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01.

arXiv (CS.CL) 2026-06-19 DOI: arXiv:2606.19379

How Linear Is a Transformer Feed-Forward Block? Per-Block Linear Recoverability Is Learned, Not Architectural

作者:

Stuart Whipp↗

Transformer feed-forward networks (FFNs) are often treated as nonlinear stores of computation, yet how nonlinear a trained FFN block actually is has rarely been measured. We treat each FFN as a position-wise input-to-output map and split it into the exact least-squares linear approximation plus a residual. The held-out variance the closed-form linear map explains defines a block's linear recoverability (R^2_lin), an optimiser-free measure of its linearity. Across all twelve blocks of GPT-2, Pythia-160m, and llama-160m, R^2_lin is highly heterogeneous and non-monotone with depth, ranging from near-linear (>0.99) to strongly nonlinear (

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02.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2606.15206

AI Contagion in Social Networks

作者:

Olivier Bos↗Stefano Bosi↗

arXiv:2606.15206v1 Announce Type: cross Abstract: We study how artificial intelligence (AI) interacts with social communication networks to shape the stability of collective knowledge. Agents exchange information through a network while receiving AI-generated content, and AI systems retrain on the aggregate social information they influence. This interaction generates two feedback forces: an AI contagion channel, through which distortions diffuse across the network, and an AI social distortion multiplier, through which retraining amplifies past errors. Despite the high dimensionality of the environment, we show that the long-run behavior of the system admits a two-dimensional representation whose spectral radius determines whether AI-mediated information systems are dynamically stable or unstable. We characterize a sharp regulatory frontier identifying the minimum filtering required for stability and show how network topology shapes systemic informational risk.

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03.

bioRxiv (Bioinfo) 2026-06-19 DOI: HASH:8d9bcc8969e61939289cca4a14c3af3f

StickForStats: automated statistical assumption validation for reproducible computational biology

作者:

Bharti↗Chakraborty↗

Reproducible computational biology depends on statistical decisions that routine workflows often skip: verifying that a differential-expression test's assumptions hold across all genes, that a strategy-comparison ANOVA is robust to non-normality, or that a meta-analysis is not distorted by publication bias. Surveys consistently find that fewer than 20% of published biomedical studies report checking these assumptions, and existing statistical software leaves validation to the analyst as an optional step. We present StickForStats, an open-source web platform that reframes assumption validation as a default precondition for every analysis. Its Guardian system–a middleware pipeline of eight validators (normality, variance homogeneity, independence, outliers, sample size, modality, linearity, homoscedasticity)–checks assumptions before execution and, on critical violations, reroutes to an appropriate nonparametric alternative with a documented decision trail. At genome scale, applying Guardian to a 91-sample synovial-sarcoma RNA-seq study (GSE271517) cascaded 90.6% of 27,221 genes to a rank-based test and flipped the differential-expression verdict for 553 genes–479 rescued from an under-powered t-test and 74 outlier-driven false positives rejected–materially changing the gene list a biologist would act on. The same automatic validation generalizes across domains: a CRISPR editing-strategy comparison (ANOVA F = 1122, with Guardian recommending Kruskal-Wallis H = 36.6), an ordinal correlation (Pearson r = 0.476 corrected to Spearman {rho} = 0.479), and a sixteen-trial clinical meta-analysis revealing severe publication bias (Egger's t = -5.78, p < 0.001); a complementary module extends the same validators to published manuscripts, checking claims against CONSORT, STROBE, ICH-E9, and JARS-Quant reporting standards. By making assumption validation automatic and transparent, StickForStats targets a tractable, under-served contributor to irreproducibility. The platform is MIT-licensed, validated against SciPy and R, and freely available at https://github.com/visvikbharti/stickforstats_new.

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04.

arXiv (CS.LG) 2026-06-16 DOI: arXiv:2606.16341

Filtered ANN as a Phase Transition: When Selectivity-Estimation Error Causes Plan Regret

作者:

