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The problem was because of the hidden nodes in the compounds which make them empty. Now, user should give all elements to the layout including the hidden ones, but the layout will not consider hidden ones during the layout (actually spectral part considers but cose part doesn't consider).
@hasanbalci thanks I confirm the fix with the extension demo. @osamazafar980 can you please check this in IAM application as well (please note the comment above for its usage).
Looks like when there are empty compound nodes in the graph, these compound nodes are not taken into account, messing up the layout.
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