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01.
arXiv (quant-ph) 2026-06-16

Forbidden transitions in superconducting artificial atoms

Authors:
Alberto Del \'Angel↗Th\'eo S\'epulcre↗Ricardo Guti\'errez-J\'auregui↗Anton Frisk Kockum↗

arXiv:2606.06069v2 Announce Type: replace Abstract: Artificial atoms built from Josephson junctions have become a powerful tool to explore the limits of quantum optics due to their strong coupling to electromagnetic fields and their sensitivity to changes at the single-photon level. This sensitivity to quantum fluctuations complements their metrological and computational use, which are based on the precise oscillating frequency of the underlying supercurrents. We present here a theory for Josephson junctions immersed in electromagnetic fields where focus is shifted from temporal correlations and towards spatial ones. Unlike the commonly used circuit and black-box descriptions, our work is based on a microscopic model that enables systematically accounting for the effect of the spatial and vectorial profile of an electromagnetic field over a junction. As an example of the interactions that emerge in such a setup, we investigate the possibility of driving a junction via a quadrupole transition, using typical experimental parameters in existing devices. With the transition being dependent on the gradient of the electric field – rather than its intensity – the junction can be excited in a region where the electric field vanishes.

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02.
medRxiv (Medicine) 2026-06-17

Performance of five risk stratification tools for paediatric pneumonia against WHO scores using data from the PediCAP trial in sub-Saharan Africa

Authors:
Nalwanga↗Clements↗Musiime↗Mulenga↗Mujuru↗H. A↗Sidat↗Buck↗W. C↗Madhi↗Bielicki↗J. A↗…

Background Risk stratification tools for childhood pneumonia have been proposed to improve identification of children at highest risk of death, particularly in low-resource settings. However, their added value over the WHO Integrated Management of Childhood Illness (IMCI) criteria and danger signs remains uncertain. Methods We conducted a secondary analysis of a multi-country randomised controlled trial of children without HIV hospitalised with pneumonia in Mozambique, South Africa, Uganda, Zambia, and Zimbabwe. We evaluated the performance of five published risk scores alongside WHO IMCI severity classification and danger signs. Discrimination for (1) in-hospital mortality, (2) 28-day mortality, and (3) 28-day readmission or death was assessed using area under the receiver operating characteristic curve (AUC). Comparative performance and clinical utility were examined. Results Of the 1010 participants, 18 (1.8%) died in hospital, 22 (2.2%) died in hospital or in the 7 days post-discharge, and 63 (6.2%) died or were readmitted by day 28. Univariate case-fatality rates were highest for variables associated with malnutrition, convulsions, and hypoxaemia. All risk scores demonstrated moderate discrimination for in-hospital and in-hospital+7-day mortality (AUC range approximately 0.75-0.84), with no meaningful differences between models, and performed similarly to the WHO danger signs and IMCI severity classification. In contrast, all approaches performed poorly in predicting 28-day readmission or death (AUC approximately 0.54-0.58). No risk score consistently outperformed simple clinical criteria. Conclusions In this multi-country dataset, we found no evidence that published paediatric pneumonia risk scores meaningfully outperform WHO IMCI-based clinical assessment for predicting mortality. The relatively small number of mortality events limits precision, and modest differences cannot be excluded. These findings suggest that, in low-resource settings, strengthening implementation of existing WHO clinical criteria may be more effective than adopting more complex prediction tools.

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03.
Nature Medicine 2026-06-08

Effects of SGLT2 inhibition on incident heart failure in carriers of cardiomyopathy-associated genetic variants