Madhulatha Mandarapu↗Sandeep Kunkunuru↗

arXiv:2606.16341v1 Announce Type: new Abstract: A filtered approximate-nearest-neighbor (ANN) query returns the k nearest vectors among those satisfying an attribute predicate P of selectivity s. The best execution strategy – pre-filter, post-filter, or in-filter – changes with s, so a system must estimate s and choose. We model this as an argmax over a landscape with phases (regions where each strategy wins) separated by boundaries, and show that selectivity-estimation error produces plan regret – recall lost versus the oracle strategy – only in the critical regions around those boundaries. The regret is a wedge of log-width equal to the multiplicative estimation error epsilon and height equal to the local cliff |V'(s*)| epsilon; the flip-margin 1/|V'(s*)| is the condition number of a sibling cardinality-estimation study reappearing as the local boundary theory. The two phase boundaries follow from independent mathematics: order statistics place the post-filter cliff at s ~ k/K, and site percolation places the in-filter cliff at s_c ~ 0.83/M for graph degree M (corpus-size independent). Criticality exists only under a constrained budget B < sqrt(k n). Under pre-registered decision rules we confirm, on synthetic sweeps and real SIFT1M, that regret concentrates ~290x at the boundary and that the regret curves obey a finite-size scaling collapse onto one universal wedge across two decades of corpus size. A real approximate index does not mis-locate the boundary, but a biased cost model opens a persistent miscalibration band that estimation-error robustness cannot fix. The contribution is a characterization, not a new index. Code and the full pre-registration are public.

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05.

arXiv (quant-ph) 2026-06-15 DOI: arXiv:2512.12103

Perturbative Input-Output Theory of Floquet Cavity Magnonics and Magnon Energy Shifts

作者:

T. Aguiar↗M. C. de Oliveira↗

arXiv:2512.12103v2 Announce Type: replace-cross Abstract: We develop a perturbative input-output formalism to compute the reflectance and transmittance spectra of cavity magnonics systems subject to a Floquet modulation. The method exploits the strong hierarchy between the magnetic-dipole couplings transverse (drive field) and parallel (modulation field) to the static bias field, which naturally introduces the small parameter $\epsilon = (2Ns)^{-1/2}$ associated with the total spin $Ns$ of the ferromagnet. By organizing the cavity and magnon fields in a systematic expansion in $\epsilon$, we obtain compact analytic expressions for the spectra up to second order. Using these results, we reproduce the characteristic sideband structure observed in recent Floquet cavity electromagnonics experiments. Furthermore, accounting for the Zeeman interaction between the modulation field and the fully polarized ground state - a contribution typically neglected in previous treatments - we predict an additional magnon detuning of approximately $0.8\,\mathrm{GHz}$, independent of both modulation frequency and sample size and determined solely by the spatial volume occupied by the modulation field. This identifies a measurable and previously overlooked shift relevant for the interpretation and design of cavity magnonics experiments.

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06.

arXiv (CS.AI) 2026-06-18 DOI: arXiv:2606.19042

Where Did the Variability Go? From Vibe Coding to Product Lines by Regeneration

作者:

Xhevahire T\"ernava↗

arXiv:2606.19042v1 Announce Type: cross Abstract: In vibe coding, an emerging AI-driven paradigm, an LLM generates an entire program from a natural language prompt, but what happens to the variability that traditional software engineering carefully builds into code? To answer this question, we conducted an exploratory analysis on 10 vibe coded C/C++ projects, which suggests that there is near-zero in-artifact variability, i.e., at compile and runtime. All variability decisions are resolved at a single new binding time, generation time, the moment the LLM produces the source code. Rather than treating this as a defect to fix, we propose Variability by Regeneration (VbR), to our knowledge the first product-line approach in which the LLM acts as the derivation engine, generating a purpose-built, free of dead code binary for each variant from a declarative specification, while a variant dispatcher transparently routes user requests to the matching binary. We formalise VbR, contrast it with classical SPL derivation, and demonstrate its full pipeline on a wc product family. For SPL engineering, variability in AI-generated software belongs in the specification, not in the code.

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07.

arXiv (CS.LG) 2026-06-11 DOI: arXiv:2606.11844

TaskFusion: Continual Anomaly Detection for Heterogeneous Tabular Data

作者:

Dayananda Herurkar↗Federico Raue↗Joachim Folz↗J\"orn Hees↗Andreas Dengel↗

arXiv:2606.11844v1 Announce Type: new Abstract: Continual anomaly detection in tabular data is challenging and remains largely underexplored, particularly in settings with heterogeneous feature schemas, distribution shifts, and severe class imbalance. In many real-world applications, data arrive sequentially from diverse domains, rendering conventional continual learning methods ineffective due to their reliance on a fixed input space. We propose a continual learning (CL) method, which can overcome these challenges and continually learn from different tasks. Our method consists of three main parts: our AGF model, Taskfusion augmentation, and outlier exposure. The AGF-model maps task-specific features into a shared space, then aligns distributions to reduce representation drift, and learns anomaly decision boundaries in the aligned space. To improve stability, we introduce Taskfusion augmentation, combining boundary-aware interpolation within tasks to refine the model anomaly boundaries and cross-task mixing to transfer anomaly structure across datasets. To handle class imbalance and memory constraints, we employ tabular dataset distillation to store compact synthetic replay samples, which are jointly used with augmented data in an outlier exposure objective for robust anomaly detection. We evaluate the approach on 21 heterogeneous datasets across multiple domains. Results show that our approach substantially improves continual anomaly detection performance over sequential fine-tuning and other CL baselines while reducing catastrophic forgetting and maintaining stable detection across heterogeneous datasets.

