Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

Introduction: Substance use disorders (SUDs) have emerged as a pressing public health crisis in the United States, with adolescent substance use often leading to SUDs in adulthood. Effective strategies are needed to prevent this progression. To help in filling this need, we develop a novel and the first-ever absolute risk prediction model for cannabis use disorder (CUD) for adolescent or young adult cannabis users. Methods: We train a Bayesian machine learning model that provides a personalized CUD absolute risk for adolescent or young adult cannabis users using data from the National Longitudinal Study of Adolescent to Adult Health. Model performance is assessed using 5-fold cross-validation (CV) with area under the curve (AUC) and ratio of the expected to observed number of cases (E/O). External validation of the final model is conducted using two independent datasets. Results: The proposed model has five risk factors: biological sex, delinquency, and scores on personality traits of conscientiousness, neuroticism, and openness. For predicting CUD risk within five years of first cannabis use, AUC and E/O, computed via 5-fold CV, were 0.68 and 0.95, respectively. For the same type of prediction in external validation, AUC values were 0.64 and 0.75, with E/O values of 0.98 and 1, indicating good discrimination and calibration performances of the model. Discussion and Conclusion: The proposed model is the first absolute risk prediction model for an SUD. It can aid clinicians in identifying adolescent/youth substance users at a high risk of developing CUD in future for clinically appropriate interventions.

Accurate molecular quantification is essential for advancing research and diagnostics in fields such as infectious diseases, cancer biology, and genetic disorders. Droplet digital PCR (ddPCR) has emerged as a gold standard for achieving absolute quantification. While computational ddPCR technologies have advanced significantly, achieving automatic interpretation and consistent adaptability across diverse operational environments remains a challenge. To address these limitations, we introduce the intelligent interpretable droplet digital PCR (I2ddPCR) assay, a comprehensive framework integrating front-end predictive models (for droplet segmentation and classification) with GPT-4o multimodal large language model (MLLM, for context-aware explanations and recommendations) to automate and enhance ddPCR image analysis. This approach surpasses the state-of-the-art models, affording 99.05% accuracy in processing complex ddPCR images containing over 300 droplets per image with varying signal-to-noise ratios (SNRs). By combining specialized neural networks and large language models, the I2ddPCR assay offers a robust and adaptable solution for absolute molecular quantification, achieving a sensitivity capable of detecting low-abundance targets as low as 90.32 copies/{\mu}L. Furthermore, it improves model's transparency through detailed explanation and troubleshooting guidance, empowering users to make informed decisions. This innovative framework has the potential to benefit molecular diagnostics, disease research, and clinical applications, especially in resource-constrained settings.

Mapping land surface disturbances supports disaster response, resource and ecosystem management, and climate adaptation efforts. Synthetic aperture radar (SAR) is an invaluable tool for disturbance mapping, providing consistent time-series images of the ground regardless of weather or illumination conditions. Despite SAR's potential for disturbance mapping, processing SAR data to an analysis-ready format requires expertise and significant compute resources, particularly for large-scale global analysis. In October 2023, NASA's Observational Products for End-Users from Remote Sensing Analysis (OPERA) project released the near-global Radiometric Terrain Corrected SAR backscatter from Sentinel-1 (RTC-S1) dataset, providing publicly available, analysis-ready SAR imagery. In this work, we utilize this new dataset to systematically analyze land surface disturbances. As labeling SAR data is often prohibitively time-consuming, we train a self-supervised vision transformer - which requires no labels to train - on OPERA RTC-S1 data to estimate a per-pixel distribution from the set of baseline imagery and assess disturbances when there is significant deviation from the modeled distribution. To test our model's capability and generality, we evaluate three different natural disasters - which represent high-intensity, abrupt disturbances - from three different regions of the world. Across events, our approach yields high quality delineations: F1 scores exceeding 0.6 and Areas Under the Precision-Recall Curve exceeding 0.65, consistently outperforming existing SAR disturbance methods. Our findings suggest that a self-supervised vision transformer is well-suited for global disturbance mapping and can be a valuable tool for operational, near-global disturbance monitoring, particularly when labeled data does not exist.

Measurement quality assurance (QA) practices play a key role in the safe use of Intensity Modulated Radiation Therapies (IMRT) for cancer treatment. These practices have reduced measurement-based IMRT QA failure below 1%. However, these practices are time and labor intensive which can lead to delays in patient care. In this study, we examine how conformal prediction methodologies can be used to robustly triage plans. We propose a new training-aware conformal risk control method by combining the benefit of conformal risk control and conformal training. We incorporate the decision making thresholds based on the gamma passing rate, along with the risk functions used in clinical evaluation, into the design of the risk control framework. Our method achieves high sensitivity and specificity and significantly reduces the number of plans needing measurement without generating a huge confidence interval. Our results demonstrate the validity and applicability of conformal prediction methods for improving efficiency and reducing the workload of the IMRT QA process.

