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University of California, San Diego
UNIVERSITY OF CALIFORNIA, SAN DIEGO Computational Methods for Parameter Estimation in Nonlinear Models A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Physics with a Specialization in Computational Physics by Bryan Andrew Toth Committee in charge: Professor Henry D. I. Abarbanel, Chair Professor Philip Gill Professor Julius Kuti Professor Gabriel Silva Professor Frank Wuerthwein 2011 Copyright Bryan Andrew Toth, 2011 All rights reserved. The dissertation of Bryan Andrew Toth is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2011 iii DEDICATION To my grandparents, August and Virginia Toth and Willem and Jane Keur, who helped put me on a lifelong path of learning. iv EPIGRAPH An Expert: One who knows more and more about less and less, until eventually he knows everything about nothing. |Source Unknown v TABLE OF CONTENTS Signature Page . iii Dedication . iv Epigraph . v Table of Contents . vi List of Figures . ix List of Tables . x Acknowledgements . xi Vita and Publications . xii Abstract of the Dissertation . xiii Chapter 1 Introduction . 1 1.1 Dynamical Systems . 1 1.1.1 Linear and Nonlinear Dynamics . 2 1.1.2 Chaos . 4 1.1.3 Synchronization . 6 1.2 Parameter Estimation . 8 1.2.1 Kalman Filters . 8 1.2.2 Variational Methods . 9 1.2.3 Parameter Estimation in Nonlinear Systems . 9 1.3 Dissertation Preview . 10 Chapter 2 Dynamical State and Parameter Estimation . 11 2.1 Introduction . 11 2.2 DSPE Overview . 11 2.3 Formulation . 12 2.3.1 Least Squares Minimization . -
An Algorithm Based on Semidefinite Programming for Finding Minimax
Takustr. 7 Zuse Institute Berlin 14195 Berlin Germany BELMIRO P.M. DUARTE,GUILLAUME SAGNOL,WENG KEE WONG An algorithm based on Semidefinite Programming for finding minimax optimal designs ZIB Report 18-01 (December 2017) Zuse Institute Berlin Takustr. 7 14195 Berlin Germany Telephone: +49 30-84185-0 Telefax: +49 30-84185-125 E-mail: [email protected] URL: http://www.zib.de ZIB-Report (Print) ISSN 1438-0064 ZIB-Report (Internet) ISSN 2192-7782 An algorithm based on Semidefinite Programming for finding minimax optimal designs Belmiro P.M. Duarte a,b, Guillaume Sagnolc, Weng Kee Wongd aPolytechnic Institute of Coimbra, ISEC, Department of Chemical and Biological Engineering, Portugal. bCIEPQPF, Department of Chemical Engineering, University of Coimbra, Portugal. cTechnische Universität Berlin, Institut für Mathematik, Germany. dDepartment of Biostatistics, Fielding School of Public Health, UCLA, U.S.A. Abstract An algorithm based on a delayed constraint generation method for solving semi- infinite programs for constructing minimax optimal designs for nonlinear models is proposed. The outer optimization level of the minimax optimization problem is solved using a semidefinite programming based approach that requires the de- sign space be discretized. A nonlinear programming solver is then used to solve the inner program to determine the combination of the parameters that yields the worst-case value of the design criterion. The proposed algorithm is applied to find minimax optimal designs for the logistic model, the flexible 4-parameter Hill homoscedastic model and the general nth order consecutive reaction model, and shows that it (i) produces designs that compare well with minimax D−optimal de- signs obtained from semi-infinite programming method in the literature; (ii) can be applied to semidefinite representable optimality criteria, that include the com- mon A−; E−; G−; I− and D-optimality criteria; (iii) can tackle design problems with arbitrary linear constraints on the weights; and (iv) is fast and relatively easy to use. -
Julia, My New Friend for Computing and Optimization? Pierre Haessig, Lilian Besson
