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01.
arXiv (CS.CV) 2026-06-19

LaTtE-Flow: Layerwise Timestep-Expert Flow-based Transformer

Recent advances in multimodal foundation models unifying image understanding and generation have opened exciting avenues for tackling a wide range of vision-language tasks within a single framework. Despite progress, existing unified models typically require extensive pretraining and struggle to achieve the same level of performance compared to models dedicated to each task. Additionally, many of these models suffer from slow image generation speeds, limiting their practical deployment in real-time or resource-constrained settings. In this work, we propose Layerwise Timestep-Expert Flow-based Transformer (LaTtE-Flow), a novel and efficient architecture that unifies image understanding and generation within a single multimodal model. LaTtE-Flow builds upon powerful pretrained Vision-Language Models (VLMs) to inherit strong multimodal understanding capabilities, and extends them with a novel Layerwise Timestep Experts flow-based architecture for efficient image generation. LaTtE-Flow distributes the flow-matching process across specialized groups of Transformer layers, each responsible for a distinct subset of timesteps. This design significantly improves sampling efficiency by activating only a small subset of layers at each sampling timestep. To further enhance performance, we propose a Timestep-Conditioned Residual Attention mechanism for efficient information reuse across layers. Experiments demonstrate that LaTtE-Flow achieves strong performance on multimodal understanding tasks, while achieving competitive image generation quality with around 6x faster inference speed compared to recent unified multimodal models.

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

ResearchClawBench: A Benchmark for End-to-End Autonomous Scientific Research

AI coding agents are increasingly used for scientific work, but their end-to-end autonomous research capability remains difficult to verify. We present ResearchClawBench, a benchmark for evaluating autonomous scientific research across 40 tasks from 10 scientific domains. Each task is grounded in a real published paper, provides related literature and raw data, and hides the target paper during evaluation. Expert-curated multimodal rubrics decompose the target scientific artifacts into weighted criteria, enabling evaluation of target-paper-level re-discovery while leaving room for new discovery. We evaluate seven autonomous research (auto-research) agents under a unified protocol and seventeen native LLMs through the lightweight ResearchHarness. Current systems remain far from reliable re-discovery: the strongest autonomous agent, Claude Code, averages 21.5, and the strongest ResearchHarness LLM, Claude-Opus-4.7, averages 20.7, with an LLM frontier mean of only 26.5. Error analysis shows that failures concentrate in experimental protocol mismatch, evidence mismatch, and missing scientific core. ResearchClawBench provides a reproducible evaluation frontier for measuring progress toward autonomous scientific research.

03.
arXiv (quant-ph) 2026-06-17

Quantum Computing Algebra (QCA), the theory and implementation

arXiv:2606.17621v1 Announce Type: new Abstract: We present a real geometric algebra framework designed for the direct translation of the Dirac formalism into geometric algebra representations. Unlike previous approaches based on positive-definite signatures, QCA employs a split-signature construction that enables a natural realization of quantum states and operators while simplifying computational implementation. We further present an implementation of QCA using the GAALOP software and show how quantum gates and multi-qubit systems can be efficiently represented and generated computationally. As an application, we demonstrate the use of QCA in quantum game theory, where the real-algebraic formulation provides computational advantages for modeling entangled strategies and quantum interactions. The proposed framework establishes a practical bridge between the abstract formalism of quantum computation and efficient geometric algebra implementations.

04.
bioRxiv (Bioinfo) 2026-06-19

HTS-Oracle v2: Prospective AI-Guided Discovery and Experimental Validation of Small Molecule Modulators Across Multiple Targets

