Merge branch 'master' of gitlab.ensta.fr:Dreo/sho into simulated_annealing

LESSON.md

-Metaheuristics (IA-308)
-=======================
-
-Compile as PDF: `pandoc -f markdown --toc -o LESSON.pdf LESSON.md`.
-
 Introduction
-------------
-
-Metaheuristics are mathematical optimization algorithms solving $argmin_{x \in X} f(x)$ (or argmax).
+============
 
-Synonyms:
+> Metaheuristics are mathematical optimization algorithms solving $\argmin_{x \in X} f(x)$.
+>
+> Synonyms:
+>
+> - search heuristics,
+> - evolutionary algorithms,
+> - stochastic local search.
+>
+> The general approach is to only look at the solutions, by trial and error, without further information on its structure.
+> Hence the problem is often labelled as "black-box".
+>
+> Link to NP-hardness/curse of dimensionality: easy to evaluate, hard to solve.
+> Easy to evaluate = fast, but not as fast as the algorithm itself.
+> Hard to solve, but not impossible.
 
-- search heuristics,
-- evolutionary algorithms,
-- stochastic local search.
 
-The general approach is to only look at the solutions, by trial and error, without further information on its structure.
-Hence the problem is often labelled as "black-box".
+Hard optimization
+-----------------
 
-Link to NP-hardness/curse of dimensionality: easy to evaluate, hard to solve.
-Easy to evaluate = fast, but not as fast as the algorithm itself.
-Hard to solve, but not impossible.
+Metaheuristics are algorithms which aim at solving "hard" mathematical optimization problems.
 
+A mathematical optimization problem is defined by a "solution" $x$
+and an "objective function" $f:x\mapsto\reals$ :
+$$\argmin_{x \in X} f(x)$$
 
-Algorithmics
-------------
-
-Those algorithms are randomized and iteratives (hence stochastics) and manipulates a sample (synonym population)
-of solutions (s. individual) to the problem, each one being associated with its quality (s. cost, fitness).
+One can consider using $\argmax$ without loss of genericity[^argminmax].
+Usually, the set $X$ is defined intentionally and constraints on $x$ are managed separately.
+For example, using a function $g:x\mapsto \{0,1\}$:
+$$\argmin_{x\in[0,1]^n} f(x),\quad\text{s.t.}\quad g(x)=0$$
 
-Thus, algorithms have a main loop, and articulate functions that manipulates the sample (called "operators").
 
-Main design problem: exploitation/exploration compromise (s. intensification/diversification).
-Main design goal: raise the abstraction level.
-Main design tools: learning (s. memory) + heuristics (s. bias).
 
-Forget metaphors and use mathematical descriptions.
+[^argminmax]: In the metaheuristics literature, $\argmax$ is often assumed for evolutionary algorithms, whether $\argmin$ is often assumed for local search or simulated annealing.
 
-Seek a compromise between complexity, performances and explainability.
 
-The is no better "method".
-Difference between model and instance, for problem and algorithm.
-No Free Lunch Theorem.
-But there is a "better algorithm instances on a given problem instances set".
-
-The better you understand it, the better the algorithm will be.
+Algorithmics
+============
+
+> Those algorithms are randomized and iteratives (hence stochastics) and manipulates a sample (synonym population)
+> of solutions (s. individual) to the problem, each one being associated with its quality (s. cost, fitness).
+> 
+> Thus, algorithms have a main loop, and articulate functions that manipulates the sample (called "operators").
+> 
+> Main design problem: exploitation/exploration compromise (s. intensification/diversification).
+> Main design goal: raise the abstraction level.
+> Main design tools: learning (s. memory) + heuristics (s. bias).
+> 
+> Forget metaphors and use mathematical descriptions.
+> 
+> Seek a compromise between complexity, performances and explainability.
+> 
+> The is no better "method".
+> Difference between model and instance, for problem and algorithm.
+> No Free Lunch Theorem.
+> But there is a "better algorithm instances on a given problem instances set".
+> 
+> The better you understand it, the better the algorithm will be.
 
 
 Problem modelization
---------------------
-
-Way to assess the quality: fitness function.
-Way to model a solution: encoding.
-
+====================
 
-### Main models
+> Way to assess the quality: fitness function.
+> Way to model a solution: encoding.
 
-Encoding:
 
-- continuous (s. numeric),
-- discrete metric (integers),
-- combinatorial (graph, permutation).
+## Main models
 
-Fitness:
+> Encoding:
+> 
+> - continuous (s. numeric),
+> - discrete metric (integers),
+> - combinatorial (graph, permutation).
+> 
+> Fitness:
+> 
+> - mono-objective,
+> - multi-modal,
+> - multi-objectives.
 
-- mono-objective,
-- multi-modal,
-- multi-objectives.
 
+## Constraints management
 
-### Constraints management
-
-Main constraints management tools for operators:
-- penalization,
-- reparation,
-- generation.
+> Main constraints management tools for operators:
+> - penalization,
+> - reparation,
+> - generation.
 
 
 Performance evaluation
-----------------------
-
-### What is performance
-
-Main performances axis:
-
-- time,
-- quality,
-- probability.
-
-Additional performance axis:
-
-- robustness,
-- stability.
-
-Golden rule: the output of a metaheuristic is a distribution, not a solution.
-
-
-### Empirical evaluation
-
-Proof-reality gap is huge, thus empirical performance evaluation is gold standard.
-
-Empirical evaluation = scientific method.
-
-Basic rules of thumb:
-
-- randomized algorithms => repetition of runs,
-- sensitivity to parameters => design of experiments,
-- use statistical tools,
-- design experiments to answer a single question,
-- test one thing at a time.
-
-### Useful statistical tools
-
-Statistical tests:
-
-- classical null hypothesis: test equality of distributions.
-- beware of p-value.
-
-How many runs?
-
-- not always "as many as possible",
-- maybe "as many as needed",
-- generally: 15 (min for non-parametric tests) -- 20 (min for parametric-gaussian tests).
-
-Use robust estimators: median instead of mean, Inter Quartile Range instead of standard deviation.
-
-
-### Expected Empirical Cumulative Distribution Functions
-
-On Run Time: ERT-ECDF.
-
-$$ERTECDF(\{X_0,\dots,X_i,\dots,X_r\}, \delta, f, t) := \#\{x_t \in X_t | f(x_t^*)>=\delta \}$$
-
-$$\delta \in \left[0, \max_{x \in \mathcal{X}}(f(x))\right]$$
-
-$$X_i := \left\{\left\{ x_0^0, \dots, x_i^j, \dots, x_p^u | p\in[1,\infty[ \right\} | u \in [0,\infty[ \right\} \in \mathcal{X}$$
-
-with $p$ the sample size, $r$ the number of runs, $u$ the number of iterations, $t$ the number of calls to the objective
-function.
-
-The number of calls to the objective function is a good estimator of time because it dominates all other times.
-
-The dual of the ERT-ECDF can be easily computed for quality (EQT-ECDF).
-
-3D ERT/EQT-ECDF may be useful for terminal comparison.
-
-
-### Other tools
-
-Convergence curves: do not forget the golden rule and show distributions:
-
-- quantile boxes,
-- violin plots,
-- histograms.
+======================
+
+## What is performance
+
+> Main performances axis:
+> 
+> - time,
+> - quality,
+> - probability.
+> 
+> Additional performance axis:
+> 
+> - robustness,
+> - stability.
+> 
+> Golden rule: the output of a metaheuristic is a distribution, not a solution.
+
+
+## Empirical evaluation
+
+> Proof-reality gap is huge, thus empirical performance evaluation is gold standard.
+> 
+> Empirical evaluation = scientific method.
+> 
+> Basic rules of thumb:
+> 
+> - randomized algorithms => repetition of runs,
+> - sensitivity to parameters => design of experiments,
+> - use statistical tools,
+> - design experiments to answer a single question,
+> - test one thing at a time.
+
+## Useful statistical tools
+
+> Statistical tests:
+> 
+> - classical null hypothesis: test equality of distributions.
+> - beware of p-value.
+> 
+> How many runs?
+> 
+> - not always "as many as possible",
+> - maybe "as many as needed",
+> - generally: 15 (min for non-parametric tests) -- 20 (min for parametric-gaussian tests).
+> 
+> Use robust estimators: median instead of mean, Inter Quartile Range instead of standard deviation.
+
+
+## Expected Empirical Cumulative Distribution Functions
+
+> On Run Time: ERT-ECDF.
+> 
+> $$ERTECDF(\{X_0,\dots,X_i,\dots,X_r\}, \delta, f, t) := \#\{x_t \in X_t | f(x_t^*)>=\delta \}$$
+> 
+> $$\delta \in \left[0, \max_{x \in \mathcal{X}}(f(x))\right]$$
+> 
+> $$X_i := \left\{\left\{ x_0^0, \dots, x_i^j, \dots, x_p^u | p\in[1,\infty[ \right\} | u \in [0,\infty[ \right\} \in \mathcal{X}$$
+> 
+> with $p$ the sample size, $r$ the number of runs, $u$ the number of iterations, $t$ the number of calls to the objective
+> function.
+> 
+> The number of calls to the objective function is a good estimator of time because it dominates all other times.
+> 
+> The dual of the ERT-ECDF can be easily computed for quality (EQT-ECDF).
+> 
+> 3D ERT/EQT-ECDF may be useful for terminal comparison.
+
+
+## Other tools
+
+> Convergence curves: do not forget the golden rule and show distributions:
+> 
+> - quantile boxes,
+> - violin plots,
+> - histograms.
 
 
 Algorithm Design
-----------------
-
-### Neighborhood
-
-Convergence definition(s):
-
-- strong,
-- weak.
-
-Neighborhood: subset of solutions atteinable after an atomic transformation:
-
-- ergodicity,
-- quasi-ergodicity.
-
-Relationship to metric space in the continuous domain.
-
-
-### Structure of problem/algorithms
-
-Structure of problems to exploit:
-
-- locality (basin of attraction),
-- separability,
-- gradient,
-- funnels.
-
-Structure with which to capture those structures:
-
-- implicit,
-- explicit,
-- direct.
-
-Silver rule: choose the algorithmic template that adhere the most to the problem model.
-
-- taking constraints into account,
-- iterate between problem/algorithm models.
-
-
-### Grammar of algorithms
-
-Parameter setting < tuning < control.
-
-Portfolio approaches.
-Example: numeric low dimensions => Nelder-Mead Search is sufficient.
-
-Algorithm selection.
-
-Algorithms are templates in which operators are interchangeable.
-
-Most generic way of thinking about algorithms: grammar-based algorithm selection with parameters.
-Example: modular CMA-ES.
+================
+
+## Neighborhood
+
+> Convergence definition(s):
+> 
+> - strong,
+> - weak.
+> 
+> Neighborhood: subset of solutions atteinable after an atomic transformation:
+> 
+> - ergodicity,
+> - quasi-ergodicity.
+> 
+> Relationship to metric space in the continuous domain.
+
+
+## Structure of problem/algorithms
+
+> Structure of problems to exploit:
+> 
+> - locality (basin of attraction),
+> - separability,
+> - gradient,
+> - funnels.
+> 
+> Structure with which to capture those structures:
+> 
+> - implicit,
+> - explicit,
+> - direct.
+> 
+> Silver rule: choose the algorithmic template that adhere the most to the problem model.
+> 
+> - taking constraints into account,
+> - iterate between problem/algorithm models.
+
+
+## Grammar of algorithms
+
+> Parameter setting < tuning < control.
+> 
+> Portfolio approaches.
+> Example: numeric low dimensions => Nelder-Mead Search is sufficient.
+> 
+> Algorithm selection.
+> 
+> Algorithms are templates in which operators are interchangeable.
+> 
+> Most generic way of thinking about algorithms: grammar-based algorithm selection with parameters.
+> Example: modular CMA-ES.
 
 Parameter setting tools:
 
@@ -216,6 +230,7 @@ Parameter setting tools:
 Design tools:
 
 - ParadisEO,
+- IOH profiler
 - jMetal,
 - Jenetics,
 - ECJ,
@@ -223,13 +238,13 @@ Design tools:
 - HeuristicLab.
 
 
-### Landscape-aware algorithms
-
-Fitness landscapes: structure of problems as seen by an algorithm.
-Features: tool that measure one aspect of a fitness landscape.
-
-We can observe landscapes, and learn which algorithm instance solves it better.
-Examples: SAT, TSP, BB.
+## Landscape-aware algorithms
 
-Toward automated solver design.
+> Fitness landscapes: structure of problems as seen by an algorithm.
+> Features: tool that measure one aspect of a fitness landscape.
+> 
+> We can observe landscapes, and learn which algorithm instance solves it better.
+> Examples: SAT, TSP, BB.
+> 
+> Toward automated solver design.
 

docs/commands.tex

+\usepackage{amssymb}
+\def\reals{\mathbb{R}}
+
+% thin space, limits underneath in displays
+\DeclareMathOperator*{\argmin}{arg\,min}
+\DeclareMathOperator*{\argmax}{arg\,max}

docs/config_pdf.yaml

+metadata:
+    title: "Metaheuristics Lesson"
+    author: Johann Dreo
+variables:
+    documentclass: memoir
+include-in-header:
+    - docs/style_quote.tex
+    - docs/style_paragraph.tex
+    - docs/commands.tex
+table-of-contents: true
+toc-depth: 3

docs/style_paragraph.tex

+\usepackage{enumitem}
+\setlist[itemize]{noitemsep, topsep=0pt}
+
+\setlength{\parskip}{0.5em}
+

docs/style_quote.tex

+
+\usepackage{tcolorbox}
+
+\definecolor{summary}{cmyk}{0.80, 0.13, 0.14, 0.04, 1.00}
+
+\newtcolorbox{myquote}{
+    title=Key concepts,
+    colback=summary!5!white,
+    colframe=summary!75!black
+}
+
+% redefine the 'quote' environment to use this 'myquote' environment
+\renewenvironment{quote}
+    {\begin{myquote}
+        \setlength{\parskip}{0.5em}
+    }
+    {\end{myquote}}
+

make_doc.sh

+#!/bin/sh
+pandoc -f markdown --defaults docs/config_pdf.yaml -o LESSON.pdf LESSON.md
+

snp.py

@@ -24,7 +24,7 @@ if __name__=="__main__":
             help="Sensors' range (as a fraction of domain width, max is √2)")
 
     can.add_argument("-w", "--domain-width", metavar="NB", default=30, type=int,
-            help="Domain width (a number of cells)")
+            help="Domain width (a number of cells). If you change this you will probably need to update `--target` accordingly")
 
     can.add_argument("-i", "--iters", metavar="NB", default=100, type=int,
             help="Maximum number of iterations")