Systems and methods for quantifying the impact of biological perturbations are disclosed. Systems and methods are provided for generating a biological impact factor that quantifies the perturbation of a biological system using response data and computational network models of the underlying biological mechanisms. The biological impact factor may represent the long-term effect of the perturbation on an outcome. As an example, the systems and methods may generate a biological impact factor representing the progression of a disease such as lung cancer - based on an exposure to an agent such as cigarette smoke.