Figure 1:

Key concepts underlying the CellCap model and its interpretable workflow. (a) A linearly decoded VAE is the backbone of CellCap, which encodes the perturbed single-cell data into basal state $z^{\left(\text{basal}\right)}$ and reconstructs $z_{nk}^{\left(\text{basal}\right)}+\mathrm{\Delta }{z}_{nk}^{\left(\text{pert}\right)}+\mathrm{\Delta }{z}_{nk}^{(\text{cov)}}$ back to the observed gene expression count matrix $x_{ng}$ via a linear decoder. (b) Graphical presentations of individual components of CellCap. (c-f) Various downstream applications of CellCap. (c) Understanding the relationship between bulk and cell-state-specific perturbation effects; (d) Interpretability of the transcriptional response programs with a linear decoder; (e) Uncovering characteristics of cell states that respond to each transcriptional program; (f) Uncovering cell-state-dependent response amplitude to each response program.