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01.
arXiv (quant-ph) 2026-06-19

Optimal multi-spectral squeezing via deterministic 2D-phase optimization

arXiv:2606.20192v1 Announce Type: new Abstract: Optimization routines are ubiquitous in quantum information technologies and essential to reach the resource levels required by quantum protocols. Specifically, multi-spectral squeezing for use in such protocols requires that losses be kept minimal at every stage, including coherent detection, which is performed by interfering the signal with a classical local-oscillator beam. This in turn requires control over all optical degrees of freedom of the beam in order to optimize the detection. The most general framework for this optimization relies on agnostic, off-the-shelf machine-learning techniques. Here we take the opposite approach: by focusing on a physical description of the specific optical process, we develop a deterministic sequential algorithm that provably reaches the global maximum of the visibility in a pixel basis and scales linearly with the number of pixels, thereby offering an efficient and theoretically grounded alternative to black-box optimization. In our waveguide-based setup, the optimized mask increases the visibility from 76% to 84%, corresponding to a 20% gain in mode-matching efficiency. Multi-spectral squeezing measurements confirm that this improvement translates directly into quantum readout: for the most squeezed spectral mode, the squeezing increases from $-2.08$ dB to $-2.64$ dB, consistent with the inferred efficiency gain. These results establish deterministic spatial phase shaping as an effective, interpretable route to enhanced multimode squeezing in waveguide platforms.

02.
arXiv (quant-ph) 2026-06-19

Phase locking nuclear spins in silicon with spin-orbit coupling

arXiv:2606.20340v1 Announce Type: new Abstract: Because they have such long coherence times, nuclear spins have extraordinary potential for use in quantum information processing devices. However, coherent nuclear spin control generally requires external phase references, such as microwave control fields. Here, we phase-lock a $^{29}$Si nuclear spin ensemble in a silicon quantum dot using only the internal electronic spin-orbit coupling as a phase reference. When driven with the quantum-dot electrons, the nuclear spins align themselves to a phase determined by the electronic spin-orbit coupling and the timing of the drive protocol. This enables us to measure the coherent precession and inhomogeneous dephasing of the nuclear spins. We corroborate our results with detailed numerical simulations of the many-body electron nuclear system. Our work opens new routes for coherently controlling solid-state nuclear spin ensembles.

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

Anti-causal domain generalization: Leveraging unlabeled data

arXiv:2602.17187v2 Announce Type: replace-cross Abstract: The problem of domain generalization concerns learning predictive models that are robust to distribution shifts when deployed in new, previously unseen environments. Existing methods typically require labeled data from multiple training environments, limiting their applicability when labeled data are scarce. In this work, we study domain generalization in an anti-causal setting, where the outcome causes the observed covariates. Under this structure, environment perturbations that affect the covariates do not propagate to the outcome, which motivates regularizing the model's sensitivity to these perturbations. Crucially, estimating these perturbation directions does not require labels, enabling us to leverage unlabeled data from multiple environments. We propose two methods that penalize the model's sensitivity to variations in the mean and covariance of the covariates across environments, respectively, and prove that these methods have worst-case optimality guarantees under certain classes of environments. Finally, we demonstrate the empirical performance of our approach on a controlled physical system and a physiological signal dataset.

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

Multi-View In-Cabin Monitoring System for Public Transport Vehicles

We introduce a multi-view in-cabin monitoring dataset for public transportation with synchronized RGB and depth images from four inward-facing cameras and a rotating LiDAR covering the vehicle interior of a digitalized and partly automated German city bus. The dataset contains 9.136 synchronized samples with annotations and is accompanied by a calibration and pseudo-labeling pipeline that generates 3D human pose estimates and oriented 3D bounding boxes for occupants. We further provide a nuScenes-format conversion and benchmark representative multi-view 3D detection models (e.g., Lift-Splat-Shoot and BEVFusion), supporting comparative evaluation and small-scale training of multi-view in-cabin perception models. The dataset and tools are available at https://github.com/EvgenyGorelik/multiview_incabin_dataset.

