A recent breakthrough in Edmonds' problem showed that the noncommutative rank can be computed in deterministic polynomial time, and various algorithms for it were devised. However, only quite complicated algorithms are known for finding a so-called shrunk subspace, which acts as a dual certificate for the value of the noncommutative rank. In particular, the operator Sinkhorn algorithm, perhaps the simplest algorithm to compute the noncommutative rank with operator scaling, does not find a shrunk subspace. Finding a shrunk subspace plays a key role in applications, such as separation in the Brascamp-Lieb polytope, one-parameter subgroups in the null-cone membership problem, and primal-dual algorithms for matroid intersection and fractional matroid matching. In this paper, we provide a simple Sinkhorn-style algorithm to find the smallest shrunk subspace over the complex field in deterministic polynomial time. To this end, we introduce a generalization of the operator scaling problem, where the spectra of the marginals must be majorized by specified vectors. Then we design an efficient Sinkhorn-style algorithm for the generalized operator scaling problem. Applying this to the shrunk subspace problem, we show that a sufficiently long run of the algorithm also finds an approximate shrunk subspace close to the minimum exact shrunk subspace. Finally, we show that the approximate shrunk subspace can be rounded if it is sufficiently close. Along the way, we also provide a simple randomized algorithm to find the smallest shrunk subspace. As applications, we design a faster algorithm for fractional linear matroid matching and efficient weak membership and optimization algorithms for the rank-2 Brascamp-Lieb polytope.