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01.
arXiv (CS.LG) 2026-06-15

Geometric Domain Adaptation via Optimal Transport for Linear Regression in R^2

arXiv:2606.14023v1 Announce Type: cross Abstract: Optimal Transport has become recently a powerful method for domain adaptation by aligning source and target distributions. We study a supervised domain adaptation problem where source and target domains are related by a rotation or a translation or a homothety in $\mathbb{R}^2$. We prove that the optimal transport map recovers the underlying map when using a $p-$norm cost with $p \geq 2$. Based on this insight, we develop a method combining $K-$means and optimal transport to estimate the underlying map, enabling adaptation of linear regression models when target data is scarce. Simulations demonstrate improved performance over baseline methods. Rather than relying on highly expressive deep learning architectures, we focus on classical machine learning models to emphasize interpretability and theoretical insight. This perspective allows us to explicitly characterize the role of optimal transport in recovering geometric transformations such as rotations, translations, and homotheties. Our contributions include a theoretical result linking optimal transport and rotations, translations and homothecies in $\mathbb{R}^2$, and a practical method for adaptation in linear regression offering both conceptual clarity and applied value in domain adaptation tasks in this space.

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

A PubMed-Scale Dataset of Structured Biomedical Abstracts

Structured abstracts are important for biomedical literature processing, by facilitating information retrieval, text mining, and knowledge synthesis. However, a vast portion of abstracts indexed in PubMed remain unstructured, presenting a significant bottleneck for downstream text-processing workflows and applications. To resolve this limitation, we introduce Structured PubMed, a comprehensive corpus of section-labeled biomedical abstracts compiled from the complete PubMed database, encompassing over 23.2 million research-article records. The corpus is divided into two distinct subsets: a collection of 5.9 million author-structured abstracts parsed from official XML files, and an automatically labeled collection of 17.2 million originally unstructured abstracts structured via a verbatim-extraction Large Language Model pipeline. Every record is harmonized under a unified five-section schema and mapped to its original PubMed identifier, publication type, and publication date. This dataset can be utilized to train sentence-classification models, benchmark text-segmentation architectures, and perform large-scale, section-specific information extraction at an unprecedented PubMed-wide scale.

03.
arXiv (CS.AI) 2026-06-11

Skill-Augmented AI Agents for Medical Research Analysis: An Exploratory Multi-Model Human Evaluation in an NSCLC Transcriptomic Biomarker Task

arXiv:2606.11830v1 Announce Type: new Abstract: Background. Large language models and AI agents are increasingly used to support biomedical research, but native model outputs may omit key analytical steps, misuse methods, or overstate conclusions. We evaluated whether autonomous access to a medical research skill package was associated with higher-quality AI-generated transcriptomic research-analysis outputs compared with native AI without skills. Methods. We conducted an exploratory multi-model human evaluation using a non-small cell lung cancer immunotherapy biomarker task. Six model backbones were tested. The evaluation included 21 anonymized outputs: 9 native-AI outputs and 12 skill-augmented outputs generated through an AI agent implementation represented by OpenClaw. Four non-expert biomedical reviewers and two blinded experts evaluated each output, with two ratings from each reviewer type. The primary outcome was expert-rated overall quality. Results. Skill-augmented outputs showed directionally higher expert overall quality than native-AI outputs (mean 5.50 vs 5.11; difference=0.39; bootstrap 95\% CI, -0.04 to 0.90; Welch p=0.156). Non-expert reviewer quality showed the same direction (mean 4.72 vs 4.47; difference=0.26; bootstrap 95\% CI, -0.25 to 0.80; Welch p=0.373). Expert agreement was limited (single-rating ICC=-0.15), and model-specific effects were descriptive and heterogeneous. Conclusions. Autonomous skill access showed a directional quality signal in this exploratory sample, but the signal was smaller than expert-rating noise and should not be interpreted as confirmatory evidence. The findings primarily motivate larger evaluations of skill-augmented AI agents with stronger reliability controls, platform replication, and biological-validity assessment.

