Proteins, Particles, and Pseudo-Max-Marginals: A Submodular Approach
Abstract
Variants of max-product (MP) belief propagation effectively find modes of many complex graphical models, but are limited to discrete distributions. Diverse particle max-product (D-PMP) robustly approximates max-product updates in continuous MRFs using stochastically sampled particles, but previous work was specialized to tree-structured models. Motivated by the challenging problem of protein side chain prediction, we extend D-PMP in several key ways to create a generic MAP inference algorithm for loopy models. We define a modified diverse particle selection objective that is provably submodular, leading to an efficient greedy algorithm with rigorous optimality guarantees, and corresponding max-marginal error bounds. We further incorporate tree-reweighted variants of the MP algorithm to allow provable verification of global MAP recovery in many models. Our general-purpose Matlab library is applicable to a wide range of pairwise graphical models, and we validate our approach using optical flow benchmarks. We further demonstrate superior side chain prediction accuracy compared to baseline algorithms from the state-of-the-art Rosetta package.
BibTeX
@InProceedings{pmlr-v37-pacheco15,
title = {Proteins, Particles, and Pseudo-Max-Marginals: A Submodular Approach},
author = {Pacheco, Jason and Sudderth, Erik},
booktitle = {Proceedings of the 32nd International Conference on Machine Learning},
pages = {2200--2208},
year = {2015},
editor = {Bach, Francis and Blei, David},
volume = {37},
series = {Proceedings of Machine Learning Research},
address = {Lille, France},
month = {07--09 Jul},
publisher = {PMLR},
pdf = {http://proceedings.mlr.press/v37/pacheco15.pdf},
url = {https://proceedings.mlr.press/v37/pacheco15.html},
abstract = {Variants of max-product (MP) belief propagation effectively find modes of many complex graphical models, but are limited to discrete distributions. Diverse particle max-product (D-PMP) robustly approximates max-product updates in continuous MRFs using stochastically sampled particles, but previous work was specialized to tree-structured models. Motivated by the challenging problem of protein side chain prediction, we extend D-PMP in several key ways to create a generic MAP inference algorithm for loopy models. We define a modified diverse particle selection objective that is provably submodular, leading to an efficient greedy algorithm with rigorous optimality guarantees, and corresponding max-marginal error bounds. We further incorporate tree-reweighted variants of the MP algorithm to allow provable verification of global MAP recovery in many models. Our general-purpose Matlab library is applicable to a wide range of pairwise graphical models, and we validate our approach using optical flow benchmarks. We further demonstrate superior side chain prediction accuracy compared to baseline algorithms from the state-of-the-art Rosetta package.}
}