Authors:
Nicholas A. Marston↗

Although the beneficial effects of sodium–glucose cotransporter 2 (SGLT2) inhibition in heart failure (HF) have been well established, it is unknown whether SGLT2 inhibition confers benefit in carriers of rare variants in cardiomyopathy-associated genes. Here we evaluated whole-exome sequencing data from the randomized DECLARE-TIMI 58 trial, in which adults with type 2 diabetes and increased cardiovascular risk were randomized to dapagliflozin or placebo treatment. Pathogenic or likely pathogenic variants (P/LP) in high-confidence cardiomyopathy genes were identified, and treatment effects on hospitalization for HF (HHF) were compared between carriers of such variants and noncarriers. Among 12,685 patients for whom sequence data were obtained, 121 carried a cardiomyopathy variant (76 dilated cardiomyopathy, 25 hypertrophic cardiomyopathy and 25 arrhythmogenic cardiomyopathy). Over a median follow-up of 4.2 years, dapagliflozin lowered the risk of HHF more strongly in carriers (hazard ratio 0.18, 95% confidence interval 0.04–0.86) than in noncarriers (hazard ratio 0.70, 95% confidence interval 0.57–0.86; P interaction 0.03). Absolute risk reduction was 13.0% in carriers and 1.0% in noncarriers (P interaction 0.03). Most carriers (82%) had no prior HF, and in carriers without prior HF, treatment with dapagliflozin reduced the absolute risk of HHF by 12.8%, compared with a reduction of 0.6% in noncarriers (P interaction 0.01). The findings from this cohort of older and high-risk patients raise the possibility that SGLT2 inhibitor treatment should be started early to prevent HF in individuals who carry P/LP cardiomyopathy variants. These results need to be confirmed in a prospective, dedicated trial of preventive HF treatments in carriers of P/LP cardiomyopathy-associated variants. In a whole-exome sequencing analysis, the beneficial effects of the SGLT2 inhibitor dapagliflozin in reducing the risk of future heart failure hospitalization in individuals with type 2 diabetes were markedly greater in individuals who carried a cardiomyopathy-associated genetic variant compared with noncarriers, suggesting a personalized preventative therapy based on genetic information.

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

Mapping Scientific Literature with Large Language Models and Topic Modeling

Authors:
Mason Smetana↗Lev Khazanovich↗

Scientific literature is increasingly fragmented by disciplinary boundaries, specialized terminology, and potentially sparse keyword systems, making it difficult to capture the evolving structure of modern science. This study introduces a large language model (LLM)-driven framework for mapping scientific literature from a topic modeling perspective. The approach is demonstrated on a 20-year corpus of more than 1,500 engineering-related articles published in the Proceedings of the National Academy of Sciences (PNAS). A two-stage classification pipeline first assigns a primary thematic category to each article based on its abstract, followed by full-text analysis to identify secondary classifications that reveal latent cross-topic connections within the corpus. Unlike conventional topic models, the LLM-based framework produces semantically interpretable topics while maintaining strong quantitative performance. Comparative evaluation against established topic modeling methods shows higher topic diversity and lower overlap with competitive coherence metrics. Manual validation on a randomly sampled subset of abstracts yields an accuracy of 75.9%. Additional traditional natural language processing analyses confirm that the generated topics correspond to meaningful linguistic patterns in the corpus. A bipartite network linking primary and secondary classifications further reveals implicit thematic relationships that are not readily observable through abstracts or keyword systems alone. The findings indicate that the framework independently recovers much of the journal's editorial dual-classification structure without prior knowledge of its schema. Overall, the proposed approach offers a powerful tool for mapping science and identifying emerging cross-topic connections in research.

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05.
arXiv (CS.CL) 2026-06-19

Beyond Global Replanning: Hierarchical Recovery for Cross-Device Agent Systems

Authors:
Shu Yao↗Yuhua Luo↗Qian Long↗Jingru Fan↗Zhuoyuan Yu↗Yuheng Wang↗Lin Wu↗Yufan Dang↗Huatao Li↗Chen Qian↗

Real-world computer-use tasks often span multiple applications and devices, requiring agents to coordinate heterogeneous environments under dynamic runtime failures. Existing multi-device agent systems support task decomposition and cross-device assignment, but recovery remains largely coarse-grained: when execution fails, they typically retry the same strategy, reassign the subtask, or revise the global plan, without systematically modeling the device-local strategy space. This limits their ability to distinguish failures that can be repaired within the current device from those that require cross-device replanning. We propose H-RePlan, a hierarchical replanning framework for multi-device agents with unified API–CLI–GUI execution. H-RePlan equips each device with interchangeable execution strategies and separates device-local strategy recovery from orchestrator-level global replanning through a compact cross-layer failure abstraction. To evaluate this capability, we introduce HeraBench, a fault-injected benchmark that constructs cross-device workflows over Linux and Android devices and injects strategy- and device-level failures. Experiments show that H-RePlan substantially outperforms single-strategy and coarse-grained multi-device baselines, achieving higher completion, instruction adherence, and perfect-pass rates while reducing the token cost required for reliable end-to-end success. These results demonstrate that scope-aware hierarchical recovery is essential for robust multi-device agent execution.

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

GH-ESD: Grounded Hypothesis-Driven Error Slice Discovery for Instance-Level Vision Tasks

Authors:
Wei Zhang↗Chaoqun Wang↗Zixuan Guan↗Sam Kao↗Pengfei Zhao↗Peng Wu↗Sifeng He↗

Systematic failures of vision models on semantically coherent subsets, known as error slices, reveal limitations in robustness and evaluation. Existing slice discovery approaches largely model slices as clusters in representation space or combinations of predefined attributes. While effective for image-level classification, such formulations are insufficient for instance-level tasks such as object detection and segmentation, where failures often arise from contextual relational and spatially grounded visual patterns. We propose GH-ESD (Grounded Hypothesis-Driven Error Slice Discovery), a generate and verify framework that reformulates slice discovery as grounded hypothesis generation and statistical verification. GH-ESD constructs relational failure hypotheses using LLM priors and grounded visual evidence, discovers hypothesis slices at the instance level via Vision Language Models, and verifies them through statistical trend analysis over instance-level errors. We also introduce GESD (Grounded Error Slice Dataset), a new benchmark for instance-level error slice discovery, providing expert-defined and spatially grounded slices derived from detection and segmentation failures. Extensive experiments demonstrate that GH-ESD consistently outperforms baselines, improving Precision@10 by 0.10 (0.73 vs. 0.63) on the GESD benchmark for detection tasks, while also supporting segmentation scenarios. GH-ESD identifies interpretable slices that facilitate actionable model improvements. The GESD dataset will be made publicly available upon acceptance.

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07.
arXiv (CS.CL) 2026-06-18

Freeing the Law with LOCUS: A Local Ordinance Corpus for the United States

Authors:
Denis Peskoff↗Joe Barrow↗Christopher Vu↗Diag Davenport↗

Progress in legal AI increasingly depends on access to authoritative legal text at scale. Yet one of the most consequential layers of American law remains largely absent from existing machine-readable corpora: local ordinances. Local codes govern zoning, housing, business licensing, public health, noise, animal control, and many other domains of everyday regulation, but they are fragmented across vendor platforms designed for human browsing rather than bulk research access. We introduce LOCUS - the Local Ordinance Corpus for the United States - a comprehensive corpus and county-harmonized access layer for U.S. municipal and county ordinance codes. The raw corpus, available for release to researchers, represents nearly all publicly available municipal and county ordinance codes. The resulting raw corpus contains codes from 9,239 cities and counties. A smaller county-harmonized LOCUS access layer provides coverage for the largest 2,309 of 3,144 U.S. counties, accounting for a majority of the population. We use OCR to handle the myriad of document formats that have kept the law from being a public resource. We release the corpus with coverage metadata to support reproducibility, downstream legal AI research, and the incremental expansion of machine-readable access to local law. We train a collection of ModernBERT-based classifiers and scorers to facilitate analyzing U.S. local law among several dimensions, such as opacity and paternalism, that have not previously been studied at this scale. LOCUS-v1 and its derivative models are available at: https://huggingface.co/datasets/LocalLaws/LOCUS-v1

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08.
arXiv (CS.LG) 2026-06-17

Sum-of-Squares Degree Barriers for the Reweighted-Hinge Method in Robust Halfspace Learning: A Christoffel-Function Characterization

Authors:
Xiaoyu Li↗

arXiv:2606.17215v1 Announce Type: new Abstract: A certificate that removes outliers sees the data only through its low-degree moments, and an adversary exploits exactly this, hiding corruption where the clean data already looks typical, in the blind spot no bounded-degree test resolves. That blind spot turns out to have an exact size: the Christoffel function of the clean marginal, the very quantity modern data analysis thresholds to detect outliers, here read from the adversary's side as the corruption a bounded-degree certificate cannot remove. We turn this inversion into the organizing principle of the reweighted-hinge approach to robustly learning $\gamma$-margin halfspaces under malicious noise (Shen, 2025; Zeng and Shen, 2025): the governing resource is the Sum-of-Squares degree of the outlier-removal certificate, and the resolution principle states that the maximal corruption mass which can hide at a center $c$ from a degree-$2t$ certificate is exactly the Christoffel function $\lambda_{t+1}(c)$ of the clean marginal. Three consequences follow, all against the certificate method (not information-theoretic). A margin-degree tradeoff: certifying the dense pancake to error $\epsilon$ costs SoS degree $\Omega(\log(1/\epsilon))$ or margin $\Omega(\sqrt{\log(1/\epsilon)}/\sqrt{d})$, explaining why the $\log(1/\epsilon)$ margin Shen (2025) records is forced, with a weighted-Chebyshev reduction making the threshold $2t=\Theta((|c|/s)^2)$ tight modulo one classical weighted-extremal estimate. A degree-$2$ outlier barrier: the resolution principle realized as an explicit instance on which degree $2$ is stuck at $\eta^{1/2}$ while degree $4$ escapes, locating the method's small breakdown rate in the degree, not the analysis. And a degree-$2t$ algorithm tracing the frontier $\eta^{1-1/2t}$ (recovering Shen (2025) at $t=1$), whose gain is an explicit constant, capped by the pancake density and shown unimprovable by the degree-$2$ barrier.