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

CausalDrive: Real-time Causal World Models for Autonomous Driving

World models have emerged as a promising paradigm for scaling autonomous driving (AD) data, yet existing video generative models fall short as interactive simulators. Layout-conditioned renderers rely on "oracle" future trajectories of all background agents, rendering them strictly non-reactive. Conversely, pure action-conditioned predictors lack semantic control over complex interactions and suffer from prohibitive diffusion latencies, hindering closed-loop policy learning. To bridge this gap, we present CausalDrive, a controllable, real-time foundation driving world renderer. CausalDrive operates solely on the initial front-view frame, the ego-vehicle's trajectory, and a macroscopic text prompt. By excluding future NPC layouts, we compel the model to intrinsically predict causal interactions, enabling text-driven control over Driving Sociology, allowing users to dynamically orchestrate diverse counterfactual reactions to identical ego-actions. To overcome the efficiency bottleneck and address the covariate shift in autoregressive generation, we propose a novel Context-Forced DMD architecture. This combines continuous flow-matching with a self-correcting distillation objective, achieving interactive speeds of 12 FPS. This breakthrough transforms the passive video generator into a playable neural simulator. We demonstrate its versatility across three downstream applications: (1) generative closed-loop evaluation with significantly mitigated collision artifacts, (2) large-scale Reinforcement Learning (RL) post-training driven by a Video2Reward module, and (3) real-time human-in-the-loop simulation. Extensive experiments validate that policies trained within CausalDrive's reactive scenarios exhibit superior interaction capabilities in the real world.

05.
arXiv (CS.CV) 2026-06-17

A geometric and deep learning reproducible pipeline for monitoring floating anthropogenic debris in urban rivers using in situ cameras

The proliferation of floating anthropogenic debris in rivers has emerged as a pressing environmental concern, exerting a detrimental influence on biodiversity, water quality, and human activities such as navigation and recreation. The present study proposes a novel methodological framework for the monitoring the aforementioned waste, utilising fixed, in-situ cameras. This study provides two key contributions: (i) the continuous quantification and monitoring of floating debris using deep learning and (ii) the identification of the most suitable deep learning model in terms of accuracy and inference speed under complex environmental conditions. These models are tested in a range of environmental conditions and learning configurations, including experiments on biases related to data leakage. Furthermore, a geometric model is implemented to estimate the actual size of detected objects from a 2D image. This model takes advantage of both intrinsic and extrinsic characteristics of the camera. The findings of this study underscore the significance of the dataset constitution protocol, particularly with respect to the integration of negative images and the consideration of temporal leakage. In conclusion, the feasibility of metric object estimation using projective geometry coupled with regression corrections is demonstrated. This approach paves the way for the development of robust, low-cost, automated monitoring systems for urban aquatic environments.

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

Triangular Consistency as a Universal Constraint for Learning Optical Flow

arXiv:2606.19938v1 Announce Type: cross Abstract: We propose triangular consistency as a first-principled constraint for optical flow, which is agnostic to network architecture, supervision type, and dataset, and applies to both image-pair and multi-frame settings. This simple but powerful constraint is to compose two flows to induce a third flow and enforce consistency among the three. The composed flows may arise from (i) image pairs, yielding cycle consistency; (ii) multiple video frames, producing longer-range motion through temporal chaining; or (iii) image pairs combined with controlled synthetic transformations, which becomes data augmentation. This triangular consistency introduces negligible computational overhead and requires no additional annotations. Since it is derived directly from the geometry of optical flow, it does not rely on model-specific assumptions and serves as a ``universal'' plug-and-play component for optical flow training. Experiments show consistent improvement across supervised, unsupervised, and transfer learning settings.

07.
arXiv (CS.CV) 2026-06-19

Relighting as a Probe of Visual Priors via Augmented Latent Intrinsics

Image-to-image relighting requires representations that separate illumination from scene properties while preserving dense geometry, material, and photometric cues. We use this task as a probe of visual priors: unlike recognition tasks that reward invariance, relighting tests whether visual features retain the information needed for light transfer. Through a controlled generative relighting framework, we find that strong semantic encoders can degrade relighting quality, exposing a semantic–photometric trade-off between abstraction and physical fidelity. We introduce Augmented Latent Intrinsics (ALI), which balances this trade-off by fusing dense, pixel-aligned visual features into a latent-intrinsic relighting model and refining it with self-supervision on unlabeled real image pairs. ALI improves relighting quality, especially on glossy, metallic, and transparent materials, and demonstrates that generative relighting is an effective tool for quantifying what visual encoders encode about the physical world.

