Chem2Gen-Bench: Benchmarking Chemical-to-Genetic Translation in Perturbation Response Space

Chem2Gen-Bench is a newly introduced benchmark that includes 260,084 chemical and 1,099,045 genetic perturbation profiles organized by cell-target contexts to facilitate the evaluation of chemical-to-genetic translation. The benchmark assesses various aspects such as pairwise alignment and retrieval success, revealing that while translation fidelity exists, it is inconsistent and background adjustment can negatively impact retrieval outcomes. This framework is significant for practitioners as it provides a systematic approach to evaluate the alignment of chemical and genetic perturbations, informing the development of more effective predictive models in biomedical research.