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01.
arXiv (CS.CV) 2026-06-11

Finding Sparse Subnetworks in One Training Cycle via Progressive Magnitude-Based Pruning

Neural network pruning reduces model size by removing less important parameters while aiming to preserve predictive performance. Although the Lottery Ticket Hypothesis (LTH) shows that sparse subnetworks can match dense networks when trained from suitable initializations, its iterative pruning procedure requires multiple complete training cycles. This work evaluates progressive magnitude-based pruning as a single-cycle alternative. The method gradually increases sparsity during training using a linear schedule and updates pruning masks based on active weight magnitudes. We conduct systematic experiments on CIFAR-10 and MNIST across ResNet, VGG-style, and LeNet architectures, comparing the proposed method with representative iterative and initialization-based pruning baselines, including LTH, SNIP, and GraSP. On CIFAR-10, the method achieves 95.12\% accuracy on ResNet-18 at 72.9\% sparsity, compared with 90.5\% reported for LTH. At extreme sparsity, it achieves 93.13\% accuracy on a VGG-like architecture at 97\% sparsity, compared with approximately 92.0\% for SNIP, and 93.44\% accuracy on VGG-19 at 97.97\% sparsity, compared with 92.19\% for GraSP at 98\% sparsity. A sparsity-accuracy analysis on ResNet-18 further shows that accuracy remains within 0.1 percentage points of the dense baseline across 70–85\% sparsity. These results indicate that progressive magnitude-based pruning provides an effective single-cycle approach for neural network sparsification under the evaluated settings.

02.
arXiv (CS.CL) 2026-06-12

EurekAgent: Agent Environment Engineering is All You Need For Autonomous Scientific Discovery

LLM-based agents have shown increasing potential in automating scientific discovery. Given an optimizable metric and an execution environment, they can propose, validate, and iterate scientific solutions, and have produced results that outperform human-designed approaches. As model capabilities continue to improve, we argue that the bottleneck for autonomous scientific discovery is shifting from prescribing agent workflows to designing agent environments: the resources, constraints, and interfaces that shape agent behavior. We frame this as environment engineering: building environments that amplify productive behaviors, such as open-ended exploration, systematic artifact management, and inter-agent collaboration, while suppressing harmful behaviors, such as reward hacking and high-friction human oversight. We present EurekAgent, an environment-engineered agent system for metric-driven autonomous scientific discovery. EurekAgent engineers the environment along four dimensions: permissions engineering for bounded agent execution and isolated evaluation; artifact engineering for filesystem and Git-based collaboration; budget engineering for budget-aware exploration; and human-in-the-loop engineering for easy human supervision and intervention. EurekAgent sets new state-of-the-art results on multiple mathematics, kernel engineering, and machine learning tasks, including new state-of-the-art 26-circle packing results discovered with less than $11 in total API cost. We open-source our code and results, and call for environment engineering as a core research direction for developing reliable autonomous research agents.

03.
arXiv (CS.CV) 2026-06-12

Modality-Aware Feature Matching in Visual and Vision-Language Applications: A Comprehensive Survey

Feature matching is a cornerstone task in computer vision, essential for applications such as image retrieval, stereo matching, 3D reconstruction, and SLAM. This survey comprehensively reviews modality-based feature matching, exploring traditional handcrafted methods and emphasizing contemporary deep learning approaches across various modalities, including RGB images, depth images, 3D point clouds, LiDAR scans, medical images, and vision-language interactions. Traditional methods, leveraging detectors like Harris corners and descriptors such as SIFT and ORB, demonstrate robustness under moderate intra-modality variations but struggle with significant modality gaps. Contemporary deep learning-based methods, exemplified by detector-free strategies like CNN-based SuperPoint and transformer-based LoFTR, substantially improve robustness and adaptability across modalities. We highlight modality-aware advancements, such as geometric and depth-specific descriptors for depth images, sparse and dense learning methods for 3D point clouds, attention-enhanced neural networks for LiDAR scans, and specialized solutions like the MIND descriptor for complex medical image matching. Cross-modal applications, particularly in medical image registration and vision-language tasks, underscore the evolution of feature matching to handle increasingly diverse data interactions.