08.
arXiv (quant-ph) 2026-06-17

Helical Dirac Current with Local Coupling to a Chiral Potential

arXiv:2606.17618v1 Announce Type: new Abstract: We show that exact Dirac eigenstates in cylindrical confinement carry a definite helical conserved-current texture even in the zero orbital angular momentum channel l = 0. For the lowest confined mode, the Dirac current contains a nonvanishing azimuthal component together with longitudinal transport and exhibits opposite handedness in the two spin-resolved sectors. The structure also persists into the evanescent region. We further derive the channel-resolved matrix-element kernel generated by a static chiral scalar potential acting on the confined l = 0 Dirac modes. The resulting spin-selective coupling arises from the Dirac current texture and the scalar chiral potential, and yields a geometric selection rule in which diagonal channels vanish while off-diagonal conversion channels survive. The coupling strength is governed by an internal sampled-current overlap Jchi(k), defined as the integral from 0 to R of f(rho) times jphi_up(rho, k) times rho d rho. This quantity measures the spatial overlap between the chiral radial profile and the spin-up azimuthal Dirac-current density. The mechanism is fully local and texture-based, without external magnetic fields or spin-orbit coupling. Within standard Dirac theory, this work identifies the minimal static Dirac-geometric kernel underlying spin-selective response, establishing a baseline structure from which dynamical-medium, scattering, and transport formalisms can be systematically developed toward a complete description of spin-polarization phenomena such as CISS.

09.
medRxiv (Medicine) 2026-06-11

Advancing Clinical Implementation of Cardiovascular Polygenic Risk Scores Through Patient-Level Robustness Assessment

Background and Aims: Polygenic risk scores (PRSs) for atherosclerotic cardiovascular disease (ASCVD) can perform equivalently at the population level yet disagree for individual patients. We examined whether such intra-individual variability reflects genuinely complementary risk information or mainly statistical and methodological uncertainty, and whether it affects clinical classification once PRSs are integrated into SCORE2-OP. Methods: In 4,137 ASCVD-free participants of the CoLaus|PsyCoLaus cohort (478 incident events over a median 14.4 years), we identified 16 ASCVD-PRSs with practically equivalent population-level performance using Bayesian equivalence testing. We quantified intra-individual variability (standard deviation, coefficient of variation, intraclass correlation, Cohen's kappa, extreme discordance), tested whether discordance exceeded chance, decomposed scores into shared and unique genetic components, and assessed variability after integration into SCORE2-OP, benchmarked against perturbation of systolic blood pressure. Results: For a typical individual, risk estimates varied by 18 percentile points across PRSs. Discordance matched chance expectations under a shared-signal model, with no distinct phenotypic profile among discordant individuals, and predictive power resided overwhelmingly in the shared genetic component. Variability tracked PRS size and weighting rather than distinct variants. After integration into SCORE2-OP, 75.6% of participants were placed in different categories by at least one model and 54.6% as both low and high risk; instability was concentrated near guideline thresholds and far exceeded that from blood-pressure measurement error. Conclusions: Equivalent population-level performance is not sufficient to treat PRSs as interchangeable at the individual level, and methodological standardisation and pragmatic clinical trials remain necessary to determine whether PRS integration improves long-term cardiovascular outcomes.

