Question: The amortized cost analysis shows that even though some dequeue operations might have a higher actual cost ( when the helper queue is involved )

The amortized cost analysis shows that even though some dequeue operations might have a higher actual cost (when the helper queue is involved), the credit "prepaid" by enqueue operations (which have a higher potential increase) is sufficient to cover them. This ensures the total running time of any sequence of n operations is O(n)

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