Julia, my new friend for computing and optimization? Pierre Haessig, Lilian Besson To cite this version: Pierre Haessig, Lilian Besson. Julia, my new friend for computing and optimization?. Master. France. 2018. cel-01830248 HAL Id: cel-01830248 https://hal.archives-ouvertes.fr/cel-01830248 Submitted on 4 Jul 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. « Julia, my new computing friend? » | 14 June 2018, IETR@Vannes | By: L. Besson & P. Haessig 1 « Julia, my New frieNd for computiNg aNd optimizatioN? » Intro to the Julia programming language, for MATLAB users Date: 14th of June 2018 Who: Lilian Besson & Pierre Haessig (SCEE & AUT team @ IETR / CentraleSupélec campus Rennes) « Julia, my new computing friend? » | 14 June 2018, IETR@Vannes | By: L. Besson & P. Haessig 2 AgeNda for today [30 miN] 1. What is Julia? [5 miN] 2. ComparisoN with MATLAB [5 miN] 3. Two examples of problems solved Julia [5 miN] 4. LoNger ex. oN optimizatioN with JuMP [13miN] 5. LiNks for more iNformatioN ? [2 miN] « Julia, my new computing friend? » | 14 June 2018, IETR@Vannes | By: L. Besson & P. Haessig 3 1. What is Julia ? Open-source and free programming language (MIT license) Developed since 2012 (creators: MIT researchers) Growing popularity worldwide, in research, data science, finance etc… Multi-platform: Windows, Mac OS X, GNU/Linux.. -
[20Pt]Algorithms for Constrained Optimization: [ 5Pt]
SOL Optimization 1970s 1980s 1990s 2000s 2010s Summary 2020s Algorithms for Constrained Optimization: The Benefits of General-purpose Software Michael Saunders MS&E and ICME, Stanford University California, USA 3rd AI+IoT Business Conference Shenzhen, China, April 25, 2019 Optimization Software 3rd AI+IoT Business Conference, Shenzhen, April 25, 2019 1/39 SOL Optimization 1970s 1980s 1990s 2000s 2010s Summary 2020s SOL Systems Optimization Laboratory George Dantzig, Stanford University, 1974 Inventor of the Simplex Method Father of linear programming Large-scale optimization: Algorithms, software, applications Optimization Software 3rd AI+IoT Business Conference, Shenzhen, April 25, 2019 2/39 SOL Optimization 1970s 1980s 1990s 2000s 2010s Summary 2020s SOL history 1974 Dantzig and Cottle start SOL 1974{78 John Tomlin, LP/MIP expert 1974{2005 Alan Manne, nonlinear economic models 1975{76 MS, MINOS first version 1979{87 Philip Gill, Walter Murray, MS, Margaret Wright (Gang of 4!) 1989{ Gerd Infanger, stochastic optimization 1979{ Walter Murray, MS, many students 2002{ Yinyu Ye, optimization algorithms, especially interior methods This week! UC Berkeley opened George B. Dantzig Auditorium Optimization Software 3rd AI+IoT Business Conference, Shenzhen, April 25, 2019 3/39 SOL Optimization 1970s 1980s 1990s 2000s 2010s Summary 2020s Optimization problems Minimize an objective function subject to constraints: 0 x 1 min '(x) st ` ≤ @ Ax A ≤ u c(x) x variables 0 1 A matrix c1(x) B . C c(x) nonlinear functions @ . A c (x) `; u bounds m Optimization -
Numericaloptimization
Numerical Optimization Alberto Bemporad http://cse.lab.imtlucca.it/~bemporad/teaching/numopt Academic year 2020-2021 Course objectives Solve complex decision problems by using numerical optimization Application domains: • Finance, management science, economics (portfolio optimization, business analytics, investment plans, resource allocation, logistics, ...) • Engineering (engineering design, process optimization, embedded control, ...) • Artificial intelligence (machine learning, data science, autonomous driving, ...) • Myriads of other applications (transportation, smart grids, water networks, sports scheduling, health-care, oil & gas, space, ...) ©2021 A. Bemporad - Numerical Optimization 2/102 Course objectives What this course is about: • How to formulate a decision problem as a numerical optimization problem? (modeling) • Which numerical algorithm is most appropriate to solve the problem? (algorithms) • What’s the theory behind the algorithm? (theory) ©2021 A. Bemporad - Numerical Optimization 3/102 Course contents • Optimization modeling – Linear models – Convex models • Optimization theory – Optimality conditions, sensitivity analysis – Duality • Optimization algorithms – Basics of numerical linear algebra – Convex programming – Nonlinear programming ©2021 A. Bemporad - Numerical Optimization 4/102 References i ©2021 A. Bemporad - Numerical Optimization 5/102 Other references • Stephen Boyd’s “Convex Optimization” courses at Stanford: http://ee364a.stanford.edu http://ee364b.stanford.edu • Lieven Vandenberghe’s courses at UCLA: http://www.seas.ucla.edu/~vandenbe/ • For more tutorials/books see http://plato.asu.edu/sub/tutorials.html ©2021 A. Bemporad - Numerical Optimization 6/102 Optimization modeling What is optimization? • Optimization = assign values to a set of decision variables so to optimize a certain objective function • Example: Which is the best velocity to minimize fuel consumption ? fuel [ℓ/km] velocity [km/h] 0 30 60 90 120 160 ©2021 A. -
