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01.
arXiv (CS.AI) 2026-06-18

Domain-Shift Aware Neural Networks for Unbalance Characterization in Rotating Systems

arXiv:2606.18882v1 Announce Type: cross Abstract: This work investigates the application of a domain-shift aware neural network for regression tasks aimed at estimating unbalance masses in rotating shafts under varying operating conditions. Experimental data were collected from a test rig in which a primary shaft, equipped with a flange carrying unbalanced masses, was driven at different rotational speeds, while a secondary shaft could be optionally activated to introduce domain discrepancy. The unbalance masses were positioned at a fixed radial distance, and the dynamic response of the system was recorded using triaxial accelerometers. The inverse problem of mass estimation is formulated within a domain adaptation framework, where the network is trained with a maximum mean discrepancy strategy to align feature representations across source and target distributions. The results demonstrate the effectiveness of explicitly addressing domain shift in improving prediction accuracy, especially when the system's physical behavior and sources of domain discrepancy are not fully known and fall outside the training conditions. These findings highlight the potential of domain-shift aware models for regression tasks in Structural Health Monitoring.

02.
arXiv (CS.AI) 2026-06-15

ANSR-DT: A Neuro-Symbolic Framework for Adaptive and Explainable Digital Twins

arXiv:2501.08561v4 Announce Type: replace Abstract: Digital twins are increasingly used to monitor and optimize industrial systems, yet many existing frameworks remain difficult to interpret, slow to adapt, and limited in their ability to incorporate explicit domain knowledge. This paper presents ANSR-DT, an adaptive neuro-symbolic framework that unifies temporal anomaly detection, symbolic reasoning, and reinforcement-learning-based decision support within a single digital twin pipeline. ANSR-DT combines a CNN-LSTM model for multivariate pattern recognition with Prolog-based reasoning that converts learned signals into explicit rules, enabling transparent diagnoses and traceable decision paths. A PPO-based adaptation layer further refines operational responses under changing conditions while preserving interpretability. Experiments against 8 baselines show that ANSR-DT delivers competitive predictive performance together with stable rule extraction, scalable symbolic reasoning, and actionable explanations. Additional validation on the Skoltech Anomaly Benchmark (SKAB) further indicates that the framework transfers beyond synthetic settings. These findings position ANSR-DT as a practical foundation for trustworthy, adaptive, and explainable industrial digital twins.

03.
medRxiv (Medicine) 2026-06-18

Early-life Urban Environment, Nutrition, and Pubertal Timing in Southern Europe: An Exposome Analysis

Background: Urban environmental and lifestyle factors during early life may influence pubertal timing, but the combined effects of multiple environmental exposures within an exposome analytical framework remain poorly understood. Objective: To examine the association between early-life urban environmental exposures and pubertal timing, and to explore whether these exposures interact with early-life nutritional factors, namely breastfeeding duration and childhood diet quality. Methods: Data from two European population-based birth cohorts were analysed: Generation XXI (G21, Portugal; n=5263; 51.5% girls) and INfancia y Medio Ambiente (INMA, Spain; n=1019; 50.1% girls). Urban environmental exposures including indicators of air pollution, traffic, built environment, and natural spaces were estimated at 4 early-life stages at both cohorts: pregnancy (INMA only), birth, 1 year, and 4-5 years of age. Pubertal development timing was assessed using Tanner staging and/or the Pubertal Development Scale (PDS), and age at menarche was self-reported. Exposome-Wide Association Study (ExWAS) models and unsupervised clustering followed by ordinal logistic regression models were used to examine single- and multi-exposure associations, respectively. Regression models were fitted adjusting for relevant child characteristics, maternal factors, and household socioeconomic conditions, and corrected for multiple testing. Results: Individuals living in more unfavourable urban environments characterised by higher building density, air pollution, and lower access to natural spaces showed earlier pubertal timing according to multiple outcomes, across multiple early-life exposure periods, and in both cohorts. In the G21 cohort, these environmental profiles were associated with earlier age at menarche, particularly for exposures at 1-1.5 and 4-5 years (e.g., 1-1.5y: {beta}=-0.172, FDR-adjusted p-value=0.041), while in the INMA cohort, boys exposed to more unfavourable environmental profiles showed more advanced pubertal development, also particularly for exposures at 1-1.5 and 4-5 years of age (e.g., 1-1.5y; {beta}=0.572, FDR-adjusted p-value=0.008). Among environmental domains, air pollution and traffic were the factors most consistently associated with pubertal timing. Regarding early-life nutritional factors, longer duration of exclusive breastfeeding was associated with a lower Tanner stage among girls in G21. No significant interactions between breastfeeding duration and environmental exposure clusters were observed. Conclusion: Early-life urban environmental exposures, particularly air pollution and traffic, may influence pubertal timing. Exclusive breastfeeding may have a protective role against earlier pubertal development. These findings highlight the importance of improving urban environmental conditions and promoting breastfeeding to support healthy developmental trajectories.

