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01.
arXiv (CS.AI) 2026-06-16

ToolMenuBench: Benchmarking Tool-Menu Filtering Strategies for Reliable and Efficient LLM Agents

arXiv:2606.15508v1 Announce Type: new Abstract: Tool-augmented large language model agents increasingly operate over large tool libraries, but existing evaluations often focus on whether a model can call a tool correctly rather than how the visible tool menu shapes reliability, efficiency, and safety-relevant risk exposure. We introduce ToolMenuBench, a benchmark for evaluating tool-menu construction in multi-step LLM agents. ToolMenuBench varies tool-menu size, distractor type, state-dependent task structure, and risk exposure, and reports both filter-level and downstream agent metrics, including visible-tool count, risky-tool exposure, task success, wrong-tool calls, premature actions, and token usage. In a controlled evaluation across seven model backends, three tool-menu sizes, six filtering methods, and seven evaluation settings, CMTF improves task success from 32.1% under all-tools exposure to 85.7%, while reducing average token usage by roughly 98%. Causal minimal tool filtering achieves the strongest overall tradeoff, reducing visible tools, wrong-tool calls, premature actions, and risky-tool exposure relative to unfiltered exposure, lexical filtering, state-aware filtering, and broader causal-path baselines. ToolMenuBench provides a reusable evaluation framework for studying the agent-interface problem: which tools should be visible, when they should be visible, and under what cost or risk constraints.

02.
bioRxiv (Bioinfo) 2026-06-11

HalluDesign-NA: Extending HalluDesign for De Novo Nucleic Acid Design

AlphaFold3 has revolutionized the prediction of biomolecular structures and interactions, including atomic-level modeling of nucleic acids. However, the de novo design of structured and functional nucleic acids remains a significant challenge. Here, we extend our HalluDesign framework to nucleic acid design by integrating NA-MPNN for nucleic acid sequence optimization and design. This new framework, HalluDesign-NA, enables iterative sequence-structure co-optimization, facilitating the de novo design of nucleic acids. Computational benchmarking across ssDNA, ssRNA, and aptamer design tasks demonstrates consistent improvements in confidence scores (pLDDT, ipTM), supporting the feasibility of de novo nucleic acid design under various constraints, such as sequence length, symmetry, and protein structure context. We anticipate that HalluDesign-NA will accelerate the de novo design of functional nucleic acids for applications in biotechnology and medicine. The source code for HalluDesign-NA is available at https://github.com/MinchaoFang/HalluDesign_NA.

03.
arXiv (CS.AI) 2026-06-24

Zero-Shot Test-Time Canonicalization using Out-of-Distribution Scoring

arXiv:2606.24178v1 Announce Type: cross Abstract: Pretrained vision models often misclassify inputs that are rotated, scaled, or sheared, even though these affine transformations leave the object class unchanged. Robustness is usually restored either by building equivariance into the architecture or by retraining with augmentation, both of which require changing or retraining the model. Test-time canonicalization instead leaves the classifier untouched. It undoes the transformation of each input, mapping it to a canonical form near the training distribution before classification. Existing canonicalizers, however, rely on a narrow set of logit-based energy scores and bespoke search procedures, leaving the design space of scoring functions and optimizers unexplored. We reframe canonicalization as out-of-distribution (OOD) detection, which lets any OOD score serve as the energy minimized over transformations. Across benchmarks ranging from handwritten characters and sketches to natural images and 3D point clouds, we systematically evaluate around twenty OOD scores and nine search algorithms, finding that distance-based scores paired with random search and local refinement perform best overall. Because canonicalizing an already-aligned input can hurt accuracy, we add a gated mechanism that transforms an input only when its OOD score indicates this is needed, preserving most in-distribution accuracy while retaining the robustness gains on transformed inputs. Code is available at github.com/johschm/its.