Recently there have been many shared tasks targeting the detection of generated text from Large Language Models (LLMs). However, these shared tasks tend to focus either on cases where text is limited to one particular domain or cases where text can be from many domains, some of which may not be seen during test time. In this shared task, using the newly released RAID benchmark, we aim to answer whether or not models can detect generated text from a large, yet fixed, number of domains and LLMs, all of which are seen during training. Over the course of three months, our task was attempted by 9 teams with 23 detector submissions. We find that multiple participants were able to obtain accuracies of over 99% on machine-generated text from RAID while maintaining a 5% False Positive Rate -- suggesting that detectors are able to robustly detect text from many domains and models simultaneously. We discuss potential interpretations of this result and provide directions for future research.

Background: Adolescents are particularly vulnerable to mental disorders, with over 75% of cases manifesting before the age of 25. Research indicates that only 18 to 34% of young people experiencing high levels of depression or anxiety symptoms seek support. Digital tools leveraging smartphones offer scalable and early intervention opportunities. Objective: Using a novel machine learning framework, this study evaluated the feasibility of integrating active and passive smartphone data to predict mental disorders in non-clinical adolescents. Specifically, we investigated the utility of the Mindcraft app in predicting risks for internalising and externalising disorders, eating disorders, insomnia and suicidal ideation. Methods: Participants (N=103; mean age 16.1 years) were recruited from three London schools. Participants completed the Strengths and Difficulties Questionnaire, the Eating Disorders-15 Questionnaire, Sleep Condition Indicator Questionnaire and indicated the presence/absence of suicidal ideation. They used the Mindcraft app for 14 days, contributing active data via self-reports and passive data from smartphone sensors. A contrastive pretraining phase was applied to enhance user-specific feature stability, followed by supervised fine-tuning. The model evaluation employed leave-one-subject-out cross-validation using balanced accuracy as the primary metric. Results: The integration of active and passive data achieved superior performance compared to individual data sources, with mean balanced accuracies of 0.71 for SDQ-High risk, 0.67 for insomnia, 0.77 for suicidal ideation and 0.70 for eating disorders. The contrastive learning framework stabilised daily behavioural representations, enhancing predictive robustness. This study demonstrates the potential of integrating active and passive smartphone data with advanced machine-learning techniques for predicting mental health risks.

Recent work proposed the computation of so-called PI-explanations of Naive Bayes Classifiers (NBCs). PI-explanations are subset-minimal sets of feature-value pairs that are sufficient for the prediction, and have been computed with state-of-the-art exact algorithms that are worst-case exponential in time and space. In contrast, we show that the computation of one PI-explanation for an NBC can be achieved in log-linear time, and that the same result also applies to the more general class of linear classifiers. Furthermore, we show that the enumeration of PI-explanations can be obtained with polynomial delay. Experimental results demonstrate the performance gains of the new algorithms when compared with earlier work.

The COVID-19 pandemic has profoundly impacted billions globally. It challenges public health and healthcare systems due to its rapid spread and severe respiratory effects. An effective strategy to mitigate the COVID-19 pandemic involves integrating testing to identify infected individuals. While RT-PCR is considered the gold standard for diagnosing COVID-19, it has some limitations such as the risk of false negatives. To address this problem, this paper introduces a novel Deep Learning Diagnosis System that integrates pre-trained Deep Convolutional Neural Networks (DCNNs) within an ensemble learning framework to achieve precise identification of COVID-19 cases from Chest X-ray (CXR) images. We combine feature vectors from the final hidden layers of pre-trained DCNNs using the Choquet integral to capture interactions between different DCNNs that a linear approach cannot. We employed Sugeno-$\lambda$ measure theory to derive fuzzy measures for subsets of networks to enable aggregation. We utilized Differential Evolution to estimate fuzzy densities. We developed a TensorFlow-based layer for Choquet operation to facilitate efficient aggregation, due to the intricacies involved in aggregating feature vectors. Experimental results on the COVIDx dataset show that our ensemble model achieved 98\% accuracy in three-class classification and 99.50\% in binary classification, outperforming its components-DenseNet-201 (97\% for three-class, 98.75\% for binary), Inception-v3 (96.25\% for three-class, 98.50\% for binary), and Xception (94.50\% for three-class, 98\% for binary)-and surpassing many previous methods.

Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular biology", capturing intricate gene expression patterns at the single-cell level. However, interacting with this "language" through conventional tools is often inefficient and unintuitive, posing challenges for researchers. To address these limitations, we present InstructCell, a multi-modal AI copilot that leverages natural language as a medium for more direct and flexible single-cell analysis. We construct a comprehensive multi-modal instruction dataset that pairs text-based instructions with scRNA-seq profiles from diverse tissues and species. Building on this, we develop a multi-modal cell language architecture capable of simultaneously interpreting and processing both modalities. InstructCell empowers researchers to accomplish critical tasks--such as cell type annotation, conditional pseudo-cell generation, and drug sensitivity prediction--using straightforward natural language commands. Extensive evaluations demonstrate that InstructCell consistently meets or exceeds the performance of existing single-cell foundation models, while adapting to diverse experimental conditions. More importantly, InstructCell provides an accessible and intuitive tool for exploring complex single-cell data, lowering technical barriers and enabling deeper biological insights.