Towards virtual cells - the need for actionable, robust perturbation models

Abstract

Computational cell biology is evolving from descriptive atlases to predictive, actionable models — from mapping what cells are to simulating what they do. In this talk, I will outline progress toward virtual cells, focusing on machine learning approaches that enable robust perturbation modeling.

Among others, I will present scConcept, a framework that differs from large-scale foundation models such as Geneformer by learning in the latent space through control-based objectives. Rather than passively embedding cellular states, scConcept explicitly models transitions between them, capturing how cells move through gene-expression space in response to context and perturbation.

Building on this foundation, I will introduce CellFlow, a generative perturbation model that predicts how interventions — such as drugs, cytokines, or gene edits — reshape cellular phenotypes. By learning causal directions of change, CellFlow enables in silico experimentation and virtual screening of differentiation protocols.

Together, these developments point toward virtual cells: computational counterparts capable of robustly predicting and designing biological behavior.

Speaker Bio

Prof. Fabian Theis is internationally recognized for pioneering work at the interface of artificial intelligence, machine learning, and biomedicine. As Head of the Computational Health Center at Helmholtz Munich and Chair for Mathematical Models of Biological Systems at the Technical University of Munich, he leads cutting-edge research on multimodal data integration, single-cell and spatial omics, and AI-powered modeling of cell states in health and disease.

A founding force behind Helmholtz.AI and co-director of several national and European AI initiatives, Theis plays a key role in shaping the biomedical AI landscape. He is a core contributor to the Human Cell Atlas and has driven the development of widely adopted computational tools in the life sciences.

His achievements have been recognized with numerous honors, including the Gottfried Wilhelm Leibniz Prize (2023), the ISCB Innovator Award (2025), and an ERC Advanced Grant (2022). In 2025, he was elected to the German National Academy of Sciences Leopoldina and appointed Chair of the Bavarian AI Council.

Beyond academia, Theis actively advises biotech companies and drives translational AI research towards clinical applications and precision medicine.