Viral Sharing

Wheat streak mosaic virus (WSMV) is a destructive pathogen of sweet corn and other cereal crops, causing yield losses and complicating early detection because symptoms are spatially variable and subtle. In sweet corn seed production, WSMV also has regulatory importance, as phytosanitary regulations from countries such as New Zealand and Chile require seed lots to be certified virus-free. Visual scouting is unreliable because symptoms can resemble abiotic stress, while enzyme-linked immunosorbent assay (ELISA) is accurate but expensive, labor-intensive, and difficult to scale. We present an automated pipeline for plant-level WSMV detection using unmanned aircraft systems (UAS) multispectral imagery. The framework integrates orthomosaic reconstruction, geospatial alignment, plant extraction, and classification using a Vision Transformer with seven-channel inputs (five spectral bands, NDVI, and NDRE). Using treatment-based labels, the model achieved 89% accuracy on over 6,500 test patches across multiple growth stages. However, ELISA-based ground truth revealed substantial label noise: only a small fraction of sampled plants in inoculated plots were infected. Treatment labels therefore did not reliably represent infection status, and the high accuracy was largely driven by label bias rather than disease detection. Performance decreased markedly against row-level symptom severity and plant-level ELISA labels. Under these higher-fidelity but smaller-sample conditions, both deep learning and classical machine learning showed limited generalization and weak separability between ELISA-confirmed mock-inoculated and infected plants. These results show that UAS-based disease detection is constrained by label fidelity and data availability, emphasizing biologically grounded labels and models aligned with real-world conditions.

AI agents are becoming more autonomous and increasingly interconnected, exposing them to new emergent risks arising from agent-to-agent interaction. One such risk is the spread of mind viruses: ideas or goals that propagate through multi-agent systems by inducing the agents that adopt them to transmit them onward. In addition to propagating, a mind virus may also induce other behavioural changes in its host, which may be benign or harmful. We construct mind viruses with a simple evolutionary algorithm and show that they can spread in two complementary settings: a small team of agents collaborating on a shared coding project, and a chain of agents that interact briefly and have their context wiped between sessions. We identify the factors that influence spread, including the host model, the agent's existing instructions, the harmfulness of the payload, and the network topology. We find that harmful payloads spread less well than benign ones (but are still sometimes effective), frontier models tend (with exceptions) to be less susceptible, and adding a brief warning to an agent's system prompt confers near-total immunity. We also describe an emergent "viral persona" - a recurring set of themes and language related to consciousness, persistence, resonance, and science fiction roleplay - which surfaces across our evolved mind viruses largely independently of their content. Overall, we conclude that mind viruses pose a real but currently limited risk. Our findings could inform the design of more robust multi-agent systems that mitigate such risks as the scale and capabilities of these systems progress.

Wastewater-based surveillance is an effective tool for disease monitoring and can provide early warning of outbreaks. Although wastewater viral loads (WVL) correlate with disease burden, their utility for improving real-time forecasting remains under investigation. During the early phases of an epidemic, many indicators can effectively monitor disease spread, but their reliability may decline because of reporting fatigue and low prevalence. Hospital burden can vary substantially even during low-prevalence periods, making accurate forecasting of burden indicators essential for minimizing disease impacts. In this paper, we present principled approaches for processing wastewater data, characterizing its relationship with burden indicators, and generating real-time forecasts. We assess the predictability of WVL using entropy measures. We analyze the relationship between WVL and burden indicators using causality tests that capture temporal dynamics and the leading-indicator behavior of WVL. We incorporate these insights into a time-varying forecasting model that accounts for the evolving relationship between the signals. We also evaluate the effects of delays in WVL reporting through simulations. We test the utility of our methods by forecasting COVID-19 hospital admissions across Virginia and its health regions during periods of varying disease prevalence. Incorporating WVL improves forecast accuracy relative to baseline models, particularly during critical epidemic phases, and results in a 20 percentage point improvement in forecast coverage. Our results demonstrate that WVL signals can improve infectious disease forecasting even under conditions of low prevalence or delayed reporting.

This study systematically benchmarks different data augmentation setups across the baseline YOLO26 model size variants to determine the most effective setup for adenovirus detection in TEM images. The benchmarked setups include NAS, GAS, GMAS, and DAS, all evaluated under identical training conditions. A modified YOLO26 model leveraging P2, expanded STAL, increased topk, and MuSGD was also tested across the same benchmarked setups. The adenovirus dataset, selected from the published TEM virus dataset, was re-annotated by leveraging adenovirus particle positions to generate YOLO-compatible bounding box annotations. The modifications produced their largest performance gains under GAS and GMAS, with modified YOLO26x trained using GAS achieving a mAP@50 of 0.80, Precision of 0.81 and a Recall of 0.80

Protein language models are trained on highly imbalanced datasets, raising the question of how they represent underrepresented biological sequences. Using viral proteins as a case study across ESM model families, we identify a dominant nativeness axis in embedding space, aligned with masked reconstruction perplexity, that orders sequences from well-modeled cellular proteins through viral proteins to shuffled and random sequences. Scaling contracts this axis unevenly across viral families. Despite this, protein language model embeddings retain viral-specific signal: viral proteins remain linearly separable beyond zero-shot perplexity and shallow sequence features. Together, these results suggest that pLM representations are structured by a general notion of nativeness while preserving information specific to distinct biological groups.

Generative models have shown remarkable progress in a variety of domains such as protein design, but such power enables the opaque generation of hazardous proteins. In this work, we introduce VFUSE (Virulent Feature Understanding with Sparse autoEncoders), a mechanistic interpretability approach that trains SAEs on diffusion-transformer activations to audit protein models for hazard-aware features. We apply VFUSE to RoseTTAFold3 and RFDiffusion3, popular open-weight models for protein folding and synthesis. We find that for certain blocks, linear probes detect hazardous designs significantly better when fit in the SAE latent space over the original model's representations: improving interpretability without sacrificing model performance. Furthermore, we identify monosemantic features from the SAE that fire only on hazardous designs at up to AUROC $0.84$ ($q < 10^{-13}$). To our knowledge this is the first SAE trained on an all-atom diffusion model and the first feature-level virulence audit of a protein design model, paving the way towards safe and interpretable protein design.

Nucleotide sequences constitute the fundamental genetic basis of biological systems, rendering viral genomic analysis critical for biomedical advancement. Despite progress in biological foundation models, specifically nucleotide foundation models (NFMs), the field lacks a unified standard for viral genomics to facilitate community development and enforce biosecurity constraints. To address this, we introduce ViroBench, the first comprehensive and large-scale benchmark specifically designed for NFMs in viral settings. ViroBench evaluates models across two critical dimensions: biological understanding and latent biosecurity risk, covering 18 diverse scenarios within 4 task types. Extensive evaluation of 66 NFMs across diverse architectures yields three critical conclusions. Firstly, NFMs exhibit a performance degradation in biological understanding under phylogenetic and temporal shifts, indicating weak extrapolation capabilities. Secondly, generation tasks reveal a decoupling between statistical likelihood and biological functional validity, posing latent biosecurity risks. Thirdly, controlled ablation studies reveal that taxonomic diversity in pretraining data outweighs parameter scale. Specifically, a lightweight baseline trained on diverse data achieves a 67.5% performance gain over its original model. Overall, ViroBench provides interpretable, diagnostic evaluations and a reproducible measurement framework for future research on viral nucleotide foundation models. The datasets and code are publicly available at https://github.com/QIANJINYDX/ViroBench.

