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

Can Neural Networks Achieve Optimal Computational-statistical Tradeoff? An Analysis on Single-Index Model

arXiv:2606.15219v1 Announce Type: new Abstract: In this work, we tackle the following question: Can neural networks trained with gradient-based methods achieve the optimal computational-statistical tradeoff in learning Gaussian single-index models? Prior research has shown that any polynomial-time algorithm under the statistical query (SQ) framework requires $\Omega(d^{s^\star/2}\lor d)$ samples, where $s^\star$ is the generative exponent representing the intrinsic difficulty of learning the underlying model. However, it remains unknown whether neural networks can achieve this sample complexity. Inspired by prior techniques such as label transformation and landscape smoothing for learning single-index models, we propose a unified gradient-based algorithm for training a two-layer neural network in polynomial time. Our method is adaptable to a variety of loss and activation functions, covering a broad class of existing approaches. We show that our algorithm learns a feature representation that strongly aligns with the unknown signal $\theta^\star$, with sample complexity $\widetilde{O} (d^{s^\star/2} \lor d)$, matching the SQ lower bound up to a polylogarithmic factor for all generative exponents $s^\star\geq 1$. Furthermore, we extend our approach to the setting where $\theta^\star$ is $k$-sparse for $k = o(\sqrt{d})$ by introducing a novel weight perturbation technique that leverages the sparsity structure. We derive a corresponding SQ lower bound of order $\widetilde{\Omega}(k^{s^\star})$, matched by our method up to a polylogarithmic factor. Our framework, especially the weight perturbation technique, is of independent interest, and suggests potential gradient-based solutions to other problems such as sparse tensor PCA.

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

Deep Q-Learning on Hölder Spaces

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arXiv:2606.16846v1 Announce Type: cross Abstract: We study the operator-theoretic core of Q-learning in continuous-time stochastic control with continuous states and actions. In value-based reinforcement learning, each Q-learning or DQN update is built from a Bellman optimality target; our analysis isolates this target in a diffusion setting and studies its regularity and approximation complexity. Under uniform ellipticity and Hölder-regular coefficients, we show that a Bellman update maps bounded inputs into an anisotropic regularity class, smoothing the state variable while leaving only Lipschitz dependence on the action variable. This yields a compact family of Bellman iterates and motivates a tensor-product DeepONet architecture adapted to the mixed regularity of the problem. We then derive explicit approximation and resource bounds, together with a stiffness–complexity trade-off as the time step $\delta \to 0$. The resulting theory makes a direct contribution to Q-learning theory at the level of Bellman target regularity and approximation in continuous stochastic control. At the same time, we do not claim a full convergence theorem for practical sampled Q-learning with exploration, replay, and stochastic gradient updates.

03.
medRxiv (Medicine) 2026-06-11

Population-scale detection of methylation outliers from long-read genome sequencing

Background: Aberrant DNA methylation can mediate the functional effects of rare genetic variation and contribute to imprinting disorders, repeat expansion diseases, and other pathogenic regulatory mechanisms. Long-read sequencing technologies now enable genome-wide detection of CpG methylation alongside genetic variation from a single assay. However, methods for systematic identification and interpretation of methylation outliers from long-read sequencing data remain limited. Methods: We developed METAFORA, a computational workflow for detecting methylation outlier regions from PacBio and Oxford Nanopore long-read sequencing data. METAFORA constructs population-level methylation references, segments the genome into correlated CpG blocks, infers technical and biological sources of variation through hidden factor estimation, models uncertainty due to variable depth sequencing, and computes covariate-adjusted methylation outlier scores for individual samples. We applied METAFORA across large long-read sequencing cohorts and integrated methylation outliers with multi-omic data. METAFORA is implemented as a snakemake workflow available at https://github.com/tjense25/METAFORA. Results: METAFORA identified methylation outlier regions associated with rare structural variants, tandem repeat expansions, and imprinting abnormalities. We found outlier regions were enriched for molecular outliers across transcriptomic and chromatin accessibility datasets, supporting their functional relevance in gene regulation. In a representative case, METAFORA identified an imprinting defect affecting the GNAS locus associated with an STX16 deletion. Conclusions: METAFORA enables scalable detection and interpretation of methylation outliers from long-read sequencing data and provides a framework for integrating epigenetic outliers with genomic and multi-omic analyses. These approaches may improve interpretation of rare regulatory variation and support discovery of clinically relevant epigenetic abnormalities in genomic medicine.