04.
arXiv (CS.LG) 2026-06-15

Scalable Deep Unfolding of Conic Optimizers

arXiv:2606.13825v1 Announce Type: cross Abstract: Deep unfolding (DU) accelerates iterative optimizers by introducing learnable components and training them through unrolled iterations, but extending DU to the large-scale semidefinite programs (SDPs) common in robotics has remained limited. Unrolling a full-update conic solver such as COSMO exposes two obstacles that prior work on learned conic solvers has not: backpropagating through the per-iteration linear-system solve incurs memory quadratic in the problem size once the coefficient matrix is formed explicitly, and backpropagating through the positive semidefinite (PSD) cone projection becomes numerically unstable when eigenvalues coincide. We address the first obstacle with a matrix-free implicit differentiation rule that operates entirely through matrix-vector products, reducing memory from $O(n^2)$ to $O(n)$ and enabling backpropagation at scales where direct factorization runs out of memory. We address the second with a backward rule based on the Dalečkii–Krein representation of the Fréchet derivative, which remains well-defined under repeated eigenvalues. Together these make it possible to learn lightweight hyperparameter policies and warm-starts for a full-update conic solver. We evaluate on nonlinear covariance steering problems solved via sequential convex programming (SCP), as well as standalone SDPs and second-order cone programs ranging from max-cut and Lovász $\vartheta$ SDPs to robust estimation and control problems. The learned policies outperform state-of-the-art solvers across all problems, and can provide up to a 50$\times$ speedup depending on the class. When used as a subroutine in SCP, the learned approach delivers over a 30$\times$ speedup compared to COSMO.

05.
medRxiv (Medicine) 2026-06-23

Sex-Specific TMPRSS2 Response and Reduced Peripheral RNA Concentration Following AstraZeneca COVID-19 Vaccination in Nigeria.

Background: ChAdOx1 nCoV-19 remains a cornerstone COVID-19 vaccine in sub-Saharan Africa, yet population-specific molecular responses are understudied. We examined peripheral blood ACE2 and TMPRSS2 expression, total RNA concentration, and coagulation indices in Nigerians >=6 months post-vaccination. Methods: In a case-control study in Port Harcourt, Nigeria, 51 ChAdOx1-vaccinated adults and 51 age/sex-matched unvaccinated controls provided venous blood for RNA extraction, qRT-PCR, and coagulation assays. Multivariable linear models assessed effects of vaccination, sex, and age on molecular parameters. Results: Vaccinated participants had 37% lower total RNA concentration than controls (4.02 +/- 0.09 vs 6.38 +/- 0.14 ng/uL, p=6 months post-ChAdOx1, Nigerians show reduced peripheral blood RNA without sustained ACE2/TMPRSS2 upregulation. The sex-specific TMPRSS2 pattern suggests hormone and vaccine interactions previously unreported in African cohorts and highlights the need for sex-disaggregated molecular surveillance. Region-specific reference gene validation is recommended for Nigerian transcriptomic studies.

06.
medRxiv (Medicine) 2026-06-17

Adverse Childhood Experiences Reorganise the Brain-Personality Network Across the Psychosis Spectrum

Exposure to adverse childhood experiences is a pervasive risk factor for psychosis, exhibiting a linear relationship across the psychosis spectrum from subclinical schizotypal traits to schizophrenia spectrum disorders. While this association is often conceptualised within the vulnerability-stress framework, the systemic mechanisms through which childhood trauma reconfigures the brain-personality interactome remain poorly understood. We examined clinical, neuropsychological, and neuroimaging data from a sample of low- and high-schizotypy individuals, and patients with a diagnosis of schizophrenia spectrum disorder (N=120). Our aim was to map how trauma reconfigures interactions between neurobiology and schizotypal phenomenology. We adopted a mixed graphical model approach to jointly estimate conditional dependencies between childhood trauma, regional brain morphometry, and schizotypal traits across the psychosis spectrum. Our results show that childhood trauma reconfigures the brain-personality network, shifting it from a state driven by cognitive processes to one anchored in emotional (limbic) reactivity. This transition is marked by the increased influence of impulsive traits and a significant strengthening of connections within the salience network. These changes converge with a reduced thickness of the frontal executive regions, the brain's control centres, identified in our models. Collectively, our results suggest a structural phenomenological decoupling, where trauma conditioned affective circuits may bypass weakened top-down regulatory controls. These findings highlight the necessity of using integrative frameworks to capture how trauma fundamentally reshapes the relationship between the brain and schizotypal personality.