04.
arXiv (CS.AI) 2026-06-16

The Quality-Utility Paradox: Why High-Reward Data Impairs Small Model Mathematical Reasoning

arXiv:2606.16152v1 Announce Type: new Abstract: Knowledge distillation from powerful reasoning models is widely used to improve Small Language Models (SLMs) on mathematical reasoning, often assuming that traces with higher reward model scores provide more useful supervision. We identify a counterintuitive Quality-Utility Paradox in mathematical reasoning distillation. Data refined or synthesized by a stronger Oracle obtains higher perceived quality according to reward models, yet consistently underperforms traces generated by the SLM itself and selected through rejection sampling across Qwen2.5, LLaMA-3, and DeepSeek families. Our analysis shows that Oracle refinement couples logical repair with distributional drift away from the SLM's native reasoning distribution. This drift increases the learner's adaptation cost and can outweigh the benefit of improved reasoning logic. To test this mechanism, we introduce Style-Aligned Refinement, which preserves the native trajectory of the SLM while retaining logical repair from the Oracle. This intervention lowers adaptation cost and restores downstream utility. These findings suggest that effective mathematical reasoning distillation should jointly optimize perceived solution quality and learner-data compatibility, rather than relying solely on reward-model scores. The datasets and code are available at https://github.com/Dracoqhl/Quality-Utility-Paradox.

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

Hierarchical Multi-Modal Retrieval for Knowledge-Grounded News Image Captioning

Traditional image captioning methods often struggle to generate comprehensive, context-rich descriptions, especially for details not directly observable from visual cues. To overcome this, we propose a novel retrieval-augmented image captioning framework that generates captions with deeper insights, such as object attributes, event context, and underlying significance, by leveraging external knowledge. Our approach features a hierarchical multi-modal article retrieval mechanism that moves beyond monolithic text entities. This retrieval considers article structure-aware features, including weighted textual components (e.g., headlines, body sections) and visual placement patterns, alongside multi-faceted similarity computations (content–visual, visual–visual, and discourse positioning). A subsequent contextual relevance refinement stage further enhances the retrieved information. The retrieved articles then serve as the knowledge base for caption generation: first, a VLM generates a concise image description; second, we segment relevant information from the retrieved articles based on this description; and finally, an LLM utilizes both the description and extracted knowledge to generate a comprehensive, contextually detailed caption. We participated in the ACM Multimedia EVENTA 2025 Challenge and achieved 5th place with an overall score of 0.2824 on the private test set of the OpenEvent-V1 dataset. Source code is publicly released at https://github.com/mf0212/EVENTA-Challange.

