Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

A Performance-Explainability-Fairness Framework For Benchmarking ML Models

Machine learning (ML) models have achieved remarkable success in various applications; however, ensuring their robustness and fairness remains a critical challenge. In this research, we present a comprehensive framework designed to evaluate and benchmark ML models through the lenses of performance, explainability, and fairness. This framework addresses the increasing need for a holistic assessment of ML models, considering not only their predictive power but also their interpretability and equitable deployment. The proposed framework leverages a multi-faceted evaluation approach, integrating performance metrics with explainability and fairness assessments. Performance evaluation incorporates standard measures such as accuracy, precision, and recall, but extends to overall balanced error rate, overall area under the receiver operating characteristic (ROC) curve (AUC), to capture model behavior across different performance aspects. Explainability assessment employs state-of-the-art techniques to quantify the interpretability of model decisions, ensuring that model behavior can be understood and trusted by stakeholders. The fairness evaluation examines model predictions in terms of demographic parity, equalized odds, thereby addressing concerns of bias and discrimination in the deployment of ML systems. To demonstrate the practical utility of the framework, we apply it to a diverse set of ML algorithms across various functional domains, including finance, criminology, education, and healthcare prediction. The results showcase the importance of a balanced evaluation approach, revealing trade-offs between performance, explainability, and fairness that can inform model selection and deployment decisions. Furthermore, we provide insights into the analysis of tradeoffs in selecting the appropriate model for use cases where performance, interpretability and fairness are important. In summary, the Performance-Explainability-Fairness Framework offers a unified methodology for evaluating and benchmarking ML models, enabling practitioners and researchers to make informed decisions about model suitability and ensuring responsible and equitable AI deployment. We believe that this framework represents a crucial step towards building trustworthy and accountable ML systems in an era where AI plays an increasingly prominent role in decision-making processes

The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health.

Food and human health are inextricably linked. As such, revolutionary impacts on health have been derived from advances in the production and distribution of food relating to food safety and fortification with micronutrients. During the past two decades, it has become apparent that the human microbiome has the potential to modulate health, including in ways that may be related to diet and the composition of specific foods. Despite the excitement and potential surrounding this area, the complexity of the gut microbiome, the chemical composition of food, and their interplay in situ remains a daunting task to fully understand. However, recent advances in high-throughput sequencing, metabolomics profiling, compositional analysis of food, and the emergence of electronic health records provide new sources of data that can contribute to addressing this challenge. Computational science will play an essential role in this effort as it will provide the foundation to integrate these data layers and derive insights capable of revealing and understanding the complex interactions between diet, gut microbiome, and health. Here, we review the current knowledge on diet-health-gut microbiota, relevant data sources, bioinformatics tools, machine learning capabilities, as well as the intellectual property and legislative regulatory landscape. We provide guidance on employing machine learning and data analytics, identify gaps in current methods, and describe new scenarios to be unlocked in the next few years in the context of current knowledge

Automatic segmentation of multiple cardiovascular structures from cardiac computed tomography angiography images using deep learning.

OBJECTIVES:To develop, demonstrate and evaluate an automated deep learning method for multiple cardiovascular structure segmentation. BACKGROUND:Segmentation of cardiovascular images is resource-intensive. We design an automated deep learning method for the segmentation of multiple structures from Coronary Computed Tomography Angiography (CCTA) images. METHODS:Images from a multicenter registry of patients that underwent clinically-indicated CCTA were used. The proximal ascending and descending aorta (PAA, DA), superior and inferior vena cavae (SVC, IVC), pulmonary artery (PA), coronary sinus (CS), right ventricular wall (RVW) and left atrial wall (LAW) were annotated as ground truth. The U-net-derived deep learning model was trained, validated and tested in a 70:20:10 split. RESULTS:The dataset comprised 206 patients, with 5.130 billion pixels. Mean age was 59.9 ± 9.4 yrs., and was 42.7% female. An overall median Dice score of 0.820 (0.782, 0.843) was achieved. Median Dice scores for PAA, DA, SVC, IVC, PA, CS, RVW and LAW were 0.969 (0.979, 0.988), 0.953 (0.955, 0.983), 0.937 (0.934, 0.965), 0.903 (0.897, 0.948), 0.775 (0.724, 0.925), 0.720 (0.642, 0.809), 0.685 (0.631, 0.761) and 0.625 (0.596, 0.749) respectively. Apart from the CS, there were no significant differences in performance between sexes or age groups. CONCLUSIONS:An automated deep learning model demonstrated segmentation of multiple cardiovascular structures from CCTA images with reasonable overall accuracy when evaluated on a pixel level

Early Prediction of Diabetes Using Deep Learning Convolution Neural Network and Harris Hawks Optimization

 Owing to the gravity of the diabetic disease the minimal level symptoms for diabetic failure in the early stage must be forecasted. The prediction system instantaneous and prior must thus be developed to eliminate serious medical factors. Information gathered from Pima Indian Diabetic dataset are synthesized through a profound learning approach that provides features for diabetic level information. Metadata is used to enhance the recognition process for the profound learned features. The distinct details retrieved by integrated machine and computer technology, including glucose level, health information, age, insulin level, etc. Due to the efficacious Hawks Optimization Algorithm (HOA), the data's insignificant participation in diabetic diagnostic processes is minimized in process analysis luminosity. Diabetic disease has been categorized with Deep Learning Convolution Networks (DLCNN) from among the chosen diabetic characteristics. The process output developed is measured on the basis of test results in terms of error rate, sensitivity, specificity and accuracy