Pysp: Modeling and Solving Stochastic Programs in Python
Noname manuscript No. (will be inserted by the editor) PySP: Modeling and Solving Stochastic Programs in Python Jean-Paul Watson · David L. Woodruff · William E. Hart Received: September 6, 2010. Abstract Although stochastic programming is a powerful tool for modeling decision- making under uncertainty, various impediments have historically prevented its wide- spread use. One key factor involves the ability of non-specialists to easily express stochastic programming problems as extensions of deterministic models, which are often formulated first. A second key factor relates to the difficulty of solving stochastic programming models, particularly the general mixed-integer, multi-stage case. Intri- cate, configurable, and parallel decomposition strategies are frequently required to achieve tractable run-times. We simultaneously address both of these factors in our PySP software package, which is part of the COIN-OR Coopr open-source Python project for optimization. To formulate a stochastic program in PySP, the user speci- fies both the deterministic base model and the scenario tree with associated uncertain parameters in the Pyomo open-source algebraic modeling language. Given these two models, PySP provides two paths for solution of the corresponding stochastic program. The first alternative involves writing the extensive form and invoking a standard deter- ministic (mixed-integer) solver. For more complex stochastic programs, we provide an implementation of Rockafellar and Wets’ Progressive Hedging algorithm. Our particu- lar focus is on the use of Progressive Hedging as an effective heuristic for approximating Jean-Paul Watson Sandia National Laboratories Discrete Math and Complex Systems Department PO Box 5800, MS 1318 Albuquerque, NM 87185-1318 E-mail: [email protected] David L. -
TOMLAB –Unique Features for Optimization in MATLAB
TOMLAB –Unique Features for Optimization in MATLAB Bad Honnef, Germany October 15, 2004 Kenneth Holmström Tomlab Optimization AB Västerås, Sweden [email protected] ´ Professor in Optimization Department of Mathematics and Physics Mälardalen University, Sweden http://tomlab.biz Outline of the talk • The TOMLAB Optimization Environment – Background and history – Technology available • Optimization in TOMLAB • Tests on customer supplied large-scale optimization examples • Customer cases, embedded solutions, consultant work • Business perspective • Box-bounded global non-convex optimization • Summary http://tomlab.biz Background • MATLAB – a high-level language for mathematical calculations, distributed by MathWorks Inc. • Matlab can be extended by Toolboxes that adds to the features in the software, e.g.: finance, statistics, control, and optimization • Why develop the TOMLAB Optimization Environment? – A uniform approach to optimization didn’t exist in MATLAB – Good optimization solvers were missing – Large-scale optimization was non-existent in MATLAB – Other toolboxes needed robust and fast optimization – Technical advantages from the MATLAB languages • Fast algorithm development and modeling of applied optimization problems • Many built in functions (ODE, linear algebra, …) • GUIdevelopmentfast • Interfaceable with C, Fortran, Java code http://tomlab.biz History of Tomlab • President and founder: Professor Kenneth Holmström • The company founded 1986, Development started 1989 • Two toolboxes NLPLIB och OPERA by 1995 • Integrated format for optimization 1996 • TOMLAB introduced, ISMP97 in Lausanne 1997 • TOMLAB v1.0 distributed for free until summer 1999 • TOMLAB v2.0 first commercial version fall 1999 • TOMLAB starting sales from web site March 2000 • TOMLAB v3.0 expanded with external solvers /SOL spring 2001 • Dash Optimization Ltd’s XpressMP added in TOMLAB fall 2001 • Tomlab Optimization Inc. -
