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01.
arXiv (CS.LG) 2026-06-18

Acceleration of an algebraic multigrid pressure solver using graph neural networks

arXiv:2606.19251v1 Announce Type: cross Abstract: Solving the pressure-Poisson equation remains the primary computational bottleneck in incompressible unstructured flow solvers primarily due to the inherent sensitivity of traditional linear solvers to mesh irregularities. This work introduces a data-driven algebraic multigrid (AMG) smoother that uses a modified graph convolutional isomorphism network (GCIN). The graph neural network predicts optimal polynomial coefficients to construct a sparse pseudo-inverse operator across diverse grid topologies. The coefficients are optimized to reduce the residual after each V-cycle iteration. By directly capturing the algebraic structure of the system from the sparse coefficient matrix, the proposed method maintains the solver's linearity while adapting to local anisotropies in unstructured grids. Our framework demonstrates significant performance gains by reducing the number of V-cycles required for a given tolerance and delivering wall-clock speedups from 4% to 37% across diverse benchmarks. Notably, the model exhibits robust generalization by maintaining efficiency on meshes up to 128 times larger than those seen in training, and by accelerating the solver's convergence on unseen industry-relevant problems such as the AirfRANS dataset.

02.
arXiv (CS.LG) 2026-06-12

Robustness Verification of Recurrent Neural Networks with Abstraction Refinement

arXiv:2606.12490v1 Announce Type: new Abstract: Certified local robustness verification for recurrent neural networks (RNNs) is challenging because approximation errors introduced by nonlinear relaxations can propagate through recurrent connections and accumulate over time. As a result, scalable linear bound propagation methods often become overly conservative and fail to certify inputs that are in fact robust, especially when many pre-activation intervals cross zero. We propose an abstraction-refinement framework for RNN verification that partitions such intervals to remove the dominant relaxation error: on each refined branch, ReLU becomes exact, and smooth activations such as tanh and sigmoid admit substantially tighter linear envelopes. To control the combinatorial cost of splitting in long sequences, we introduce a SHAP-guided timestep selection strategy that ranks hidden states by their contribution to the verification objective and refines only the most critical timesteps in temporal order. Experiments on CIFAR10 and MNIST stroke benchmarks demonstrate consistent improvements in verification success and robustness-margin tightness over abstraction-only baselines, while exposing clear runtime trade-offs between ReLU and tanh models.

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

RoSE: Round-robin Synthetic Data Evaluation for Selecting LLM Generators without Human Test Sets

LLMs are powerful generators of synthetic data, which are used for training smaller, specific models. This is especially valuable for low-resource languages, where human-labelled data is scarce but LLMs can still produce high-quality text. However, LLMs differ in how useful their outputs are for training. Selecting the best LLM as a generator is challenging because extrinsic evaluation requires costly human annotations (which are often unavailable for low-resource languages), while intrinsic metrics correlate poorly with downstream performance. We introduce Round robin Synthetic data Evaluation (RoSE), a proxy metric for selecting the best LLM generator without human test sets. RoSE trains a small model on the outputs of a candidate generator (LLM) and then evaluates it on generated synthetic examples from all other candidate LLMs. The final RoSE score is the mean performance of this small model. Across six LLMs, eleven languages, and three tasks (sentiment, topic, intent), RoSE identifies the optimal generator more often than any other intrinsic heuristics. RoSE outperforms intrinsic heuristics and comes within 0.76 percentage points of the optimal generator baseline. This result is measured in terms of downstream performance, obtained by training a small model on the chosen generator's outputs (optimal vs. proxy metric selected) and evaluating it on human-labelled test data. Additionally, RoSE is the only metric to achieve a positive correlation with performance on human test data.

04.
arXiv (CS.LG) 2026-06-17

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

作者:

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.

