Papers

Some classic papers in various fields.

Machine Learning and Neural Network

Theories, Methods, Algorithms

2018 S. M. Ali Eslami et al., Neural scene representation and rendering (image representation learning)

2016 Kaiming He, Xiangyu Zhang, Shaoqing Ren and Jian Sun, Deep Residual Learning for Image Recognition (ResNet, shortcuts between remote layers)

2015 D. P. Kingma and Jimmy L. Ba, Adam: A Method for Stochastic Optimization (Adam optimizer)

2015 Yann LeCun, Yoshua Bengio and Geoffrey Hinton, Deep learning, Nature 521, 436–444 (review)

2015 Christian Szegedy, Wei Liu, Yangqing Jia, Pierre Sermanet, Scott Reed, Dragomir Anguelov, Dumitru Erhan, Vincent Vanhoucke, Andrew Rabinovich, Going Deeper with Convolutions (GoogleNet, Inception)

2014 Ian J. Goodfellow, Jean Pouget-Abadie, Mehdi Mirza, Bing Xu, David Warde-Farley, Sherjil Ozair, Aaron Courville, Yoshua Bengio, Generative Adversarial Networks (GAN)

2014 Pankaj Mehta, David J. Schwab, An exact mapping between the Variational Renormalization Group and Deep Learning, arXiv:1410.3831

2013 Matthew D Zeiler, Rob Fergus, Visualizing and Understanding Convolutional Networks, arXiv:1311.2901 (see what each layer is picking up in CNN)

2012 A Krizhevsky, I Sutskever, GE Hinton, ImageNet Classification with Deep Convolutional Neural Networks, Advances in Neural Information Processing Systems 25 (NIPS 2012) (AlexNet)

2006 G. E. Hinton, R. R. Salakhutdinov, Reducing the Dimensionality of Data with Neural Networks (restricted Boltzmann machine autoencoder)

1998 Y. Lecun ; L. Bottou ; Y. Bengio ; P. Haffner, Gradient-based learning applied to document recognition (LeNet-5, CNN for MNIST)

1989 Kurt Hornik, Maxwell Stinchcombe, Halbert White, Multilayer feedforward networks are universal approximators (proof of MLP with one hidden layer and enough units can approximate any function)

1986 David E. Rumelhart, Geoffrey E. Hinton & Ronald J. Williams, Learning representations by back-propagating errors (backpropagation)

1985 D. J. Amit, and H. Gutfreund and H. Sompolinsky, Spin-glass models of neural networks (spin glass)

1982 J J Hopfield, Neural networks and physical systems with emergent collective computational abilities (Hopfield network, associative memory)

1980 Kunihiko Fukushima, Neocognitron: A self-organizing neural network model for a mechanism of pattern recognition unaffected by shift in position (early ideas on CNN)

1943 Warren S. McCulloch, Walter Pitts, A logical calculus of the ideas immanent in nervous activity (activation of a single perceptron, logic gate e.g. XOR)

1901 Karl Pearson, On Lines and Planes of Closest Fit to Systems of Points in Space (PCA)

Application

2018 Marwin H. S. Segler, Mike Preuss & Mark P. Waller, Planning chemical syntheses with deep neural networks and symbolic AI, Nature (organic synthesis)

2018 Maciej Koch-Janusz and Zohar Ringel, Mutual information, neural networks and the renormalization group, Nature Phys. (use RBM to do RG by minimizing cross entropy)

2018 Kermany et. al., Identifying Medical Diagnoses and Treatable Diseases by Image-Based Deep Learning, Cell (CNN medical image)

2018 Capper et. al., DNA methylation-based classification of central nervous system tumours, Nature (random forrest cancer flassification)

2017 Evert P. L. van Nieuwenburg, Ye-Hua Liu & Sebastian D. Huber, Learning phase transitions by confusion, Nature Phys (small NN, three lattice models, W-shape performance P(c') gives the transition c when exploring a<c'<b)

2017 Juan Carrasquilla & Roger G. Melko, Machine learning phases of matter, Nature Phys (supervised, NN and CNN, spin models, X=configuration, y=phase label)

2017 David Silver et. al., Mastering the game of Go without human knowledge, Nature

2016 David Silver et. al., Mastering the game of Go with deep neural networks and tree search, Nature

Ising Model

Ernst Ising, Beitrag zur Theorie des Ferromagnetismus, Zeitschrift für Physik 31, 253-258 (1925) (the model)