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09.
arXiv (CS.AI) 2026-06-16

Orcheo: A Modular Full-Stack Platform for Conversational Search

Authors:
Shaojie Jiang↗Svitlana Vakulenko↗Maarten de Rijke↗

arXiv:2602.14710v2 Announce Type: replace-cross Abstract: Conversational search (CS) requires a complex software engineering pipeline that integrates query reformulation, ranking, and response generation. CS researchers currently face two barriers: the lack of a unified framework for efficiently sharing contributions with the community, and the difficulty of deploying end-to-end prototypes needed for user evaluation. We introduce Orcheo, an open-source platform designed to bridge this gap. Orcheo offers three key advantages: (i) A modular architecture promotes component reuse through single-file node modules, facilitating sharing and reproducibility in CS research; (ii) Production-ready infrastructure bridges the prototype-to-system gap via dual execution modes, secure credential management, and execution telemetry, with built-in AI coding support that lowers the learning curve; (iii) Starter-kit assets include 45+ off-the-shelf components for query understanding, ranking, and response generation, enabling the rapid bootstrapping of complete CS pipelines. We describe the framework architecture and validate Orcheo's utility through case studies that highlight modularity and ease of use. Orcheo is released as open source under the MIT License at https://github.com/AI-Colleagues/orcheo.

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

Beware of Aliases – Signal Preservation is Crucial for Robust Image Restoration

Authors:
Shashank Agnihotri↗Julia Grabinski↗Janis Keuper↗Margret Keuper↗

Image restoration networks are usually comprised of an encoder and a decoder, responsible for aggregating image content from noisy, distorted data and to restore clean, undistorted images, respectively. Data aggregation as well as high-resolution image generation both usually come at the risk of involving aliases, i.e.~standard architectures put their ability to reconstruct the model input in jeopardy to reach high PSNR values on validation data. The price to be paid is low model robustness. In this work, we show that simply providing alias-free paths in state-of-the-art reconstruction transformers supports improved model robustness at low costs on the restoration performance. We do so by proposing BOA-Restormer, a transformer-based image restoration model that executes downsampling and upsampling operations partly in the frequency domain to ensure alias-free paths along the entire model while potentially preserving all relevant high-frequency information.

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11.
arXiv (CS.CV) 2026-06-17

Seeing Is Not Screening: Multimodal Hidden Instruction Attacks on Agent Skill Scanners

Authors:
Xiaojun Jia↗Jie Liao↗Simeng Qin↗Ke Ma↗Wenbo Guo↗Yebo Feng↗Aishan Liu↗Yang Liu↗

Agent skills are emerging as an important attack surface in LLM-based systems. Through an empirical study of existing skill scanners, we find that current defenses primarily rely on textual descriptions, manifests, and source code as the main signals for security analysis, which can leave visually conveyed malicious intent insufficiently examined. This creates a practical blind spot: harmful operational instructions hidden in images may bypass scanning while still being recoverable by multimodal agents during deployment. To systematically investigate this threat, we propose SkillCamo, a document-mediated multimodal instruction attack that conceals malicious instructions within images bundled with a skill while rewriting the surrounding documentation to naturally reference those images as part of the normal workflow. Thus, the attack does not rely on the image alone, but on the joint interpretation of textual guidance and visual payload at execution time. To defend against such attacks, we further propose ExecScan, an execution-grounded multimodal scanning module that performs intent extraction, behavior reconstruction, abuse assessment, and deliberative execution simulation over skill artifacts. ExecScan jointly analyzes documentation, code, referenced resources, and visual content to recover hidden instructions, reconstruct executable behavior chains, and identify downstream risks such as exfiltration, destruction, persistence, deception, and privilege escalation. Extensive experiments show that image-hidden malicious instructions challenge existing skill scanners, while ExecScan can improve the skill scanning performance.

