Non-negative tensor factorization workflow for time series biomedical data

Koki Tsuyuzaki, Naoki Yoshida, Tetsuo Ishikawa, Yuki Goshima, Eiryo Kawakami

Research output: Contribution to journalArticlepeer-review

Abstract

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

Original languageEnglish
Article number102318
JournalSTAR Protocols
Volume4
Issue number3
DOIs
Publication statusPublished - 2023 Sept 15

Keywords

  • Bioinformatics
  • Computer sciences
  • Health Sciences

ASJC Scopus subject areas

  • General Neuroscience
  • General Biochemistry,Genetics and Molecular Biology
  • General Immunology and Microbiology

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