04.
arXiv (quant-ph) 2026-06-17

DRAG-Compatible Leakage Suppression in Landau–Zener Control via Isoprobability Twins

arXiv:2506.19572v4 Announce Type: replace Abstract: Analytically solvable models – particularly the Landau-Majorana-Stückelberg-Zener (LMSZ) and Allen-Eberly-Hioe (AEH) models – underpin many quantum-gate implementations and population-transfer protocols. However, their canonical pulse shapes are incompatible with modern leakage-suppression techniques and some systems. Most notably, the constant Rabi envelope of the LMSZ pulse prevents many leakage-suppression approaches, which require smoothness. We address both limitations by developing the concept of isoprobability twin models: distinct pairs of Rabi frequency $\Omega(t)$ and detuning $\Delta(t)$ that yield identical post-pulse transition probabilities based on the Delos-Thorson transformation. In this work, we formalise the method by experimentally demonstrating the equivalence of multiple LMSZ and AEH twin models on IBM's ibm_kyiv processor. Finally, we show a staggering leakage reduction by more than 3 orders of magnitude using a custom DRAG implementation of a cosine LMSZ isoprobability model.

05.
medRxiv (Medicine) 2026-06-15

SPIRIT-CONSORT-ELM: Element-Level Assessment of Randomized Controlled Trial Reporting Using Large Language Models

Randomized controlled trials (RCTs) play a central role in assessing the benefits and harms of interventions. Incomplete reporting in RCT publications can compromise the verifiability and usefulness of RCTs. SPIRIT and CONSORT reporting guidelines aim to improve the completeness of RCT protocols and results publications, respectively. However, many RCTs are not reported completely. Checking manuscripts automatically could help authors improve the completeness of reports prior to publication. We previously annotated SPIRIT-CONSORT-TM, a corpus of 200 articles (comprising 100 protocol-results publication pairs) using 83 checklist items drawn from SPIRIT 2013 and CONSORT 2010. We also trained machine learning models to automatically assess reporting at the item level. Each checklist item can include multiple constituent elements (i.e., specific details required for that item), and an item might be considered fully reported when all of its elements are present. However, prior work does not explicitly capture or evaluate reporting at the element level. To address this gap, we extended SPIRIT-CONSORT-TM by incorporating element-level annotations and using them to assess reporting completeness (SPIRIT-CONSORT-ELM). We formulated element-level assessment as a machine reading comprehension task, operationalized through 119 questions, where each question targets a specific reporting element within a checklist item. Using the 200 articles included in SPIRIT-CONSORT-TM, two annotators independently answered 119 questions for 50 articles (25 protocol-results pairs) and resolved any discrepancies through discussion; the remaining 150 articles (75 protocol-results pairs) were assessed by a single annotator. We then developed an automated pipeline for element-level assessment using SPIRIT-CONSORT-ELM. The pipeline first applies a PubMedBERT-based model to identify sentences containing item-level reporting information, then it uses a generative large language model (LLM; GPT-5) with chain-of-thought reasoning to answer element-level questions based on the retrieved evidence. Agreement between the two annotators was high (Gwet's AC1: 0.782) and our pipeline achieved high accuracy in identifying element-level reporting evidence (F1: 0.822, Gwet's AC1: 0.796). Ablation studies indicate that chain-of-thought reasoning and the inclusion of illustrative in-context examples modestly improve LLM performance on the machine reading comprehension task. SPIRIT-CONSORT-ELM provides a benchmark for evaluating reporting guideline completeness at the element level, enabling assessment of RCT transparency beyond the simple presence or absence of checklist items and is publicly available at https://osf.io/kznx4/. The automated pipeline establishes a robust baseline for assessing RCT reporting and demonstrates potential as a practical aid for authors, reviewers, and editors to identify and address gaps in completeness and transparency of RCT reports.