Pyomo Documentation Release 5.6.2.Dev0
Pyomo Documentation Release 5.6.2.dev0 Pyomo Feb 06, 2019 Contents 1 Installation 3 1.1 Using CONDA..............................................3 1.2 Using PIP.................................................3 2 Citing Pyomo 5 2.1 Pyomo..................................................5 2.2 PySP...................................................5 3 Pyomo Overview 7 3.1 Mathematical Modeling.........................................7 3.2 Overview of Modeling Components and Processes...........................9 3.3 Abstract Versus Concrete Models....................................9 3.4 Simple Models.............................................. 10 4 Pyomo Modeling Components 17 4.1 Sets.................................................... 17 4.2 Parameters................................................ 23 4.3 Variables................................................. 24 4.4 Objectives................................................ 25 4.5 Constraints................................................ 26 4.6 Expressions................................................ 26 4.7 Suffixes.................................................. 31 5 Solving Pyomo Models 41 5.1 Solving ConcreteModels......................................... 41 5.2 Solving AbstractModels......................................... 41 5.3 pyomo solve Command....................................... 41 5.4 Supported Solvers............................................ 42 6 Working with Pyomo Models 43 6.1 Repeated Solves............................................. 43 6.2 Changing -
Research and Development of an Open Source System for Algebraic Modeling Languages
Vilnius University Institute of Data Science and Digital Technologies LITHUANIA INFORMATICS (N009) RESEARCH AND DEVELOPMENT OF AN OPEN SOURCE SYSTEM FOR ALGEBRAIC MODELING LANGUAGES Vaidas Juseviˇcius October 2020 Technical Report DMSTI-DS-N009-20-05 VU Institute of Data Science and Digital Technologies, Akademijos str. 4, Vilnius LT-08412, Lithuania www.mii.lt Abstract In this work, we perform an extensive theoretical and experimental analysis of the char- acteristics of five of the most prominent algebraic modeling languages (AMPL, AIMMS, GAMS, JuMP, Pyomo), and modeling systems supporting them. In our theoretical comparison, we evaluate how the features of the reviewed languages match with the requirements for modern AMLs, while in the experimental analysis we use a purpose-built test model li- brary to perform extensive benchmarks of the various AMLs. We then determine the best performing AMLs by comparing the time needed to create model instances for spe- cific type of optimization problems and analyze the impact that the presolve procedures performed by various AMLs have on the actual problem-solving times. Lastly, we pro- vide insights on which AMLs performed best and features that we deem important in the current landscape of mathematical optimization. Keywords: Algebraic modeling languages, Optimization, AMPL, GAMS, JuMP, Py- omo DMSTI-DS-N009-20-05 2 Contents 1 Introduction ................................................................................................. 4 2 Algebraic Modeling Languages ......................................................................... -
Robert Fourer, David M. Gay INFORMS Annual Meeting
AMPL New Solver Support in the AMPL Modeling Language Robert Fourer, David M. Gay AMPL Optimization LLC, www.ampl.com Department of Industrial Engineering & Management Sciences, Northwestern University Sandia National Laboratories INFORMS Annual Meeting Pittsburgh, Pennsylvania, November 5-8, 2006 Robert Fourer, New Solver Support in the AMPL Modeling Language INFORMS Annual Meeting, November 5-8, 2006 1 AMPL What it is . A modeling language for optimization A system to support optimization modeling What I’ll cover . Brief examples, briefer history Recent developments . ¾ 64-bit versions ¾ floating license manager ¾ AMPL Studio graphical interface & Windows COM objects Solver support ¾ new KNITRO 5.1 features ¾ new