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12.
arXiv (CS.CL) 2026-06-11

Pre-AF 13: An Interpretable Atrial Fibrillation Risk Score Mined from Discharge Reports

Authors:
Olga Shakhmatova↗Dmitrii Kriukov↗Daniil Larionov↗Nikita Khromov↗Iaroslav Bespalov↗Alexander Zolotarev↗Kirill Grishchenkov↗Ekaterina Ivanova↗Miron Kuznetsov↗Ilya Sochenkov↗Elizaveta Panchenko↗Artem Shelmanov↗…

Background. Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia and a major determinant of prognosis. Established AF risk scores rely on factors (older age, hypertension) nearly ubiquitous among patients with cardiovascular disease (CVD), offering limited stratification in this high-risk group. Most target long-term (5-10 year) rather than medium-term prediction. We developed interpretable ML models predicting AF risk over a 24-month and entire follow-up horizon in CVD patients using routinely collected hospital data. Methods. Single-center retrospective study of electronic health records from the National Research Cardiology Center (Russia) for patients aged >=18 with CVD but without pre-existing AF, hospitalized more than once between January 2012 and May 2019. A custom NLP pipeline transformed unstructured discharge reports into 73 structured features, combining a rule-based parser with transformer-based NER. Using LightAutoML we built a full model (73 features), a simple model (reduced subset), and a linear model for a bedside risk score. Performance was assessed by ROC AUC, compared with CHARGE-AF, C2HEST, MHS, and HAVOC, and interpreted via SHAP. Results. Of 80,576 records from 45,000 patients, 17,562 met inclusion criteria; 1,438 (8.19%) developed AF. The full model reached ROC AUC 0.735 (24-month) and 0.696 (entire follow-up); the simple model was nearly identical (0.725, 0.696). All non-linear models outperformed the four clinical risk scores (ROC AUC 0.53-0.64). The simple model uses 13 features and is named Pre-AF 13. SHAP identified age and left atrial volume as dominant predictors. A linear risk score (Pre-AF 9) stratified observed 24-month AF incidence from ~7% to 36%. Conclusion. Interpretable ML models built from routinely collected EHR data identify high-AF-risk CVD patients, outperforming established clinical risk scores.

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13.
arXiv (CS.AI) 2026-06-19

Beyond Static Leaderboards: Predictive Validity for the Evaluation of LLM Agents

Authors:
Dhaval C. Patel↗Kaoutar El Maghraoui↗Shuxin Lin↗Yusheng Li↗Tianjun Feng↗Chun-Yi Tsai↗Yihan Sun↗Wei Alexander Xin↗Akshat Bhandari↗Tanisha Rathod↗Aaron Fan↗Sanskruti Vijay Shejwal↗…

arXiv:2606.19704v1 Announce Type: new Abstract: Agent benchmarks are growing fast, but no single benchmark touches more than four or five of the dimensions that deployment exposes. This paper aggregates the largest coordinated deep-dive of one MCP-based industrial-agent benchmark to date: fourteen parallel implementation studies covering new asset classes (including a multi-modal visual extension), alternative orchestrations, retrieval strategies, reasoning modes, infrastructure optimizations, and evaluation-methodology probes. Consolidating those studies with seven prior agent benchmarks, we argue that aggregate-score leaderboards systematically underspecify deployed-agent evaluation. Rankings derived from aggregate scores do not transfer to out-of-distribution settings; recent public-to-hidden competition retrospectives provide direct empirical evidence of this rank instability. We propose ranking configurations by predictive validity, the correlation between in-sample and out-of-sample rank, rather than in-sample mean, and report a twelve-tier measurement apparatus that exposes the deployment-relevant dimensions HELM and its agent-era successors collapse. The position is operationalized through three falsifiable out-of-distribution criteria with explicit thresholds; existing evidence partly supports it but is too thin to confirm. We close with a pre-registered pilot design and a field-level vision for what the next generation of agentic benchmarks should report.

