GeneSpeak-FP: Target and Compound Retrieval from Observed Cell-Level Perturbation Signatures
Large-scale single-cell perturbation atlases make it possible to ask an inverse question: given an observed transcriptional response, which annotated targets and compounds in a fixed library are most consistent with that response? We present \model, a Transformer retrieval model for this closed-library setting. Each input is a cell-level perturbation signature formed by contrasting one treated cell with a cell-line-specific mean DMSO reference. The encoder maps the signature to a target-retrieval vector and a molecular-embedding vector, trained jointly with supervised target losses and structure--transcriptome alignment. We evaluate on Tahoe-100M conditions with mapped target annotations ...
| Authors | Kseniia Vaniushkina, Jeongmin Lim, Jinyong Park |
|---|---|
| Primary category | cs.LG |
| Published | 20 July 2026 |
| Last updated at source | 20 July 2026 |
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