05.
arXiv (CS.CL) 2026-06-12

Helping Figures Tell their Story! Paper-Grounded Video Generation Explaining Complex Scientific Figures

Scientific figures compress complex pipelines into a single canvas, yet understanding them requires paper-grounded, step-by-step narration aligned with visual highlights a capability missing from current video generation systems and benchmarks. To address this, we introduce paper-grounded figure-to-video generation: generating narrated, region-grounded walkthrough videos from a figure and its paper. We propose MINARD (Multimodal Interpretation of Narrated Architecture via Region Decomposition), a pipeline that generates paper-grounded narrations and sequentially grounds them to figure regions. We also release FigTalk, a benchmark with new sequential and component-level grounding metrics derived. On FigTalk, MINARD generates humanlike, paper-faithful narrations and outperforms narration-conditioned figure spatial grounding compared to existing approaches in both automatic and human evaluation

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

Learning the Context of Errors: Black-Box Online Adaptation of Time Series Foundation Models

arXiv:2606.14222v1 Announce Type: new Abstract: The rapid evolution of Time Series Foundation Models (TSFMs) has advanced zero-shot forecasting across diverse domains. Inspired by the current form of Large Language Models, future TSFMs may be offered as commercialized, closed-source API services. However, many existing online adaptation methods still rely on white-box access for parameter fine-tuning or gradient backpropagation. This paradigm mismatch raises a question: In black-box online adaptation for TSFMs, what should we learn? We answer this with an insight: the predictive errors of the base model are conditioned on both the input and output of the base model (i.e., the context of errors). To validate this insight, we propose ORCA (Online Residual Contextual Adaptation). We conduct extensive experiments across 5 state-of-the-art TSFMs and 8 datasets to demonstrate the effectiveness of our approach. Furthermore, through ablation studies, we quantitatively analyze the impact of different adapter learning hypotheses on the final adaptation performance in black-box online adaptation. Code available at https://github.com/Fifthky/ORCA.

07.
arXiv (CS.CV) 2026-06-15

Pix2Fact: When Vision Is Not Enough – Benchmarking Fine-Grained VQA with Web Verification on High-Resolution Real-World Scenes

Despite progress on general tasks, vision-language models (VLMs) still struggle with challenges that demand both fine-grained visual grounding and external knowledge, a synergy overlooked by existing benchmarks that evaluate these abilities in isolation. To fill this void, we introduce Pix2Fact, a visual question-answering benchmark designed to assess expert-level visual perception and knowledge search. Pix2Fact comprises 1,000 high-resolution (4K+) images spanning eight scenarios. Its questions and answers are meticulously crafted by PhD-holding annotators from top global universities across diverse disciplines. Each question requires detailed visual grounding and the integration of external knowledge. Evaluating ten state-of-the-art VLMs, including proprietary models such as Gemini-3.1-Pro and GPT-5.4, we find that Pix2Fact poses a formidable challenge: the most advanced model (Gemini-3.1-Pro) achieves only 51.7% average accuracy, even with access to visual ground truth and search tools. Our analysis attributes this low accuracy to three factors, frequent visual grounding errors even with visual ground truth, shallow search harnessing, and VLM's inability to retrieve long-tail, unstructured local information. This striking gap exposes the limitations of current models in assisting humans with real-world scenarios that demand overwhelming visual comprehension. We believe Pix2Fact will serve as a critical benchmark to drive the next generation of language-vision agents that seamlessly integrate fine-grained perception with robust knowledge search.