06.
PLOS Medicine 2026-05-20

Prescribed hormonal contraceptive use trends in the Estonian Biobank: A longitudinal observational study

by Jelisaveta Džigurski, Märt Möls, Kristi Läll, Hannah Currant, Mall Eltermaa, Estonian Biobank Research Team , Reedik Mägi, Lili Milani, Triin Laisk Background Hormonal contraceptives (HCs) are widely used and have well-documented population-level statistics. Previous studies with short follow-ups have focussed on individual HC use and side effects. However, the same aspects over longer periods, HC formulation switching, and the impact of genetic factors on HC side effects remain understudied due to the limited availability of suitable datasets. We investigated whether the Estonian Biobank (EstBB) is suitable for studying genetic risk for HC side effects. Methods and findings This is a longitudinal descriptive study combining prescribed HC purchase data collected from 2004 to 2022 with genetic and health data from 73,071 female EstBB HC users aged 15–55 at the time of purchase. HC usage was defined by the Anatomical Therapeutic Chemical (ATC) codes G02B, G03A, and G03HB01. Methods included calculating age-stratified annual user prevalence, inferring usage periods from purchases, assessing formulation switching, identifying the International Classification of Diseases, Tenth Revision (ICD-10)-based side effect-related diagnoses and thromboembolism risk factors, and assessing carrier status for Factor V Leiden (FVL, rs6025) and prothrombin G20210A (PTM, rs1799963) genetic variants as proof-of-concept. Over 19 years, 20 HC formulations with five administration routes (oral pills, transdermal patches, vaginal rings, subdermal implants, intrauterine devices) were used. In the EstBB, combined HCs were the most commonly used among users aged 15–29, while progestin-only HC use increased with age and over time, comparable to the Estonian population. Overall, 64.2% (n = 46,920) of users switched formulations at least once, with 17.7% (n = 12,929) being rapid switchers. Side effect-related diagnoses were observed in 23.1% (n = 2,982) of rapid switchers, with excessive/irregular menstrual bleeding being the most common. Genetic analysis revealed that 5.3% (n = 3,886) of users carried at least one variant previously associated with increased thrombosis risk (3.5% (n = 2,556) carried FVL only, 1.8% (n = 1,276) PTM only, and 0.07% (n = 54) both). Carriers of thrombosis-associated variants had a significantly higher percentage of thrombosis (6.5%) than non-carriers (4.2%; OR = 1.61, 95% CI [1.40, 1.84], p 

07.
arXiv (CS.AI) 2026-06-17

Constitutional On-Policy Safe Distillation

arXiv:2606.03089v2 Announce Type: replace-cross Abstract: On-policy self-distillation (OPSD) has emerged as an efficient post-training paradigm by using a teacher conditioned on privileged information to provide dense token-level supervision. Prior work has shown that OPSD can collapse in verifiable reasoning tasks, but safety alignment differs in that it is guided by high-level constitutions rather than explicit target answers, making it a natural setting to revisit dense distillation. However, our pilot study show that safety OPSD still suffers from severe collapse: constitutional conditioning contracts the teacher distribution toward short and overly conservative responses, and Reverse KL further amplifies this contraction into reduced expressiveness. We formalize this effect as geometric leakage under safety boundaries in a non-orthogonal semantic space, where safety pressure transfers into the expressiveness dimension. Based on this analysis, we propose Constitutional On-Policy Safe Distillation (COPSD), which first calibrates the teacher through a Cross-SFT cold-start and then performs constitution-conditioned on-policy distillation. Experiments on 12 benchmarks show that COPSD achieves a consistently stronger safety–helpfulness trade-off than baselines while substantially reducing the safety tax on general reasoning ability.