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08.

arXiv (CS.LG) 2026-06-19 DOI: arXiv:2606.20357

On the Variance of Temporal Difference Learning and its Reduction Using Control Variates

作者:

Hsiao-Ru Pan↗Bernhard Sch\"olkopf↗

arXiv:2606.20357v1 Announce Type: new Abstract: We analyze the variance of temporal difference (TD) learning using the phased setting with tabular representation, and show that one of the mechanisms behind its ability to reduce variance is by effectively aggregating over a larger number of independent trajectories. Based on this insight, we demonstrate that (1) the variance of TD is asymptotically bounded from above by Monte Carlo (MC) estimators, and (2) shorter horizon updates incurs less variance for a fixed number of samples. Beyond TD, we show that Direct Advantage Estimation (DAE), a method for estimating the advantage function, can be seen as a type of regression-adjusted control variate, which achieves a tighter bound on the variance compared to TD in the large-sample limit. Finally, we numerically illustrate the behaviors of these estimators with carefully designed environments.

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09.

bioRxiv (Bioinfo) 2026-06-15 DOI: HASH:0d90a2da2a3d2d78dece637f14838033

oxo-flow: compiled, memory-safe bioinformatics workflow orchestration

作者:

Wang↗

Bioinformatics analyses depend on workflow engines to coordinate dozens of computational tools across complex dependency chains. The most widely adopted engines-Snakemake, Nextflow, the Common Workflow Language (CWL), and the Workflow Description Language (WDL)-run on interpreted or just-in-time (JIT) compiled language runtimes, incurring hundreds of milliseconds of startup latency and providing no compile-time safety guarantees from the host language. We developed oxo-flow, a workflow engine written in Rust that compiles to a single native binary. On an Apple M5 processor, oxo-flow parses, validates, and dry-runs a production-scale workflow in roughly 22 milliseconds-before Snakemake or Nextflow have finished loading their runtime environments. Peak memory usage is 16 megabytes, representing six- to seven-fold reductions relative to Snakemake and Nextflow. Dry-run latency is essentially independent of workflow size: a hundred-fold increase in rule count adds approximately 0.4 milliseconds. oxo-flow integrates 31 command-line tools, a REST interface with 60 endpoints, an embedded web application, and native cluster submission into a single 10-megabyte binary. It provides per-rule environment isolation across seven backends, checkpoint-based fault tolerance with cryptographic output verification, and a formal installation and operational qualification protocol for regulated laboratory environments. Ten curated workflows and three demonstration pipeline repositories are available. oxo-flow is freely available under Apache License 2.0 at https://github.com/Traitome/oxo-flow.

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10.

arXiv (CS.CL) 2026-06-16 DOI: arXiv:2606.15643

Extending Item Response Theory for Efficient and Meaningful Multilingual Evaluation

作者:

Gili Lior↗Tzviel Frostig↗Gabriel Stanovsky↗Matan Eyal↗

Multilingual benchmarks are central to evaluating large language models (LLMs) across languages, but they suffer from three issues: exhaustive evaluation scales linearly with the number of languages, automatic translation introduces errors that are easily missed at scale, and some items conflate general and culture-specific knowledge. We address all three with a unified statistical framework, Multilingual-IRT, which extends Item Response Theory with per-language difficulty deviations, split discriminability separating content from language effects, and per-language ability residuals. Fitting Multilingual-IRT on 25 LLMs across 29 languages of MMLU-Pro-X, we show that its fitted parameters support three practical applications: predicting unobserved (item, LLM, language) instances with 11-16% lower binary cross-entropy than the strongest accuracy-based baseline, surfacing candidate translation errors distributed across all 28 non-English languages, whereas accuracy-based baselines concentrate detections in a few languages, and recovering culture-specific items that accuracy-based baselines miss.

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11.

arXiv (CS.CV) 2026-06-18 DOI: arXiv:2606.19162

The Reward Was in Your Data All Along: Correcting Flow Matching with Discriminator-Guided RL

作者:

Nicolas Beltran-Velez↗Felix Friedrich↗Zhang Xiaofeng↗Reyhane Askari-Hemmat↗Xiaochuang Han↗Adriana Romero-Soriano↗Michal Drozdzal↗

