From 7797f3ea40ff5f3c5db37300044c8d59c5b89338 Mon Sep 17 00:00:00 2001 From: Younes Strittmatter Date: Thu, 2 Nov 2023 15:31:37 -0400 Subject: [PATCH] feat: add documentation/enhance interface --- README.md | 29 +- dev/burn.py | 65 ++ docs/Additional Example.ipynb | 72 -- docs/Basic Usage.ipynb | 757 +++++++++++++++++- docs/img/logo.png | Bin 0 -> 31814 bytes docs/index.md | 35 +- docs/quickstart.md | 5 +- docs/user-guide/equation-formats.md | 16 + docs/user-guide/sampling.md | 2 + mkdocs.yml | 92 ++- mkdocs/base.yml | 25 - mkdocs/gen_ref_pages.py | 39 + mkdocs/hooks.py | 12 + mkdocs/overrides/main.html | 15 + pyproject.toml | 11 + src/equation_tree/__init__.py | 4 +- .../data/_hashed_probabilities.json | 2 +- src/equation_tree/defaults.py | 8 + src/equation_tree/prior.py | 2 + src/equation_tree/sample.py | 21 +- src/equation_tree/src/__init__.py | 0 src/equation_tree/tree.py | 13 + src/equation_tree/util/__init__.py | 0 23 files changed, 1071 insertions(+), 154 deletions(-) create mode 100644 dev/burn.py delete mode 100644 docs/Additional Example.ipynb create mode 100644 docs/img/logo.png create mode 100644 docs/user-guide/equation-formats.md create mode 100644 docs/user-guide/sampling.md delete mode 100644 mkdocs/base.yml create mode 100644 mkdocs/gen_ref_pages.py create mode 100644 mkdocs/hooks.py create mode 100644 mkdocs/overrides/main.html create mode 100644 src/equation_tree/src/__init__.py create mode 100644 src/equation_tree/util/__init__.py diff --git a/README.md b/README.md index f1fd935..84cb6ba 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,25 @@ -# Quickstart Guide +# Equation Tree -You will need: +The Equation Tree package is an equation toolbox with symbolic regression in mind. It represents +expressions as incomplete binary trees and has various features tailored towards testing symbolic +regression algorithms or training models. The main features are: -- `python` 3.8 or greater: [https://www.python.org/downloads/](https://www.python.org/downloads/) +- Equation sampling (including priors) +- Feature Extraction from equation distributions +- Distance metrics between equations -```shell -pip install -U equation-tree -``` +## Getting Started +Check out the documentation at +[https://autoresearch.github.io/equation-tree](https://autoresearch.github.io/equation-tree). -Check your installation by running: -```shell -python -c "from equation_tree import EquationTree" -``` +## About + +This project is in active development by +the Autonomous Empirical Research +Group +(package developer: Younes Strittmatter, +PI: Sebastian Musslick. This research program is supported by +Schmidt Science Fellows, in partnership with the Rhodes Trust, as well as the Carney BRAINSTORM +program at Brown University. \ No newline at end of file diff --git a/dev/burn.py b/dev/burn.py new file mode 100644 index 0000000..7aea8fe --- /dev/null +++ b/dev/burn.py @@ -0,0 +1,65 @@ +from equation_tree.sample import burn +from equation_tree.defaults import DEFAULT_PRIOR + +prior_0 = { + 'structures': {'[0, 1, 1]': .3, '[0, 1, 2]': .3, '[0, 1, 2, 3, 2, 3, 1]': .4}, + 'features': {'constants': .2, 'variables': .8}, + 'functions': {'sin': .5, 'cos': .5}, + 'operators': {'+': .8, '-': .2} +} + + + +prior_1 = { + 'structures': {'[0, 1, 1]': .3, '[0, 1, 2]': .3, '[0, 1, 2, 3, 2, 3, 1]': .4}, + 'features': {'constants': .2, 'variables': .8}, + 'functions': {'sin': .5, 'cos': .5}, + 'operators': {'+': .5, '-': .5}, + 'function_conditionals': { + 'sin': { + 'features': {'constants': 0., 'variables': 1.}, + 'functions': {'sin': 0., 'cos': 1.}, + 'operators': {'+': .5, '-': .5} + }, + 'cos': { + 'features': {'constants': 0., 'variables': 1.}, + 'functions': {'cos': 1., 'sin': 0.}, + 'operators': {'+': 0., '-': 1.} + } + }, + 'operator_conditionals': { + '+': { + 'features': {'constants': .5, 'variables': .5}, + 'functions': {'sin': 1., 'cos': 0.}, + 'operators': {'+': 1., '-': 0.