2025-08-28 スイス連邦工科大学ローザンヌ校(EPFL)
<関連情報>
- https://actu.epfl.ch/news/advanced-ai-models-are-not-always-better-than-simp/
- https://www.nature.com/articles/s41587-025-02777-8
Systema:系統的変動を超えた遺伝子撹乱応答予測評価のためのフレームワーク Systema: a framework for evaluating genetic perturbation response prediction beyond systematic variation
Ramon Viñas Torné,Maciej Wiatrak,Zoe Piran,Shuyang Fan,Liangze Jiang,Sarah A. Teichmann,Mor Nitzan & Maria Brbić
Nature Biotechnology Published:25 August 2025
DOI:https://doi.org/10.1038/s41587-025-02777-8
Abstract
Predicting transcriptional responses to genetic perturbations is challenging in functional genomics. While recent methods aim to infer effects of untested perturbations, their true predictive power remains unclear. Here, we show that current methods struggle to generalize beyond systematic variation, the consistent transcriptional differences between perturbed and control cells arising from selection biases or confounders. We quantify this variation in ten datasets, spanning three technologies and five cell lines, and show that common metrics are susceptible to these biases, leading to overestimated performance. To address this, we introduce Systema, an evaluation framework that emphasizes perturbation-specific effects and identifies predictions that correctly reconstruct the perturbation landscape. Using this framework, we uncover insights into the predictive capabilities of existing methods and show that predicting responses to unseen perturbations is substantially harder than standard metrics suggest. Our work highlights the importance of heterogeneous gene panels and disentangles predictive performance from systematic effects, enabling biologically meaningful developments in perturbation response modeling.