H. A. Kramers and G. H. Wannier, Statistics of the Two-Dimensional Ferromagnet. Part I, Phys. Rev. 60, 252 (1941) (transfer matrix; sinh J/kTc = 1, Tc=2.269117)

H. A. Kramers and G. H. Wannier, Statistics of the Two-Dimensional Ferromagnet. Part II, Phys. Rev. 60, 263 (1941)

Lars Onsager,Crystal Statistics. I. A Two-Dimensional Model with an Order-Disorder Transition, Phys. Rev. 65, 117-149 (1944) (2D exact solution, Cv)

G. H. Wannier, The Statistical Problem in Cooperative Phenomena, Rev. Mod. Phys. 17, 50 (1945)

Bruria Kaufman, Crystal Statistics. II. Partition Function Evaluated by Spinor Analysis, Phys. Rev. 76, 1232 (1949) (simplification of Onsager's solution)

C. N. Yang, The Spontaneous Magnetization of a Two-Dimensional Ising Model, Phys. Rev. 85, 808-816 (1952) (2D magnetization exact solution, beta=1/8)

M. Kac and J. C. Ward, A Combinatorial Solution of the Two-Dimensional Ising Model, Phys. Rev. 88, 1332 (1952)

Roy J. Glauber, Time‐Dependent Statistics of the Ising Model, J. Math. Phys. 4, 294 (1963)

Kyozi Kawasaki, Diffusion Constants near the Critical Point for Time-Dependent Ising Models. I, Phys. Rev. 145, 224–230 (1966)

Arthur E. Ferdinand and Michael E. Fisher, Bounded and Inhomogeneous Ising Models. I. Specific-Heat Anomaly of a Finite Lattice, Phys. Rev. 185, 832 (1969)

Paul D. Beale, Exact Distribution of Energies in the Two-Dimensional Ising Model, Phys. Rev. Lett. 76, 78 (1996)

Monte Carlo Methods

Nicholas Metropolis, Arianna W. Rosenbluth, Marshall N. Rosenbluth, Augusta H. Teller, and Edward Teller, Equation of State Calculations by Fast Computing Machines, J. Chem. Phys. 21, 1087 (1953) (importance sampling)

W. K. Hastings, Monte Carlo Sampling Methods Using Markov Chains and Their Applications, Biometrika 57, 97–109 (1970)

Molecular Dynamics

B. J. Alder and T. E. Wainwright, Studies in Molecular Dynamics. I. General Method, J. Chem. Phys. 31, 459 (1959) ( step potential, event-driven collision dynamics, time table, cell list)

A. Rahman, Correlations in the Motion of Atoms in Liquid Argon, Phys. Rev. 136, A405 (1964) (first MD study of realistic system, a predictor-corrector algorithm, g(r), D, G(r,t))

Molecular dynamics with coupling to an external bath (1984) (Berendsen thermostat)

A molecular dynamics method for simulations in the canonical ensemble (1984) (Nose-Hoover thermostat)

Free Energy Calculation

Daan Frenkel and Anthony Ladd, New Monte Carlo method to compute the free energy of arbitrary solid phases. Application to the FCC and HCP phases of hard spheres, J. Chem. Phys. 81, 3188 (1984) (thermodynamic integration from Einstein crystal to hard sphere )

M. Watanabe and W. P. Reinhardt, Direct dynamical calculation of entropy and free energy by adiabatic switching, Phys. Rev. Lett. 65, 3301 (1990) (adiabatic switching)

C. Jarzynski, Nonequilibrium equality for free energy differences, Phys. Rev. Lett. 78, 2690 (1997) (Jarzynski equality, valid for isolated and weak coupling systems)

Maurice de Koning, A. Antonelli, and Sidney Yip, Optimized Free-Energy Evaluation Using a Single Reversible-Scaling Simulation, Phys. Rev. Lett. 83, 3973 (1999) (integral over temperature T = T0/lambda)

Finite-Size Scaling

K. Binder, Finite Size Scaling Analysis of Ising Model Block Distribution Functions, Z. Phys. B - Condensed Matter 43, 119 (1981) (Binder cumulant, magnetization distribution)

Histogram Reweighting

A. M. Ferrenberg and D. P. Landau, Critical behavior of the three-dimensional Ising model: A high-resolution Monte Carlo Study, Phys. Rev. B 44, 5081 (1991) (Ising universality critical exponent, finite-size scaling)

