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01.
medRxiv (Medicine) 2026-06-15

Supporting people to access social security payments through the Special Rules for End of Life: a qualitative study of the perspectives of patients, carers and health care professionals

Authors:
Davies↗J. M↗Marshall↗Hussain↗Diggle↗French↗Stone↗Fimister↗Ogden↗Sleeman↗K. E↗Bradshaw↗…

Background: People living with terminal illness face a double financial burden from additional costs and loss of earning for themselves and their carers. Social security benefits are intended to help alleviate some of this financial pressure, and in the UK and other countries people are eligible for fast-tracked access to financial support via the Special Rules for End of Life. One in 3 people who are eligible miss out on this support, yet there is limited evidence on the reasons for this take-up deficit. Objectives: The aim of this study is to understand the barriers and facilitators to claiming benefits for terminally ill people from the perspectives of patients, carers, and health care professionals. Methods: This is a qualitative study combining i) focus groups with healthcare professionals recruited via professional networks and social media, and ii) interviews with patients and carers recruited in hospital and hospice settings. We analysed the data using Practical Thematic Analysis Results: Fifty-five multidisciplinary healthcare professionals participated in 11 focus groups, and we interviewed 10 patients and carers. We constructed five descriptive themes to summarise the data: Navigating priorities and uncertainty; positive impacts alongside a sense of shame and stigma; talking about money, difficulties and dividends; everybodys, yet nobodys, responsibility; and sticking points in the system. Conclusion: The themes reveal several challenges that may contribute to people not taking up this financial support. However, discussions about access to benefits were also seen as a core part of holistic care, a positive way to offer support and a gateway to other discussions about end-of-life care preferences and decisions. Recommendations for policy and practice include evaluating the adoption of a diagnostic rather than a prognostic eligibility criteria, integrating discussions about benefits into existing processes such as advance care planning, and improving education and support for clinicians.

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

Entity Labels Are Not Entity Signals: A Framework for Observable Relevance in Document Re-Ranking

Authors:
Utshab Kumar Ghosh↗Shubham Chatterjee↗

Entity-aware document retrieval uses query-associated entities as ranking signals, assuming that semantically relevant entities are also useful retrieval signals. We show this assumption is insufficient- and explain why. Unlike terms, which are ground-truth observations, entity links are hypotheses produced by an imperfect linker: an entity can be topically central yet provide no discriminative signal if the linker fires indiscriminately across relevant and non-relevant documents. We formalize this as a distinction between Conceptual Entity Relevance (CER)- whether an entity is topically related to a query- and Observable Entity Relevance (OER)- whether its observed presence in a collection discriminates relevant from non-relevant documents. Across four collections and annotation sources including human entity judgments, CER and OER exhibit near-chance agreement ($\kappa \approx 0$), while OER operationalizations agree substantially ($\kappa \approx 0.5$), confirming CER as the systematic outlier. CER-based supervision selects topically plausible but weakly discriminative entities, pruning fewer than 4% of non-relevant documents on some collections. Aligning supervision with OER improves non-relevant pruning by up to 10x and open-world MAP by 0.051 over BM25. Our findings motivate a shift from conceptual to observable notions of entity relevance in entity-aware retrieval.

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03.
arXiv (CS.CL) 2026-06-16

Formalize Once, Edit the Rest: Efficient Lean-Based Answer Selection for Math Reasoning

Authors:
Ji Feng↗Zhouxing Shi↗

With large language models (LLMs) increasingly applied to mathematical reasoning, formal proof assistants such as Lean can be leveraged to verify reasoning outputs with machine-checkable rigor, enabling use cases such as answer selection in test-time scaling with K sampled candidate answers. However, employing Lean requires that LLM outputs, originally in natural language, first be formalized. Existing Lean-based answer-selection work uses an autoformalization model to generate a formal statement in Lean for each candidate answer independently, incurring a significant computational cost. We propose BASE, a base-and-edit pipeline that formalizes a single base candidate per problem and derives the remaining K-1 statements by editing the answer expression in place. To facilitate this, we train a rewriter model LEANSCRIBE to localize the answer in the base formalization and generate a reusable edit function for the other K-1 candidates. BASE simultaneously improves selection accuracy and reduces formalization cost - a Pareto improvement that holds on all 12 (dataset, solver) configurations across four benchmarks and three solvers, cutting autoformalizer calls by about 5x at K=8, with the reduction expected to become larger as K grows. Code is available at https://github.com/ucr-rai/base-and-edit.

