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

Doeblin Curves

arXiv:2606.19859v1 Announce Type: cross Abstract: Recent research on Doeblin coefficients has shed light on their usefulness as a multi-way generalization of the Dobrushin contraction coefficient for TV distance, in a separate vein from their classic role in the theory of Markov chain ergodicity. However, strong conditions, such as being bounded away from 0, are typically necessary for Doeblin coefficients to establish the existence of information contraction. Building on recently formulated concepts of nonlinear information contraction, we aim to propose a finer-grained Doeblin-based characterization of multi-way contraction behavior which yields non-vacuous contraction guarantees even for channels whose Doeblin coefficient is 0. To this end, we introduce the notion of a Doeblin curve – a nonlinear function which quantifies the contraction behavior of a Markov kernel on collections of input distributions at specific levels of divergence and power. Through the course of our analysis, we develop a new variational characterization of Doeblin coefficients, present several properties of Doeblin curves, define several versions of power-constrained Doeblin curves, and derive upper and lower bounds using our aforementioned variational characterization. We then utilize these results in diverse areas, including generalization bounds for noisy iterative optimization, error bounds for reliable computation with noisy circuits, and differential privacy guarantees for online iterative algorithms. In particular, we extend results in these areas to broader domains or group settings, leveraging Doeblin curves to reveal finer-grained contraction phenomena than Doeblin coefficients.

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

Unstable Features, Reproducible Subspaces: Understanding Seed Dependence in Sparse Autoencoders

Sparse autoencoders (SAEs) are widely used to interpret neural network representations, but their utility depends on whether the learned features are reproducible across training runs. We study this question through feature stability: for each SAE feature, we estimate the probability that a similar feature reappears in an independently trained SAE. This yields a scalable per-feature signal that separates stable from unstable features. In a large-scale study across seeds, models, layers, dictionary sizes, and SAE variants, we find a pronounced functional asymmetry: stable features carry most of the reconstruction- and prediction-relevant signal, while unstable features have weak marginal impact and are dominated by low-frequency surface-form triggers in both activation statistics and automatic explanations. Geometrically, unstable features are individually non-reproducible but concentrate in reproducible lower-rank subspaces, suggesting that seed dependence often reflects basis ambiguity within a shared region of activation space rather than pure noise. A controlled synthetic model makes this mechanism explicit, showing that low-rank ground-truth features can be recovered at the subspace level while remaining non-identifiable as individual SAE latents across seeds. Finally, by pooling unique cross-seed features, we construct more stable SAEs while preserving explained variance in this setting. Together, these results show that unstable features are not merely failed or noisy latents: they have weak individual functional impact, but reflect reproducible low-dimensional structure that standard SAEs resolve differently across seeds.

03.
arXiv (CS.CV) 2026-06-18

Low-Rank Tensor Completion Based on Fractional Regularization with Ky Fan p-k Norm

This paper addresses low-rank tensor completion (LRTC) by proposing a novel nonconvex surrogate, namely the ratio of the tensor nuclear norm to the tensor Ky Fan p-k norm (TNPK), to accurately approximate the tensor tubal rank. The TNPK possesses appealing properties, including scale invariance, parameter flexibility, and the existence of closed-form solutions under specific choices of p and k. With specific parameter settings of p and k, it reduces to the ratio of the tensor nuclear norm to the tensor Ky Fan k norm (TNK) or the ratio of the tensor nuclear norm to the tensor Frobenius norm (TNF). We construct a LRTC model and, under the tensor null space property (NSP), prove that low-rank tensors are local minimizers of the proposed model. Moreover, we derive the proximal operator of the Ky Fan p-k inverse-norm and further develop an efficient alternating direction method of multipliers (ADMM) algorithm with guaranteed subsequential convergence under mild conditions. Extensive experiments on synthetic and real-world datasets validate the superior performance of our method against state-of-the-art competitors.

04.
arXiv (CS.AI) 2026-06-11

Search Discipline for Long-Horizon Research Agents

arXiv:2606.11522v1 Announce Type: new Abstract: Autoresearch agents now propose, evaluate, and select scientific candidates against a metric, and that metric is usually an aggregate reduced over a heterogeneous space of regions, slices, or cohorts. We show that when scientific validity lives in that disaggregated structure, the aggregate can rank the wrong candidate first. The headline number improves while the structure underneath inverts, so a decision made on the number accepts a candidate that quietly breaks the model. The failure is not domain-specific. It appears wherever a candidate's validity is multi-dimensional but its verifier is a single reduction. We demonstrate the inversion on a fire-model task in the Ecosystem Demography model. The highest-scoring candidate and a slightly lower one are within noise of each other on global score, yet the top-scoring one collapses the protected boreal regions while the other preserves them. What separates them is the per-region behavior, not the headline number. This decision should not be left to the agent that produced the candidates. The agent optimizing the score is the last party likely to catch the score being wrong, and a prompt has no remaining turn once the agent has stopped. We move the decision to an external control loop that audits each candidate on its disaggregated behavior and acts after the agent has decided. It can demote a candidate the agent would have accepted, and it can reopen a run the agent had declared finished. Our contribution is the inversion finding itself, and a search-discipline protocol that decides on reviewable candidate-effect evidence instead of the score.

05.
arXiv (CS.CV) 2026-06-16

CoIRL-AD: Collaborative-Competitive Imitation-Reinforcement Learning in Latent World Models for Autonomous Driving

End-to-end autonomous driving models trained with imitation learning (IL) often generalize poorly, particularly in long-tail scenarios where expert demonstrations are sparse. Reinforcement learning (RL) can provide complementary task-level supervision, but applying RL to real-world autonomous driving is challenging in offline settings without interactive simulators, where datasets are dominated by expert actions and provide limited behavioral diversity. We propose CoIRL-AD, a competitive dual-policy framework that integrates IL and RL under a unified offline training regime. CoIRL-AD decouples imitation and reward optimization into separate actors to alleviate objective conflicts, uses imagined future rollouts for long-horizon reward estimation, and introduces a competition mechanism that selectively transfers beneficial behaviors while keeping RL anchored to expert-like driving. Experiments on the nuScenes benchmark show that CoIRL-AD consistently improves robustness over strong IL-based baselines, with especially large gains in cross-city generalization and long-tail scenarios. Code is available at: https://github.com/SEU-zxj/CoIRL-AD.

06.
arXiv (CS.CL) 2026-06-17

Rethinking Groups in Critic-Free RLVR

Reinforcement learning (RL) has become a central paradigm for post-training large language models. Existing critic-free RL methods typically generate a group of rollouts for the same question to estimate value baselines for advantage computation. However, this design suffers from data inefficiency, group synchronization barriers, and inflexibility with structured rollouts. In this work, we revisit the role of the ``group'' and show that its underlying function is not merely to estimate baselines but to prevent false penalties on negative samples. Building on this insight, we propose negative token filtering, a simple and effective strategy that enables stable single-rollout training. We apply it to two batch-level advantage methods, achieving comparable performance on reasoning tasks and stronger performance on agentic tasks relative to group-based RL techniques.

07.
arXiv (CS.CV) 2026-06-16

LIBERO-Occ: Evaluating and Improving Vision-Language-Action Models under Scene-Induced Occlusion via Viewpoint Imagination

Vision-Language-Action (VLA) models achieve strong performance on standard manipulation benchmarks, but most evaluations assume that task-relevant objects are fully visible. This assumption often fails in realistic settings, where occlusion makes manipulation partially observable. In this paper, we study scene-induced occlusion as a fundamental challenge for VLA models and introduce LIBERO-Occ, an occlusion-oriented extension of LIBERO. Experiments show that state-of-the-art VLAs suffer substantial performance degradation under occlusion. To address this issue, we propose Viewpoint Imagination (VIM), which generates a complementary view from an occluded primary observation and conditions action prediction on both observed and imagined evidence. VIM improves robustness across task suites, occlusion types, and severity levels without requiring additional cameras at deployment time, suggesting that viewpoint imagination is an promising mechanism for perception completion in partially observable manipulation. Our benchmark and corresponding code are available at: \href{https://github.com/litsh/Libero-Occ}{https://github.com/litsh/Libero-Occ}.

08.
arXiv (quant-ph) 2026-06-19

Locally Gentle State Certification for High Dimensional Quantum Systems

arXiv:2602.04550v3 Announce Type: replace Abstract: Standard approaches to quantum statistical inference rely on measurements that induce a collapse of the wave function, effectively consuming the quantum state to extract information. In this work, we investigate the fundamental limits of locally-gentle quantum state certification, where the learning algorithm is constrained to perturb the state by at most $\alpha$ in trace norm, thereby allowing for the reuse of samples. We analyze the hypothesis testing problem of distinguishing whether an unknown state $\rho$ is equal to a reference $\rho_0$ or $\epsilon$-far from it. We derive the minimax sample complexity for this problem, quantifying the information-theoretic price of non-destructive measurements. Specifically, by constructing explicit measurement operators, we show that the constraint of $\alpha$-gentleness imposes a sample size penalty of $\frac{d}{\alpha^2}$, yielding a total sample complexity of $n = \Theta(\frac{d^3}{\epsilon^2 \alpha^2})$. Our results clarify the trade-off between information extraction and state disturbance, and highlight deep connections between physical measurement constraints and privacy mechanisms in quantum learning. Crucially, we find that the sample size penalty incurred by enforcing $\alpha$-gentleness scales linearly with the Hilbert-space dimension $d$ rather than the number of parameters $d^2-1$ typical for high-dimensional private estimation.

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

MAD: Manifold Attracted Diffusion

arXiv:2509.24710v3 Announce Type: replace-cross Abstract: Score-based diffusion models are a highly effective method for generating samples from a distribution of images. We consider scenarios where the training data comes from a noisy version of the target distribution, and present an efficiently implementable modification of the inference procedure to generate noiseless samples. Our approach is motivated by the manifold hypothesis, according to which meaningful data is concentrated around some low-dimensional manifold of a high-dimensional ambient space. The central idea is that noise manifests as low magnitude variation in off-manifold directions in contrast to the relevant variation of the desired distribution which is mostly confined to on-manifold directions. We introduce the notion of an extended score and show that, in a simplified setting, it can be used to reduce small variations to zero, while leaving large variations mostly unchanged. We describe how its approximation can be computed efficiently from an approximation to the standard score and demonstrate its efficacy on toy problems, synthetic data, and real data.

10.
arXiv (quant-ph) 2026-06-11

Polarization-Resolved Photon Statistics of Cavity Quantum Materials

arXiv:2606.11550v1 Announce Type: cross Abstract: By forming hybrid light-matter states, optical cavities offer a route for engineering material properties, however, unambiguously probing the effects of light-matter coupling remains difficult. Here, we show that the polarization-resolved statistics of photons transmitted through a cavity, measurable via $g^{(2)}$, provide one such diagnostic. By relating $g^{(2)}$ to matter correlation functions such as the Raman structure factor, we link photon bunching and antibunching to material properties. By applying this method to the stripy-to-antiferromagnetic transition in the Kitaev-Heisenberg spin model, we find that polarization-dependent patterns of bunching and antibunching encode the magnetic point-group symmetries of each phase and characterize the behavior at the phase boundary. Finally, we predict measuring $g^{(2)}$ for output photon pairs polarized orthogonal to the input field will isolate higher-order light-matter scattering processes that probe higher-order material correlations.

