Differential geometric MCMC methods and applications
暂无分享,去创建一个
[1] Antonietta Mira,et al. Zero variance Markov chain Monte Carlo for Bayesian estimators , 2010, Stat. Comput..
[2] Kevin H. Knuth,et al. Foundations of Inference , 2010, Axioms.
[3] Hans-Georg Müller,et al. Functional Data Analysis , 2016 .
[4] Mark Girolami,et al. Statistical analysis of nonlinear dynamical systems using differential geometric sampling methods , 2011, Interface Focus.
[5] Hervé Delingette,et al. Efficient probabilistic model personalization integrating uncertainty on data and parameters: Application to eikonal-diffusion models in cardiac electrophysiology. , 2011, Progress in biophysics and molecular biology.
[6] Radford M. Neal. MCMC Using Hamiltonian Dynamics , 2011, 1206.1901.
[7] Kamil Erguler,et al. Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models. , 2011, Molecular bioSystems.
[8] Michael P H Stumpf,et al. Sensitivity, robustness, and identifiability in stochastic chemical kinetics models , 2011, Proceedings of the National Academy of Sciences.
[9] M. Girolami,et al. Riemann manifold Langevin and Hamiltonian Monte Carlo methods , 2011, Journal of the Royal Statistical Society: Series B (Statistical Methodology).
[10] Mark K Transtrum,et al. Geometry of nonlinear least squares with applications to sloppy models and optimization. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.
[11] Michael Andrew Christie,et al. Population MCMC methods for history matching and uncertainty quantification , 2010, Computational Geosciences.
[12] Radford M. Neal. Probabilistic Inference Using Markov Chain Monte Carlo Methods , 2011 .
[13] William W. Chen,et al. Classic and contemporary approaches to modeling biochemical reactions. , 2010, Genes & development.
[14] D. Xiu. Numerical Methods for Stochastic Computations: A Spectral Method Approach , 2010 .
[15] T. Maiwald,et al. Materials and Methods SOM Text Figs. S1 to S16 References Materials and Methods , 2022 .
[16] Stephen M. Stigler,et al. Darwin, Galton and the Statistical Enlightenment , 2010 .
[17] M. Girolami,et al. Inferring Signaling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species , 2010, Science Signaling.
[18] T. Banchoff,et al. Differential Geometry of Curves and Surfaces , 2010 .
[19] M. Koornneef,et al. The development of Arabidopsis as a model plant. , 2010, The Plant journal : for cell and molecular biology.
[20] Juha Karhunen,et al. Approximate Riemannian Conjugate Gradient Learning for Fixed-Form Variational Bayes , 2010, J. Mach. Learn. Res..
[21] Jean Clairambault,et al. Circadian timing in cancer treatments. , 2010, Annual review of pharmacology and toxicology.
[22] Ryan P. Adams,et al. Elliptical slice sampling , 2009, AISTATS.
[23] James C. Spall,et al. Efficient Monte Carlo computation of Fisher information matrix using prior information , 2007, Comput. Stat. Data Anal..
[24] Shun-ichi Amari,et al. Divergence, Optimization and Geometry , 2009, ICONIP.
[25] Neil Dalchau,et al. Systems analyses of circadian networks. , 2009, Molecular bioSystems.
[26] Mark A. Girolami,et al. Estimating Bayes factors via thermodynamic integration and population MCMC , 2009, Comput. Stat. Data Anal..
[27] Ursula Klingmüller,et al. Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood , 2009, Bioinform..
[28] S. McDougall,et al. Multiscale modelling and nonlinear simulation of vascular tumour growth , 2009, Journal of mathematical biology.
[29] H. Rue,et al. Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations , 2009 .
[30] Paul H. C. Eilers,et al. Bayesian density estimation from grouped continuous data , 2009, Comput. Stat. Data Anal..
[31] Carl E. Rasmussen,et al. Gaussian processes for machine learning , 2005, Adaptive computation and machine learning.
[32] Robert J. Smith,et al. WHEN ZOMBIES ATTACK!: MATHEMATICAL MODELLING OF AN OUTBREAK OF ZOMBIE INFECTION , 2009 .
[33] Neil D. Lawrence,et al. Latent Force Models , 2009, AISTATS.
[34] Catherine F. Higham. Bifurcation analysis informs Bayesian inference in the Hes1 feedback loop , 2009, BMC Systems Biology.
[35] David Welch,et al. Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems , 2009, Journal of The Royal Society Interface.