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04.
arXiv (CS.AI) 2026-06-19

ScaleWoB: Guiding GUI Agents with Coding Agents via Large-Scale Environmental Synthesis

Authors:
Guohong Liu↗Jialei Ye↗Pengzhi Gao↗Wei Liu↗Jian Luan↗Yunxin Liu↗Yuanchun Li↗

arXiv:2605.25160v2 Announce Type: replace Abstract: GUI agents powered by large language models are advancing rapidly, creating urgent needs for evaluation and training based on realistic environments. However, directly doing so in real-world environments introduces some challenges that cannot be overlooked. Real-world environments are complex and uncontrollable, making it difficult to construct verifiable rewards and to save or reset states. Existing works prioritize reproducibility but are often limited to open-source apps or file-operation tasks for reliable reward building, leaving a persistent gap from real-world usage. Furthermore, relying on virtual machines or docker images demand high resource requirements and suffer from slow response speeds, which limit the efficiency. We present \sys, a framework that could produce high-fidelity synthesized interactive environments for GUI agents across platforms with verifiable rewards. These environments behave as backend-free webpages accessible via URL, requiring near-zero setup and low resource cost, making the approach suitable for both large-scale evaluation and downstream agent training. We support multiple GUI platforms including mobile, desktop, and automotive/in-vehicle interfaces based on the same pipeline, covering 100+ environments and 1000+ verifiable tasks. Among them, 120 challenging tasks across 63 simulated mobile applications are released as a fully synthesized mobile GUI agent benchmark. Experiment results on five state-of-the-art mobile GUI agents reveal substantial headroom – the average success rate is only 27.92\%, dropping to 17.82\% on long-horizon subset – while humans reach 92.08\%. A comparison against real-world sample tasks shows that assessments made in our synthetic environments generalize to real apps. The project website is at https://scalewob.github.io.

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

Latent Space Reinforcement Learning for Inverse Material Estimation in Food Fracture Simulation

Authors:
Adrian Ramlal↗Yuhao Chen↗John S. Zelek↗

Realistic visual simulation of food manipulation requires accurate material parameters, yet these are difficult to measure directly and vary across the heterogeneous regions of a single food item. We address the inverse problem of estimating material parameters from a target description of fracture behavior in a non-differentiable continuum damage mechanics simulator. Using orange peeling as a test case, we train a neural surrogate on 2,000 forward simulations and compare Covariance Matrix Adaptation Evolution Strategy (CMA-ES, a gradient-free evolutionary optimizer) with Proximal Policy Optimization (PPO, a reinforcement learning algorithm) across the original 9-dimensional parameter space and two learned 4-dimensional latent representations. Since different oranges have different material properties, a practical inverse system must handle arbitrary targets without retraining. We train a goal-conditioned PPO policy that learns a general inverse mapping: given any target description of peeling behavior, the policy produces a material parameter estimate in a single forward pass (8 surrogate evaluations, approximately 10ms). Operating in a normalizing flow latent space with a shared surrogate evaluator, the goal-conditioned policy achieves 0.642 actual recovery when validated through the simulator, outperforming the original parameter space by 23%. A warm-start extension that initializes CMA-ES refinement from the policy's output further improves recovery to 0.828 with 540 evaluations. These findings provide a practical framework for inverse food physics and lay groundwork for vision-driven material identification from video observations of food manipulation.

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

GENIE: A Fine-Grained Measure for Novelty

Authors:
Ramya Namuduri↗Manya Wadhwa↗Anshun Asher Zheng↗Greg Durrett↗Junyi Jessy Li↗

Large Language Models have consistently demonstrated a lack of creativity and diversity across tasks. Prior work has focused on addressing whether models are capable of generating creative outputs. Here, we aim to consider novelty and investigate what makes model-generated content novel or not novel in a task-specific manner. We propose a fine-grained evaluation metric GENIE to measure the novelty of responses along task-specific features with respect to a population of responses. We show that unlike GENIE, holistic metrics struggle to capture the high-dimensionality of novelty and do not provide insight on which properties they target. Finally, we use GENIE to measure the effectiveness of mitigation methods that address creativity to better understand where these methods can improve novelty.

