Abstract
Cancer prognosis prediction is typically carried out without integrating scientific knowledge available on genomic pathways, the effect of drugs on cell dynamics, or modeling mutations in the population. Recent work addresses some of these problems by formulating an uncertainty class of Boolean regulatory models for abnormal gene regulation, assigning prognosis scores to each network based on intervention outcomes, and partitioning networks in the uncertainty class into prognosis classes based on these scores. For a new patient, the probability distribution of the prognosis class was evaluated using optimal Bayesian classification, given patient data. It was assumed that (1) disease is the result of several mutations of a known healthy network and that these mutations and their probability distribution in the population are known and (2) only a single snapshot of the patient's gene activity profile is observed. It was shown that, even in ideal settings where cancer in the population and the effect of a drug are fully modeled, a single static measurement is typically not sufficient. Here, we study what measurements are sufficient to predict prognosis. In particular, we relax assumption (1) by addressing how population data may be used to estimate network probabilities, and extend assumption (2) to include static and time-series measurements of both population and patient data. Furthermore, we extend the prediction of prognosis classes to optimal Bayesian regression of prognosis metrics. Even when time-series data is preferable to infer a stochastic dynamical network, we show that static data can be superior for prognosis prediction when constrained to small samples. Furthermore, although population data is helpful, performance is not sensitive to inaccuracies in the estimated network probabilities.