\
convert original.pdf -negate new.pdf
other formats may work, need to try.

for i in `ls source/*.pdf`; do convert -negate  ${i%.*}.pdf target/${i%.*}_inv.pdf; done

bulk inverting in mse21f/ (current directory):
 [wangwc@101 mse21f]$ cd notes_mse21f/
 [wangwc@101 notes_mse21f]$ for i in `ls *.pdf`; do convert -negate  ${i%.*}.pdf ../notes_mse21f_inverted/${i%.*}_inv.pdf; done

This will convert all .pdf files in notes_mse21f/
and store them in notes_mse21f_inverted/
(both are existing subdirectories of mse21f/).