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

Mapping Geopolitical Bias in 11 Large Language Models: A Bilingual, Dual-Framing Analysis of U.S.-China Tensions

Large language models are how hundreds of millions of people now encounter contested political questions, raising a subtle measurement problem: a model that simply agrees with whatever it is told can masquerade as biased, contaminating any claim that models hold political opinions. We address this by importing balanced keying from survey psychometrics, posing each proposition and its swapped reverse and signing the response so acquiescence cancels and genuine conviction accumulates. The result is a reproducible, quantitative instrument that maps geopolitical stance across 11 models and 2 languages (19,712 responses). Developer origin, query language and issue domain emerge as three near-equal, additive factors; every model, including those built in the United States, leans more Pro-China in Mandarin; and two models with identical agreement bias are told apart, one neutral, one biased. We release it as an open, interactive tool that extends to any contested-opinion domain.

09.
arXiv (CS.LG) 2026-06-17

The Implicit Bias of Steepest Descent with Mini-batch Stochastic Gradient

arXiv:2602.11557v2 Announce Type: replace Abstract: A variety of widely used optimization methods like SignSGD and Muon can be interpreted as instances of steepest descent under different norm-induced geometries. In this work, we study the implicit bias of mini-batch stochastic steepest descent in multi-class classification, characterizing how batch size, momentum, and variance reduction shape the limiting max-margin behavior and convergence rates under general entry-wise and Schatten-$p$ norms. We show that, without momentum, worst-case convergence and successful classification can only be guaranteed with full-batch gradient. In contrast, momentum enables small-batch convergence to an approximate max-margin solution through a batch-momentum trade-off, though it slows convergence. This approach provides fully explicit, dimension-free rates that improve upon prior results. Moreover, we prove that variance reduction can recover the exact full-batch implicit bias for any batch size, albeit at a slower convergence rate. Finally, we further investigate the batch-size-one steepest descent without momentum, and reveal its convergence to a fundamentally different bias via a concrete data example, which reveals a key limitation of purely stochastic updates. Overall, our unified analysis clarifies when stochastic optimization aligns with full-batch behavior, and paves the way for perform deeper explorations of the training behavior of stochastic gradient steepest descent algorithms.

10.
arXiv (quant-ph) 2026-06-16

A short proof of the modified Kretschmann-Schlingemann-Werner conjecture

Authors:

arXiv:2606.16418v1 Announce Type: new Abstract: Let $\Phi_1, \Phi_2 : \mathbb{M}_d(\mathbb{C})\to \mathbb{M}_n(\mathbb{C})$ be two quantum channels with respective Stinespring isometries $V_1, V_2 : \mathbb{C}^{d}\to \mathbb{C}^{n} \otimes \mathbb{C}^{m}$ on any common dilation space $\mathbb{C}^{m}$. We prove that there exists a unitary $U$ on $\mathbb{C}^{m}$ such that $\|V_1-({\bf1}\otimes U)V_2\|_\infty\leq\sqrt{2\|\Phi_1-\Phi_2\|_\diamond},$ thus resolving vom Ende's modification of the Kretschmann-Schlingemann-Werner conjecture in the affirmative.

11.
Nature (Science) 2026-06-10

Whole-genome duplication shaped cell-type evolution in the vertebrate brain

Authors:

The complex brains of vertebrates have more cell types than those of their closest relatives. Whole-genome duplications (WGDs) occurred during early vertebrate evolution1, but it is unclear whether the duplicated genes (ohnologues) facilitated cell-type evolution. Here using brain single-cell transcriptomes from five chordates—human2, mouse3, lizard4, lamprey5 and amphioxus—we report that many cell-type families with conserved core transcription factors in vertebrates do not show one-to-one homology with amphioxus. Moreover, ohnologues, particularly those from the first WGD, were more important than small-scale duplication paralogues for vertebrate cell-type evolution. To explore whether ohnologues are mechanistically important for this process, we predicted ancestral cell-type states and compared them to amphioxus and experimentally investigated macroglia. The findings indicate that ohnologues had a role in early vertebrate cell-type diversification. Moreover, by examining paralogue expression across cell types and species, we show that expression changes were mainly driven by dosage selection and subfunctionalization. We also link ohnologues to cellular diversity at different anatomical and cell-type scales. Our findings demonstrate the importance of WGDs for the evolution of early vertebrate brain complexity and highlight that the resultant ohnologues continued to capacitate cell-type evolution long after they were formed. Analyses of brain single-cell transcriptomes from human, mouse, lizard, lamprey and amphioxus reveal that duplicated genes (ohnologues) played a pivotal part in early vertebrate cell-type diversification.