04.
bioRxiv (Bioinfo) 2026-06-12

Systematic functional annotation of thousands of BAHD acyltransferases in plant genomes using Protein Language Model and phylogenomic tools

The functional annotation of plant genes lags significantly behind their genomic annotation. Closing this gap requires thorough cataloging of reported protein activities alongside predictive methods that scale beyond sequence-similarity inference. Focusing on the BAHD acyltransferase enzyme family as a model, we assembled FuncZymeDB-BAHD, a large database of 2,705 LLM-retrieved and curated enzyme-acceptor-donor activities covering 336 BAHDs from 156 plant species, a 2-to-6-fold expansion over Swiss-Prot and prior compilations. We further developed FuncPred-OG, which maps queries to orthologous groups and previously characterized enzymes in FuncZymeDB-BAHD, returning hits with high evidence provenance. FuncPred-OG enabled functional prediction of over half of BAHDs across 85 plant proteomes, of which five novel predictions were validated via in vitro assays and recent studies. For the remaining BAHDs without FuncPred-OG annotation, we developed FuncPred-AI, where logistic-regression classifiers trained on protein language model embeddings achieved high Area-Under-the-Precision-Recall-curve (AUPR) scores and correct-hit rates up to 93%. FuncPred-AI yielded >1 probable donor/acceptor annotation for 99.9% (8894/8897) of BAHDs in our pan-plant dataset. Finally, the FuncPred workflow and datasets were deployed on a web portal for broader utilization, potentially reducing experimentalist efforts for selecting candidates from days to minutes. Overall, this framework provides a generalizable template for functional annotation of entire enzyme families.

05.
arXiv (CS.AI) 2026-06-15

Q-Net: Queue Length Estimation via Kalman-based Neural Networks

arXiv:2509.24725v4 Announce Type: replace-cross Abstract: Estimating queue lengths at signalized intersections is a long-standing challenge in traffic management. Partial observability of vehicle flows complicates this task despite the availability of two privacy-preserving data sources: (i) aggregated vehicle counts from loop detectors near stop lines, and (ii) aggregated floating car data (aFCD) that provide segment-wise average speed measurements. However, how to integrate these sources with differing spatial and temporal resolutions for queue length estimation is rather unclear. Addressing this question, we present Q-Net: a queue estimation framework built upon a state-space formulation. This design addresses key challenges in queue modeling, such as violations of traffic conservation assumptions. Q-Net follows the Kalman predict-update structure and maintains physical interpretability in both the state evolution and measurement models. Q-Net uses an AI-augmented Kalman filter to learn time-varying gain dynamics from data. The framework supports real-time implementation and improves spatial transferability by grouping aFCD measurements into fixed-size local groups, making the number of learnable parameters independent of section length. Evaluations on urban main roads in Rotterdam, the Netherlands, show that Q-Net outperforms baseline methods, tracks queue formation and dissipation accurately, and mitigates aFCD-induced delays. By combining data efficiency, interpretability, real-time applicability, and spatial transferability, Q-Net makes accurate queue length estimation possible without costly sensing infrastructure like cameras or radar.

06.
medRxiv (Medicine) 2026-06-15

Dysplasia-Stratified Management of Barrett's Esophagus: An Incidence-Based U.S. Cost-Effectiveness Analysis

作者:

