Evo-velocity is a method that simulates evolution using PLMs pseudoperplexity values (1). It was tested on numerous viral and eukaryotic proteins and predicted fitness trajectories align reasonably well with improvements in fitness. However, (2) argue that PLMs are unable to reason about evolution.
Ref (1)
1.
Hie BL, Yang KK, Kim PS. Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins. Cell Systems. 2022;13(4):274-285.e6. Available from: https://doi.org/10.1016/j.cels.2022.01.003
2.
Ektefaie Y, Shen A, Jain L, Farhat M, Zitnik M. Evolutionary Reasoning Does Not Arise in Standard Usage of Protein Language Models. openRxiv; 2025. Available from: https://doi.org/10.1101/2025.01.17.633626