Workflow from Scientific Research

GEARS model architecture. (i) For each gene in the unperturbed state, GEARS initializes a gene embedding vector (green) and a gene perturbation embedding vector (red) (ii). These embedding vectors are assigned as node features in the gene relationship graph and the perturbation relationship graph (iii). A GNN is used to combine information between neighbors in each graph. Each resulting gene embedding is summed with the perturbation embedding of each perturbation in the perturbation set (iv). The output is combined across all genes using the cross-gene layer and fed into gene-specific output layers (v). The final result is postperturbation gene expression; MLP, multilayer perceptron.

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