Score-informed note separation seeks to extract the performed waveform of all individual notes, often from a polyphonic recording. Existing deep learning systems generally only target instrument-level stems. We present, to our knowledge, the first deep learning approach to score-informed note separation, NoteSep. NoteSep extracts the queried notes by applying an extraction stage model, NoteGrab, once per note. Conditioned on pitch, onset, and offset, NoteGrab separates harmonic and percussive components in two U-Nets linked by bidirectional cross-attention; selective harmonic gating suppresses lower-octave interference while preserving percussive attacks. Finally, a joint separation stage applies Adaptive Set Ownership (ASO) to compare concurrent NoteGrab estimates and reallocate mixture energy. We curate SCNS-Train (25,729 mixtures and 743,920 targets) for training and SCNS-Eval (16 instruments, disjoint scores and libraries) for evaluation. On SCNS-Eval, NoteSep reaches a median SI-SDR of 7.39~dB, compared with 2.49~dB for our strongest baseline. See the demo page at https://benschou.com/notesep.

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