Genes no longer queue by index in attention: SPEAR folds co-expression geometry and perturbation-time repositioning into rotation angles
Transformer models for single-cell perturbation prediction need a position for each gene, yet genes have no natural order, and static co-expression masks cannot reflect the regulatory rewiring a perturbation induces. SPEAR replaces that position with continuous coordinates from the co-expression graph Laplacian and, at every layer, re-derives a scalar position from the perturbation-conditioned hidden state, summing both into one rotation angle. On genetic, pharmacological and cytokine perturbation benchmarks it beats baselines including scDFM on differential-expression direction and magnitude, with the largest gap on held-out combinations.