11.
arXiv (CS.AI) 2026-06-17

Structural Preservation and the Logical Expressiveness of Graph Neural Networks

arXiv:2606.17882v1 Announce Type: new Abstract: Bridges between graph neural networks (GNNs) and logical formalisms have been established by fixing architectural choices, such as the types of aggregation, combination, and activation functions. These choices define restricted classes of GNNs for which tight correspondences with logical formalisms can be obtained, by showing that logical formulae can be translated into equivalent GNNs and, conversely, that GNNs can be translated into equivalent formulae. In this paper we take a semantic perspective by establishing the logical expressiveness of classes of GNN classifiers that are preserved under structural properties: embeddings (extensions), injective homomorphisms, and homomorphisms. We show that, for each such property, there exists a fragment of graded modal logic characterising the class of GNNs. In particular, preservation under embeddings, injective homomorphisms, and homomorphisms corresponds to existential graded modal logic, its existential-positive fragment, and existential-positive modal logic, respectively. These results characterise the expressiveness of broad classes of GNNs independently of specific architectural choices, but we also show that each of these classes admits a GNN architecture of the same expressiveness. Technically, our approach uses a new well-quasi-order result for trees of bounded height, yielding finite representations of unravelling-invariant classes.

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

PANDA: An LLM-Enhanced Performance-Driven Analog Design Framework Bridging Design Intent and Layout Generation

arXiv:2606.15052v1 Announce Type: cross Abstract: Traditional design of analog circuits heavily relies on manual interventions across topology, sizing, and layout, with prior automation addressing stages in isolation. In this work, we propose PANDA, an LLM-enhanced framework that bridges high-level design intent to final layout by actively managing cross-stage dependencies through guided topology synthesis, substructure-aware sizing, and constraint-driven layout generation. This shifts automation from algorithm-centric execution to intent-centric co-design, reducing turnaround time from days or weeks to hours while improving design performance.

13.
arXiv (quant-ph) 2026-06-19

Recursive perturbation approach to time-convolutionless master equations: Explicit construction of generalized Lindblad generators for arbitrary open systems

arXiv:2506.04095v2 Announce Type: replace Abstract: We develop a recursive perturbative expansion for the time-convolutionless (TCL) generator of an open quantum system in a generalized Lindblad form. This formulation provides a systematic approach to derive the generator at arbitrary order while preserving a Lindblad-like structure, without imposing assumptions on the system or environment beyond an initially uncorrelated state. The generator is written, at all orders, in a canonical form, which also corresponds to the minimal dissipation condition, which uniquely specifies the decomposition of the generator into Hamiltonian and dissipative contributions. To validate the method and show its effectiveness in addressing non-Markovian dynamics and strong-coupling effects, we compute the generator explicitly up to fourth order.

14.
bioRxiv (Bioinfo) 2026-06-14

Transposable elements as evolutionary substrates of proteindisorder in the human proteome

Intrinsically disordered regions (IDRs) are central contributors to protein function, evolution and human disease, yet the evolutionary routes that seed new disordered segments within pre-existing proteins are still poorly understood. Sequence insertions provide a powerful mechanism for disorder expansion, but the genomic donors of inserted IDR and its long-term conformational fate remain largely unknown. Transposable elements (TEs), abundant mobile genetic elements with distinctive compositional biases, represent compelling candidates for generating disorder within proteins. Here, we systematically mapped TE-derived segments across human proteins and isoforms, and we found that these insertions are strongly enriched in intrinsic disorder. The structural consequences of their insertion are shaped by TE class and family, reflecting the sequence biases of the elements from which they originate. Recent, Primate specific insertions preferentially generate disordered segments, whereas older insertions more frequently occupy ordered structural contexts, revealing an age-dependent transition in the conformational state of TE-derived sequences. TE-containing isoforms are expressed at lower levels than TE-free isoforms, particularly when insertions are young and disorder-rich, suggesting that intrinsic disorder may constrain the cellular tolerance of newly exonized sequences. These findings identify TEs as a major evolutionary mechanism linking genome mobility to the emergence of new disordered conformational ensembles in the human proteome.

