IP is protecting its usage (real world applications, ideally, with assessed damages), rather than the implementation. The analogy is: bulb is patented, but the patent shouldn't cover the bulb factory as well. You can pay for the damage, or shut down the factory, but you cannot force to dis-integrate the factory.

You can use patent algorithms if you have proper license, but it shouldn't forbidden various implementations from ground up. (however, you can form the argument that the implementation is dedicated to violate the patent rights, thus, should be responsible as well).

As always, software patent is a bch. Without a court trial, no one knows the exact answer.