08.
arXiv (CS.CV) 2026-06-16

HSQ-VLM: A Novel Spatially-Constrained Quadrant Segmentation VLM Model for Explainability in Diabetic Retinopathy

Diabetic Retinopathy (DR) is an aggressive retinal disease and a leading cause of global blindness, yet its clinical management is currently hindered by the black-box nature of diagnostic AI. While deep learning models achieve high classification accuracy, there is a critical lack of explainability methods capable of detailing the exact anatomical landmarks and lesion distributions that lead to a clinical decision for DR. Therefore, we propose HSQ-VLM, a novel quadrant segmentation pipeline on fundus images that utilizes a Landmark-Anchored Cartesian Cross-Attention mechanism to unify visual feature extraction with structured clinical reasoning. Unlike traditional methods that rely on arbitrary image partitioning, our pipeline implements 4-quadrant Topological Latent Partitioning (TLP) to dynamically align retinal features with a fovea-centered coordinate system. This allows the Vision-Language Model to generate natural language reports that quantify pathology with anatomical precision. On a dataset of 3,500 high-resolution fundus images, this innovative methodology achieved a lesion detection sensitivity of 99.6% for hemorrhages and 96.4% for microaneurysms, while demonstrating a significant reduction in boundary-ambiguity errors compared to standard segmentation baselines.

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

LearnOpt: Recovering the Latent Cognitive Structure of Standardized Examinations via Knowledge Graphs and Constrained Optimization

arXiv:2606.15349v1 Announce Type: cross Abstract: Standardized examinations are typically treated as uniform syllabus coverage problems. We argue they are better understood as adversarial systems with stable latent cognitive structures diverging systematically from official syllabi. We introduce LearnOpt, which recovers this structure from historical question papers and generates personalized, time-bounded study plans. Applied to nine years of NEET questions (2016-2024, n=1,496), LearnOpt builds an exam knowledge graph from LLM-tagged questions, extracts a five-category latent skill distribution, and formulates study planning as a knapsack-variant optimization over prerequisite-aware subgraphs with Bayesian Knowledge Tracing. Central finding: NEET's latent skill distribution is stable within a syllabus regime (consecutive-year KL divergence 0.004-0.032 for 2016-2021, non-significant under permutation testing) but shifts significantly with NCERT's 2023 syllabus rationalization: pooling 2016-2021 (n=1,072) vs 2023-2024 (n=392) gives KL=0.040 (p=0.0005), with Elimination/Negation questions rising from ~20-29% to ~31-35%. Latent structure, while not permanently stationary, is piecewise stable, with shifts detectable and attributable to curricular events. Within either regime, subject predicts skill profile more strongly than year. An optimization evaluation, using one real and two synthetic mastery profiles, shows the skill-weighted objective produces a modest but real reordering of recommended topics over a mastery-conditioned frequency baseline. Applying the pipeline to JEE Advanced reveals a profile dominated by Multi-concept Integration (80.9% vs. 33.3% for NEET), with a JEE-vs-NEET divergence (KL=0.505) exceeding NEET's largest cross-subject divergence: exam tier shapes latent cognitive structure more than subject, which shapes it more than time within a regime. Code, knowledge graph, and annotated dataset are released publicly.

10.
arXiv (CS.LG) 2026-06-19

Score Approximation for Diffusion Models on Arbitrary Low-Dimensional Structures

arXiv:2606.19894v1 Announce Type: new Abstract: The remarkable success of score-based diffusion models has spurred significant efforts to establish their theoretical foundations. However, existing complexity bounds for score approximation rely heavily on restrictive assumptions like Lipschitz continuous densities or smooth manifold supports, which are routinely violated by the singularities, sharp boundaries, and disjoint clusters inherent to real-world perceptual data. This work establishes a universal score approximation theorem that works for any distribution supported on any compact set of upper Minkowski dimension $d$. Using a novel discrete-mixture formulation, we prove that the score function can be approximated with a ReLU network whose complexity grows exponentially only with $d$, thus breaking the exponential curse of ambient dimensionality. Combined with existing theories on accurately solving the backward diffusion SDE for arbitrary compact distributions, our work shows that diffusion models readily adapt to irregular, non-smooth data structures, explaining their competence in real-world generative tasks.

