We address a version of the set-cover problem where we do not know the sets initially (and hence referred to as covert) but we can query an element to find out which sets contain this element as well as query a set to know the elements. We want to find a small set-cover using a minimal number of such queries. We present a Monte Carlo randomized algorithm that approximates an optimal set-cover of size $OPT$ within $O(\log N)$ factor with high probability using $O(OPT \cdot \log^2 N)$ queries where $N$ is the input size. We apply this technique to the network discovery problem that involves certifying all the edges and non-edges of an unknown $n$-vertices graph based on layered-graph queries from a minimal number of vertices. By reducing it to the covert set-cover problem we present an $O(\log^2 n)$-competitive Monte Carlo randomized algorithm for the covert version of network discovery problem. The previously best known algorithm has a competitive ratio of $\Omega (\sqrt{n\log n})$ and therefore our result achieves an exponential improvement.

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