[36] Ciaran L. Kelly,et al. The Circadian Clock in Arabidopsis Roots Is a Simplified Slave Version of the Clock in Shoots , 2008, Science.
[37] Neil D. Lawrence,et al. Accelerating Bayesian Inference over Nonlinear Differential Equations with Gaussian Processes , 2008, NIPS.
[38] J. Tyson,et al. Design principles of biochemical oscillators , 2008, Nature Reviews Molecular Cell Biology.
[39] L. Abbott,et al. Theoretical Neuroscience Rising , 2008, Neuron.
[40] Erin L. McDearmon,et al. The genetics of mammalian circadian order and disorder: implications for physiology and disease , 2008, Nature Reviews Genetics.
[41] Neil D. Lawrence,et al. Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities , 2008, ECCB.
[42] A. Pettitt,et al. Marginal likelihood estimation via power posteriors , 2008 .
[43] Bryan C. Daniels,et al. Sloppiness, robustness, and evolvability in systems biology. , 2008, Current opinion in biotechnology.
[44] Mark A. Girolami,et al. Bayesian ranking of biochemical system models , 2008, Bioinform..
[45] M. Vallisneri. Use and abuse of the Fisher information matrix in the assessment of gravitational-wave parameter-estimation prospects , 2007, gr-qc/0703086.
[46] B. Calderhead. A study of Population MCMC for estimatingBayes Factors over nonlinear ODE models , 2008 .
[47] Karine David,et al. ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light. , 2007, Nature.
[48] S. Kay,et al. PRR7 protein levels are regulated by light and the circadian clock in Arabidopsis. , 2007, The Plant journal : for cell and molecular biology.
[49] Ajay Jasra,et al. On population-based simulation for static inference , 2007, Stat. Comput..
[50] C. Tomlin,et al. Biology by numbers: mathematical modelling in developmental biology , 2007, Nature Reviews Genetics.
[51] H. Steven Wiley,et al. Cell Surface Receptors for Signal Transduction and Ligand Transport: A Design Principles Study , 2007, PLoS Comput. Biol..
[52] Aki Vehtari,et al. Sparse Log Gaussian Processes via MCMC for Spatial Epidemiology , 2007, Gaussian Processes in Practice.
[53] Christopher R. Myers,et al. Universally Sloppy Parameter Sensitivities in Systems Biology Models , 2007, PLoS Comput. Biol..
[54] A. Hajian. Efficient cosmological parameter estimation with Hamiltonian Monte Carlo technique , 2006, astro-ph/0608679.
[55] S. Oliver,et al. Bayesian Methods of Astronomical Source Extraction , 2005, astro-ph/0512597.
[56] R. Sidman. Discussion of paper by B. B. Garber , 1972, In Vitro.
[57] Jiguo Cao,et al. Parameter estimation for differential equations: a generalized smoothing approach , 2007 .
[58] Tony O’Hagan. Bayes factors , 2006 .
[59] B. Walsh,et al. Models for navigating biological complexity in breeding improved crop plants. , 2006, Trends in plant science.
[60] Heikki Haario,et al. DRAM: Efficient adaptive MCMC , 2006, Stat. Comput..
[61] J. Skilling. Nested sampling for general Bayesian computation , 2006 .
[62] Anthony Hall,et al. Disruption of Hepatic Leptin Signaling Protects Mice From Age- and Diet-Related Glucose Intolerance , 2010, Diabetes.
[63] Tania Nolan,et al. Quantification of mRNA using real-time RT-PCR , 2006, Nature Protocols.
[64] Anand Rangarajan,et al. A New Closed-Form Information Metric for Shape Analysis , 2006, MICCAI.
[65] Xavier Pennec,et al. Intrinsic Statistics on Riemannian Manifolds: Basic Tools for Geometric Measurements , 2006, Journal of Mathematical Imaging and Vision.
[66] D. Wilkinson. Stochastic Modelling for Systems Biology , 2006 .
[67] C. Robertson McClung,et al. Plant Circadian Rhythms , 2006, The Plant Cell Online.
[68] H. Philippe,et al. Computing Bayes factors using thermodynamic integration. , 2006, Systematic biology.
[69] C. Holmes,et al. Bayesian auxiliary variable models for binary and multinomial regression , 2006 .
[70] P. James McLellan,et al. Parameter estimation in continuous-time dynamic models using principal differential analysis , 2006, Comput. Chem. Eng..
[71] Mats Jirstrand,et al. Systems biology Systems Biology Toolbox for MATLAB : a computational platform for research in systems biology , 2006 .
