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categories: ["foundations", "genetics"]categories: ["foundations", "genetics"]tags: ["machine learning", "systems biology", "simulation", "computational modelling", "single cell", "foundation models"]tags: ["machine learning", "systems biology", "simulation", "computational modelling", "single cell", "foundation models"]summary: "Computational models that simulate a cell's molecular behaviour, from complete cell cycles of minimal bacteria to learned predictions of how human cells respond to perturbation."summary: "Computational models that simulate a cell's molecular behaviour, from complete cell cycles of minimal bacteria to learned predictions of how human cells respond to perturbation."updated: "2026-08-22"updated: "2026-08-23"humanEvidence: "Complete whole-cell models exist only for minimal bacteria; learned models of human cell lines predict part of the transcriptional response to gene silencing, and none is validated as a model of a whole human cell."humanEvidence: "Complete whole-cell models exist only for minimal bacteria; learned models of human cell lines predict part of the transcriptional response to gene silencing, and none is validated as a model of a whole human cell."access: "Most models and datasets are public, including Recon3D, Geneformer, scGPT and Arc's State; commercial world models are proprietary and released as previews to selected academic and industry users."access: "Most models and datasets are public, including Recon3D, Geneformer, scGPT and Arc's State; commercial world models are proprietary and released as previews to selected academic and industry users."reversibility: "context"reversibility: "context"lines 48–53 → 48–5733 unchanged lines not shown
The cost is that the parameters have to come from somewhere. That model needed roughly 1,800 ofThe cost is that the parameters have to come from somewhere. That model needed roughly 1,800 ofthem, assembled from the published literature on an organism with about 525 genes. A human cell hasthem, assembled from the published literature on an organism with about 525 genes. A human cell hasroughly twenty thousand.roughly twenty thousand. ```figure{"key": "mycoplasma-3d-cell-model", "caption": "A spatial model of the same bacterium the 2012 dynamical model simulated: a molecular census placed in space at one instant. No model of any cell yet combines this structure with dynamics."}``` Learned models take the opposite route and assume nothing about mechanism. Geneformer converts eachLearned models take the opposite route and assume nothing about mechanism. Geneformer converts eachcell's expression profile into a sequence of gene tokens ranked by abundance and trains acell's expression profile into a sequence of gene tokens ranked by abundance and trains aremoved, struck through added, underlinedLine numbers count the serialised markdown of each revision, frontmatter included.
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