CPLEX 10.1 features Robert Fourer, New Solver Support in the AMPL Modeling Language INFORMS Annual Meeting, November 5-8, 2006 2 Ex 1: Airline Fleet Assignment set FLEETS; set CITIES; set TIMES circular; set FLEET_LEGS within {f in FLEETS, c1 in CITIES, t1 in TIMES, c2 in CITIES, t2 in TIMES: c1 <> c2 and t1 <> t2}; # (f,c1,t1,c2,t2) represents the availability of fleet f # to cover the leg that leaves c1 at t1 and # whose arrival time plus turnaround time at c2 is t2 param leg_cost {FLEET_LEGS} >= 0; param fleet_size {FLEETS} >= 0; Robert Fourer, New Solver Support in the AMPL Modeling Language INFORMS Annual Meeting, November 5-8, 2006 3 Ex 1: Derived Sets set LEGS := setof {(f,c1,t1,c2,t2) in FLEET_LEGS} (c1,t1,c2,t2); # the set of all legs that can be covered by some fleet set SERV_CITIES {f in FLEETS} := union {(f,c1,c2,t1,t2) -
Julia: a Modern Language for Modern ML
Julia: A modern language for modern ML Dr. Viral Shah and Dr. Simon Byrne www.juliacomputing.com What we do: Modernize Technical Computing Today’s technical computing landscape: • Develop new learning algorithms • Run them in parallel on large datasets • Leverage accelerators like GPUs, Xeon Phis • Embed into intelligent products “Business as usual” will simply not do! General Micro-benchmarks: Julia performs almost as fast as C • 10X faster than Python • 100X faster than R & MATLAB Performance benchmark relative to C. A value of 1 means as fast as C. Lower values are better. A real application: Gillespie simulations in systems biology 745x faster than R • Gillespie simulations are used in the field of drug discovery. • Also used for simulations of epidemiological models to study disease propagation • Julia package (Gillespie.jl) is the state of the art in Gillespie simulations • https://github.com/openjournals/joss- papers/blob/master/joss.00042/10.21105.joss.00042.pdf Implementation Time per simulation (ms) R (GillespieSSA) 894.25 R (handcoded) 1087.94 Rcpp (handcoded) 1.31 Julia (Gillespie.jl) 3.99 Julia (Gillespie.jl, passing object) 1.78 Julia (handcoded) 1.2 Those who convert ideas to products fastest will win Computer Quants develop Scientists prepare algorithms The last 25 years for production (Python, R, SAS, DEPLOY (C++, C#, Java) Matlab) Quants and Computer Compress the Scientists DEPLOY innovation cycle collaborate on one platform - JULIA with Julia Julia offers competitive advantages to its users Julia is poised to become one of the Thank you for Julia. Yo u ' v e k i n d l ed leading tools deployed by developers serious excitement. -
Methods of Distributed and Nonlinear Process Control: Structuredness, Optimality and Intelligence
Methods of Distributed and Nonlinear Process Control: Structuredness, Optimality and Intelligence A THESIS SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA BY Wentao Tang IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Advised by Prodromos Daoutidis May, 2020 c Wentao Tang 2020 ALL RIGHTS RESERVED Acknowledgement Before meeting with my advisor Prof. Prodromos Daoutidis, I was not determined to do a Ph.D. in process control or systems engineering; after working with him, I could not imagine what if I had chosen a different path. The important decision that I made in the October of 2015 turned out to be most correct, that is, to follow an advisor who has the charm to always motivate me to explore the unexploited lands, overcome the obstacles and make achievements. I cherish the freedom of choosing different problems of interest and the flexibility of time managing in our research group. Apart from the knowledge of process control, I have learned a lot from Prof. Daoutidis and will try my best to keep learning, about the skills to write, present and teach, the pursuit of knowledge and methods with both elegance of fundamental theory and a promise of practical applicability, and the pride and fervor for the undertaken works. \The high hill is to be looked up to; the great road is to be travelled on."1 I want to express my deepest gratitude to him. Prof. Qi Zhang always gives me very good suggestions and enlightenment with his abundant knowledge in optimization since he joined our department.