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01.
arXiv (CS.CV) 2026-06-15

SAFformer:Improving Spiking Transformer via Active Predictive Filtering

Spiking Neural Networks (SNNs) offer notable advantages in biological plausibility and energy efficiency, making them promising candidates for building low-power Transformers. However, existing Spiking Transformers largely adhere to a passive reactive paradigm, which struggles to focus on task-relevant information and incurs substantial computational overhead when processing redundant visual data. To overcome this fundamental yet underexplored limitation, we propose SAFformer, a novel Spiking Transformer architecture based on an active predictive filtering paradigm. Inspired by the brain's predictive coding mechanism, SAFformer actively suppresses predictable signals and focuses on salient visual features. Extensive experiments show that SAFformer establishes new state-of-the-art performance on CIFAR-10/100 and CIFAR10-DVS. Remarkably, on ImageNet-1K, it achieves 80.44% Top-1 accuracy with only 26.58M parameters and an energy consumption of 5.88 mJ, demonstrating an exceptional balance between accuracy and efficiency.

02.
arXiv (CS.LG) 2026-06-24

A Differentially Private Weighted Empirical Risk Minimization Procedure and its Application to Outcome Weighted Learning

arXiv:2307.13127v3 Announce Type: replace-cross Abstract: Data used to train predictive models via empirical risk minimization (ERM) often contain sensitive personal information. While differential privacy (DP) provides mathematically provable bounds to protect such data, previous work has focused almost exclusively on unweighted ERM. We consider weighted ERM (wERM) – an important generalization where individual contributions to the objective function vary. We propose the first DP algorithm for general wERM with formal privacy guarantees and derive both its empirical and population excess risk bounds. Crucially, this general wERM framework provides a pathway for deriving privacy-preserving learning methods for individualized treatment rules, including the popular outcome-weighted learning (OWL) approach. We evaluate DP-wERM applied to OWL in simulated and real data experiments. Our empirical results demonstrate that training OWL models via wERM provides strong DP guarantees while maintaining robust performance, proving the method is practical for sensitive, real-world data.

03.
arXiv (CS.CL) 2026-06-12

When Does Mixing Help? Analyzing Query Embedding Interpolation in Multilingual Dense Retrieval

While mixed-language querying is ubiquitous in multilingual communities, the sensitivity of dense retrievers to such queries remains poorly understood. We present a ratio-controlled study on mMARCO that systematically evaluates retrieval performance by varying the mixing proportion of parallel query translations via embedding-level mixing – constructing mixed queries as an interpolation of monolingual embeddings. Experiments with BGE-M3 demonstrate that an optimal mixing ratio outperforms the best monolingual endpoint in 88/105 cases. We uncover a distinct asymmetry driven by English dominance: mixing is uniformly beneficial when retrieving from non-English document indices, whereas indices containing English are best served by pure English queries. Furthermore, English acts as the strongest mixing partner for every non-English document language. Finally, when controlling for English dominance, mixing gains correlate negatively with typological distance. We conclude that language-mix sensitivity is structured and predictable, and we validate the robustness of these patterns across model families and scales.

05.
arXiv (CS.LG) 2026-06-24

Target-Aware Linear Regression Under Distribution Shift

arXiv:2606.22775v2 Announce Type: replace-cross Abstract: Distribution shift between training and deployment is a pervasive challenge for modern AI systems. In many cases, the target marginals of covariates and response are known or specified through population-level observations, boundary conditions, properties of simulator configurations, or alignment-time distributional constraints. Such knowledge may provide valuable side information for regression estimation. We study this problem in the multivariate linear regression setting with a stable conditional mean $E[Y\mid X]$ across source and target, and identify the hybrid-loss estimator, which jointly incorporates both target marginals, as a benchmark target-aware estimator. Its direct computation, however, requires solving a coupled nonlinear optimization that is expensive at scale. Our main contribution is to develop and evaluate two computationally tractable alternatives: a constrained moment-matching estimator and a two-stage estimator that augments ordinary least squares with a calibration step. For all three estimators, we derive and compare closed-form asymptotic mean squared errors, yielding conditions under which the tractable alternatives match or closely approximate the hybrid benchmark, and regimes in which they do not. Monte Carlo experiments across three controlled shift regimes validate the theoretical results, investigate the accuracy-runtime tradeoffs among the three estimators, and translate into guidance on estimator choice. In particular, the two-stage estimator nearly matches the hybrid benchmark in the high signal-to-noise regime at essentially no additional cost, providing theoretical grounding for empirical observations in nonlinear settings.

06.
medRxiv (Medicine) 2026-06-15

Pulmonary extracellular vesicles drive alveolar macrophage dysfunction via microRNA transfer in Acute Respiratory Distress Syndrome

Background: Alveolar macrophage (AM) dysfunction contributes to Acute Respiratory Distress Syndrome (ARDS) pathogenesis. We investigated the role of extracellular vesicles (EVs) in mediating this dysfunction. Methods: Pulmonary EVs were isolated from broncho-alveolar lavage and non-directed bronchial lavage samples of ventilated sepsis patients with and without ARDS, and post-operative control patients via ultracentrifugation. AMs were isolated from lung tissue resections of lobectomy patients. AMs were treated with pooled EVs for 24 hours prior to functional, metabolic and autophagy profiling. EV cargo was profiled via small RNA transcriptomics and proteomics. Mechanistic role of EV microRNAs was assessed via mimic / antagomir transfection. Results: Pulmonary EVs from sepsis patients with ARDS impaired AM efferocytosis, and control EVs had no effect. ARDS EV treatment enhanced AM mitochondrial-linked respiration, but not glycolysis. ARDS EV treatment impaired LC3B-II and LAMP1 expression, indicating dysregulated AM autophagy-lysosomal machinery. Proteomics revealed downregulation of innate immune pathways in ARDS EVs. Transcriptomics revealed enrichment of 24 microRNAs in ARDS EVs; miR-652-3p was the most enriched, validated by RT-qPCR. EV miR-652-3p was associated with 90-day mortality (9.20 vs 0.59 RQ, p=0.0295) and inversely correlated with oxygenation (PaO2/FiO2). AM transfection with miR-652-3p mimic induced similar dysregulation of function and autophagy as ARDS EVs. Transfection of ARDS EVs with antagomirs to miR-652-3p prior to AM treatment partially rescued efferocytosis and autophagy. Conclusions: Targeting EV miR-652-3p may restore alveolar macrophage function and reduce excessive inflammation, thus offering a novel therapeutic strategy for patients with ARDS.

07.
Nature (Science) 2026-06-11

Daily briefing: Deep-sea whale graveyard is a treasure trove of fossils

Authors:

Researchers have uncovered more than 400 fossilized whale bones in an ocean-floor chasm. Plus, the working lives of scientists, in pictures, and how AI could slow the pace of research publication for the better. Researchers have uncovered more than 400 fossilized whale bones in an ocean-floor chasm. Plus, the working lives of scientists, in pictures, and how AI could slow the pace of research publication for the better.

08.
arXiv (CS.CV) 2026-06-11

FronTalk: Benchmarking Front-End Development as Conversational Code Generation with Multi-Modal Feedback

We present FronTalk, a benchmark for front-end code generation that pioneers the study of a unique interaction dynamic: conversational code generation with multi-modal feedback. In front-end development, visual artifacts such as sketches, mockups and annotated creenshots are essential for conveying design intent, yet their role in multi-turn code generation remains largely unexplored. To address this gap, we focus on the front-end development task and curate FronTalk, a collection of 100 multi-turn dialogues derived from real-world websites across diverse domains such as news, finance, and art. Each turn features both a textual instruction and an equivalent visual instruction, each representing the same user intent. To comprehensively evaluate model performance, we propose a novel agent-based evaluation framework leveraging a web agent to simulate users and explore the website, and thus measuring both functional correctness and user experience. Evaluation of 20 models reveals two key challenges that are under-explored systematically in the literature: (1) a significant forgetting issue where models overwrite previously implemented features, resulting in task failures, and (2) a persistent challenge in interpreting visual feedback, especially for open-source vision-language models (VLMs). We propose a strong baseline to tackle the forgetting issue with AceCoder, a method that critiques the implementation of every past instruction using an autonomous web agent. This approach significantly reduces forgetting to nearly zero and improves the performance by up to 9.3% (56.0% to 65.3%). Overall, we aim to provide a solid foundation for future research in front-end development and the general interaction dynamics of multi-turn, multi-modal code generation. Code and data are released at https://github.com/shirley-wu/frontalk

