Вот один из способов использования re.sub
:
import re
literal_eval(','.join(re.sub(r'(?<=\d)(\s+)(?=-?\d)', ',', s).splitlines()))
[[0.03694573, 0.01084746, 0.01306414, 0.00499198, 0.00307188],
[0.03780498, 0.02610241, 0.00967986, 0.02228694, -0.01153102],
[0.03837708, 0.02111896, 0.01370878, -0.00136839, 0.01906253],
[0.03490672, -0.02791057, 0.08824896, -0.01991765, 0.01964361],
[0.0811892, 0.28361901, 0.21539196, -0.00259571, 0.28737829],
[0.20022041, 0.16184418, 0.25939959, 0.00546446, 0.36415219],
[0.22920615, 0.27439767, 0.36991198, 0.00624375, 0.39911759]]