07.
medRxiv (Medicine) 2026-06-18

Instantaneous-Frequency EEG Microstate Dynamics Stratify Motor Subtypes in Parkinson's Disease

Parkinson's disease (PD) is clinically heterogeneous, yet objective electrophysiological markers of its postural-instability/gait-difficulty (PIGD) and tremor-dominant (TD) motor subtypes are lacking. We tested whether the temporal dynamics of instantaneous-frequency (IF) microstates in resting-state electroencephalography (EEG) distinguish these subtypes from each other and from healthy controls (HC). In a publicly available cohort (OpenNeuro ds007526) comprising 28 HC and 97 PD patients classified as PIGD (n=50) or TD (n=47), the spatial distribution of the IF was reduced by principal component analysis and modeled with a Gaussian hidden Markov model, yielding three recurrent microstates. Per-participant mean dwell time, occupancy, and state-transition probabilities were compared across the three groups and, within PD, correlated with clinical scores. We found that the dynamics of one microstate varied systematically across groups: its dwell time, occupancy, and self-transition probability increased monotonically from HC through TD to PIGD, while outgoing transitions decreased, so that the state became an increasingly persistent attractor. For dwell time, all three pairwise contrasts survived correction (HC versus PIGD, Hedges' g=1.06; HC versus TD, g=0.59; PIGD versus TD, g=0.40). None of the dynamic indices was associated with clinical severity, disease duration, or medication dose within PD. IF-microstate dynamics thus stratify the PD motor subtypes along a graded continuum without tracking continuous disease severity. The approach offers a candidate objective EEG marker for motor-subtype stratification, complementing spectral characterizations of PD.

08.
arXiv (CS.AI) 2026-06-19

Evaluating and Enhancing Negation Comprehension in Remote Sensing MLLMs

arXiv:2606.20177v1 Announce Type: cross Abstract: Multimodal Large Language Models (MLLMs) have demonstrated remarkable success in various Remote Sensing (RS) tasks. However, their ability to comprehend negation remains underexplored, limiting deployment in real-world applications where models must explicitly identify what is false or absent, e.g., emergency responders need to locate non-flooded routes for evacuation. To comprehensively study this limitation, we introduce RS-Neg, the first benchmark to evaluate negation understanding across region-level to scene-level tasks. Specifically, we design an automated data generation pipeline for RS imagery, using LLMs to synthesize diverse negation queries, and introduce a dynamic visual focus module for verification. Our evaluation reveals that advanced RS MLLMs struggle with negation, exhibiting hallucinations and substantial performance degradation. To close this gap, we propose NeFo, a novel test-time learning method that explicitly incorporates the logical role of negation into the model optimization. Remarkably, using about 5\% unlabeled test samples, NeFo significantly improves the negation understanding of models and shows strong generalization to unseen tasks. Code and data will be released upon acceptance.

09.
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.

