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We now set the minimum path setting to four and extract the key pathway components for insulin resistance.
Optimum performance is reached with a minimum path setting of four genes.
From Figure 2, the optimal clustering performance is observed to be at a minimum path setting of nine genes.
This relatively small minimum path setting indicates that insulin resistance is the result of metabolism of only a few critical compounds.
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By means of Boolean algebra simplification, the minimum path sets of the system are achieved.
Once the minimum covering path set is computed and the node layers are established, the final table can be built by walking through every path and, for each node, reporting its contribution to the table headers and cell values, where such contribution consists of the node attributes mentioned above.
The quality of the 3M clustering for each minimum path length setting is evaluated using a 5-fold cross-validated Normalized Mutual Information (NMI).
The minimum path length is set to [2, 6, 10], number of paths to be extracted is set to K = [1000, 5000, 10 000] and the network size is increased in terms of number of genes (nodes) until the entire KEGG yeast metabolic network is analyzed.
We now set the minimum path parameter to nine genes and analyze the clustering results.
Among the 46 secondary pain disease proteins, 27 proteins have direct interactions with the pain disease protein set, and the minimum path lengths between any of the other 17 secondary pain disease proteins and the pain disease protein set (except for the proteins themselves) are 2, and the minimum path lengths are 3 and 4 for the remaining two secondary pain disease proteins.
Minimum path decompositions are not unique and hence a single given path may result in multiple sets of intermediate destinations.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com