Score- and flow-matching models often rely on preference-based reinforcement learning for two purposes: aligning with subjective preferences and, surprisingly, recovering properties such as visual realism and coherent object structure that matching-based training is intended to learn from the data itself. We argue that this reflects a structural mismatch. Matching losses measure $\ell_2$ regression error on the velocity or score field under training-time marginals, a proxy poorly aligned with the visual and semantic properties that determine sample quality at inference. Given a reward aligned with these properties, RL sidesteps the mismatch by evaluating the model on its own samples and following the reward landscape directly. The challenge is to obtain such a reward without relying on human preferences, which are expensive and conflate data realism with annotator inclinations. We propose Discriminator-Guided RL (DRL). DRL trains a discriminator to separate data from base-model samples in a pretrained representation space and uses its logit as the reward in KL-regularized RL. The pretrained space restricts the discriminator to perceptually meaningful directions, and the logit estimates the log-likelihood ratio between data and model, which is the optimal reward for targeting the data distribution. Across SiT, JiT, REPA, and RAE, DRL reduces guidance-free FID (e.g., $9.38 \to 2.62$ on SiT) and semantic-space FD (e.g., $88.2 \to 19.3$ on DINOv3 for SiT), with consistent gains across all backbones, and improves human-preference rewards without training on them. It also yields a better Pareto frontier between preference reward and image fidelity under subsequent preference-based post-training, increasing alignment while reducing low-level artifacts such as oversaturation and excessive brightness.

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12.

bioRxiv (Bioinfo) 2026-06-19 DOI: HASH:4e27796b09c01d0ba5d3c28788b6796b

Nickel-Driven Dynamics of Urease in Sporosarcina pasteurii: Integrated Computational and Experimental Insights

作者:

Al-Thawadi↗S. M↗

Urease is a nickel-dependent enzyme that plays an important role in urea hydrolysis and in a process named as microbial-induced calcium carbonate precipitation (MICP), which is widely used in sustainable environmental biotechnology. Despite its ecological importance, urease powers Biogrout (biocementation), a promising green technology for soil stabilization and infrastructure repair. Yet, the relationship between nickel availability, enzyme activation, and bacterial fitness remains poorly understood. In this study, we reveal a striking dual effect of nickel on Sporosarcina pasteurii: while high Ni2+ concentrations strongly inhibit growth (IC50 {approx} 637.7 {micro}M), they simultaneously boost specific urease activity up to six-fold. This uncoupling between biomass and enzymatic efficiency highlights a previously overlooked adaptive strategy under metal stress. Using structural bioinformatics and molecular docking, we show that Ure1–the catalytic subunit–exhibits the strongest nickel affinity (-4.3 kcal{middle dot}mol-1), supported by highly conserved active-site residues, whereas accessory proteins UreE and UreG display moderate and weak binding, consistent with their roles in metal delivery and GTP-dependent maturation. In addition, microscopic observations confirmed that calcium carbonate precipitation was most pronounced at intermediate nickel concentrations (approximately 400-1000 {micro}M), whereas higher concentrations ([&ge;]1000-1300 {micro}M) led to reduced mineral formation due to loss viable cells. Taken together, these results indicates that nickel availability controls both urease activation and bacterial fitness, and that an optimal balance is required to maximize biomenerilization efficiency in environmental applications, particularly in biocementation technology.

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13.

arXiv (CS.AI) 2026-06-11 DOI: arXiv:2606.05551

Conformal Risk-Averse Decision Making with Action Conditional Guarantee

作者:

Zihan Zhu↗Shayan Kiyani↗George Pappas↗Hamed Hassani↗

arXiv:2606.05551v2 Announce Type: replace-cross Abstract: Reliable decision making pipelines powered by machine learning models require uncertainty quantification (UQ) methods that come with explicit safety guarantees. Conformal prediction provides such UQ by wrapping ML predictions into prediction sets, and recent work by Kiyani et al. (2025b) established that these sets can be translated into optimal risk-averse decision policies – yet only inheriting marginal safety guarantees. We generalize and strengthen their results by (i) introducing action-conditional conformal prediction, which yields safety guarantees conditioned explicitly on each action taken by the decision maker, (ii) showing that action-conditional prediction sets serve as a proxy for the feasible decision space for risk-averse decision makers aiming to optimize action-conditional value-at-risk, and (iii) proposing a principled finite-sample algorithm based on pinball-loss minimization, connecting the framework of Gibbs et al. (2025) to action-conditional guarantees. Experiments on two real-world datasets confirm that our approach significantly improves action-conditional performance over conformal baselines.

