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01.
arXiv (math.PR) 2026-06-25

Imprecise Transition Matrices for Markov Cohort Models: Lower and Upper Expectations with a Practical Health Economic Application

arXiv:2606.25716v1 Announce Type: cross Abstract: In applied health research, Markov cohort models are built on a precisely specified transition probability matrix. However, in many applications, the available evidence – transition counts, structural constraints, and treatment-effect data – identifies a set of admissible matrices rather than one uniquely justified matrix. This paper formulates an imprecise-probability extension in which inference yields lower and upper expectations over an evidence-compatible set of precise Markov cohort models. The contribution differs from existing imprecise Markov-chain work by focusing on finite-horizon cohort trajectories, additive accumulated outcomes, and transition matrices constructed from empirical transition counts. Under non-empty compact separately specified outgoing-row sets, the lower and upper accumulated outcomes are computed exactly by Bellman-style lower and upper transition operators. We prove the envelope theorem, reduction to the classical model, coherence properties of the lower transition operator, and algebraic conditions under which a single selected matrix yields a non-robust decision. We then show how multinomial transition counts induce admissible matrix sets through the Imprecise Dirichlet Model. A real-world cost-effectiveness example of patent foramen ovale closure after cryptogenic stroke illustrates the practical consequence: the empirical transition matrix slightly favors closure, whereas the imprecise analysis yields an incremental net monetary benefit interval crossing zero. The method provides both a rigorous lower-expectation formulation and a practical diagnostic for decisions that depend on transition probabilities not fully resolved by the evidence.

02.
arXiv (CS.LG) 2026-06-16

Functional Gradient Descent with Adaptive Representations

arXiv:2606.16926v1 Announce Type: cross Abstract: Functional optimization problems are typically solved by optimizing the parameters of a fixed representation, such as a neural network, resulting in highly nonconvex losses that complicate both training and theoretical analysis. An interesting alternative is functional gradient descent (FGD), that is, gradient descent directly in function space, which benefits from strong convergence results and admits a clean theory. However, FGD is difficult to implement in practice because functional gradients are infinite-dimensional, and thus cannot be fully computed nor stored in memory. Existing implementations therefore rely on fixed approximations, which introduce approximation error. We propose a new, theoretically-grounded FGD algorithm that adapts the representation of the functional gradients over the course of optimization. By explicitly incorporating this approximation into the analysis, we establish convergence to a stationary point (for smooth losses) and to a global minimizer (under smoothness + a Polyak-Lojasiewicz-type condition) regardless of our approximations. To the best of our knowledge, this is the first implementable FGD method with such guarantees in a general setting. We demonstrate the effectiveness of our method on regression, numerical solution of PDEs, and modern computer vision. Across settings, our method consistently outperforms both FGD with fixed approximations and neural network baselines in efficiency and accuracy.

03.
arXiv (CS.CL) 2026-06-25

Beyond Function Calling: Benchmarking Tool-Using Agents under Tool-Environment Unreliability

Large language models are increasingly deployed as agents that solve tasks by interacting with external tool environments. Although recent tool-use benchmarks increasingly cover complex task settings, they still largely assume clean, stable, and trustworthy tool environments, leaving tool-environment unreliability insufficiently examined. We introduce ToolBench-X, a benchmark for evaluating agents under recoverable reliability hazards. ToolBench-X contains executable multi-step tasks across diverse domains and sequential, parallel, and mixed workflows, each paired with deterministic tools and a canonical final answer for automatic evaluation. Starting from clean tool environments, ToolBench-X injects five structured hazard types: Specification Drift, Invocation Error, Execution Failure, Output Drift, and Cross-source Conflict. Crucially, each injected instance remains solvable through at least one valid recovery path, such as retrying, fallback, verification, or cross-checking. Experiments reveal a substantial reliability gap: agents that perform well with reliable tools often fail under recoverable hazards. Further analysis shows that failures are driven less by tool-use volume or inference budget than by limited hazard diagnosis and ineffective recovery. Targeted recovery hints recover many failed tasks, while test-time scaling yields more limited gains. These results suggest that tool-use evaluation should move beyond function-call accuracy toward task completion under unreliable tool environments. The code and data is available at https://github.com/Foreverskyou/ToolBench-X.