Background and Aims Barrett's esophagus (BE) is the principal precursor of esophageal adenocarcinoma (EAC), whose incidence has risen sharply in Western countries since the 1960s. Effective, dysplasia stratified surveillance strategies are needed to prevent progression. This study evaluated the cost effectiveness of dysplasia stratified surveillance intervals and endoscopic eradication therapy (EET) across the BE spectrum. Methods We developed an incidence-based Markov state transition model of BE progression calibrated to U.S. epidemiologic data from a healthcare sector perspective over a lifetime horizon. Four hypothetical cohorts of 50-year-old individuals with short segment BE (SSBE), nondysplastic BE (NDBE), low grade dysplasia (LGD), or high-grade dysplasia (HGD) were evaluated. Strategies included no surveillance; surveillance at 1-, 2-, 3-, 4-, 5-, or 10-year intervals; standard or AI assisted endoscopy; non endoscopic screening (sponge, breath, miRNA tests); and EET for LGD and HGD. Outcomes included costs, quality adjusted life years (QALYs), incremental cost effectiveness ratios (ICERs), net monetary benefits (NMBs), EAC cases, and EAC-related deaths. Sensitivity analyses used a willingness to pay threshold of US$100,000 per QALY. Results No surveillance was the most cost-effective strategy for SSBE and NDBE. For LGD, upfront EET was more cost effective than all surveillance strategies, with results sensitive to EAC incidence and recurrence. For HGD, EET was cost saving and yielded the greatest QALYs, with findings robust in 99.9% of simulations. EET prevented 12,614 and 44,295 EAC related deaths per 100,000 individuals with LGD and HGD, respectively. Conclusion Dysplasia-stratified management is essential for optimizing surveillance and treatment strategies in BE. Any degree of dysplasia should receive EET followed by targeted post-treatment monitoring, establishing EET as the central therapeutic pathway for dysplastic BE.

07.
arXiv (CS.CL) 2026-06-11

An Ontology-Guided Multi-Anchor Graph Retrieval Framework for Traffic Legal Liability Determination

Traffic law liability determination is critical for assigning legal penalties, requiring the simultaneous identification of interdependent statutory provisions across multiple legal dimensions. However, existing retrieval-augmented generation methods suffer from a multi-dimensional retrieval bottleneck: single axis architectures compress complex legal queries into a single pathway, causing interdependent statutory dimensions to be overlooked. To address this, we propose OMAGR, an ontology-guided framework that decomposes queries into ontology-aligned anchors and executes parallel graph retrieval across each dimension, ensuring independent retrieval across dimensions before fusion. To evaluate the proposed method, we created the TrafficLaw-QA dataset, an expert-validated benchmark dataset containing 200 questions and 527 legal provisions. Results show that TrafficOmni-RAG outperforms baselines on Context Precision and Faithfulness metrics. The findings demonstrate that parallel multi-anchor retrieval effectively resolves the multi-dimensional retrieval bottleneck, offering a promising direction for traffic law liability determination research.

08.
arXiv (CS.CV) 2026-06-16

A Generalizable Light Transport 3D Embedding for Global Illumination

Global illumination (GI) is essential for realistic rendering but remains computationally expensive due to the complexity of simulating indirect light transport. Recent neural methods have mainly relied on per-scene optimization, sometimes extended to handle changes in camera or geometry. Efforts toward cross-scene generalization have largely stayed in 2D screen space, such as neural denoising or G-buffer based GI prediction, which often suffer from view inconsistency and limited spatial understanding. We propose a generalizable 3D light transport embedding that approximates global illumination directly from 3D scene configurations, without using rasterized or path-traced cues. Each scene is represented as a point cloud with geometric and material features. A scalable transformer models global point-to-point interactions to encode these features into neural primitives. At render time, each query point retrieves nearby primitives via nearest-neighbor search and aggregates their latent features through cross-attention to predict the desired rendering quantity. We demonstrate results on diffuse global illumination prediction across diverse indoor scenes with varying layouts, geometry, and materials. The embedding trained for irradiance estimation can be quickly adapted to new rendering tasks with limited fine-tuning. We also present preliminary results for spatial-directional radiance field estimation for glossy materials and show how the normalized field can accelerate unbiased path guiding. This approach highlights a path toward integrating learned priors into rendering pipelines without explicit ray-traced illumination cues.

09.
arXiv (CS.LG) 2026-06-12

Variational Graph Neural Networks for Uncertainty Quantification in Inverse Problems

arXiv:2603.29515v2 Announce Type: replace Abstract: The increasingly wide use of deep machine learning techniques in computational mechanics has significantly accelerated simulations of problems that were considered unapproachable just a few years ago. However, in critical applications such as Digital Twins for engineering or medicine, fast responses are not enough; reliable results must also be provided. In certain cases, traditional deterministic methods may not be optimal as they do not provide a measure of confidence in their predictions or results, especially in inverse problems where the solution may not be unique or the initial data may not be entirely reliable due to the presence of noise, for instance. Classic deep neural networks also lack a clear measure to quantify the uncertainty of their predictions. In this work, we present a variational graph neural network (VGNN) architecture that integrates variational layers into its architecture to model the probability distribution of weights. Unlike computationally expensive full Bayesian networks, our approach strategically introduces variational layers exclusively in the decoder, allowing us to estimate cognitive uncertainty and statistical uncertainty at a relatively lower cost. In this work, we validate the proposed methodology in two cases of solid mechanics: the identification of the value of the elastic modulus with nonlinear distribution in a 2D elastic problem and the location and quantification of the loads applied to a 3D hyperelastic beam, in both cases using only the displacement field of each test as input data. The results show that the model not only recovers the physical parameters with high precision, but also provides confidence intervals consistent with the physics of the problem, as well as being able to locate the position of the applied load and estimate its value, giving a confidence interval for that experiment.