} + }, + '-': { + 'features': {'constants': .3, 'variables': .7}, + 'functions': {'cos': .5, 'sin': .5}, + 'operators': {'+': .9, '-': .1} + } + }, +} + +# import random +for _ in range(1, 5): + burn(DEFAULT_PRIOR, + _, + "../src/equation_tree/data/_hashed_probabilities.json", + 10_000, + 0.5, + ) + burn( + prior_0, + 2, + "../src/equation_tree/data/_hashed_probabilities.json", + 10_000, + 0.5, + ) + burn( + prior_1, + 2, + "../src/equation_tree/data/_hashed_probabilities.json", + 10_000, + 0.5, + ) \ No newline at end of file diff --git a/docs/Additional Example.ipynb b/docs/Additional Example.ipynb deleted file mode 100644 index b211083..0000000 --- a/docs/Additional Example.ipynb +++ /dev/null @@ -1,72 +0,0 @@ -{ - "cells": [ - { - "attachments": {}, - "cell_type": "markdown", - "metadata": { - "collapsed": false - }, - "source": [ - "# Additional Example\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "from autora.equation_tree.equation_tree import Example" - ] - }, - { - "attachments": {}, - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Include inline mathematics like this: $4 < 5$\n", - "\n", - "Include block mathematics like this (don't forget the empty lines above and below the block):\n", - "\n", - "$$ \n", - "y + 1 = 4 \n", - "$$\n", - "\n", - "... or this:\n", - "\n", - "\\begin{align}\n", - " p(v_i=1|\\mathbf{h}) & = \\sigma\\left(\\sum_j w_{ij}h_j + b_i\\right) \\\\\n", - " p(h_j=1|\\mathbf{v}) & = \\sigma\\left(\\sum_i w_{ij}v_i + c_j\\right)\n", - "\\end{align}" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.6" - } - }, - "nbformat": 4, - "nbformat_minor": 0 -} diff --git a/docs/Basic Usage.ipynb b/docs/Basic Usage.ipynb index 1881b81..adc205b 100644 --- a/docs/Basic Usage.ipynb +++ b/docs/Basic Usage.ipynb @@ -7,37 +7,662 @@ "collapsed": false }, "source": [ - "# Basic Usage\n" + "# Basic Usage\n", + "Here, we demonstrate core functionalities of the Equation Tree:\n", + "- Basic Functionality for sampling and processing equations\n", + "- Advanced settings for sampling equations\n", + "\n", + "## Installation" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": { "collapsed": false }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Requirement already satisfied: equation_tree in /Users/younesstrittmatter/Documents/GitHub/AutoRA/equation-tree/src (0.0.11.dev27+g1da6b63.d20231102)\r\n", + "Requirement already satisfied: numpy in /Users/younesstrittmatter/Documents/GitHub/AutoRA/equation-tree/venv/lib/python3.11/site-packages (from equation_tree) (1.25.2)\r\n", + "Requirement already satisfied: sympy in /Users/younesstrittmatter/Documents/GitHub/AutoRA/equation-tree/venv/lib/python3.11/site-packages (from equation_tree) (1.12)\r\n", + "Requirement already satisfied: importlib_resources in /Users/younesstrittmatter/Documents/GitHub/AutoRA/equation-tree/venv/lib/python3.11/site-packages (from equation_tree) (6.0.1)\r\n", + "Requirement already satisfied: tqdm in /Users/younesstrittmatter/Documents/GitHub/AutoRA/equation-tree/venv/lib/python3.11/site-packages (from equation_tree) (4.66.1)\r\n", + "Requirement already satisfied: mpmath>=0.19 in /Users/younesstrittmatter/Documents/GitHub/AutoRA/equation-tree/venv/lib/python3.11/site-packages (from sympy->equation_tree) (1.3.0)\r\n", + "\r\n", + "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip is available: \u001B[0m\u001B[31;49m23.1.2\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m23.3.1\u001B[0m\r\n", + "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\r\n" + ] + } + ], "source": [ - "from equation_tree import" + "import random\n", + "!pip install equation_tree" ] }, { "cell_type": "markdown", "source": [ - "Include inline mathematics like this: $4 < 5$\n", + "## Basic Functionality\n", + "\n", + "### Sampling With Default Settings\n", + "First, we need to import the functionality. Here we also set a seed to ensure reproducible results." + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": 2, + "outputs": [], + "source": [ + "from equation_tree import sample\n", + "\n", + "# To