04.
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.

05.
arXiv (quant-ph) 2026-06-12

Intermediate State Formation of Topologically Associated Chromatin Domains using Quantum Annealing

arXiv:2505.23289v2 Announce Type: replace Abstract: Topologically Associating Chromatin Domains are spatially distinct chromatin regions that regulate transcription by segregating active and inactive genomic elements. Empirical studies show that their formation correlates with local patterns of epigenetic markers, yet the precise mechanisms linking 1D epigenetic landscapes to 3D chromatin folding remain unclear. Recent models represent chromatin as a spin system, where nucleosomes are treated as discrete-state variables coupled by interaction strengths derived from genomic and epigenetic data. Classical samplers struggle with these models due to high frustration and dense couplings. Here, we present a quantum annealing (QA) approach to efficiently sample chromatin states, embedding an epigenetic Ising model into the topology of D-Wave quantum processors. Rather than reconstructing exact TAD size distributions or insulation scores, our method reproduces statistical features, such as mean marker incidences and intra-/inter-nucleosome correlations, while generating configurations that exhibit TAD-like structural motifs. These results demonstrate QA as an alternative to explore the chromatin architecture and provide a foundation in epigenetic modeling.

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

Fundamental limit on the heralded single photons' spectral brightness

arXiv:2510.24439v3 Announce Type: replace Abstract: Heralded single photons (HSPs) are the versatile flying qubits in quantum communication and networks due to their ability to remove the randomness of arrival time and enhance the transmission reliability. As the generation rate of HSPs increases or their linewidth narrows, both of which are desirable for quantum information processing, the fundamental limit of spectral brightness (SB), defined as the generation rate per unit linewidth, remains unclear. To examine the existence and value of such a limit, we systematically studied the SB together with the cross-correlation function, or equivalently, the signal-to-background ratio (SBR). We ultimately derive an upper bound on SB that applies universally to all types of HSP sources. A newly defined quantity governs this limit, the quality factor, which is the product of SBR and effective SB. The quality factor indicates how closely an HSP source approaches an ideal noise-free source. Furthermore, by employing an HSP source based on hot atomic vapor, we achieved an SB of $(8.5\pm0.3)$$\times$$10^5$ pairs/s/MHz and a quality factor of $0.73\pm0.02$ under the single-photon criterion. Both values represent the highest reported performance to date among all HSP platforms. These results provide a unified benchmark for evaluating and optimizing HSP sources.

07.
arXiv (quant-ph) 2026-06-17

A Lindbladian for holographic Brownian motion

arXiv:2606.17909v1 Announce Type: cross Abstract: We derive a Lindbladian description of holographic Brownian motion in the high-temperature regime. Starting from the influence functional for a trailing string endpoint, we identify the corresponding quantum master equation and prove that it is completely positive and trace-preserving. We determine the coefficients of the Lindbladian explicitly for two holographic backgrounds: the BTZ black hole and the AdS$_5$ black brane, restricting in the latter case to the endpoint fluctuation along the $x^1$-direction. We then analyze the time evolution of phase-space moments, energy relaxation, and steady states.

08.
arXiv (CS.LG) 2026-06-19

PaAno+: Multiscale Encoding and Cross-Variable Attention for Time Series Anomaly Detection

arXiv:2606.20055v1 Announce Type: new Abstract: Time-series anomaly detection has significant practical value for industrial and medical monitoring, as well as other critical domains. Current Transformer- and large-model-based detection approaches incur excessive computational overhead, while existing lightweight alternatives are constrained by insufficient feature extraction and inadequate modeling of dependencies across multivariate variables. To mitigate the above drawbacks, this study develops a lightweight, efficient anomaly detection model, dubbed PaAno, within the patch-oriented representation learning paradigm. In the encoder module, a multiscale feature-extraction backbone is constructed using convolutional kernels with differentiated receptive fields to capture hierarchical temporal characteristics; subsequent cross-scale adaptive attention aggregation, combined with residual connection optimization, further stabilizes feature representation learning. A cross-variable fusion attention module is embedded to explicitly characterize inter-variable correlations, empowering the model to identify anomalous patterns amid intricate operational conditions. Moreover, a novel pretext task based on temporal patch-window sorting is customized to uncover intrinsic structural properties of time series, and triplet loss is leveraged to optimize the patch embedding space for enhanced feature discrimination. Extensive experiments on the TSB-AD benchmark demonstrate that the proposed PaAno achieves state-of-the-art detection accuracy on both univariate and multivariate tasks, yielding significant performance gains across evaluation metrics, including VUS-PR, relative to the original PaAno. Leveraging a compact network design, the presented model achieves favorable computational efficiency, enabling deployment on resource-limited terminals for real-time anomaly inference.

