Year: 2021
Type: preprint
Abstract: Selecting drugs most effective against a tumor’s specific transcriptional signature is an important challenge in precision medicine. To assess oncogenic therapy options, cancer cell lines are dosed with drugs that can differentially impact cellular viability. Here we show that basal gene expression patterns can be conditioned by learned small molecule structure to better predict cellular drug sensitivity, achieving an R 2 of 0.7190±0.0098 (a 5.61% gain). We find that 1) transforming gene expression values by learned small molecule representations outperforms raw feature concatenation, 2) small molecule structural features meaningfully contribute to learned representations, and 3) an affine transformation best integrates these representations. We analyze conditioning parameters to determine how small molecule representations modulate gene expression embeddings. This ongoing work formalizes in silico cellular screening as a conditional task in precision oncology applications that can improve drug selection for cancer treatment.
Authors: Will Connell, Michael Keiser
Institution: University of California, San Francisco
Language: English
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W3138842050