09.
arXiv (CS.CV) 2026-06-11

DroneShield-AI: A Multi-Modal Sensor Fusion Framework for Real-Time Autonomous Drone Threat Detection, Behavioral Intent Classification, and Swarm Intelligence in Contested Airspace

Unmanned Aerial Vehicle (UAV) threats have emerged as a defining security challenge of the 21st century. This paper presents DroneShield-AI, a unified open framework integrating six processing layers: RF signal classification, acoustic motor-signature detection, YOLOv8-based visual detection, evidence-weighted sensor fusion, a Behavioral Intent Classification Engine (BICE), and a Graph Neural Network Swarm Intelligence Module (GNN-SIM). BICE introduces the first systematic six-class threat taxonomy for drone flight patterns, enabling predictive operator alerts with a 30-second advance-warning horizon. GNN-SIM is the first open framework for adversarial multi-drone formation analysis using Graph Attention Networks. Evaluated on three publicly available real-world datasets, the fused pipeline achieves 96.1% detection accuracy, 3.2% false alarm rate, AUC-ROC: 0.981, and 142ms end-to-end latency on commodity CPU-class hardware at approximately $500-$780 USD total system cost. All code, model weights, and simulation datasets are publicly released at submission.

10.
medRxiv (Medicine) 2026-06-22

Starting, stopping and restarting. Patterns of Methylphenidate Use over 14 years in a large public health system

Background Persistence with stimulant medication is poor in children and adolescents with ADHD, and the evidence base is derived predominantly from high-income countries. We describe methylphenidate utilisation patterns and predictors of 12-month retention across 14 years in a large South African public health service. Methods Retrospective cohort study using routine pharmacy data from the Western Cape provincial health service (2011-2024). Children aged 5-18 at first prescription were included. Treatment episodes were defined as continuous prescription sequences with no gap exceeding 90 days and classified as initiations or restarts. Logistic regression modelled 12-month retention against early visit frequency and formulation type as pre-specified exposures. Findings 421,925 prescription events for 23,243 children across 115 facilities generated 65,885 treatment episodes. Median age at first prescription was 10 years (IQR 8-12); 77.6% were male. Kaplan-Meier 12-month survival was 28.2% for initiations and 15.4% for restarts, substantially below high-income country comparators. A quarter of all initiating prescriptions were not followed by a subsequent dispensing event; nearly 40% of patients had three or more treatment episodes. Early visit frequency was the strongest predictor of 12-month retention (high vs low: OR 2.85, 95% CI 2.65-3.06). The sustained-release formulation effect was present but attenuated on multivariable adjustment. Treatment re-initiations showed a marked seasonal pattern consistent with the South African school calendar. Interpretation Twelve-month retention was markedly lower than high-income country rates. Against a backdrop of high attrition, both early visit frequency and sustained-release formulation access predicted persistence; clinical engagement and reducing structural barriers to access are modifiable factors in this setting. Funding None.

11.
arXiv (CS.AI) 2026-06-15

FreoStream:Enhancing Stream Guardrails via Future-Aware Reasoning and Safety-Aligned Optimization

arXiv:2606.13737v1 Announce Type: cross Abstract: Stream guardrails enable token-level safety detection before full responses are generated. However, they often make overly conservative judgements and block those sensitive but safe tokens, which is known as over-refusal. Due to lack of full context, they also fail to detect implicitly harmful content from jailbreaking. To address these challenges, we propose FreoStream, a novel streaming guardrail framework. Specifically, FreoStream fine-tunes a LoRA module to perform Future-Aware Reasoning when the base guardrail detects unsafe tokens. The reasoning process follows a Future-Reason-Judge paradigm: predict the future, reason about the full context and give the final judgement. This design can effectively reduce over-refusal by incorporating the future information. Moreover, we introduce the Safety-Aligned Optimization module that extracts the safety-aligned component from the reasoning gradients to update the base guardrail model, thereby enhancing streaming safety detection. Extensive experiments on various safety benchmarks demonstrate that FreoStream achieves lower over-refusal rates and better jailbreak defense compared to existing streaming guardrails.