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07.
bioRxiv (Bioinfo) 2026-06-16

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets

Authors:
Gao↗Cui↗

Large-scale clinical and biomedical datasets increasingly contain both diverse subgroup attributes (e.g., demographic or clinical subgroups) and multiple prediction targets. Although various machine learning approaches can address subgroup differences or multi-target prediction, they often consider these aspects independently rather than jointly. To more effectively capture the shared and subgroup-specific information in such complex datasets, we propose the Integrative Transfer Network (ITN), a deep neural network designed to leverage data across subgroups and multiple related outcomes simultaneously. In extensive experiments, including time-to-event and classification tasks where demographic subgroups and multiple disease endpoints are prevalent, ITN demonstrates consistent improvements in subgroup-specific prediction by borrowing strength from other subgroups and outcomes. We envision ITN as a unified framework for learning from heterogeneous datasets where subgroup-specific insights are critical.

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

SIGMA: Search-Augmented On-Demand Knowledge Integration for Agentic Mathematical Reasoning

Authors:
Ali Asgarov↗Umid Suleymanov↗Aadyant Khatri↗

Solving mathematical reasoning problems requires not only accurate access to relevant knowledge but also careful, multi-step thinking. However, current retrieval-augmented models often rely on a single perspective, follow inflexible search strategies, and struggle to effectively combine information from multiple sources. We introduce SIGMA (Search-Augmented On-Demand Knowledge Integration for AGentic Mathematical reAsoning), a unified framework that orchestrates specialized agents to independently reason, perform targeted searches, and synthesize findings through a moderator mechanism. Each agent generates hypothetical passages to optimize retrieval for its analytic perspective, ensuring knowledge integration is both context-sensitive and computation-efficient. When evaluated on challenging benchmarks such as MATH500, AIME, and PhD-level science QA GPQA, SIGMA consistently outperforms both open- and closed-source systems, achieving an absolute performance improvement of 7.4%. Our results demonstrate that multi-agent, on-demand knowledge integration significantly enhances both reasoning accuracy and efficiency, offering a scalable approach for complex, knowledge-intensive problem-solving. We will release the code upon publication.

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09.
arXiv (quant-ph) 2026-06-24

Universal Dynamical Response to Slow Driving in Chaotic Systems

Authors:
Nachiket Karve↗Nathan Rose↗David Campbell↗Anatoli Polkovnikov↗

arXiv:2606.23810v1 Announce Type: cross Abstract: We propose a unified perspective on classical and quantum chaos based on the stability of a system's stationary states under slow driving. We probe this sensitivity via the system's susceptibility to the average protocol speed, which we call the ``speed-Fisher information," and relate it to irreversible entropy production in the system. We show that chaotic dynamics manifests as a divergence of the speed-Fisher information with the protocol time, and that this response is controlled by the perturbation's low-frequency spectral weight. This approach to chaos applies to both classical and quantum Hamiltonian systems, and naturally extends to non-Hamiltonian classical flows. We illustrate this framework with simple classical and quantum examples, along with a non-Hamiltonian flow that qualitatively exhibits analogous low-frequency spectral behavior.

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10.
arXiv (CS.LG) 2026-06-17

Credibility-Weighted Pricing of Autonomous Vehicle Liability Under Operational Design Domain Shift

Authors:
Doyeon Jang↗

arXiv:2606.17451v1 Announce Type: new Abstract: Automated Driving System deployments create a foundational ratemaking challenge: sparse experience, shifting operational design domains, and non-stationary risk across software releases. We propose a hierarchical Bayesian credibility framework pooling across cities, software versions, and territories via a learned ODD-similarity kernel, nesting Buhlmann-Straub as a limiting case. Demonstrated on 648 verified-engaged Waymo crashes across four U.S. metros from the NHTSA Standing General Order database against 116 million matched miles, city-aggregate credibility weights are moderate (0.12-0.46), partial pooling decisively outperforms no pooling, and a power analysis shows the learned kernel's advantage becomes detectable at approximately twelve deployed cities.