10.
bioRxiv (Bioinfo) 2026-06-15

Multiple Fault Analysis and Drug Therapy on Signaling Pathways Using Dynamic Bayesian Network-based Model

Cell growth is an intricate biological phenomenon that is closely regulated by the interplay between various growth factors and transcription factors. Signaling pathways are the main mediators in this event, which provide the driving force for mitosis or sometimes meiosis. However, when malfunctions occur within the biological network, they can cause uncontrolled cell division, regardless of external stimuli. By employing Dynamic Bayesian Networks (DBNs), these malfunctions can be explicitly simulated, offering insights into their effects on cellular behavior and growth regulation. To a significant extent, the resultant outcomes can be mitigated through the use of reduced drug combinations. This study delves into the intricacies of signaling pathway behavior under the influence of concurrent malfunctions. Initially, we replicate the effects of these dysfunctions within DBNs. Subsequently, drug therapy is applied to alleviate their impact. Our methodology introduces a parameter known as efficiency_score, enabling the identification of optimized drug combinations without prior knowledge of specific dysfunctions. Particularly relevant in the context of realistic cancer conditions, these tailored drug inhibition points demonstrate enhanced efficacy compared to conventional treatments. Leveraging GPU acceleration throughout the modeling process accelerates the analysis of multiple faults within the biological networks, rendering our approach notably faster and more efficient.

11.
PLOS Computational Biology 2026-06-02

Data-driven model reveals increased stability of CAG-expanded <i>huntingtin</i> RNA due to MID1 binding

作者:

by Yuhong Liu, Annika Reisbitzer, Domagoj Dorešić, Jan Hasenauer, Sybille Krauß, Tatjana Tchumatchenko RNA-binding proteins (RBP) are important regulators of RNA metabolism. In neurodegenerative disorders such as Huntington’s Disease (HD), disrupted RBP-RNA interactions contribute to neuronal dysfunction. One such RBP, Midline 1 (MID1), has been shown to aberrantly associate with mutant huntingtin (Htt) RNA, enhancing its translation, yet the mechanism driving this effect remains unknown. Here, we develop a computational model to understand the role of MID1. Based on previously published data, our model predicts that MID1 increases the stability of the Htt RNA. We experimentally validate this prediction, showing that overexpression of MID1 significantly prolongs the half-life of mutant Htt RNA. Furthermore, we evaluate model refinements, including clustering of MID1-bound RNA, which allow capturing all key observations in the data. Together, we provide a data-driven framework that underlines the importance of RBP-RNA interaction in post-transcriptional regulation. This framework also shows how individual molecular reactions jointly determine RNA stability and protein levels in HD.

12.
Nature (Science) 2026-06-17

A 98-qubit trapped-ion quantum computer with all-to-all connectivity

Quantum computers require both high-fidelity operations and large qubit numbers to surpass classical capabilities1. Trapped-ion platforms have demonstrated the highest gate fidelities of any modality2–6 but scaling to larger qubit numbers while preserving performance has remained a central challenge. We report on Quantinuum Helios, a 98-qubit trapped-ion quantum processor based on the quantum charge-coupled device (QCCD) architecture7. Helios features 137Ba+ hyperfine qubits8,9, all-to-all connectivity enabled by a rotatable ion storage ring connecting two quantum operation regions by a junction10,11, speed improvements from parallelized operations12 and a new software stack with real-time compilation of dynamic programs13. Averaged over all operational zones in the system, we achieve average infidelities of 2.5(1) × 10−5 for single-qubit (1Q) gates, 7.9(2) × 10−4 for two-qubit (2Q) gates and 3.3(5) × 10−4 for state preparation and measurement (SPAM), none of which are fundamentally limited and probably able to be improved. These component infidelities are predictive of system-level performance in both random Clifford circuits and random circuit sampling (RCS), the latter demonstrating that Helios operates well beyond the reach of classical simulation and establishes a new frontier of fidelity and complexity for quantum computers14. A new quantum computer, Quantinuum Helios, which is a 98-qubit trapped-ion quantum processor built on the QCCD architecture, demonstrates performance well beyond classical capabilities and provides a path for scaling up quantum computing.

