The self-assembly of solitons into nonlinear superpositions of multiple solitons plays a key role in the complex dynamics of mode-locked lasers. These states are extensively studied in light of their potential technological applications and their resemblance to molecules that offer opportunities for studying molecular interactions. However, progress along these endeavors is still held back by the lack of effective means to manipulate multi-soliton waveforms. Here we show it is possible to control inter-soliton interactions in mode-locked fiber lasers using a single control knob, the laser gain. We experimentally demonstrate a 2-orders-of-magnitude reduction in the separation of bound soliton pairs by sweeping the pumping current of the laser. The sweep induces a dynamical transition between a phase-incoherent loosely bound state and a phase-locked tightly bound state. Using numerical simulations and a simplified analytical model, we find that the dynamical transition is governed by noise-mediated interactions, which can be switched between repulsion and attraction. The discovery of a single control parameter that sets the nature of the inter-soliton interaction points to possibilities for controlling multi-soliton states for optical communication systems and pump-probe spectroscopy.