05.
arXiv (CS.CL) 2026-06-11

Doc-to-Atom: Learning to Compile and Compose Memory Atoms

Long input sequences are central to document understanding and multi-step reasoning in Large Language Models, yet the quadratic cost of attention makes inference both memory-intensive and slow. Context distillation mitigates this by compressing contextual information into model parameters, and recent work such as Doc-to-LoRA amortizes context distillation into a single forward pass that generates one LoRA adapter per document. However, producing a single monolithic adapter for all queries leads to irrelevant-query interference, limited compositional recall, and poor scalability to long-document reasoning. To address these challenges, we propose Doc-to-Atom (Doc2Atom), a compositional parametric memory framework that decomposes each document into semantically typed knowledge atoms. Each atom is compiled into an independent micro-LoRA adapter and a provenance retrieval key. At inference time, a lightweight query router selects and assembles only the relevant atoms into a query-specific adapter, which is then injected into a frozen base model. The entire system is trained end-to-end through a multi-objective distillation framework. Experiments on six diverse QA benchmarks demonstrate that Doc2Atom outperforms Doc-to-LoRA baselines while reducing the memory cost of document internalization.

06.
medRxiv (Medicine) 2026-06-17

Clinical Study Protocol of the 'Biomarkers of Severity of COVID-19 Patients' (BIOMARCOVID) Project

Introduction The coronavirus disease 2019 (COVID-19) pandemic has challenged health care systems worldwide, in certain areas exceeding hospital capacities and human resources. This has underscored the importance of having better tools to predict the outcome of potentially severe respiratory infections such as SARS-CoV-2. Predicting COVID-19 severity may allow physicians to better manage ICU beds and increase the chances of patient survival through appropriate management. During the toughest months of the pandemic, most physicians tried to identify patients that might develop severe forms based primarily on clinical features on admission (e.g., BMI, age). In this context, significant research has focused on identifying comorbidities, clinical manifestations, and routine blood biomarkers to predict disease severity. However, despite the demonstrated value of untargeted metabolomics in assessing severity, limited data exist on its use for identifying novel metabolite biomarkers that could improve both the sensitivity and specificity of outcome prediction. Our goal is to identify metabolite biomarkers that could enhance the predictive accuracy of standard medical biology data and clinical parameters. Methods and analysis This is a retrospective, observational, monocentric cohort study conducted at the Centre Hospitalier Universitaire Grenoble Alpes (CHUGA). The maximum number of eligible patients admitted for PCR-confirmed COVID-19 between March and December 2020 will be included. Severity outcome is defined using the WHO 10-category ordinal scale (mild: categories 4-5; severe: >5). Blood samples were collected within 48 hours of admission and analyzed for 62 routine blood tests and untargeted multiplatform LC-MS/MS metabolomics across four national platforms. Statistical analysis will include logistic regression with variable selection for the primary aim, and multi-block chemometric integration of clinical, biological, and metabolomics data as a secondary aim. Ethics and dissemination A study steering committee has been formed to ensure the accuracy of the collected data by thoroughly reviewing it prior to the data lock. All aspects of the study comply with ethical standards, including approval by the CHUGA institutional review board and adherence to CNIL Reference Methodology MR004 for the protection of participants' rights, privacy, and confidentiality. This study is registered on the French Health Data Hub (number F20210218154851). Results will be disseminated through peer-reviewed publications, presentations at national and international scientific and clinical conferences, and reports shared with key healthcare system stakeholders.

07.
arXiv (CS.CL) 2026-06-16

Rapid Poison: Practical Poisoning Attacks Against the Rapid Response Framework

The Rapid Response (RR) framework, deployed in production systems, including Anthropic's ASL-3 safeguards, continuously improves jailbreak-detection classifiers. When new jailbreaks emerge that bypass these classifiers, Rapid Response generates synthetic variants for training, helping the model generalize from the new attacks and quickly adapt. We reveal that prompt injection can infiltrate this pipeline to deliver poisoned samples into the classifier's training set, enabling two attack objectives: (I) targeted poisoning attacks that create false positives on harmless samples by categorizing them as a jailbreak, with a specific desired feature (e.g., certain formatting, subject, or keyword), (II) concept-based backdoor attacks that induce false negatives on jailbreak inputs, generalizing even to jailbreaks from attack strategies the defender explicitly trained against, when the backdoor trigger is present. Importantly, our threat model restricts adversaries to modifying only jailbreak samples (not benign data or labels), a constraint unexplored by prior work that makes the second objective particularly challenging. We address this with Omission Attack, which exploits a new phenomenon: when training on concept-absent unsafe samples, the classifier misassociates that concept's presence with the safe label. Both attacks cause substantial and in some cases near-complete label flipping at only a 1% poisoning rate, achieving up to 100% false positive rates and up to 96% false negative rates.

