{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Thebe Github Pages\n", "> Swarm Intelligence from social interaction\n", "\n", "- toc: false \n", "- badges: true\n", "- comments: true\n", "- hide: true\n", "- image: images/copied_from_nb/my_icons/static_pso.png\n", "- categories: [jupyter, optimisation, visualisation]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
print(\"HellSSo!\")\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Why are we here?" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "I'm hoping it's to read about **Swarm Intelligence!** I'm also hoping you're interested to read about the **_interactive dashboard_** side of things too so we can play with it at the end. \n", "\n", "If that sounds like too much and you just want to play with it now, **you can use it on PyViz examples here: https://particle-swarms.pyviz.demo.anaconda.com**\n", "\n", "We're going to build the dashboard using some of [Anacondas](https://www.anaconda.com/)'s [HoloViz](https://holoviz.org/) tools (Holoviews, Panel and Bokeh) to **get the result from the tweet below.**" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " > twitter: https://twitter.com/_ScottCondron/status/1293605204013846530" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Finding the \"just right\" Goldilocks Zone using Swarm Intelligence" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Say you're building a house and you want to maximise the number of rooms you can fit in your plot of land, maybe saying that all rooms have to be a certain size or bigger. That's the kind of thing that optimisation algorithms are useful for.\n", "\n", "Optimisation methods like **Particle Swarm Optimisation** are used when you want to find the _best_/_optimum_ for some system / problem. **You could just try every possible input** but that might take a while so smarter people than me have invented better ways." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## No death\n", "\n", "This is going to be pretty similar to my [Genetic Algorithm blog post](https://www.scottcondron.com/jupyter/optimisation/visualisation/2020/07/20/interactive-genetic-algorithm-dashboard-from-scratch-in-python.html) except this time there will be a lot less death. You won’t necessarily need to have read that blog post but I will be referring back to it once or twice so you may want to go back and read that first.\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Make it interactive because" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's build a dashboard in which you can **control parameters of Particle Swarm Optimisation, click a target and see the little dots flock towards it**. Like an interactive, 2D version of this plot on Wikipedia." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![pso_gif.gif](https://www.scottcondron.com/images/copied_from_nb/my_icons/pso_gif.gif \"Source: Wikipedia\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Swarm Intelligence" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Wait, why no death?\n", "\n", "Genetic algorithm is based on genetic evolution where for each generation there is survival-of-the-fittest-style well... death. In the case of Particle Swarm Optimisation, **there is the same population throughout** because we want them to **remember where they were when they were at their fittest**. Like looking back at yourself on your wedding day or after a health kick. **Each particles position is a potential solution to your problem so they're all trying to find the _best position_ together.** :heart_eyes:\n", "\n", "## Adding velocity to the mix\n", "\n", "In the case of Genetic Algorithm each member of the population was just a few numbers (their X and Y position), the parameters that you’re trying to optimise. In this case each particle will not just have a X and Y position, **they also have a velocity**. We also need a way to know how to improve the particles in our swarm..." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Closer (smaller distance) is better" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The same as with Genetic Algorithm, we'll need to **find the fittest member of the population using euclidean distance** / mean squared error (which particle is closest to the target). " ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "#collapse-hide\n", "def mean_squared_error(y_true, y_pred):\n", " return ((y_true - y_pred)**2).mean(axis=0)\n", "\n", "target_x, target_y = 0,0 \n", "def problem(soln):\n", " global target_x #using globals so we can link this to the click event later\n", " global target_y\n", " return mean_squared_error(soln, [target_x, target_y])\n", "\n", "def assess_fitness(individual, problem):\n", " \"Determines the fitness of an individual using the given problem\"\n", " return problem(individual)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Nostalgic by design" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**Each member is going to keep track of their fittest position**, this can help them if they explore a worse direction, or want to tell other particles (but we'll get to that later). They also keep an ID so that we can colour them across iterations. \n", "\n", "## A portrait of a particle\n", "\n", "The big red blob is one particle which has an X and Y position, a velocity and is constantly reminiscing about it's fittest position." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![pso.png](https://www.scottcondron.com/images/copied_from_nb/my_icons/particle.png \"A portrait of a particle\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Here's that in code (before we add any of the update logic)." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "\n", "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var force = true;\n", "\n", " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", " root._bokeh_onload_callbacks = [];\n", " root._bokeh_is_loading = undefined;\n", " }\n", "\n", " if (typeof 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monospace;\\n}\\n.json-formatter-dark.json-formatter-row,\\n.json-formatter-dark.json-formatter-row a,\\n.json-formatter-dark.json-formatter-row a:hover {\\n color: white;\\n text-decoration: none;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-row {\\n margin-left: 1rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty {\\n opacity: 0.5;\\n margin-left: 1rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty:after {\\n display: none;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-object:after {\\n content: \\\"No properties\\\";\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-children.json-formatter-empty.json-formatter-array:after {\\n content: \\\"[]\\\";\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-string,\\n.json-formatter-dark.json-formatter-row .json-formatter-stringifiable {\\n color: #31F031;\\n white-space: pre;\\n word-wrap: break-word;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-number {\\n color: #66C2FF;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-boolean {\\n color: #EC4242;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-null {\\n color: #EEC97D;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-undefined {\\n color: #ef8fbe;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-function {\\n color: #FD48CB;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-date {\\n background-color: rgba(255, 255, 255, 0.05);\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-url {\\n text-decoration: underline;\\n color: #027BFF;\\n cursor: pointer;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-bracket {\\n color: #9494FF;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-key {\\n color: #23A0DB;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler-link {\\n cursor: pointer;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler {\\n line-height: 1.2rem;\\n font-size: 0.7rem;\\n vertical-align: middle;\\n opacity: 0.6;\\n cursor: pointer;\\n padding-right: 0.2rem;\\n}\\n.json-formatter-dark.json-formatter-row .json-formatter-toggler:after {\\n display: inline-block;\\n transition: transform 100ms ease-in;\\n content: \\\"\\\\25BA\\\";\\n}\\n.json-formatter-dark.json-formatter-row > a > .json-formatter-preview-text {\\n opacity: 0;\\n transition: opacity 0.15s ease-in;\\n font-style: italic;\\n}\\n.json-formatter-dark.json-formatter-row:hover > a > .json-formatter-preview-text {\\n opacity: 0.6;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > .json-formatter-toggler-link .json-formatter-toggler:after {\\n transform: rotate(90deg);\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > .json-formatter-children:after {\\n display: inline-block;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open > a > .json-formatter-preview-text {\\n display: none;\\n}\\n.json-formatter-dark.json-formatter-row.json-formatter-open.json-formatter-empty:after {\\n display: block;\\n}\\n\");\n", " },\n", " function(Bokeh) {\n", " inject_raw_css(\"table.panel-df {\\n margin-left: auto;\\n margin-right: auto;\\n border: none;\\n border-collapse: collapse;\\n border-spacing: 0;\\n color: black;\\n font-size: 12px;\\n table-layout: fixed;\\n width: 100%;\\n}\\n\\n.panel-df tr, th, td {\\n text-align: right;\\n vertical-align: middle;\\n padding: 0.5em 0.5em !important;\\n line-height: normal;\\n white-space: normal;\\n max-width: none;\\n border: none;\\n}\\n\\n.panel-df tbody {\\n display: table-row-group;\\n vertical-align: middle;\\n border-color: inherit;\\n}\\n\\n.panel-df tbody tr:nth-child(odd) {\\n background: #f5f5f5;\\n}\\n\\n.panel-df thead {\\n border-bottom: 1px solid black;\\n vertical-align: bottom;\\n}\\n\\n.panel-df tr:hover {\\n background: lightblue !important;\\n cursor: pointer;\\n}\\n\");\n", " },\n", " function(Bokeh) {\n", " /* BEGIN bokeh.min.js */\n", " /*!\n", " * Copyright (c) 2012 - 2020, Anaconda, Inc., and Bokeh Contributors\n", " * All rights reserved.\n", " * \n", " * Redistribution and use in source and binary forms, with or without modification,\n", " * are permitted provided that the following conditions are met:\n", " * \n", " * Redistributions of source code must retain the above copyright notice,\n", " * this list of conditions and the following disclaimer.\n", " * \n", " * Redistributions in binary form must reproduce the above copyright notice,\n", " * this list of conditions and the following disclaimer in the documentation\n", " * and/or other materials provided with the distribution.\n", " * \n", " * Neither the name of Anaconda nor the names of any contributors\n", " * may be used to endorse or promote products derived from this software\n", " * without specific prior written permission.