09.
arXiv (CS.LG) 2026-06-24

Dirac-Frenkel dynamics with inertia for nonlinearly parametrized solutions of evolution problems

arXiv:2606.24769v1 Announce Type: cross Abstract: Even when Dirac-Frenkel dynamics determine a well-defined evolution in function space, the corresponding parameter dynamics can be non-unique or ill-conditioned for redundant nonlinear parametrizations such as neural networks or mixture models. We propose to add inertia to the Dirac-Frenkel dynamics and show that this allows useful parameter velocity information to persist from the past trajectory in directions that are weakly informed, while well-informed parameter velocity directions continue to follow the Dirac-Frenkel dynamics. We prove that the inertial formulation yields well-posed parameter dynamics and provide a posteriori error bounds. After time discretization, the method requires the solution of the same type of regularized linear least-squares problem as standard Dirac-Frenkel dynamics, but with the previous velocity appearing as an anchor. Numerical experiments demonstrate the increased robustness obtained with inertia.

10.
bioRxiv (Bioinfo) 2026-06-12

Evaluating cell type annotations in single-cell omics in the absence of ground truth

Accurate cell type annotation is essential for single-cell transcriptomics, directly shaping downstream analyses and biological interpretations. Yet, objective evaluation of annotation quality remains a major challenge. Here, we argue that a cell type or cell state label has practical utility only if it captures a molecular pattern that is reproducible across biological replicates. Based on this principle, we introduce inter-sample consistency (ISC), a quantitative framework to assess annotation quality in single-cell RNA-seq datasets. Unlike existing cluster validation approaches, ISC distinguishes annotations that generalize across samples and individuals from those driven by technical or unwanted variation, thereby providing principled criteria for annotation quality and transferability. When applied to published single-cell atlases, ISC reveals widespread reproducibility gaps and provides actionable guidance for repairing inconsistent annotations. Notably, ISC enables benchmarking of automated cell type annotation tools even when ground-truth labels are unavailable, providing interpretable metrics to guide their development and evaluation. Implemented as the scTypeEval Bioconductor package, this framework offers a broadly applicable resource for evaluating and improving cell type annotations in single-cell RNA-seq experiments.

11.
medRxiv (Medicine) 2026-06-17

Low-Density Lipoprotein Cholesterol and Dementia Risk: Integrating Mendelian Randomization and Target Trial Emulation Within the Heart-Brain Axis

Background: The heart-brain axis links cardiovascular and neurodegenerative disease through shared vascular and inflammatory mechanisms. Although low-density lipoprotein cholesterol (LDL-C) is an established causal factor in atherosclerotic cardiovascular disease (ASCVD), its relationship with dementia remains uncertain, with midlife elevations associated with increased risk but late-life associations often appearing null or inverse. To address this cholesterol paradox, we integrated mendelian randomization (MR) with an active-comparator new-user target trial emulation. Methods: We applied a triangulated causal inference framework integrating two-sample MR with observational target trial emulation. Genetic variants associated with LDL-C were used as instrumental variables to evaluate Alzheimer disease (AD), dementia with Lewy bodies (DLB), frontotemporal dementia (FTD), and any dementia (AnyDem), with causal estimates derived using inverse-variance weighted models and sensitivity analyses for heterogeneity and pleiotropy. In parallel, an active-comparator new-user design compared statin versus ezetimibe initiation among adults aged 60 years or older using propensity score (PS) overlap weighting and Cox proportional hazards models to evaluate cardiovascular and dementia outcomes. Results: Genetically predicted LDL-C was associated with increased risk of DLB (OR 1.65, 95% CI 1.30-2.10; p