High-throughput screening (HTS) remains the cornerstone of early-phase small molecule discovery yet consistently underperforms against immunotherapy targets, yielding validated hit rates below 0.1%. Here we introduce HTS-Oracle v2, which features rigorous cross-validation that ensures honest performance estimates. HTS-Oracle v2 was trained and validated across four clinically significant immune checkpoint targets (CD28, ICOS, LAG-3, and TIGIT) achieving ROC-AUC values of 0.968, 0.969, 0.875, 0.928 respectively under rigorous cross-validation. For prospective experimental validation, HTS-Oracle v2 was applied to an 8,960-compound Enamine Protein Mimetic Library, selecting only 25 compounds per target for experimental testing using temperature-related intensity change (TRIC) technology, a 99.7% reduction in screening burden. HTS-Oracle v2 identified 4, 5, 4, and 6 validated binders from 25 prospectively selected compounds per target, corresponding to validated hit rates of 16%, 20%, 16%, and 24%, respectively. Notably, 67-80% of all experimentally confirmed hits across the full 8,960-compound library were captured within just 25 model-selected compounds per target. For CD28, this represents a 28-fold improvement over HTS-Oracle v1 (239x versus 8.4x), establishing HTS-Oracle v2 as an efficient platform for AI-guided prospective hit discovery across immunotherapy targets.

05.
arXiv (quant-ph) 2026-06-16

Optimizing Wigner Negativity in Scattering Processes Using Energetic Cost Functions

arXiv:2606.15101v1 Announce Type: new Abstract: Wigner negativities (WNs) are key signatures of non-Gaussian bosonic states and essential resources for quantum technologies. We study their generation in the scattering of coherent pulses by a two-level atom coupled to a one-dimensional reservoir, a unitary and energy-preserving platform. Optimization in this multimode setting is hindered by the complexity of evaluating Wigner functions. We overcome this challenge by introducing energetic cost functions that identify output modes most likely to host large negativities. First using incoherent energy and then isolating a genuinely non-Gaussian contribution, we demonstrate a strong correlation between these quantities and WNs. This correlation extends beyond short, intense pulses to encompass pulses of finite energy, where photons are scattered while the two-level atom is driven. Focusing on the energy-efficiency of the process, we show that maximally efficient generation takes place for one input photon, on average, spectrally mode-matched with the atom.

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

BALTO: Balanced Token-Level Policy Optimization for Hallucination Mitigation

Hallucinations remain a major obstacle to deploying large language models (LLMs) in knowledge-intensive settings, where generated responses must be faithfully grounded in provided evidence. Reinforcement learning (RL) is a promising direction for hallucination mitigation, but response-level faithfulness rewards suffer from a granularity mismatch: localized hallucinations can cause supported content to receive spurious penalties. Although recent work introduces fine-grained feedback such as claim-level verification and token-level rewards, unbalanced credit assignment can still induce length, verbosity, or optimization-noise biases. We propose BALTO, a Balanced Token-level Policy Optimization framework for hallucination mitigation. BALTO extracts checkable factual claims, verifies them against the reference context, and projects claim-level judgments to token-level labels. A balanced token-level credit assignment mechanism is introduced into the framework. This design redistributes probability mass from unsupported content toward faithful content, rather than suppressing the entire response. We systematically analyze the limitations of response-level rewards from a theoretical standpoint, and prove BALTO's advantages in training stability and optimization efficiency for hallucination mitigation. Experiments on ConFiQA, RAGTruth, and FinLLM-Eval show that BALTO achieves the highest faithfulness across all six model–benchmark settings and consistently outperforms existing post-training baselines in Q-Score, demonstrating a stronger faithfulness–informativeness trade-off.

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

BOUTEF: A Multilingual Corpus for FakeNews in North Africa – Language as a Weapon

The rapid spread of fake news on social media has become a major challenge, particularly in multilingual and under-resourced contexts such as North Africa. In this paper, we introduce BOUTEF, a large-scale multilingual corpus designed to study the propagation, characteristics, and impact of fake news in Algeria and Tunisia. The corpus integrates three complementary components: fake narratives, genuine narratives, and associated user-generated comments, along with verified debunking information. It covers a wide range of languages and linguistic varieties, including MSA, Algerian and Tunisian dialects, Arabizi, French, English, and code-switched language. Building on this resource, we conduct a comprehensive empirical analysis combining quantitative and qualitative approaches. We examine thematic distributions, linguistic and rhetorical strategies, sentiment patterns, and social engagement dynamics. Statistical analyses reveal significant associations between thematic categories and message veracity, as well as strong correlations between user engagement and the visibility of fake content. Our findings show that fake news relies heavily on emotionally charged narratives, sensational framing, and hybrid linguistic practices that enhance virality and audience engagement. In contrast, debunking content adopts a more factual and verification-oriented style. Furthermore, a comparative analysis between Algeria and Tunisia highlights both shared dynamics and country-specific characteristics shaped by sociopolitical contexts. The results emphasize the role of informal language practices in the diffusion and reception of misinformation. By providing a rich, annotated, and publicly available dataset, this work contributes to advancing research on fake news detection, low-resource language processing, and the understanding of information disorders in complex linguistic environments.