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14.

arXiv (CS.CV) 2026-06-18 DOI: arXiv:2510.21615

Epipolar Geometry Improves Video Generation Models

作者:

Orest Kupyn↗Th\'eo Uscidda↗Marta Tintore Gazulla↗Fabian Manhardt↗Federico Tombari↗Christian Rupprecht↗

Video generation models have advanced significantly through the latent diffusion transformers trained with rectified flow techniques. Yet these models still struggle with geometric inconsistencies, unstable motion, and visual artifacts that break the illusion of realistic 3D scenes. 3D-consistent video generation could significantly impact numerous downstream applications in generation and reconstruction tasks. We explore how epipolar geometry constraints improve modern video diffusion models. Despite using massive training data, these models fail to capture fundamental geometric principles. We align diffusion models using pairwise epipolar geometry constraints via preference-based optimization, directly addressing unstable trajectories and geometric artifacts through mathematically principled geometric enforcement. Our approach efficiently enforces geometric principles without requiring end-to-end differentiability. Evaluation demonstrates that classical geometric constraints provide more stable optimization signals than modern learned metrics. Training on static scenes with dynamic cameras ensures metric quality while the model generalizes to various dynamic scenes. By bridging data-driven learning with classical computer vision, we reduce epipolar error by 31% and improve human-rated consistency from 54% to 72% without compromising visual quality.

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15.

medRxiv (Medicine) 2026-06-16 DOI: HASH:09c2f5e2407b10ffb1f04328fce24c48

Validating an Early Pregnancy HbA1c as the Screening Test for Gestational Diabetes Mellitus: Findings from PRISMA Pakistan Cohort

作者:

Naz↗Yazdani↗Hoodbhoy↗Ghebremihael-Weldeselassie↗Mazhar↗Hotwani↗Jehan↗Nisar↗M. I↗Iqbal↗

Background: Early identification of gestational diabetes mellitus (GDM) is critical to improving maternal and neonatal outcomes, particularly in resource-constrained settings where universal oral glucose tolerance testing (OGTT) is burdensome. We assessed whether early-pregnancy HbA1c alone or combined with common risk factors can predict GDM and reduce the burden of OGTT requirements in a peri-urban cohort in Karachi, Pakistan. Methods: We conducted a secondary analysis of the Pregnancy Risk Infant Surveillance and Measurement Alliance (PRISMA) Pakistan cohort. Women enrolled before 20 weeks' gestation with available early-pregnancy HbA1c and a 2-hour 75g OGTT at 24 to 28 weeks were included. We externally validated GDM prediction models originally developed in the STRiDE-India cohort. Model performance was evaluated using receiver operating characteristic (ROC) curves and area under the curve (AUC). We assessed four models: HbA1c alone (Model 1a); age, BMI, and family history of diabetes mellitus (FH DM) (Model 1b); HbA1c combined with age, BMI, and FH DM (Model 2); and an extended model, i.e., Model 2 combined with socioeconomic status, gestational age, parity, systolic and diastolic blood pressure (Model 3). A dual-threshold approach was applied to assess rule-in and rule-out performance. Results: Among 2,489 women, GDM incidence was 7.5% (n=186). Models with a broader set of predictors demonstrated higher AUC values, with Model 2 achieving an AUC of 0.61 (95% CI: 0.57, 0.66). Including additional factors (Model 3) did not further improve predictive ability (AUC: 0.62; 95% CI: 0.58, 0.66). In addition, at predefined thresholds, Model 2 achieved sensitivity of 73.7% (rule-out) and specificity of 83.5% (rule-in), with the potential to reduce OGTT requirements (58.5%). Conclusions: Early-pregnancy risk stratification using HbA1c combined with simple clinical predictors offers a pragmatic approach to streamline GDM screening among high-risk pregnant women. A dual-threshold strategy using Model 2 could reduce reliance on universal OGTT while prioritizing high-risk women for confirmatory testing.

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16.

arXiv (CS.AI) 2026-06-12 DOI: arXiv:2606.12841

TimeROME-DLM: Temporal Causal Tracing and Low-Rank Inference-Time Knowledge Editing for Masked Diffusion Language Models

作者:

Zhengtao Yao↗Liuyang Song↗Hongbo Zhang↗Chenhao Wei↗Haoyan Xu↗Guang Yang↗Siheng Wang↗

arXiv:2606.12841v1 Announce Type: cross Abstract: Masked diffusion language models (MDLMs) such as LLaDA now rival autoregressive (AR) LLMs, but every existing knowledge-editing and unlearning method (ROME, MEMIT, etc.) targets AR transformers and either makes assumptions that fail under iterative denoising, or requires gradient updates whose backward-pass activations cost tens of GB of extra VRAM and which collapse MDLMs at standard learning rates. We introduce TimeROME-DLM, the first training-free, gradient-free, inference-time knowledge-editing framework for MDLMs. It couples two components: a Temporal Indirect Effect (TIE) causal-tracing protocol that identifies, for each fact, the coordinate whose intervention most strongly drives the object prediction at later denoising steps; and a closed-form, low-rank residual edit memory that aggregates subject keys and target deltas across all forget facts and applies a single ridge-regularised update at that coordinate at every diffusion forward, with sparsification to limit utility spillover. Backbone weights stay frozen; only three hyperparameters (alpha, lambda, q) are tuned on a small validation split. On TOFU forget01 with TOFU-finetuned LLaDA-8B-Base, TimeROME-DLM cuts forget-set log-probability by roughly 83 nats. The same configuration transfers to LLaDA-8B-Instruct, Dream-7B, MMaDA-8B, DiffuLLaMA-7B, and LLaDA-MoE-1.4B. It keeps retain-set log-probability nearly flat (within ~1 nat at the utility-safe operating point) across 50 sequentially inserted facts, delivers a four- to fourteen-fold wall-clock speedup with zero additional VRAM over the strongest converged training-time baseline, and scales sub-linearly to 400 facts. TimeROME-DLM closes the locate-then-edit gap between AR LLMs and MDLMs at a fraction of the computational cost.