obtain reproducible results, we set a seed for the following section\n", + "import numpy as np\n", + "np.random.seed(42)\n", + "# Adjusting the input dimension of the equations" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "markdown", + "source": [ + "We use this to sample an equation:" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": 3, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/younesstrittmatter/Documents/GitHub/AutoRA/equation-tree/src/equation_tree/util/io.py:27: UserWarning: No hashed prior found. Sample frequencies may diverge from the prior. Consider burning this prior first.\n", + " warnings.warn(\n", + "Processing: 100%|██████████| 1/1 [00:00<00:00, 9.77iteration/s]\n" + ] + } + ], + "source": [ + "equation = sample()" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "markdown", + "source": [ + "### Equation Representations And Features\n", + "\n", + "First, lets look at the type of the equation" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "code", + "execution_count": 4, + "outputs": [ + { + "data": { + "text/plain": "list" + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "type(equation)" + ], + "metadata": { + "collapsed": false + } + }, + { + "cell_type": "markdown", + "source": [ + "It is a list! 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This research program is supported by +Schmidt Science Fellows, in partnership with the Rhodes Trust, as well as the Carney BRAINSTORM +program at Brown University. \ No newline at end of file diff --git a/docs/quickstart.md b/docs/quickstart.md index 8771d5d..ac62c8f 100644 --- a/docs/quickstart.md +++ b/docs/quickstart.md @@ -7,11 +7,10 @@ You will need: ```shell pip install -U equation-tree -"] ``` Check your installation by running: ```shell -python -c "from autora.equation_tree.equation_tree import Example" -``` +python -c "from equation_tree import EquationTree" +``` \ No newline at end of file diff --git a/docs/user-guide/equation-formats.md b/docs/user-guide/equation-formats.md new file mode 100644 index 0000000..5b71620 --- /dev/null +++ b/docs/user-guide/equation-formats.md @@ -0,0 +1,16 @@ +# Equation Formats +Equations can be represented in multiple formats. Depending on the use case, some of these formats might be more useful than others. While the underlying format of the Equation Tree is a incomplete binary tree, it supports multiple formats as initialisation and output. + +## Tree Representation +### Tree Structure +coming soon + + +## String Representation +coming soon + +## Prefix Notation +coming soon + + + diff --git a/docs/user-guide/sampling.md b/docs/user-guide/sampling.md new file mode 100644 index 0000000..faabcad --- /dev/null +++ b/docs/user-guide/sampling.md @@ -0,0 +1,2 @@ +# Sampling Method +coming soon \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index ac0dd82..430b315 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,12 +1,86 @@ -# yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json -INHERIT: mkdocs/base.yml # use the shared AutoRA configuration by default - -site_name: AutoRA equation-tree +site_name: AutoRA Equation Tree repo_url: 'https://github.com/AutoResearch/equation-tree' +site_url: 'https://autoresearch.github.io/equation-tree/' +edit_uri: 'blob/main/docs/' + +extra: + colab_base_url: 'https://colab.research.google.com/github/AutoResearch/equation-tree/blob/gh-pages/' + social: + - icon: fontawesome/brands/github-alt + link: https://github.com/AutoResearch + nav: -- Home: 'index.md' -- Quickstart: 'quickstart.md' -- Examples: - - Basic Usage: 'Basic Usage.ipynb' - - Additional Example: 'Additional Example.ipynb' + - Introduction: 'index.md' + - Quickstart: 'quickstart.md' + - User Guide: + - Sampling: 'user-guide/sampling.md' + - Equation Formats: 'user-guide/equation-formats.md' + - Tutorials: + - Equation Sampling: Equation Sampling.ipynb + - Code Reference: reference/ + +theme: + name: material + features: + + language: en + logo: img/logo.png + palette: + # Palette