Critical comparison of maxcal and other stochastic modeling approaches in analysis of gene networks

Learning the underlying details of a gene network with feedback is critical in designing new synthetic circuits. Yet, quantitative characterization of these circuits remains limited. This is due to the fact that experiments can only measure partial information from which the details of the circuit must be inferred. One potentially useful avenue is to harness hidden information from single-cell stochastic gene expression time trajectories measured for long periods of time—recorded at frequent intervals—over multiple cells. This raises the feasibility vs. accuracy dilemma while deciding between different models of mining these stochastic trajectories. We demonstrate that inference based on the Maximum Caliber (MaxCal) principle is the method of choice by critically evaluating its computational efficiency and accuracy against two other typical modeling approaches: (i) a detailed model (DM) with explicit consideration of multiple molecules including protein-promoter interaction, and (ii) a coarse-grain model (CGM) using Hill type functions to model feedback. MaxCal provides a reasonably accurate model while being significantly more computationally efficient than DM and CGM. Furthermore, MaxCal requires minimal assumptions since it is a top-down approach and allows systematic model improvement by including constraints of higher order, in contrast to traditional bottom-up approaches that require more parameters or ad hoc assumptions. Thus, based on efficiency, accuracy, and ability to build minimal models, we propose MaxCal as a superior alternative to traditional approaches (DM, CGM) when inferring underlying details of gene circuits with feedback from limited data.