Literature DB >> 31404441

A high-bias, low-variance introduction to Machine Learning for physicists.

Pankaj Mehta1, Ching-Hao Wang1, Alexandre G R Day1, Clint Richardson1, Marin Bukov2, Charles K Fisher3, David J Schwab4.   

Abstract

Machine Learning (ML) is one of the most exciting and dynamic areas of modern research and application. The purpose of this review is to provide an introduction to the core concepts and tools of machine learning in a manner easily understood and intuitive to physicists. The review begins by covering fundamental concepts in ML and modern statistics such as the bias-variance tradeoff, overfitting, regularization, generalization, and gradient descent before moving on to more advanced topics in both supervised and unsupervised learning. Topics covered in the review include ensemble models, deep learning and neural networks, clustering and data visualization, energy-based models (including MaxEnt models and Restricted Boltzmann Machines), and variational methods. Throughout, we emphasize the many natural connections between ML and statistical physics. A notable aspect of the review is the use of Python Jupyter notebooks to introduce modern ML/statistical packages to readers using physics-inspired datasets (the Ising Model and Monte-Carlo simulations of supersymmetric decays of proton-proton collisions). We conclude with an extended outlook discussing possible uses of machine learning for furthering our understanding of the physical world as well as open problems in ML where physicists may be able to contribute.

Entities:  

Year:  2019        PMID: 31404441      PMCID: PMC6688775          DOI: 10.1016/j.physrep.2019.03.001

Source DB:  PubMed          Journal:  Phys Rep        ISSN: 0370-1573            Impact factor:   25.600


  51 in total

1.  Nonlinear dimensionality reduction by locally linear embedding.

Authors:  S T Roweis; L K Saul
Journal:  Science       Date:  2000-12-22       Impact factor: 47.728

2.  A global geometric framework for nonlinear dimensionality reduction.

Authors:  J B Tenenbaum; V de Silva; J C Langford
Journal:  Science       Date:  2000-12-22       Impact factor: 47.728

3.  On the momentum term in gradient descent learning algorithms.

Authors:  Ning Qian
Journal:  Neural Netw       Date:  1999-01

4.  Training products of experts by minimizing contrastive divergence.

Authors:  Geoffrey E Hinton
Journal:  Neural Comput       Date:  2002-08       Impact factor: 2.026

5.  Density matrix formulation for quantum renormalization groups.

Authors: 
Journal:  Phys Rev Lett       Date:  1992-11-09       Impact factor: 9.161

6.  A fast learning algorithm for deep belief nets.

Authors:  Geoffrey E Hinton; Simon Osindero; Yee-Whye Teh
Journal:  Neural Comput       Date:  2006-07       Impact factor: 2.026

7.  Weak pairwise correlations imply strongly correlated network states in a neural population.

Authors:  Elad Schneidman; Michael J Berry; Ronen Segev; William Bialek
Journal:  Nature       Date:  2006-04-09       Impact factor: 49.962

8.  Reducing the dimensionality of data with neural networks.

Authors:  G E Hinton; R R Salakhutdinov
Journal:  Science       Date:  2006-07-28       Impact factor: 47.728

9.  'Infotaxis' as a strategy for searching without gradients.

Authors:  Massimo Vergassola; Emmanuel Villermaux; Boris I Shraiman
Journal:  Nature       Date:  2007-01-25       Impact factor: 49.962

10.  Entanglement renormalization.

Authors:  G Vidal
Journal:  Phys Rev Lett       Date:  2007-11-28       Impact factor: 9.161

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  40 in total

Review 1.  Big-Data Science in Porous Materials: Materials Genomics and Machine Learning.