10.
arXiv (CS.CV) 2026-06-16

Dynamic Black-hole Emission Tomography with Physics-informed Neural Fields

With the success of static black-hole imaging, the next frontier is the dynamic and 3D imaging of black holes. Recovering the dynamic 3D gas near a black hole would reveal previously-unseen parts of the universe and inform new physics models. However, only sparse radio measurements from a single viewpoint are possible, making the dynamic 3D reconstruction problem significantly ill-posed. Previously, BH-NeRF addressed the ill-posed problem by assuming Keplerian dynamics of the gas, but this assumption breaks down near the black hole, where the strong gravitational pull of the black hole and increased electromagnetic activity complicate fluid dynamics. To overcome the restrictive assumptions of BH-NeRF, we propose PI-DEF, a physics-informed approach that uses differentiable neural rendering to fit a 4D (time + 3D) emissivity field given EHT measurements. Our approach jointly reconstructs the 3D velocity field with the 4D emissivity field and enforces the velocity as a soft constraint on the dynamics of the emissivity. In experiments on simulated data, we find significantly improved reconstruction accuracy over both BH-NeRF and a physics-agnostic approach. We demonstrate how our method may be used to estimate other physics parameters of the black hole, such as its spin.

11.
arXiv (quant-ph) 2026-06-15

Quantum-Classical Hierarchical Equations of Motion

作者:

arXiv:2606.14363v1 Announce Type: new Abstract: We develop a quantum-classical hierarchical equations of motion (QC-HEOM) approach for simulating non-Markovian open quantum systems. The method combines the ensemble-averaged classical path reference of the quantum-classical path integral formalism with a hierarchy of auxiliary quantum influence functionals. By incorporating thermal fluctuations through an ensemble average over reference trajectories, the hierarchy is required to represent only the residual quantum memory associated with the imaginary part of the bath response function. Consequently, unlike conventional hierarchical equations of motion, QC-HEOM does not require Matsubara or Padé expansions of the thermal kernel and exhibits only weak temperature dependence of the hierarchy size. Furthermore, because thermal fluctuations are supplied through reference classical trajectories, the framework naturally extends beyond harmonic baths and enables the incorporation of anharmonic and molecular environments through externally generated trajectories. We derive the formalism and demonstrate its exactness for a harmonic bath. Applications to an asymmetric spin-boson model and the seven-site Fenna–Matthews–Olson complex illustrate the accuracy of QC-HEOM. It reproduces benchmark quasi-adiabatic path integral and hierarchical equations of motion results while requiring substantially fewer auxiliary objects, particularly at low temperatures. These results establish QC-HEOM as an efficient framework for treating residual quantum memory in quantum-classical descriptions of open-system dynamics. The separation of thermal fluctuations from residual quantum memory through the use of Wigner trajectories provides an approximate route toward hierarchical treatments of complex anharmonic environments that are inaccessible to conventional HEOM approaches.

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

Bridging the Usability Gap: Lessons from Interpreting Studies for Machine Interpreting Design

Machine interpreting (MI), the live, real-time branch of speech translation, has achieved remarkable progress on standard benchmarks, with some systems approaching human parity on textual fidelity. Yet the user experience remains far inferior to interpreter-mediated communication, revealing what we term the accuracy illusion: systems that appear accurate on paper but fail in practice to support smooth, goal-oriented interaction. This paper defines MI as a distinct subfield of speech translation, with its own characteristics and the need for evaluation methods grounded in communicative effectiveness rather than isolated fidelity metrics. Drawing on insights from interpreting studies, we identify critical dimensions of professional interpreting practice that are overlooked by current systems, and consolidate them into three interdependent design priorities for future MI: agency (context-sensitive initiative and repair), grounding (multimodal and discourse-level situational awareness), and experience (adaptive improvement through real interaction). Together, these priorities chart a path toward closing the usability gap and enabling systems that can sustain authentic multilingual communication in real time.