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

OmniVideo-100K: A Dataset for Audio-Visual Reasoning through Structured Scripts and Evidence Chains

Current automated pipelines for audio-visual Question Answering (QA) generally adopt a ``video-caption-QA'' paradigm. However, these methods typically segment videos into short clips and generate separate descriptions for audio and visual modalities. This decoupled processing severs inherent associations between sounds and their visual sources, while independent clip processing often causes inconsistent descriptions of the same entity across segments. Furthermore, coupling long-text comprehension and QA synthesis into a single step often restricts models to localized events, yielding questions lacking long-term temporal connections and deep cross-modal reasoning. To address these issues, we propose an automated data engine featuring two mechanisms: (1) Entity-Anchored Video Scripting transforms videos into structured scripts, comprising summaries, main entity lists, and segment-wise audio-visual descriptions. The entity list serves as a global prior to ensure cross-segment referential consistency and reconstruct audio-visual associations. (2) Clue-Guided QA Generation prompts models to first mine cross-segment, multimodal clues from the script, and subsequently generate QA pairs based on these high-value clues. Leveraging this pipeline, we construct the instruction-tuning dataset OmniVideo-100K and a human-verified test set, OmniVideo-Test. Fine-tuning VITA-1.5, Qwen2.5-Omni-7B and Qwen3-Omni-30B on OmniVideo-100K yields performance gains of up to 20.59% on OmniVideo-Test, demonstrating strong generalization (up to 12.64% improvements) across established benchmarks like Daily-Omni and JointAVBench.

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

Critic Architecture Matters: Dual vs. Unified Critics for Humanoid Loco-Manipulation

arXiv:2606.11891v1 Announce Type: cross Abstract: Multi-objective reinforcement learning for humanoid robots must coordinate locomotion and manipulation within a single policy. A natural design choice is whether to use a single (unified) critic that estimates the combined value of all objectives, or separate (dual) critics with disjoint reward signals. We present a controlled comparison on the Unitree G1 humanoid (23 active DoF) in NVIDIA Isaac Lab, training loco-manipulation policies through a sequential curriculum spanning 13 levels from stationary reaching to walking with variable-orientation targets. In standardized evaluation, dual-critic policies reach targets 3.5$\times$ faster (6.5 vs. 22.6 simulation steps), achieve 2$\times$ higher throughput (14.3 vs. 7.0 validated reaches per 1,000 steps), and attain higher validated reach rates (65.2% vs. 53.8%) compared to the unified-critic policy. Notably, additional anti-gaming reward mechanisms provide no further improvement beyond the architectural change alone (60.9% vs. 65.2%). These results have direct implications for the emerging paradigm of RL fine-tuning of imitation-learned policies: when refining a pre-trained manipulation policy with RL, a unified critic risks suppressing the learned behavior through competing locomotion gradients. These findings demonstrate that critic architecture is a primary - and often overlooked - design choice in multi-objective humanoid RL, with greater impact than reward engineering on reaching efficiency.

14.
bioRxiv (Bioinfo) 2026-06-21

SPA-C: an hybrid tool to accurately scaffold genomes using Hi-C and Deep-Learning

Genome assembly is a computational pipeline designed to reconstruct chromosomes from small sequencing reads. Following their assembly, contiguous sequences (contigs) are arranged into chromosome-long sequences during scaffolding. Hi-C, a long-range linkage information between regions of the genome widely used in recent large sequencing projects, is often required to correctly order contigs. Several tools have been developed to automate this task following either statistical or deep-learning approaches. Statistical approaches summarise 2D Hi-C matrices into contact densities across sequences, thus ignoring informative visual patterns. The sole existing deep-learning tool uses a transformer-based computer vision model to correct the assembly. It has been trained on several species and uses Hi-C matrices directly. Yet it comes as a supplementary step in the scaffolding process, introducing extra computation time, and has been trained on a dataset that might contain labelling errors, which could provide sub-optimal results. We propose SPA-C, an hybrid pipeline combining the strengths of both approaches. Linkage prediction is handled with a frugal CNN-based model and a graph-solving algorithm is used to generate the scaffolds. Through our input's design, the model is able to both correct errors within assemblies and link contigs, leveraging small, local Hi-C contact matrices. We handled low-complexity regions that might induce erroneous predictions using an external tool, improving the overall accuracy of generated assemblies. On a benchmark of six various genomes and four standard metrics, SPA-C outperformed four out of four state-of-the-art methods while achieving comparable start-to-end computation time.Python and Bash scripts are available on GitHub (https://github.com/SPA-C/SPA-C.git) and Zenodo (https://doi.org/10.5281/zenodo.19000361).