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

Pareto LoRA: Mitigating Modality Imbalance in Unified Multimodal Models via Pareto-Optimal Gradient Integration

Unified multimodal models (UMMs) have recently emerged as a promising paradigm for integrating multimodal understanding and generation within a single autoregressive transformer. However, during multimodal instruction tuning, these models often exhibit pronounced modality imbalance: language gradients dominate optimization, thus leading to lower image generation quality, especially under parameter-efficient fine-tuning such as LoRA. In this work, we systematically analyze modality imbalance in LoRA-based fine-tuning of UMMs for interleaved text-image generation. We show that vision modality performance degrades substantially more than text modality performance when compared to unimodal counterparts, and that modality-specific gradients can differ by orders of magnitude across various tasks and layers. Motivated by this observation, we reformulate the multimodal instruction tuning as a bi-objective optimization problem and propose Pareto LoRA, a Pareto-optimal gradient integration strategy that balances the text and image objectives by modulating the gradient direction and strength. Experiments on the CoMM benchmark with Emu2 demonstrate that Pareto LoRA consistently improves multimodal generation balance, achieving up to 44.9% gains in perceptual image quality over vanilla LoRA while maintaining comparable text performance.

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

Demystifying Variance in Circuit Discovery of LLMs

arXiv:2606.16920v1 Announce Type: cross Abstract: Circuit discovery is a key technique in mechanistic interpretability to pinpoint the model components that are crucial for performing a given task. Although the current state-of-the-art method (EAP-IG) performs well on the metric of (un)faithfulness, it suffers from substantial variability. This includes resampling variance, where the circuit changes when we probe with a new batch of data from the same distribution; rephrasing variance, where the discovered circuit shifts when the prompts are rephrased; and sample-wise variance, where a circuit with low population unfaithfulness exhibits large fluctuations in unfaithfulness across individual samples. This paper studies the roots of these variances. We demonstrate that CEAP, our new circuit discovery method that improves upon EAP-IG with a theoretical guarantee, can substantially lessen resampling variance. We further show that rephrasing variance arises because prompts with different templates tend to activate different circuits in the model. This leads us to argue that it may be challenging to find a comprehensive circuit that explains and controls the model's behavior on a task, which can be expressed in countless templates, suggesting that LLMs may be inherently hard to steer. We show that sparsity, which has been claimed to form more compact and interpretable task circuits, fails to solve this problem. Regarding sample-wise variance, we argue that it is largely benign: extremely poor unfaithfulness scores often stem from how unfaithfulness is defined, rather than from defects in the measured circuits. We show that the magnitude of unfaithfulness is affected by selective contribution scaling, a neural mechanism that accounts for the extremely poor scores sometimes observed.

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

Temporal Motif-aware Graph Test-time Adaptation for OOD Blockchain Anomaly Detection

arXiv:2605.29526v2 Announce Type: replace-cross Abstract: Ever-evolving transaction patterns have significantly hindered anomaly detection on emerging cryptocurrency blockchains due to the vast number of addresses and diverse anomalous behaviors. Recently, advanced Graph Anomaly Detection (GAD) approaches applied to blockchains have faced two critical challenges: adversarial pattern evolution by malicious actors and the out-of-distribution (OOD) problem caused by varied transaction semantics on blockchains. To address these challenges, we propose a novel framework termed TEmporal Motif-aware Graph Test-Time Adaptation (TEMG-TTA). First, we comprehensively capture the 3-node temporal motif distribution of each active address using an efficient computational mechanism, enabling downstream temporal motif-aware graph learning. Second, we design a simple yet effective test-time adaptation strategy to facilitate the sharing of common patterns between training and testing graphs. Extensive experiments on 5 real-world datasets demonstrate that our proposed TEMG-TTA outperforms state-of-the-art GAD approaches by an average of 54.88\%. A further case study on interpretable motif patterns reveals that TEMG-TTA explicitly characterizes the complex transaction patterns of anomalous addresses, thereby verifying the effectiveness of our technical designs. Our code is publicly available at https://github.com/LuoXishuang0712/TEMG-TTA/.

