scTREAT: Latent Diffusion for Single-Cell Drug-Response Prediction

Abstract

Generating drug-induced transcriptional responses requires a model to account for cellular background together with molecular identity and dose. We present scTREAT, the first diffusion framework to factorize state and drug guidance for single-cell drug-response prediction. A shared latent expression space connects baseline and response, while Guided Decomposable Attention (GD-Attn) injects a baseline representation and a dose-conditioned molecular embedding. Independent channel dropout exposes four conditioning states during training; inference combines three conditional predictions with separately specified state and drug coefficients, and dose modulates drug-guidance strength. On condition-level pseudobulk profiles derived from the Tahoe-100M single-cell atlas, scTREAT achieves the best value on 10 of 12 metrics for unseen cell line-drug combinations (UC) and 11 of 12 for unseen drugs (UD). Ablations examine condition injection, molecular representation, and guidance design. On UD, the relative gains over the second-best model reach 36.11% and 34.21% for DEG logFC-Spearman and logFC-Pearson. These results demonstrate the effectiveness of combining shared latent expression modeling with explicit state and drug conditioning for response prediction.

arXiv comment16 pages