[72] Stephen Emmott,et al. Towards 2020 Science , 2006 .
[73] Eric J Kunkel,et al. Systems biology in drug discovery. , 2006, Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference.
[74] Kaare Brandt Petersen,et al. The Matrix Cookbook , 2006 .
[75] P. Atzberger. The Monte-Carlo Method , 2006 .
[76] M. Barenco,et al. Ranked prediction of p53 targets using hidden variable dynamic modeling , 2006, Genome Biology.
[77] J. Spall. Monte Carlo Computation of the Fisher Information Matrix in Nonstandard Settings , 2005 .
[78] Xiuwen Liu,et al. A Computational Approach to Fisher Information Geometry with Applications to Image Analysis , 2005, EMMCVPR.
[79] Carol S. Woodward,et al. Enabling New Flexibility in the SUNDIALS Suite of Nonlinear and Differential/Algebraic Equation Solvers , 2020, ACM Trans. Math. Softw..
[80] Paul E. Brown,et al. Extension of a genetic network model by iterative experimentation and mathematical analysis , 2005, Molecular systems biology.
[81] M S Turner,et al. Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana. , 2005, Journal of theoretical biology.
[82] T. Mizuno,et al. Pseudo-Response Regulators (PRRs) or True Oscillator Components (TOCs). , 2005, Plant & cell physiology.
[83] J. Rosenthal,et al. Scaling limits for the transient phase of local Metropolis–Hastings algorithms , 2005 .
[84] Muffy Calder,et al. When kinases meet mathematics: the systems biology of MAPK signalling , 2005, FEBS letters.
[85] Leonhard Held,et al. Gaussian Markov Random Fields: Theory and Applications , 2005 .
[86] B. Leimkuhler,et al. Simulating Hamiltonian Dynamics: Hamiltonian PDEs , 2005 .
[87] Christian P. Robert,et al. Monte Carlo Statistical Methods , 2005, Springer Texts in Statistics.
[88] Albert Tarantola,et al. Inverse problem theory - and methods for model parameter estimation , 2004 .
[89] Ovidiu Calin,et al. Geometric Mechanics on Riemannian Manifolds: Applications to Partial Differential Equations , 2004 .
[90] E. Hairer,et al. Geometric Numerical Integration: Structure Preserving Algorithms for Ordinary Differential Equations , 2004 .
[91] R. Baierlein. Probability Theory: The Logic of Science , 2004 .
[92] J. Stelling,et al. Robustness properties of circadian clock architectures. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[93] B. Frieden. Science from Fisher Information , 2004 .
[94] Jens Timmer,et al. Parameter Identification Techniques for Partial Differential Equations , 2004, Int. J. Bifurc. Chaos.
[95] C. Sawyers,et al. Targeted cancer therapy , 2004, Nature.
[96] Carl E. Rasmussen,et al. Warped Gaussian Processes , 2003, NIPS.
[97] A. P. Dawid,et al. Gaussian Processes to Speed up Hybrid Monte Carlo for Expensive Bayesian Integrals , 2003 .
[98] Thore Graepel,et al. Solving Noisy Linear Operator Equations by Gaussian Processes: Application to Ordinary and Partial Differential Equations , 2003, ICML.
[99] N. Monk. Oscillatory Expression of Hes1, p53, and NF-κB Driven by Transcriptional Time Delays , 2003, Current Biology.
[100] K. S. Brown,et al. Statistical mechanical approaches to models with many poorly known parameters. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[101] J. Timmer,et al. Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[102] Guy Lebanon,et al. Learning Riemannian Metrics , 2002, UAI.
[103] Carl von Linné,et al. Linnaeus' Philosophia Botanica , 2003 .
[104] Timothy J. Robinson,et al. Sequential Monte Carlo Methods in Practice , 2003 .
[105] Radford M. Neal. Slice Sampling , 2000, physics/0009028.
[106] M. Koornneef,et al. A fortunate choice: the history of Arabidopsis as a model plant , 2002, Nature Reviews Genetics.
[107] Andrew J. Millar,et al. The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana , 2002, Nature.
[108] Elton P. Hsu. Stochastic analysis on manifolds , 2002 .
[109] Neil D. Lawrence,et al. Fast Sparse Gaussian Process Methods: The Informative Vector Machine , 2002, NIPS.
[110] Carl E. Rasmussen,et al. Derivative Observations in Gaussian Process Models of Dynamic Systems , 2002, NIPS.