18.
arXiv (CS.LG) 2026-06-19

QMaxCal: Path-Space Regularization for Open Quantum Control via Girsanov's Theorem

arXiv:2606.19947v1 Announce Type: cross Abstract: Reliable quantum control in the presence of decoherence requires policies that combat the effect of environmental noise on the controlled dynamics. Open quantum systems under continuous monitoring generate classical measurement records whose drift depends on the noise experienced by the system; the records of two evolutions sharing the same decoherence channels differ only in this drift, so Girsanov's theorem yields a closed-form, differentiable estimator of the KL divergence between their trajectory distributions. We instantiate this estimator with two physically motivated reference measures, yielding two regularizers that both drive the system toward states where the effects of decoherence are minimal: the Wiener KL (KL_W), which is empirically more effective under certain conditions on the noise model, and the drift-variance regularizer (R_DV), which works for all noise models. Both are qualitatively distinct from existing penalties on control fluence or smoothness: they penalize the observable consequences of control on the decoherence channels rather than the control amplitude itself. The regularizers outperform unregularized gradient-based and reinforcement-learning baselines across a range of open quantum systems – including single- and multi-qubit benchmarks and a multi-qubit chain calibrated to a published snapshot of the IBM Kingston processor – along several axes of evaluation: final-state fidelity, robustness to mismatch in the assumed noise model (gains grow from +17 pp at training noise to +27 pp under 2.5x noise mismatch), and occupation of forbidden states. The regularizers reduce infidelity by up to 50%, with ~16% gains on the calibrated IBM Kingston chain.

19.
arXiv (math.PR) 2026-06-11

Consensus on Dynamic Stochastic Block Models: Fast Convergence and Phase Transitions

arXiv:2209.03999v2 Announce Type: replace Abstract: We introduce two models of consensus following a majority rule on time-evolving stochastic block models (SBM), in which the network evolution is Markovian or non-Markovian. Under the majority rule, in each round, each agent simultaneously updates their opinion according to the majority of their neighbors. Our network has a community structure and randomly evolves with time. In contrast to the classic setting, the dynamics is not purely deterministic, and reflects the structure of SBM by resampling the connections at each step, making agents with the same opinion more likely to connect than those with different opinions. In the Markovian model, connections between agents are resampled at each step according to the SBM law and each agent updates their opinion via the majority rule. We prove a power-of-one type result, i.e., any initial bias leads to a non-trivial advantage of winning in the end, uniformly in the size of the network. In the non-Markovian model, a connection between two agents is resampled according to the SBM law only when at least one of them changes opinion and is otherwise kept the same. We identify the phase-transition threshold, up to the second-order leading term, between halting and fast convergence to consensus. We also give sufficient initial-lead conditions for consensus to occur within one, two, or three rounds.

20.
Nature Medicine 2026-06-22

Biological aging and generational shifts in early-onset cancer risk

作者:

Incidence of early-onset cancer is rising globally in recent generations, which underscores the need to elucidate the influence of emerging generational risk factors. Systemic and organ-specific aging reflects the cumulative impact of exposures and may provide an integrative and complementary approach to understand early-onset cancer risk. Here among 154,169 young adults from the United Kingdom Biobank, systemic aging measured by PhenoAge increased across birth cohorts, with 23% s.d. increase for those born 1965–1974 versus 1950–1954, and was associated with early-onset solid cancer risk (hazard ratio (HR)per s.d. 1.08; 95% confidence interval (CI), 1.03–1.13), driven by lung, gastrointestinal and uterine cancers, independent of genetic risks of aging and cancer. Patterns were consistent using alternative systemic aging measures, including the Klemera–Doubal method-defined age gap and metabolomic-based age gap. These findings were validated partially among 10,262 participants in the United States All of Us Research Program. Proteomics-based organ-specific aging analyses linked immune aging with early-onset lung cancer (HRper s.d. 1.89; CI, 1.20–2.97) and adipose tissue aging to early-onset colorectal cancer (HR 1.60; CI, 1.11–2.32). Greater age gap, reflecting more advanced biological aging relative to chronological age, may serve as a driver associated with risk of early-onset solid cancers, highlighting the importance of uncovering underlying mechanisms to guide effective prevention strategies. Analyses of population cohorts found that young adults exhibited earlier systemic and organ-specific aging, which was associated with increased risk of early-onset cancer compared with older adults born decades earlier.