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

TS-ICL: A Flexible Time-Indexed Foundation Model for Time Series via In-Context Learning

arXiv:2606.05878v2 Announce Type: replace Abstract: Foundation models mark a profound paradigm shift in time series modeling, with task-specific models being superseded by general-purpose zero-shot models. Yet, current approaches primarily focus on forecasting, while real-world time series are often irregularly and partially observed, requiring models that can jointly forecast, impute missing values, and handle degraded sampling conditions. To address these challenges, we introduce TS-ICL, a novel probabilistic In-Context Learning encoder–regressor Transformer that unifies forecasting and imputation. TS-ICL formulates time series tasks as timestamp-aligned regression and naturally incorporates covariates by training on synthetic dependency structures generated from a novel causal data prior. Empirically, TS-ICL achieves a new state-of-the-art in imputation, while remaining competitive with leading forecasting foundation models across both univariate and covariate-aware benchmarks. It shows particularly strong performance in forecasting with partially observed look-back windows.

09.
arXiv (quant-ph) 2026-06-16

Towards Quantum Limited Spatial Resolution of NV-Diamond Magnetometry

arXiv:2508.13438v2 Announce Type: replace Abstract: Optically addressable ensembles of solid-state defects, such as nitrogen vacancy (NV) centers, are a leading modality for imaging-based magnetometry, thermometry and strain sensing. However, monitoring the fluorescence of individual defects within a sub-diffraction ensemble remains an outstanding challenge that currently limits access to atomic-scale features and dynamics. For compact clusters of NVs, we formulate imaging-based atomic sensing as a low-dimensional multiparameter estimation task in which one seeks to localize each defect and quantify the field strength in its immediate vicinity. In this work, we employ optical spatial mode demultiplexing (SPADE) to enhance localization and brightness estimation accuracy at sub-diffraction scales. Specifically, we develop a two-stage sensing protocol that augments direct imaging by projecting the incoming optical field onto point spread function (PSF)-adapted, i.e., PAD spatial modes and Yuen-Kennedy-Lax (YKL) spatial modes enabling efficient extraction of emitter positions and brightnesses. The YKL-SPADE measurement employed for brightness estimation is shown to be quantum-optimal in the case of two emitters and establishes a new connection between quantum detection and estimation theories. We numerically evaluate the statistical performance of our protocol for sub-diffraction optically detected magnetic resonance (ODMR) and Rabi sensing experiments. Compared to conventional focal plane intensity measurements, our protocol improves emitter localization accuracy by 6$\times$ and brightness estimation accuracy by 2$\times$ for tightly confined ensembles, residing well below the diffraction limit.

10.
arXiv (CS.CV) 2026-06-19

Exploring Multi-Modal Large Language Models and Two-Stage Fine-Tuning for Fashion Image Retrieval

Composed image retrieval retrieves a target image using a composed query of a reference image and a modified text description. In the fashion domain, this task requires understanding subtle attribute variations such as color, pattern, and texture. However, existing approaches face limitations due to scarce annotated data and simplistic negative sampling. We propose a novel framework that integrates a multi-modal large language model (LLaVA) to generate attribute-aware triplets and introduces a two-stage fine-tuning strategy to enhance contrastive learning. We leverage pretrained vision-language models, such as CLIP-ViT/B32, to generate and concatenate sentence-level prompts with the relative caption and to scale the number of negatives using static representations. Experimental results demonstrate enhanced compositional reasoning and improved fine-grained retrieval behavior, underscoring the feasibility and potential of the proposed framework for fashion retrieval.