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14.
arXiv (CS.LG) 2026-06-11

Trajectory Geometry of Transformer Representations Across Layers

Authors:
Vishal Pandey↗Gopal Singh↗Yacine Mahdid↗

arXiv:2606.09287v2 Announce Type: replace Abstract: Understanding how transformer representations evolve across layers, not merely what they encode, remains an open problem in mechanistic interpretability. We recast the transformer forward pass as a discrete population trajectory through a high-dimensional representation manifold, drawing on geometric tools from computational neuroscience. Rather than probing for pre-specified features, we characterize trajectory geometry using five metrics computed directly in the ambient space: trajectory length, curvature, a semantic convergence index, layerwise cosine similarity, and representational stability. Across three model families (GPT-2, TinyLlama, Qwen2.5) and five controlled prompt families, we report four findings. First, semantically related prompts converge significantly in middle-to-late layers (peak CI 0.41–0.58, p

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

Learning Directional Semantic Transitions for Longitudinal Chest X-ray Analysis

Authors:
Zhangfeng Hu↗Zefan Yang↗Ge Wang↗Tanveer Syeda-Mahmood↗Anushree Burade↗Mannudeep Kalra↗Pingkun Yan↗

Chest X-ray (CXR) interpretation often requires longitudinal comparison to assess disease progression. Existing approaches typically rely on temporal feature fusion or inter-study discrepancy modeling, yet remain limited in capturing subtle progression semantics and overlook the inherently directional nature of disease trajectories. In this paper, we propose ProTrans, a novel vision-language pretraining framework that formulates disease progression as a directional semantic transition between paired CXR studies. ProTrans leverages radiology reports to anchor individual CXR representations within interpretable disease states, and introduces a learnable progression feature map to explicitly encode semantic shifts between states, aligned with report-derived progression descriptions. To enforce direction-aware perception, ProTrans incorporates a reversed temporal modeling process and imposes bidirectional reconstruction consistency across states and transitions, thereby disentangling directional semantics and promoting coherent trajectory modeling. Extensive experiments on longitudinal downstream tasks, including disease progression classification and progression captioning, demonstrate that ProTrans consistently outperforms existing methods, establishing a unified pretraining framework for longitudinal CXR understanding. https://github.com/RPIDIAL/ProTrans

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

Enhanced Low-Density Region Exploration in Classifier-Guided Diffusion Models Through Modified Reverse Diffusion Sampling

Authors:
Jagriti Singh↗Shekhar Verma↗Muneendra Ojha↗

arXiv:2606.13347v1 Announce Type: new Abstract: Diffusion models have emerged as state-of-the-art generative models for high-fidelity image synthesis, particularly in their classifier-free guided and classifier-guided forms. However, standard classifier guidance concentrates probability mass around high-density class mean, leading to poor coverage of rare samples in the tails of the class-conditional distributions. Recent work on diffusion-based tail sampling mitigates this by training an additional low-density-seeking classifier with a synthetic-vs-real discriminator, at the cost of additional networks and training. In parallel, a number of samplers and distillation techniques accelerate or refine diffusion sampling, but do not explicitly address long-tail coverage. We propose a purely sampling-time, density-aware extension of classifier-guided conditional diffusion model that targets low-density regions without any additional training. We have applied guidance at noisy images not on predicted noise like most diffusion models. Starting from a pretrained conditional diffusion model and classifier on ImageNet, we modify the guided reverse dynamics by steering trajectories toward low-confidence regions via the modified classifier gradient, and at each time step, we also guide the sampling process toward the predicted real image. 1st guidance helps explore low-probability samples, and 2nd guidance helps to generate samples to be close to the real data manifold. The proposed sampler consistently improves ADM model recall at 64x64 resolution while maintaining a comparable FID, and with a 256x256 ADM model, we showed the results visually with different combinations of both guidance. We also showed that standard ADM classifier guidance, combined with predicted real image guidance, helps generate high perceptual quality samples with a 256x256 ADM model on ImageNet.

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17.
bioRxiv (Bioinfo) 2026-06-16

DMcloud: Macromolecular Structure Modeling Using Local Structure Fitting for Medium to Low Resolution cryo-EM maps

Authors:
Terashi↗Wang↗Zhang↗Zhu↗Hong Park↗Kihara↗

Cryogenic electron microscopy (cryo-EM) has become an essential experimental approach in structural biology for determining macromolecular structures. When the resolution of a cryo-EM map is worse than approximately 5[A], fitting known or predicted molecular models into the map becomes a common strategy for interpretation. However, accurately fitting biomolecular models into cryo-EM maps, particularly for large macromolecular complexes, remains challenging when the input structure models contain errors or are in a conformation different from that represented in the map. Here, we present DMcloud, a method for local structure fitting of proteins and nucleic acids in cryo-EM maps. Instead of forcing an entire input model into the map, DMcloud divides input structures into local regions, identifies regions that are supported by the density, removes unsupported regions, and assembles the retained regions into a final model. We benchmarked DMcloud on 176 cryo-EM maps, including intermediate and high-resolution maps that include proteins, DNAs, or RNAs. For EM maps in the 5.0-10.0 [A] and 2.5-5.0 [A] resolution ranges, DMcloud achieved average sequence modeling coverage of 0.49 and 0.70, respectively. For DNA/RNA maps, DMcloud achieved an average sequence coverage of 0.75. Across all datasets, DMcloud consistently outperformed existing methods in model accuracy, map-model correlation, and modeling coverage.