[111] J. Rosenthal,et al. Optimal scaling for various Metropolis-Hastings algorithms , 2001 .
[112] Steve A. Kay,et al. Reciprocal Regulation Between TOC1 and LHY/CCA1 Within the Arabidopsis Circadian Clock , 2001, Science.
[113] Yoram Baram,et al. Manifold Stochastic Dynamics for Bayesian Learning , 1999, Neural Computation.
[114] Jun S. Liu,et al. Monte Carlo strategies in scientific computing , 2001 .
[115] George Boole,et al. The Calculus of Logic , 2001 .
[116] Jim Albert,et al. Ordinal Data Modeling , 2000 .
[117] A. Hall,et al. Functional independence of circadian clocks that regulate plant gene expression , 2000, Current Biology.
[118] N. Čencov. Statistical Decision Rules and Optimal Inference , 2000 .
[119] Stefano Tarantola,et al. Sensitivity Analysis as an Ingredient of Modeling , 2000 .
[120] Shun-ichi Amari,et al. Methods of information geometry , 2000 .
[121] P. Marriott,et al. Applications of differential geometry to econometrics: List of contributors , 2000 .
[122] Lingyu Chen,et al. Exploring Hybrid Monte Carlo in Bayesian Computation , 2000 .
[123] Francis Sullivan,et al. The Metropolis Algorithm , 2000, Computing in Science & Engineering.
[124] 남홍길. Control of Circadian Rhythms and Photoperiodic Flowering by the Arabidopsis GIGANTEA Gene , 1999 .
[125] S. Howison,et al. Applied Partial Differential Equations , 1999 .
[126] Neil Gershenfeld,et al. The nature of mathematical modeling , 1998 .
[127] J. M. Corcuera,et al. A Characterization of Monotone and Regular Divergences , 1998 .
[128] Bradley P. Carlin,et al. Markov Chain Monte Carlo in Practice: A Roundtable Discussion , 1998 .
[129] Gareth O. Roberts,et al. Markov‐chain monte carlo: Some practical implications of theoretical results , 1998 .
[130] Shun-ichi Amari,et al. Natural Gradient Works Efficiently in Learning , 1998, Neural Computation.
[131] J. Rosenthal,et al. Optimal scaling of discrete approximations to Langevin diffusions , 1998 .
[132] R. Kass,et al. Geometrical Foundations of Asymptotic Inference , 1997 .
[133] D. C. Rapaport,et al. The Art of Molecular Dynamics Simulation , 1997 .
[134] Dani Gamerman,et al. Sampling from the posterior distribution in generalized linear mixed models , 1997, Stat. Comput..
[135] R. Tweedie,et al. Exponential convergence of Langevin distributions and their discrete approximations , 1996 .
[136] Berend Smit,et al. Understanding molecular simulation: from algorithms to applications , 1996 .
[137] John Skilling,et al. Data analysis : a Bayesian tutorial , 1996 .
[138] David B. Dunson,et al. Bayesian Data Analysis , 2010 .
[139] P. Green. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination , 1995 .
[140] S. Chib,et al. Understanding the Metropolis-Hastings Algorithm , 1995 .
[141] Geoffrey E. Hinton,et al. Bayesian Learning for Neural Networks , 1995 .
[142] Yoshua Bengio,et al. Pattern Recognition and Neural Networks , 1995 .
[143] David J. Spiegelhalter,et al. Machine Learning, Neural and Statistical Classification , 2009 .
[144] N. Shephard,et al. Stochastic Volatility: Likelihood Inference And Comparison With Arch Models , 1996 .
[145] Michael I. Miller,et al. REPRESENTATIONS OF KNOWLEDGE IN COMPLEX SYSTEMS , 1994 .
[146] Paul Marriott,et al. Preferred Point Geometry and the Local Differential Geometry of the Kullback-Leibler Divergence , 1994 .
[147] I. Chavel. Riemannian Geometry: Subject Index , 2006 .
[148] Paul Marriott,et al. Preferred Point Geometry and Statistical Manifolds , 1993 .
[149] M. Murray,et al. Differential Geometry and Statistics , 1993 .
[150] Charles J. Geyer,et al. Practical Markov Chain Monte Carlo , 1992 .
[151] G. Sussman,et al. Chaotic Evolution of the Solar System , 1992, Science.
[152] J. Skilling. Bayesian Solution of Ordinary Differential Equations , 1992 .
[153] T. Bayes. An essay towards solving a problem in the doctrine of chances , 2003 .