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17.

arXiv (CS.CV) 2026-06-11 DOI: arXiv:2606.12072

World Model Self-Distillation: Training World Models to Solve General Tasks

作者:

Sebastian Stapf↗Pablo Acuaviva Huertos↗Aram Davtyan↗Paolo Favaro↗

Pretrained video generators are promising visual world models that exhibit emergent task-solving abilities; however, their reliance on detailed textual descriptions limits their direct use for planning and decision-making. Existing approaches either outsource this reasoning to language or vision-language models, or rely on supervised fine-tuning with paired task-execution videos, which are costly to collect and difficult to scale. We propose a scalable framework that elicits task-solving ability in such models by combining self-distillation with reinforcement learning. Given an unlabeled scene image, a vision-language model generates a candidate task and a detailed step-by-step solution. The solution conditions a pretrained video diffusion model, the Demonstrator; we distill its behavior into an Executor conditioned only on the image and a short task prompt. This transfers execution knowledge from caption-guided generation to instruction-conditioned task solving without curated task-video supervision. We further improve the Executor with reinforcement learning from VLM feedback, exploiting the asymmetry between judging whether a sampled video satisfies a task and generating the solution. Experiments on our proposed WorldTasks-Benchmark and the DreamGen robotics benchmark show that the Executor surpasses the Demonstrator under our VLM-based evaluation protocol and transfers competitively to robotic tasks.

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18.

arXiv (CS.LG) 2026-06-18 DOI: arXiv:2604.14906

Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning

作者:

Mariia Ivonina↗Jakub Rydzewski↗

arXiv:2604.14906v3 Announce Type: replace-cross Abstract: The pseudoknot secondary structure in SARS-CoV-2 RNA is essential for regulating protein synthesis through $-$1 programmed ribosomal frameshifting ($-1$ PRF), a mechanism that allows the virus to generate both structural and non-structural proteins from overlapping reading frames. This pseudoknot exhibits both threaded and unthreaded long-lived topologies. The influence of ligand binding on its folding is a process critical for the development of $-$1 PRF small-molecule inhibitors. Understanding this process through unbiased molecular dynamics (MD) simulations can be facilitated by introducing collective variables (CVs) that capture the corresponding slowest dynamical modes. Here, we use spectral map (SM), a thermodynamics-driven machine learning technique, to learn such CVs directly from all-atom MD trajectories of the SARS-CoV-2 RNA pseudoknot in complex with the $-$1 PRF inhibitor merafloxacin and its two structural analogs in neutral and ionized forms. Free-energy landscapes (FELs) derived from the learned CVs indicate that ligand-induced destabilization is topology-selective. In the threaded pseudoknot, the inhibitors destabilize the S2 stem, while in the unthreaded pseudoknot, destabilization occurs in the S1 and S3 stems. Furthermore, the extent to which each ligand reshapes the FEL matches experimentally reported antiviral potency, whereas the protonation state qualitatively alters dynamics within the same RNA topology. Overall, our results show how pseudoknot topology, ligand type, and protonation state collectively influence the slow conformational dynamics of viral RNA and establish physiological protonation as a critical factor for modeling RNA-targeted drug action.

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19.

arXiv (quant-ph) 2026-06-12 DOI: arXiv:2606.13606

Diffusive Dynamics of Nonstabilizerness

作者:

Zhenyu Xiao↗Shinsei Ryu↗

arXiv:2606.13606v1 Announce Type: new Abstract: Symmetries shape the quantum-information dynamics of many-body systems, but their effect on nonstabilizerness, the resource complementary to entanglement, is less understood. We compute the stabilizer Rényi entropy, a measure of nonstabilizerness, in $\mathrm{U}(1)$-symmetric one-dimensional random circuits. The disorder-averaged dynamics is captured by a four-replica tensor network, which we evaluate by $S_4$-adapted infinite time-evolving block decimation (iTEBD) directly in the thermodynamic limit. Together with a hydrodynamic argument, our results identify a diffusive universality class for the late-time approach of nonstabilizerness to its random-state value, with the stabilizer Rényi entropy gap closing as $1/t$. The same scaling is verified in an energy-conserving nonintegrable Ising chain. More broadly, our framework provides a hydrodynamic perspective on nonstabilizerness generation and offers insight into the design of approximate Haar-random states in Hamiltonian dynamics.