15.
arXiv (CS.AI) 2026-06-24

TIP-Search: Time-Predictable Inference Scheduling for Market Prediction under Uncertain Load

Authors:

arXiv:2506.08026v4 Announce Type: replace Abstract: Real-time market prediction services need correct predictions before a decision deadline; a correct prediction delivered late is not usable. TIP-Search studies time-predictable inference scheduling over fixed market predictors under uncertain load. It filters conformal latency-quantile feasible models, dispatches over finite workers, and uses shielded constrained online experts to trade accuracy, queue pressure, and deadline risk. On the optimized deployable pool, TIP-Search reaches 0.994 raw accuracy and 0.991 timely accuracy. On official TLOB FI-2010 h=10, TIP-Search++ raises timely accuracy from 0.156 to 0.239 and deadline satisfaction from 0.391 to 0.962. In matched h10 profiled systems replay, OCO-ACPO reaches 0.303 timely accuracy and 0.951 deadline satisfaction, with paired gains over RAMSIS/SneakPeek/utility-style comparators of $+0.00285$ timely accuracy ($p=0.0118$) and $+0.0146$ deadline satisfaction ($p=1.5{\times}10^{-5}$). SA-OCO-ACPO improves timely/deadline service by 0.188–0.417 over CPO under nonstationary stress. The claim is a systems scheduling result, not a broad LOB classifier leaderboard.

16.
arXiv (CS.LG) 2026-06-19

Optimal Coarse Correlated Equilibria in Mean Field Games: Linear Programming and No-Regret Learning

arXiv:2606.20062v1 Announce Type: cross Abstract: We introduce optimal coarse correlated equilibria for continuous-time mean field games. A coarse correlated equilibrium is a randomized recommendation scheme from which no player can gain by ignoring the recommendation and switching to an alternative strategy. The problem is as follows: a moderator selects, among all mean-field coarse correlated equilibria, one that optimizes a prescribed performance criterion, which may differ from the representative player's objective. After formulating the problem, we develop a linear programming (LP) formulation, prove the existence of optimal LP coarse correlated equilibria, and relate the LP characterization to the original probabilistic setting. Building on this characterization, we design a no-regret primal-dual algorithm, based on an equivalent Lagrangian formulation of the external-regret constraint, for learning such equilibria. We provide explicit convergence rates for the learning algorithm, and numerical examples illustrate the method.

17.
bioRxiv (Bioinfo) 2026-06-18

Identification of environmental factors and growth stages in the prediction of fibre yield and fibre quality traits in rain-grown cotton

Context Understanding how and when environmental conditions influence overall crop performance is crucial for optimising the development of genotypes to a specific breeding target environment. We focused on economically important traits of Australian rain-grown cotton including fibre yield and quality traits, which have not been investigated comprehensively. The aim of the study was to identify relevant environmental factors, and the timing and extent of their impact on rain-grown cotton production. Methods We used a data driven approach to analyse the relationship between ten climate related environmental factors across various plant growth stages and eight fibre yield and quality traits, using a large-scale field dataset of 9,283 records collected over 23 years at 4 locations, with 53 unique year-location combinations. We applied eight complementary statistical models including stepwise, penalised and Bayesian linear regression, regression-tree based ensemble methods and deep learning frameworks to (1) select the most essential environmental covariates affecting rain-grown cotton production, and (2) evaluate the predictive performance of these models. Results The environmental impacts on rain-grown cotton production were trait and growth-stage specific. Number of rainy days and solar radiation were identified as the most influential environmental factors for fibre yield traits, vapour pressure deficit at maximum daily temperature was the most influential factor for majority of fibre quality traits. However, each analysed trait was influenced by multiple environmental factors across multiple growth stages (rather than a single factor or a single growth stage). These influential covariates explained a wide range of variation in the traits, accounting for 5.8% to 68.2%. Using the best-fit random forest model, our findings revealed non-linear relationships between key environmental covariates and the traits. Conclusions Environmental factors at different rain-grown cotton growth stages are key determinants for the performance of end-of-season fibre yield and fibre quality parameters. These findings highlight the need to account for environment conditions when developing cotton varieties optimised for rain-grown production systems. Potential strategies are proposed whereby these key environmental factors can be used to increase the rate of genetic gain in rain-grown cotton production systems. Implications The results of this study will be crucial for future genetic evaluations and analyses of genotype-by-environment interaction effects in rain-grown cotton, which must account for the influence of the environment on plant performance. Furthermore, these methods can be applied to other species to identify critical growth stages and environmental factors which most influence crop performance.