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

CLAP: Contrastive Latent Action Pretraining for Learning Vision-Language-Action Models from Human Videos

Generalist Vision-Language-Action models remain constrained by the scarcity of robotic data relative to the abundance of human video demonstrations. Existing Latent Action Models attempt to use video data but often suffer from visual entanglement, encoding noise rather than manipulation skills. To address this limitation, we propose Contrastive Latent Action Pretraining (CLAP), a framework that first uses Act-VAE to learn an executable action-token vocabulary from robot trajectories and then aligns human visual transitions with this vocabulary through contrastive learning. This alignment maps unlabeled human videos into a physically grounded latent action space rather than reconstructing appearance. Building on the aligned tokens, we train CLAP-NTP as an autoregressive VLA using robot demonstrations and pseudo-labeled human videos, preserving instruction following and object generalization. For deployment and target-domain adaptation, we further introduce a post-training strategy that combines CLAP-RF, a Rectified Flow action head for low-latency continuous action chunk prediction, with Knowledge Matching regularization to preserve pretrained semantic knowledge during fine-tuning. Extensive experiments show that CLAP achieves strong performance against competitive baselines while enabling effective skill transfer from human videos to robotic execution.

13.
arXiv (CS.AI) 2026-06-16

A Learning Method with Gap-Aware Generation for Heterogeneous DAG Scheduling

arXiv:2603.23249v2 Announce Type: replace-cross Abstract: Efficient scheduling of directed acyclic graphs (DAGs) is a core problem in large-scale data-intensive computing systems, where query plans, data-processing workloads, and computation graphs consist of dependent tasks competing for limited heterogeneous resource pools. In practice, achieving high-performance execution requires schedulers to adapt across environments with varying resource pools and task types, while generating schedules under tight runtime budgets. We propose WeCAN, an end-to-end reinforcement learning framework for heterogeneous DAG scheduling that addresses task-pool compatibility coefficients and generation-induced optimality gaps. It adopts a two-stage single-pass design: a single forward pass produces task-pool scores and global parameters, followed by a generation map that constructs schedules without repeated network calls. Its weighted cross-attention encoder models task-pool interactions gated by compatibility coefficients, and is size-agnostic to environment fluctuations. Moreover, widely used list-scheduling maps can incur generation-induced optimality gaps from restricted reachability. We introduce an order-space analysis that characterizes the reachable set of generation maps via feasible schedule orders, explains the mechanism behind generation-induced gaps, and yields sufficient conditions for gap elimination. Guided by these conditions, we design a skip-extended realization with an analytically parameterized decreasing skip rule, which enlarges the reachable order set while preserving single-pass efficiency. Experiments on real-world TPC-H query DAGs, resource-intensive workload datasets, and ML-compiler computation graphs demonstrate improved makespan over strong baselines, with inference time comparable to classical heuristics and faster than multi-round neural schedulers.

14.
arXiv (CS.CV) 2026-06-17

Detail++: Training-Free Detail Enhancer for Text-to-Image Diffusion Models

Recent advances in text-to-image (T2I) generation have led to impressive visual results. However, these models still face significant challenges when handling complex prompt, particularly those involving multiple subjects with distinct attributes. Inspired by the human drawing process, which first outlines the composition and then incrementally adds details, we propose Detail++, a training-free framework that introduces a novel Progressive Detail Injection (PDI) strategy to address this limitation. Specifically, we decompose a complex prompt into a sequence of simplified sub-prompts, guiding the generation process in stages. This staged generation leverages the inherent layout-controlling capacity of self-attention to first ensure global composition, followed by precise refinement. To achieve accurate binding between attributes and corresponding subjects, we exploit cross-attention mechanisms and further introduce a Centroid Alignment Loss at test time to reduce binding noise and enhance attribute consistency. Extensive experiments on T2I-CompBench and a newly constructed style composition benchmark demonstrate that Detail++ significantly outperforms existing methods, particularly in scenarios involving multiple objects and complex stylistic conditions.