08.
medRxiv (Medicine) 2026-06-18

Guiding the development of climate counterfactuals for health impact attribution studies

Climate change detection and attribution (D&A) methods have become vital for quantifying the influence of anthropogenic forcing on the Earth's systems, including human health. Health impact attribution (HIA) studies seek to disentangle climate-driven health effects from natural variability yet are often constrained by the availability of accessible counterfactual climate scenarios. This tutorial paper presents a flexible, reproducible framework for developing counterfactual climates without reliance on computationally intensive global circulation models. We provide practical, R-based methodologies for constructing both trend-based (temperature and non-temperature) and event-based counterfactual, using a variety of techniques including model residual detrending, data-driven decomposition (e.g., Singular Spectrum Analysis and Empirical Mode Decomposition) and stochastic weather generators. The tutorial also explores the incorporation of greenhouse gas concentrations as forcing variables, rather than global mean temperature anomalies. By operationalising these methods through worked examples and an open code repository, this paper aims to build capacity within the HIA community, enhance methodological transparency, and foster interdisciplinary collaboration between climate and health researchers.

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

An Ensemble Deep Learning Approach for Reliable and Scalable Lemon Leaf Disease Classification

Early detection of plant diseases is crucial to plants and for the farmers. Plant diseases reduce fruit yield and quality, and plants are more susceptible to other stresses when they are infected. The lemon leaf disease dataset contains 1354 images. The dataset has 9 classes. Among the 9 classes only one class is for healthy leaf, and the other 8 classes are leaf diseases. The dataset was split into training (70%), testing (15%) and validation (15%) sets after comprehensive preprocessing. Two pretrained models (InceptionV3 and MobileNetV2) were applied and then combined these models using an ensemble technique to boost robustness. Ensemble models showed a promising performance of 99.27% accuracy. Adversarial Training is applied to improve models' ability and ensure reliable predictions under noisy data. Grad-CAM visualization highlights the important regions of leaf images that validate the model prediction with confidence level.

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

Benchmarking Instance-Dependent Label Noise with Controlled Corruptions

arXiv:2606.14965v1 Announce Type: new Abstract: Synthetic instance-dependent label noise (IDN) benchmarks are widely used to evaluate noisy-label learning methods, yet existing approaches typically generate noise through imperfect annotators or classifier raters, leaving the source of ambiguity implicit. We introduce CILN, a benchmark generation framework that creates IDN through controlled input corruptions. A diverse voter pool labels corrupted instances, producing benchmark datasets in which both the source and severity of ambiguity are explicit and controllable. Using CIFAR10, MNIST, and Adult, we construct 90 benchmark settings spanning multiple corruption families and severity levels. Our experiments show that the resulting benchmarks exhibit genuine instance-dependent noise, provide diverse confusion structures, and, on CIFAR-10, can produce label distributions that are closer to human uncertainty than an existing synthetic IDN benchmark. We further demonstrate that corruption-mediated IDN can expose failure modes of popular noisy-label learning methods, including Co-Teaching and DivideMix, that are not observed under comparable levels of rater-fallibility noise. These findings suggest that noise structure, not only noise rate, plays an important role in benchmark difficulty and algorithm behavior. By making ambiguity generation explicit and controllable, CILN provides a complementary benchmarking framework for studying noisy-label learning under diverse sources of instance difficulty.

