Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. Towards multimodal foundation models in molecular cell biology
 
research article

Towards multimodal foundation models in molecular cell biology

Cui, Haotian
•
Tejada-Lapuerta, Alejandro
•
Brbić, Maria  
Show more
April 17, 2025
Nature

The rapid advent of high-throughput omics technologies has created an exponential growth in biological data, often outpacing our ability to derive molecular insights. Large-language models have shown a way out of this data deluge in natural language processing by integrating massive datasets into a joint model with manifold downstream use cases. Here we envision developing multimodal foundation models, pretrained on diverse omics datasets, including genomics, transcriptomics, epigenomics, proteomics, metabolomics and spatial profiling. These models are expected to exhibit unprecedented potential for characterizing the molecular states of cells across a broad continuum, thereby facilitating the creation of holistic maps of cells, genes and tissues. Context-specific transfer learning of the foundation models can empower diverse applications from novel cell-type recognition, biomarker discovery and gene regulation inference, to in silico perturbations. This new paradigm could launch an era of artificial intelligence-empowered analyses, one that promises to unravel the intricate complexities of molecular cell biology, to support experimental design and, more broadly, to profoundly extend our understanding of life sciences.

  • Details
  • Metrics
Type
research article
DOI
10.1038/s41586-025-08710-y
Scopus ID

2-s2.0-105003389985

Author(s)
Cui, Haotian

University of Toronto

Tejada-Lapuerta, Alejandro

Helmholtz Center Munich German Research Center for Environmental Health

Brbić, Maria  

École Polytechnique Fédérale de Lausanne

Saez-Rodriguez, Julio

Universitätsklinikum Heidelberg

Cristea, Simona

Dana-Farber Cancer Institute

Goodarzi, Hani

Arc Institute

Lotfollahi, Mohammad

Wellcome Sanger Institute

Theis, Fabian J.

Helmholtz Center Munich German Research Center for Environmental Health

Wang, Bo

University of Toronto

Date Issued

2025-04-17

Published in
Nature
Volume

640

Issue

8059

Article Number

83

Start page

623

End page

633

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
MLBIO  
FunderFunding(s)Grant NumberGrant URL

Pfizer

Sanofi

Available on Infoscience
May 5, 2025
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/249712
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés