Timezone: »

 
Poster
Sampling with Riemannian Hamiltonian Monte Carlo in a Constrained Space
Yunbum Kook · Yin-Tat Lee · Ruoqi Shen · Santosh Vempala

Thu Dec 01 02:00 PM -- 04:00 PM (PST) @ Hall J #723
in Poster Session 6 »

We demonstrate for the first time that ill-conditioned, non-smooth, constrained distributions in very high dimension, upwards of 100,000, can be sampled efficiently \emph{in practice}. Our algorithm incorporates constraints into the Riemannian version of Hamiltonian Monte Carlo and maintains sparsity. This allows us to achieve a mixing rate independent of smoothness and condition numbers. On benchmark data sets in systems biology and linear programming, our algorithm outperforms existing packages by orders of magnitude. In particular, we achieve a 1,000-fold speed-up for sampling from the largest published human metabolic network (RECON3D). Our package has been incorporated into a popular Bioinformatics library.

Keywords: Sampling · Hamiltonian Monte Carlo

Author Information

Yunbum Kook (Georgia Institute of Technology)
Yin-Tat Lee
Ruoqi Shen (University of Washington)
Santosh Vempala (Georgia Tech)

More from the Same Authors