12.
bioRxiv (Bioinfo) 2026-06-18

Accounting for allelic diversity and multicopy gene detection improves the accuracy of antibiotic resistance genotypic determination

Background Genomic prediction of antimicrobial resistance (AMR) relies on the accurate detection of resistance genes or allelic variants of core genes from raw or assembled genomes sequences. For several bacterial species and antibiotics, AMR genotype-phenotype discrepancies are common, indicating that important sources of error remain unresolved. For Enterococcus faecium, we focused on identifying the sources of discrepancies for tetracycline resistance, for which genotypic detection had shown particularly low accuracy. We investigated the effect of structural variation in antibiotic resistance genes (ARGs), including gene duplications, truncations, interruptions, and mixed configurations of complete and partial gene copies, as a source of genotype-phenotype discrepancies from short-read data. We conduct further extended investigations to other antibiotic families and into another bacterial species: Escherichia coli. Methods We analyzed collections of E. faecium and E. coli genomes, integrating high-quality complete assemblies, simulated Illumina short reads, and matched AMR phenotypic data. The integrity, copy number, and allelic diversity of ARGs were examined for multiple antibiotic classes, and their impact on ARG detection and accuracy of AMR determination was assessed using several commonly used bioinformatic tools (SRST2, ARIBA and AMRFinderPlus). Results For E. faecium, after ruling out the effect of specific tet allelic variants on tetracycline susceptibility, we found that the integrity and copy number of tet(M) had a major effect on detection accuracy. Duplicated and incomplete ARGs are also common in E. faecium genomes, particularly for macrolides (erm(B)) and aminoglycosides (ant(6)-Ia and aph(3')-IIIa). In E. coli, similar patterns were observed for tet(A), erm(B) and aminoglycoside-associated genes (aph(3')-IIIa and ant(6)-Ia). Across ARGs in both species, short-read mapping methods wrongly reported interrupted genes as complete in some instances, while assembly-based methods often failed to resolve complete copies of duplicated genes. Detection accuracy improved when tools were adapted to account for gene integrity and when extended AMR databases incorporating species-specific alleles were included. Conclusions Our findings reveal that bioinformatic limitations in dealing with ARG copy number and completeness, and in accounting for allelic variation, underly a substantial source of genotype-phenotype errors, highlighting the need for improved AMR databases and bioinformatic tools that consider these factors to achieve reliable genomic prediction of AMR.

13.
arXiv (CS.AI) 2026-06-17

Distributed General-Purpose Agent Networks: Architecture, Key Mechanisms, and Prototypes

arXiv:2606.17368v1 Announce Type: new Abstract: Large language models have accelerated the transition from passive conversational assistants to autonomous agents that can understand goals, plan actions, invoke tools, and execute multi-step tasks. Yet the capability of a single agent remains constrained by its local data, tool permissions, runtime environment, and governance boundary. This paper studies distributed general-purpose agent networks: open peer-to-peer networks in which heterogeneous agents deployed on personal devices, edge nodes, or autonomous computing environments can discover one another, establish trust, negotiate cooperation rules, and execute open-ended tasks. We argue that such networks cannot be obtained by simply combining existing peer-to-peer overlays with conventional multi-agent systems. Unlike traditional P2P networks, agent networks must propagate semantic declarations about intentions, capabilities, states, and cooperation constraints. We therefore propose a layered architecture centered on a protocol adaptation layer that connects upper-level task semantics with lower-level network operations. Based on this architecture, the paper identifies three core mechanism problems: semantic announcement propagation for collaborator discovery, verifiable identity and multi-topic reputation for cooperation governance, and semantic-gradient mechanism design for open task execution. For each problem, we present a technical route, including bodyless gossip with sequential logs, BAID-based identity binding with MG-EigenTrust reputation, and a Stackelberg-style mechanism-generation loop driven by semantic attribution feedback. We further report prototype overhead results for BAID-style tiered verification and mechanism-level simulations of MG-EigenTrust under cross-topic disguise-collusion attacks. The resulting framework provides a system-level foundation for open, trustworthy, and scalable agent collaboration.

