Table. 1 List of symbols and notations used in the paper
Symbol | Description |
|---|---|
\({{{{{{\boldsymbol{X}}}}}}}_{{{{{{\boldsymbol{1}}}}}}}\) | The control profiles treated with DMSO |
\({{{{{{\boldsymbol{X}}}}}}}_{{{{{{\boldsymbol{2}}}}}}}\) | The transcriptional profiles treated with compounds |
\({{{{{\boldsymbol{\Delta }}}}}}{{{{{\boldsymbol{X}}}}}}\) | The differential expression genes \(\left({X}_{2}-{X}_{1}\right)\) |
\({\hat{{{{{{\boldsymbol{X}}}}}}}}_{{{{{{\boldsymbol{1}}}}}}}\) | The reconstructed control profiles |
\({\hat{{{{{{\boldsymbol{X}}}}}}}}_{{{{{{\boldsymbol{2}}}}}}}\) | The reconstructed transcriptional profiles |
\({{{{{\boldsymbol{\Delta }}}}}}\hat{{{{{{\boldsymbol{X}}}}}}}\) | The reconstructed differential expression genes \(\left({\hat{X}}_{2}-{X}_{1}\right)\) |
\({{{{{{\boldsymbol{X}}}}}}}_{{{2}}}^{{{\prime} }}\) | The predicted transcriptional profiles from \({X}_{1}\) and perturbation representation |
\({{{{{\boldsymbol{\Delta }}}}}}{{{{{\boldsymbol{X}}}}}}^{{{\prime} }}\) | The predicted differential expression genes \(\left({X}_{2}^{\prime} -{X}_{1}\right)\) |
\({{{{{{\boldsymbol{Z}}}}}}}_{{{{{{\boldsymbol{1}}}}}}}\) | The latent representation of \({X}_{1}\) |
\({{{{{{\boldsymbol{Z}}}}}}}_{{{{{{\boldsymbol{2}}}}}}}\) | The latent representation of \({X}_{2}\) |
\({{{{{{\boldsymbol{Z}}}}}}}_{{{{{{\boldsymbol{2}}}}}}}{{{{{\boldsymbol{F}}}}}}{{{{{{\boldsymbol{Z}}}}}}}_{{{{{{\boldsymbol{1}}}}}}}\) | The latent representation from \({X}_{1}\) and perturbation representation |
\({{{{{{\boldsymbol{C}}}}}}}_{{{{{{\boldsymbol{mol}}}}}}}\) | The input representation of the compounds |
\({{{{{{\boldsymbol{Z}}}}}}}_{{{{{{\boldsymbol{mol}}}}}}}\) | The hidden representation of the compounds |
\({{{{{{\boldsymbol{encoder}}}}}}}_{{{{{{\boldsymbol{x}}}}}}{{{{{\boldsymbol{1}}}}}}}\) | The encoder for \({X}_{1}\) |
\({{{{{{\boldsymbol{decoder}}}}}}}_{{{{{{\boldsymbol{x}}}}}}{{{{{\boldsymbol{1}}}}}}}\) | The decoder for \({X}_{1}\) |
\({{{{{{\boldsymbol{encoder}}}}}}}_{{{{{{\boldsymbol{x}}}}}}{{{{{\boldsymbol{2}}}}}}}\) | The encoder for \({X}_{2}\) |
\({{{{{{\boldsymbol{decoder}}}}}}}_{{{{{{\boldsymbol{x}}}}}}{{{{{\boldsymbol{2}}}}}}}\) | The decoder for \({X}_{2}\) |