11.
bioRxiv (Bioinfo) 2026-06-11

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

Long-read RNA sequencing enables haplotype- and isoform-resolved allelic analysis of transcriptomes, yet extending this capability to single cells and distinct cell types remains computationally challenging due to sparse coverage, sequencing errors, incomplete variant information, and reference-biased transcript assignment. Here we present ANCHOR, a haplotype-aware framework for single-cell long-read RNA sequencing that performs de novo expressed-variant discovery, molecule-level haplotype assignment and isoform-resolved allelic quantification. ANCHOR combines a signed-graph variant caller, pair hidden Markov modelling and beta-binomial UMI aggregation to infer parental allele counts for genes and splice-resolved isoforms, without requiring a pre-existing phased genotype or deep learning. In human single-cell long-read RNA benchmarks, ANCHOR improved variant-calling performance over tested long-read RNA callers at single-cell and low-to-moderate coverage, and its beta-binomial model reduced depth-driven false positives in allele-specific expression testing. Applied to newly generated single-cell long-read RNA-seq data from reciprocal mouse crosses during gastrulation, ANCHOR resolved cell-type- and isoform-specific parent-of-origin imprinting and identified an antagonistic maternally biased Sgce isoform. ANCHOR provides a general framework for allele- and isoform-resolved analysis of diploid single-cell long-read transcriptomes.

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

Visored: A Controlled-Natural-Language Prover for LLM-Generated Mathematics

arXiv:2606.17581v1 Announce Type: cross Abstract: We present a dependent-type-based prover designed around the way LLMs (and humans) tend to write mathematics, complementing existing systems such as Lean and Rocq. Its core design choices are a surface that imitates mathematical natural language and a rule-driven automation layer that closes the routine steps a textbook would omit, so that an accepted proof can be re-emitted as a checked Lean file. Early experiments suggest that, even without any prover-specific training data, LLMs can learn to use it effectively on the miniF2F benchmark. Lean output excerpts: https://github.com/xiyuzhai-husky-lang/visored/

13.
Science (Express) 2026-04-16

Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase | Science

作者: 未知作者

Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), synthesizes alternating poly(GT/AC) double-stranded DNA. Cryo–electron microscopy structures at 2.6 Å resolution reveal a D3-symmetric 6:6:6 complex of Drt3a, Drt3b, and ncRNA. Drt3a produces the poly(GT) strand using a conserved ACACAC template within the ncRNA. Notably, Drt3b synthesizes a complementary, protein-primed poly(AC) strand in the complete absence of a nucleic acid template, using conserved active site residues specific to Drt3b to enforce precise base alternation. These findings expand the functional landscape of nucleic acid polymerases, revealing a protein-templated mechanism for sequence-specific DNA synthesis.

14.
arXiv (CS.CV) 2026-06-16

Avoiding Exponential Blow-Up in Distributive Lattice Submodular Minimization

作者:

Submodular function minimization has gained a lot of interest in recent years. They are highly applicable in the area of Computer Vision and Machine Learning. Often such applications require to work with submodular functions defined on distributive lattice. Current best way of dealing with it is using a transformation which extrapolates the submodular function for the respective boolean lattice. It makes optimization system too inefficient due to enlargement of the working space. Quantitatively, the expanded space has additional exponential (in set size) number of elements. We propose a generic framework for dealing with distributive lattice which only works within distributive lattice. Our framework allows one to use already established submodular function minimization algorithms for boolean lattice. In our experiment, we show the huge improvement in terms of running time over tranditional methods for handling distributive lattice.