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

CoffeeBench: Benchmarking Long-Horizon LLM Agents in Heterogeneous Multi-Agent Economies

arXiv:2606.16613v1 Announce Type: new Abstract: As LLM agents become capable of increasingly long-horizon tasks, evaluating their performance in economic systems is becoming increasingly important. Unlike existing benchmarks that primarily evaluate a single agent interacting with a passive environment, economic systems are inherently multi-agent, requiring autonomous agents to communicate, negotiate, and transact while pursuing their own objectives over extended periods. We introduce CoffeeBench, a benchmark for evaluating LLM agents in a long-horizon multi-agent economy composed of heterogeneous firms. In CoffeeBench, two farmers, two roasters, and two retailers autonomously operate their businesses over a 90-day simulation, each seeking to maximize cumulative net income through communication and transactions while managing cash, inventory, and pricing. The evaluated model controls one coffee roaster, while the remaining firms are controlled by fixed reference agents. Across several recent open-weight and proprietary LLMs, all models outperform a passive baseline that takes no actions, with most achieving positive net income. Analysis of agent behavior reveals substantial differences in long-horizon economic interaction: higher-performing models communicate more actively with other firms, whereas Claude~Haiku~4.5 exhibits an idle-drift failure mode, repeatedly choosing inaction despite producing coherent assessments and plans. We release our code and agent trajectories to support future research.

19.
bioRxiv (Bioinfo) 2026-06-15

oxo-flow: compiled, memory-safe bioinformatics workflow orchestration

Authors:

Bioinformatics analyses depend on workflow engines to coordinate dozens of computational tools across complex dependency chains. The most widely adopted engines-Snakemake, Nextflow, the Common Workflow Language (CWL), and the Workflow Description Language (WDL)-run on interpreted or just-in-time (JIT) compiled language runtimes, incurring hundreds of milliseconds of startup latency and providing no compile-time safety guarantees from the host language. We developed oxo-flow, a workflow engine written in Rust that compiles to a single native binary. On an Apple M5 processor, oxo-flow parses, validates, and dry-runs a production-scale workflow in roughly 22 milliseconds-before Snakemake or Nextflow have finished loading their runtime environments. Peak memory usage is 16 megabytes, representing six- to seven-fold reductions relative to Snakemake and Nextflow. Dry-run latency is essentially independent of workflow size: a hundred-fold increase in rule count adds approximately 0.4 milliseconds. oxo-flow integrates 31 command-line tools, a REST interface with 60 endpoints, an embedded web application, and native cluster submission into a single 10-megabyte binary. It provides per-rule environment isolation across seven backends, checkpoint-based fault tolerance with cryptographic output verification, and a formal installation and operational qualification protocol for regulated laboratory environments. Ten curated workflows and three demonstration pipeline repositories are available. oxo-flow is freely available under Apache License 2.0 at https://github.com/Traitome/oxo-flow.

20.
arXiv (CS.CV) 2026-06-16

XMedFusion: A Knowledge-Guided Multimodal Perception and Reasoning Framework for Autonomous Medical Systems

Autonomous medical and robotic systems increasingly rely on intelligent perception and reasoning capabilities to interpret visual data and support clinical decision making. Radiology report generation represents a critical component of such automated diagnostic workflows, yet existing end-to-end multimodal models often suffer from weak visual grounding, resulting in unreliable interpretations and omission of subtle clinical findings. This paper presents XMedFusion, a modular AI framework designed as an intelligent perception and reasoning module for autonomous medical systems. The proposed framework decomposes visual information into coordinated functional components that emulate expert-driven analysis, including a visual perception agent that extracts image-grounded evidence, a knowledge graph construction agent that structures clinically relevant findings, and a retrieval-guided drafting process that ensures a consistent reporting structure. A synthesis agent iteratively integrates visual and structured evidence through reasoning-driven verification to produce reliable and interpretable diagnostic outputs. Experimental evaluation on a public chest radiograph dataset demonstrates significant improvements over baseline vision-language models, achieving gains from 0.0493 to 0.3359 in BLEU-1, 0.0863 to 0.2440 in ROUGE-L, and 0.0829 to 0.1708 in METEOR, along with substantial improvements in semantic evaluation metrics such as Consistency (2.38 to 7.80) and Accuracy (2.34 to 6.93). The results highlight the effectiveness of structured multi-agent perception and reasoning for enhancing robustness, transparency, and automation in intelligent medical imaging systems, enabling integration into autonomous healthcare and robotic diagnostic workflows.