[154] R. Ghanem,et al. Stochastic Finite Elements: A Spectral Approach , 1990 .
[155] R. T. Cox. Probability, frequency and reasonable expectation , 1990 .
[156] Adrian F. M. Smith,et al. Sampling-Based Approaches to Calculating Marginal Densities , 1990 .
[157] A. Kennedy. The theory of hybrid stochastic algorithms , 1990 .
[158] Creutz. Global Monte Carlo algorithms for many-fermion systems. , 1988, Physical review. D, Particles and fields.
[159] J. Banavar,et al. Computer Simulation of Liquids , 1988 .
[160] R. Fletcher. Practical Methods of Optimization , 1988 .
[161] Derek J. Pike,et al. Empirical Model‐building and Response Surfaces. , 1988 .
[162] A. Kennedy,et al. Hybrid Monte Carlo , 1988 .
[163] Calyampudi R. Rao,et al. Chapter 3: Differential and Integral Geometry in Statistical Inference , 1987 .
[164] K. Wilson,et al. Langevin simulations of lattice field theories. , 1985, Physical review. D, Particles and fields.
[165] Scott Kirkpatrick,et al. Optimization by simulated annealing: Quantitative studies , 1984 .
[166] S. Eguchi. Second Order Efficiency of Minimum Contrast Estimators in a Curved Exponential Family , 1983 .
[167] C. R. Rao,et al. Entropy differential metric, distance and divergence measures in probability spaces: A unified approach , 1982 .
[168] S. Amari. Differential Geometry of Curved Exponential Families-Curvatures and Information Loss , 1982 .
[169] C. R. Rao,et al. On the convexity of some divergence measures based on entropy functions , 1982, IEEE Trans. Inf. Theory.
[170] J. Varah. A Spline Least Squares Method for Numerical Parameter Estimation in Differential Equations , 1982 .
[171] K. Chung. Lectures from Markov processes to Brownian motion , 1982 .
[172] P. Ferreira,et al. Extending Fisher's measure of information , 1981 .
[173] C. Atkinson. Rao's distance measure , 1981 .
[174] M. Benson,et al. Parameter fitting in dynamic models , 1979 .
[175] J. Kent. Time-reversible diffusions , 1978, Advances in Applied Probability.
[176] J. D. Doll,et al. Brownian dynamics as smart Monte Carlo simulation , 1978 .
[177] A. Dawid. Further Comments on Some Comments on a Paper by Bradley Efron , 1977 .
[178] Harold L. Friedman,et al. Brownian dynamics: Its application to ionic solutions , 1977 .
[179] C. Dodson,et al. Tensor Geometry: The Geometric Viewpoint and its Uses , 1977 .
[180] M. Spivak. A comprehensive introduction to differential geometry , 1979 .
[181] B. Efron. Defining the Curvature of a Statistical Problem (with Applications to Second Order Efficiency) , 1975 .
[182] Piet Hemker,et al. Nonlinear parameter estimation in initial value problems , 1974 .
[183] Yonathan Bard,et al. Nonlinear parameter estimation , 1974 .
[184] P. Peskun,et al. Optimum Monte-Carlo sampling using Markov chains , 1973 .
[185] Robert K. Tsutakawa,et al. Design of Experiment for Bioassay , 1972 .
[186] I. Csiszár. A class of measures of informativity of observation channels , 1972 .
[187] C. W. Gear,et al. The automatic integration of ordinary differential equations , 1971, Commun. ACM.
[188] W. K. Hastings,et al. Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .
[189] A. Barker. Monte Carlo calculations of the radial distribution functions for a proton-electron plasma , 1965 .
[190] N. G. Parke,et al. Ordinary Differential Equations. , 1958 .
[191] N. Metropolis,et al. Equation of State Calculations by Fast Computing Machines , 1953, Resonance.
[192] R. A. Leibler,et al. On Information and Sufficiency , 1951 .
[193] H. Jeffreys. An invariant form for the prior probability in estimation problems , 1946, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.
[194] Helly. Grundbegriffe der Wahrscheinlichkeitsrechnung , 1936 .
[195] L. M. M.-T.. Theory of Probability , 1929, Nature.
[196] I. Holopainen. Riemannian Geometry , 1927, Nature.
[197] C. Darwin,et al. The 'Power of movement in plants.'--1880. , 1888 .
[198] W. T. THISELTON DYER,et al. The Effects of Cross- and Self-Fertilisation in the Vegetable Kingdom , 1877, Nature.