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

A Diffusion Approximation for Temporal-Difference Learning with Linear Features under Markovian Noise

arXiv:2606.18183v1 Announce Type: cross Abstract: Temporal difference (TD) learning with linear function approximation is a core method for policy evaluation. Its classical continuous-time description is an ordinary differential equation (ODE), which captures the asymptotic mean dynamics but neglects stochastic fluctuations determining the error floor. We introduce a stochastic differential equation (SDE) approximation for linear TD(0) under Markovian noise. The resulting model distinguishes the contraction dynamics governed by the projected Bellman operator from the influence of Markovian sampling. As a consequence, the model explains the constant-stepsize error floor through the interaction between Markovian long-run covariance and the contraction geometry of the projected Bellman operator.

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

FoundCause: Causal Discovery with Latent Confounders from Observational Data

arXiv:2606.17516v1 Announce Type: cross Abstract: Causal discovery from observational data remains challenging due to the need to recover directed structure and latent confounding without interventions. We propose FoundCause, an amortized causal discovery model trained entirely on synthetic data that maps datasets directly to causal graphs in a single forward pass. By learning from large collections of simulated structural causal models, FoundCause captures transferable statistical patterns that generalize beyond individual datasets. The architecture incorporates several key inductive biases for causal discovery. It uses a permutation-invariant transformer encoder with alternating attention over samples and variables to jointly model cross-variable dependence and per-variable distributions. Pairwise statistical features derived from classical asymmetry measures are injected through statistics-conditioned attention, guiding the model toward known causal signals. A factorized decoder separates edge existence from direction, while a triangular refinement module enables reasoning over higher-order causal motifs such as chains and colliders. In addition, a dedicated confounder module based on learnable latent tokens explicitly models hidden common causes, and the model explicitly handles missing data via its masked input representation. To our knowledge, FoundCause is the first amortized causal discovery approach to explicitly model latent confounding. FoundCause outperforms 11 classical non-amortized methods (e.g., PC, GES, NOTEARS-style optimization) and 4 amortized causal discovery methods on 15 real-world datasets, achieving +9.6% improvement in $F_1$, +1.2% in AUROC, and an 18.9% reduction in structural Hamming distance relative to the strongest non-amortized methods, while performing inference in a single forward pass.

08.
medRxiv (Medicine) 2026-06-24

Pilot Validation of an AI-based Audiovisual Fatigue Assessment Tool (mAI Fatigue) in Chronic Liver Disease: A Multicentre Study

Fatigue affects over half of patients with chronic liver disease (CLD) and is a major driver of impaired quality of life, yet it remains underrecognised because assessment relies almost entirely on subjective patient-reported outcomes (PROs). This proof of concept study evaluated whether audiovisual (AV) markers from facial and vocal expressions, captured via the mAI Fatigue tool (Blueskeye), could serve as objective correlates of fatigue in CLD. In a prospective, multicentre, case-control study at three sites in India, 111 adults (aged 18 to 65 years) were enrolled as healthy controls (n=55) or CLD patients with moderate to severe fatigue (n=56). Over four weeks, participants completed ten assessments combining validated PROs, Psychomotor Vigilance Task (PVT) reaction times and AV recordings. CLD participants had significantly slower PVT reaction times than controls (882 vs 776 ms; p=0.0047). Session-level AV-PRO correlations were modest (r=-0.17 to -0.27), but participant-level aggregation strengthened associations (r=-0.47; p{approx}0.002) in the high-quality audio subset (n=41), where a predictive model achieved R=0.75 to 0.76 (p