15.
arXiv (CS.CV) 2026-06-12

Augmentation techniques for video surveillance in the visible and thermal spectral range

In intelligent video surveillance, cameras record image sequences during day and night. Commonly, this demands different sensors. To achieve a better performance it is not unusual to combine them. We focus on the case that a long-wave infrared camera records continuously and in addition to this, another camera records in the visible spectral range during daytime and an intelligent algorithm supervises the picked up imagery. More accurate, our task is multispectral CNN-based object detection. At first glance, images originating from the visible spectral range differ between thermal infrared ones in the presence of color and distinct texture information on the one hand and in not containing information about thermal radiation that emits from objects on the other hand. Although color can provide valuable information for classification tasks, effects such as varying illumination and specialties of different sensors still represent significant problems. Anyway, obtaining sufficient and practical thermal infrared datasets for training a deep neural network poses still a challenge. That is the reason why training with the help of data from the visible spectral range could be advantageous, particularly if the data, which has to be evaluated contains both visible and infrared data. However, there is no clear evidence of how strongly variations in thermal radiation, shape, or color information influence classification accuracy. To gain deeper insight into how Convolutional Neural Networks make decisions and what they learn from different sensor input data, we investigate the suitability and robustness of different augmentation techniques...

16.
Science (Express) 2026-05-21

Nodeless superconducting gap and electron-boson coupling in (La,Pr,Sm)3Ni2O7 films | Science

Authors: Unknown Author

The discovery of superconductivity in Ruddlesden-Popper (RP) bilayer nickelate films under ambient pressure provides an opportunity to directly investigate electronic energy scales of the superconducting state and the pairing mechanism. We report angle-resolved photoemission spectroscopy measurements of superconducting (La,Pr,Sm) 3 Ni 2 O 7 thin films by developing an ultra-high vacuum cryogenic sample quenching and transfer technique. A superconducting gap of ~18 meV with coherence peaks is observed along the Brillouin zone diagonal. The finite gap persists across the entire Brillouin zone, revealing the absence of gap nodes. A kink is observed in the energy-momentum dispersion at ~70 meV below Fermi level, indicating an electron-boson coupling. The simultaneous observation of a nodeless superconducting gap and electron-boson coupling provides insight into the pairing symmetry and gluing mechanism in RP bilayer nickelates.

17.
arXiv (CS.CV) 2026-06-16

CEVAR: Centerline Embedding Extraction for Endovascular Aneurysm Repair

Long-term mortality rates after endovascular aneurysm repair (EVAR) remain elevated due to post-EVAR rupture caused by loss of seal in stent graft sealing zones. Structured CT review using centerline measurements improves detection, but current workflows require manual centerline editing and expert operators. We propose a transformer framework for automated, protocol-driven sealing zone assessment that combines 3D centerline tracking with embedding-based geometric prediction. Two state-of-the-art image-to-graph models are evaluated for aorto-iliac centerline extraction from follow-up CT and for measurement of stent position, vessel diameters, and seal lengths according to EVAR4C protocol. Across the full test set and a challenging no-contrast subset, the proposed fully automatic method outperforms the commercial semi-automatic workflow.

