Improving Omics-Based Classification: The Role of Feature Selection and Synthetic Data Generation

Given the increasing complexity of omics datasets, a key challenge is not only improving classification performance but also enhancing the transparency and reliability of model decisions. Effective model performance and feature selection are fundamental for explainability and reliability. In many cases, high dimensional omics datasets suffer from limited number of samples due to clinical constraints, patient conditions, phenotypes rarity and others conditions. Current omics based classification models often suffer from narrow interpretability, making it difficult to discern meaningful insights where trust and reproducibility are critical. This study presents a machine learning based classification framework that integrates feature selection with data augmentation techniques to achieve high standard classification accuracy while ensuring better interpretability. Using the publicly available dataset (E MTAB 8026), we explore a bootstrap analysis in six binary classification scenarios to evaluate the proposed model's behaviour. We show that the proposed pipeline yields cross validated perfomance on small dataset that is conserved when the trained classifier is applied to a larger test set. Our findings emphasize the fundamental balance between accuracy and feature selection, highlighting the positive effect of introducing synthetic data for better generalization, even in scenarios with very limited samples availability.

Uncovering Population PK Covariates from VAE-Generated Latent Spaces

Population pharmacokinetic (PopPK) modelling is a fundamental tool for understanding drug behaviour across diverse patient populations and enabling personalized dosing strategies to improve therapeutic outcomes. A key challenge in PopPK analysis lies in identifying and modelling covariates that influence drug absorption, as these relationships are often complex and nonlinear. Traditional methods may fail to capture hidden patterns within the data. In this study, we propose a data-driven, model-free framework that integrates Variational Autoencoders (VAEs) deep learning model and LASSO regression to uncover key covariates from simulated tacrolimus pharmacokinetic (PK) profiles. The VAE compresses high-dimensional PK signals into a structured latent space, achieving accurate reconstruction with a mean absolute percentage error (MAPE) of 2.26%. LASSO regression is then applied to map patient-specific covariates to the latent space, enabling sparse feature selection through L1 regularization. This approach consistently identifies clinically relevant covariates for tacrolimus including SNP, age, albumin, and hemoglobin which are retained across the tested regularization strength levels, while effectively discarding non-informative features. The proposed VAE-LASSO methodology offers a scalable, interpretable, and fully data-driven solution for covariate selection, with promising applications in drug development and precision pharmacotherapy.