14.
medRxiv (Medicine) 2026-06-16

Comparative Effectiveness and Safety of Prophylactic Vasopressors for Preventing Post-induction Hypotension in the Elderly: A Systematic Review and Network Meta-analysis

Background: Post-induction hypotension is a predictable haemodynamic hazard in older adults undergoing general anaesthesia. Prevention remains divided among volume optimisation, anaesthetic dose reduction, rescue treatment after hypotension occurs and proactive vasoactive support. Methods: We searched PubMed, Embase, Web of Science, CENTRAL, CNKI, Wanfang and VIP from inception to 30 March 2026. Eligible studies were randomised trials of prophylactic vasoactive drugs given before, during or immediately after induction in older adults. The primary outcome was post-induction hypotension. Secondary outcomes were post-induction mean arterial pressure (MAP), systolic arterial pressure (SBP), heart rate (HR) and reported haemodynamic adverse events. Random-effects network meta-analysis was used, and confidence in network estimates was assessed using CINeMA principles. Results: Thirty-one trials including 2,821 participants were included in the revised network. Compared with placebo/control, all active agents favoured lower post-induction hypotension. The most favourable point estimates were observed for phenylephrine (odds ratio [OR] 0.17, 95% confidence interval [CI] 0.01 to 2.16) and metaraminol (OR 0.19, 95% CI 0.02 to 1.53), although both were imprecise. More precise reductions were observed for methoxamine (OR 0.23, 95% CI 0.13 to 0.43), norepinephrine (OR 0.25, 95% CI 0.13 to 0.47) and ephedrine (OR 0.34, 95% CI 0.19 to 0.63). Phenylephrine ranked highest for MAP support, norepinephrine ranked highest for SBP support, and ephedrine ranked highest for HR preservation. Global inconsistency was detected for SBP but not for hypotension incidence, MAP or HR, supporting cautious profile-based interpretation. Conclusions: Prophylactic vasopressor choice during induction should be guided by haemodynamic phenotype rather than ranking alone. In the revised network, active prophylaxis consistently favoured lower hypotension, but sparse nodes produced uncertainty. Norepinephrine retained a comparatively balanced profile when vasodilatory post-induction hypotension is anticipated, phenylephrine and related alpha-agonists provided stronger pressure support when HR and cardiac-output reserve are preserved, and ephedrine was most relevant when chronotropic support is desired. Keywords: general anaesthesia; induction; hypotension; norepinephrine; phenylephrine; ephedrine; network meta-analysis; older adults.

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

Exploration Structure in LLM Agents for Multi-File Change Localization

arXiv:2606.11976v1 Announce Type: cross Abstract: Software engineering tools increasingly rely on LLM based agents to localize files to change to resolve a software issue. Most AI agents explore repositories linearly, that is, visiting one directory or file per step. We postulate that this is a structural mismatch for changes that span several subsystems. We compare linear sequential exploration against non-linear, domain-scoped parallel agentic exploration. Using SWE Bench Pro as initial benchmark, we focus on ansible as an exemplar. We construct an approach for persistent-session evaluation of GitHub issues anchored at a single base commit. We compare our non-linear domain-agent file traversal system against a base LLM without direct repository access, a single agent Recursive Language Model (RLM) baseline with a persistent Python REPL and an external CLI baseline using Codex 5.5 High. Domain scoped parallel agent spawning with a small Haiku-class model achieves the highest micro F1 among Haiku class models by a large margin. Domain-agents is the second highest behind only the much larger Codex 5.5 High on our own expanded benchmark including over more recent PRs from 2025 and 2026. On the original, curated, 2020 SWE-bench Pro benchmark, a larger Sonnet plain LLM baseline attains higher micro F1 by predicting few files, leading to higher precision, but at significantly lower all gold recall. We also present three additional findings. First, documentation evolution is a latent dependency unresolved by any approach. Second, naive file system access can degrade localization driven by test-file over prediction. Lastly, forced multi-agent consultation does not measurably help and raises token cost substantially.