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20.

arXiv (CS.LG) 2026-06-19 DOI: arXiv:2510.19893

EQPO: Equitable Group Relative Policy Optimization for Clinical Reasoning

作者:

Shiqi Dai↗Wei Dai↗Jiaee Cheong↗Paul Pu Liang↗

arXiv:2510.19893v2 Announce Type: replace Abstract: Medical AI systems demonstrated impressive diagnostic performance, yet they routinely show uneven accuracy across demographic groups, disadvantaging underrepresented populations. Although multimodal reasoning foundation models have pushed clinical diagnosis forward, reinforcement learning-based post-training tends to absorb and magnify the biases present in majority-dominated training corpora. We propose Equitable Group Relative Policy Optimization (EQPO), a hierarchical reinforcement learning method that encourages balanced learning across heterogeneous clinical populations by adaptively reweighting samples according to subgroup representation, task difficulty, and data source. As demographic annotations are frequently missing in real-world clinical data, EQPO additionally applies unsupervised clustering to recover latent subpopulations when they are unavailable. On 7 diagnostic benchmarks covering 5 modalities (X-ray, CT, dermoscopy, mammography, ultrasound), EQPO reduces F1 standard deviation by 43.9% and the maximum cross-group F1 gap by 42.7% on QoQ-Med3-8B over vanilla GRPO, and narrows predictive parity gaps by 27.2% on MedGemma-4B over bias-mitigated RL baselines while raising F1 by 12.5% even without any demographic labels. Examining the training trajectory shows that EQPO steadily improves fairness over the course of optimization, in contrast to baseline methods whose fairness degrades as training proceeds, and the discovered implicit groups remain stable and align with masked demographic attributes. We further release EquiMedGemma-4B and EquiQoQ-Med3-8B, equitability-aware clinical VLLMs that attain state-of-the-art accuracy with markedly smaller demographic gaps.

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21.

arXiv (quant-ph) 2026-06-17 DOI: arXiv:2605.27841

Coherent Dark State Formation of a Lead-Vacancy Spin Qubit in Diamond

作者:

Yiyang Chen↗Koyo Hirai↗Tzyy Zheng Neo↗Eiki Ota↗Takashi Taniguchi↗Masashi Miyakawa↗Shinobu Onoda↗Toshiharu Makino↗Mutsuko Hatano↗Takayuki Iwasaki↗

arXiv:2605.27841v2 Announce Type: replace Abstract: A lead-vacancy (PbV) center in diamond exhibits coherent emission above the liquid helium temperature, making it highly attractive for quantum network applications. Here, we report the magneto-optical and spin properties of PbV centers in diamond. We record a spin lifetime of 12 ms at 7.5 K under large off-axis magnetic field. Furthermore, we observe formation of the coherent dark state by coherent population trapping and estimate a spin dephasing time of 177 ns at 6.5 K. This work demonstrates the outstanding thermal robustness of the PbV spin compared to other group-IV centers above 4 K.

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22.

arXiv (CS.LG) 2026-06-18 DOI: arXiv:2606.19138

INDEQS: Informed Neural controlled Differential EQuationS

作者:

Michael Detzel↗Gabriel Nobis↗Kristiyan Blagov↗Juri Schubert↗Jackie Ma↗Wojciech Samek↗

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

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23.

arXiv (CS.AI) 2026-06-12 DOI: arXiv:2512.15133

HD-Prot: A Protein Language Model for Joint Sequence-Structure Modeling with Continuous Structure Tokens

作者:

Yi Zhou↗Haohao Qu↗Yunqing Liu↗Shanru Lin↗Le Song↗Wenqi Fan↗

arXiv:2512.15133v3 Announce Type: replace-cross Abstract: Proteins inherently possess a consistent sequence-structure duality. The abundance of protein sequence data, which can be readily represented as discrete tokens, has driven fruitful developments in protein language models (pLMs). A key remaining challenge, however, is how to effectively integrate continuous structural knowledge into pLMs. Current methods often discretize protein structures to accommodate the language modeling framework, which inevitably results in the loss of fine-grained information and limits the performance potential of multimodal pLMs. In this paper, we argue that such concerns can be circumvented: a sequence-based pLM can be extended to incorporate the structure modality through continuous tokens, i.e., high-fidelity protein structure latents that avoid vector quantization. Specifically, we propose a hybrid diffusion protein language model, HD-Prot, which embeds a continuous-valued diffusion head atop a discrete pLM, enabling seamless operation with both discrete and continuous tokens for joint sequence-structure modeling. It captures inter-token dependencies across modalities through a unified absorbing diffusion process, and estimates per-token distributions via categorical prediction for sequences and continuous diffusion for structures. Extensive results demonstrate that HD-Prot achieves competitive performance in unconditional sequence-structure co-generation, motif-scaffolding, protein structure prediction, and inverse folding tasks. Furthermore, our method can perform on par with state-of-the-art multimodal pLMs, despite being developed under limited computational resources (i.e., less than one-tenth the budget for modality extension fine-tuning). It highlights the viability of simultaneously estimating categorical and continuous distributions within a unified language model architecture, offering a promising alternative direction for multimodal pLMs.

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24.

arXiv (CS.AI) 2026-06-11 DOI: arXiv:2603.09555

Compiler-First State Space Duality and Portable $O(1)$ Autoregressive Caching for Inference

作者:

Cosmo Santoni↗Anmol Thapar↗

arXiv:2603.09555v2 Announce Type: replace-cross Abstract: High-throughput Mamba-2 inference is usually tied to fused CUDA and Triton kernels, limiting portability across accelerator backends. We show that the state space duality (SSD) recurrence has a compiler-friendly structure: diagonal per-head dynamics, fixed-size chunking, einsum-dominated compute, and static control flow. Expressing this structure in standard JAX primitives gives a single-source inference path with no custom kernels, a registered JAX PyTree cache, and a compiled on-device autoregressive loop. On a single Google Cloud TPU v6e, batch-1 prefill reaches approximately 140 TFLOPS, or 15% model FLOP utilisation (MFU), the roofline ceiling for this regime, and cached decode reaches up to 64% hardware bandwidth utilisation (HBU). At a 4096-token context, cached decode is 27x–36x faster than full-prefix recomputation across five Mamba-2 checkpoints from 130M to 2.7B parameters. The same source runs unmodified on NVIDIA L40S, where cached decode remains sequence-length independent across all model scales. WikiText-103 validation perplexity matches the Triton reference mamba_ssm v2.2.2 within +/-0.0005 points, and hidden states agree to float32 rounding tolerance. Code is available at https://github.com/CosmoNaught/mamba2-jax.

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25.

Nature (Science) 2026-06-10 DOI: HASH:823795ad4ab18e3c726b57ddbe6002d9

Mutation-dependent responses to sleep and exercise in clonal haematopoiesis

作者:

Teresa Gerhardt↗

Clonal haematopoiesis (CH) activates inflammation and increases the risk of atherosclerosis1,2. Whether lifestyle alters CH clone expansion or the phenotypic programming of CH mutant cells, thereby affecting atherosclerosis, is unknown. Here, in humans and mice and across mutations in Jak2, Tet2, Trp53 and Dnmt3a, we demonstrate mutation-dependent responses to sleep and exercise in CH and show that mutant cells are uniquely sensitive to lifestyle. In two human datasets, moderate-to-vigorous physical activity was associated with lower prevalence of non-DNMT3A-driven CH. In atherogenic mice with Jak2V617F or Tet2 loss of function (LOF), but not Trp53 LOF or Dnmt3aR878H CH, uninterrupted sleep or exercise curtails clone expansion. In CH with the Jak2V617F mutation, sleep and exercise reduces clone expansion by selectively reprogramming mutant, but not cohabitant wild type, haematopoietic progenitor cells towards antiproliferative and metabolically healthy phenotypes by tempering bone marrow macrophage–haematopoietic progenitor cell IL-1β signalling. Sleep or exercise also lessens Jak2V617F-driven, Tet2 LOF-driven and Trp53 LOF-driven, but not Dnmt3aR878H-driven, atherosclerosis by locally reprogramming mutant vascular macrophages, independent of peripheral clone dynamics. In Jak2V617F, but not adjacent wild type, aortic macrophages, uninterrupted sleep blunts CLEC4E-dependent inflammasome activation, consequently diminishing lesions. Exercise, meanwhile, activates PAC1+ neurons in the locus coeruleus, raising the levels of peripheral noradrenaline, which signals through adrenergic receptor β2 (ADRβ2) whose expression is preserved by exercise in Jak2V617F, but not cohabitant wild type, aortic macrophages, selectively repressing their inflammatory programming and atherosclerosis. Our findings establish that healthy lifestyles gene-specifically diminish CH and selectively reprogram mutant haematopoietic progenitor cells and macrophages to maintain cardiovascular health. Sleep and exercise can slow clonal haematopoiesis and limit mutant cell-driven atherosclerosis.

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