iTARGET: Interpretable Tailored Age Regression for Grouped Epigenetic Traits

Accurately predicting chronological age from DNA methylation patterns is crucial for advancing biological age estimation. However, this task is made challenging by Epigenetic Correlation Drift (ECD) and Heterogeneity Among CpGs (HAC), which reflect the dynamic relationship between methylation and age across different life stages. To address these issues, we propose a novel two-phase algorithm. The first phase employs similarity searching to cluster methylation profiles by age group, while the second phase uses Explainable Boosting Machines (EBM) for precise, group-specific prediction. Our method not only improves prediction accuracy but also reveals key age-related CpG sites, detects age-specific changes in aging rates, and identifies pairwise interactions between CpG sites. Experimental results show that our approach outperforms traditional epigenetic clocks and machine learning models, offering a more accurate and interpretable solution for biological age estimation with significant implications for aging research.

Molecular Dynamics of Polymer-lipids in Solution from Supervised Machine Learning

Machine learning techniques including neural networks are popular tools for materials and chemical scientists with applications that may provide viable alternative methods in the analysis of structure and energetics of systems ranging from crystals to biomolecules. However, efforts are less abundant for prediction of dynamics. Here we explore the ability of three well established recurrent neural network architectures for forecasting the energetics of a macromolecular polymer-lipid aggregate solvated in ethyl acetate at ambient conditions. Data models generated from recurrent neural networks are trained and tested on nanoseconds-long time series of the intra-macromolecules potential energy and their interaction energy with the solvent generated from Molecular Dynamics and containing half million points. Our exhaustive analyses convey that the three recurrent neural network investigated generate data models with limited capability of reproducing the energetic fluctuations and yielding short or long term energetics forecasts with underlying distribution of points inconsistent with the input series distributions. We propose an in silico experimental protocol consisting on forming an ensemble of artificial network models trained on an ensemble of series with additional features from time series containing pre-clustered time patterns of the original series. The forecast process improves by predicting a band of forecasted time series with a spread of values consistent with the molecular dynamics energy fluctuations span. However, the distribution of points from the band of forecasts is not optimal. Although the three inspected recurrent neural networks were unable of generating single models that reproduce the actual fluctuations of the inspected molecular system energies in thermal equilibrium at the nanosecond scale, the proposed protocol provides useful estimates of the molecular fate