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11.
arXiv (quant-ph) 2026-06-12

Where a Quantum Reservoir Works: A Transferable Operating Band

Authors:
Markus Baumann↗Itamar Fink↗Johannes Wittmann↗Claudia Linnhoff-Popien↗Jonas Stein↗

arXiv:2606.13284v1 Announce Type: new Abstract: In quantum reservoir computing, a fixed quantum system transforms an input signal, while learning reduces to training a simple linear readout on its measured outputs. Since the quantum dynamics themselves are never optimized, the method is well suited to today's hardware. Yet these dynamics must still be chosen carefully, because their settings remain fixed throughout training and inference. It therefore remains an open question where, in its control space, a fixed quantum system learns well. We address this question for a dissipative reservoir by mapping performance over three central physical controls: the strength of the input drive, the coupling between neighboring qubits, and the rate of dissipation. Good performance concentrates in a single, well-defined operating region of this control space. This region transfers across tasks and reservoir initializations, and the same memory-defined regime persists under architectural changes. It is also mechanistically grounded, since it disappears whenever any of the mechanisms that create it is removed. Finally, the region can be located cheaply before any task is run, using a simple memory diagnostic.

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12.
medRxiv (Medicine) 2026-06-11

Incremental costs of transitioning from four to eight WHO-recommended antenatal care visits in Uganda: A costing analysis from a societal perspective

Authors:
Atuhumuza↗E. B↗Atukunda↗E. C↗Musiimenta↗Mugyenyi↗G. R↗Haberer↗Obua↗Siedner↗M. J↗Matthews↗…

Background In 2016, the World Health Organization revised its antenatal care (ANC) recommendation from four to eight visits. For low- and middle-income countries like Uganda, where achieving even four visits remains a challenge, this transition has significant cost implications for both the health system and households. This study estimated the incremental costs of adopting the eight-visit model from a societal perspective. Methods The study was conducted in six government health facilities in southwestern Uganda. A micro-costing approach estimated health facility costs (personnel, equipment, consumables, and overhead). Costs incurred at patients end (transport, ultrasound, medical expenses, and time) were collected from 785 women using a questionnaire, with all costs in 2025 USD. Results For an average of 4.3 visits, total cost per woman was $100.1: facility costs $43.7 (43.7%), and patient costs $56.4 (56.3%). Transitioning to eight visits would increase total cost by $57.8 (57.8%), of which $36.4 (63.0%) would fall on households, equivalent to 68.8% of average monthly household income. Total costs would rise by 55.4% ($115.5 to $179.5) at Health Center IVs and 64.3% ($102.3 to $168.1) at Health Center IIIs, with facility costs up 43.4% and 62.9% and patient costs up 61.2% and 65.7%, respectively. Conclusion Transitioning to eight ANC visits would impose a large financial burden on households, with the incremental patient cost equivalent to more than two-thirds of average monthly household income. Equitable implementation requires improving availability of medicines and diagnostics, subsidizing transport, exploring telemedicine or community-based models, and improving efficiency at lower-tier health centers.

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13.
arXiv (CS.AI) 2026-06-11

WeaveBench: A Long-Horizon, Real-World Benchmark for Computer-Use Agents with Hybrid Interfaces

Authors:
Wanli Li↗Bowen Zhou↗Yunyao Yu↗Zhou Xu↗Yifan Yang↗Dongsheng Li↗Caihua Shan↗

