Explainable artificial intelligence and microbiome data for food geographical origin: the Mozzarella di Bufala Campana PDO Case of Study.

Identifying the origin of a food product holds paramount importance in ensuring food safety, quality, and authenticity. Knowing where a food item comes from provides crucial information about its production methods, handling practices, and potential exposure to contaminants. Machine learning techniques play a pivotal role in this process by enabling the analysis of complex data sets to uncover patterns and associations that can reveal the geographical source of a food item. This study aims to investigate the potential use of explainable artificial intelligence for identifying the food origin. The case of study of Mozzarella di Bufala Campana PDO has been considered by examining the composition of the microbiota in each samples. Three different supervised machine learning algorithms have been compared and the best classifier model is represented by Random Forest with an Area Under the Curve (AUC) value of 0.93 and the top accuracy of 0.87. Machine learning models effectively classify origin, offering innovative ways to authenticate regional products and support local economies. Further research can explore microbiota analysis and extend applicability to diverse food products and contexts for enhanced accuracy and broader impact.

Air pollution and mortality for cancer of the respiratory system in Italy: an explainable artificial intelligence approach.

Respiratory system cancer, encompassing lung, trachea and bronchus cancer, constitute a substantial and evolving public health challenge. Since pollution plays a prominent cause in the development of this disease, identifying which substances are most harmful is fundamental for implementing policies aimed at reducing exposure to these substances. We propose an approach based on explainable artificial intelligence (XAI) based on remote sensing data to identify the factors that most influence the prediction of the standard mortality ratio (SMR) for respiratory system cancer in the Italian provinces using environment and socio-economic data. First of all, we identified 10 clusters of provinces through the study of the SMR variogram. Then, a Random Forest regressor is used for learning a compact representation of data. Finally, we used XAI to identify which features were most important in predicting SMR values. Our machine learning analysis shows that NO, income and O3 are the first three relevant features for the mortality of this type of cancer, and provides a guideline on intervention priorities in reducing risk factors.

Insights from Explainable Artificial Intelligence of Pollution and Socioeconomic Influences for Respiratory Cancer Mortality in Italy.

Respiratory malignancies, encompassing cancers affecting the lungs, the trachea, and the bronchi, pose a significant and dynamic public health challenge. Given that air pollution stands as a significant contributor to the onset of these ailments, discerning the most detrimental agents becomes imperative for crafting policies aimed at mitigating exposure. This study advocates for the utilization of explainable artificial intelligence (XAI) methodologies, leveraging remote sensing data, to ascertain the primary influencers on the prediction of standard mortality rates (SMRs) attributable to respiratory cancer across Italian provinces, utilizing both environmental and socioeconomic data. By scrutinizing thirteen distinct machine learning algorithms, we endeavor to pinpoint the most accurate model for categorizing Italian provinces as either above or below the national average SMR value for respiratory cancer. Furthermore, employing XAI techniques, we delineate the salient factors crucial in predicting the two classes of SMR. Through our machine learning scrutiny, we illuminate the environmental and socioeconomic factors pertinent to mortality in this disease category, thereby offering a roadmap for prioritizing interventions aimed at mitigating risk factors.

Explainable artificial intelligence for microbiome data analysis in colorectal cancer biomarker identification.

Background: Colorectal cancer (CRC) is a type of tumor caused by the uncontrolled growth of cells in the mucosa lining the last part of the intestine. Emerging evidence underscores an association between CRC and gut microbiome dysbiosis. The high mortality rate of this cancer has made it necessary to develop new early diagnostic methods. Machine learning (ML) techniques can represent a solution to evaluate the interaction between intestinal microbiota and host physiology. Through explained artificial intelligence (XAI) it is possible to evaluate the individual contributions of microbial taxonomic markers for each subject. Our work also implements the Shapley Method Additive Explanations (SHAP) algorithm to identify for each subject which parameters are important in the context of CRC. Results: The proposed study aimed to implement an explainable artificial intelligence framework using both gut microbiota data and demographic information from subjects to classify a cohort of control subjects from those with CRC. Our analysis revealed an association between gut microbiota and this disease. We compared three machine learning algorithms, and the Random Forest (RF) algorithm emerged as the best classifier, with a precision of 0.729 ± 0.038 and an area under the Precision-Recall curve of 0.668 ± 0.016. Additionally, SHAP analysis highlighted the most crucial variables in the model's decision-making, facilitating the identification of specific bacteria linked to CRC. Our results confirmed the role of certain bacteria, such as Fusobacterium, Peptostreptococcus, and Parvimonas, whose abundance appears notably associated with the disease, as well as bacteria whose presence is linked to a non-diseased state. Discussion: These findings emphasizes the potential of leveraging gut microbiota data within an explainable AI framework for CRC classification. The significant association observed aligns with existing knowledge. The precision exhibited by the RF algorithm reinforces its suitability for such classification tasks. The SHAP analysis not only enhanced interpretability but identified specific bacteria crucial in CRC determination. This approach opens avenues for targeted interventions based on microbial signatures. Further exploration is warranted to deepen our understanding of the intricate interplay between microbiota and health, providing insights for refined diagnostic and therapeutic strategies.

