Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains

The Chemical Master Equation (CME) is a cornerstone of stochastic analysis and simulation of models of biochemical reaction networks. Yet direct solutions of the CME have remained elusive. Although several approaches overcome the infinite dimensional nature of the CME through projections or other means, a common feature of proposed approaches is their susceptibility to the curse of dimensionality, i.e. the exponential growth in memory and computational requirements in the number of problem dimensions. We present a novel approach that has the potential to “lift” this curse of dimensionality. The approach is based on the use of the recently proposed Quantized Tensor Train (QTT) formatted numerical linear algebra for the low parametric, numerical representation of tensors. The QTT decomposition admits both, algorithms for basic tensor arithmetics with complexity scaling linearly in the dimension (number of species) and sub-linearly in the mode size (maximum copy number), and a numerical tensor rounding procedure which is stable and quasi-optimal. We show how the CME can be represented in QTT format, then use the exponentially-converging -discontinuous Galerkin discretization in time to reduce the CME evolution problem to a set of QTT-structured linear equations to be solved at each time step using an algorithm based on Density Matrix Renormalization Group (DMRG) methods from quantum chemistry. Our method automatically adapts the “basis” of the solution at every time step guaranteeing that it is large enough to capture the dynamics of interest but no larger than necessary, as this would increase the computational complexity. Our approach is demonstrated by applying it to three different examples from systems biology: independent birth-death process, an example of enzymatic futile cycle, and a stochastic switch model. The numerical results on these examples demonstrate that the proposed QTT method achieves dramatic speedups and several orders of magnitude storage savings over direct approaches.Author Summary: Stochastic models of chemical networks are necessary to quantitatively describe random fluctuations and other probabilistic phenomena within living cells. The Chemical Master Equation (CME) describes the time evolution of molecular abundance probabilities in these models, and is a basis for many stochastic simulation and analysis methods. Yet the CME is difficult to solve directly except for very simple structures. Indeed current approaches are susceptible to the curse of dimensionality, that is, the exponential growth of memory and computational requirements in the number of problem dimensions. In this paper, we propose a novel approach that has the potential to overcome the curse of dimensionality. It is based on the use of the recently proposed Quantized Tensor Train (QTT) formatted numerical linear algebra for numerical representation of tensors, using algorithms for basic tensor arithmetics with complexity scaling linearly in the number of reacting species considered, and sub-linearly in the maximum allowed copy number per species. We present this approach and demonstrate its effectiveness by applying it to three problems from systems biology. Numerical experiments are reported which show that several orders of magnitude memory savings is typically afforded by the new approach presented here.