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

LLM-Based Synthetic Ground Truth Generation for Audio-Based Emotion Classification via In-Context Learning

arXiv:2606.14784v1 Announce Type: cross Abstract: Understanding human states and interaction dynamics is a core goal of human-computer interaction (HCI). As interaction paradigms become more immersive, virtual reality (VR) has emerged as a powerful platform for studying collaborative work. In such settings, evaluating team collaboration states, including team performance and team resilience, requires continuous and reliable inference of latent team-level cognitive and affective states from multi-modal sensor data, such as speech signals. However, generating ground truth labels for these latent states remains challenging due to sensor-induced noise, contextual variability, and sparse expert annotations. Traditional self-reporting approaches provide only static and delayed measurements and are therefore insufficient for capturing dynamic team processes reflected in continuous speech data. In this work, we propose a large language model (LLM)-driven, agentic inference workflow for automated emotion-related synthetic ground truth generation from streaming speech data in multi-user VR environments. Leveraging the generalization capabilities of LLMs, we use In-Context Learning (ICL) with few-shot demonstrations of paired audio-based samples and their corresponding transcriptions. ICL tends to achieve task adaptation comparable to model fine-tuning while circumventing the computational overhead of parameter updates. To construct informative and robust in-context prompts, we adopt a retrieval-based selection strategy that dynamically identifies relevant audio demonstrations based on similarity in the acoustic feature space.

02.
arXiv (CS.AI) 2026-06-17

FinAcumen: Financial Multimodal Reasoning via Self-Evolving Experience Memory Harness

arXiv:2606.17642v1 Announce Type: new Abstract: Financial multimodal reasoning requires agents to coordinate numerical computation, retrieval, visual interpretation, and temporal grounding across heterogeneous evidence sources. Existing tool-augmented agents improve execution fidelity, yet remain largely stateless across episodes, repeatedly rediscovering reasoning strategies and failure patterns. In high-stakes financial settings, this leads to unreliable tool routing, noisy retrieval, and hallucination-prone reasoning. We present FinAcumen, a financial reasoning agent framework centered on selective experience memory for tool-augmented multimodal reasoning. FinAcumen accumulates financially grounded reasoning experience from prior trajectories, distilling successful strategies and failure-derived cautionary rules into a persistent memory bank. During inference, retrieved experiences condition reasoning only when semantic relevance exceeds a calibrated threshold, while irrelevant memory is explicitly suppressed through a fallback mechanism. A deterministic financial tool environment further grounds numerical computation, retrieval, visual decoding, and answer verification.Across four financial multimodal reasoning benchmarks, FinAcumen consistently improves a frozen 8B vision-language model over finance-specialized models and approaches leading proprietary general-purpose models. Further analysis shows that selective experience activation improves reasoning reliability under retrieval uncertainty. Our code is anonymously available at https://anonymous.4open.science/r/FinAcumen

04.
arXiv (CS.LG) 2026-06-19

AgentArmor: A Framework, Evaluation, \& Mitigation of Coding Agent Failures

arXiv:2606.19380v1 Announce Type: cross Abstract: Software engineering and deployment are increasingly being delegated to AI coding agents. The scale of their adoption is surfacing rare, but highly destructive, failure modes. In this paper, we study these failure modes as stemming from three distinct mechanisms: underspecification, where default model behavior is unsafe; capability errors, where the safe action is available but the model does not adhere to it due to bias or capability limitations; and agent harness errors, where the model fails to execute the safe action through the harness. We evaluate these across 8 different evaluations, each inspired by real-life deployment failures, totaling 20 coding environments and 59 synthetic transcript templates. Based on this evaluation, we propose AgentArmor, an agent harness modification, to mitigate these errors. By adding an extended system prompt, a separate command classifier, a ``3 strikes'' policy, deterministic guardrails, and tools for the agent to edit its own context, we show that AgentArmor is safer across a statistically significant number of samples. Thus, we suggest concrete mitigations for current coding agents and a design philosophy for future agent harness features.

