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The two views (papers citing and cited by the seeds) can naturally be visualized together. Such a view will not only show more relevant information but will also simplify the user interaction by skipping the choice.
Any (or both) of these two approaches can be used to distinguish the citing from the cited by nodes:
I agree with the DAGification as the better option, but I'd also like to add a note:
If you do end up adding directed edges of some form, there's UX research (I can dig up the citations IFF you insist.) showing that tapering edges (thick at the start, thin at the end) function as much better visual indicators of direction than arrows do.
The two views (papers citing and cited by the seeds) can naturally be visualized together. Such a view will not only show more relevant information but will also simplify the user interaction by skipping the choice.
Any (or both) of these two approaches can be used to distinguish the citing from the cited by nodes:
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