10.
arXiv (CS.LG) 2026-06-12

Fourier Multi-Component and Multi-Layer Neural Networks: Unlocking High-Frequency Potential

arXiv:2502.18959v3 Announce Type: replace Abstract: The architecture of a neural network and the choice of its activation function are both fundamental to its performance. Equally important is ensuring that these two elements are well matched, as their alignment is key to effective representation and learning. In this paper, we introduce the Fourier Multi-Component and Multi-Layer Neural Network (FMMNN), a model that combines sine-type activations with the multi-component and multi-layer structure of MMNNs. In an FMMNN, each component is represented as a trainable linear combination of fixed random sine-type basis functions, while multi-layer composition generates more complex and adaptive high-frequency features. We establish that FMMNNs retain exponential expressive power for function approximation even under a low-rank architectural structure. We also analyze the optimization landscape of FMMNNs and find it to be substantially more favorable than that of standard fully connected neural networks, especially for high-frequency targets. In addition, we propose a scaled random initialization method for the first-layer weights in FMMNNs, which accelerates training and improves final performance when sufficient samples are available. Extensive numerical experiments support our theoretical insights, showing that FMMNNs achieve strong accuracy and favorable convergence behavior on oscillatory function-approximation benchmarks.

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

Deep Spectral Learning of Embedded Latent Transfer Operators for Stochastic Dynamical Systems

arXiv:2606.14079v1 Announce Type: new Abstract: We propose a spectral learning method for stochastic nonlinear dynamical systems represented with embedded latent transfer operators in deep feature spaces. We instantiate the method as Deep Spectral Encoder (DSE), an operator-based latent state-space model in which a time-invariant neural encoder implements learnable nonlinear feature maps from observations, and these features define Markovian latent states whose temporal evolution and observation mapping are described by the transfer and observation operators, respectively. Functional canonical correlation analysis in a learnable Galerkin-projected feature space provides state coordinates from past and future observations, and the two linear operators are estimated on the state coordinates as ridge-regularized closed-form solutions that coincide with Galerkin projections of the associated covariance operators. On this representation, we generalize sequential Bayesian filtering and Koopman spectral mode decomposition in feature space. Experiments on several scenarios show stable and superior performance with sequential Bayesian filtering and dynamic mode decomposition baselines even under noise and partial observability.

12.
Nature (Science) 2026-06-17

Confined migration induces non-lethal DNA damage in developing neurons

Migratory cells tend to have soft nuclei that deform and penetrate narrow spaces1,2. Extensive nuclear deformation during migration can cause nuclear-envelope rupture and DNA damage in cancer cells, which may contribute to malignant transformation during tumour progression3–6. However, the importance of DNA damage in physiological migration is less well understood. Here we demonstrate that the migration of neurons in developing cerebral and cerebellar cortices is accompanied by massive DNA double-stranded breaks (DSBs) due to mechanostress during passage through narrow interstitial spaces. In contrast to many other migratory cells, these DSBs occur without detectable nuclear envelope rupture. Confined migration increases topoisomerase-IIβ covalently bound DSBs, and these lesions are repaired through non-homologous end-joining during brain development without causing cell death. Genome sequencing revealed that DSBs tend to occur at transcriptionally inactive regions. The deletion of ligase IV at the onset of neuronal migration leads to persistent DSB accumulation in cerebellar neurons with moderate transcriptional changes in genes related to synaptic function, neuronal development and stress and immune responses. The mutant mouse develops mild motor deficits in later life, suggesting that the DNA damage generated during normal brain development poses a potential disease risk if left unrepaired. The migration of neurons in developing cerebral and cerebellar cortices is accompanied by massive DNA double-strand breaks due to mechanostress during passage through narrow interstitial spaces.

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

Cross-Modal Benchmarking for Robotic Perception in Natural Environments

Natural environments present a complex challenge to robotics perception systems. Current models, particularly vision foundation models, are largely trained on structured, urban environments leading to weaknesses in their perception for field robotics tasks. We showcase the limitations of current models using our recently released WildCross benchmark, a new cross-modal benchmark for place recognition and metric depth estimation in large-scale natural environments. WildCross comprises over 476K sequential RGB frames with semi-dense depth and surface normal annotations, each aligned with accurate 6DoF pose and synchronized dense lidar submaps. In this work, we provide an expanded analysis of the benchmark results from the recent WildCross benchmark, with particular emphasis on expanded metric depth estimation experiments. Access to the code repository and dataset for this work can be found at https://csiro-robotics.github.io/WildCross.