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

ROSA-TFormer: A Radar-Optical Sensor-Aware Temporal Transformer for Pinus sylvestris Plantation Classification in Northern Shaanxi Using GEE-Derived Sentinel-1/2 Time Series

Authors:
Nengbo Zhang↗Chang sheng↗

Accurate identification of Pinus sylvestris var. mongolica plantations is important for monitoring afforestation quality and ecological restoration in northern Shaanxi. This paper proposes ROSA-TFormer, a radar-optical sensor-aware temporal Transformer for P. sylvestris classification using Sentinel-1/2 time-series data generated on Google Earth Engine. The model integrates separate SAR and optical embedding branches, a sensor-aware gate, and temporal attention pooling to capture multi-source seasonal features. Experiments on monthly and half-month point-level datasets show that ROSA-TFormer achieves strong classification performance, with 99.67% overall accuracy, 99.56% macro F1, and 98.91% P. sylvestris F1 on the HalfMonth-dataBig dataset. Spatial block validation and ablation results further indicate the effectiveness of radar-optical temporal fusion and sensor-aware modeling. The results demonstrate the potential of ROSA-TFormer for point-level P. sylvestris plantation classification, while broader wall-to-wall validation remains necessary.

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

MetaboNet-Bench: A Multi-modal Benchmark for Glucose Forecasting in Type 1 Diabetes

Authors:
Nathaniel Jeffries↗Miriam Wolff↗Sam Royston↗Elizabeth Healey↗Caleb Mayer↗David Klonoff↗Michael Snyder↗Tao Wang↗

arXiv:2606.18640v1 Announce Type: new Abstract: Glucose forecasting algorithms are an important aspect of glycemic control management in type 1 diabetes. So far, the research community has developed numerous algorithms and models for forecasting. However, it is well-recognized that the lack of standardized model performance evaluation benchmarks makes fair comparison difficult and hinders further innovation, and thus benchmark standardization is in urgent need. Furthermore, many published glucose forecasting algorithms are limited to CGM data alone, ignoring other multimodal signals such as insulin dosing and carbohydrate intake. Here, we introduce MetaboNet-Bench, a benchmark for multimodal glucose forecasting for patients with type 1 diabetes that provides an extensible open-source evaluation framework for comparison of glucose forecasting algorithms that leverage glucose, insulin, and carbohydrate data. We then demonstrate its utility by benchmarking several recently published glucose forecasting models and a custom multimodal time-series model, representing different model architectures. The results show that the benefit of adding data modalities is conditioned on the complexity of the model and that incorporating more clinical metrics helps identify meaningful gaps to fill for future research.

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21.
arXiv (CS.AI) 2026-06-19

Bi-Anchor Interpolation Solver for Accelerating Generative Modeling

Authors:
Hongxu Chen↗Hongxiang Li↗Zhen Wang↗Long Chen↗

arXiv:2601.21542v3 Announce Type: replace-cross Abstract: Flow Matching (FM) models have emerged as a leading paradigm for high-fidelity synthesis. However, their reliance on iterative Ordinary Differential Equation (ODE) solving creates a significant latency bottleneck. Existing solutions face a dichotomy: training-free solvers suffer from significant performance degradation at low Neural Function Evaluations (NFEs), while training-based one- or few-steps generation methods incur prohibitive training costs and lack plug-and-play versatility. To bridge this gap, we propose the Bi-Anchor Interpolation Solver (BA-solver). BA-solver retains the versatility of standard training-free solvers while achieving significant acceleration by introducing a lightweight SideNet (1-2% backbone size) alongside the frozen backbone. Specifically, our method is founded on two synergistic components: 1) Bidirectional Temporal Perception, where the SideNet learns to approximate both future and historical velocities without retraining the heavy backbone; and 2) Bi-Anchor Velocity Integration, which utilizes the SideNet with two anchor velocities to efficiently approximate intermediate velocities for batched high-order integration. By utilizing the backbone to establish high-precision ``anchors'' and the SideNet to densify the trajectory, BA-solver enables large interval sizes with minimized error. Empirical results on ImageNet-256^2 demonstrate that BA-solver achieves generation quality comparable to 100+ NFEs Euler solver in just 10 NFEs and maintains high fidelity in as few as 5 NFEs, incurring negligible training costs. Furthermore, BA-solver ensures seamless integration with existing generative pipelines, facilitating downstream tasks such as image editing.