arXiv:2606.09426v2 Announce Type: replace Abstract: Computer-use agents (CUAs) increasingly operate in runtimes that combine visual desktop control, command-line execution, code editing, browsers, and external tools. Existing benchmarks, however, often evaluate these interfaces as separable capabilities, leaving long-horizon cross-interface orchestration under-tested. Thus, we introduce WeaveBench, a long-horizon hybrid-interface benchmark with 114 tasks across 8 real-world work domains, grounded in real user requests and publicly verifiable artifacts. Each task requires agents to combine GUI observations/actions with CLI/code operations within a single trajectory. We evaluate these tasks on a real Ubuntu desktop inside deployed CLI-agent runtimes, augmented with a minimal desktop-control plugin. We also propose a companion trajectory-aware judge that inspects deliverables, files, screenshots, logs, and action traces, while detecting shortcut behaviors such as fabricated visual evidence or hard-coded metrics. Across frontier model-runtime pairings, the best PassRate reaches only 41.2%, showing the benchmark remains far from saturated. The trajectory-aware judge further reveals that outcome-only grading substantially overestimates agent performance. Overall, WeaveBench exposes a critical gap in CUA evaluation and provides an effective testbed to measure whether agents can orchestrate GUI, CLI, and code operations across long-horizon real-world tasks.

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14.
arXiv (CS.LG) 2026-06-18

Stealthy World Model Manipulation via Data Poisoning

Authors:
Yibin Hu↗Xiaolin Sun↗Zizhan Zheng↗

arXiv:2606.18697v1 Announce Type: new Abstract: Model-based learning agents use learned world models to predict future states, plan actions, and adapt to new environments. However, the process of updating world models from collected experience creates a training-time attack surface: adversarially poisoned fine-tuning trajectories can manipulate the learned dynamics and thereby corrupt downstream planning. In this paper, we propose SWAAP, the first two-stage data poisoning framework for learned world models. In the first stage, SWAAP identifies a harmful target world model that induces low-return behavior under planning while remaining close to clean dynamics, using first-order bilevel optimization enabled by a transition-gradient theorem. In the second stage, SWAAP realizes this target through stealth-constrained gradient matching, modifying only a limited fraction of fine-tuning transition targets so that the induced training gradients steer the victim model toward the adversarial target, while a prediction-error regularizer encourages the poisoned targets to remain close to the world model's natural approximation error. To assess attack stealthiness, we evaluate defenses and detectability across three stages of the poisoning pipeline: pre-training detection of poisoned transitions, robust training during fine-tuning, and test-time monitoring of the resulting world model. Across diverse continuous-control tasks, SWAAP causes substantial performance degradation while keeping poisoned transitions close to clean data and evading the evaluated non-adaptive residual/CUSUM/TRIM-style defenses. These results reveal a practical vulnerability in world-model adaptation pipelines and highlight the need for robustness methods that protect both world-model training data and learned dynamics.

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

Toward General Digraph Contrastive Learning: A Dual Spatial Perspective

Authors:
Zhengyu Wu↗Daohan Su↗Yang Zhang↗Xunkai Li↗Rong-Hua Li↗Guoren Wang↗

arXiv:2510.16311v2 Announce Type: replace Abstract: Graph Contrastive Learning (GCL) has emerged as a powerful tool for extracting consistent representations from graphs, independent of labeled information. However, existing methods predominantly focus on undirected graphs, disregarding the pivotal directional information that is fundamental and indispensable in real-world networks (e.g., social networks and recommendations).In this paper, we introduce S2-DiGCL, a novel framework that emphasizes spatial insights from complex and real domain perspectives for directed graph (digraph) contrastive learning. From the complex-domain perspective, S2-DiGCL introduces personalized perturbations into the magnetic Laplacian to adaptively modulate edge phases and directional semantics. From the real-domain perspective, it employs a path-based subgraph augmentation strategy to capture fine-grained local asymmetries and topological dependencies. By jointly leveraging these two complementary spatial views, S2-DiGCL constructs high-quality positive and negative samples, leading to more general and robust digraph contrastive learning. Extensive experiments on 7 real-world digraph datasets demonstrate the superiority of our approach, achieving SOTA performance with 4.41% improvement in node classification and 4.34% in link prediction under both supervised and unsupervised settings.

