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Persistent free radicals (PFRs) are emerging substances with diverse impacts in biochar applications, necessitating accurate prediction of their content and types prior to their optimal use and minimal adverse effects. This prediction task is challenging due to the nonlinearity and intricate variable relationships of biochar. Herein, we employed data-driven techniques to compile a dataset from peer-reviewed publications, aiming to systematically predict the PFRs by developing supervised machine learning models. Notably, extreme gradient boosting (XGBoost) model exhibited the best predictive performance for both regression and classification tasks in predicting the PFRs, achieving a test R2 value of 0.95 for PFR content prediction, along with an Area Under the Receiver Operating Curve (AUROC) of 0.92 for PFR type prediction, respectively. Based on XGBoost model, a graphical user interface (GUI) was developed to access PFRs predictions. Analysis of feature importance revealed that the biochar properties, such as metal/non-metal doping, pyrolysis temperature, carbon content, and specific surface area were identified as the four most significant factors influencing PFRs contents. Regarding the types of PFRs in biochar, specific surface area, pyrolysis temperature, carbon content, and feedstock were top-ranked influencing factors. These findings provide valuable guidance for accurately predicting both the contents and types of PFRs in biochar, and also hold significant potential for highly efficient utilization of biochar across various applications. Highlights: • Recognizing dual nature of PFRs, a machine-learning framework predicts them in biochar. • XGBoost excels, achieving an R2 (0.95) for PFR content and an AUROC (0.92) for PFR type. • Important factors of PFR: doping, pyrolysis temp, carbon, and surface area. • GUI enhances accessibility, enabling PFR predictions before biochar preparation. [ABSTRACT FROM AUTHOR]

Introduction: Microbes are increasingly (re)considered for environmental assessments because they are powerful indicators for the health of ecosystems. The complexity of microbial communities necessitates powerful novel tools to derive conclusions for environmental decision-makers, and machine learning is a promising option in that context. While amplicon sequencing is typically applied to assess microbial communities, metagenomics and total RNA sequencing (herein summarized as omics-based methods) can provide a more holistic picture of microbial biodiversity at sufficient sequencing depths. Despite this advantage, amplicon sequencing and omics-based methods have not yet been compared for taxonomy-based environmental assessments with machine learning. Methods: In this study, we applied 16S and ITS-2 sequencing, metagenomics, and total RNA sequencing to samples from a stream mesocosm experiment that investigated the impacts of two aquatic stressors, insecticide and increased fine sediment deposition, on stream biodiversity. We processed the data using similarity clustering and denoising (only applicable to amplicon sequencing) as well as multiple taxonomic levels, data types, feature selection, and machine learning algorithms and evaluated the stressor prediction performance of each generated model for a total of 1,536 evaluated combinations of taxonomic datasets and data-processing methods. Results: Sequencing and data-processing methods had a substantial impact on stressor prediction. While omics-based methods detected a higher diversity of taxa than amplicon sequencing, 16S sequencing outperformed all other sequencing methods in terms of stressor prediction based on the Matthews Correlation Coefficient. However, even the highest observed performance for 16S sequencing was still only moderate. Omics-based methods performed poorly overall, but this was likely due to insufficient sequencing depth. Data types had no impact on performance while feature selection significantly improved performance for omicsbased methods but not for amplicon sequencing. Discussion: We conclude that amplicon sequencing might be a better candidate for machine-learning-based environmental stressor prediction than omics-based methods, but the latter require further research at higher sequencing depths to confirm this conclusion. More sampling could improve stressor prediction performance, and while this was not possible in the context of our study, thousands of sampling sites are monitored for routine environmental assessments, providing an ideal framework to further refine the approach for possible implementation in environmental diagnostics. [ABSTRACT FROM AUTHOR]

Microbiome data predictive analysis within a machine learning (ML) workflow presents numerous domain-specific challenges involving preprocessing, feature selection, predictive modeling, performance estimation, model interpretation, and the extraction of biological information from the results. To assist decision-making, we offer a set of recommendations on algorithm selection, pipeline creation and evaluation, stemming from the COST Action ML4Microbiome. We compared the suggested approaches on a multi-cohort shotgun metagenomics dataset of colorectal cancer patients, focusing on their performance in disease diagnosis and biomarker discovery. It is demonstrated that the use of compositional transformations and filtering methods as part of data preprocessing does not always improve the predictive performance of a model. In contrast, the multivariate feature selection, such as the Statistically Equivalent Signatures algorithm, was effective in reducing the classification error. When validated on a separate test dataset, this algorithm in combination with random forest modeling, provided the most accurate performance estimates. Lastly, we showed how linear modeling by logistic regression coupled with visualization techniques such as Individual Conditional Expectation (ICE) plots can yield interpretable results and offer biological insights. These findings are significant for clinicians and nonexperts alike in translational applications. [ABSTRACT FROM AUTHOR]