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

Pruning via Causal Attribution Preserves Reasoning Performance in Large Language Models

Large language models (LLMs) excel at multi-step reasoning but incur substantial inference cost. We introduce Causal Attribution Pruning (CAP), a training-free method that identifies critical attention heads by measuring their causal impact on reasoning tasks and uses these head-level scores to guide fine-grained weight pruning. For each attention head, CAP estimates the expected performance degradation when the head is masked during forward passes on a small calibration set of reasoning problems. These causal scores are then converted into weight-level importance values for the corresponding projection matrices. Unlike magnitude-only or activation-based criteria, CAP's interventional measurement directly captures each head's functional contribution, yielding relative accuracy gains of up to 61% over Wanda on ARC-Challenge at 20% sparsity. We evaluate CAP on GSM8K, StrategyQA, and ARC-Challenge using Llama-3-8B-Instruct and Mistral-7B-Instruct at 10%, 20%, and 50% sparsity. At moderate sparsity (10-20%), CAP improves over Wanda in most model-benchmark configurations. with especially large gains on ARC-Challenge for Llama-3. Our results suggest that attention-head-level causal attribution can better preserve reasoning performance on downstream benchmarks than correlational pruning criteria at equivalent sparsity, while remaining limited by coarse MLP attribution at 50% sparsity.

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

Topological Data Analysis for High-Dimensional Dynamic Process Monitoring

arXiv:2606.20443v1 Announce Type: cross Abstract: Real-time process monitoring requires methods that extract actionable information from high-dimensional time-series data. In this work, we present a new approach for process monitoring that combines tools of topological data analysis (TDA) and machine learning. In the proposed approach, we represent multivariate time-series data as manifolds and use topological descriptors to summarize the structure of such data; we then use a neural ordinary differential equation to learn the dynamic evolution of the topological structure of the system. Using real data from an industrial process, we show that this trajectory-based event detection approach is effective at detecting diverse types of events. We contrast this approach against reconstruction-based approaches such as principal component analysis and autoencoders and against a trajectory-based approach that uses Koopman autoencoders.

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

Critique of Agent Model

arXiv:2606.23991v1 Announce Type: new Abstract: What is an agent? What constitutes agency? With the rise of Large Language Model (LLM) systems marketed as ``coding agents'', ``AI co-scientists'', and other ``agentic" tools that promise to drive up productivity, and at the same time, ``existential" concerns such as AI escaping human control with destructive power under a speculative ``machine agency" against humans, it has become essential to clarify where automation ends and agency begins, both for building capable systems and for understanding whether and what to fear. Drawing on Descartes' grounding of agency in independent thought, and on portrayals of autonomous beings in science fiction, we survey the current landscape of AI agents, and analyze agent architectures along five dimensions: goal, identity, decision-making, self-regulation, and learning. Specifically, we argue that genuine agency requires these structures to be internalized within the system itself rather than assembled through external scaffolding. This distinction between agentic systems, whose competence resides in engineered workflows, and agentive systems, whose capabilities (including social interaction) arise endogenously, defines the boundary between systems designed for prescribed tasks, and those capable of operating in the open world with true autonomy. Building on this analysis, we propose the Goal-Identity-Configurator (GIC) architecture for a general-purpose agent model, combining hierarchical goal decomposition, identity evolution, simulative reasoning grounded in a separately trained world model, learned self-regulation, and self-directed learning from both real and simulated experience. Furthermore, we share insight on the auditability, controllability, and safety of agentive systems that possess greater autonomy and ``agency", but remain under human oversight.