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

AnnotateAnything: Automatic Annotation of 3D Assets for Robot Manipulation

Simulation enables scalable robot data collection, but raw 3D assets provide only geometry, lacking the semantic, interactive, and physical knowledge needed to specify where and how robots should act. In this work, we present AnnotateAnything, a general automatic annotation framework that converts passive 3D assets into manipulation-ready assets with structured, diverse, and executable manipulation labels. AnnotateAnything is built around two complementary pipelines. First, a unified visual-language annotation pipeline using vision-language reasoning to infer object semantics, interaction constraints, and 3D-grounded cues, providing human-prior guidance for identifying meaningful interaction regions. Second, a fully automatic and massively parallel physics annotation pipeline grounds these priors in each asset's geometry and physical constraints through candidate generation, geometry optimization and trajectory generation. This pipeline produces diverse and executable action annotations, including grasp poses, dexterous contacts, articulation waypoints, insertion directions, hanging affordances, and navigation targets. Using the generated annotations, we further build an asynchronous parallel simulation data-collection system across diverse objects, tasks, and robot embodiments. Experiments demonstrate that AnnotateAnything achieves superior annotation efficiency, data-collection efficiency, and task success rates over existing annotation and data-generation pipelines, while also supporting downstream tasks such as affordance detection, robotic VQA, and visual instruction finetuning. We provide project materials on the project page and plan to release the full code, annotations, and benchmark to facilitate future research. Videos, code, demo assets, and annotations are provided in supplementary materials Project page: https://tourmaline-caramel-169490.netlify.app.

16.
bioRxiv (Bioinfo) 2026-06-10

Is level-1 blob reconstruction under the network multispecies coalescent easy?

作者:

Hybridization is an important evolutionary process, commonly modeled by the network multispecies coalescent. Reconstructing evolutionary histories under this model is notoriously costly, even for level-1 networks where hybridization events are isolated from each other. The widely used methods that combine speed with statistical guarantees rely on quartet concordance factors computed for all subsets of four species, resulting in an o(n^4k) bottleneck that severely limits scalability to large numbers of species (n) and genes (k). Among quartet-based methods, NANUQ+ is notable because it decomposes the problem into two steps: first reconstructing a tree of blobs, which compresses each non-treelike part of the network, called a blob, into a single vertex, and second reconstructing the internal structure of each level-1 blob, specifically its circular order and hybrid vertex. Here, we investigate whether level-1 blob reconstruction is difficult once the tree of blobs is known. We present a fast and statistically consistent algorithm, called NetCS, based on two simple primitives: majority voting and merge sort, circumventing the bottleneck of computing all quartet concordance factors. In simulations, NetCS achieved comparable accuracy to NANUQ+ and was dramatically faster, enabling analyses of 200 taxa and 1000 genes in only a few minutes. Both methods attained near-perfect accuracy when given the true tree of blobs; however, their performance degraded in end-to-end pipelines due to errors in tree of blobs reconstruction. Strikingly, even methods that reconstruct level-1 networks directly struggled to accurately predict hybrid ancestry. Our results suggest that reconstructing level-1 blobs is unexpectedly easy once the tree of blobs is known, and that a major challenge for phylogenetic network inference lies in accurate tree of blobs reconstruction.

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

Compatibility-Aware Dynamic Fine-Tuning for Large Language Models

Supervised Fine-Tuning (SFT) is the predominant paradigm for aligning large language models (LLMs), yet it suffers from optimization instability and limited generalization. Recent work attributes this issue to pathological gradient scaling and proposes Dynamic Fine-Tuning (DFT) to correct it at the token level. However, DFT assumes all demonstrations are equally suitable learning targets, an assumption violated by the strong heterogeneity of large-scale instruction data, where demonstration-policy mismatch induces high-variance updates at the sample level. We introduce Compatibility-Aware Dynamic Fine-Tuning (CADFT), a principled extension of DFT that controls sample-level optimization variance. CADFT derives a dynamic, policy-dependent compatibility signal from model likelihoods to modulate supervised updates, suppressing high-variance gradients from incompatible demonstrations. We further propose a delayed, low-frequency compatibility-guided rewriting strategy to transform persistently incompatible demonstrations into learnable targets. We show that CADFT can be interpreted as a variance-controlled estimator that generalizes token-level stabilization in DFT to the sample level. Extensive experiments demonstrate improved stability, generalization, and cold-start reinforcement learning initialization, while remaining fully supervised and independent of explicit reward modeling.