21.
medRxiv (Medicine) 2026-06-11

Plasma protein prioritisation in rheumatoid arthritis reveals druggable targets and shared biology with cardiovascular diseases

Abstract Background Rheumatoid arthritis (RA) is an autoimmune inflammatory disease with complex and incompletely understood molecular mechanisms. Understanding circulating proteins associated with RA may improve understanding of disease biology and clarify its pathological links with cardiometabolic comorbidities. Methods A proteome-wide two-sample Mendelian randomisation (MR) drug target analysis was conducted using plasma proteins measured in 54,219 participants from the UK Biobank Pharma Proteomics Project as exposures and RA and cardiometabolic diseases as the outcomes. Summary statistics for RA included 53,663 cases and 1,070,200 controls. Colocalisation analysis was performed to confirm shared single causal variants and prioritise RA proteins supported by both MR and colocalisation. The prioritised proteins were then evaluated in the Accelerating Medicines Partnership RA Phase II synovial single-cell dataset for cell-type expression patterns. Druggability was then assessed followed by analysis of genetic overlap between RA-associated proteins and cardiometabolic diseases. Results 37 plasma proteins had a causal effect on RA risk, supported by combined evidence from MR and conditional colocalisation. In synovial tissue, TPPP3, RARRES2, AKAP12, and GGT5 were predominantly expressed in stromal and endothelial cell clusters. Druggability assessment identified IFNGR2, IL6R, CD40, and FCGR2B as Tier 1 targets. However, several biologically relevant proteins, including RARRES2, AKAP12, TPPP3, and SNX2, had limited available druggability data. Genetic overlap analysis demonstrated shared protein signals between RA and cardiovascular diseases, including overlap of RARRES2 and TPPP3 with coronary artery disease (CAD) and FCGR2B with atrial fibrillation (AF). To approximate the therapeutic effect of target inhibition, the direction of effect estimates for proteins showing overlap between RA-CAD and RA-AF was reversed. Conclusion This study identified circulating proteins involved in RA pathogenesis and reveals shared mechanisms between RA and cardiovascular diseases. While some proteins showed clear translational potential targets, several prioritised proteins had limited available druggability information and could not be confidently classified. Addressing these gaps may help identify new targets relevant to RA management. Future work should also use phenome-wide MR studies to evaluate potential on-target adverse effects of protein inhibition across RA-CAD and RA-AF.

22.
medRxiv (Medicine) 2026-06-24

Mask-Based Breath Sampling for Detection of Pseudomonas aeruginosa in Adults with Cystic Fibrosis and Bronchiectasis

Background: Monitoring Pseudomonas aeruginosa (P. aeruginosa) infection in people with cystic fibrosis (pwCF) is essential for early detection, targeted treatment, and prevention of chronification. Sputum culture is the current standard, yet many patients, particularly those receiving CFTR modulator therapy, struggle to expectorate sputum. Microbial aerosols from the respiratory tract offer a non-invasive alternative. This proof-of-principle study assessed the accuracy and feasibility of the AveloMask, a novel breath aerosol collection kit paired with qPCR detection. Methods: Adult pwCF and bronchiectasis patients attending routine monitoring visits and healthy controls were enrolled in a cross-sectional study. Participants wore the mask for 30 minutes, followed by 20 instructed coughs. Mask filters were tested with a triplex qPCR assay targeting P. aeruginosa specific ecfX and gyrB, and human RPP30 as an endogenous control. Accuracy was evaluated using a composite reference standard (sputum culture and PCR). Results: Of 25 patients enrolled, 23 were included in the analyses. Sensitivity was 12/19 (63.2%) for breath qPCR versus 15/19 (78.9%) for sputum culture. Breath qPCR missed 5 cases detected by sputum culture but detected 2 sputum culture-negative/qPCR-positive cases. Specificity of breath qPCR was 100% in 4 patients and 15 healthy controls. RPP30 was detected in all mask samples. AveloMask was perceived as easy to use, with many patients preferring it over sputum collection. Discussion: Mask-based breath collection demonstrated promising diagnostic accuracy for detection of P. aeruginosa. Breath sampling may complement or partially substitute sputum-based diagnostics, especially in patients unable to expectorate. Further studies are needed to define its clinical role.