18.
arXiv (CS.CL) 2026-06-12

PolyAlign: Conditional Human-Distribution Alignment

Post-training methods such as supervised fine-tuning (SFT) and preference optimization typically align language models toward a single global assistant behavior. While effective for improving average helpfulness, this can suppress the natural variation of human responses across languages, tasks, and dialogue settings. We study this problem as conditional human-distribution alignment: models should match the human response distribution appropriate to the current interaction context, rather than a universal response style. We introduce PolyAlign, a distribution-aware alignment framework that organizes bilingual interaction data into bucket-specific human reference distributions defined by language, interaction track, response family, and length. PolyAlign combines Bucket-Aware SFT, which balances optimization across heterogeneous buckets, with Human-Distribution Preference Optimization (HDPO), which regularizes preference learning using critic-estimated distance to bucket-specific human support. Across a bilingual evaluation suite covering English and Chinese single- and multi-turn settings, PolyAlign improves conditional naturalness and distributional faithfulness while preserving competitive task utility. The results suggest that post-training should move beyond global alignment objectives toward interaction-aware alignment with human response distributions.

19.
arXiv (CS.AI) 2026-06-17

STAR: SpatioTemporal Adaptive Reward Allocation for Text-to-Image RL Post-Training

arXiv:2606.17979v1 Announce Type: new Abstract: Existing RL post-training methods for text-to-image generation usually convert the final-image reward into a single scalar advantage and apply it with the same strength to the entire generative trajectory. However, text-to-image generation naturally has temporal and spatial structure: different denoising steps are responsible for different generation stages, and the content that truly determines text alignment often appears only in part of the image. This granularity mismatch makes it difficult for policy updates to focus on the generative components that actually affect the reward. To address this issue, we propose SpatioTemporal Adaptive Reward (STAR) Allocation for RL post-training of text-to-image diffusion and flow models. STAR uses text-image attention inside the generative model and starts from the core content that the user truly cares about in the prompt. It constructs spatial allocation maps that dynamically vary across denoising steps and rollouts, and allocates the same group-relative advantage to more relevant latent regions with almost no additional computational overhead. STAR then applies stronger policy updates to these regions through a spatially resolved policy objective. We use Stable Diffusion 3.5 Medium as the base model and evaluate on three tasks: GenEval, OCR text rendering, and PickScore. Experimental results show that STAR improves compositional semantic alignment, text rendering, and preference optimization without changing the external reward source, achieving $\mathbf{0.9759}$, $\mathbf{0.9757}$, and $\mathbf{23.60}$ on GenEval, OCR, and PickScore, respectively.

20.
arXiv (CS.AI) 2026-06-19

FM-Agent: Scaling Formal Methods to Large Systems via LLM-Based Hoare-Style Reasoning

arXiv:2604.11556v2 Announce Type: replace-cross Abstract: LLM-assisted software development has become increasingly prevalent, and can generate large-scale systems, such as compilers. It becomes crucial to strengthen the correctness of the generated code. However, automated reasoning for large-scale systems remains challenging due to code complexity. Hoare logic offers an approach to decomposing a large system into smaller components and reasoning about them separately (i.e., compositional reasoning). However, existing works still struggle to scale, because Hoare logic requires writing formal specifications for each function, imposing a heavy human burden. The problem is exacerbated when code is generated by LLMs, as developers lack a deep understanding of each function's expected behavior. This paper presents FM-Agent, the first framework that realizes automated compositional reasoning for large-scale systems. Leveraging LLMs, FM-Agent introduces a top-down paradigm to automatically generate function-level specifications. Specifically, FM-Agent derives the specification of a function from how its callers expect the function to behave, so the generated specifications can reflect the developer's intent of a function even if the implementation is buggy. Developers' intent is usually expressed in natural language, while existing verifiers only support formulas. Therefore, FM-Agent generalizes Hoare-style inference to reason about functions against natural-language specifications. Finally, to confirm bug existence and explain bug causes, FM-Agent automatically generates test cases to trigger potential bugs. In our evaluation, FM-Agent successfully reasons about large-scale systems within 2 days, each of which has up to 143k LoC. These systems have already been tested by their developers, but FM-Agent still finds 522 newly discovered bugs. These bugs can cause serious consequences, including system crashes and incorrect execution results.

