Large-scale models require substantial computational resources for analysis and studying treatment conditions. Specifically, estimating treatment effects using simulations may require a lot of infeasible resources to allocate at every treatment condition. Therefore, it is essential to develop efficient methods to allocate computational resources for estimating treatment effects. Agent-based simulation allows us to generate highly realistic simulation samples. FRED (A Framework for Reconstructing Epidemiological Dynamics) is an agent-based modeling system with a geospatial perspective using a synthetic population constructed based on the U.S. census data. Given its synthetic population, FRED simulations present a baseline for comparable results from different treatment conditions and treatment conditions. In this paper, we show three other methods for estimating treatment effects. In the first method, we resort to brute-force allocation, where all treatment conditions have an equal number of samples with a relatively large number of simulation runs. In the second method, we try to reduce the number of simulation runs by customizing individual samples required for each treatment effect based on the width of confidence intervals around the mean estimates. In the third method, we use a regression model, which allows us to learn across the treatment conditions such that simulation samples allocated for a treatment condition will help better estimate treatment effects in other conditions. We show that the regression-based methods result in a comparable estimate of treatment effects with less computational resources. The reduced variability and faster convergence of model-based estimates come at the cost of increased bias, and the bias-variance trade-off can be controlled by adjusting the number of model parameters (e.g., including higher-order interaction terms in the regression model).