11.
arXiv (CS.CV) 2026-06-16

Context-Aware RL for Agentic and Multimodal LLMs

Large language models (LLMs) often fail when answering requires identifying a small but decisive piece of evidence within a long or complex context, such as a single line in a tool trace or a subtle detail in an image. We propose ContextRL, a context-aware reinforcement learning (RL) method that improves long-horizon reasoning and multimodal performance through an indirect auxiliary objective. Instead of supervising only the final answer, ContextRL presents the model with a query, an answer, and two highly similar contexts, and rewards it for selecting the context that supports the query–answer pair, thereby encouraging fine-grained grounding. We construct contrastive context data in two domains: for coding agents, trajectories serve as contexts, yielding 1k pairs built via condition filtering; for multimodal reasoning, images serve as contexts, yielding 7K pairs built via generative editing and similarity search. ContextRL achieves average gains of +2.2% over standard GRPO on 5 long-horizon benchmarks, and +1.8% across 12 diverse visual question answering benchmarks. To disentangle the effect of the proposed objective from that of additional data, we compare against data-augmentation baselines that repurpose the same contrastive contexts as standard query–context–answer examples. These baselines provide little to no improvement, showing that the gains arise from the proposed context-selection objective rather than from the contrastive data alone.

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

Quantum iterative approach to the Traveling Salesman Problem

arXiv:2606.11843v1 Announce Type: new Abstract: The Traveling Salesman Problem (TSP) is a classical NP-hard problem in combinatorial optimization, where determining the shortest route among a set of cities becomes computationally prohibitive as the problem size increases. This work explores quantum computing as an alternative approach to address this complexity. Unlike existing methods that primarily rely on quantum annealing, we propose a quantum iterative framework integrating Quantum Phase Estimation (QPE) and Grover's search algorithm. Route costs are encoded as quantum phases, enabling QPE to efficiently evaluate them, while Amplitude Amplification, implemented via the Grover-Long algorithm, iteratively refines the solution space toward the optimal route. A proof-of-concept case study on a small-scale TSP instance demonstrates the feasibility of this approach and its potential for scaling to larger optimization problems. Furthermore, under an expectation-based analysis, the algorithm exhibits an expected computational complexity of $O(\frac{m^2\log_2(m)\log_2(1/\epsilon)}{\sqrt{\epsilon}})$ which depends on the error tolerance parameter $\epsilon$. This estimation omits the initialization term, which we expect future refinements to render subdominant to Phase Estimation.

13.
medRxiv (Medicine) 2026-06-10

Trajectories of brain structure and function in young adult carriers of genetic frontotemporal dementia variants

Background and Objectives: Converging evidence hints at neurodevelopmental effects in genetic frontotemporal degeneration (FTD). In cross-sectional studies, for some genes, young adult FTD variant carriers show differences in brain volumes and cognition compared to familial non-carriers. However, longitudinal trajectories may more sensitively capture FTD-related neurodevelopmental vs. neurodegenerative changes than cross-sectional approaches. This study examined longitudinal trajectories of brain volumes, executive function, and plasma biomarkers in young adult carriers compared to familial non-carriers, as measures of neurodevelopmental and neurodegenerative outcomes of FTD-causing variants. Methods: This longitudinal cohort study comprised participants, aged 18-30 years, from the FTD Prevention Initiative across Europe, Canada, and the USA. Genetic groups included C9orf72 (47%), MAPT (30%), and GRN (23%). Linear mixed-effects models were computed to assess longitudinal outcomes across age between groups, controlling for sex, scanner (for brain volumes), and education (for executive function); random effects accounted for between-subject variability nested within family membership. Results: Variant carriers (n=147) and familial non-carriers (n=113) did not differ in age (mean{+/-}SD, 25.9{+/-}3.2 years), sex (53% female), or number of visits (2.1{+/-}1.7). Young adult C9orf72 repeat expansion carriers exhibited smaller thalamic volumes than non-carriers at the reference age of 26 years (b=-982.8mm3, SE=317.0, p=0.0046, f2=0.32), with relatively stable trajectories across ages 18-30 (i.e., no change over time). Trajectories of rostral anterior cingulate volumes differed in C9orf72 carriers and non-carriers across age, where carriers showed relatively stable trajectories and non-carriers showed age-appropriate declines (b=64.4mm3, SE=29.9, p=0.035, f2=0.07). For MAPT and GRN, there were little to no differences in total brain, cortical, or subcortical volumes between groups and over time. No longitudinal differences were observed between carriers and non-carriers in executive function, or plasma NfL or GFAP for any genetic group. Discussion: C9orf72 repeat expansions were linked to smaller average thalamic volumes and stable trajectories between ages 18 to 30, supporting potential neurodevelopmental origins. The modest evidence supporting an absence of difference in neurodegenerative biomarkers and executive function suggests minimal early neurodegeneration and functional preservation in young adulthood.

