedite pain biomarker research, and introduces presurgical biomarkers t0 consider in future TKA-CPSP biosignature derivation.

19.
arXiv (CS.AI) 2026-06-15

Hidden in Plain Sight: Benchmarking Agent Safety Against Decomposition Attacks with DECOMPBENCH

arXiv:2606.13994v1 Announce Type: cross Abstract: LLM-based Agents are becoming increasingly capable and widely deployed, creating growing incentives for adversarial misuse in the real-world. A key emerging threat is Decomposition Attacks [glukhov2024breach, jones2024adversaries] in which a harmful task is broken into simpler, benign subtasks that evade safety mechanisms when executed separately but cumulatively fulfill the malicious intent. Although recent benchmarks assess agent safety in multi-turn and multi-tool-use settings, they do not explicitly capture this form of decompositional misuse and may not represent realistic adversarial execution flows. To this end, we introduce DeCompBench, a benchmark designed specifically to evaluate agentic safety under decomposition attacks. DeCompBench is created with a decomposition-by-design principle using a graphical framework and enables harmful task decomposition into individually benign and executable subtasks with realistic workflows. Our experiments using a custom decomposer show that state-of-the-art agents exhibit high refusal rates on monolithic harmful tasks, but significantly lower refusal rates on their decomposed variants, while often inadvertently fulfilling the adversarial objectives. These findings underscore the need for safety evaluations against decomposition attacks and corresponding defenses. Our dataset is publicly available and can be found at https://huggingface.co/datasets/decompositionbench/DeCompBench.

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

Distributional Biases in Post-Training: A Markovian Analysis of Reasoning Trajectories

arXiv:2511.07368v3 Announce Type: replace-cross Abstract: Foundation models exhibit broad knowledge but limited task-specific reasoning, motivating post-training strategies such as RL with verifiable rewards (RLVR) and test-time scaling (TTS). While recent work highlights the role of exploration in improving pass@K, empirical evidence points to a paradox: RLVR and ORM/PRM typically reinforce existing paths rather than expanding the reasoning scope, raising the question of why exploration helps if no new patterns emerge. To reconcile this paradox, we adopt the perspective of Kim et al. (2025), viewing easy (e.g., simplifying a fraction) versus hard (e.g., discovering the some symmetry) reasoning steps as low versus high probability Markov transitions. In this tractable model, pretraining corresponds to tree-graph discovering, while post-training corresponds to CoT reweighting. We provably show that, both RLVR and ORM/PRM would favor heavily to several high-probability paths, and thereby forget rare-but-crucial CoTs. Building on this, we further prove that exploration strategies such as rejecting easy instances and KL regularization help preserve rare CoTs. Empirical simulations corroborate our theoretical results.

21.
bioRxiv (Bioinfo) 2026-06-13

Virus-human protein-protein interactions predict viral phenotypes

Viral phenotypes such as host and tissue tropism are critical determinants of viral infection and transmission. Inferring viral phenotypes presents unique challenges compared to cellular organisms, as viruses rely entirely on host machinery for replication and survival. Current methods for predicting viral phenotypes mainly rely on viral genomic data, often overlooking host-related information. Here, we evaluated the utility of predicted virus-human protein-protein interactions (PPIs) in inferring diverse viral phenotypes using machine-learning algorithms. For predicting human infectivity, a PPI-based machine learning model outperformed both virus genomic and protein sequence-based models that used large language model embeddings. It also surpassed previous methods that incorporated both viral and host genomic data. The human proteins identified by the model were significantly enriched in functions related to viral infection and immune response. In predicting various phenotypes of human RNA viruses, PPI-based models performed better than virus sequence-based models in forecasting virulence, human transmissibility and transmission routes, while showing comparable performance to genomic sequence-based models in predicting tissue tropism. Finally, we demonstrated that a PPI-based model could distinguish high-risk HPV genotypes from low-risk ones. Proteins associated with high-risk HPV were involved in apoptosis and immune regulation, whereas those linked to low-risk HPV were enriched in telomere maintenance and DNA repair. Collectively, this study is the first to demonstrate the value of predicted virus-human PPIs in inferring viral phenotypes, thereby enhancing our understanding of the molecular mechanisms underlying these phenotypes. It also provides effective tools for risk assessment of emerging viruses, contributing to improved pandemic preparedness.