12.
arXiv (CS.AI) 2026-06-19

Which Pairs to Compare for LLM Post-Training?

arXiv:2606.19607v1 Announce Type: new Abstract: Preference-based post-training has become a central paradigm for aligning language models. A common data-collection strategy is to generate a small set of completions for each prompt and label the resulting comparison pairs. However, human preference labels are often much more expensive than generating additional completions, suggesting a different use of the same labeling budget: generate a larger pool of completions, but label only the most informative comparison pairs. This paper studies which pairs should be compared in preference-based post-training. We formulate comparison curation as a sampling-design problem and evaluate designs by the quality of the final policy under the preference-based post-training objective. We instantiate this framework for Direct Preference Optimization (DPO), analyzing how the choice of labeled pairs propagates through DPO training to downstream policy performance. Our main results provide matching upper and lower bounds on the post-training optimality gap of the DPO-trained policy. The bounds show that comparison selection affects downstream performance through a single design-dependent information matrix, which links label allocation to parameter estimation error and policy suboptimality. This yields an explicit optimization criterion for budgeted comparison curation and motivates practical sampling designs for selecting informative pairs from large generated completion pools. Experiments on synthetic settings and language-model post-training benchmarks show that the proposed designs consistently improve sample efficiency over common comparison-selection heuristics.

13.
bioRxiv (Bioinfo) 2026-06-24

ComplexDesign: sequence-hallucination design of protein binders bridging multiple proteins

Motivation: Designing multichain protein complexes requires coordinating the folding of component proteins with the formation of their interfaces. The existing methods, however, remain limited in their ability to satisfy these requirements simultaneously, especially for trimeric and tetrameric complexes. As an important practical scenario, designing a binder that bridges two target proteins into a ternary complex requires flexibility in the relative arrangement of the two targets, adding an additional challenge to existing design methods. Results: We present ComplexDesign, a hallucination-based approach for multichain protein design. ComplexDesign performs structure-prediction-guided sequence optimization to simultaneously fold each protein chain and form inter-chain interactions that bind them together. To provide the flexibility required to appropriately arrange these target proteins, ComplexDesign introduces a specialized masking mechanism that enables exploration of possible relative arrangements rather than being limited to the predefined ones. Across a comprehensive set of benchmarks with various chain lengths, ComplexDesign outperformed existing methods in the unconditional design of dimers, trimers, and tetramers, achieving a high design success rate exceeding 50%, supporting its capability for multichain complex design. Furthermore, in the case of multi-target binder design, ComplexDesign produced high-confidence, self-consistent ternary complexes for 8 out of 10 target pairs. These results establish ComplexDesign as an effective tool for multichain protein design, with particular utility for designing binders that bridge two target proteins. Availability and implementation: The source code of ComplexDesign will be made publicly available upon publication.

14.
arXiv (quant-ph) 2026-06-24

Dissipative ground-state preparation of a quantum spin chain on a trapped-ion quantum computer

arXiv:2601.08137v2 Announce Type: replace Abstract: We demonstrate a dissipative protocol for ground-state preparation of a quantum spin chain on a trapped-ion quantum computer. As a first step, we derive a Kraus representation of a dissipation channel for the protocol recently proposed by Ding et al. [Phys. Rev. Res. 6, 033147 (2024)] that still holds for arbitrary temporal discretization steps, extending the analysis beyond the Lindblad dynamics regime. The protocol guarantees that the fidelity with the ground state monotonically increases (or remains unchanged) under repeated applications of the channel to an arbitrary initial state, provided that the ground state is the unique steady state of the dissipation channel. Using this framework, we implement dissipative ground-state preparation of a transverse-field Ising chain for up to 19 spins on the trapped-ion quantum computer Reimei provided by Quantinuum. Despite the presence of hardware noise, the dynamics consistently converges to a low-energy state far away from the maximally mixed state even when the corresponding quantum circuits contain as many as 4110 entangling gates, demonstrating the intrinsic robustness of the protocol. By applying zero-noise extrapolation, the resulting energy expectation values are systematically improved to agree with noiseless simulations within statistical uncertainties.