Packing

--Hard Spheres

J. D. Bernal, A Geometrical Approach to the Structure of Liquids, Nature 183, 141 (1959)

J. D. Bernal, Geometry of the Structure of Monatomic Liquids, Nature 185, 68 (1960)

G. D. Scott, Packing of Spheres, Nature 188, 908 (1960)

J. D. Bernal and J. Mason, Coordination of Randomly Packed Spheres, Nature 188, 910 (1960)

J. L. Finney, Random packings and the structure of simple liquids I. The geometry of random close packing, Proc. Roy. Soc. Lond. A. 319, 479 (1970)

J. L. Finney, Random packings and the structure of simple liquids II. The molecular geometry of simple liquids, Proc. Roy. Soc. Lond. A. 319, 495 (1970)

J. L. Finney, Modelling the structures of amorphous metals and alloys, Nature 266, 309 (1977)

S. Yerazunis, S. W. Cornell and B. Wintner, Dense random packing of binary mixtures of spheres, Nature 207, 835 (1965) (theory to infinite size ratio)

A. S. Clarke and J. D. Wiley, Numerical simulation of the dense random packing of a binary mixture of hard spheres: Amorphous metals, Phys. Rev. B 35, 7350 (1987) (collective rearrangement algorithm with random growth and movement, size ratio 1.0-2.0)

Simple Liquid

J. G. Kirkwood, Statistical Mechanics of Fluid Mixtures, J. Chem. Phys. 3, 300 (1935) (Kirkwood integration;coupling parameter)

Léon Van Hove, Correlations in Space and Time and Born Approximation Scattering in Systems of Interacting Particles, Phys. Rev. 95, 249 (1954) (Van Hove function G(r,t))

R. W. Zwanzig, High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases, J. Chem. Phys. 22, 1420 (1954) (perturbation formula: exp (-beta(A-A0)) = <exp (-betaV1)>_0)

Glass

Walter. Kauzmann, The Nature of the Glassy State and the Behavior of Liquids at Low Temperatures, Chem. Rev. 43, 219 (1948) (Kauzmann temperature TK, entropy crisis)

C. A. Angell, Formation of Glasses from Liquids and Biopolymers, Science 267, 1924 (1995) (Angell plot: fragile vs strong glasses)

Frank H. Stillinger, A Topographic View of Supercooled Liquids and Glass Formation, Science 267, 1935 (1995) (inherent structure and energy landscape)

P. G. Debenedetti and F. H. Stillinger, Supercooled liquids and the glass transition, Nature 410, 259 (2001)

G. Parisi and F. Zamponi, Mean-field theory of hard sphere glasses and jamming, Rev. Mod. Phys. 82, 789 (2010)

Water Glass

Ashely Smart, "Melting" ice yields hints of a second liquid water, Physics Today 66, 16 (2013) (novel experiment reveals two glass transitions supporting the existence of two liquid phase, HDL and LDL)

Bulk Metallic Glass (BMG)

Mark Telford, The case for bulk metallic glass, Materials Today 7, 36 (2004) (review of history, properties and applications)

A. Lindsay Greer, Metallic Glasses, Science 267, 1947 (1995) (confusion rule)

Jan Schroers, Glasses made from pure metals, Nature 512, 142 (2014)

Li Zhong, Jiangwei Wang, Hongwei Sheng, Ze Zhang and Scott X. Mao, Formation of monatomic metallic glasses through ultrafast liquid quenching, Nature 512, 177 (2014) (pure metallic glass)

Nucleation

F. C. Frank, Supercooling of Liquids, Proc. Roy. Soc. London 215, 43 (1952) (the physics: close-packing vs dodecahedron)

Colloid

Valerie J. Anderson and Henk N. W. Lekkerkerker, Insights into phase transition kinetics from colloid science, Nature 416, 811 (2002) (hard sphere, long-range attraction, short-range attraction, protein suspension, colloid-polymer mixture, crystallization, nucleation, glass transition, depletion force, spinodal decomposition, aggregation, gelation)

Packing

R. S. Hoy, J. Harwayne-Gidansky, and C. S. O'Hern, Structure of finite sphere packings via exact enumeration: Implications for colloidal crystal nucleation, Phys. Rev. E 85, 051403 (2012) (number of packings M(N, Nc) of N spheres with Nc contacts)

Jamming

A. J. Liu and S. R. Nagel, Jamming is not just cool any more, Nature 396, 21 (1998) (T-Stress-Density phase diagram)

S. Torquato, T. M. Truskett, and P. G. Debenedetti, Is Random Close Packing of Spheres Well Defined?, Phys. Rev. Lett. 84, 2064 (2000) (maximally random jammed, i.e. minimizes order parameter)