17.
arXiv (CS.AI) 2026-06-15

Optimizing Agentic Reasoning with Retrieval via Synthetic Semantic Information Gain Reward

arXiv:2602.00845v3 Announce Type: replace Abstract: Agentic reasoning enables large reasoning models (LRMs) to dynamically acquire external knowledge, but yet optimizing the retrieval process remains challenging due to the lack of dense, principled reward signals. In this paper, we introduce InfoReasoner, a unified framework that incentivizes effective information seeking via a synthetic semantic information gain reward. Theoretically, we redefine information gain as uncertainty reduction over the model's belief states, establishing guarantees, including non-negativity, telescoping additivity, and channel monotonicity. Practically, to enable scalable optimization without manual retrieval annotations, we propose an output-aware intrinsic estimator that computes information gain directly from the model's output distributions using semantic clustering via bidirectional textual entailment. This intrinsic reward guides the policy to maximize epistemic progress, enabling efficient training via Group Relative Policy Optimization (GRPO). Experiments across seven question-answering benchmarks demonstrate that InfoReasoner consistently outperforms strong retrieval-augmented baselines, achieving up to 5.4% average accuracy improvement. Our work provides a theoretically grounded and scalable path toward agentic reasoning with retrieval. The code is available at https://github.com/dl-m9/InfoReasoner

18.
arXiv (CS.CL) 2026-06-24

AdversaBench: Automated LLM Red-Teaming with Multi-Judge Confirmation and Cross-Model Transferability

Scaling adversarial evaluation of large language models requires both a method for generating hard inputs and a reliable way to confirm that resulting failures are real. We present AdversaBench, an end-to-end red-teaming pipeline that mutates seed prompts with five structured operators, queries a target model, and confirms failures through a three-judge panel with a meta-judge tiebreaker. We report experiments on 45 seeds across three categories: reasoning, instruction-following, and tool use. Every seed produced a confirmed failure. Four findings stand out. First, operator effectiveness varies sharply by category: inject_distractor scores 0.00 mean reward on instruction-following seeds but 0.80-0.83 on reasoning and tool-use. Second, binary failure rate hides difficulty: instruction-following seeds required 2.4 attacker iterations on average versus 1.1 for other categories, a gap visible in survival curves. Third, pairwise judge agreement of 80-87% coexists with near-zero Cohen's kappa due to label skew; category-level disagreement rates are more informative. Fourth, adversarial prompts generated against Llama 3.1 8B transfer zero-shot to Llama 3.3 70B, suggesting the mutations exploit general behavioral patterns rather than model-specific weaknesses. Code, dataset, and analysis scripts are available at https://github.com/khanak0509/AdversaBench .

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

Enhancing Spectral Embedding through Robust and Flexible Knowledge Transfer in Electronic Health Records

arXiv:2606.11570v1 Announce Type: cross Abstract: We propose a spectral-based, unsupervised representation learning framework to derive low-dimensional embeddings for clinical concepts and patients in rare disease cohorts from electronic health records, where data are high-dimensional but sample sizes are limited. To overcome this challenge, we incorporate a knowledge matrix extracted from a broader population that shares a partially overlapping subspace with the rare-disease cohort. Our method departs from existing approaches by relaxing restrictive one-to-one signal-alignment assumptions between the latent data matrix and knowledge matrix, allowing more flexible and realistic forms of structured sharing. We introduce a novel two-step spectral embedding procedure: first, we identify and remove irrelevant components from the knowledge matrix; then, we apply a projection-based method to separately recover shared and heterogeneous components. Simulations and an analysis of a real-world multiple sclerosis cohort show that the proposed method outperforms competing approaches, particularly in challenging scenarios where shared signals are weak and only partially aligned, as is common in rare-disease data.

20.
arXiv (CS.CL) 2026-06-24

When Retrieval Metrics Mislead: Measuring Policy Signal in Long-Horizon Tool-Use Agents

Exact-match retrieval recall is often used as a proxy for whether a retriever supplies useful policy context to a downstream decision model. We test this proxy for pre-action policy classification in tau-bench using Qwen2.5-3B/7B classifiers. Under gold-policy conditioning, a compact structured state improves macro-F1 over raw trajectories by 0.13-0.17 after tuning. We then replace the benchmark-designated policy clause with the top-ranked clause retrieved from decision-time context. Although the exact governing clause is retrieved at rank 1 for only 7% of airline states, the primary 3B classifier obtains macro-F1 0.58 with retrieved clauses versus 0.60 with gold clauses (Delta=-0.02, task-cluster 95% CI [-0.23,+0.21]); mismatched-policy and no-policy controls score 0.32 and 0.21. We do not detect a macro-F1 difference between retrieved and gold clauses in this configuration, although the interval remains too wide to establish non-inferiority. The same qualitative pattern appears with a second retriever and at 7B, while varying across fine-tuning configurations. These results indicate that exact-match clause recall can underestimate downstream policy utility in this benchmark setting, motivating evaluation with retrieved policies in the classification loop rather than recall alone.