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

MoCo-AIS: A Contrastive Learning Framework for Similarity Computation of Vessel Trajectories

arXiv:2606.17978v1 Announce Type: new Abstract: Trajectory similarity is a fundamental task in analyzing mobility patterns, essential for applications such as route pattern extraction, mobility prediction, and anomaly detection. Traditional distance-based measures for computing similarity incur high computational cost, driving the adoption of lightweight learning-based approaches. Supervised methods rely on extensive labels derived from traditional distance measures and often reproduce these metrics, which limits generalization. While self-supervised learning addresses this issue through contrastive learning, it lacks a unified framework, making it difficult to compare deep learning (DL) models for consistent trajectory representation. Accordingly, this paper presents MoCo-AIS, a unified framework for learning vessel trajectory embeddings based on the Momentum Contrast (MoCo) paradigm, which formulates similarity learning through positive and negative trajectory pairs. Within this framework, we evaluate a diverse set of leading DL models on large-scale, real-world vessel-tracking AIS datasets that capture diverse navigation behaviors and operating conditions. Results demonstrate that our framework significantly improves similarity learning over existing baselines, while providing a benchmarking platform for evaluating trajectory representation models.

10.
arXiv (CS.LG) 2026-06-24

SEED: Semi-supervised Continual MalwarE Detection for Tackling ConcEpt Drift on a BuDget

arXiv:2605.24903v2 Announce Type: replace-cross Abstract: Machine learning based malware detectors become obsolete over time due to concept drift in benign and malware applications. Recent methods rely on fully labeled data and use hierarchical contrastive loss (HCL) with active learning to improve robustness against drift by exploiting semantic structure in malware representations. However, obtaining labeled data in the security domain is difficult. Under partially labeled settings, HCL suffers significant performance degradation in detecting unseen malware, especially on datasets such as BODMAS where strong semantic structure may not exist. In this paper, we propose SEED, a semantic-structure-agnostic method for malware detection under limited supervision. SEED combines a tailored binary cross-entropy objective with semi-supervised continual learning and active learning. For partially labeled seen tasks, unlabeled samples are projected into a representation space constructed from previously seen data using singular value decomposition, and paired with suitable labeled samples to encourage representation consistency. For unseen tasks with fully unlabeled data, uncertainty is quantified using cosine distance in representation space, and the most uncertain samples are selected for analyst labeling. We evaluate SEED on both Windows and Android malware datasets. Using only 20% labeled data on seen tasks, SEED achieves average AUT improvements of 40% on BODMAS and 14% on AndroZoo for unseen malware detection compared to HCL* (the semi-supervised adaptation of HCL), while remaining competitive on APIGraph. Finally, we introduce a delayed buffer update strategy to reduce label noise propagation during replay and improve learning stability.

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

FlowMaps: Modeling Long-Term Multimodal Object Dynamics with Flow Matching

arXiv:2606.20209v1 Announce Type: cross Abstract: Joint spatial and temporal understanding of 3D scenes is a crucial requirement for robots deployed in everyday household environments. Such agents must not only comprehend and navigate spatial layouts, but also reason about how these spaces evolve over time. In particular, humans interact with objects daily, causing them to change position throughout the environment and making it difficult for robots to reliably associate current observations with previously seen objects. However, these interactions are not random: human habits and routines induce spatio-temporally consistent patterns in object locations, which robotic agents can potentially learn and then exploit for downstream tasks such as navigation. To this end, we introduce FlowMaps, a latent flow matching model for estimating multimodal distributions over the future locations of dynamic objects in a continuous 3D space. By learning the implicit dependencies among objects and their temporal evolution, FlowMaps predicts likely changes in object locations conditioned on past human interactions, while supporting generalization across previously unseen environments that share similar object routines. To demonstrate the utility of this method, we deploy FlowMaps in a downstream dynamic Object Navigation task in both simulated and real-world environments. Across more than 600 episodes, FlowMaps outperforms state-of-the-art approaches, showing that modeling object dynamics through continuous, multimodal spatio-temporal distributions improves robotic search and navigation in changing household environments. Code and additional material is available at https://fra-tsuna.github.io/flowmaps/.