13.
arXiv (CS.CL) 2026-06-15

MASLab: A Unified and Comprehensive Codebase for LLM-based Multi-Agent Systems

LLM-based multi-agent systems (MAS) have demonstrated significant potential in enhancing single LLMs to address complex and diverse tasks in practical applications. Despite considerable advancements, the field lacks a unified codebase that consolidates existing methods, resulting in redundant re-implementation efforts, unfair comparisons, and high entry barriers for researchers. To address these challenges, we introduce MASLab, a unified, comprehensive, and research-friendly codebase for LLM-based MAS. (1) MASLab integrates over 20 established methods across multiple domains, each rigorously validated by comparing step-by-step outputs with its official implementation. (2) MASLab provides a unified environment with various benchmarks for fair comparisons among methods, ensuring consistent inputs and standardized evaluation protocols. (3) MASLab implements methods within a shared streamlined structure, lowering the barriers for understanding and extension. Building on MASLab, we conduct extensive experiments covering 10+ benchmarks and 8 models, offering researchers a clear and comprehensive view of the current landscape of MAS methods. MASLab will continue to evolve, tracking the latest developments in the field, and invite contributions from the broader open-source community.

14.
arXiv (CS.LG) 2026-06-19

Enhancing Graph Neural Networks Using Proximity Graphs for Dust Source Emission Forecasting

arXiv:2606.19825v1 Announce Type: new Abstract: Accurate prediction of dust source emissions is critical for mitigating the significant environmental and health hazards posed by dust storms. Traditional forecasting methods often struggle to capture the complex spatiotemporal dynamics of these phenomena. In this paper, we demonstrate that proximity graphs enable Graph Neural Networks (GNNs) to effectively model the intricate spatial and temporal relationships between data points. Specifically, we use proximity graphs–such as Delaunay triangulation, Gabriel graph, k-Nearest Neighbor graph, and Yao graph–as the input for GNNs (including GraphSAGE, Graph Convolutional Networks, and Graph Attention Networks) to perform message passing. Our approach highlights the effectiveness of integrating proximity graphs with GNNs for robust and accurate dust source forecasting. To emphasize the importance of proximity graph representations, we compare our method against GNNs using random graphs for message passing. The results show that GNNs with proximity graphs significantly outperform those with random graphs and are also far superior to Long Short-Term Memory (LSTM) model in dust source emission forecasting.

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

RLCSD: Reinforcement Learning with Contrastive On-Policy Self-Distillation

On-policy self-distillation (OPSD) provides dense, token-level supervision for reasoning models by aligning a model's own distribution with the distribution it produces under privileged context, typically a verified solution. However, we show that the learning signal drawn from this distributional gap concentrates on style tokens rather than task-bearing ones, as the hinted model tends to produce more direct, shorter outputs. We term this pathology privilege-induced style drift, which destabilizes training or causes response length to shrink. To address this, we propose RLCSD (Reinforcement Learning with Contrastive on-policy Self-Distillation), which mitigates this drift by contrasting the teacher-student gap under a correct hint against that under a wrong hint, suppressing the style shift that conditioning on a hint tends to induce regardless of correctness, and yielding a signal that is more concentrated on task-bearing tokens. Experiments on Qwen3 (1.7B/4B/8B) and Olmo-3-7B-Think across mathematical and logical reasoning show that RLCSD consistently outperforms GRPO and prior OPSD methods. We further show that the contrastive principle is general: it plugs into existing OPSD methods to improve them, and its underlying insight extends to the broader cross-model on-policy distillation setting.