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

JointEdit3D: Feed-Forward 3D Scene Editing in a Unified Latent Space

Existing 3D scene editing methods typically rely on per-scene optimization over explicit 3D representations or cascaded edit-and-reconstruct pipelines, resulting in high test-time cost, limited 3D awareness, and structural inconsistencies. To couple appearance synthesis and geometry prediction during editing, we build on a unified RGB-geometry reconstruction-generation latent space and adapt it to feed-forward 3D scene editing. The resulting framework, JointEdit3D, performs asymmetric latent inpainting by observing only a single edited RGB reference latent and generating the remaining RGB views and edited geometry latent under source-scene anchoring. JointEdit3D introduces a dedicated SceneAnchor Branch to inject source-scene structure without forcing direct copying, and adopts edit/background-aware losses to balance edited-region fidelity with unedited-content preservation. To address the lack of paired resources for standardized 3D scene editing evaluation, we introduce SceneEdit3D-15K, a dataset with 15K paired editing samples and renderer-provided 3D annotations, together with SceneEdit3D-Bench, a curated 100-sample benchmark. Experiments show that JointEdit3D improves edited-region quality and 3D structural completeness over prior baselines while maintaining competitive background preservation.

16.
arXiv (CS.AI) 2026-06-11

Bridging the Morphology Gap: Adapting VLA Models to Dexterous Manipulation via Intent-Conditioned Fine-Tuning

arXiv:2606.12109v1 Announce Type: cross Abstract: Vision-Language-Action (VLA) models have demonstrated remarkable zero-shot generalization in robotic manipulation, yet the vast majority of pre-trained pipelines remain strictly confined to low-DoF parallel grippers. Adapting these rich semantic priors to high-DoF dexterous hands introduces a severe morphology gap, direct end-to-end joint fine-tuning inherently causes catastrophic forgetting of spatial reasoning and acute action manifold collapse due to data scarcity. In this paper, we present InDex, a novel, data-efficient adaptation framework rooted in cross-morphology semantic inheritance. Rather than discarding the pre-trained 1-DoF parallel grasp output, we repurpose it as a continuous, macroscopic virtual grasp intent proxy to sequentialize the control topology. We implement a two-stage decoupled learning architecture: the first stage parameter-efficiently aligns the VLA backbone to predict continuous arm trajectories and the scalar grasp intent; the second stage freezes this spatial backbone and leverages an intent-conditioned denoising diffusion head to decode fine-grained joint articulations for multi-fingered end-effectors. Extensive simulation benchmarks across a suite of multi-stage, contact-rich dexterous manipulation tasks demonstrate that InDex effectively masters intricate skills with minimal demonstration data, substantially outperforming monolithic baselines while preserving the robust spatial generalizability of the original VLA prior.

17.
medRxiv (Medicine) 2026-06-10

Documented clinical genetic testing among carriers of hereditary breast and ovarian cancer variants: Ancestry and socioeconomic disparities in the All of Us research program

Importance: Hereditary breast and ovarian cancer (HBOC) variant carriers benefit from risk-reducing interventions, but only if identified. The extent to which carriers are clinically recognized, and whether recognition is equitable across diverse populations, is poorly characterized in a single large U.S. cohort. Objective: To estimate P/LP HBOC carrier prevalence across genetic ancestry groups, quantify documented clinical genetic testing among carriers, and evaluate ancestry and socioeconomic disparities in testing. Design, Setting, and Participants: Cross-sectional analysis of the All of Us Research Program Controlled Tier (Curated Data Repository v8/C2024Q3R9), comprising participants with short-read whole genome sequencing and linked electronic health record (EHR) and survey data. Carriers were ascertained from research genomic data independent of clinical testing. Exposures: Genetically inferred ancestry (African [AFR], Admixed American [AMR], East Asian [EAS], European [EUR], Middle Eastern [MID], South Asian [SAS]); self-reported household income and educational attainment. Main Outcomes and Measures: (1) Carrier prevalence with Wilson 95% CIs; (2) documented clinical genetic testing (procedure codes) among carriers; (3) adjusted odds of documented testing among women, by ancestry, before and after socioeconomic adjustment, using multivariable logistic regression. Results: Among 414,830 participants, P/LP HBOC carrier prevalence was 1.42% (95% CI, 1.38-1.45) overall and similar across ancestry groups (AFR 1.24%, AMR 1.32%, EAS 1.19%, EUR 1.52%, MID 1.68%, SAS 1.33%; overlapping CIs). Among 250,071 women in the testing analysis, documented clinical genetic testing was rare: only 74 of 5,878 carriers overall (1.3%) and 59 of 3,572 European-ancestry carriers (1.7%) had a documented test, with counts below reportable thresholds in all other ancestry groups. African-ancestry women had lower adjusted odds of documented testing than European-ancestry women (Model 1 adjusted odds ratio [aOR], 0.32; 95% CI, 0.27-0.39), an association that attenuated but persisted after adjustment for income and education (Model 2 aOR, 0.48; 95% CI, 0.40-0.58; P < 0.001); Admixed American women also had reduced adjusted odds (aOR, 0.71; 95% CI, 0.61-0.84). Lower income and lower education were independently and dose-dependently associated with lower testing odds (income