23.
PLOS Medicine 2026-05-14

Antibody fine specificity correlates with protection from malaria for the RTS,S vaccine in young African children: A post hoc analysis of a phase IIb randomised controlled trial

Authors:

by Alessia Hysa, D. Herbert Opi, Joshua Waterhouse, Sandra Chishimba, Jessica L. Horton, Natalie Kingston, Hans J. Netter, David Wetzel, Michael Piontek, Gaoqian Feng, Jahit Sacarlal, Carlota Dobaño, Liriye Kurtovic, James G. Beeson Background The RTS,S/AS01 malaria vaccine was recently approved for implementation in children, but only provides modest and short-lived efficacy against malaria. RTS,S targets a portion of the Plasmodium falciparum (Pf) circumsporozoite protein (CSP), comprising the central NANP-repeat region and C-terminal domain. Mechanisms of immunity and correlates of protection for the RTS,S vaccine are not well defined, hindering progress towards generating highly effective CSP-based vaccines. Methods and findings We investigated epitope specificity and cross-reactivity of vaccine-induced antibodies to six peptides representing CSP epitopes in the N-terminal and central NANP-repeat region. We evaluated antibody reactivity in preclinical mouse vaccine studies, among CSP-specific monoclonal antibodies (mAbs), and in a large RTS,S phase IIb clinical trial in young children 1–4 years old (n = 735).The preclinical mouse vaccine studies and CSP-specific mAbs were used to initially evaluate IgG responses to the six peptides. Mice immunised with the central NANP-repeat region had IgG with cross-reactivity to an epitope in the N-terminal region. Additionally, we demonstrated that a single CSP-specific mAb could display cross-reactivity to several CSP epitopes. Through post hoc quantification and analysis of antibody responses in the RTS,S phase IIb clinical trial, we found that a subset of children generated IgG with specificity for a short NANP-repeat epitope (NANP2; amino acid sequence: NANPNANP) and cross-reactivity to an N-terminal epitope (J1; amino acid sequence: KQPADGNPDPNANPN). Notably, children with high IgG responses to NANP2 and J1 had a significantly reduced risk of clinical malaria, compared to children with low responses (IgG to NANP2 (aHR: 0.838 (95% CI [0.716, 0.981]; p = 0.028)) and J1 (aHR: 0.718 (95% CI [0.611, 0.844]; p 

24.
arXiv (CS.AI) 2026-06-17

Conservation Laws for Modern Neural Architectures

arXiv:2606.17816v1 Announce Type: cross Abstract: Understanding gradient descent dynamics is key to explaining the success of over-parameterized models, where implicit bias manifests through conservation laws in gradient flow. While such laws are well understood for linear and ReLU networks, they remain largely unexplored for modern architectures. This work develops a unified framework to characterize conservation laws for contemporary models, including feedforward networks with GELU, SiLU, and SwiGLU activations, multihead attention with sinusoidal and rotary positional encodings, and Mixture-of-Experts architectures under diverse gating designs. Our theoretical findings are supported by experiments that validate the predicted invariants.

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

C-QUERI: Congressional Questions, Exchanges, and Responses in Institutions Dataset

Questions in political interviews and hearings serve strategic purposes beyond information gathering including advancing partisan narratives and shaping public perceptions. However, these strategic aspects remain understudied due to the lack of large-scale datasets for studying such discourse. Congressional hearings provide an especially rich and tractable site for studying political questioning: Interactions are structured by formal rules, witnesses are obliged to respond, and members with different political affiliations are guaranteed opportunities to ask questions, enabling comparisons of behaviors across the political spectrum. We develop a pipeline to extract question-answer pairs from unstructured hearing transcripts and construct a novel dataset of committee hearings from the 108th–117th Congress. Our analysis reveals systematic differences in questioning strategies across parties, by showing the party affiliation of questioners can be predicted from their questions alone. Our dataset and methods not only advance the study of congressional politics, but also provide a general framework for analyzing question-answering across interview-like settings.