21.
Nature (Science) 2026-06-17

<i>CHPO</i> coordinates chilling recovery and nitrogen use in rice

作者:

Global rice production faces mounting challenges from abnormal temperature fluctuations and nitrogen-fertilizer-driven environmental pollution1–7. Developing varieties that balance chilling resilience and nitrogen-use efficiency (NUE) offers a promising solution, but the molecular networks coordinating these traits remain poorly understood. Here we identify CHILLING PHOENIX (CHPO), a major gene underlying the quantitative trait locus shared by both chilling tolerance and resilience. It encodes a MYB transcription factor that acts as a key regulator coordinating post-chilling recovery with nitrogen use in rice. Natural variation in a GCG-repeat-encoded polyalanine tract alters CHPO DNA-binding preference and redirects regulatory outputs between the japonica-type (CHPOjap) and indica-type (CHPOind), causing opposing effects on chilling tolerance and resilience. This allelic variation is shaped by domestication selection, with the CHPOjap allele probably derived from Chinese wild rice. CHPOjap directly targets OsTCP19 and OsNRT2.4 to fine-tune NUE, thereby enhancing chilling tolerance and resilience. These findings provide a mechanistic framework for a chilling-induced high-nitrogen-utilization module that alleviates the damage caused by chilling stress, and a potential molecular design&nbsp;strategy for breeding rice varieties with both chilling resilience and high NUE at the&nbsp;recovery stage. A rice gene, CHPO, links chilling resilience with nitrogen-use efficiency, revealing a domestication-shaped regulatory mechanism that could guide breeding of climate-resilient, sustainable rice varieties.

22.
bioRxiv (Bioinfo) 2026-06-11

Machine Learning-Guided Discovery of Bacterial-Selective Membrane-Active Compounds Reveals Mechanistic Bias in Antibiotic Training Datasets

The rise of antibiotic resistance necessitates the discovery of antibacterial compounds with novel mechanisms of action (MoAs). Recent machine learning approaches have shown promise in antibacterial compound discovery, but often identify derivatives of known antibiotic classes rather than mechanistically novel compounds. Previous approaches applied Tanimoto similarity filters at the end of screening pipelines, but this method has substantial drawbacks: Tanimoto similarity can be misleading in chemical space, and post-hoc filtering does not influence what activity models learn to prioritize. Here, we present a machine learning pipeline that addresses chemical novelty upfront by employing an XGBoost-based MoA classifier to explicitly prioritize compounds predicted to have mechanisms distinct from known antibiotic classes, combined with graph neural networks for antibacterial activity and toxicity prediction. Applied to the Zinc20 database, our approach successfully identified non-toxic antibacterial compounds structurally distinct from known antibiotics. Notably, the majority of these hits exhibited membrane-targeting activity with selectivity for bacterial cells over mammalian cells, suggesting potential for next-generation membrane-active antibiotics. However, we did not identify compounds with novel protein targets. Systematic analysis revealed that this limitation stems from mechanistic bias in training data rather than model architecture. Specifically, our activity model learned to preferentially score compounds similar to specific groups in the training data, thus overrepresenting certain MoA classes including membrane-active compounds. Even substantial model architecture and training data enhancements did not overcome this constraint. Our findings demonstrate that the primary bottleneck for discovering mechanistically novel antibiotics is the scarcity of diverse, mechanistically-annotated training data. This work provides both a methodological framework for mechanism-aware screening and critical insights into data requirements for genuinely novel antibiotic discovery.