05.
arXiv (CS.AI) 2026-06-16

Deep Neural Networks: A Formulation Via Non-Archimedean Analysis

arXiv:2402.00094v3 Announce Type: replace-cross Abstract: We introduce a new class of deep neural networks (DNNs) with multilayered tree-like architectures. The architectures are codified using numbers from the ring of integers of non-Archimdean local fields. These rings have a natural hierarchical organization as infinite rooted trees. Natural morphisms on these rings allow us to construct finite multilayered architectures. The new DNNs are robust universal approximators of real-valued functions defined on the mentioned rings. We also show that the DNNs are robust universal approximators of real-valued square-integrable functions defined in the unit interval.

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

Latent Geometric Chords for Query-Efficient Decision-Based Adversarial Attacks

While decision-based black-box adversarial attacks present a severe security threat, current methodologies suffer from fundamental limitations. Pixel-wise attacks frequently introduce unnatural, high-frequency visual artifacts, while latent-space frameworks are confined by the limited search space of low-dimensional manifolds and inherent reconstruction flaws. To resolve these limitations, we propose Latent Geometric Chords (LGC) for Query-Efficient Decision-Based Adversarial Attacks alongside a variant, LGC-H. At its core, LGC navigates decision boundaries by executing a curvature-aware geometric search within a compressed semantic manifold. To guarantee high visual fidelity and circumvent dimensionality bottlenecks, we introduce a Residual-based Adversarial Generation (RAG) mechanism. RAG isolates semantic perturbations as geometric chords and superimposes them directly onto the original source image. RAG substantially resolves baseline reconstruction flaws and effectively doubles the permissible search space dimensions. Experimental results demonstrate that LGC achieves robust cross-dataset transferability and substantially outperforms state-of-the-art baselines. Notably, our method, LGC, minimizes perturbation magnitudes while achieving state-of-the-art visual fidelity–with a Structural Similarity Index Measure (SSIM) exceeding 0.99 and a Learned Perceptual Image Patch Similarity (LPIPS) below 0.01 at 5000 queries–and sustaining high attack success rates under stringent perceptual constraints, successfully compromising adversarially trained robust models. The source code is available at: https://github.com/eihmuekhine/Latent-Geometric-Chords.

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

CONCORD: Asynchronous Sparse Aggregation for Device-Cloud RAG under Document Isolation

arXiv:2606.15179v1 Announce Type: new Abstract: Retrieval-augmented generation (RAG) has emerged as a pivotal technique for improving language models by incorporating external knowledge at inference time. As device-cloud collaborative inference makes it feasible to deploy small language models on edge devices, a new setting arises in which private documents remain on the device and public knowledge resides in the cloud. Privacy and policy constraints often forbid raw document exchange, creating a document-isolated dual-end RAG setting. However, existing methods rely on frequent remote synchronization and dense evidence transfer, limiting throughput under realistic latency and bandwidth conditions. To address this issue, we propose CONCORD, an asynchronous sparse aggregation framework for dual-end RAG under document isolation. CONCORD treats the cloud as an asynchronously arriving evidence source rather than a continuously synchronized co-generator. Specifically, we introduce waiting debt control to decide whether each decoding step should continue waiting for remote participation based on the observed return of waiting. We also design a certificate-guided minimal supplementation mechanism that requests only the remote evidence needed to determine the current greedy decision. Steps that consult the cloud preserve the same greedy token as dense dual-end aggregation, while the remaining steps commit locally without remote evidence. Experiments on Natural Questions and WikiText-2 show that CONCORD improves end-to-end throughput over baselines by $1.66\times$ and $2.15\times$, respectively, while reducing per-token communication by over two orders of magnitude and maintaining comparable answer quality and perplexity.

