Proteins, particles, and pseudo-max-marginals: A submodular approach

Jason L. Pacheco, Erik B. Sudderth

Research output: Chapter in Book/Report/Conference proceedingConference contribution

8 Scopus citations


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.

Original languageEnglish (US)
Title of host publication32nd International Conference on Machine Learning, ICML 2015
EditorsFrancis Bach, David Blei
PublisherInternational Machine Learning Society (IMLS)
Number of pages9
ISBN (Electronic)9781510810587
StatePublished - 2015
Externally publishedYes
Event32nd International Conference on Machine Learning, ICML 2015 - Lile, France
Duration: Jul 6 2015Jul 11 2015

Publication series

Name32nd International Conference on Machine Learning, ICML 2015


Other32nd International Conference on Machine Learning, ICML 2015

ASJC Scopus subject areas

  • Human-Computer Interaction
  • Computer Science Applications


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