14.
arXiv (CS.CV) 2026-06-16

Trusting Right Predictions for Wrong Reasons: A LIME Based Analysis of Deep Learning Interpretability in Lung Cancer Diagnosis

Lung cancer is the leading cause of cancer-related mortality, with approximately 2.5 million new cases and 1.8 million deaths annually, making reliable diagnosis a clinical priority. Although deep learning models have achieved strong performance in lung cancer classification, evaluation has largely focused on predictive accuracy, leaving their decision-making processes insufficiently examined. This study compares three architecturally distinct models: a Convolutional Neural Network (CNN), a pretrained ResNet50, and a Vision Transformer (ViT), trained on the IQ-OTH/NCCD lung cancer CT dataset. Local Interpretable Model-Agnostic Explanations (LIME) were applied to investigate model reasoning. In addition to standard performance metrics, a dual-correlation framework was introduced to measure both prediction agreement and explanation agreement across model pairs. All three models achieved strong classification performance, with ResNet50 attaining 98.61% accuracy, CNN 97.91%, and ViT 93.75%, while all achieved ROC-AUC scores of 0.99. Prediction correlations exceeded 0.99 across all model pairs, indicating highly consistent outputs. However, LIME explanation correlations remained below 0.26, revealing substantial differences in the image regions used to reach those predictions. Analysis of misclassified samples further identified a consistent spatial pattern: incorrect predictions were associated with attention outside the lung parenchyma, whereas correct predictions focused primarily within lung regions. These findings demonstrate that prediction agreement is a poor proxy for reasoning consistency, and that interpretability evaluation must be treated as an independent validation criterion alongside predictive performance in clinical AI systems.

15.
arXiv (quant-ph) 2026-06-17

Photon anti-bunching in high harmonic generation

arXiv:2606.17620v1 Announce Type: new Abstract: Photon anti-bunching is the direct evidence for the existence of photons without having a classical counterpart. Unlike bunching of photons, which can have a semi-classical description, the effect of photon anti-bunching can only be understood with quantized electromagnetic fields. However, for the process of high harmonic generation (HHG), where many photons of the driving field are upconverted to a single photon of higher energy, there is yet no clear evidence for the presence of individual photon emission. The key result of this work is the prediction of photon anti-bunching in the process of HHG, marking it the first theoretical discovery of non-classicality in the temporal correlations of HHG photons. While other non-classical signatures in HHG, such as sub-Poissonian statistics or squeezing, have been discussed for an ensemble of photons, the anti-bunching signature reported here is a signature of a single photon. This is achieved by using the recently developed Heisenberg picture approach for quantum optical HHG, revealing clear anti-bunching signatures in the intensity correlation function across the entire harmonic spectrum.