21.
medRxiv (Medicine) 2026-06-24

The role of Mediterranean diet adherence, smoking and their interactions in epigenetic age acceleration: A cross-sectional analysis of the Airwave cohort.

Background: Epigenetic clocks are markers of biological aging that may vary in their sensitivity to environmental stressors and lifestyle modifiers. To evaluate the utility of these biomarkers as sensors of the human exposome, we investigated how they respond to two powerful and opposing exposures: smoking, a source of oxidative stress, and the antioxidant-rich Mediterranean diet. Objectives: We assessed the sensitivity of eleven epigenetic clocks to diet and smoking and evaluated whether Mediterranean diet adherence modifies associations between smoking and epigenetic aging. Methods: We analysed 928 participants (mean age 41 years, 59% male) from the Airwave Health Monitoring Study. Linear regression models assessed associations between Mediterranean Diet Score (MDS) and epigenetic age acceleration (EAA), alongside smoking status and blood cotinine. Interaction terms between smoking status and MDS were included to detect dietary attenuation of smoking-related EAA. Models were adjusted for demographic, socioeconomic, lifestyle, and psychological covariates. Results: Higher MDS was associated with lower EAA for GrimAge ({beta} = -0.07 SD; 95% CI: -0.13, -0.01) and Bernabeu ({beta} = -0.08 SD; 95% CI: -0.14, -0.02) after false discovery rate correction. Smoking was strongly associated with increased EAA, particularly for GrimAge, Bernabeu, and DunedinPACE. Among current smokers, effect sizes were greater in those with lower dietary adherence (e.g. GrimAge: 1.79 SD, 95% CI: 1.54, 2.04) compared with those with higher adherence (1.35 SD, 95% CI: 1.01, 1.68; P_interaction < 0.001). Similar attenuation patterns were observed for Bernabeu. Higher intake of fruits, vegetables, and whole grains contributed most to the attenuation of smoking-related EAA. Conclusions: Our findings indicate that certain epigenetic clocks effectively capture the tension between harmful and protective exposures within the exposome. Rather than suggesting that diet neutralises the risks of tobacco, these results demonstrate that specific clocks are sensitive enough to monitor how lifestyle factors modify molecular responses to environmental toxins. This highlights the value of second-generation clocks in quantifying biological resilience.

22.
arXiv (CS.CV) 2026-06-11

i1: A Simple and Fully Open Recipe for Strong Text-to-Image Models

Diffusion models have consistently driven progress in text-to-image generation. However, it is challenging to attribute recent progress to specific modeling and data choices: state-of-the-art open-weight models provide limited ablations, and do not disclose their training data and full training details. The research community needs fully open (weights, data, and code) models as a foundation for further research; yet existing fully open models still fall significantly short of leading models in performance. In this project, we conduct a systematic investigation of the modeling and data design choices in text-to-image diffusion training and inference with 300+ controlled experiments totaling 700K+ TPU v6e hours. Our experiments highlight several empirical findings (e.g., equal weighting is a strong default for mixing curated datasets) and simple design decisions (e.g., larger text encoder adapters improve performance with minimal added parameters) for training strong models. Guided by these insights, we train i1, a 3B-parameter text-to-image diffusion model using only publicly available datasets. i1 is competitive with leading models on five representative benchmarks (GenEval, DPG, PRISM, CVTG-2K, and LongText), and outperforms the best existing fully open model by 29.5 absolute percentage points on average. We provide the i1 checkpoints, training and inference code, and the data processing pipeline. Together, our findings and the i1 recipe establish a practical foundation for future open research in text-to-image diffusion models. Our code is available at https://github.com/zlab-princeton/i1.