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

TMASC: Transmasculine Attitude and Speech Corpus

作者:

We introduce the Transmasculine Attitudes and Speech Corpus (TMASC), a multimodal corpus of 196 transmasculine individuals, including questionnaire responses and 66 audio recordings. The questionnaire includes items exploring the vocal health of transmasculine individuals. The audio recordings include cough and throat-clearing samples, a reading passage, and additional session-specific questions. This paper outlines the development of this corpus and the data collection procedures. To illustrate the utility of this corpus, we present three case studies demonstrating how this crowd-sourced multimodal corpus can be used to support transmasculine individuals. These include the integration of perceptual and acoustic data, the identification of group-level characteristics, and the calibration of acoustic measurements.

19.
arXiv (quant-ph) 2026-06-15

Implementation of two-qubit Rydberg operations on neutral Rb-87 atoms in systems with different intermediate states

arXiv:2606.13975v1 Announce Type: new Abstract: This work presents an experimental setup for implementing two-qubit operations on neutral atoms ($^{87}$Rb) with the possibility of using two different Rydberg excitation schemes. One of them uses 5P$_{1/2}$ as the intermediate level and applies the second-stage beam locally to the addressed atoms. The second scheme uses the 6P$_{3/2}$ level; in this scheme, the particles to be entangled are moved to a separate zone through which both Rydberg beams pass. The advantages and limitations of both schemes are analyzed. Based on numerical modeling performed with a Julia package developed by the authors, it is demonstrated that the spatial configuration has a greater effect on quantum-operation fidelity than the choice of intermediate level. An experimental implementation of the scheme using the 6P$_{3/2}$ level is demonstrated, making it possible to achieve a two-qubit operation fidelity of 94%.

21.
bioRxiv (Bioinfo) 2026-06-16

Expanding gene regulatory networks from transcriptome data through graphical modeling with heterogeneous priors

Gene regulatory network inference is widely used to reconstruct large-scale networks and identify functional genes from transcriptome data. Meanwhile, in many biological fields, core regulatory genes have been extensively studied, leading to the establishment of small-scale gene regulatory networks, and novel genes connected to these networks remain to be identified. However, methods for expanding existing gene networks by identifying novel regulatory interactions, rather than reconstructing the entire network, are not well established. Here, we propose a method for gene network expansion that incorporates known regulatory relationships and evaluates each candidate gene individually to infer its regulatory connections to the existing network. Using simulated datasets from the DREAM4 benchmark and the PRECISE-1K experimental dataset, our method outperformed conventional methods by incorporating prior knowledge. In particular, it improved the ability to distinguish true regulatory interactions from indirect associations arising from strong correlations among genes in the existing network. The method also showed strong performance for interactions involving genes with high outdegree or centrality. Furthermore, it maintained stable performance as the size of the existing network increased and was robust to noise in prior information. These results demonstrate that our method provides an effective framework for expanding existing gene regulatory networks by leveraging prior knowledge.

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

DragMesh-2: Physically Plausible Dexterous Hand-Object Interaction with Articulated Objects

Dexterous interaction with articulated objects is important for household, assistive, and humanoid manipulation, where multi-finger hands can provide compliant contact patterns beyond parallel-jaw grasping. However, articulated-object manipulation differs from static-object manipulation: the target part cannot be directly actuated, and its motion must emerge through sustained physical hand–handle contact. This makes the transition from object-centric articulated generation to hand-driven dexterous hand–object interaction non-trivial, since geometric trajectory replay or open-loop execution does not model the contact dynamics required to move the articulated part. Moreover, policies trained only for task completion under fixed dynamics can overfit nominal contact loads, especially without tactile or force feedback, and may degrade when the contact load changes. To address these challenges, we present DragMesh-2, a contact-driven framework for dexterous interaction with articulated objects that extends articulated interaction from object-centric generation to hand-driven dexterous hand–object interaction, where articulated motion must arise through physical contact. We further propose PICA, a physically informed contact-aware training mechanism that injects physical signals into policy learning without tactile or force feedback, improving robustness and task success under changing contact loads. Finally, we conduct systematic evaluation across multiple damping conditions and articulated-object categories to study robustness under contact-load variation, and provide a pure-geometry dexterous interaction resource to support future loco-manipulation and humanoid hand–object interaction research. Across seven GAPartNet objects, DragMesh-2 achieves stronger robustness under contact-load variation than the compared methods while maintaining high task success across damping conditions.