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

NEST3D: A High-Resolution Multimodal Dataset of Sociable Weaver Tree Nests

Sociable weaver nests function as complex ecological structures offering thermoregulatory microhabitats and sustaining diverse species; however, datasets used in prior studies lack fine-grained 3D structural detail. Producing usable and accurate 3D weaver nest data is challenging due to their irregular geometry and integration with complex host vegetation. We bridge this gap with an open-access, 1.4 TB multimodal drone dataset of 104 nest-bearing trees, comprising 27,945 RGB images, 111,780 multispectral images, approximately 781 million 3D points, and expert-annotated semantic segmentation labels. We benchmark semantic segmentation using KPConv, RandLA-Net, and Point Transformer V3, with PT-v3 achieving an mIoU of 86.35% on the test set. While the results demonstrate strong performance for transformer-based and point-wise methods, they also highlight architecture-dependent challenges, particularly for convolution-based approaches such as KPConv. By uniquely combining spectral, spatial, and structural information, the presented dataset advances 3D reconstruction, segmentation, and classification algorithms, enabling ecological applications from nest volume estimation to species conservation, and serves as a demanding benchmark that exposes architecture-dependent performance under extreme class imbalance.

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

INFRAMIND: Infrastructure-Aware Multi-Agent Orchestration

arXiv:2606.11440v1 Announce Type: new Abstract: Existing multi-agent LLM orchestration methods, ranging from brute-force ensembles to learned routers, select models and topologies based on task and model features. However, these methods do not consider the runtime state of the serving infrastructure. On shared GPU clusters under concurrent load, this infrastructure blindness causes systematic resource underutilization: preferred models accumulate deep request queues while equally capable alternatives sit idle. In multi-agent pipelines, where each query triggers multiple sequential model calls, these delays then compound across every downstream step. Closing this gap is challenging because the relevant infrastructure signals (queue depths, KV-cache pressure, latencies) are dynamic and noisy, and they must drive three different decisions: planning, per-step routing, and scheduling. We introduce INFRAMIND, a framework that makes the entire multi-agent stack infrastructure-aware. An infra-aware planner conditions topology and role selection on real-time system load and remaining budget, biasing toward simpler graphs under congestion and richer ones at low load. An infra-aware executor then observes per-model queue depths, cache utilization, and response latencies at each agent step to decide which model to call and how deeply to reason; a budget-aware scheduler further reorders each model's queue so that urgent requests are served first. Cast as a hierarchical constrained MDP and solved end-to-end via reinforcement learning, the system learns to balance quality against latency automatically. Across five benchmarks, INFRAMIND delivers up to +7.6 pp accuracy over the prior baseline at low load with up to 7x lower latency, and sustains up to 99.9% SLO compliance under high load where every baseline drops below 50%.

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

A Distributionally Robust Reinforcement Learning Framework for Constrained Urban EV Dispatch

arXiv:2604.25848v2 Announce Type: replace Abstract: We study city-scale control of electric-vehicle (EV) ride-hailing fleets where dispatch, repositioning, and charging decisions must respect charger and feeder limits under uncertain, spatially correlated demand and travel times. We formulate the problem as a hex-grid semi-Markov decision process (semi-MDP) with mixed actions – discrete actions for serving, repositioning, and charging, together with continuous charging power – and variable action durations. To guarantee physical feasibility during both training and deployment, the policy learns over high-level intentions produced by a masked, temperature-annealed actor. These intentions are projected at every decision step through a time-limited rolling mixed-integer linear program (MILP) that strictly enforces state-of-charge, port, and feeder constraints. To mitigate distributional shifts, we optimize a Soft Actor-Critic (SAC) agent against a Wasserstein-1 ambiguity set with a graph-aligned Mahalanobis ground metric that captures spatial correlations. The robust backup uses the Kantorovich-Rubinstein dual, a projected subgradient inner loop, and a primal-dual risk-budget update. Our architecture combines a two-layer Graph Convolutional Network (GCN) encoder, twin critics, and a value network that drives the adversary. Experiments on a large-scale EV fleet simulator built from NYC taxi data show that PD-RSAC achieves the highest net profit, reaching \$1.22M, compared with \$0.58M-\$0.70M for strong heuristic, single-agent RL, and multi-agent RL baselines, including Greedy, SAC, MAPPO, and MADDPG, while maintaining zero feeder-limit violations.