23.
arXiv (CS.LG) 2026-06-11

Phase Transitions in Attention: A Bayesian Theory of Copy Head Emergence

arXiv:2606.12058v1 Announce Type: cross Abstract: Attention is the key mechanism underlying in-context learning in transformers, and attention patterns have been observed empirically to emerge abruptly during training. We present a Bayesian theory of feature learning in attention; we then focus on how the copy subcircuit in the first layer of an induction head is learned by analyzing a single-layer softmax attention network trained on a copy task. We derive a closed-form posterior over the attention matrix and reduce it to a low-dimensional order parameter space. This reduction reveals a phase transition in the amount of training data, which we verify using both Bayesian sampling and standard training with Adam. We contrast our results with linear attention and find that softmax attention exhibits a first-order phase transition while in linear attention an initial second-order phase transition is followed by a smooth, continuous evolution toward the structured attention pattern (crossover). Our work provides a first-principles theoretical account of the abrupt emergence of the copy subcircuit, reminiscent of the one observed in training large language models.

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

AI Sovereignty as National Learning Capacity: A Human-Centered Learning Mechanics Viewpoint on France, the United States, and China

arXiv:2606.00729v2 Announce Type: replace Abstract: Artificial intelligence in France is often discussed through separate dimensions such as investment, compute, regulation, employment, sovereignty, and education. This viewpoint paper proposes a unified interpretation: France can be analyzed as a national AI learning system. Building on Human-Centered Learning Mechanics (HCLM), we use HCLM not as a validated econometric model, but as a conceptual and diagnostic lens for interpreting national AI development as a balance between information injection, absorptive capacity, and institutional dissipation. Information injection includes compute, data, talent, research, capital, industrial deployment, and policy experimentation. Institutional dissipation refers to avoidable frictions such as administrative overload, coordination failures, energy constraints, regulatory uncertainty, talent mobility pressures, and weak industrial absorption. Regulation is not treated as mere friction: adaptive governance, trusted data spaces, and safety-oriented standards may increase long-term learning capacity by improving legitimacy, interoperability, and social trust. The central claim is not that a country follows neural-network equations, but that AI sovereignty depends on how effectively it converts distributed information into absorbed, coordinated, and socially legitimate capability. The paper connects HCLM with neural scaling laws, endogenous growth theory, creative destruction, absorptive capacity, and coordination mechanisms. It offers a formal heuristic, policy indicators, illustrative scenarios, and implications for France. The numerical results are diagnostic scenarios, not econometric estimates or official rankings. The proposed viewpoint reframes AI policy as the governance of an open, strategic, non-equilibrium learning system that should be tested with historical and cross-country data.

25.
arXiv (quant-ph) 2026-06-16

Interaction and non-Hermiticity controlled transmission in extended Su-Schrieffer-Heeger models

arXiv:2606.15245v1 Announce Type: cross Abstract: We study the transport characteristics of an extended version of the Su-Schrieffer-Heeger (SSH) model with next-nearest-neighbor (NNN) interactions and non-Hermitian onsite energies. We observed that transport in such a system is significantly modified by the NNN interaction and the non-Hermitian terms. The transmission coefficient exhibits oscillatory behavior as the strength of the NNN interaction varies in a fixed-length chain. Moreover, the transmission coefficient also shows oscillation with system size for a fixed strength of the NNN interaction. We find that novel oscillatory behavior of the transmission coefficient, arising form the NNN interaction, is a unique feature of such a model and has not been reported previously. The presence of the non-Hermitian terms also enhances/reduces the transmission coefficient depending on the values of the other system parameters like intra-, inter- and NNN hopping. It appears from our study that both the NNN interaction and the non-Hermiticity introduce significant changes in the transport properties of the extended SSH chain, which are not observed in the standard Hermitian nearest-neighbour variant of the SSH model.