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Table 1 Hierarchical optimization framework based on four objectives for AVTD

From: Fuzzy optimization for identifying antiviral targets for treating SARS-CoV-2 infection in the heart

The objectives of the outer optimization problem are as follows:

1

To eliminate the viral biomass growth rate (VBGR) of HV cells as much as possible under the target treatment

2

To maximize the ATP production rate for treated HV cells and perturbed HT cells during treatment

3

To evaluate the fuzzy similarity between the metabolic patterns of treated HV cells and perturbed HT cells and those of HT cells

4

To evaluate the fuzzy dissimilarity between the metabolic patterns of treated HV cells and perturbed HT cells and those of HV cells

The objectives of the inner optimization problem, which is subject to a constraint-based model, are as follows:

1

To conduct FBA and solve UFD problems for the treated HV cells

2

To conduct FBA and solve UFD problems for the perturbed HT cells

  1. The source code for the AVTD algorithm and the cell-specific GSMMs is implemented using the General Algebraic Modeling System (GAMS, https://www.gams.com/) and can be found at http://doi.org/10.5281/zenodo.8103559