Age Prediction by DNA Methylation in Neural Networks

Integrating ensemble and machine learning models for early prediction of pneumonia mortality using laboratory tests

Background

The recent use of artificial intelligence (AI) in medical research is noteworthy. However, most research has focused on medical imaging. Although the importance of laboratory tests in the clinical field is acknowledged by clinicians, they are undervalued in medical AI research. Our study aims to develop an early prediction AI model for pneumonia mortality, primarily using laboratory test results.

Materials and methods

We developed a mortality prediction model using initial laboratory results and basic clinical information of patients with pneumonia. Several machine learning (ML) models and a deep learning method-multilayer perceptron (MLP)-were selected for model development. The area under the receiver operating characteristic curve (AUROC) and F1-score were optimized to improve model performance. In addition, an ensemble model was developed by blending several models to improve the prediction performance. We used 80,940 data instances for model development.

Results

Among the ML models, XGBoost exhibited the best performance (AUROC = 0.8989, accuracy = 0.88, F1-score = 0.80). MLP achieved an AUROC of 0.8498, accuracy of 0.86, and F1-score of 0.75. The performance of the ensemble model was the best among the developed models, with an AUROC of 0.9006, accuracy of 0.90, and F1-score of 0.81. Several laboratory tests were conducted to identify risk factors that affect pneumonia mortality using the "Feature importance" technique and SHapley Additive exPlanations. We identified several laboratory results, including systolic blood pressure, serum glucose level, age, aspartate aminotransferase-to-alanine aminotransferase ratio, and monocyte-to-lymphocyte ratio, as significant predictors of mortality in patients with pneumonia.

Conclusions

Our study demonstrates that the ensemble model, incorporating XGBoost, CatBoost, and LGBM techniques, outperforms individual ML and deep learning models in predicting pneumonia mortality. Our findings emphasize the importance of integrating AI techniques to leverage laboratory test data effectively, offering a promising direction for advancing AI applications in medical research and clinical decision-making.

A multi-organization epigenetic age prediction based on a channel attention perceptron networks

DNA methylation indicates the individual's aging, so-called Epigenetic clocks, which will improve the research and diagnosis of aging diseases by investigating the correlation between methylation loci and human aging. Although this discovery has inspired many researchers to develop traditional computational methods to quantify the correlation and predict the chronological age, the performance bottleneck delayed access to the practical application. Since artificial intelligence technology brought great opportunities in research, we proposed a perceptron model integrating a channel attention mechanism named PerSEClock. The model was trained on 24,516 CpG loci that can utilize the samples from all types of methylation identification platforms and tested on 15 independent datasets against seven methylation-based age prediction methods. PerSEClock demonstrated the ability to assign varying weights to different CpG loci. This feature allows the model to enhance the weight of age-related loci while reducing the weight of irrelevant loci. The method is free to use for academics at www.dnamclock.com/#/original.

Evaluation of different computational methods for DNA methylation-based biological age

In recent years there has been a widespread interest in researching biomarkers of aging that could predict physiological vulnerability better than chronological age. Aging, in fact, is one of the most relevant risk factors for a wide range of maladies, and molecular surrogates of this phenotype could enable better patients stratification. Among the most promising of such biomarkers is DNA methylation-based biological age. Given the potential and variety of computational implementations (epigenetic clocks), we here present a systematic review of such clocks. Furthermore, we provide a large-scale performance comparison across different tissues and diseases in terms of age prediction accuracy and age acceleration, a measure of deviance from physiology. Our analysis offers both a state-of-the-art overview of the computational techniques developed so far and a heterogeneous picture of performances, which can be helpful in orienting future research.

Development of Machine-Learning Model to Predict COVID-19 Mortality: Application of Ensemble Model and Regarding Feature Impacts

This study was designed to develop machine-learning models to predict COVID-19 mortality and identify its key features based on clinical characteristics and laboratory tests. For this, deep-learning (DL) and machine-learning (ML) models were developed using receiver operating characteristic (ROC) area under the curve (AUC) and F1 score optimization of 87 parameters. Of the two, the DL model exhibited better performance (AUC 0.8721, accuracy 0.84, and F1 score 0.76). However, we also blended DL with ML, and the ensemble model performed the best (AUC 0.8811, accuracy 0.85, and F1 score 0.77). The DL model is generally unable to extract feature importance; however, we succeeded by using the Shapley Additive exPlanations method for each model. This study demonstrated both the applicability of DL and ML models for classifying COVID-19 mortality using hospital-structured data and that the ensemble model had the best predictive ability.