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

LabOSBench: Benchmarking Computer Use Agents for Scientific Instrument Control

arXiv:2606.16802v1 Announce Type: new Abstract: Current computer-use benchmarks primarily focus on software operation tasks in virtualized systems, whereas scientific instrumentation scenarios require coordinated control over complex interfaces, and feedback-driven parameter adjustment. However, directly evaluating agents on physical high-precision instruments is impractical due to high cost, safety risks, limited accessibility, and difficulty in ensuring reproducible evaluation. This motivates the need for a simulated yet realistic testbed that preserves the operational challenges of scientific instruments while enabling scalable and safe benchmarking. To this end, we introduce LabOSBench, a challenging benchmark for multimodal GUI agents built on a suite of web-based scientific-instrument simulators. Operating directly via a browser, LabOSBench avoids resource-heavy OS virtualization while supporting flexible task configuration and execution-based evaluation. Specifically, LabOSBench constructs 96 subtasks across eight instrument simulators, covering workflows from sample loading, alignment, parameter tuning, and data acquisition to result inspection. We evaluate general-purpose vision-language models, specialized GUI agent models, and advanced agentic frameworks at both subtask and end-to-end levels. Our experiments reveal that while existing agents can complete many structured GUI subtasks, they still struggle with feedback-driven operations and long-horizon workflow execution. Overall, LabOSBench provides a reproducible, low-cost testbed for advancing computer-using agents toward scientific-instrument control.

17.
arXiv (CS.LG) 2026-06-18

Generative models for decision-making under distributional shift

arXiv:2604.04342v2 Announce Type: replace Abstract: Many data-driven decision problems are formulated using a nominal distribution estimated from historical data, while performance is ultimately determined by a deployment distribution that may be shifted, context-dependent, partially observed, or stress-induced. This tutorial presents modern generative models, particularly flow- and score-based methods, as mathematical tools for constructing decision-relevant distributions. From an operations research perspective, their primary value lies not in unconstrained sample synthesis but in representing and transforming distributions through transport maps, velocity fields, score fields, and guided stochastic dynamics. We present a unified framework based on pushforward maps, continuity, Fokker-Planck equations, Wasserstein geometry, and optimization in probability space. Within this framework, generative models can be used to learn nominal uncertainty, construct stressed or least-favorable distributions for robustness, and produce conditional or posterior distributions under side information and partial observation. We also highlight representative theoretical guarantees, including forward-reverse convergence for iterative flow models, first-order minimax analysis in transport-map space, and error-transfer bounds for posterior sampling with generative priors. The tutorial provides a principled introduction to using generative models for scenario generation, robust decision-making, uncertainty quantification, and related problems under distributional shift.

18.
bioRxiv (Bioinfo) 2026-06-16

Orion: Towards Lab Automation with Computer-Using Agents

Laboratory discovery increasingly depends on computational workflows that connect experimental data to analysis, interpretation and follow-up hypotheses. Yet these workflows remain constrained by labor-intensive use of specialized software, visual inspection through graphical user interfaces, and integration of knowledge across multiple sources. Here, we present Orion, a computer-using AI agent for biomedical image analysis and interpretation that moves towards lab automation by automating this computational layer of laboratory work. Orion combines large language models with terminal execution, GUI control and adaptive multi-step reasoning in a shared computing environment. It can inspect visual data, operate standard scientific software, mine web resources and conduct end-to-end analysis and interpretation workflows without requiring bespoke software integrations. Across benchmarks, Orion achieved over 90% accuracy on biomedical database and literature retrieval tasks, learned to use the popular tools CellProfiler and QuPath for quantitative analysis of cellular and tissue images, respectively, and facilitated autonomous discovery in experimental imaging data. In 100 hours of autonomous exploration of a large-scale perturbation imaging dataset, Orion generated 52 research reports, of which human scientist review prioritized 22 plausible mechanistic hypotheses. These results show that computer-using AI agents can substantially expand the reach of laboratory automation, providing a scalable and auditable route from experimental imaging data to quantitative analysis, reports and biologically grounded hypotheses.