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

DSB: Dynamic Sliding Block Scheduling for Diffusion LLMs

Authors:
Lizhuo Luo↗Shenggui Li↗Yonggang Wen↗Tianwei Zhang↗

Diffusion large language models (dLLMs) have emerged as a promising alternative for text generation, distinguished by their native support for parallel decoding. In practice, block inference is crucial for avoiding order misalignment in global bidirectional decoding and improving output quality. However, the widely-used fixed, predefined block (naive) schedule is agnostic to semantic difficulty, making it a suboptimal strategy for both quality and efficiency: it can force premature commitments to uncertain positions while delaying easy positions near block boundaries. In this work, we analyze the limitations of naive block scheduling and disclose the importance of dynamically adapting the schedule to semantic difficulty for reliable and efficient inference. Motivated by this, we propose Dynamic Sliding Block (DSB), a training-free block scheduling method that uses a sliding block with a dynamic size to overcome the rigidity of the naive block. To further improve efficiency, we introduce DSB Cache, a training-free KV-cache mechanism tailored to DSB. Extensive experiments across multiple models and benchmarks demonstrate that DSB, together with DSB Cache, consistently improves both generation quality and inference efficiency for dLLMs. Code is released at https://github.com/lizhuo-luo/DSB.

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

FlowMPC: Improving Flow Matching policies with World Models

Authors:
Chandon Hamel↗

arXiv:2606.16286v1 Announce Type: cross Abstract: Flow Matching (FM) is a powerful approach for behavior cloning in multimodal action spaces [Jiang et al., 2025], but because it is not trained to directly maximize expected return, there is still room to improve how FM policies act at test time. This work investigates whether a learned world model can improve FM policies by enabling Model Predictive Path Integral (MPPI) planning over candidate action sequences proposed by the policy. Building on TD-MPC2 [Hansen et al., 2024], I introduce FlowMPC, a framework that combines an imitation-learned FM policy with a learned world model for test-time planning in ManiSkill manipulation tasks [Tao et al., 2025]. Across PickCube and PickSingleYCB, adding the world model improved performance over the FM policy alone, with especially clear gains in end-of-episode success. These results suggest that world-model-based planning can effectively complement flow-based imitation policies without modifying the FM training objective.

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

Scaling Generative Foundation Models for Chest Radiography with Rectified Flow Transformers

Authors:
Fabio De Sousa Ribeiro↗Emma A. M. Stanley↗Charles Jones↗Tian Xia↗Dominic C. Marshall↗Laurent Renard Trich\'e↗Christopher V. Cosgriff↗Panagiotis Dimitrakopoulos↗Sotirios A. Tsaftaris↗Ben Glocker↗

arXiv:2606.19460v1 Announce Type: cross Abstract: We introduce the first generative foundation model for chest radiograph synthesis trained from scratch at the billion-parameter scale. Existing radiographic AI models often suffer from poor generalisation across patient subpopulations, institutions, and acquisition settings, resulting in limited real-world clinical utility. Controlled, high-fidelity synthesis of chest radiographs is a promising path toward diversifying clinical datasets and evaluating the robustness of diagnostic models. Therefore, we present the largest specialist generative foundation model for chest radiographs to date, with over 1.3B parameters, trained for 1.6T tokens on a curated, heterogeneous dataset comprising 1.2M radiographs and clinical expert-guided metadata. Our model supports controllable radiograph generation and editing across multiple demographic subgroups, acquisition views, and a dozen pathologies. Moreover, we significantly advance the state of the art in radiograph synthesis fidelity, producing images that are indistinguishable from real radiographs to clinical experts.

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19.
arXiv (math.PR) 2026-06-16

Probabilities

Authors:
Jean-Yves Ouvrard↗Xavier Ouvrard↗

arXiv:2601.18853v4 Announce Type: replace-cross Abstract: Probabilities is the English translation of the book Probabilités Tome 1 and Tome 2. The mathematic content is authored by Prof. Jean-Yves Ouvrard. The English version has been done by his eldest son Dr. Xavier Ouvrard. This probability theory book covers not only an introduction to this field, but also advanced concepts based on measure theory. The first part introduces the fundamentals of probability theory across 7 chapters, targeting bachelor level, including event algebras, random variables, independence, conditional probabilities, moments of discrete and continuous random variables, generating functions, and limit theorems. The second part contains 10 chapters and corresponds to master level. Following a brief introduction to measure theory, this part develops more advanced topics: probability measures and their complements, distributions and moments of random variables, modes of convergence, laws of large numbers, conditional expectation, Fourier transforms and characteristic functions, Gaussian random variables, convergence of measures, convergence in distribution, discrete-time stochastic processes, martingales, and Markov chains. The reader's work is greatly facilitated by the inclusion, in every chapter, of numerous exercises, all accompanied by detailed solutions that often provide substantial extensions to the theoretical material.