12.
arXiv (CS.CL) 2026-06-25

Aligning Human-AI-Interaction Trust for Mental Health Support: Survey and Position for Multi-Stakeholders

Building trustworthy AI systems for mental health support is a shared priority across stakeholders from multiple disciplines. However, "trustworthy" remains loosely defined and inconsistently operationalized. AI research often focuses on technical criteria (e.g., robustness, explainability, and safety), while therapeutic practitioners emphasize therapeutic fidelity (e.g., appropriateness, empathy, and long-term user outcomes). To bridge the fragmented landscape, we propose a three-layer trust framework, covering human-oriented, AI-oriented, and interaction-oriented trust, integrating the viewpoints of key stakeholders (e.g., practitioners, researchers, regulators). Using this framework, we systematically review existing AI-driven research in mental health domain and examine evaluation practices for ``trustworthy'' ranging from automatic metrics to clinically validated approaches. We highlight critical gaps between what NLP currently measures and what real-world mental health contexts require, and outline a research agenda for building socio-technically aligned and genuinely trustworthy AI for mental health support.

13.
arXiv (CS.AI) 2026-06-25

UC-Search: Risk-Aware Test-Time Search for Delayed Constrained Time-Series Control

作者:

arXiv:2606.25274v1 Announce Type: cross Abstract: Time-series models are usually scored as forecasters, yet deployed systems often require delayed decisions under uncertainty and hard feasibility constraints. UC-Search is a model-agnostic test-time wrapper: a backbone emits forecasts or action scores, a feasibility automaton rolls candidate paths forward, and bounded search returns the first action of a risk-adjusted feasible trajectory. We instantiate UC-Beam and a UCT-style UC-MCTS diagnostic, using epistemic, aleatoric, and propagated uncertainty mainly as path-risk terms. A myopic-collapse/separation theorem states when search reduces to one-step risk-greedy and when delayed feasible-set coupling can create non-myopic value. Primary evidence comes from a predeclared public $9$-family, $33$-series delayed-control suite with six held-out starts per series: UC-Pareto is positive versus validation-selected CEM, MPPI, and risk-aware random at the normalized threshold ($+3.1675/+2.3328/+2.5038$), and remains positive in a compute-matched audit ($+2.8466/+2.7418/+2.7429$). ETT/LTSF delayed-inventory validation supports the same compute-frontier claim. A 48-series raw M4 standard periodic-review lost-sales inventory audit is positive versus the strongest classic base-stock control ($+13556.7547$), CEM ($+64900.2207$), and risk-random ($+52881.6042$), while MPPI remains family-mixed. FI-2010, official-forecast adapters, SB3/FQI controls, direction/capacity/intervention checks, and synthetic mechanism tests are reported as boundary or mechanism evidence rather than broad dominance claims.

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

Efficient Image-to-Image Schrödinger Bridge for CT Field of View Extension

Computed tomography (CT) is a cornerstone imaging modality for non-invasive, high-resolution visualization of internal anatomical structures. However, when the scanned object exceeds the scanner's field of view (FOV), projection data are truncated, resulting in incomplete reconstructions and pronounced artifacts near FOV boundaries. Conventional reconstruction algorithms struggle to recover accurate anatomy from such data, limiting clinical reliability. Deep learning approaches have been explored for FOV extension, with diffusion generative models representing the latest advances in image synthesis. Yet, conventional diffusion models are computationally demanding and slow at inference due to their iterative sampling process. To address these limitations, we propose an efficient CT FOV extension framework based on the image-to-image Schrödinger Bridge (I$^2$SB) diffusion model. Unlike traditional diffusion models that synthesize images from pure Gaussian noise, I$^2$SB learns a direct stochastic mapping between paired limited-FOV and extended-FOV images. This direct correspondence yields a more interpretable and traceable generative process, enhancing anatomical consistency and structural fidelity in reconstructions. I$^2$SB achieves superior quantitative performance, with root-mean-square error (RMSE) values of 49.8 HU on simulated noisy data and 152.0 HU on real data, outperforming state-of-the-art diffusion models such as conditional denoising diffusion probabilistic models (cDDPM) and patch-based diffusion methods. Moreover, its one-step inference enables reconstruction in just 0.19 s per 2D slice, representing over a 700-fold speedup compared to cDDPM (135 s) and surpassing DiffusionGAN (0.58 s), the second fastest. This combination of accuracy and efficiency indicates that I$^2$SB has potential for real-time or clinical deployment.