19.
bioRxiv (Bioinfo) 2026-06-19

Tox21mer, A transformer foundation model for Tox21 high-throughput concentration-response curves data

The U.S. Tox21 collaboration has generated a large reference library of high-throughput concentration-response assays. Here we present Tox21mer, a 43.5-million-parameter transformer that encodes each Tox21 concentration-response curve together with assay metadata into a 768-dimensional representation. Tox21mer was pretrained on ~2.5 million curves from 102 assay protocols and 6,727 compounds using masked-response reconstruction as the primary objective, with low-weight auxiliary supervision on assay outcome and AC50. To evaluate the learned representation, we trained lightweight probes on frozen embeddings from concentration-response curves of held-out compounds. The representation supported a macro-F1 of 0.985 for three-class outcome prediction (agonist, antagonist, inactive), a binary F1 of 0.994 for active/inactive prediction, and an R2 of 0.87 for log10(AC50). The learned embeddings formed coherent groupings by curve-class category. A masked-only pretraining variant retained near-baseline probe performance, indicating that the representation is learned largely from the self-supervised objective rather than from auxiliary labels. Ablation analyses further showed that predictive performance depends mainly on curve-level response-value distributions conditioned on assay context, with limited reliance on detailed within-curve ordering. Tox21mer thus provides a reusable foundation representation for Tox21 concentration-response data that can support extrapolation to untested compounds through integration with chemical features or distillation into chemistry-only student models for large-scale external screening.

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

Configurable Clinical Information Extraction with Agentic RAG: What Works, What Breaks, and Why

arXiv:2606.19602v1 Announce Type: new Abstract: Patient contexts span hundreds of heterogeneous documents and thousands of structured data points, yet the document-level metadata that AI systems need for retrieval and triage is absent or incomplete. Standard retrieval-augmented generation fails on this data, mishandling temporal reasoning, cross-document dependencies, and missing metadata. We deploy ACIE (Agentic Clinical Information Extraction) at University Medicine Essen: an on-premise agentic RAG pipeline that reasons over complete patient contexts and grounds every answer in source passages for clinician verification. We quantify the metadata gap, trace the architectural decisions it shaped, and evaluate extraction alongside an independent retrospective lymphoma registry study, in which nuclear-medicine physicians verify every extracted value against its cited sources. Across 7,326 judgments, clinicians accepted 96.5\% of extractions, with per-type acceptance ranging from 80\% to 99\%.

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

Not all Jensen-Shannon Divergence Estimators are Equal

arXiv:2606.16411v1 Announce Type: new Abstract: The Jensen-Shannon divergence is widely reported as a scalar measure of fidelity for synthetic tabular data. Yet, in practice, it is estimated from finite samples using protocols that are often underspecified. This creates a measurement problem. Although the population divergence is well defined, the empirical value depends on the estimator family, sampling protocol, calibration, dimensionality, and class balance. We show that different protocols can yield non-comparable values: marginal-based estimators ignore dependencies in the joint distribution and can severely underestimate divergence, while classifier-based estimators capture joint structure but exhibit strong estimator dependence. We systematically study this behavior across controlled settings with reference divergences and real-world synthetic tabular benchmarks. Our analysis reveals dependence blindness in marginal estimators, prior-shift bias under class imbalance, and estimator sensitivity in high dimensions. To address prior shift, we derive a closed-form posterior correction for classifier-based Jensen-Shannon estimation. Our results show that empirical Jensen-Shannon divergence values are inherently protocol-dependent, making explicit specification of the estimation procedure necessary for meaningful comparison. We provide practical guidelines and an open-source tool for estimator-aware Jensen-Shannon evaluation.

22.
arXiv (CS.CV) 2026-06-18

Objective Quality Assessment of Point Clouds Using Multi-scale Implicit Structural Similarity