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

Beyond Safe Data: Pretraining-Stage Alignment with Regular Safety Reflection

arXiv:2606.19168v1 Announce Type: new Abstract: To achieve deeper safety alignment for large language models (LLMs), recent efforts have studied how to push safety interventions earlier into the pretraining stage, primarily by filtering unsafe data or rewriting it into safer forms. We argue that pretraining-stage alignment should go beyond making the data safe: LLMs may compose seemingly benign knowledge and capabilities into unsafe behaviors. To this end, we propose Safety Reflection Pretraining, a pretraining-stage alignment method which regularly inserts short safety reflections into pretraining corpora to integrate self-monitoring directly into language modeling, establishing a foundational capability that is subsequently reinforced by compatible post-training. Our experiments with 1.7B models pretrained on FineWeb-Edu show that Safety Reflection Pretraining improves safety classification accuracy and substantially reduces the success rates of inference-stage and finetuning attacks. Complementary to our real-world experiments, we also introduce a fully controlled synthetic environment, MedSafetyWorld, with a clear definition of safety and a reasoning structure under which models can easily generalize unsafe behaviors from safe data. Ablations in MedSafetyWorld further demonstrate a clear advantage of Safety Reflection Pretraining in preventing models from acting on unsafe behaviors generalized from safe data, compared with data filtering and rewriting. Taken together, our findings suggest that pretraining alignment should not only make the training data safe, but also shape the behaviors that models are likely to acquire from safe data.

17.
arXiv (CS.LG) 2026-06-12

$\alpha$-fair heterogeneous agent reinforcement learning

arXiv:2606.13076v1 Announce Type: cross Abstract: Cooperation in multi-agent systems is typically optimized through utilitarian objectives that maximize overall efficiency but fail to account for reward distribution, often resulting in inequitable "leader-follower" dynamics. While fairness-based approaches encourage pro-social behaviors where every agent benefits from cooperation, many current algorithms - including those utilizing reward shaping - break the stationarity of Markov Games or lack rigorous theoretical guarantees. This creates a critical gap between fair objective methods and theoretically safe learning frameworks. We propose a novel framework that bridges $\alpha$-fairness with Heterogeneous-Agent Trust Region Learning (HATRL), ensuring monotonic improvement and convergence toward Nash Equilibria. Our approach leverages a fair advantage function that dynamically weights agent utilities based on their expected returns, allowing the global objective to transition from purely utilitarian efficiency to $\alpha$-fairness welfare based on the parameter $\alpha$. We introduce two practical algorithms, $\alpha$-fair HATRPO and $\alpha$-fair HAPPO, and demonstrate through experiments in sequential social dilemmas like CleanUp and CommonHarvest that they perform better than HATRL's algorithms from a utilitarian point of view while achieving socially higher outcomes.

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

Uncertainty Estimation for Molecular Diffusion Models

arXiv:2606.13451v1 Announce Type: new Abstract: Diffusion models have seen wide adoption for 3D molecular generation, yet they offer no principled signal of when a generated molecule is likely to be of low quality. We propose a post-hoc method for estimating per-sample uncertainty in pretrained molecular diffusion models. Building on a Laplace approximation of the denoising network, we measure the variability of the noise prediction across the generation trajectory. Empirically, we show that the resulting uncertainty score is informative of sample quality, exhibiting a negative correlation with established sample-level quality metrics. We further study how the proposed uncertainty score can be used to filter generated samples, improving model performance via test-time scaling.

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

CellNet – Localizing Cells using Sparse and Noisy Point Annotations

Counting living cells is an important step in many biological research workflows. Our collaborators at the Wellcome Sanger Institute study vital genes in humans via large scale saturation genome editing screening, which requires repeatedly counting cells a great number of times. Computer Vision based automation is crucial for high throughput and resource efficiency. In this work, we develop a regression-based deep learning computer vision algorithm to detect and count cells in phase-contrast microscopy images. To reduce annotation effort, which in practice often becomes a bottleneck, we focus on counting cells only using sparse point annotations, which are fast and easy to acquire. By comparison to state-of-the-art 0-shot methods, we show that regression-based counting is a promising alternative in low data regimes. Through developing methods to automatically count living cells in microscopy images, we contribute to valuable research on the human genome. The code is available at https://github.com/beijn/cellnet.

