2017/02/28 by H. Chau Nguyen, Riccardo Zecchina, Johannes Berg · 2 citations
Physics and Astronomy · Biochemistry, Genetics and Molecular Biology · #cond-mat.dis-nn #q-bio.GN #q-bio.MN #q-bio.NC
paper · pdf · doi:10.1080/00018732.2017.1341604
published as Advances in Physics, 66 (3), 197-261 (2017) · Review article, 45 pages
arxiv created 2017/11/06 · arxiv updated 2017/11/07
Inverse problems in statistical physics are motivated by the challenges of `big data' in different fields, in particular high-throughput experiments in biology. In inverse problems, the usual procedure of statistical physics needs to be reversed: Instead of calculating observables on the basis of model parameters, we seek to infer parameters of a model based on observations. In this review, we focus on the inverse Ising problem and closely related problems, namely how to infer the coupling strengths between spins given observed spin correlations, magnetisations, or other data. We review applications of the inverse Ising problem, including the reconstruction of neural connections, protein structure determination, and the inference of gene regulatory networks. For the inverse Ising problem in equilibrium, a number of controlled and uncontrolled approximate solutions have been developed in the statistical mechanics community. A particularly strong method, pseudolikelihood, stems from statistics. We also review the inverse Ising problem in the non-equilibrium case, where the model parameters must be reconstructed based on non-equilibrium statistics.