18.
bioRxiv (Bioinfo) 2026-06-23

Early Tracheal and Salivary miRNAs in Extremely Preterm Infants Predict BPD-related Pulmonary Hypertension

Pulmonary hypertension (BPD-PH) associated with bronchopulmonary dysplasia (BPD) in preterm infants associates with high morbidity and mortality within the first two years of life. In a previous unbiased study, we identified a panel miRNAs in tracheal aspirates (TA) that were differentially expressed in extremely low gestational age newborns (ELGANs) with BPD-PH compared to those with BPD but no PH. To explore the predictive potential of these miRNAs, we studied TA exosomes from 7 days old ELGANs and analysed a curated panel of 16 miRNAs through logistic regression and calculated the predictive AUROC to diagnose BPD-PH at 36 weeks PMA. AUROC of TA miRNAs was 0.76 with sensitivity and specificity of 53% and 93%, respectively. Adding sex and gestational age to the variables improved the AUROC to 0.78 with sensitivity and specificity of 61 and 87% respectively. Due to challenges of obtaining TA in non-invasively ventilated infants, we collected saliva samples from ELGANs at 7 days of age and compared the log expression of these 16 miRNAs in both biofluids and found significant correlation in their expression (pearson r=0.92, p

19.
arXiv (CS.CV) 2026-06-11

Slots, Transitions, Loops: Learning Composable World Models for ARC

ARC tests in-context rule induction: given a few input-output demonstrations, a model must infer the hidden rule and apply it to a new query. While many approaches express ARC rules through language, code, or symbolic programs, ARC itself is visual-symbolic: rules appear as grid transitions over objects, colors, shapes, and spatial relations. We introduce Loop-OWM, an object-centric world-modeling architecture that learns these rules as composable transitions over structured states. It combines color-prototype slots, demonstration-conditioned task summaries, and a looped transition model with dense propagation and slot-conditioned correction. On both ARC-1 and ARC-2, Loop-OWM outperforms non-looped and looped baselines with comparable or fewer parameters. These results suggest that ARC rules can be learned not only as language descriptions or searched programs, but also as transitions over visual-symbolic world states.

20.
arXiv (quant-ph) 2026-06-15

Conditional squeezing induced by a two-level system: arbitrary-time Magnus coefficients in the quantum Rabi model

arXiv:2508.03506v5 Announce Type: replace Abstract: We present a systematic Magnus expansion treatment of the quantum Rabi model beyond the Rotating Wave Approximation. We show that at the second order of Magnus series, the second-order evolution operator contains a term that induces conditional squeezing of the field mode depending on the state of the atom, in addition to the energy shifts. We analyze the scaling behavior of the conditional squeezing coefficient for $^{87}\mathrm{Rb}$ $5^2S_{1/2}\rightarrow5^2P_{1/2}$ transition line and show that the slow envelope of the squeezing coefficient is maximized at half-detuning cycles, and that it scales with $\frac{4g^2}{\omega_0|\Delta|}$. We also show that the quadrature squeezing angle suggests a possible route towards quantum non-demolition readouts, while further investigation is required for a full first-order suppression. We then connect our work to the well-studied AC-Stark shift and Bloch-Siegert shift using the effective Hamiltonian theory. Finally, we show how the energy shifts and the conditional squeezing arise, as a whole $\mathrm{SU}(1,1)$ algebra, and how they can be disentangled as individual unitary evolutions.