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20.
PLOS Computational Biology 2026-06-01

Supervised deep learning with gene functional annotation for cell classification

Authors:
Zhexiao Lin↗

by Zhexiao Lin, Yuanyuan Gao, Wei Sun Gene-by-gene differential expression analysis is a widely used supervised approach for interpreting single-cell RNA-sequencing (scRNA-seq) data. However, modern scRNA-seq datasets often contain large numbers of cells, leading to the identification of many differentially expressed genes with extremely small p-values but negligible effect sizes, thus making biological interpretation difficult. To overcome this challenge, we developed Supervised Deep learning with gene functional ANnotation (SDAN), a method that integrates gene functional annotation information (e.g., protein-protein interaction) with gene-expression profiles through a graph neural network. SDAN identifies functionally coherent gene sets that optimally classify cells, and the resulting cell-level classification scores can be aggregated to make individual-level predictions. We evaluated SDAN alongside three representative existing methods in three real-data applications aimed at identifying gene sets associated with severe COVID-19, dementia, and cancer immunotherapy response. Across all applications, SDAN consistently outperformed the alternative approaches by achieving two objectives simultaneously: accurate outcome classification and clear assignment of genes to functionally related gene sets.

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

FORTIS: Benchmarking Over-Privilege in Agent Skills

Authors:
Shawn Li↗Chenxiao Yu↗Han Wang↗Wei Yang↗Ryan Rossi↗Franck Dernoncourt↗Xiyang Hu↗Philip Yu↗Chaowei Xiao↗Huan Zhang↗Yue Zhao↗

arXiv:2605.09163v3 Announce Type: replace Abstract: Large language model agents increasingly operate through an intermediate skill layer that mediates between user intent and concrete task execution. This layer is widely treated as an organizational abstraction, but we argue it is also a privilege boundary that current models routinely exceed. We present FORTIS, a benchmark that evaluates over-privilege in agent skills across two stages: whether a model selects the minimally sufficient skill from a large overlapping library, and whether it executes that skill without expanding into broader tools or actions than the skill permits. Across ten frontier models and three domains, we find that over-privileged behavior is the norm rather than the exception. Models consistently reach for higher-privilege skills and tools than the task requires, failing at both stages at rates that remain high even for the strongest available models. Failure is especially severe under the ordinary conditions of real user interaction: incomplete specification, convenience framing, and proximity to skill boundaries. None of these requires adversarial construction. The results indicate that the skill layer, far from containing agent behavior, is itself a primary source of privilege escalation in current systems.

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22.
arXiv (quant-ph) 2026-06-24

Non-adiabatic transitions in the density matrix formalism

Authors:
Pasquale Di Bari↗Shreya Pandit↗Ye-Ling Zhou↗

arXiv:2606.24310v1 Announce Type: new Abstract: We show that a density matrix formalism provides a useful description of non-adiabatic transitions in two-state quantum systems. Compared to a traditional Hamiltonian formalism, even in the absence of decoherence when there is full equivalence between the two, the density matrix formalism provides a convenient change of variables that yields a powerful general analytical solution. This solution nicely describes a transition regime between the well known Landau-Zener-Stuckelberg-Majorana (LZSM) approximation and the extremely non-adiabatic limit. Our results have very general applications, within a large variety of problems in quantum physics, neutrino physics, cosmology.

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23.
arXiv (CS.CV) 2026-06-15

Improving Lunar Topography with Deep Learning Schrödinger Bridges

Authors:
Matthew Repasky↗Erwan Mazarico↗Michael K. Barker↗Stefano Bertone↗Terence J. Sabaka↗Yao Xie↗

Increasing the resolution of planetary topography models can enable a better understanding of surface processes and geomorphology; however, existing analytical super-resolution methods are expensive and difficult to apply at large scales. Generative models provide the tools to learn complex relationships within data and can be applied at scale due to hardware accelerators and parallelization. We present a diffusion-based Schrödinger Bridge (SB) generative modeling approach for lunar topography super-resolution, connecting the distribution of low-resolution topography to that of high-resolution topography, incorporating physically-constraining optical imagery. Our approach is inspired by existing Shape-from-Shading methods, which improve a priori low-resolution topography by using optical images at the target resolution. We train SBs on a novel dataset of rendered lunar topography, emulating optical imagery from the Lunar Reconnaissance Orbiter Narrow Angle Camera. The result is a flexible approach for topography super-resolution which can provide pixel-level uncertainties in the reconstruction.

