Literature DB >> 26156455

Perspective: Sloppiness and emergent theories in physics, biology, and beyond.

Mark K Transtrum1, Benjamin B Machta2, Kevin S Brown3, Bryan C Daniels4, Christopher R Myers5, James P Sethna5.   

Abstract

Large scale models of physical phenomena demand the development of new statistical and computational tools in order to be effective. Many such models are "sloppy," i.e., exhibit behavior controlled by a relatively small number of parameter combinations. We review an information theoretic framework for analyzing sloppy models. This formalism is based on the Fisher information matrix, which is interpreted as a Riemannian metric on a parameterized space of models. Distance in this space is a measure of how distinguishable two models are based on their predictions. Sloppy model manifolds are bounded with a hierarchy of widths and extrinsic curvatures. The manifold boundary approximation can extract the simple, hidden theory from complicated sloppy models. We attribute the success of simple effective models in physics as likewise emerging from complicated processes exhibiting a low effective dimensionality. We discuss the ramifications and consequences of sloppy models for biochemistry and science more generally. We suggest that the reason our complex world is understandable is due to the same fundamental reason: simple theories of macroscopic behavior are hidden inside complicated microscopic processes.

Mesh:

Year:  2015        PMID: 26156455     DOI: 10.1063/1.4923066

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  48 in total

1.  Visualizing probabilistic models and data with Intensive Principal Component Analysis.

Authors:  Katherine N Quinn; Colin B Clement; Francesco De Bernardis; Michael D Niemack; James P Sethna
Journal:  Proc Natl Acad Sci U S A       Date:  2019-06-24       Impact factor: 11.205

2.  Identifiability analysis for stochastic differential equation models in systems biology.

Authors:  Alexander P Browning; David J Warne; Kevin Burrage; Ruth E Baker; Matthew J Simpson
Journal:  J R Soc Interface       Date:  2020-12-16       Impact factor: 4.118

3.  Chance, long tails, and inference in a non-Gaussian, Bayesian theory of vocal learning in songbirds.

Authors:  Baohua Zhou; David Hofmann; Itai Pinkoviezky; Samuel J Sober; Ilya Nemenman
Journal:  Proc Natl Acad Sci U S A       Date:  2018-08-20       Impact factor: 11.205

4.  Exploring the landscape of model representations.

Authors:  Thomas T Foley; Katherine M Kidder; M Scott Shell; W G Noid
Journal:  Proc Natl Acad Sci U S A       Date:  2020-09-14       Impact factor: 11.205

5.  Untangling the Hairball: Fitness-Based Asymptotic Reduction of Biological Networks.

Authors:  Félix Proulx-Giraldeau; Thomas J Rademaker; Paul François
Journal:  Biophys J       Date:  2017-10-17       Impact factor: 4.033

6.  Maximizing the information learned from finite data selects a simple model.

Authors:  Henry H Mattingly; Mark K Transtrum; Michael C Abbott; Benjamin B Machta
Journal:  Proc Natl Acad Sci U S A       Date:  2018-02-06       Impact factor: 11.205

Review 7.  How to deal with parameters for whole-cell modelling.

Authors:  Ann C Babtie; Michael P H Stumpf
Journal:  J R Soc Interface       Date:  2017-08-02       Impact factor: 4.118

8.  Cellular packing, mechanical stress and the evolution of multicellularity.

Authors:  Shane Jacobeen; Jennifer T Pentz; Elyes C Graba; Colin G Brandys; William C Ratcliff; Peter J Yunker
Journal:  Nat Phys       Date:  2018-03       Impact factor: 20.034

9.  Numerical Parameter Space Compression and Its Application to Biophysical Models.

Authors:  Chieh-Ting Jimmy Hsu; Gary J Brouhard; Paul François
Journal:  Biophys J       Date:  2020-01-29       Impact factor: 4.033

10.  Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants.

Authors:  Tal Einav; Rob Phillips
Journal:  J Phys Chem B       Date:  2017-02-21       Impact factor: 2.991

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