23.
arXiv (math.PR) 2026-06-16

Eyring-Kramers asymptotics for infinite-dimensional stochastic gradient systems

arXiv:2606.16083v1 Announce Type: new Abstract: We study small-noise asymptotics for a class of reversible stochastic evolution equations in infinite dimensions. The dynamics are of the form \[ dX_t=-A\nabla F(X_t)\,dt+\sqrt{2\beta^{-1}A}\,dW_t, \] where $F$ is a regular multi-well potential, $A$ is a selfadjoint mobility operator, $W$ is a cylindrical Brownian motion and $\beta\gg 1$ is the inverse noise strength. The invariant measure is a Gibbs perturbation of a Gaussian reference measure, and the resulting framework covers, in particular, the stochastic Allen-Cahn and stochastic Cahn-Hilliard equations on bounded intervals. In the double-well case, we derive a sharp asymptotic formula for the first nonzero eigenvalue of the generator. This gives an infinite-dimensional Eyring-Kramers law for the spectral gap, with exponential rate determined by the communication height and leading prefactor determined by the local quadratic behavior at the relevant minima and saddle points. Our approach provides a general strategy for lifting finite-dimensional Eyring-Kramers analysis to infinite-dimensional stochastic gradient systems.

24.
arXiv (CS.CV) 2026-06-18

Posterior Continuation with Noise-Conditioned Frequency Exposure for Diffusion Inverse Problems

Diffusion posterior sampling solves inverse problems by combining a pretrained diffusion prior with measurement-consistency guidance. However, full-band guidance can be unreliable at high noise levels, where clean estimates contain score-induced errors and high-frequency measurement directions are weakly identifiable. We argue that posterior guidance should expose measurement frequencies according to the instantaneous diffusion noise level. Based on this principle, we propose a posterior continuation framework that constructs a family of intermediate posteriors whose likelihood emphasizes currently reliable frequency bands and gradually returns to full-band consistency. We instantiate this framework with a stabilized sampler that combines a diffusion predictor, frequency-limited likelihood refinement, and a Haar-domain commitment rule that commits reliable coarse corrections while deferring weakly identifiable details. Across super-resolution, inpainting, and deblurring, our method achieves competitive-to-state-of-the-art restoration performance, including up to 5 dB PSNR improvement on motion deblurring over strong baselines in evaluations on FFHQ and ImageNet.

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

Pre-Training for Simulation-Based Science: A Study on Jet Foundation Model Training Objectives

arXiv:2606.14870v1 Announce Type: cross Abstract: Foundation models (FMs) trained on large datasets and fine-tuned on downstream tasks have emerged as a powerful paradigm in AI for science. Industrial FMs are typically trained using self-supervision with masking due to the lack of labels. In many scientific domains, accurate simulations are plentiful and facilitate large, labeled datasets. This opens up new possibilities for pre-training. We present a systematic comparison of pre-training methods using the OmniLearned High Energy Physics FM framework. We test supervised classification, flow-matching generation, and self-supervised masked particle modeling. All models are pre-trained on the JetClass dataset and fine-tuned on two representative downstream tasks, top jet classification and JetNet conditional generation. Among other observations, for classification tasks, we find that pure classifier pre-training is optimal when downstream labels and model capacity are plentiful, but combining it with self-supervised masked particle modeling (MPM) is uniquely powerful in the low-finetuning label regime. Flow matching-based generative pre-training seems to provide little benefit for downstream classification, and interestingly, for downstream generation, we find that flow matching must be in the pre-training objective to see a significant finetuning advantage, hinting at the orthogonality of classification and generation tasks. That is, for a model to transfer to both generative and classification downstream tasks, it must be pre-trained on both. This study provides a template for controlled scaling analysis of pre-training objectives for foundation models in simulation-based sciences.