LEOPARD : missing view completion for multi-timepoint omics data via representation disentanglement and temporal knowledge transfer

Han, Siyu (author), Adamski, Jerzy (author), Wang-Sattler, Rui (author)

Longitudinal multi-view omics data offer unique insights into the temporal dynamics of individual-level physiology, which provides opportunities to advance personalized healthcare. However, the common occurrence of incomplete views makes extrapolation tasks difficult, and there is a lack of tailored methods for this critical issue. Here, we introduce LEOPARD, an innovative approach specifically designed to complete missing views in multi-timepoint omics data. By disentangling longitudinal omics data into content and temporal representations, LEOPARD transfers the temporal knowledge to the omics-specific content, thereby completing missing views. The effectiveness of LEOPARD is validated on four real-world omics datasets constructed with data from the MGH COVID study and the KORA cohort, spanning periods from 3 days to 14 years. Compared to conventional imputation methods, such as missForest, PMM, GLMM, and cGAN, LEOPARD yields the most robust results across the benchmark datasets. LEOPARD-imputed data also achieve the highest agreement with observed data in our analyses for age-associated metabolites detection, estimated glomerular filtration rate-associated proteins identification, and chronic kidney disease prediction. Our work takes the first step toward a generalized treatment of missing views in longitudinal omics data, enabling comprehensive exploration of temporal dynamics and providing valuable insights into personalized healthcare.

• Language: English
• Keywords: multi-timepoint omics data, representation, temporal knowledge transfer
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: MF - Faculty of Medicine
• Publication status: Published
• Publication version: Version of Record
• Year: 2025
• Number of pages: 20 str.
• Numbering: Vol. 16, art. 3278
• PID: 20.500.12556/RUL-181916
• UDC: 577:61
• ISSN on article: 2041-1723
• DOI: 10.1038/s41467-025-58314-3
• COBISS.SI-ID: 264903171
• Publication date in RUL: 20.04.2026

Record is a part of a journal

• Title: Nature communications
• Shortened title: Nat. Commun.
• Publisher: Nature Publishing Group
• ISSN: 2041-1723
• COBISS.SI-ID: 2315876

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: veččasovni omični podatki, reprezentacija, časovni prenos znanja