21.
bioRxiv (Bioinfo) 2026-06-24

Development of Deep-Learning Models that Predict Quantitative Protein-Ligand Interac-tions in Glycobiology as a part of a Capstone Course

Glycans coat the surface of all cells, and every glycan is recognised by specific glycan-binding pro-teins (GBPs). There are no general tools that can accurately estimate the binding strength between glycan and GBP from the amino acid sequence of the GBP and the molecular structure of the glycan, represented as SMILES string. We describe models for predicting such binding strengths developed as a part of a Capstone Course at the University of Alberta. The models are trained on a dataset that combines BindingDB, a published database of small-molecule protein interactions, and data from glycan arrays measured by Consortium of Functional Glycomics (CFG). In this hybrid dataset of protein-ligand interactions the ligands are both glycans from CFG and small molecules from BindingDB; similarly, proteins include GBP and proteins from BindingDB. Three models are presented (i) ProMax which fuses ESM-2, MolFormer, and MolCLR features; (ii) APEX which constrains learning to a predetermined form, a physical model of binding; (iii) UltraMax adds inter-atomic distances for the ligands. To address the dataset's severe long-tail distribution, the models employ tail-aware losses for rare high-binding instances. Trained and evaluated on approximately one million protein–ligand pairs using hold-out splits for unseen molecules, the three models provide a unified framework for quantitative glycan-protein binding prediction. We observed that learning glycan-protein binding is harder than the similar task of learning small-molecule-protein interactions. Simple mirror-inversion tests led us to postulate that insufficient use of chiral features is an important source of difficulty in learning these interactions.

22.
arXiv (CS.CV) 2026-06-11

Atlas H&E-TME: Scalable AI-Based Tissue Profiling at Expert Pathologist-Level Accuracy

Hematoxylin and eosin (H&E) staining is the cornerstone of histopathology, yet scalable, quantitative analysis of H&E whole-slide images (WSIs) remains a central challenge in computational pathology. We present Atlas H&E-TME, an AI-based system built on the Atlas family of pathology foundation models that predicts tissue quality, tissue region, and cell type labels across multiple cancer types, yielding over 4,500 quantitative readouts per slide at cell-level resolution. A key challenge to validating such systems is overcoming morphological ambiguity inherent to H&E-only ground truth and the limited scalability of more informed references drawing on modalities such as immunohistochemistry (IHC). We address this with a dual validation framework combining biologically grounded depth with technical and morphological breadth. For depth, we propose an IHC-informed multi-pathologist consensus protocol that substantially improves inter-rater agreement over conventional H&E-only annotation. This yields a molecularly grounded reference against which we compare Atlas H&E-TME and pathologists working from H&E alone. For breadth, we benchmark Atlas H&E-TME on over 200,000 high-confidence H&E-only pathologist annotations across 1,500+ cases spanning eight cancer types and their most common metastatic sites, with subtypes covering >90% of clinical cases per cancer type, drawn from 25+ sources and 8+ scanner models. Benchmarked against the IHC-informed consensus, Atlas H&E-TME matches or exceeds pathologist H&E-only performance and generalizes consistently and robustly across this broad morphological and technical scope. In doing so, Atlas H&E-TME turns the H&E slide – the most ubiquitous data in pathology – into a scalable, quantitative window into the tumor and its microenvironment, laying a foundation for the next generation of tissue-based biomarkers in translational and clinical research.

