Pretrained-Guided Conditional Diffusion Models for Microbiome Data Analysis
This addresses data quality issues in microbiome analysis for cancer research, though it is incremental as it builds on existing diffusion and VAE techniques.
The paper tackles missing data in microbiome-cancer studies by introducing mbVDiT, a pre-trained conditional diffusion model that uses unmasked data and patient metadata for imputation, achieving improved performance on datasets from three cancer types compared to existing methods.
Emerging evidence indicates that human cancers are intricately linked to human microbiomes, forming an inseparable connection. However, due to limited sample sizes and significant data loss during collection for various reasons, some machine learning methods have been proposed to address the issue of missing data. These methods have not fully utilized the known clinical information of patients to enhance the accuracy of data imputation. Therefore, we introduce mbVDiT, a novel pre-trained conditional diffusion model for microbiome data imputation and denoising, which uses the unmasked data and patient metadata as conditional guidance for imputating missing values. It is also uses VAE to integrate the the other public microbiome datasets to enhance model performance. The results on the microbiome datasets from three different cancer types demonstrate the performance of our methods in comparison with existing methods.