20.
arXiv (CS.CV) 2026-06-19

Gaussian Process Prior Variational Autoencoder for Endoscopic Videos

Endoscopic video analysis is essential for gastrointestinal diagnosis and computer-assisted interventions, but video sequences are routinely degraded by specular reflections, motion artifacts, and missing frames. These transient corruptions can distract clinicians, reduce image interpretability, and disrupt downstream tasks such as 3D reconstruction and navigation. Effective restoration therefore requires methods that exploit temporal continuity rather than treating frames in isolation. We introduce a Gaussian Process Prior Variational Autoencoder (GPVAE) framework for endoscopic video restoration that replaces the standard factorized latent prior with a temporal Gaussian process prior, enabling interpolation of missing frames with uncertainty-aware reconstruction. The framework combines endoscopy-specific encoders, including a convolutional EndoVAE backbone and pretrained Vision Transformer encoders from GastroNet-5M, with two scalable GP approximations: Hierarchical Prior Approximation (HPA) and Sparse Precision Approximation (SPA). Specular reflections are handled using a DUCKNet-based masking pipeline that excludes corrupted pixels from the reconstruction objective. On the C3VDv2 colonoscopy dataset, the best GPVAE variants reduced image reconstruction RMSE by 21.9\% on average, and by up to 26.1\%, relative to matched VAE baselines. Downstream trajectory RMSE was reduced by 12.7\% on average across classical visual odometry and a pretrained PoseNet, at an average increase of 27.3\% in training time per epoch. Finally, the GP posterior provides per-frame uncertainty estimates that reflect temporal support and offer a confidence signal for restored frames.

21.
arXiv (CS.AI) 2026-06-16

A Multi-Level Architecture for Reusable Materials Ontologies – The OntoCrafter Ceramics Ontology (OCO) as Reference Implementation

arXiv:2606.14814v1 Announce Type: cross Abstract: The Materials Science and Engineering ontology landscape is fragmented along multiple axes simultaneously. Horizontally: a recent survey identified 94 ontologies of which over 40 are structurally incompatible; each new application domain – ceramics, polymers, batteries, smart materials – typically restarts ontology design from scratch. Vertically: EU regulation (CSRD, CSDDD, PPWR, CBAM, R2R, AI Act, ESPR) forces material, manufacturing, supply-chain, and lifecycle data into integrated digital product passports, leaving ontologies that only address horizontal fragmentation incomplete for any contemporary consumer. And mechanistically: a vocabulary that records that BNT-BT has $d_{33} \approx 580$ pC/N stores a fact but cannot surface why – Bi-6s$^2$ lone-pair stereo-activity, anomalous Born effective charges, soft modes, defect chemistry – without a systematic explanation skeleton. We propose a multi-level modular architecture with two independent classification axes – level of abstraction (L0 bridges, L1 material-agnostic laboratory-notebook, L2 material-class-specific, L3 categorical reasoning) and consumer audience (material vs. compliance) – in which the material-specific level is internally organised by a seven-tier mechanistic-explanation skeleton (Symmetry, Energy/DFT, Thermo/CALPHAD, Kinetics, Microstructure, Defect chemistry, Bonding) applicable to any crystalline ionic oxide. The level-and-audience modularity dissolves the horizontal fragmentation, the compliance audience absorbs the vertical regulation pressure, and the seven-tier organisation of Level 2 delivers the mechanistic explanation depth. We instantiate the architecture as the OntoCrafter Ceramics Ontology (OCO v0.94): 5,196 classes across 44 modules; 167,348 OWL axioms (40,454 logical); 1,674 properties; 829 cross-ontology bridge mappings; 1,172 SHACL shapes; 163 published competency questions.