13.
medRxiv (Medicine) 2026-06-15

International Consensus Guideline on Management of Genitourinary Adverse Events Associated with Prostate Cancer Radiotherapy

Purpose/Objective: Genitourinary (GU) adverse events (AEs) are common during and after pelvic radiation therapy (RT) for prostate cancer and can substantially impact quality of life. We convened an international committee to establish consensus in the prevention, mitigation, and management of radiation-related acute and late GU AEs, as there are no relevant evidence-based consensus guidelines to inform treating providers. Materials/Methods: A systematic evidence review focused on mitigation and management of radiation-related acute and late GU AEs was performed in PubMed, Embase and Cochrane. The following topics were addressed: management of acute GU AEs in the intact and post-operative settings; RT techniques; bladder outlet obstruction procedures; and indications for urology referral or hyperbaric oxygen therapy (HBO). Evidence-based consensus recommendations were developed using a Delphi process. We highlight the current state of evidence and evidence gaps worthy of future study. Results: Consensus was reached for 31 key questions. For management of lower urinary tract symptoms (LUTS), most evidence comes from trials in patients without cancer and not undergoing RT. A consensus algorithm for medical management of acute GU AEs was developed with the following highlights: (a) alpha blockers as 1st-line for obstructive symptoms in the intact setting, (b) anti-spasmodics as 1st -line for irritative symptoms in the intact setting, and (c) anti-spasmodics as 1st -line in the post-operative setting. The consensus algorithm provides an ordered list of medications to offer if 1st -line options afford inadequate relief. For RT fractionation, randomized clinical trial (RCT) data are available. 40% of panelists rarely or never use standard fractionation over moderate hypofractionation for patients with baseline LUTS, but most consider moderate hypofractionation over SBRT for AUA IPSS > 15. For patients with severe obstructive LUTS (most commonly AUA IPSS >20), the panel recommends a prophylactic bladder outlet obstruction procedure and, if obstructive symptoms improve, consideration of moderate hypofractionation or SBRT, based on retrospective data. There is one RCT supporting use of HBO for late radiation cystitis. Conclusions: The consensus guideline synthesizes available evidence and expert opinion across key clinical decision points to provide practical guidance in the prevention, mitigation, and management of radiation-related acute and late GU AEs in prostate cancer RT. Envisioned as a living document with periodic updates, this guideline serves as a resource for practicing radiation oncologists by outlining expert-derived consensus recommendations of evidence-based care in areas where high-quality data is limited.

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

A Comprehensive Survey of Medical Image Segmentation: Challenges, Benchmarks, and Beyond

Medical image segmentation plays a critical role in clinical diagnostics, treatment planning, disease monitoring, and neurological disorder identification. This article presents a comprehensive review of its systematic development, covering widely used public datasets, representative methods built on the U-Net, Transformer, and SAM architectures, and key evaluation metrics with their differences, followed by an analysis of major challenges from multiple perspectives. Unlike surveys that focus on a single model family or a specific clinical application, this review organizes U-Net-, Transformer-, and SAM-based methods within a unified analytical framework, with a particular focus on their effectiveness in improving segmentation accuracy and efficiency. This work aims to guide future research and support clinical translation of medical image segmentation, with all related resources publicly available in our GitHub repository: https://github.com/andrew-pengyu/Awsome_MedSeg/tree/main.

15.
arXiv (quant-ph) 2026-06-11

The quantum harmonic oscillator and the real Hilbert space

arXiv:2606.12060v1 Announce Type: new Abstract: The harmonic oscillator is considered within generalized frameworks using complex and quaternionic numbers. The classical oscillator is considered in terms of a complex position function, and quantum oscillators are examined in terms of complex wave functions, and in terms of quaternionic wave functions as well. Both of the quantum solutions are obtained within the real Hilbert space formalism. The results reveal the complex and quaternionic descriptions as suitable frameworks for non-stationary processes, including damped oscillations, forced oscillations, and additionally self-interacting processes that cannot be appropriately described otherwise.

