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Gao, CY; Zhou, HJ; Aurell, E3,4,5
Correlation-compressed direct-coupling analysis
Source PublicationPHYSICAL REVIEW E
Language英语
KeywordSTRUCTURE PREDICTION PROTEIN-STRUCTURE CONTACTS IDENTIFICATION MODEL SEQUENCES FAMILIES HUMANS
AbstractLearning Ising or Potts models from data has become an important topic in statistical physics and computational biology, with applications to predictions of structural contacts in proteins and other areas of biological data analysis. The corresponding inference problems are challenging since the normalization constant (partition function) of the Ising or Potts distribution cannot be computed efficiently on large instances. Different ways to address this issue have resulted in a substantial amount of methodological literature. In this paper we investigate how these methods could be used on much larger data sets than studied previously. We focus on a central aspect, that in practice these inference problems are almost always severely under-sampled, and the operational result is almost always a small set of leading predictions. We therefore explore an approach where the data are prefiltered based on empirical correlations, which can be computed directly even for very large problems. Inference is only used on the much smaller instance in a subsequent step of the analysis. We show that in several relevant model classes such a combined approach gives results of almost the same quality as inference on the whole data set. It can therefore provide a potentially very large computational speedup at the price of only marginal decrease in prediction quality. We also show that the results on whole-genome epistatic couplings that were obtained in a recent computation-intensive study can be retrieved by our approach. The method of this paper hence opens up the possibility to learn parameters describing pairwise dependences among whole genomes in a computationally feasible and expedient manner.
2018
ISSN2470-0045
Volume98Issue:3Pages:32407
Subject AreaPhysics
MOST Discipline CataloguePhysics, Fluids & Plasmas ; Physics, Mathematical
DOI10.1103/PhysRevE.98.032407
Indexed BySCIE
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Cited Times:1[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/22820
Collection理论物理所科研产出_SCI论文
Affiliation1.Chinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China
2.Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China
3.Hunan Normal Univ, Synerget Innovat Ctr Quantum Effects & Applicat, Changsha 410081, Hunan, Peoples R China
4.KTH Royal Inst Technol, Dept Computat Biol, S-10044 Stockholm, Sweden
5.Aalto Univ, Dept Appl Phys, Aalto 00076, Finland
6.Aalto Univ, Dept Comp Sci, Aalto 00076, Finland
Recommended Citation
GB/T 7714
Gao, CY,Zhou, HJ,Aurell, E. Correlation-compressed direct-coupling analysis[J]. PHYSICAL REVIEW E,2018,98(3):32407.
APA Gao, CY,Zhou, HJ,&Aurell, E.(2018).Correlation-compressed direct-coupling analysis.PHYSICAL REVIEW E,98(3),32407.
MLA Gao, CY,et al."Correlation-compressed direct-coupling analysis".PHYSICAL REVIEW E 98.3(2018):32407.
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