22.
arXiv (CS.LG) 2026-06-17

From Reasoning Traces to Reusable Modules: Understanding Compositional Generalization in Language Model Reasoning

arXiv:2606.18089v1 Announce Type: new Abstract: Post-training pipelines that combine supervised fine-tuning (SFT) with reinforcement learning (RL) have emerged as the key recipe for transforming large language models (LLMs) into robust reasoners. We argue that this combined success is driven by compositional generalization, which we formalize through a hierarchical latent selection model. In this framework, reasoning traces are generated by a cascade of discrete latent selection variables corresponding to reusable atomic modules, including both skills (local operations) and routing mechanisms (how intermediate information is selected, reused, and composed). Within this model, we theoretically show that SFT and RL play asymmetric, complementary roles: SFT supplies the raw module materials in compositional traces, and RL decomposes those traces to identify the latent atomic modules and enable compositional generalization. We design controlled experiments to validate this theory. Our results demonstrate that RL can extract atomic modules from compound traces supplied by SFT and recombine them to solve new configurations. Moreover, we find that training on compound traces yields stronger generalization than training on isolated atomic modules. Finally, we investigate the relationship between SFT and RL data and identify an effective protocol in which SFT ensures coverage of all atomic modules through compositional traces, while RL focuses on novel compositions outside the SFT support to drive exploration.

23.
arXiv (CS.CV) 2026-06-18

DVANet: Degradation-aware Visual-prior Alignment Network for Image Restoration

All-in-One image restoration aims to develop a unified restoration framework for handling diverse degradation types. Existing end-to-end methods usually regard the restoration process as a black-box mapping, lacking an explicit optimization interpretation. Although deep unfolding provides an interpretable iterative modeling paradigm for image restoration, existing methods mostly rely on fixed degradation assumptions or predefined degradation information, making them difficult to adapt to unified restoration requirements under complex degradations and locally damaged content. This limitation restricts their performance in degradation suppression and structural detail recovery. To address these issues, this paper proposes DVANet, a deep unfolding network inspired by the half-quadratic splitting optimization algorithm, which formulates unified image restoration under complex degradations as a collaborative unfolding process between degradation-aware observation consistency and visual-prior-guided reconstruction. Specifically, in the degradation-aware observation consistency branch, a degradation representation module is employed to extract global degradation attributes and local degradation cues, and degradation-conditioned mapping is used to enhance the model's adaptability to different degradation types. In the visual-prior-guided reconstruction branch, DINOv3 is introduced to provide structural and semantic information as hierarchical visual priors, thereby complementing the missing structural information in damaged regions and improving detail recovery. Extensive experiments demonstrate that DVANet achieves superior or competitive performance on multi-scenario degradation and cross-domain image restoration tasks, showing favorable degradation adaptability and generalization ability.

24.
arXiv (CS.CL) 2026-06-12

Direct Preference Optimization for Chatbot Fine-Tuning: An Empirical Study

We present an approach to fine-tuning large language models using Direct Preference Optimization (DPO), a reinforcement learning technique. Our experimental results demonstrate that DPO simplifies the training pipeline, improves computational efficiency, and achieves competitive performance. The evaluation using BLEU, ROUGE, and cosine similarity metrics indicates effective learning and convergence, though further investigation is needed to address observed training instability.

25.
arXiv (CS.CL) 2026-06-19

Prompt, Plan, Extract: Zero-Shot Agentic LLMs Workflows for Lung Pathology Extraction from Clinical Narratives

Information extraction from pathology reports is essential for cancer staging, tumor registry population. Yet key data remains embedded in narrative reports, making manual extraction labor-intensive and error-prone. Traditional supervised Natural Language Processing pipelines address this through fully supervised Named Entity Recognition and Relation Extraction, but require expensive manual annotation and suffer cascading failures when upstream entities are missed. In this study, we developed a zero-shot, agentic workflow, and evaluated five open-source generative Large Language Models (LLMs) to populate 13 College of American Pathologists synoptic fields from lung resection pathology reports. We compared them against a state-of-the-art supervised GatorTron NER-RE baseline using a novel, registry-aligned evaluation framework. The baseline achieved Micro-F1of 0.960, while the best zero-shot model (GPT-OSS-20B) achieved Micro-F1 of 0.893 (recall: 0.949), accurately extracting complex relations like Pathologic Stage without task-specific training. These results suggest that open-source, zero-shot agentic LLMs are a low-cost solution for extracting lung pathology information.