15.
arXiv (CS.CV) 2026-06-16

Continuous Splatting meets Retinex: Continuous Gaussian Splatting and Implicit Reflectance Modeling for Low-Light Image Enhancement

Low-light image enhancement aims to recover clear images from low-illumination observations and is crucial for high-level downstream vision tasks. However, existing methods frequently encounter color distortion and structural artifacts when balancing global smooth illumination adjustment and local high-frequency detail recovery. To address these issues, we propose CGS-Retinex as the first low-light image enhancement framework based on explicit-implicit joint modeling. Our framework deeply integrates continuous Gaussian splatting with Retinex theory. Specifically, we represent the image grid as a continuous parameter field and propose a continuous Gaussian renderer to estimate the spatially continuous global illumination distribution. This approach fundamentally eliminates grid artifacts caused by discrete Gaussian sampling. Furthermore, we introduce an implicit neural representation to model reflectance independently. We leverage shallow high-frequency features to guide the network in accurately reconstructing degraded texture details. Within the Retinex framework, we incorporate physics-inspired brightness consistency constraints and illumination smoothness regularization to enable explicit illumination and implicit reflectance to maintain proper exposure and achieve high-fidelity recovery of high-frequency structures and colors. Extensive experiments demonstrate that CGS-Retinex significantly suppresses dark-region noise and overexposure while achieving exceptional high-frequency structural fidelity and color restoration by precisely decoupling illumination and texture. This work establishes a novel continuous physical representation paradigm for low-light image enhancement.

17.
bioRxiv (Bioinfo) 2026-06-15

Inferring Cell Fate Trajectories in Time-Resolved Metabolic RNA Labeling data

Single-cell RNA sequencing provides high-resolution snapshots of cellular states but lacks direct information about transcriptional dynamics. Metabolic RNA labeling addresses this limitation by distinguishing newly synthesized RNA, offering insight into the direction of cell state changes, and providing valuable information when attempting to recover the underlying continuous dynamics from static snapshots of cell distributions. However, existing trajectory inference methods do not fully exploit this additional signal. Here, we propose FLOWSATATE, a framework for single-cell trajectory inference that leverages time-resolved RNA labeling within an Optimal Transport setting. We model cell dynamics as a gradient flow in an inferred potential landscape parameterized by a neural network, integrating both total and labeled RNA across time points. The learned potential enables identification of key genes and transcription factors driving cell fate decisions and supports prediction of future cellular states. We benchmark our approach on its ability to generalize unseen data and recover coherent trajectories. We also apply it to study colorectal cancer response to demethylation treatment as well as neuronal differentiation of embryonic stem cells.

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

Localization for non-stationary Anderson models in three dimensions

作者:

arXiv:2603.17810v2 Announce Type: replace-cross Abstract: We prove localization (near the bottom of the spectrum) for certain non-stationary variants of the Anderson model in three dimensions. More specifically, we prove a Wegner estimate, which implies localization by existing work. Two key inputs are a deterministic quantitative unique continuation theorem by Li and Zhang [Duke Math. J. 171(2): 327-415, 2022] and some combinatorial decompositions/bounds for non-stationary random potentials proved by the author [Commun. Math. Phys. 407:64, 2026].

