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Actually, they are taking a "big picture" approach, since it's easier to find out the chord produced by an unknown number of instruments than to find out how many instruments are playing and what they are playing, separately. Doing these things you describe would require the second option, I believe.

From the article itself:

“The problem with ‘full polyphonic transcription’ is that the computer doesn’t know how many voices and instruments sound together and what the characteristics are of these instruments,” says De Haas.

“When you transcribe chords, we examine the mixture as a whole and examine what the prominent frequencies are in the spectrum.”



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