How can you bypass the Law of Equivalent Exchange?

Answer

You can't.

but there was a stone (The Philosopher's Stone)

A genuine Philosopher's Stone is capable of amazing feats, among them complete human transmutation and allowing a soul to be transferred into a new body. Such transference comes at the cost of a fraction of the alchemist's soul, and runs the risk of the new host body decomposing into a living corpse. In the manga, "Full Metal Alchemist," the Philosopher's Stone is the main ingredient in the creation of a Homunculus, while in the anime the Homunculi seek it to obtain humanity. Even a true Philosopher's Stone is not immune to Equivalent Exchange: every time it is used, a bit of it vanishes, and its power is likewise reduced.

it can be used up so therefor it is not a true bypass

..... true i guess lol