  We report that single interatomic potential, developed using Gaussian
regression of density functional theory calculation data, has high accuracy and
flexibility to describe phonon transport with ab initio accuracy in two
different atomistic configurations: perfect crystalline Si and crystalline Si
with vacancies. The high accuracy of second- and third-order force constants
from the Gaussian approximation potential (GAP) are demonstrated with phonon
dispersion, Gr\"uneisen parameter, three-phonon scattering rate, phonon-vacancy
scattering rate, and thermal conductivity, all of which are very close to the
results from density functional theory calculation. We also show that the
widely used empirical potentials (Stillinger-Weber and Tersoff) produce much
larger errors compared to the GAP. The computational cost of GAP is higher than
the two empirical potentials, but five orders of magnitude lower than the
density functional theory calculation. Our work shows that GAP can provide a
new opportunity for studying phonon transport in partially disordered
crystalline phases with the high predictive power of ab initio calculation but
at a feasible computational cost.