The unstructured and irregular nature of points poses a significant challenge for accurate point cloud quality assessment (PCQA), particularly in establishing accurate perceptual feature correspondence. To tackle this, we propose the Multi-scale Implicit Structural Similarity Measurement (MS-ISSM). Unlike traditional point-to-point matching, MS-ISSM utilizes radial basis function (RBF) to represent local features continuously, transforming distortion measurement into a comparison of implicit function coefficients. This approach effectively circumvents matching errors inherent in irregular data. Additionally, we propose a ResGrouped-MLP quality assessment network, which robustly maps multi-scale feature differences to perceptual scores. The network architecture departs from traditional flat multi-layer perceptron (MLP) by adopting a grouped encoding strategy integrated with residual blocks and channel-wise attention mechanisms. This hierarchical design allows the model to preserve the distinct physical semantics of luma, chroma, and geometry while adaptively focusing on the most salient distortion features across High, Medium, and Low scales. Experimental results on multiple benchmarks demonstrate that MS-ISSM outperforms state-of-the-art metrics in both reliability and generalization. The source code is available at: https://github.com/ZhangChen2022/MS-ISSM.

23.
medRxiv (Medicine) 2026-06-19

The Impact of Pregnant Womens Dietary Behavior on the Physiological Adaptation Paradox and Maternal-Fetal Resource Conflict in Conflict Settings: A Predictive Analytical Study

This scientific study aims to assess the level of awareness, nutritional knowledge, and actual behavioral practices among pregnant women in the Capital District of Sanaa, Republic of Yemen, and to determine their impact on the health and clinical indicators of the mother and fetus under complex conflict conditions. The study employed a descriptive-analytical approach based on a simple random sample of 200 pregnant women attending government-run hospitals and specialized medical centers in the Capital District. Field data were collected during December 2025 using a structured and validated questionnaire consisting of 42 items measuring demographic variables, awareness, practices, barriers, and health outcomes. The results of the statistical analysis using SPSS software showed a high level of nutritional awareness (87%) and healthy dietary practices (80%) among the sample participants. Simple and multiple linear regression tests revealed a statistically significant effect of awareness and practices in explaining 20.2% of the variance in the health status of the mother and fetus (R{superscript 2}= 0.204, p < 0.001). The study demonstrated that actual behavioral practices have greater predictive power ({beta}=0.316, p=0.001) compared to theoretical cognitive awareness ({beta}=0.232, p=0.005) in determining clinical outcomes for the mother and fetus, highlighting the widening gap between knowledge and behavior under structural pressures. "Morning sickness" (80%) and the deterioration of "family economic status" (71%) emerged as the greatest physiological and material barriers to proper nutrition. With their inferential impact established as an extension of the maternal-fetal resource allocation conflict in a physiologically and economically challenging environment, the study also identified significant differences in nutritional behavior and health outcomes in favor of housewives and mothers who are more educated and have higher incomes, while no significant differences were recorded attributable to obstetric variables such as stage or order of pregnancy. The study offers a unique theoretical and practical contribution by formulating an integrated causal model that demonstrates that the fetus acts as a biological drain on the mothers cellular and mineral reserves in a war environment, which necessitates directing antenatal care and support programs toward effective behavioral empowerment and nutritional support to overcome the structural and material barriers faced by pregnant women.

24.
arXiv (CS.AI) 2026-06-18

QSignAI: Quantum-Randomness-Seeded Identity Signatures at the Intersection of AI for Science and Science for AI

arXiv:2605.27729v2 Announce Type: cross Abstract: The 2024-2025 Nobel and Turing awards recognised AI and quantum science simultaneously. Yet no deployed system has brought these streams together for the public. This paper presents QSignAI, a production-deployed platform demonstrating a bidirectional AI-quantum relationship in a real-time event participation system. We address three questions: can quantum-randomness generation via a two-source extractor be embedded in an AI-driven social platform with acceptable latency; can an AI bot make quantum phenomena perceptually legible to general audiences; and does the combined system work in practice? A conversational bot routes each participant's first message through a quantum pipeline comprising a Toeplitz two-source extractor over independent single-qubit Hadamard measurements on SV1 and DM1 simulators, plus a 2-qubit Bell state, producing a unique quantum-randomness-seeded identity signature per participant. The first two questions are answered through system architecture and qualitative deployment evidence from live events; the third through successful production deployment. The current deployment uses cloud quantum simulators; physical QPU randomness is the near-term extension. Measurable benchmarks are identified as priority future work.