Several studies have pointed out the need for accurate mid-level representations of music signals for information retrieval and signal processing purposes. In this paper, we propose a new mid-level representation based on the decomposition of a signal into a small number of sound atoms or molecules bearing explicit musical instrument labels. Each atom is a sum of windowed harmonic sinusoidal partials whose relative amplitudes are specific to one instrument, and each molecule consists of several atoms from the same instrument spanning successive time windows. We design efficient algorithms to extract the most prominent atoms or molecules and investigate several applications of this representation, including polyphonic instrument recognition and music visualization.