Authors:  Kevin Maik Jablonka; Daniele Ongari; Seyed Mohamad Moosavi; Berend Smit
Journal:  Chem Rev       Date:  2020-06-10       Impact factor: 60.622

2.  DOME: recommendations for supervised machine learning validation in biology.

Authors:  Ian Walsh; Dmytro Fishman; Dario Garcia-Gasulla; Tiina Titma; Gianluca Pollastri; Jennifer Harrow; Fotis E Psomopoulos; Silvio C E Tosatto
Journal:  Nat Methods       Date:  2021-07-27       Impact factor: 28.547

3.  Detecting Examinees With Item Preknowledge in Large-Scale Testing Using Extreme Gradient Boosting (XGBoost).

Authors:  Cengiz Zopluoglu
Journal:  Educ Psychol Meas       Date:  2019-04-02       Impact factor: 2.821

4.  Learning moment closure in reaction-diffusion systems with spatial dynamic Boltzmann distributions.

Authors:  Oliver K Ernst; Thomas M Bartol; Terrence J Sejnowski; Eric Mjolsness
Journal:  Phys Rev E       Date:  2019-06       Impact factor: 2.529

Review 5.  Proposed Requirements for Cardiovascular Imaging-Related Machine Learning Evaluation (PRIME): A Checklist: Reviewed by the American College of Cardiology Healthcare Innovation Council.

Authors:  Partho P Sengupta; Sirish Shrestha; Béatrice Berthon; Emmanuel Messas; Erwan Donal; Geoffrey H Tison; James K Min; Jan D'hooge; Jens-Uwe Voigt; Joel Dudley; Johan W Verjans; Khader Shameer; Kipp Johnson; Lasse Lovstakken; Mahdi Tabassian; Marco Piccirilli; Mathieu Pernot; Naveena Yanamala; Nicolas Duchateau; Nobuyuki Kagiyama; Olivier Bernard; Piotr Slomka; Rahul Deo; Rima Arnaout
Journal:  JACC Cardiovasc Imaging       Date:  2020-09

6.  Defective glycosylation and multisystem abnormalities characterize the primary immunodeficiency XMEN disease.

Authors:  Juan C Ravell; Mami Matsuda-Lennikov; Samuel D Chauvin; Juan Zou; Matthew Biancalana; Sally J Deeb; Susan Price; Helen C Su; Giulia Notarangelo; Ping Jiang; Aaron Morawski; Chrysi Kanellopoulou; Kyle Binder; Ratnadeep Mukherjee; James T Anibal; Brian Sellers; Lixin Zheng; Tingyan He; Alex B George; Stefania Pittaluga; Astin Powers; David E Kleiner; Devika Kapuria; Marc Ghany; Sally Hunsberger; Jeffrey I Cohen; Gulbu Uzel; Jenna Bergerson; Lynne Wolfe; Camilo Toro; William Gahl; Les R Folio; Helen Matthews; Pam Angelus; Ivan K Chinn; Jordan S Orange; Claudia M Trujillo-Vargas; Jose Luis Franco; Julio Orrego-Arango; Sebastian Gutiérrez-Hincapié; Niraj Chandrakant Patel; Kimiyo Raymond; Turkan Patiroglu; Ekrem Unal; Musa Karakukcu; Alexandre Gr Day; Pankaj Mehta; Evan Masutani; Suk S De Ravin; Harry L Malech; Grégoire Altan-Bonnet; V Koneti Rao; Matthias Mann; Michael J Lenardo
Journal:  J Clin Invest       Date:  2020-01-02       Impact factor: 14.808

7.  Unsupervised Learning Methods for Molecular Simulation Data.

Authors:  Aldo Glielmo; Brooke E Husic; Alex Rodriguez; Cecilia Clementi; Frank Noé; Alessandro Laio
Journal:  Chem Rev       Date:  2021-05-04       Impact factor: 60.622

8.  Microswimmers learning chemotaxis with genetic algorithms.

Authors:  Benedikt Hartl; Maximilian Hübl; Gerhard Kahl; Andreas Zöttl
Journal:  Proc Natl Acad Sci U S A       Date:  2021-05-11       Impact factor: 11.205

9.  Molecular insights on ABL kinase activation using tree-based machine learning models and molecular docking.

Authors:  Philipe Oliveira Fernandes; Diego Magno Martins; Aline de Souza Bozzi; João Paulo A Martins; Adolfo Henrique de Moraes; Vinícius Gonçalves Maltarollo
Journal:  Mol Divers       Date:  2021-06-30       Impact factor: 3.364

10.  Extracting multi-way chromatin contacts from Hi-C data.

Authors:  Lei Liu; Bokai Zhang; Changbong Hyeon
Journal:  PLoS Comput Biol       Date:  2021-12-06       Impact factor: 4.475

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