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

Lost in a Single Vector: Improving Long-Document Retrieval with Chunk Evidence Aggregation

Dense retrieval ranks one query vector against one document vector. On long documents, this interface can fail when a short but decisive span is weakened during document encoding before ranking. We study this failure mode as document-side early compression and introduce the Evidence Dilution Index (EDI) to measure how far a document-level representation falls below the strongest chunk-level evidence within the same gold document. Guided by this view, we propose DICE (Document Inference via Chunk Evidence), a training-free document-side strategy that splits documents into chunks, encodes them independently with a frozen model, and aggregates them back into a single vector while preserving the standard one-query-one-document interface. On LongEmbed, DICE improves retrieval across four backbones, with the largest gains on slices beyond 4k tokens: for Dream, Passkey >4k rises from 30.0 to 90.0 and Needle >4k from 23.3 to 74.0. Across 12,779 filtered samples, DICE yields lower EDI than the single-vector baseline in 92.8% of cases. These results establish document-level encoding as a practical and underexplored lever for long-document retrieval.

20.
arXiv (quant-ph) 2026-06-24

Ultra-Low-Rate Information Reconciliation: Repetition Coding or Dedicated Codes?

arXiv:2606.23726v1 Announce Type: new Abstract: We compare repetition-based ultra-low-rate information reconciliation with dedicated ultra-low-rate codes for CV-QKD. Repetition coding offers a favorable performance-complexity trade-off, incurring only a moderate error-rate penalty while reducing decoding complexity by $2\times$, making it attractive for implementation-constrained systems.

21.
Science (Express) 2026-04-23

Structural N- and O-glycans revealed by high-resolution cryo-EM analysis of tubular mastigonemes | Science

作者: 未知作者

The chemical complexity and non-templated biosynthesis of glycans have posed significant challenges for establishing sequence-structure relationships. Here we report cryo-EM structures of tubular mastigonemes from a golden alga species, Ochromonas danica , in which a large number of N- and O-glycans are resolved at 1.8-2.2 Å resolution. Beyond high-mannose and complex N-glycans, we identify a non-canonical N-glycan on the Ala- Asn -Asp (A N D) motif. The surface spikes comprise dense O-glycans coating PSXX tetrapeptide repeats, with two glycans linked on trihydroxylated proline and one on serine per repeat. In addition to various types of sugars and their covalent modifiers, water molecules (>10% of resolved volume) and cations are clearly resolved and mediate the structural assembly. Our study establishes a framework for investigating glycan folding in high-order biological assemblies.

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

Graph2Idea:Retrieval-Augmented Scientific Idea Generation with Graph-Structured Contexts

arXiv:2606.09105v3 Announce Type: replace Abstract: Generating novel, feasible, and high-quality research ideas is an important yet challenging task in scientific discovery. Recent Large Language Model (LLM)-based methods often ground idea generation with retrieved literature, but the retrieved evidence is usually provided as flat text, such as titles, abstracts, or summaries. Such flat contexts may contain redundant or weakly relevant information, while making cross-paper relations among problems, methods, mechanisms, and findings difficult to identify and trace. To address this challenge, we propose Graph2Idea, a knowledge graph-guided framework for retrieval-augmented scientific idea generation.Graph2Idea first retrieves papers according to the input topic, transforms them into structured knowledge triples, and dynamically constructs a target-centered knowledge graph to make literature relations explicit. It then extracts compact graph-derived contexts that retain target-relevant relational evidence while reducing noisy textual input. Based on these contexts, a two-stage generation process first identifies promising research directions and then guides the LLM to synthesize candidate ideas from graph-grounded evidence. Experiments on a scientific idea generation benchmark show that Graph2Idea outperforms representative baselines under the automatic evaluation protocol. Compared with the strongest baseline scores, it improves Novelty from 0.45 to 0.52, Quality from 0.24 to 0.29, and Feasibility from 0.22 to 0.28. These results suggest that graph-structured evidence helps LLMs generate research ideas through more explicit, compact, and traceable recombination of prior scientific knowledge.