16.
medRxiv (Medicine) 2026-06-15

Recruitment, Retention Approaches and Community Engagement in the THRIVE pilot Trial: Lessons Learned from a Food is Medicine Trial

Background: Recruitment of underrepresented populations, including Black and Hispanic populations, for Food is Medicine (FIM) and cardiovascular trials, may pose significant challenges. Methods: We implemented a multi-component recruitment approach for the THRIVE (AdapTive personalized dietitian coacHing and messaging with pRoduce prescrIptions to improVE healthy dietary behaviors) pilot trial to engage primarily Black and Hispanic adults in a Food is Medicine for hypertension intervention. The recruitment approaches included community engagement at approximately 40 community events (cultural festivals and neighborhood gatherings); partnerships with 8 community and faith-based service hubs and food distribution sites; recruitment through safety net primary care clinics, digital outreach via the study website, and social media campaigns; and direct recruitment at places of worship. We report lessons learned from the community engagement process, recruitment efficiency, representativeness, and retention outcomes. Results: Within 6 months, the enrollment target was exceeded by 40%, with an accrual index of 1.04. Over 1,000 individuals were reached through the direct-to-community engagement process, while faith-based partnerships engaged about 900 adults. There were 2,673 visits to the study webpage, and social media achieved 12,259 impressions with 399 clicks. About 95% of participants resided within 10 miles of the faith-based recruitment sites. Face-to-face engagement at the food distribution sites within faith-based organizations or community service hubs outperformed digital methods. Faith leader endorsements and follow-up in-person meetings (following unsuccessful email outreach) dramatically increased recruitment. Regarding retention, pre-randomization attrition was 6%, and 82% of participants completed the study. Conclusion: Culturally tailored, community-engaged recruitment grounded in faith-based and local community partnerships, was highly effective in engaging Black and Hispanic populations in this FIM cardiovascular trial. This provides a replicable model for implementing equitable and sustainable cardiovascular health interventions.

17.
arXiv (quant-ph) 2026-06-16

Twisted (co)homology of non-orientable Weyl semimetals

arXiv:2511.22303v3 Announce Type: replace-cross Abstract: The quasi-particle excitations in Weyl semimetals, known as Weyl fermions, are usually forced to emerge in charge-conjugate pairs by the Nielsen–Ninomiya theorem. When the Brillouin zone is non-orientable, this constraint is replaced by a $\mathbb{Z}_2$ charge cancellation, as a result of the chirality becoming ill-defined on such manifolds; this results in configurations with seemingly non-zero total chirality. Here, we set out to explain this behaviour from a purely topological perspective, and provide a classification of non-orientable Weyl semimetal topology in terms of exact sequences of twisted (co)homology groups. This leads to several discoveries of direct physical importance: in particular, we recover the $\mathbb{Z}_2$ charge cancellation in a coordinate-independent way, allowing meaningful limits to be set on its physical interpretation. A detailed discussion is provided on a specific Klein bottle-like topology induced by a momentum-space glide symmetry, including a full review of the insulating and semimetallic invariants of the system and a classification of the surface states on the non-orientable boundary. Beyond this, we provide a complete survey of all possible non-orientable Brillouin zones and their associated invariants, and extend our formalism into the realm of non-Hermitian topological physics and inversion-symmetric Weyl semimetals. Our work exemplifies the vast potential of fundamental mathematical descriptions to not only aid the corresponding physical intuition, but also predict novel and hitherto overlooked phenomena of great relevance throughout the physics research forefront.

18.
arXiv (math.PR) 2026-06-16

The distribution of the de Moivre experiment

arXiv:2606.15178v1 Announce Type: new Abstract: In this paper, we focus on de Moivre random experience which allows us to introduce the $ s- $Bernoulli distribution and the bi$ ^s $nomial distribution. We present some probabilistic properties such as the expectation, the variance, the skewness and kurtosis coefficients, the moments and the generating functions. Then we establish that for $ s\in\mathbb{N} $, the bi$ ^s $nomial distribution converges to a limiting Poisson and normal distributions when $ n\rightarrow\infty. $