19.
medRxiv (Medicine) 2026-06-22

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

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

20.
arXiv (CS.CL) 2026-06-19

A Layered Security Framework Against Prompt Injection in RAG-Based Chatbots

Prompt injection is ranked as the most critical vulnerability in large language model (LLM) deployments by the OWASP Top 10 for LLM Applications, yet existing defenses operate at isolated pipeline stages and remain incomplete. Input filters cannot inspect retrieved documents, while output monitors cannot prevent malicious payloads from reaching the model. Consequently, retrieval-augmented generation (RAG) chatbots remain vulnerable to indirect injection, where a poisoned knowledge-base document compromises every user whose query retrieves it. We present a three-layer framework that intercepts both direct and indirect prompt injection throughout the inference pipeline. Layer 1 screens user input using a rule-based pattern library and a fine-tuned semantic anomaly classifier. Layer 2 enforces a provenance-based instruction hierarchy during context assembly, preventing retrieved content from overriding operator policy. Layer 3 audits model output using a policy rule engine and semantic drift detector before delivery. A continuous audit loop aggregates structured logs and supports retraining to adapt the classifier to emerging attack patterns. The framework is model-agnostic and deploys as middleware without modifying the underlying LLM. Evaluation on 5,080 samples across GPT-4o, Llama 3, and Mistral 7B shows that the framework reduces Attack Success Rate (ASR) from 71.4\% to 11.3\%, outperforming the best single-layer baseline by 27.3 percentage points and a published guardrail system by 23.8 percentage points, while maintaining a 4.8\% false positive rate and a median latency overhead of 61.2 ms. Ablation studies confirm that all three layers provide complementary protection and that their combined effect exceeds the sum of individual contributions.

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

Adaptive Inference-Time Scaling via Early-Step Latent Verification for Image Editing

Instruction-based image editing has made notable progress with recent advances in generative models. However, the quality of the edited result is still influenced by the randomly sampled initial noise, particularly in complex editing scenarios. An unsuitable initial noise may lead to unsatisfactory editing results. Recent inference-time scaling methods address this issue by sampling multiple initial noises and selecting better candidates. Nevertheless, most of them follow a decode-then-verify scheme which introduces an efficiency-accuracy trade-off. When decoding is performed after limited inference steps, the decoded images often remain too noisy for reliable assessment, whereas sufficiently denoised images require much higher computational cost. To address this issue, we propose VeriLatent, a plug-and-play adaptive inference-time scaling framework with early-step latent verification for image editing. Specifically, we propose a novel verifier that scores each initial noise through a latent-space editing activation map at an early stage. It identifies promising candidates by assessing whether they can induce an effective edit in the correct region. This enables efficient early pruning without decoding latents into images. Building on this, we further develop an adaptive search strategy for inference-time scaling. It allocates inference budgets according to editing difficulty, thereby reducing the number of function evaluations (NFE). Extensive experiments on multiple benchmarks and different base models demonstrate that VeriLatent consistently improves both editing performance and inference-time scaling efficiency.

22.
arXiv (CS.AI) 2026-06-19

Emyx: Fast and efficient all-atom protein generation

arXiv:2606.19377v1 Announce Type: cross Abstract: Computational enzyme design requires generating proteins that scaffold catalytic residues and ligands, a task that demands both geometric accuracy and structural diversity from the underlying generative model. Current all-atom generators inherit expensive architectures from structure prediction, leading to high training costs and limited sample diversity. We argue that much of this complexity is unnecessary for generators, which condition on sparse geometric constraints rather than rich co-evolutionary signals. Emyx is a 140M-parameter conditional flow matching model that concentrates capacity within standard transformer blocks, replacing heavy embedding stacks with lightweight conditional representations and sparse connectivity. We additionally derive an exact reparametrisation of the flow matching interpolant into the EDM noise-level framework, bridging flow matching training efficiency with state-of-the-art sampling methods designed for diffusion models without retraining. Despite being the smallest model, Emyx outperforms both Proteína-Complexa and RFdiffusion3 against the AME enzyme design benchmark across success rate under strict evaluation requiring both global fold recovery and catalytic geometry accuracy, structural novelty, scaffold diversity, and geometric validity, while training in just $682$ GPU-hours, roughly $4\times$ less than RFdiffusion3.