C. S. O'Hern, S. A. Langer, A. J. Liu, and S. R. Nagel, Force distributions near jamming and glass transitions, Phys. Rev. Lett. 86, 111 (2001) (distribution of force P(F) plateaus or peaks around average force <F> as approaching the glass/jamming transition)

C. S. O'Hern, S. A. Langer, A. J. Liu, and S. R. Nagel, Random Packings of Frictionless Particles, Phys. Rev. Lett. 88, 075507 (2002) (T=0, finite-range repulsive particle, energy minimization; pressure p and shear stress G scales around the jamming threshold phic; distribution P(phic) of the jamming threshold narrows and peaks to the random close packing as N increases)

I. K. Ono, C. S. O'Hern, D. J. Durian, S. A. Langer, A. J. Liu, and S. R. Nagel, Effective Temperatures of a Driven System Near Jamming, Phys. Rev. Lett. 89, 095703 (2002) (define effective temperatures in driven athermal systems, e.g. sheared foam, by pressure fluctuation Tp, shear stress Txy, energy fluctuation Tu, diffusion TD and entropy change Ts.)

C. S. O'Hern, L. E. Silbert, A. J. Liu, and S. R. Nagel, Jamming at zero temperature and zero applied stress: The epitome of disorder, Phys. Rev. E 68, 011306 (2003) (comprehensive summary of the author's previous work.)

R. D. Kamien and A. J. Liu, Why is Random Close Packing Reproducible?, Phys. Rev. Lett. 99, 155501 (2007) (metastable liquid pressure diverges at RCP)

Chaoming Song, Ping Wang and Hernán A. Makse, A phase diagram for jammed matter, Nature 453, 629 (2008) ()

Ning Xu, D. Frenkel, and A. J. Liu, Direct Determination of the Size of Basins of Attraction of Jammed Solids, Phys. Rev. Lett. 106, 245502 (2011) (a free-energy integration method that calculates the volume of potential-energy basins and number of distinct potential-energy minima)

Stochastic Processes

D. T. Gillespie, Exact Stochastic Simulations of Coupled Chemical Reactions, J. Phys. Chem. 81, 2340-2361 (1977) (stochastic simulation algorithm instead of solving master equation)

Evolutionary Dynamics

M. Kimura, Evolutionary Rate at the Molecular Level, Nature 217, 624 (1968) (neutral theory)

R. Axelrod and W. D. Hamilton, The Evolution of Cooperation, Science 211, 1390 (1981) (tit-for-tat strategy in the Prisoner's Dilemma game with reciprocity)

M. A. Nowak, Five Rules for the Evolution of Cooperation, Science 314, 1560 (2006)

Evolutionary Game Theory

J. Nash, Equilibrium Points in N-Person Games, PNAS 36, 48 (1950) (Nash equilibrium)

Ian Stewart, A Puzzle for Pirates, Scientific American May, 98 (1999)

Networks

S. Milgram, The Small-World Problem, Psychology Today, May, 61 (1967) (six degree of separation)

S. Redner, How Popular is Your Paper? An Empirical Study of the Citation Distribution, Eur. Phys. J. B 4, 131-134 (1998)

D. J. Watts and S. H. Strogatz, Collective Dynamics of 'Small-World' Networks, Nature 393, 440 (1998)

A-L. Barabasi and R. Albert, Emergence of Scaling in Random Networks, Science 286, 509 (1999) (power law distribution)

Biophysics

Alex Mogilner, Jun Allard, and Roy Wollman, Cell Polarity: Quantitative Modeling as a Tool in Cell Biology, Science 336, 175 (2012)

Luis G. Morelli, Koichiro Uriu, Saúl Ares, Andrew C. Oates, Computational Approaches to Developmental Patterning, Science 336, 187 (2012) (four embryonic patterning strategies: signaling molecule gradient, activator-inhibitor system, synchronization of genetic oscillation, mechanical deformation)

Protein Folding

Hao Li, Robert Helling, Chao Tang, Ned Wingreen, Emergence of Preferred Structures in a Simple Model of Protein Folding, Science 273, 666 (1996)

Hao Li, Chao Tang, Ned Wingreen, Are protein folds atypical?, PNAS 95, 4987 (1998)

Polymer

Kurt Kremer and Gary S Grest, Dynamics of entangled linear polymer melts: A molecular‐dynamics simulation, The Journal of Chemical Physics 92, 5057 (1990) (benchmark simulation of the bead-spring polymer model)