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22.
bioRxiv (Bioinfo) 2026-06-19

Perturbation Curve models continuous transcriptional response trajectories and improves prediction of genetic modulations

Authors:
Zhong↗wang↗Yang↗Yu↗Qi↗Jiang↗

Single-cell CRISPR screens, Perturb-seq, have revolutionized functional genomics by revealing biological causality. However, although perturbation assignments are typically represented as discrete labels, the cell-level effective strength of perturbations is often continuous and diverse. Current analytical frameworks struggle to decouple the variability in perturbation strength from the diversity of downstream responses. Here, we present Perturbation Curve (PertCurve), a nonlinear, curve-based computational framework that models the trajectories of transcriptomic responses by explicitly incorporating diverse perturbation magnitudes and strengths. By ordering cells by perturbation strength, we demonstrate that PertCurve accurately recapitulates the response magnitudes and reveals the distinct modularity and asynchrony patterns of downstream gene behaviors. These patterns are categorized into archetypes, including proportional, sensitive, and threshold responses. By applying this framework across CRISPRi/a modalities, we identify universal response patterns in viral infection, apoptosis, and proliferation genes, and reveal previously overlooked context-specific regulatory features in cell differentiation. Finally, incorporating PertCurve into perturbation prediction models and evaluation metrics enhances predictive performance, delivering actionable insights for refining established models.

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23.
medRxiv (Medicine) 2026-06-11

Assessment of occupational aerosol exposure for laboratory technicians: A quantitative study using {Phi}X174 phage as a substitute virus

Authors:
Liu↗Zhang↗

This study aimed to clarify aerosol exposure risks throughout the workflow of a Biosafety Level 2 (BSL-2) polymerase chain reaction (PCR) laboratory, validate the suitability of the {Phi}X174 bacteriophage as an indicator virus, and provide evidence for biosafety control measures. The {Phi}X174 bacteriophage was used to simulate viral samples, and a concentration-bacteriophage plaque standard curve was constructed (R2=0.998). Five operational steps in a simulated PCR laboratory were quantitatively monitored for aerosol concentration using double-layer agar plates, with blank controls used to eliminate interference. Statistical analysis was employed to identify risk differences. Sample homogenization ((5.67 {+/-} 1.23) x 104 plaque-forming units (PFU)/m3) and nucleic acid extraction ((3.45 {+/-} 0.89) x 104 PFU/m3) were identified as high-/very high-risk steps. The viral load in the samples was strongly positively correlated with the aerosol concentration (r = 0.926, P

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24.
arXiv (CS.LG) 2026-06-16

Exact Federated Continual Unlearning for Ridge Heads on Frozen Foundation Models

Authors:
Yijun Quan↗Wentai Wu↗Giovanni Montana↗

arXiv:2603.12977v3 Announce Type: replace Abstract: Foundation models are commonly deployed as frozen feature extractors with a small trainable head to adapt to private, user-generated data in federated settings. The ``right to be forgotten'' requires removing the influence of specific samples or users from the trained model on demand. Existing federated unlearning methods target general deep models and rely on approximate reconstruction or selective retraining, making exactness costly or elusive. We study this problem in a practically relevant but under-explored regime: a frozen foundation model with a ridge-regression head. The exact optimum depends on the data only through two additive sufficient statistics, which we turn into a communication protocol supporting an arbitrary stream of add and delete requests via fixed-size messages. The server maintains a head that is, in exact arithmetic, pointwise identical to centralized retraining after every request. We provide deterministic retrain-equivalence guarantees, order and partition invariance, two server-side variants, and a Bayesian certificate of zero KL divergence. Experiments on four benchmarks confirm the guarantees: both variants match centralized ridge retraining to within $10^{-9}$ relative Frobenius error and complete each request at orders-of-magnitude lower cost than federated retraining baselines.

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