Best answer I can think of is that the balloon is being acted on by a buoyant force. Helium is less dense than air, and so the average density of the balloon is less than that of air. The balloon therefore "floats" in this sea of air called the atmosphere, and the buoyant force causes it to rise. Any corrections/clarifications?
The lighter helium is buoyant in the denser air - the buoyant forces cause the helium balloon to rise with some velocity. Kinetic energy is simply 1/2 mv2.
The balloon is rising in the gravitational field, hence the mass of the balloon is gaining potential energy.