I'm working with a computational model. The model demonstrates the behaviour of a several sub metabolic systems (A, B, C, D, E, F, G, H, I and J) of a bacteria. I cluster these sub systems based on their behaviour. The dendrogram for this is in the left side.

Then I do some modifications to the model and re-cluster the sub systems (left side). I'm using the same method to cluster both cases (complete linkage). The changes introduced to the model does have an impact on the behaviour and the improved model's behaviour is slightly higher (~0.1) compared to the old model.

I used the FM index to compare the two dendrograms but it says the dendrograms are similar. I believe it is due to the slight change in the values before and after modification. But the dendrograms are clearly different. Therefore I need to compare the dendrograms visually. Would it be correct, if I were to say the following?

The height axis represents the average distance between all inter-cluster pairs. In the min-growth dendrogram the distance between inter-clusters are not that strong. Meaning there is no clear grouping. But in the enhanced- growth dendrogram the distance between the clusters are large, the clusters are well separated. Hence the two models are different.

enter image description here

  • $\begingroup$ Whether the height "represents the average distance between all inter-cluster pairs" depends on the linkage you are using for the hierarchical clustering, which you haven't stated here. Most likely, you should be doing something else to compare the effect of the change to your model, but from what you have here, I can't tell what. $\endgroup$ – gung - Reinstate Monica Jun 23 '17 at 18:14
  • $\begingroup$ Thank you. I'm using the complete linkage function. Can you please explain what you meant by "You should be doing something else to compare the effect"? I have plots for how each sub system works before and after they have been modified. They show that there is an improvement. Or did you mean something I could do with the dendrograms? $\endgroup$ – SriniShine Jun 23 '17 at 18:20
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    $\begingroup$ 1) How is FM index used to compare dendrograms? please describe or give a link to the procedure. 2) Why do you want to compare dendrograms? Why not compare the two corresponding distance matrtices? $\endgroup$ – ttnphns Jun 23 '17 at 18:34
  • $\begingroup$ Thank you. I used this link to compare the dendrograms usinf FM index. cran.r-project.org/web/packages/dendextend/vignettes/… I want to compare the dendrograms to show that the two clustering are different. Hence prove that models are different (Models are different in the sense the modifications done to the model has produced the difference in behaviour). Am I doing something wrong? $\endgroup$ – SriniShine Jun 23 '17 at 18:44

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