21.
arXiv (quant-ph) 2026-06-17

From Period Finding to Lattice Sampling: Experimental Insights into Shor's and Regev's Factoring Algorithms

arXiv:2606.17647v1 Announce Type: new Abstract: Quantum algorithms for integer factorization represent one of the most prominent applications of quantum computation, with far-reaching implications for modern cryptography. While Shor's algorithm provides a polynomial-time solution in the ideal quantum model, its practical implementation is severely constrained by the limitations of current noisy intermediate-scale quantum (NISQ) hardware. These constraints have motivated the exploration of alternative factoring algorithms with different structural and resource trade-offs. In this work, we present an experimental study of Regev's quantum factoring algorithm, implemented on real quantum hardware, and compare its behavior with that of Shor's algorithm under analogous conditions. Focusing on the case N = 15, we execute both algorithms on the QMIO quantum computer at the Centro de Supercomputacion de Galicia (CESGA) and contrast the results with one of IBM's open-access quantum computers and ideal simulations. This parallel execution enables a low-level comparison of the two algorithms, highlighting how their respective quantum implementations interact with hardware noise, limited circuit depth, and finite sampling. Our analysis emphasizes the different ways in which Shor's and Regev's algorithms encode arithmetic structure into quantum states through Fourier sampling in one and higher dimensions, respectively, and how these differences manifest in experimental outcomes. Although neither algorithm demonstrates a practical advantage in the small N regime, the results provide insight into their relative robustness and failure modes on contemporary quantum devices. This study illustrates the value of experimental benchmarking of alternative quantum factoring algorithms as a means of understanding the practical implications of algorithmic design choices in the NISQ era.

22.
arXiv (quant-ph) 2026-06-16

Minimum measurements quantum protocol for band structure calculation

arXiv:2511.04389v2 Announce Type: replace Abstract: Protocols for quantum measurement are an essential part of quantum computing. Measurements are no longer confined to the final step of computation but are increasingly embedded within quantum circuits as integral components of noise-resilient algorithms. However, each observable typically requires a distinct measurement basis, often demanding a different circuit configuration. As the number of such configurations typically grows with the number of qubits, measurements constitute a major bottleneck. Focusing on electronic structure calculations in crystalline systems, we propose a measurement protocol that restricts the required measurement configurations to an absolute minimum of just three, independent of the number of qubits. This makes it one of the few known protocols that do not scale with qubit number. In particular, we derive the measurement protocol from the symmetries of tight-binding (TB) Hamiltonians and implement it within the Orthogonal-Ansatz Variational Quantum Eigensolver (OA-VQE) algorithm. We demonstrate its performance on three systems, namely a two-dimensional CuO$_2$ square lattice (3 qubits), bilayer graphene with hexagonal (Honeycomb) lattice (4 qubits) and three-dimensional diamond lattice (10 qubits). Beyond tight-binding systems, the protocol can be extended to enable efficient initial state preparation for many-body Hamiltonians, such as multi-orbital Hubbard models in a momentum space.

23.
bioRxiv (Bioinfo) 2026-06-20

A network approach to DNA methylation clocks

Biological age predicts health and lifespan better than chronological age, but remains difficult to measure. One leading molecular proxy for biological age is DNA methylation, which underlies age predictors known as "clocks". These clocks use penalized linear regression to predict chronological age from methylation levels using selected cytosine–guanine pairs (CpGs) along DNA. Although they predict chronological age within a few years and track mortality risk, there are several issues. Different clocks share a vanishingly small number of CpG sites, many of which show weak associations with age. Also, the clocks often do not transfer across methylation array platforms. This paper takes a network approach to better understand these issues. By using 12 public datasets from human blood, we build a co-methylation network of the sites that show the strongest age correlation. After pruning weak links, we find that it has a small number of large modules of covarying CpGs surrounded by many small modules and singleton sites. These modules are biologically interpretable, as they are associated with CpG island contexts and enriched for distinct Gene Ontology functions. We also map five established clocks onto this network (Horvath, Hannum, AltumAge, Skin & Blood, and Han) and find that they select some CpGs from the same module. This suggests that they are more similar than they appear. The network structure also suggests new ways to build clocks. A simple clock that retains one CpG per module matches the performance of established clocks. A second one, built from module-level principal components, outperforms all five established clocks in three validation cohorts and is transferable across array platforms (Illumina Infinium Methylation 450K or EPIC arrays). Overall, the network perspective shifts attention from individual CpG sites to modules of covarying sites. This perspective helps explain why DNA methylation clocks perform so well despite their differences and provides a more systematic approach for developing the next generation of aging biomarkers.