23.
medRxiv (Medicine) 2026-06-22

Brain-gut axis imaging, motion correction with 11C-carfentanil total-body PET

Background: Mu-opioid receptors (MORs) are expressed throughout the body including in the brain and gastrointestinal (GI) tract. Total-body PET imaging of the brain and GI tract offers a promising approach for cross-sectional in vivo evaluation of the MOR brain-GI axis. However, intestinal motility and bladder filling introduce motion throughout the GI tract over the scan window. Here we establish analysis methodology to account for motion for dynamic imaging of the brain-GI axis, to further characterize peripheral MORs throughout the body and provide a framework for semi-automatic total-body PET modeling. Methods: 4 subjects underwent 90-min dynamic [11C]-carfentanil (cfn) total-body PET acquisitions at baseline, after intravenous naloxone (central antagonist) administration, and after orally administered loperamide (peripheral agonist and P-glycoprotein substrate). Thalamic MOR availability was measured using the Logan reference tissue model. Using CT-based segmentation, the GI tract was subdivided into anatomical segments, in addition to other peripheral organs (e.g., liver, psoas muscle). Frame-by-frame semi-automatic motion correction was performed with three distinct reference frames (11-14 min post-injection, p.i., 35-40 min p.i., and 85-90 min p.i.). The performance of these three were compared to manual correction. Compartment modeling and Logan graphical analysis were performed to estimate relevant kinetic parameters (K1, VT, VTLogan). Results: Across the 4 subjects and regions, kinetic parameter estimates were highly correlated (r>0.7) for K1, VT and VT Logan when comparing semi-automatic (reference frame at 35-40 min p.i.) and manual correction. With semi-automatic motion correction, graphical-based estimation of VTLogan in the gastrointestinal tract was significantly decreased with loperamide relative to baseline (p

24.
arXiv (quant-ph) 2026-06-12

Path integral control of open quantum systems

arXiv:2410.18635v4 Announce Type: replace Abstract: We investigate open-loop quantum state preparation for a class of open quantum systems whose dynamics follow a Gorini-Kossakowski-Lindblad-Sudarshan (GKLS) master equation that admits a trajectory-based stochastic representation. The deterministic control objective is reformulated as a stochastic optimal control problem – interpreting stochasticity as a methodological tool akin to stochastic Schrödinger equation unravelings – which situates the problem within the path integral control framework. For the class of GKLS generators under consideration, this reformulation leads to an explicit expression for the optimal control as a weighted average over stochastic quantum trajectories, thereby eliminating the need for gradient evaluations. Building on this theoretical result, we derive a control update rule for piecewise-constant control pulses and demonstrate that adaptive importance sampling progressively enhances the control estimator during optimization, culminating in the algorithm we term Path integral Quantum Control (PiQC). We further introduce an annealed variant of PiQC, wherein a synthetic noise schedule gradually steers open-system trajectories toward closed-system dynamics, enabling high-fidelity unitary state preparation. Numerical studies on a dissipative single-qubit system and a multi-qubit Nuclear Magnetic Resonance model verify that PiQC yields precise open-loop controls and displays robustness to Hamiltonian perturbations. We propose PiQC as a trajectory-based alternative to gradient-based approaches, which might offer a viable solution in quantum control problems where gradient computation is infeasible or computationally demanding.

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

An Ethical eValuation Agent (EeVA): Results of a Proof-of-Concept Test on a Prototype Agentic-like Workflow to Assist Ethical Deliberations

arXiv:2606.11218v1 Announce Type: cross Abstract: Ethical deliberation is often misunderstood as a search for single right or wrong answers, creating difficulties for non-ethically trained personnel who must address ethically laden challenges. We developed EeVA, an agentic-like LLM-based workflow designed to support comparative ethical reflection rather than deliver definitive ethical answers. EeVA was programmed in n8n using three interconnected workflows: starter, worker, and emitter. It evaluated uploaded use cases against 10 ethical frameworks through evaluator and synthesis prompts. Proof-of-concept testing used three published cases from urban mobility, peer-to-peer energy trading, and social-service resource allocation. Across all cases, EeVA produced consistently structured framework-specific evaluations and integrated syntheses. Outputs differentiated between frameworks, identified convergences and divergences, recommended modifications to increase alignment, and highlighted persistent ethical tensions. Syntheses were readable for non-specialists and shifted attention away from simplistic answers toward design conditions, safeguards, and areas where full cross-framework agreement was unlikely. The findings suggest that LLMs can be organised into usable workflows that preserve ethical plurality while helping bridge the communicative gap between ethicists and non-ethically trained personnel. EeVA's value lies not in replacing ethicists or resolving moral disagreement, but in scaffolding structured ethical deliberation. EeVA offers a promising proof of concept for supporting ethical reflection where access to ethics expertise is limited. Further work is needed on reproducibility, human evaluation, user testing, and efficiency before it can be considered a mature tool.