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

Vision-Encoder Behavioral Fingerprints of Image-to-Image Generative Models: A Training-Paradigm-Driven Taxonomy of Six Commercial APIs

作者:

We study six production image-to-image AI systems (gpt-image-1, Gemini 2.5 Flash Image, Flux Kontext, SDXL img2img, SD3 img2img, and Qwen Image Edit) under a content-adaptive sub-JND adversarial perturbation pipeline, scoring all outputs by frozen DINOv2 ViT-B/14 token distances against clean references. Across a 3,588-call corpus spanning COCO photographs, CelebA-HQ portraits, and AI-generated inputs, the six systems partition into two image-invariant behavioral bands on a 2D (patch_mean, ssim_clean) plane: edit-trained models (Flux Kontext, Qwen Edit, Gemini) cluster in a tight band, while T2I-base models adapted at sampling time (SDXL, SD3, gpt-image-1) cluster in a drift band.

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

Multiple Descents in Deep Learning as a Sequence of Order-Chaos Transitions in LSTM Networks

arXiv:2505.20030v2 Announce Type: replace-cross Abstract: We observe a novel `multiple-descent' phenomenon during the learning process of a recurrent neural network called long-short-term memory (LSTM) networks during its training on real-world task, in which the performance goes through long cycles of up and down trends multiple times after the model is overtrained. By carrying out asymptotic stability analysis of the models, we found that the cycles in performance – indicated by loss function in test data – are closely associated with the phase transition process between order and chaos of the model, and the local optimal training step are consistently at the critical transition point between the two phases. More importantly, the most optimal point of the model usually occurs at the first transition from order to chaos, where the `width' of the `edge of chaos' is often the widest, allowing the best exploration of weight configurations for learning.

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

Generative causal testing to bridge data-driven models and scientific theories in language neuroscience

Representations from large language models are highly effective at predicting BOLD fMRI responses to language stimuli. However, these representations are largely opaque: it is unclear what features of the language stimulus drive the response in each brain area. We present generative causal testing (GCT), a framework for generating concise explanations of language selectivity in the brain from predictive models and then testing those explanations in follow-up experiments using LLM-generated stimuli.This approach is successful at explaining selectivity both in individual voxels and cortical regions of interest (ROIs), including newly identified microROIs in prefrontal cortex. We show that explanatory accuracy is closely related to the predictive power and stability of the underlying predictive models. Finally, we show that GCT can dissect fine-grained differences between brain areas with similar functional selectivity. These results demonstrate that LLMs can be used to bridge the widening gap between data-driven models and formal scientific theories.

25.
arXiv (CS.CV) 2026-06-12

GeoCFNet: Geometry-Aware Confidence Field Network for Robot-Assisted Endoscopic Submucosal Dissection

Advanced surgical robotics has made robot-assisted endoscopic submucosal dissection (ESD) a promising approach for the en-bloc resection of large lesions, with the potential to reduce recurrence and improve long-term outcomes. However, the technical complexity and risk of complications in ESD demand stable and precise visual guidance to maintain an accurate dissection corridor and a safe tissue margin. Dense confidence fields provide an effective representation for this purpose by describing both the preferred dissection region and its spatial transition to surrounding tissue. However, reliable confidence field estimation remains challenging in dynamic endoscopic scenes due to smoke, specular highlights, tissue deformation, weak texture, and the thin geometric structure of the target region. To address these challenges, we formulate dissection guidance as a geometry-aware confidence field estimation problem and propose GeoCFNet, a geometry-aware confidence field network built on a pretrained DINOv3 backbone. GeoCFNet integrates a Token-Differentiated Fusion module to aggregate class-token context with dense patch representations, a SegFormer decoder for confidence regression, and Geometry-Aware Spatial Regularization (GASR) to preserve spatial coherence and local geometric transitions. Experimental results show that GeoCFNet achieves RMSE 0.0480, PSNR 27.1995, SSIM 0.3397, and CC 0.2466, indicating accurate and geometrically stable confidence field estimation for robot-assisted ESD guidance.