24.
medRxiv (Medicine) 2026-06-15

Population-scale genomics reveals divergent pathogenicity of variant classes across paralogous collagen IV genes

Monoallelic pathogenic or likely pathogenic variants in COL4A3 and COL4A4 occur in approximately 1 in 106 individuals, yet whether these paralogous genes confer equivalent pathogenicity for the same variant classes has not been tested at population scale. Using whole-genome sequencing data from the UK Biobank (UKB; n = 500,000), with replication in the All of Us Research Program (n = 414,000), we performed per-variant association testing, gene-based collapsing analyses and phenome-wide association studies (PheWAS) across haematuria, proteinuria and chronic kidney disease. We identified 64 COL4A3 and 92 COL4A4 rare variants significantly associated with haematuria or proteinuria, generating a quantitative allelic series for clinical variant interpretation. Glycine substitutions within collagenous domains conferred similar risks in both genes. In contrast, truncating and non-collagenous domain (NC1) missense variants were strongly associated with haematuria and proteinuria in COL4A4 carriers but showed substantially attenuated or absent associations in COL4A3 carriers despite comparable carrier frequencies and predicted pathogenicity scores. These findings were independently replicated in All of Us. Genome-wide association analysis identified the COL4A3/COL4A4 locus as the dominant genetic determinant of haematuria, with the signal attributable to the aggregate effects of rare coding variants and no evidence of independent common variant or trans-acting modifier effects. These findings demonstrate substantial gene-specific differences in tolerance to truncating and NC1 variants between COL4A3 and COL4A4, challenging assumptions of equivalent pathogenicity across paralogous collagen IV genes. Gene identity and not variant class alone, should inform risk stratification, variant interpretation and genetic counselling in individuals carrying collagen IV risk genotypes.

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

Human-Guided Agentic AI for Multimodal Clinical Prediction: Lessons from the AgentDS Healthcare Benchmark

arXiv:2602.19502v2 Announce Type: replace Abstract: Agentic AI systems are increasingly capable of autonomous data science workflows, yet clinical prediction tasks demand domain expertise that purely automated approaches struggle to provide. We investigate how human guidance of agentic AI can improve multimodal clinical prediction, presenting our approach to all three AgentDS Healthcare benchmark challenges: 30-day hospital readmission prediction (Macro-F1 = 0.8986), emergency department cost forecasting (MAE = $465.13), and discharge readiness assessment (Macro-F1 = 0.7939). Across these tasks, human analysts directed the agentic workflow at key decision points, multimodal feature engineering from clinical notes, scanned PDF billing receipts, and time-series vital signs; task-appropriate model selection; and clinically informed validation strategies. Our approach ranked 5th overall in the healthcare domain, with a 3rd-place finish on the discharge readiness task. Ablation studies reveal that human-guided decisions compounded to a cumulative gain of +0.065 F1 over automated baselines, with multimodal feature extraction contributing the largest single improvement (+0.041 F1). We distill three generalizable lessons: (1) domain-informed feature engineering at each pipeline stage yields compounding gains that outperform extensive automated search; (2) multimodal data integration requires task-specific human judgment that no single extraction strategy generalizes across clinical text, PDFs, and time-series; and (3) deliberate ensemble diversity with clinically motivated model configurations outperforms random hyperparameter search. These findings offer practical guidance for teams deploying agentic AI in healthcare settings where interpretability, reproducibility, and clinical validity are essential.