Inference of biochemical S-systems via mixed-variable multiobjective evolutionary optimization
Summary: Inference of the biochemical systems (BSs) via experimental data is important for understanding how biochemical components in vivo interact with each other. However, it is not a trivial task because BSs usually function with complex and nonlinear dynamics. As a popular ordinary equation (ODE) model, the S-System describes the dynamical properties of BSs by incorporating the power rule of biochemical reactions but behaves as a challenge because it has a lot of parameters to be confirmed. This work is dedicated to proposing a general method for inference of S-Systems by experimental data, using a biobjective optimization (BOO) model and a specially mixed-variable multiobjective evolutionary algorithm (mv-MOEA). Regarding that BSs are sparse in common sense, we introduce binary variables indicating network connections to eliminate the difficulty of threshold presetting and take data fitting error and the \(L_0\)-norm as two objectives to be minimized in the BOO model. Then, a selection procedure that automatically runs tradeoff between two objectives is employed to choose final inference results from the obtained nondominated solutions of the mv-MOEA. Inference results of the investigated networks demonstrate that our method can identify their dynamical properties well, although the automatic selection procedure sometimes ignores some weak connections in BSs.
- Evolutionary Multi-Criterion Optimization
- Bi-objective optimization of biochemical systems by linear programming
- Parameter reconstruction for biochemical networks using interval analysis
- Inference of \(S\)-system models of genetic networks by solving one-dimensional function optimization problems
- Inverse problem studies of biochemical systems with structure identification of S-systems by embedding training functions in a genetic algorithm
- Autoregressive models for gene regulatory network inference: sparsity, stability and causality issues
- Differential evolution -- a simple and efficient heuristic for global optimization over continuous spaces
- Evolutionary Multi-Criterion Optimization
- Review on statistical methods for gene network reconstruction using expression data
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