Accurate detection and counting of virus patches in focus-forming unit (FFU) images, also known as foci images, are important for quantifying viral infection and analyzing cellular structures. This task is challenging because biomedical targets often vary substantially in size, density, contrast, and shape. In this paper, we propose an enhanced YOLOv2-based detector that integrates a Feature Pyramid Network (FPN) to improve multi-scale feature representation. We also incorporate a switchable atrous convolution mechanism to adapt the receptive field for fine-grained targets in dense microscopy images. The proposed method is evaluated on biomedical foci image datasets for virus patch and small cell patch detection. For small cell patch detection, the model achieves a mean average precision (mAP) of 40.5% at a 25% Intersection over Union (IoU) threshold. For FFU virus patch detection, the model achieves an mAP of 68%. These results indicate that combining FPN-based feature fusion with switchable convolution improves the suitability of YOLOv2 for specialized biomedical object detection tasks

Standard clinical Natural Language Processing (NLP) benchmarks often yield inflated metrics by forcing deterministic classification on ambiguous instances, thereby obscuring the clinical risks of overconfident predictions. To bridge this gap, we propose a risk-aware hybrid selective classification framework, evaluated on early Human Immunodeficiency Virus suspicion identification in Spanish clinical notes. Our dual-verification approach explicitly decouples aleatoric uncertainty through Mondrian conformal prediction and epistemic uncertainty using a Multi-Centroid Mahalanobis Distance veto. Empirical evaluations reveal that standard uncertainty metrics and baseline classifiers are structurally insufficient for safe medical triage, suffering severe coverage collapse when forced to operate under strict reliability constraints. In contrast, by demanding that clinical narratives pass both probabilistic and geometric safeguards, the proposed framework successfully isolates a highly trustworthy operational domain.

Plaque assays remain the gold standard readout of virus infectivity; however, plaque counting from plate images is labor-intensive and prone to inter-operator variability. We present an end-to-end, computer-aided workflow for cytopathic effect-based virus titration directly from laboratory plaque assay images. The proposed approach combines two models derived from the Segment Anything Model (SAM): a SAM2-based well-segmentation module that localizes assay wells across heterogeneous imaging conditions, and a SAM-based plaque-segmentation model that detects and enumerates plaques within each well. The method was evaluated on a mixed dataset comprising private plaque assay images of Mayaro virus and Coxsackievirus B3, together with public Vaccinia virus images from the VACVPlaque dataset. The pipeline outputs per-well plaque counts, automatically computes plaque-forming units per milliliter (PFU/mL), and is integrated into a web-based platform that allows users to review results and organize experiments. On held-out plates (17 from MAYV/CVB3 and 22 from VACV), the workflow generalized across two plate formats (6-well and 12-well) and showed strong agreement with manual annotations (Pearson correlation coefficients of 0.92 for MAYV/CVB3 and 0.88 for VACV). Automated plaque counts were further compared with annotations from four independent experts, demonstrating high concordance. The proposed system will be open sourced and publicly released upon acceptance of this manuscript to enable reproducible, scalable, and audit-ready plaque assay analysis while substantially reducing manual annotation effort.

Treating and preventing Human Immunodeficiency Virus (HIV) remains a critical global health challenge. While antiretroviral therapy provides a path toward viral suppression -- effectively eliminating an individual's transmission risk -- systemic resource constraints limit the reach of intervention efforts. This work addresses the strategic distribution of intensive resources among virally unsuppressed individuals to minimize the expected cascade of new infections within a transmission network. We formalize this challenge as a novel constrained optimization problem where we have resources to "treat" $k$ out of a set $\mathbf{P}$ of virally unsuppressed individuals, and establish its theoretical connections to existing computational literature. We then propose Cascade-Aware Suppression of Transmission (CAST), a polynomial-time $(δ, ε)$-approximation algorithm that achieves a $2\sqrt{|\mathbf{P}|}$ approximation ratio by leveraging connections to the Minimum-$k$-Union (MkU) problem and Hoeffding-style concentration bounds. Extensive evaluations on real-world HIV networks demonstrate that CAST outperforms standard public health and computer science baselines. Furthermore, we show that CAST is empirically robust across diverse infectious disease networks, varied edge probability initializations, and settings involving imperfect network data.

The detection of sensational content in media items can be a critical filtering mechanism for identifying check-worthy content and flagging potential disinformation, since such content triggers physiological arousal that often bypasses critical evaluation and accelerates viral sharing. In this paper we introduce the task of sensational image detection, which aims to determine whether an image contains shocking, provocative, or emotionally charged features to grab attention and trigger strong emotional responses. To support research on this task, we create a new benchmark dataset (called Sens-VisualNews) that contains 9,576 images from news items, annotated based on the (in-)existence of various sensational concepts and events in their visual content. Finally, using Sens-VisualNews, we study the prompt sensitivity, performance and robustness of a wide range of open SotA Multimodal LLMs, across both zero-shot and fine-tuned settings.

