Fast and Numerically Stable Implementation of Rate Constant Matrix Contraction Method

TL;DR

This paper presents a numerically stable and faster implementation of the rate constant matrix contraction (RCMC) method for chemical kinetics, addressing computational bottlenecks and numerical instability in large-scale reaction networks.

Contribution

It introduces a modified LazyFastGreedy algorithm that avoids catastrophic cancellations and leverages matrix properties, significantly improving speed and stability of RCMC simulations.

Findings

The proposed method is numerically stable for chemical kinetics instances.

It achieves significant speedup over the original RCMC method.

The algorithm maintains accuracy despite the complex reaction time scales.

Abstract

The rate constant matrix contraction (RCMC) method, proposed by Sumiya et al. (2015, 2017), enables fast and numerically stable simulations of chemical kinetics on large-scale reaction path networks. Later, Iwata et al. (2023) mathematically reformulated the RCMC method as a numerical algorithm to solve master equations whose coefficient matrices, known as rate constant matrices, possess the detailed balance property. This paper aims to accelerate the RCMC method. The bottleneck in the RCMC method lies in the greedy selection of steady states, which is actually equivalent to the greedy algorithm for the MAP inference in DPPs under cardinality constraints. Hemmi et al. (2022) introduced a fast implementation of the greedy DPP MAP inference, called LazyFastGreedy, by combining the greedy algorithm of Chen et al. (2018) with the lazy greedy algorithm by Minoux (1978), a practically efficient greedy algorithm that exploits the submodularity of the objective function. However, for instances arising from chemical kinetics, the straightforward application of LazyFastGreedy suffers from catastrophic cancellations due to the wide range of reaction time scales. To address this numerical instability, we propose a modification to LazyFastGreedy that avoids the subtraction of like-sign numbers by leveraging the properties of rate constant matrices and the connection of the DPP MAP inference to Cholesky decomposition. For faster implementation, we utilize a segment tree, a data structure that manages one-dimensional arrays of elements in a semigroup. We also analyze the increase in relative errors caused by like-sign subtractions and permit such subtractions when they do not lead to catastrophic cancellations, aiming to further accelerate the process. Using real instances, we confirm that the proposed algorithm is both numerically stable and significantly faster than the original RCMC method.