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

Testing For Distribution Shifts with Conditional Conformal Test Martingales

arXiv:2602.13848v2 Announce Type: replace Abstract: We propose a sequential test for detecting arbitrary distribution shifts that allows conformal test martingales (CTMs) to work under a fixed, reference-conditional setting. Existing CTM detectors construct test martingales by continually growing a reference set with each incoming sample, using it to assess how atypical the new sample is relative to past observations. While this design yields anytime-valid type-I error control, it suffers from test-time contamination: after a change, post-shift observations enter the reference set and dilute the evidence for distribution shift, increasing detection delay and reducing power. In contrast, our method avoids contamination by design by comparing each new sample to a fixed null reference dataset. Our main technical contribution is a robust martingale construction that remains valid conditional on the null reference data, achieved by explicitly accounting for the estimation error in the reference distribution induced by the finite reference set. This yields anytime-valid type-I error control together with guarantees of asymptotic power one and bounded expected detection delay. Empirically, our method detects shifts faster than standard CTMs, providing a powerful and reliable distribution-shift detector.

24.
Nature Medicine 2026-06-22

Biological aging and generational shifts in early-onset cancer risk

作者:

Incidence of early-onset cancer is rising globally in recent generations, which underscores the need to elucidate the influence of emerging generational risk factors. Systemic and organ-specific aging reflects the cumulative impact of exposures and may provide an integrative and complementary approach to understand early-onset cancer risk. Here among 154,169 young adults from the United Kingdom Biobank, systemic aging measured by PhenoAge increased across birth cohorts, with 23% s.d. increase for those born 1965–1974 versus 1950–1954, and was associated with early-onset solid cancer risk (hazard ratio (HR)per s.d. 1.08; 95% confidence interval (CI), 1.03–1.13), driven by lung, gastrointestinal and uterine cancers, independent of genetic risks of aging and cancer. Patterns were consistent using alternative systemic aging measures, including the Klemera–Doubal method-defined age gap and metabolomic-based age gap. These findings were validated partially among 10,262 participants in the United States All of Us Research Program. Proteomics-based organ-specific aging analyses linked immune aging with early-onset lung cancer (HRper s.d. 1.89; CI, 1.20–2.97) and adipose tissue aging to early-onset colorectal cancer (HR 1.60; CI, 1.11–2.32). Greater age gap, reflecting more advanced biological aging relative to chronological age, may serve as a driver associated with risk of early-onset solid cancers, highlighting the importance of uncovering underlying mechanisms to guide effective prevention strategies. Analyses of population cohorts found that young adults exhibited earlier systemic and organ-specific aging, which was associated with increased risk of early-onset cancer compared with older adults born decades earlier.

25.
arXiv (CS.AI) 2026-06-19

Sovereign Execution Brokers: Enforcing Certificate-Bound Authority in Agentic Control Planes

arXiv:2606.20520v1 Announce Type: cross Abstract: Autonomous agents are increasingly connected to cloud, deployment, and data-control workflows, but production mutation authority should not reside inside non-deterministic reasoning processes. Existing access-control mechanisms authorize identities, while assurance layers certify proposed actions; neither alone provides a mandatory enforcement point for certified authority at the moment of mutation. This paper introduces the Sovereign Execution Broker (SEB), a runtime enforcement boundary for certificate-bound agentic infrastructure. SEB consumes certificates issued by the Sovereign Assurance Boundary (SAB), verifies that the requested mutation matches the certified execution contract, checks validity windows, policy epochs, revocation epochs, and live-state drift, mints scoped execution identity, invokes infrastructure APIs, and records signed decision and outcome records. By separating proposal, admission, and execution, SEB turns certified authority into a short-lived, revocable, auditable runtime capability, provided that production mutation APIs reject non-broker identities. We present the SEB execution model, certificate and replay-verification predicates, scoped identity semantics, bypass-prevention deployment patterns, failure behavior, and a concrete prototype implementation. We evaluate the prototype on AWS and Kubernetes clusters, measuring latency overheads, revocation propagation, drift detection, and security under fault injection.