08.
arXiv (CS.LG) 2026-06-12

Aerial Wildfire Suppression Planning with a Hybrid CNN-Cellular Automata Fire Model

arXiv:2606.13633v1 Announce Type: cross Abstract: Aerial wildfire suppression requires not only predicting fire spread, but also designing effective intervention strategies under operational and environmental uncertainty. We present a modeling and optimization framework for aerial wildfire suppression that combines a hybrid neural-cellular automaton wildfire model with gradient-based design of targeted aerial drops. The wildfire model predicts spatially varying spread behavior from terrain, fuel, and wind data, while the intervention module determines binary drop actions with continuous-valued location and orientation parameters mapped to the simulation grid. Water and retardant are represented with distinct suppression effects, corresponding to immediate reduction of active burning and persistent reduction of future spread. To evaluate the robustness of the resulting suppression plans, we quantify both aleatoric uncertainty through Monte Carlo sampling of daily fire-state realizations and epistemic uncertainty through spatially correlated prediction-error perturbations. A case study based on the 2020 Bear Fire shows that the framework can generate coherent aerial suppression schedules for reducing total fire-affected area and can support uncertainty-aware analysis of wildfire intervention strategies.

09.
Nature (Science) 2026-06-22

Stereoretentive decarbonylative C(sp<sup>3</sup>)-C(sp<sup>3</sup>) cross-coupling

作者:

While C(sp3)–C(sp3) bond-forming cross-coupling methods have become more common, stereocontrolled bond-formation remains a challenge,1 despite its importance for drug discovery, where there is a emerging demand for molecules with increased sp3 character.2-4 Enantiospecific cross-coupling approaches would complement advances in enantioselective coupling,5-8 but have been limited to specialized substrates with lower availability5,9 because stereospecific oxidative addition of more abundant chiral alkyl electrophiles is unknown.10 Inspired by the classic, stereoretentive Curtius rearrangement,11 herein we disclose a catalytic strategy that proceeds by an analogous stereoretentive decarbonylation step to form a versatile chiral alkylnickel intermediate from easily-available chiral amino-acid and α-hydroxy-acid derivatives. The chiral alkylnickel intermediates decompose and/or racemize on the order of minutes, but are sufficiently stable to enable stereoretentive cross-electrophile coupling12 with alkyl radicals (derived from alkyl iodides) at relatively low temperature (22-40 °C). This mechanistic strategy provides a straightforward approach to stereocontrolled C(sp3)–C(sp3) bond formation, including diastereomers that are inaccessible by stereoselective radical mechanisms. The “metallo-Curtius” strategy described in this study lays a mechanistic foundation for the development many new stereospecific cross-coupling reactions.

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

Does Traversal Order Matter? A Systematic Study of Tree Traversal Methods in Transformer Grammars

Transformer Grammars (TGs) enhance language modeling by incorporating syntactic tree structures. Despite the potentially significant impact on model performance of how syntactic trees are linearized in TGs, existing studies rely solely on Depth-First Traversal (DFT) for linearization. In this paper, we expand the traversal design space by exploring Breadth-First Traversal (BFT) and a novel hybrid traversal strategy, Production-Rule Traversal (PRT), which combines the structural lookahead of BFT with the early lexical generation of DFT. We integrate these traversal methods with varying tree configurations and masking strategies, and empirically evaluate their performance on language modeling, syntactic generalization and summarization. We reveal the inherent trade-offs between nested composition and global lookahead, providing actionable recommendations for designing task-aware Transformer Grammars.

12.
arXiv (CS.CL) 2026-06-17

RubricsTree: Scalable and Evolving Open-Ended Evaluation of Personal Health Agents across Health Memory and Medical Skills

The LLM-empowered personal health agents with user health (sensor) metrics have offered a promising pathway to alleviate global disparities in healthcare access. However, large-scale clinical deployment remains constrained by an open-ended evaluation bottleneck: physician annotation is reliable but costly and unscalable, while LLM-as-a-judge evaluators are scalable but subjective, inconsistent, and sometimes clinically misaligned. We introduce RubricsTree, a scalable evaluation framework with an expert-aligned hierarchical taxonomy of over 100 atomic, clinically-verifiable Boolean rubrics, evolving from the insights of 4,000 real user queries through an iterative human-in-the-loop curation protocol with an expertise panel led by an experienced physician. A context-aware adaptive router activates only the relevant auto-weighted rubric subset per query, providing the throughput needed for scalable evaluation with expert-aligned quality. Through a systematic meta-evaluation, we show that RubricsTree (i) substantially exceeds a strong large-scale evaluation baseline in expert alignment on challenging open-ended queries; (ii) reliably penalizes contextually degraded responses; and (iii) when used as structured instructions, text feedback, or training rewards for performance optimization, yields up to ~66% relative gains on HealthBench for Gemini, GPT, and Qwen model families. RubricsTree thus provides a scalable, auditable, and evolving evaluation infrastructure required for the continuous optimization of product-level personal healthcare AI.

13.
arXiv (quant-ph) 2026-06-11

Time-Frequency Grid States for Reconstruction and Correction of Channel-Induced Distortion in Entangled Photons

arXiv:2606.12216v1 Announce Type: new Abstract: Characterization of time-frequency (TF) quantum states requires reliable reconstruction of their TF distributions. However, imperfect transmission or measurement channels can distort reconstructed joint spectral intensities (JSIs), especially when the underlying perturbation mechanism is unknown. Here, we experimentally demonstrate a reconstruction and correction framework that uses a TF grid state as an intrinsic frequency-domain reference. By analyzing the displacement of the grid points, a Gaussian process regression model is employed to reconstruct a correction mapping for the nonlinear coordinate deformation without assuming a prior physical model of the distortion. The learned mapping reduces the residual coordinate deviation of the TF grid state by approximately a factor of 11 and, when applied to an independent frequency-entangled test state, improves the Gaussian-shape fidelity from 76.2\% to 90.0\%. These results establish TF grid states as practical metrological resources for diagnosing and correcting distortions in TF quantum systems, providing a pathway toward distortion-resilient quantum communication and high-dimensional quantum information processing.

14.
arXiv (CS.CV) 2026-06-17

Flux-Guard: Facial Identity Protection using diffusion models

The widespread deployment of face recognition (FR) systems exposes personal images shared on social media and public platforms to identity linkage and privacy risks. Existing adversarial privacy protection methods can degrade unauthorized FR performance but are not compatible with generative face editing. Artificial intelligence-driven face editing tools are gaining popularity, which has significantly increased user demand for personalized portrait generation and social sharing. However, current editing methods often preserve identity features, making the edited images still susceptible to tracking by malicious FR systems. Thus, this paper proposes Flux-Guard, a privacy-preserving face editing framework based on adversarial attacks, which integrates face editing and privacy protection within a unified generative process. Specifically, we design a flow trajectory control method to align semantic manipulations with the generative process and introduce latent-space adversarial optimization with an adaptive perceptual-loss-driven weighting strategy, dynamically adjusting adversarial strength to maximize attack effectiveness while preserving visual quality. Extensive experiments demonstrate that Flux-Guard supports face editing while significantly improving attack success rates against cross-domain face recognition models on the CelebA-HQ and LADN datasets. Furthermore, evaluation results for commercial APIs have confirmed its effectiveness in real-world applications. The code is released at https://github.com/JLMWang/Flux-Guard.

