Literature DB >> 34093005

Multiscale modeling meets machine learning: What can we learn?

Grace C Y Peng1, Mark Alber2, Adrian Buganza Tepole3, William R Cannon4, Suvranu De5, Salvador Dura-Bernal6, Krishna Garikipati7, George Karniadakis8, William W Lytton6, Paris Perdikaris9, Linda Petzold10, Ellen Kuhl11.   

Abstract

Machine learning is increasingly recognized as a promising technology in the biological, biomedical, and behavioral sciences. There can be no argument that this technique is incredibly successful in image recognition with immediate applications in diagnostics including electrophysiology, radiology, or pathology, where we have access to massive amounts of annotated data. However, machine learning often performs poorly in prognosis, especially when dealing with sparse data. This is a field where classical physics-based simulation seems to remain irreplaceable. In this review, we identify areas in the biomedical sciences where machine learning and multiscale modeling can mutually benefit from one another: Machine learning can integrate physics-based knowledge in the form of governing equations, boundary conditions, or constraints to manage ill-posted problems and robustly handle sparse and noisy data; multiscale modeling can integrate machine learning to create surrogate models, identify system dynamics and parameters, analyze sensitivities, and quantify uncertainty to bridge the scales and understand the emergence of function. With a view towards applications in the life sciences, we discuss the state of the art of combining machine learning and multiscale modeling, identify applications and opportunities, raise open questions, and address potential challenges and limitations. We anticipate that it will stimulate discussion within the community of computational mechanics and reach out to other disciplines including mathematics, statistics, computer science, artificial intelligence, biomedicine, systems biology, and precision medicine to join forces towards creating robust and efficient models for biological systems.

Entities:  

Keywords:  Machine learning; biomedicine; multiscale modeling; physics-based simulation

Year:  2020        PMID: 34093005      PMCID: PMC8172124          DOI: 10.1007/s11831-020-09405-5

Source DB:  PubMed          Journal:  Arch Comput Methods Eng        ISSN: 1134-3060            Impact factor:   7.302


  84 in total

1.  Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors.

Authors:  Birgit Schoeberl; Claudia Eichler-Jonsson; Ernst Dieter Gilles; Gertraud Müller
Journal:  Nat Biotechnol       Date:  2002-04       Impact factor: 54.908

Review 2.  Systems biology: a brief overview.

Authors:  Hiroaki Kitano
Journal:  Science       Date:  2002-03-01       Impact factor: 47.728

3.  Multiscale modeling of biomedical, biological, and behavioral systems (Part 1).

Authors:  Ronald White; Grace Peng; Semahat Demir
Journal:  IEEE Eng Med Biol Mag       Date:  2009 Mar-Apr

4.  Distinct roles for GABA across multiple timescales in mammalian circadian timekeeping.

Authors:  Daniel DeWoskin; Jihwan Myung; Mino D C Belle; Hugh D Piggins; Toru Takumi; Daniel B Forger
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-30       Impact factor: 11.205

5.  Optimizing computer models of corticospinal neurons to replicate in vitro dynamics.

Authors:  Samuel A Neymotin; Benjamin A Suter; Salvador Dura-Bernal; Gordon M G Shepherd; Michele Migliore; William W Lytton
Journal:  J Neurophysiol       Date:  2016-10-19       Impact factor: 2.714

6.  Solving high-dimensional partial differential equations using deep learning.

Authors:  Jiequn Han; Arnulf Jentzen; Weinan E
Journal:  Proc Natl Acad Sci U S A       Date:  2018-08-06       Impact factor: 11.205

7.  Multiscale characterization of heart failure.

Authors:  F Sahli Costabal; J S Choy; K L Sack; J M Guccione; G S Kassab; E Kuhl
Journal:  Acta Biomater       Date:  2019-01-07       Impact factor: 8.947

8.  Dermatologist-level classification of skin cancer with deep neural networks.

Authors:  Andre Esteva; Brett Kuprel; Roberto A Novoa; Justin Ko; Susan M Swetter; Helen M Blau; Sebastian Thrun
Journal:  Nature       Date:  2017-01-25       Impact factor: 49.962

Review 9.  Reinforcement Learning, Fast and Slow.

Authors:  Matthew Botvinick; Sam Ritter; Jane X Wang; Zeb Kurth-Nelson; Charles Blundell; Demis Hassabis
Journal:  Trends Cogn Sci       Date:  2019-04-16       Impact factor: 20.229

Review 10.  Bridging scales in cancer progression: mapping genotype to phenotype using neural networks.

Authors:  Philip Gerlee; Eunjung Kim; Alexander R A Anderson
Journal:  Semin Cancer Biol       Date:  2014-05-12       Impact factor: 15.707

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  13 in total

Review 1.  Predictive Design and Analysis of Drug Transport by Multiscale Computational Models Under Uncertainty.

Authors:  Ali Aykut Akalın; Barış Dedekargınoğlu; Sae Rome Choi; Bumsoo Han; Altug Ozcelikkale
Journal:  Pharm Res       Date:  2022-06-01       Impact factor: 4.580

Review 2.  Genome-Wide Association Study Statistical Models: A Review.

Authors:  Mohsen Yoosefzadeh-Najafabadi; Milad Eskandari; François Belzile; Davoud Torkamaneh
Journal:  Methods Mol Biol       Date:  2022

Review 3.  Multiscale simulations of left ventricular growth and remodeling.

Authors:  Hossein Sharifi; Charles K Mann; Alexus L Rockward; Mohammad Mehri; Joy Mojumder; Lik-Chuan Lee; Kenneth S Campbell; Jonathan F Wenk
Journal:  Biophys Rev       Date:  2021-08-25

Review 4.  ASAS-NANP symposium: mathematical modeling in animal nutrition: limitations and potential next steps for modeling and modelers in the animal sciences.

Authors:  Marc Jacobs; Aline Remus; Charlotte Gaillard; Hector M Menendez; Luis O Tedeschi; Suresh Neethirajan; Jennifer L Ellis
Journal:  J Anim Sci       Date:  2022-06-01       Impact factor: 3.338

5.  Is it safe to lift COVID-19 travel bans? The Newfoundland story.

Authors:  Kevin Linka; Proton Rahman; Alain Goriely; Ellen Kuhl
Journal:  Comput Mech       Date:  2020-08-29       Impact factor: 4.014

6.  A three-dimensional multiscale model for the prediction of thrombus growth under flow with single-platelet resolution.

Authors:  Kaushik N Shankar; Yiyuan Zhang; Talid Sinno; Scott L Diamond
Journal:  PLoS Comput Biol       Date:  2022-01-28       Impact factor: 4.475

7.  Online Machine Learning for Accelerating Molecular Dynamics Modeling of Cells.

Authors:  Ziji Zhang; Peng Zhang; Changnian Han; Guojing Cong; Chih-Chieh Yang; Yuefan Deng
Journal:  Front Mol Biosci       Date:  2022-01-27

8.  Towards a robust out-of-the-box neural network model for genomic data.

Authors:  Zhaoyi Zhang; Songyang Cheng; Claudia Solis-Lemus
Journal:  BMC Bioinformatics       Date:  2022-04-09       Impact factor: 3.169

9.  Multiscale modeling in disease.

Authors:  Ashlee N Ford Versypt
Journal:  Curr Opin Syst Biol       Date:  2021-05-08

10.  The reproduction number of COVID-19 and its correlation with public health interventions.

Authors:  Kevin Linka; Mathias Peirlinck; Ellen Kuhl
Journal:  Comput Mech       Date:  2020-07-28       Impact factor: 4.014

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