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24.
bioRxiv (Bioinfo) 2026-06-20

Seed variation impacts clustering stability in Single-Cell RNA-Seq and can be mitigated by StAbility-BasEd-Reassignment (SABER)

Authors:
Zagaria↗Tini↗Bonetti↗Mazzarella↗

Single-cell RNA-seq clustering is commonly treated as reproducible once a random seed is fixed, yet the choice of seed itself may alter cell assignments and downstream interpretation. We systematically quantified seed-induced clustering variability by running Louvain and Leiden clustering across 100 seeds in Seurat and Scanpy on 28 single-cell RNA-seq datasets from the Human Cell Atlas and IMMUcan. Using Element-Centric Consistency, we found that seed choice affected a substantial fraction of cells, with Scanpy showing more unstable assignments than Seurat on average, 40.46% versus 26.78% unstable cells, respectively. This increased stability came at a marked computational cost: Seurat required approximately 19-fold higher median memory than Scanpy. Seed-dependent clustering variability also propagated to cell-type annotation, particularly among transcriptionally related populations including macrophage/monocyte, endothelial/epithelial and T/NK cell states. To mitigate this instability, we developed StAbility-BasEd Reassignment (SABER), a Scanpy-based framework that identifies seed-sensitive cells across repeated clusterings and reassigns them to stable cluster cores using cosine similarity. SABER improved clustering quality while preserving annotation concordance and reduced median memory usage 3.5-fold compared with Seurat-Louvain. Our results identify seed choice as an underappreciated source of variability in single-cell analysis and provide a scalable strategy to improve clustering robustness.

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

Exactly Solvable Quantum Model with Spin-Dependent Coulomb Interaction

Authors:
Jiang-Lin Zhou↗Yu-Xuan Zhang↗Choo Hiap Oh↗Jing-Ling Chen↗

arXiv:2501.05103v5 Announce Type: replace Abstract: In this work, we report an exactly solvable quantum model featuring a spin-dependent Coulomb interaction, described by the spin vector potential \(\vec{\mathcal{A}} = k (\vec{r} \times \vec{S}) / r^2\) together with a Coulomb-type scalar potential \(\varphi = \kappa / r\) . The model is governed by the Schrödinger-type Hamiltonian \(\mathcal{H}_S = \vec{\Pi}^2 / (2M) + q \varphi\) in nonrelativistic quantum mechanics and by the Dirac-type Hamiltonian \(\mathcal{H}_D = c \vec{\alpha} \cdot \vec{\Pi} + \beta M c^2 + q \varphi\) in relativistic quantum mechanics, where \(\vec{\Pi} = \vec{p} - (q/c)\vec{\mathcal{A}}\) is the canonical momentum. We demonstrate two main results: (i) Just as the Coulomb-type scalar potential \(\mathcal{S}_Maxwell = \{\vec{\mathcal{A}} = 0,\ \varphi = \kappa / r\}\) is a local exact solution of Maxwell's equations on $r\neq0$, the gauge potential \(\mathcal{S}_YM = \{\vec{\mathcal{A}} = k (\vec{r} \times \vec{S}) / r^2,\ \varphi = \kappa / r\}\) constitutes a local exact solution of the Yang–Mills equations on the punctured region $r\neq0$. (ii) Both Hamiltonians \(\mathcal{H}_S\) and \(\mathcal{H}_D\) can be solved exactly in the presence of this spin-dependent Coulomb interaction. The resulting energy spectra are derived, and they naturally reduce to those of the ordinary hydrogen atom when the spin-dependent terms are neglected. Finally, we clarify the quantization conditions and the fixed-background interpretation of the model.

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