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

A Mathematical Theory of Value: a synthesis on goal-directed agency under resource constraints

作者:

arXiv:2606.12502v1 Announce Type: cross Abstract: We propose that value – the quantity goal-directed agents create, destroy, and exchange – is a lawful structural quantity in the same category as information. Following Shannon's method, we make one ruthless abstraction: value is the rate at which an agent converts a resource into goal-progress, relative to a frame fixed by its goal. A scale-invariance axiom forces a logarithmic measure, $V=\sum_i k_i \ln e_i$; compounding of a reinvested resource forces the same form via the ergodicity argument of Peters (2019). The two routes are kin rather than independent; their agreement is a consistency check, not an over-determination. We derive a coding theorem of value: $\Delta G \le I(X;Y)$, achieved by Bayes-proportional allocation; realized value decomposes as $G=D(q\|r)-D(q\|p)$, identifying misalignment with measurable waste. For populations, value is frame-relative while price is frame-independent; a fleet that pools its resource and fuses its perception inherits the ceiling $G_{\mathrm{fleet}} \le I(X;Y_{1:m}) \le H(X)$ (a corollary; an earlier sum-form claim was wrong and is corrected in v5). A dynamical layer yields an is/ought asymmetry from which alignment emerges as a control-stability condition with a closed-form residual. We test the single-frame laws on live language models in a pre-registered scale-up: perception mutual information tracks realized capability rather than parameter count (Spearman $\rho = 0.977$ pooled over 30 model$\times$domain points), out-of-sample $\Delta G$ tracks $I(X;Y)$, and over-confidence is measurable dissipation; a further pre-registered test shows the bridge is shape-invariant across four task shapes ($n=42$, slope 0.953). None of the mechanisms is individually new – generalized Kelly, Armstrong & Mindermann (2018), classical control; the contribution is their unification and the governance mapping (incentive design over oversight) that follows.

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

CRANE: Constrained Reasoning Injection for Code Agents via Nullspace Editing

Code agents must both reason over long-horizon repository state and obey strict tool-use protocols. In paired Instruct/Thinking checkpoints, these capabilities are complementary but misaligned. The Instruct model is concise and tool-disciplined, whereas the Thinking model offers stronger planning and recovery behavior but often over-deliberates and degrades agent performance. We present CRANE (Constrained Reasoning Injection for Code Agents via Nullspace Editing), a training-free parameter-editing method that treats the Thinking-Instruct delta as a directional pool of candidate reasoning edits for the Instruct backbone. CRANE combines magnitude thresholding to denoise the delta, a Conservative Taylor Gate to retain edits that are jointly beneficial for reasoning transfer and tool-use preservation, and Graduated Sigmoidal Projection to suppress format-critical update directions. By merging paired Instruct and Thinking checkpoints, CRANE delivers strong gains over either individual model while preserving Instruct-level efficiency: on Roo-Eval it achieves pass1 of 66.2% (+19.5%) for Qwen3-30B-A3B and 81.5% (+8.7%) for Qwen3-Next-80B-A3B; on SWE-bench-Verified it resolves up to 14 additional instances at both scales (122/500 and 180/500); and on Terminal-Bench v2 it improves pass1/pass5 by up to 2.3%/7.8%, reaching 7.6%/17.9% and 14.8%/30.3%, respectively, consistently outperforming alternative merging strategies across all three benchmarks.

17.
arXiv (math.PR) 2026-06-19

On creating convexity in high dimensions

arXiv:2502.10382v3 Announce Type: replace-cross Abstract: Given a subset $A$ of $\mathbb{R}^n$, we define \begin{align*} \mathrm{conv}_k(A) := \left\{ \lambda_1 s_1 + \cdots + \lambda_k s_k : \lambda_i \in [0,1], \sum_{i=1}^k \lambda_i = 1 , s_i \in A \right\} \end{align*} to be the set of vectors in $\mathbb{R}^n$ that can be written as a $k$-fold convex combination of vectors in $A$. Let $\gamma_n$ denote the standard Gaussian measure on $\mathbb{R}^n$. We show that for every $\varepsilon > 0$, there exists a subset $A$ of $\mathbb{R}^n$ with Gaussian measure $\gamma_n(A) \geq 1- \varepsilon$ such that for all $k = O_\varepsilon(\sqrt{\log \log(n)})$, $\mathrm{conv}_k(A)$ contains no convex set $K$ of Gaussian measure $\gamma_n(K) \geq \varepsilon$. This result acts as a complement to the recent affirmative resolution of Talagrand's convexity conjecture by Hua, Song, and Tudose, which states that a universal dilation of the threefold Minkowski sum $A+A+A$ of a large set $A$ guarantees a large convex subset. Our approach utilises concentration properties of random copulas and the application of optimal transport techniques to the empirical coordinate measures of vectors in high dimensions.