19.
bioRxiv (Bioinfo) 2026-06-11

An AI-Powered Trisomy 21 Research Assistant

Down syndrome, caused by trisomy 21, increases the risk of diverse co-occurring conditions. With more than 34,000 related publications indexed in PubMed as of early 2026, keeping pace with this expanding literature is challenging. While general-purpose large language models are widely used for information retrieval, they often rely on broad training data rather than specific evidence. Retrieval-augmented generation (RAG) improves rigor and reliability of responses by linking model outputs to source texts. In research, source texts are peer-reviewed articles. Standard implementations treat all manuscript sections equally, allowing background text to rank as highly as experimental results. To focus model outputs on experimentally supported responses, we developed the T21 Research Assistant, a section-aware RAG system that prioritizes Results sections to ground responses in primary experimental evidence. The system draws exclusively from 1,789 open-access Down syndrome publications from PubMed Central, including 327 NIH INCLUDE-funded studies, and uses a multistage pipeline for query validation, retrieval, reranking, synthesis, and citation verification. Built on NVIDIA Nemotron models, it generates structured, cited responses. Evaluation using expert-curated questions demonstrated strong performance, achieving a BERTScore F1 of 0.712 and recall of 0.758, comparable to or exceeding leading proprietary and open-source models. T21 Research Assistant is available at: https://bioinformatics.cuanschutz.edu/t21-res-assi/

20.
arXiv (CS.LG) 2026-06-12

Policy-driven Conformal Prediction for Trustworthy QoT Estimation

arXiv:2606.12501v1 Announce Type: new Abstract: We propose Conformal QoT, a policy-driven framework that combines statistically guaranteed QoT estimation with operational decision policies, enabling reliable lightpath-feasibility predictions under domain shift and improving accuracy from 92\% to 99.6\% on open datasets.

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

A Causal Model of Theory of Mind in Conflict for Artificial Intelligence

arXiv:2606.16944v1 Announce Type: new Abstract: Theory of mind (ToM), the capacity to ascribe mental states to others and use those ascriptions for prediction and inference, is widely assumed to be essential for effective human-machine integration. Existing AI-ToM models address how to mentalize, but leave the question of when largely unaddressed. The central question is: under what situational and agent-level conditions is ToM engagement causally warranted in conflict? This paper presents a structural causal model formalized as a directed acyclic graph (DAG), treating ToM as a mechanism activated by situational and agent-level conditions rather than as an always-on capacity. The model specifies four exogenous variables capturing situational and agent-level conditions, five endogenous mediators, and a mechanistic ToM node producing engagement states through three distinct causal pathways: a tractability pathway, a reasoning-depth pathway, and an enabling-cause pathway. The primary outcome is epistemic accuracy, which decouples social reasoning from behavioral policy and generalizes across social phenomena beyond conflict. The framework gives AI systems a principled, resource-rational decision procedure for mentalizing, with implications for efficiency, trust, and the development of robust artificial social intelligence. Simulation validation, empirical human-machine teaming studies, and ethical considerations arising from conflict-optimized mentalizing are discussed.

22.
arXiv (quant-ph) 2026-06-17

Optimizing bias-tailored quantum error correction beyond code-capacity noise

arXiv:2606.17709v1 Announce Type: new Abstract: We find that the substantial advantages predicted for bias-tailored quantum error correction (QEC) under code-capacity noise are strongly reduced once realistic syndrome extraction and circuit-level noise models are considered. We start by comparing XZZX codes to rectangular surface codes with a bias-dependent optimised anisotropy. Although code-capacity simulations predict an advantage of rectangular surface codes in the limit of high noise bias, this actually disappears under circuit-level noise, making the XZZX codes the preferred and simplest choice even for platforms that allow for a flexible variation of the code layout adapted to changes in noise calibration. Our results identify bias degradation during syndrome extraction under circuit-level noise as the central limitation of biased-tailored QEC. To partially mitigate this effect, we introduce a bias-filtering CNOT gadget that temporarily encodes the ancillary target qubit during syndrome extraction in a repetition code and, upon measurement and feed forward, manages to reduce the bias degradation. In a regime of high-bias and low-idle errors, this bias-filtering gadget yields a few-percent relative improvement of the XZZX code error threshold, demonstrating that lightweight bias-filtering strategies can recover part of the lost bias-tailoring advantage for realistic circuit-level noise.