23.
arXiv (quant-ph) 2026-06-12

Quantum-Driven Neuromorphic Computing for Million-Qubit-Scale Workloads

arXiv:2606.12968v1 Announce Type: new Abstract: We introduce Apollo, a 10000 node p-qubit neuromorphic processor fabricated in 16 nm mixed signal CMOS and operating fully at room temperature with a typical analog core power envelope of about 0.5 W. Its fundamental element, the p-qubit, is a bistable stochastic unit whose continuous time state fluctuations are driven by integrated quantum entropy units that inject true quantum derived randomness. This enables ultrafast stochastic transitions at low energy while preserving a classical state representation. Apollo combines these p-qubits with a high degree Hyperion 256 interconnect topology, allowing efficient embedding of dense Ising and QUBO problems with substantially reduced minor embedding overhead compared with sparse annealing platforms. We show that, through the Suzuki Trotter correspondence, the equilibrium statistics and annealing dynamics of the p-qubit network reproduce key properties of transverse field quantum annealing without cryogenic cooling, long lived coherence, or microwave control. Beyond device level validation, Apollo is evaluated on a three dimensional spin glass benchmark previously used to study quantum advantage in superconducting annealers. Across 300 disorder realizations, Apollo reaches substantially lower ground state energies than reported cryogenic quantum annealing hardware, while remaining distinct from classical simulated annealing and simulated quantum annealing. A 350 nm release candidate device experimentally validates the core p-qubit dynamics, thermodynamic sampling correctness, and continuous time annealing behavior. These results establish Apollo as a room temperature, industrially scalable platform for quantum driven energy based optimization, probabilistic inference, generative modeling, and hybrid classical quantum workflows.

24.
medRxiv (Medicine) 2026-06-15

Midwifery Practice in Conflict Contexts: Lived Experiences from Somalia and Nigeria

Background: Midwives are a central cadre in the health system, particularly in conflict-affected settings where they are sometimes the primary or even only skilled providers available. Yet, despite their critical role, there is limited qualitative evidence capturing their lived experiences and how these shape workforce entry, retention, and overall well-being. Methods: Drawing on a phenomenological research methodology, this qualitative study was embedded within a larger prospective longitudinal cohort of midwifery students and graduates in Somalia and Nigeria. We conducted focus group discussions with graduate midwives (n=48 in Nigeria; n=63 in Somalia) to explore their experiences transitioning into the workforce and their realities working in health systems impacted by conflict and violent insecurity. Data were analysed using inductive thematic analysis. Results: Five themes emerged from the data: (1) job search and workforce entry, which was described as fraught with challenges and shaped by a set of formal systems in Nigeria but informal networks and structural barriers in Somalia (2) working conditions that were marked by resource scarcity, infrastructural challenges, and heavy and unreasonable workloads, (3) safety, security and coping strategies that differed across the two contexts but reflected persistent exposure to violence and a reliance on ad hoc and personal coping in lieu of systematic protection, (4) community perceptions of midwives, shaped and constrained by social and gender norms and (5) mental health and emotional wellbeing, highlighting stress, burnout and moral injury experienced by this cadre. Conclusion: Our findings highlight the profound challenges faced by midwives working in conflict-affected settings, and they shine a light on the urgent need to support and invest in this critical and predominantly female health workforce.

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arXiv (CS.CV) 2026-06-16

CausalDrive: Real-time Causal World Models for Autonomous Driving

World models have emerged as a promising paradigm for scaling autonomous driving (AD) data, yet existing video generative models fall short as interactive simulators. Layout-conditioned renderers rely on "oracle" future trajectories of all background agents, rendering them strictly non-reactive. Conversely, pure action-conditioned predictors lack semantic control over complex interactions and suffer from prohibitive diffusion latencies, hindering closed-loop policy learning. To bridge this gap, we present CausalDrive, a controllable, real-time foundation driving world renderer. CausalDrive operates solely on the initial front-view frame, the ego-vehicle's trajectory, and a macroscopic text prompt. By excluding future NPC layouts, we compel the model to intrinsically predict causal interactions, enabling text-driven control over Driving Sociology, allowing users to dynamically orchestrate diverse counterfactual reactions to identical ego-actions. To overcome the efficiency bottleneck and address the covariate shift in autoregressive generation, we propose a novel Context-Forced DMD architecture. This combines continuous flow-matching with a self-correcting distillation objective, achieving interactive speeds of 12 FPS. This breakthrough transforms the passive video generator into a playable neural simulator. We demonstrate its versatility across three downstream applications: (1) generative closed-loop evaluation with significantly mitigated collision artifacts, (2) large-scale Reinforcement Learning (RL) post-training driven by a Video2Reward module, and (3) real-time human-in-the-loop simulation. Extensive experiments validate that policies trained within CausalDrive's reactive scenarios exhibit superior interaction capabilities in the real world.