For the problem of producing a bit-pattern with exactly n
set bits, I know of two practical methods, but they both have limitations I\'m not happy with.
Fir
Is this a theory problem or a practical problem?
You could still do the partial shuffle, but keep track of the order of the ones and forget the zeroes. There are log(k!) bits of unused entropy in their final order for your future consumption.
You could also just use the recurrence (n choose k) = (n-1 choose k-1) + (n-1 choose k) directly. Generate a random number between 0 and (n choose k)-1. Call it r. Iterate over all of the bits from the nth to the first. If we have to set j of the i remaining bits, set the ith if r < (i-1 choose j-1) and clear it, subtracting (i-1 choose j-1), otherwise.
Practically, I wouldn't worry about the couple of words of wasted entropy from the partial shuffle; generating a random 32-bit word with 16 bits set costs somewhere between 64 and 80 bits of entropy, and that's entirely acceptable. The growth rate of the required entropy is asymptotically worse than the theoretical bound, so I'd do something different for really big words.
For really big words, you might generate n independent bits that are 1 with probability k/n. This immediately blows your entropy budget (and then some), but it only uses linearly many bits. The number of set bits is tightly concentrated around k, though. For a further expected linear entropy cost, I can fix it up. This approach has much better memory locality than the partial shuffle approach, so I'd probably prefer it in practice.