\n", " * \n", " * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n", " * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n", " * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE\n", " * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE\n", " * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR\n", " * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF\n", " * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS\n", " * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN\n", " * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)\n", " * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF\n", " * THE POSSIBILITY OF SUCH DAMAGE.\n", " */\n", " (function(root, factory) {\n", " const bokeh = factory();\n", " if (root.Bokeh === undefined) {\n", " root.Bokeh = bokeh;\n", " }\n", " const Bokeh = root.Bokeh;\n", " Bokeh[bokeh.version] = bokeh;\n", " })(this, function() {\n", " var define;\n", " var parent_require = typeof require === \"function\" && require\n", " return (function(modules, entry, aliases, externals) {\n", " if (aliases === undefined) aliases = {};\n", " if (externals === undefined) externals = {};\n", "\n", " var cache = {};\n", "\n", " var normalize = function(name) {\n", " if (typeof name === \"number\")\n", " return name;\n", "\n", " if (name === \"bokehjs\")\n", " return entry;\n", "\n", " var prefix = \"@bokehjs/\"\n", " if (name.slice(0, prefix.length) === prefix)\n", " name = name.slice(prefix.length)\n", "\n", " var alias = aliases[name]\n", " if (alias != null)\n", " return alias;\n", "\n", " var trailing = name.length > 0 && name[name.lenght-1] === \"/\";\n", " var index = aliases[name + (trailing ? \"\" : \"/\") + \"index\"];\n", " if (index != null)\n", " return index;\n", "\n", " return name;\n", " }\n", "\n", " var require = function(name) {\n", " var mod = cache[name];\n", " if (!mod) {\n", " var id = normalize(name);\n", "\n", " mod = cache[id];\n", " if (!mod) {\n", " if (!modules[id]) {\n", " if (externals[id] === false || (externals[id] == true && parent_require)) {\n", " try {\n", " mod = {exports: externals[id] ? parent_require(id) : {}};\n", " cache[id] = cache[name] = mod;\n", " return mod.exports;\n", " } catch (e) {}\n", " }\n", "\n", " var err = new Error(\"Cannot find module '\" + name + \"'\");\n", " err.code = 'MODULE_NOT_FOUND';\n", " throw err;\n", " }\n", "\n", " mod = {exports: {}};\n", " cache[id] = cache[name] = mod;\n", " modules[id].call(mod.exports, require, mod, mod.exports);\n", " } else\n", " cache[name] = mod;\n", " }\n", "\n", " return mod.exports;\n", " }\n", "\n", " var main = require(entry);\n", " main.require = require;\n", "\n", " if (typeof Proxy !== \"undefined\") {\n", " // allow Bokeh.loader[\"@bokehjs/module/name\"] syntax\n", " main.loader = new Proxy({}, {\n", " get: function(_obj, module) {\n", " return require(module);\n", " }\n", " });\n", " }\n", "\n", " main.register_plugin = function(plugin_modules, plugin_entry, plugin_aliases, plugin_externals) {\n", " if (plugin_aliases === undefined) plugin_aliases = {};\n", " if (plugin_externals === undefined) plugin_externals = {};\n", "\n", " for (var name in plugin_modules) {\n", " modules[name] = plugin_modules[name];\n", " }\n", "\n", " for (var name in plugin_aliases) {\n", " aliases[name] = plugin_aliases[name];\n", " }\n", "\n", " for (var name in plugin_externals) {\n", " externals[name] = plugin_externals[name];\n", " }\n", "\n", " var plugin = require(plugin_entry);\n", "\n", " for (var name in plugin) {\n", " main[name] = plugin[name];\n", " }\n", "\n", " return plugin;\n", " }\n", "\n", " return main;\n", " })\n", " ([\n", " function _(e,t,_){Object.defineProperty(_,\"__esModule\",{value:!0}),e(1).__exportStar(e(2),_)},\n", " function _(t,e,n){\n", " /*! *****************************************************************************\n", " Copyright (c) Microsoft Corporation. All rights reserved.\n", " Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use\n", " this file except in compliance with the License. You may obtain a copy of the\n", " License at http://www.apache.org/licenses/LICENSE-2.0\n", " \n", " THIS CODE IS PROVIDED ON AN *AS IS* BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY\n", " KIND, EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION ANY IMPLIED\n", " WARRANTIES OR CONDITIONS OF TITLE, FITNESS FOR A PARTICULAR PURPOSE,\n", " MERCHANTABLITY OR NON-INFRINGEMENT.\n", " \n", " See the Apache Version 2.0 License for specific language governing permissions\n", " and limitations under the License.\n", " ***************************************************************************** */\n", " Object.defineProperty(n,\"__esModule\",{value:!0});var r=function(t,e){return(r=Object.setPrototypeOf||{__proto__:[]}instanceof Array&&function(t,e){t.__proto__=e}||function(t,e){for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n])})(t,e)};function o(t){var e=\"function\"==typeof Symbol&&Symbol.iterator,n=e&&t[e],r=0;if(n)return n.call(t);if(t&&\"number\"==typeof t.length)return{next:function(){return t&&r>=t.length&&(t=void 0),{value:t&&t[r++],done:!t}}};throw new TypeError(e?\"Object is not iterable.\":\"Symbol.iterator is not defined.\")}function a(t,e){var n=\"function\"==typeof Symbol&&t[Symbol.iterator];if(!n)return t;var r,o,a=n.call(t),i=[];try{for(;(void 0===e||e-- >0)&&!(r=a.next()).done;)i.push(r.value)}catch(t){o={error:t}}finally{try{r&&!r.done&&(n=a.return)&&n.call(a)}finally{if(o)throw o.error}}return i}function i(t){return this instanceof i?(this.v=t,this):new i(t)}n.__extends=function(t,e){function n(){this.constructor=t}r(t,e),t.prototype=null===e?Object.create(e):(n.prototype=e.prototype,new n)},n.__assign=function(){return n.__assign=Object.assign||function(t){for(var e,n=1,r=arguments.length;n