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

InfoGeo: Information-Theoretic Object-Centric Learning for Cross-View Generalizable UAV Geo-Localization

Cross-view geo-localization (CVGL) is fundamental for precise localization and navigation in GPS-denied environments, aiming to match ground or UAV imagery with satellite views. Existing approaches often rely on global feature alignment, but they suffer from substantial domain shifts induced by varying regional textures and weather conditions. This issue becomes even more pronounced in UAV-based scenarios, where the broader perspective inevitably introduces dense, fine-grained objects, creating significant visual clutter. To address this, we draw inspiration from Object-Centric Learning (OCL) and propose InfoGeo, an information-theoretic framework designed to enhance robustness and generalization. InfoGeo reformulates the optimization as an information bottleneck process with two core objectives: (i) maximizing view-invariant information by aligning the object-centric structural relations across views, and (ii) minimizing view-specific noisy signals through cross-view knowledge constraints. Extensive evaluations across diverse benchmarks and challenging scenarios demonstrate that InfoGeo significantly outperforms state-of-the-art methods.

19.
arXiv (quant-ph) 2026-06-12

Coarse-grained quantum thermodynamics: Observation-dependent quantities, observation-independent laws

arXiv:2507.15918v2 Announce Type: replace Abstract: In both classical and quantum thermodynamics, physical quantities are typically assigned objective values defined independently of our observations. We then refer to the 'work performed by a gas', or the 'entropy of the gas', regardless of how they are evaluated. Here, we question this conception in the context of quantum thermodynamics, estimating how the definition of pivotal thermodynamic quantities is affected by experimental instruments of limited precision. We find that the coarse-grained thermodynamic quantities frequently lead to different conclusions from those drawn in fine-grained scenarios. For instance, the irreversibility of a process, or its work payoff, can significantly vary with the instrument precision. We show nonetheless that coarse-grained thermodynamic quantities satisfy the same relations (i.e., the second law inequality, the relation between dissipation and distinguishability of a process from its time-reverse, and the quantum work fluctuation theorems) as their fine-grained counterparts. These results highlight the observation-independence of relations linking thermodynamic quantities which are themselves observation-dependent.

20.
Nature (Science) 2026-06-23

How should I respond to race-based exclusion in my lab?

作者:

A researcher in Europe feels left out of their team and held to different standards from their colleagues. How can they challenge exclusion without risking their position? A researcher in Europe feels left out of their team and held to different standards from their colleagues. How can they challenge exclusion without risking their position?

21.
arXiv (CS.CL) 2026-06-15

SuperThoughts: Reasoning Tokens in Superposition

Long Chain-of-Thought (CoT) reasoning improves LLM problem-solving but is computationally expensive due to sequential token generation. While recent works explore reasoning in continuous latent spaces to bypass discrete token generation, they often struggle with training stability and fail to scale to complex, long-horizon tasks due to lack of supervision signal. We propose SuperThoughts, which compresses pairs of consecutive CoT tokens into single latent representations and decodes two tokens per step via a lightweight Multi-Token Prediction (MTP) module. This preserves discrete token supervision at training time while doubling throughput at inference time. We finetune Qwen2.5-Math-1.5B-Instruct, Qwen2.5-Math-7B-Instruct, Qwen2.5-Math-14B-Instruct, and evaluate on MATH500, AMC, OlympiadBench, and GPQA-Diamond. With a confidence-based adaptive mechanism that falls back to standard decoding when uncertain, SuperThoughts achieves $\sim$20–30\% CoT length reduction while maintaining accuracy with minimal degradation (1-2 points accuracy drop on most tasks).

