Linear Programming Relaxations and Belief Propagation - An Empirical Study

The problem of finding the most probable (MAP) configuration in graphical models comes up in a wide range of applications. In a general graphical model this problem is NP hard, but various approximate algorithms have been developed. Linear programming (LP) relaxations are a standard method in computer science for approximating combinatorial problems and have been used for finding the most probable assignment in small graphical models. However, applying this powerful method to real-world problems is extremely challenging due to the large numbers of variables and constraints in the linear program. Tree-Reweighted Belief Propagation is a promising recent algorithm for solving LP relaxations, but little is known about its running time on large problems. In this paper we compare tree-reweighted belief propagation (TRBP) and powerful general-purpose LP solvers (CPLEX) on relaxations of real-world graphical models from the fields of computer vision and computational biology. We find that TRBP almost always finds the solution significantly faster than all the solvers in CPLEX and more importantly, TRBP can be applied to large scale problems for which the solvers in CPLEX cannot be applied. Using TRBP we can find the MAP configurations in a matter of minutes for a large range of real world problems.

[1]  Éva Tardos,et al.  A Strongly Polynomial Algorithm to Solve Combinatorial Linear Programs , 1986, Oper. Res..

[2]  Judea Pearl,et al.  Probabilistic reasoning in intelligent systems - networks of plausible inference , 1991, Morgan Kaufmann series in representation and reasoning.

[3]  Eugene Santos,et al.  On the Generation of Alternative Explanations with Implications for Belief Revision , 1991, UAI.

[4]  Roland L. Dunbrack,et al.  Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.

[5]  Solomon Eyal Shimony,et al.  Finding MAPs for Belief Networks is NP-Hard , 1994, Artif. Intell..

[6]  Aviezri S. Fraenkel Protein folding, spin glass and computational complexity , 1997, DNA Based Computers.

[7]  John N. Tsitsiklis,et al.  Introduction to linear optimization , 1997, Athena scientific optimization and computation series.

[8]  Carlo Tomasi,et al.  A Pixel Dissimilarity Measure That Is Insensitive to Image Sampling , 1998, IEEE Trans. Pattern Anal. Mach. Intell..

[9]  Robert Cowell,et al.  Advanced Inference in Bayesian Networks , 1999, Learning in Graphical Models.

[10]  Olga Veksler,et al.  Fast approximate energy minimization via graph cuts , 2001, Proceedings of the Seventh IEEE International Conference on Computer Vision.

[11]  Kevin Murphy,et al.  Bayes net toolbox for Matlab , 1999 .

[12]  M. Karplus,et al.  Effective energy function for proteins in solution , 1999, Proteins.

[13]  S. L. Mayo,et al.  Computational protein design. , 1999, Structure.

[14]  D. Baker,et al.  Native protein sequences are close to optimal for their structures. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[15]  D. Scharstein,et al.  A Taxonomy and Evaluation of Dense Two-Frame Stereo Correspondence Algorithms , 2001, Proceedings IEEE Workshop on Stereo and Multi-Baseline Vision (SMBV 2001).

[16]  Niles A Pierce,et al.  Protein design is NP-hard. , 2002, Protein engineering.

[17]  Robert E. Bixby,et al.  Solving Real-World Linear Programs: A Decade and More of Progress , 2002, Oper. Res..

[18]  Nanning Zheng,et al.  Stereo Matching Using Belief Propagation , 2002, IEEE Trans. Pattern Anal. Mach. Intell..

[19]  Yair Weiss,et al.  Approximate Inference and Protein-Folding , 2002, NIPS.

[20]  William T. Freeman,et al.  Understanding belief propagation and its generalizations , 2003 .

[21]  D. Baker,et al.  An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. , 2003, Journal of molecular biology.

[22]  Richard Szeliski,et al.  High-accuracy stereo depth maps using structured light , 2003, 2003 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2003. Proceedings..

[23]  Rina Dechter,et al.  Systematic vs. Non-systematic Algorithms for Solving the MPE Task , 2003, UAI.

[24]  William T. Freeman,et al.  Comparison of graph cuts with belief propagation for stereo, using identical MRF parameters , 2003, Proceedings Ninth IEEE International Conference on Computer Vision.

[25]  Adrian A Canutescu,et al.  A graph‐theory algorithm for rapid protein side‐chain prediction , 2003, Protein science : a publication of the Protein Society.

[26]  Vladimir Kolmogorov,et al.  What energy functions can be minimized via graph cuts? , 2002, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[27]  D. Baker,et al.  Modeling structurally variable regions in homologous proteins with rosetta , 2004, Proteins.

[28]  Daniel P. Huttenlocher,et al.  Efficient Belief Propagation for Early Vision , 2004, Proceedings of the 2004 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2004. CVPR 2004..

[29]  Pedro F. Felzenszwalb,et al.  Efficient belief propagation for early vision , 2004, CVPR 2004.

[30]  Mona Singh,et al.  Solving and analyzing side-chain positioning problems using linear and integer programming , 2005, Bioinform..

[31]  Martin J. Wainwright,et al.  On the Optimality of Tree-reweighted Max-product Message-passing , 2005, UAI.

[32]  Martin J. Wainwright,et al.  MAP estimation via agreement on trees: message-passing and linear programming , 2005, IEEE Transactions on Information Theory.

[33]  Yair Weiss,et al.  Globally optimal solutions for energy minimization in stereo vision using reweighted belief propagation , 2005, Tenth IEEE International Conference on Computer Vision (ICCV'05) Volume 1.

[34]  Martin J. Wainwright,et al.  MAP estimation via agreement on (hyper)trees: Message-passing and linear programming , 2005, ArXiv.

[35]  Vladimir Kolmogorov,et al.  Convergent Tree-Reweighted Message Passing for Energy Minimization , 2006, IEEE Transactions on Pattern Analysis and Machine Intelligence.