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Fig. 1 | BMC Bioinformatics

Fig. 1

From: TopoFilter: a MATLAB package for mechanistic model identification in systems biology

Fig. 1

TopoFilter method. a Parameter space \(\mathcal {P}=\left [p_{1}^{\text {min}},p_{1}^{\text {max}}\right ]\times \left [p_{2}^{\text {min}},p_{2}^{\text {max}}\right ]\) and viable subspace \({\tilde {P}}\) (gray). Sample parameter points (black dots), when projected to zero separately for the two coordinates (arrows), yield viable (green) or non-viable (red) reductions. Colored lines at the axes and a point at the origin denote viable (green) and non-viable (red) lower-dimensional subspaces. b Topological filtering step with a rank 1 exhaustive search, for a viable (green) model \(\mathcal {M}\) with \(\tilde {d}=4\) reducible parameters; \(\mathcal {M}_{I}\) (\(\mathcal {M}_{\setminus I}\)) denotes the model with (without) reducible parameters \(I\subseteq \left \{1,\ldots,\tilde {d}\right \}\). For a single viable parameter sample p, all rank 1 parameter reductions (1P) are tested for viability. A union of the three viable 1P reductions skips over the 2P reduction candidates (gray) and goes directly to a single 3P reduction (blue) for viability test. The remaining subspace of models (white) induced by the non-viable 1P reduction (red) is pruned from testing for the current parameter sample. Reductions that have been skipped (gray, white) may still be tested using another parameter sample or in a recursive step

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