23.
arXiv (quant-ph) 2026-06-16

Information Is Not Physical: Possibility Spaces, Erasure, and the Structure of Unrealized Alternatives

arXiv:2606.15120v1 Announce Type: cross Abstract: The slogan ``information is physical,'' introduced by Rolf Landauer and developed through quantum information theory and black-hole thermodynamics, has achieved near-axiomatic status in modern physics. Yet the ontological status of information remains surprisingly underexamined: most discussions either reduce information to a form of energy or treat it as a purely mathematical object. This paper proposes a third position. I argue that information is neither a physical substance nor a free-floating abstraction, but rather the structure of physically realizable alternatives – a counterfactual structure that a physical system instantiates in virtue of the possibility space available to it. Building on Shannon's combinatorial definition, the Landauer principle, the no-cloning theorem, and the black-hole information paradox, I show that the informational content of any physical event is constituted by the set of outcomes that could have occurred but did not. This counterfactual reading dissolves several persistent confusions: it explains why erasing information dissipates heat without making information ``material,'' why quantum superposition is informationally richer than any classical mixture, and why information loss in black holes is physically significant beyond mere bookkeeping. The proposal sits within a structural-realist framework but departs from standard structural realism by locating the relevant structure in modal, not merely actual, relations. I conclude by sketching implications for the foundations of quantum mechanics, quantum gravity, and scientific ontology more broadly.

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

AdaMame: A Training Recipe for Adaptive Multilingual Reasoning

While Large Reasoning Models (LRMs) show strong performance in English, they often fail to reason in the language of the query, a phenomenon known as language collapse. Existing RL-based fixes typically add a binary language fidelity reward to the accuracy objective, yet still incur trade-off in accuracy, mid-trace code-switching, and excessive token usage. In this work, we propose AdaMame, a two-stage training recipe for multilingual mathematical reasoning that addresses these limitations by adaptively aligning the reasoning language to the query language without compromising accuracy. The first SFT stage fine-tunes on naturally occurring reasoning traces across five languages to establish multilingual reasoning capability. In the subsequent RL stage, we introduce AdaMame-GRPO, an adaptation of Group Relative Policy Optimization (GRPO) in which a query-conditioned alignment factor grows progressively during training, guiding the model to first explore diverse reasoning languages before exploiting reasoning in the query language. Evaluated across two benchmarks, two LRMs, and 12 languages, AdaMame-GRPO achieves Pareto-optimal performance across reasoning accuracy, language fidelity, and token efficiency over all baselines, with the strongest gains on out-of-domain, lower-resource languages.

25.
arXiv (math.PR) 2026-06-18

First to reach $n$ game

arXiv:2506.08782v4 Announce Type: replace Abstract: We consider a game with two players, consisting of a number of rounds, where the first player to win $n$ rounds becomes the overall winner. Who wins each individual round is governed by a certain urn having two types of balls (type 1 and type 2). At each round, we randomly pick a ball from the urn, and its type determines which of the two players wins. We study the game under three regimes. In the first and the third regimes, a ball is taken without replacement, whilst in the second regime, it is returned to the urn with one more ball of the same colour. We study the properties of the random variables equal to the properly defined overall net profits of the players, and the results are drastically different in all three regimes.