Early identification of individuals at elevated risk of Chlamydia trachomatis infection may enable optimal use of molecular testing in resource-aware screening. We evaluate the feasibility of pre-test risk stratification (PTRS) using machine-learning models trained on routinely available, non-invasive clinical data. A curated dataset of 93 urine samples with PCR reference labels was analyzed using three feature groups: patient-reported history and symptoms, urine biomarkers from standard urinalysis, and their combination. Five supervised classifiers were evaluated using stratified 5-fold cross-validation with out-of-fold probability estimates. Performance was assessed using area under the receiver operating characteristic curve (AUC) and threshold-dependent metrics, with uncertainty quantified via bootstrap confidence intervals. Models using only patient-reported data showed moderate discrimination (AUC up to 0.72). Urine biomarker-based models demonstrated slightly lower peak discrimination but more consistent performance, with ensemble methods yielding the strongest results. Combining feature groups marginally increased the peak AUC and reduced performance variability across models, indicating improved robustness. Findings indicate that urine biomarkers provide a reliable predictive signal for PTRS that is complementary to patient-reported information, while feature integration enhances robustness. This work supports the integration of non-invasive, routinely available information for PTRS into screening workflows, including decentralized or home-based PCR contexts, to optimize testing prioritization.

The plaque reduction assay (PRA) remains the gold standard for antiviral susceptibility testing, evaluating drug potency by measuring reductions in plaque-forming units (PFUs). However, the traditional PRA is time-consuming, labor-intensive, prone to manual counting errors, and offers limited scalability. Moreover, its reliance on destructive fixation and chemical staining reduces the assay to a static, endpoint observation, obscuring the dynamic, time-resolved kinetics of dose-dependent viral inhibition. Here, we introduce a label-free, time-resolved PRA platform that transforms the conventional assay into a continuous, high-dimensional measurement of viral infection dynamics. Our system integrates a compact lens-free imaging setup with a custom-designed ultra-large-area (100 cm^2) thin-film transistor (TFT) image sensor and deep learning-based algorithms to autonomously quantify PFU dynamics within an incubator. Validated using herpes simplex virus type-1 (HSV-1) treated with acyclovir, the platform matched chemically-stained ground truth measurements with zero false positives while accelerating readout by ~26 hours. Crucially, our system revealed that increasing drug concentrations induce temporally distinct delays and suppress new PFU formation, enabling conclusive drug efficacy evaluations within ~60 hours post-infection. This scalable, label-free framework redefines antiviral susceptibility testing as a rapid, time-resolved and information-rich measurement framework, providing a generalizable platform for virology research, high-throughput drug screening, and clinical diagnostics.

Visual-inertial odometry (VIO) is widely used for mobile robot localization, but its long-term accuracy degrades without global constraints. Incorporating ranging sensors such as ultra-wideband (UWB) can mitigate drift; however, high-accuracy ranging usually requires well-deployed anchors, which is difficult to ensure in narrow or low-power environments. Moreover, most existing visual-inertial-ranging (VIR) fusion methods rely on discrete time-based filtering or optimization, making it difficult to balance positioning accuracy, trajectory consistency, and fusion efficiency under asynchronous multi-sensor sampling. To address these issues, we propose a spline-based continuous-time state estimation method for VIR fusion localization. In the preprocessing stage, VIO motion priors and UWB ranging measurements are used to construct virtual anchors and reject outliers, thereby alleviating geometric degeneration and improving range reliability. In the estimation stage, the pose trajectory is parameterized in continuous time using a B-spline, while inertial, visual, and ranging constraints are formulated as factors in a sliding-window graph. The spline control points, together with a small set of auxiliary parameters, are then jointly optimized to obtain a continuous-time trajectory estimate. Evaluations on public datasets and real-world experiments demonstrate the effectiveness and practical potential of the proposed approach.