22.
arXiv (CS.LG) 2026-06-12

A unified complexity bound for logconcave sampling

arXiv:2606.12694v1 Announce Type: cross Abstract: We give a simple, unified, and nearly tight bound for sampling arbitrary logconcave distributions from a warm start using the In-and-Out algorithm along with exponential lifting. The main new ingredient in the analysis is an improved bound on the Poincaré constant of a lifted distribution. As a consequence, the resulting convergence rate is nearly tight for both constrained settings (e.g., Gaussian restricted to a convex body) and well-conditioned settings (e.g., strongly logconcave and smooth densities).

23.
arXiv (CS.CV) 2026-06-18

PEFT-MedSAM: Efficient Fine-Tuning of Medical Foundation Models for Explainable Skin Lesion Segmentation

Automated segmentation of skin lesions using deep learning models for dermoscopic images can be very helpful in finding melanomas earlier than they would normally be detected. However, most deep learning methods available do not perform well. The aim of this paper is to present a parameter-efficient fine-tuning method called PEFT-MedSAM for adapting the Medical Segment Anything Model (MedSAM) to automatically segment dermoscopic skin lesions. The PEFT-MedSAM method uses only the lightweight mask decoder for training the model while keeping the pre-trained image encoder and prompt encoder frozen. The experiments performed on the ISIC 2018 benchmark dataset shows that PEFT-MedSAM obtains a dice coefficient of .9411 and an intersection over union value of .8918 when compared to both a fully trained U-Net baseline (.8715 dice coefficient) and zero-shot MedSAM inference (.8997 dice coefficient). The external validation of the model using PH2 dataset shows .9467 dice coefficient with +/- .0310 standard deviation. Supportive evidence for these claims include a p-value less than .0001 for Wilcoxon signed rank tests comparing the two datasets and bootstrap-estimated 95% confidence intervals of [.9364,.9447] that represent the estimated range of possible values for the average dice coefficient obtained by repeating the test. To increase clinical trustworthiness, we used Grad-CAM explainability along with a pointing game based evaluation methodology to evaluate the CNN baseline model on the validation set. The results showed that we had an accuracy rate of 98.27% on the validation set of 519 images and confirmed that the model classified regions containing skin lesions.

24.
bioRxiv (Bioinfo) 2026-06-19

Sanjeevani: A manually curated anti-cancerous phytochemical database integrated with downstream analysis tools.

Background: Cancer continues to pose a massive global health burden. While plant-derived phytochemicals offer promising therapeutic leads, existing natural product databases often lack cancer specificity, dataset downloadability, and integrated screening tools. Methods: We developed Sanjeevani, an integrative web platform cataloguing 4,823 curated anticancer phytochemicals. Using a balanced dataset of 9,646 molecules, we trained Support Vector Machine (SVM), Random Forest, and K-Nearest Neighbours classifiers using a hybrid feature representation of RDKit descriptors and 2048-bit ECFP4 fingerprints. The platform also integrates AutoDock Vina for web-based molecular docking for binding affinity, poses prediction and ADMET-AI for pharmacokinetics estimation. Results: The SVM model demonstrated the strongest predictive capability, achieving a top test accuracy of 0.966 and a ROC-AUC of 0.992. Benchmarking across five docking tools confirmed that AutoDock Vina successfully balanced computational automation with literature-consistent binding affinity replication. The final architecture provides rapid interactive 2D/3D visualizations integrated with downstream analysis tools. Conclusion: Sanjeevani provides an open-access, one-stop pipeline that bridges the gap between raw natural product data and actionable computational screening, accelerating natural product-based oncology drug discovery.

25.
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.