Unraveling the microbiome-metabolome nexus: a comprehensive study protocol for personalized management of Behçet's disease using explainable artificial intelligence.

The presented study protocol outlines a comprehensive investigation into the interplay among the human microbiota, volatilome, and disease biomarkers, with a specific focus on Behçet's disease (BD) using methods based on explainable artificial intelligence. The protocol is structured in three phases. During the initial three-month clinical study, participants will be divided into control and experimental groups. The experimental groups will receive a soluble fiber-based dietary supplement alongside standard therapy. Data collection will encompass oral and fecal microbiota, breath samples, clinical characteristics, laboratory parameters, and dietary habits. The subsequent biological data analysis will involve gas chromatography, mass spectrometry, and metagenetic analysis to examine the volatilome and microbiota composition of salivary and fecal samples. Additionally, chemical characterization of breath samples will be performed. The third phase introduces Explainable Artificial Intelligence (XAI) for the analysis of the collected data. This novel approach aims to evaluate eubiosis and dysbiosis conditions, identify markers associated with BD, dietary habits, and the supplement. Primary objectives include establishing correlations between microbiota, volatilome, phenotypic BD characteristics, and identifying patient groups with shared features. The study aims to identify taxonomic units and metabolic markers predicting clinical outcomes, assess the supplement's impact, and investigate the relationship between dietary habits and patient outcomes. This protocol contributes to understanding the microbiome's role in health and disease and pioneers an XAI-driven approach for personalized BD management. With 70 recruited BD patients, XAI algorithms will analyze multi-modal clinical data, potentially revolutionizing BD management and paving the way for improved patient outcomes.

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.

Every year, 11% of infants are born preterm with significant health consequences, with the vaginal microbiome a risk factor for preterm birth. We crowdsource models to predict (1) preterm birth (PTB; <37 weeks) or (2) early preterm birth (ePTB; <32 weeks) from 9 vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from public raw data via phylogenetic harmonization. The predictive models are validated on two independent unpublished datasets representing 331 samples from 148 pregnant individuals. The top-performing models (among 148 and 121 submissions from 318 teams) achieve area under the receiver operator characteristic (AUROC) curve scores of 0.69 and 0.87 predicting PTB and ePTB, respectively. Alpha diversity, VALENCIA community state types, and composition are important features in the top-performing models, most of which are tree-based methods. This work is a model for translation of microbiome data into clinically relevant predictive models and to better understand preterm birth.

Machine learning approaches in microbiome research: challenges and best practices.

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 non-experts alike in translational applications.

Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research.

Globally, every year about 11% of infants are born preterm, defined as a birth prior to 37 weeks of gestation, with significant and lingering health consequences. Multiple studies have related the vaginal microbiome to preterm birth. We present a crowdsourcing approach to predict: (a) preterm or (b) early preterm birth from 9 publicly available vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from raw sequences via an open-source tool, MaLiAmPi. We validated the crowdsourced models on novel datasets representing 331 samples from 148 pregnant individuals. From 318 DREAM challenge participants we received 148 and 121 submissions for our two separate prediction sub-challenges with top-ranking submissions achieving bootstrapped AUROC scores of 0.69 and 0.87, respectively. Alpha diversity, VALENCIA community state types, and composition (via phylotype relative abundance) were important features in the top performing models, most of which were tree based methods. This work serves as the foundation for subsequent efforts to translate predictive tests into clinical practice, and to better understand and prevent preterm birth.