23.
bioRxiv (Bioinfo) 2026-06-10

ECMME: an atlas of selection pressures on the mammalian extracellular matrix reveals contrasting evolutionary dynamics

The extracellular matrix (ECM) is a fundamental metazoan innovation that provides structural support and regulatory cues essential for multicellular life. While core matrisome components are subject to strong functional constraints, their evolutionary dynamics at the molecular level remain incompletely characterized. Here, we present a comprehensive per-residue analysis of selection pressures across 272 human core matrisome proteins using high-quality orthologous sequences from up to 228 placental mammal species. We developed an automated pipeline integrating ortholog identification, codon-aware alignments, and site-specific selection analyses with the MEME and FUBAR methods from the HyPhy suite. Results reveal pervasive strong purifying selection across the matrisome, consistent with its structural and functional indispensability. This is accompanied by episodic positive selection and rarer pervasive positive selection, with collagens exhibiting significantly elevated episodic positive selection compared to glycoproteins and proteoglycans. To facilitate community access, we developed ECMME (ECM Molecular Evolution) browser, an intuitive open-access web resource that visualizes selection metrics plotted directly onto protein topologies. ECMME allows researchers to seamlessly browse and investigate the data, providing a powerful framework for interpreting functional sites. It is available online and requires no local installation or set-up (https://izzilab-ecmme.share.connect.posit.cloud/).

24.
arXiv (CS.LG) 2026-06-15

FlowMo-WM: A World Model with Object Momentum and Hidden Ambient Drift

arXiv:2606.13817v1 Announce Type: cross Abstract: World models in robot learning predict future states from visual observations and actions, enabling agents to reason about the consequences of their controls. However, many action-conditioned models are evaluated in settings where motion is dominated by immediate control, whereas aquatic surface vehicles and other real-world objects continue moving under inertia and are displaced by hidden ambient drift, such as water currents or wind. We propose FlowMo-WM, an end-to-end trainable visual world model that infers object-centric motion state and a predictive long-history context associated with hidden drift from image-action histories without direct supervision of flow fields. FlowMo-WM factorizes image-action history into a short-history latent state, trained to summarize object-centric motion, and a longer-history context, trained to summarize slowly varying exogenous influences. A zero-context residual transition separates action-conditioned base dynamics from context-dependent drift effects during latent rollout. In simulated aquatic surface-vehicle environments with diverse hidden flows, disturbances, and randomized vehicle dynamics, FlowMo-WM improves long-horizon rollout accuracy over representative action-conditioned latent world models. Prediction-time context ablations, in which the inferred context is zeroed or shuffled during rollout, show that the ambient context is important for stable prediction under hidden drift, while frozen linear probes characterize information encoded in the learned factors.

25.
arXiv (CS.AI) 2026-06-11

From Architecture to Output: Structural Origins of Hallucination in Large Language Models and the Amplifying Role of Data

arXiv:2606.07537v1 Announce Type: cross Abstract: Large language models hallucinate–producing fluent, confident, factually wrong outputs–with a consistency that persists across generations and scales. Existing taxonomies classify hallucination by output type, distinguishing intrinsic from extrinsic failures and faithfulness from factuality divergence. These frameworks are descriptively rigorous but do not identify which internal mechanism produced a given instance. This paper analyses hallucination as a structural consequence of three architectural decisions that together form a compound failure system. Self-attention's co-occurrence learning substitutes statistical proximity for semantic meaning and produces entity confusion, fact misattribution, and semantic drift. The maximum likelihood estimation training objective optimises next-token probability without factual constraint, rewarding statistically plausible outputs regardless of their truth value. Autoregressive decoding's permanent left-to-right commitment under exposure bias ensures that a single wrong token cascades forward through the entire output sequence without revision. Dataset pathologies–long-tail deficiencies, training bias, and synthetic pollution–amplify these vulnerabilities but do not independently cause them. We make three contributions. First, we map each mechanism to a specific output category in the Alansari and Luqman taxonomy, locating intrinsic hallucination in self-attention, extrinsic hallucination in MLE, and logical inconsistency in autoregressive decoding. Second, we show that each commonly cited dataset pathology exploits one of these mechanisms rather than originating hallucination independently. Third, we identify the diagnostic limitation of output-type-only classification and contrast it with inference-layer mitigation approaches.