1. An apparatus of separating musical sound sources, the apparatus comprising: a separation unit to separate a plurality of mixed signals into a plurality of segments; a Nonnegative Matrix Partial Co-Factorization (NMPCF) analysis unit to perform an NMPCF analysis on the plurality of segments, and to obtain a plurality of entity matrices based on the analysis result; a target instrument signal separating unit to separate, from the mixed signals, a target instrument signal, by calculating an inner product between the plurality of entity matrices; and a signal association unit to associate the target instrument signals separated from each of the plurality of segments.