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a Overview of perturbation data with a leave-one-drug-out (LODO) training / test set split. Drug 12 is never used in training. b Causal graphical model for subset of drugs and responses (proteins and phenotypes). Drugs are exogenous variables with known targets, e.g. it is assumed known that drug 12 directly effects protein \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$X_3$$\end{document} X 3 . Black dashed lines represent hidden confounding. For example unmeasured cell cycle may effect responses \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$X_{10}$$\end{document} X 10 and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$X_8$$\end{document} X 8

Journal: BMC Bioinformatics

Article Title: Causal models and prediction in cell line perturbation experiments

doi: 10.1186/s12859-024-06027-7

Figure Lengend Snippet: a Overview of perturbation data with a leave-one-drug-out (LODO) training / test set split. Drug 12 is never used in training. b Causal graphical model for subset of drugs and responses (proteins and phenotypes). Drugs are exogenous variables with known targets, e.g. it is assumed known that drug 12 directly effects protein \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$X_3$$\end{document} X 3 . Black dashed lines represent hidden confounding. For example unmeasured cell cycle may effect responses \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$X_{10}$$\end{document} X 10 and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$X_8$$\end{document} X 8

Article Snippet: Cellbox can be fit with several envelope functions \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\phi$$\end{document} φ including identity, clipped linear, and sigmoid.

Techniques: