Non-negative tensor factorization workflow for time series biomedical data

Abstract

Summary: Non-negative tensor factorization (NTF) enables the extraction of a small number of latent components from high-dimensional biomedical data. However, NTF requires many steps, which is a hurdle to implementation. Here, we provide a protocol for TensorLyCV, an easy to run and reproducible NTF analysis pipeline using Snakemake workflow management system and Docker container. Using vaccine adverse reaction data as an example, we describe steps for data processing, tensor decomposition, optimal rank parameter estimation, and visualization of factor matrices.For complete details on the use and execution of this protocol, please refer to Kei Ikeda et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Health Sciences
• Computer sciences