toggle for light mode + - scheme: default + primary: black + toggle: + icon: material/brightness-7 + name: Switch to dark mode + - scheme: slate + primary: black + toggle: + icon: material/brightness-4 + name: Switch to light mode + custom_dir: mkdocs/overrides + + + + + + +watch: + - src/ + +plugins: + - search + - gen-files: + scripts: + - mkdocs/gen_ref_pages.py + - literate-nav: + nav_file: SUMMARY/index.html + - section-index + - mkdocstrings: + handlers: + python: + import: + - https://scikit-learn.org/stable/objects.inv + - mkdocs-jupyter: # required to convert Jupyter notebooks + include_source: true + execute: false + ignore_h1_titles: true +hooks: + - mkdocs/hooks.py + +markdown_extensions: + admonition: { } + pymdownx.details: { } + pymdownx.superfences: { } + pymdownx.arithmatex: # required for equation display + generic: true + pymdownx.snippets: { } + pymdownx.tabbed: + alternate_style: true + +extra_javascript: [ + # requirements for pymdownx.arithmetex: + "javascripts/mathjax.js", + "https://polyfill.io/v3/polyfill.min.js?features=es6", + "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js" +] \ No newline at end of file diff --git a/mkdocs/base.yml b/mkdocs/base.yml deleted file mode 100644 index 8676be1..0000000 --- a/mkdocs/base.yml +++ /dev/null @@ -1,25 +0,0 @@ -# yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json -# Shared configuration matching the rest of the AutoRA documentation. - -theme: - name: material - -plugins: - mkdocs-jupyter: # required to convert Jupyter notebooks - include_source: true - execute: false - ignore_h1_titles: true - -markdown_extensions: - admonition: {} - pymdownx.details: {} - pymdownx.superfences: {} - pymdownx.arithmatex: # required for equation display - generic: true - -extra_javascript: [ - # requirements for pymdownx.arithmetex: - "javascripts/mathjax.js", - "https://polyfill.io/v3/polyfill.min.js?features=es6", - "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js" -] \ No newline at end of file diff --git a/mkdocs/gen_ref_pages.py b/mkdocs/gen_ref_pages.py new file mode 100644 index 0000000..68069d2 --- /dev/null +++ b/mkdocs/gen_ref_pages.py @@ -0,0 +1,39 @@ +"""Generate the code reference pages and navigation.""" + +from pathlib import Path +from typing import List + +import mkdocs_gen_files + +nav = mkdocs_gen_files.Nav() + +source_paths = sorted(Path("./src/equation_tree/").rglob("*.py")) + + +special_paths: List[Path] = [] # [Path("./docs/docstrings.py")] + +for path in source_paths: + module_path = path.relative_to(".").with_suffix("") + doc_path = path.relative_to(".").with_suffix(".md") + + full_doc_path = Path("reference", doc_path) + + + parts = tuple(module_path.parts) + + if parts[-1] == "__init__": + parts = parts[:-1] + doc_path = doc_path.with_name("index.md") + full_doc_path = full_doc_path.with_name("index.md") + elif parts[-1] == "__main__": + continue + + nav[parts] = doc_path.as_posix() + + with mkdocs_gen_files.open(full_doc_path, "w") as fd: + ident = ".".join(parts) + fd.write(f"::: {ident}") + mkdocs_gen_files.set_edit_path(full_doc_path, path) + +with mkdocs_gen_files.open("reference/SUMMARY.md", "w") as nav_file: + nav_file.writelines(nav.build_literate_nav()) diff --git a/mkdocs/hooks.py b/mkdocs/hooks.py new file mode 100644 index 0000000..9074dfe --- /dev/null +++ b/mkdocs/hooks.py @@ -0,0 +1,12 @@ +import os +from urllib.parse import quote + + +def basename(path): + return os.path.basename(path) + + +def on_env(env, config, files, **kwargs): + env.filters["basename"] = basename + env.filters["quote"] = quote + return env \ No newline at end of file diff --git a/mkdocs/overrides/main.html b/mkdocs/overrides/main.html new file mode 100644 index 0000000..3a7b8a9 --- /dev/null +++ b/mkdocs/overrides/main.html @@ -0,0 +1,15 @@ +{% extends "base.html" %} + +{% block content %} +{% if page.nb_url %} + + {% include ".icons/material/download.svg" %} + + + Open In Colab + +{% endif %} +{{ super() }} +{% endblock content %} \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index ce24738..cdacef4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,6 +21,17 @@ dependencies = [ dev = [ ] +docs = [ + "mkdocs-material", + "mkdocs-gen-files", + "mkdocs-literate-nav", + "mkdocs-section-index", + "mkdocs-multirepo-plugin", + "mkdocstrings-python", + "mkdocs-jupyter", + "pymdown-extensions", +] + [project.urls] homepage = "http://www.empiricalresearch.ai" repository = "https://github.com/AutoResearch/equation-tree" diff --git a/src/equation_tree/__init__.py b/src/equation_tree/__init__.py index eebaae9..2de8411 100644 --- a/src/equation_tree/__init__.py +++ b/src/equation_tree/__init__.py @@ -1,4 +1,4 @@ from equation_tree.sample import burn, sample -from equation_tree.tree import EquationTree +from equation_tree.tree import EquationTree, instantiate_constants -__all__ = ["EquationTree", "sample", "burn"] +__all__ = ["EquationTree", "sample", "burn", "instantiate_constants"] diff --git a/src/equation_tree/data/_hashed_probabilities.json b/src/equation_tree/data/_hashed_probabilities.json index 243a582..20dd498 100644 --- 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0.5, "-": 0.5}}, "cos": {"features": {"constants": 0.0, "variables": 1.0}, "functions": {"cos": 1.0, "sin": 0.0}, "operators": {"+": 0.0, "-": 1.0}}}, "operator_conditionals": {"+": {"features": {"constants": 0.6152504745737963, "variables": 0.3847495254262038}, "functions": {"sin": 1.0, "cos": 0.0}, "operators": {"+": 1.0, "-": 0.0}}, "-": {"features": {"constants": 0.2838943217919089, "variables": 0.7161056782080912}, "functions": {"cos": 0.5054986338797814, "sin": 0.4945013661202186}, "operators": {"+": 0.9381255377114999, "-": 0.06187446228850014}}}}, "{'features': {'constants': 0.5, 'variables': 0.5}, 'functions': {'abs': 0.1111111111111111, 'acos': 0.1111111111111111, 'asin': 0.1111111111111111, 'cos': 0.1111111111111111, 'exp': 0.1111111111111111, 'log': 0.1111111111111111, 'sin': 0.1111111111111111, 'sqrt': 0.1111111111111111, 'tan': 0.1111111111111111}, 'max_num_variables': 1, 'operators': {'*': 0.14285714285714285, '+': 0.14285714285714285, '-': 0.14285714285714285, '/': 0.14285714285714285, '^': 0.14285714285714285, 'max': 0.14285714285714285, 'min': 0.14285714285714285}, 'structures': {'[0, 1, 1, 2, 2, 3]': 0.027777777777777776, '[0, 1, 1, 2, 2]': 0.027777777777777776, '[0, 1, 1, 2, 3, 2]': 0.027777777777777776, '[0, 1, 1, 2, 3, 3]': 0.027777777777777776, '[0, 1, 1, 2, 3, 4]': 0.027777777777777776, '[0, 1, 1, 2, 3]': 0.027777777777777776, '[0, 1, 1, 2]': 0.027777777777777776, '[0, 1, 1]': 0.027777777777777776, '[0, 1, 2, 1, 2, 2]': 0.027777777777777776, '[0, 1, 2, 1, 2, 3]': 0.027777777777777776, '[0, 1, 2, 1, 2]': 0.027777777777777776, '[0, 1, 2, 1]': 0.027777777777777776, '[0, 1, 2, 2, 1, 2]': 0.027777777777777776, '[0, 1, 2, 2, 1]': 0.027777777777777776, '[0, 1, 2, 2, 3, 1]': 0.027777777777777776, '[0, 1, 2, 2, 3, 3]': 0.027777777777777776, '[0, 1, 2, 2, 3, 4]': 0.027777777777777776, '[0, 1, 2, 2, 3]': 0.027777777777777776, '[0, 1, 2, 2]': 0.027777777777777776, '[0, 1, 2, 3, 1, 2]': 0.027777777777777776, '[0, 1, 2, 3, 1]': 0.027777777777777776, '[0, 1, 2, 3, 2, 1]': 0.027777777777777776, '[0, 1, 2, 3, 2, 3]': 0.027777777777777776, '[0, 1, 2, 3, 2]': 0.027777777777777776, '[0, 1, 2, 3, 3, 1]': 0.027777777777777776, '[0, 1, 2, 3, 3, 2]': 0.027777777777777776, '[0, 1, 2, 3, 3, 4]': 0.027777777777777776, '[0, 1, 2, 3, 3]': 0.027777777777777776, '[0, 1, 2, 3, 4, 1]': 0.027777777777777776, '[0, 1, 2, 3, 4, 2]': 0.027777777777777776, '[0, 1, 2, 3, 4, 3]': 0.027777777777777776, '[0, 1, 2, 3, 4, 4]': 0.027777777777777776, '[0, 1, 2, 3, 4, 5]': 0.027777777777777776, '[0, 1, 2, 3, 4]': 0.027777777777777776, '[0, 1, 2, 3]': 0.027777777777777776, '[0, 1, 2]': 0.027777777777777776}}": {"structures": {"[0, 1, 2, 3]": 0.023266666666666665, "[0, 1, 2, 3, 1]": 0.03311666666666666, "[0, 1, 2, 3, 4, 5]": 0.029416666666666664, "[0, 1, 2]": 0.021566666666666665, "[0, 1, 2, 1]": 0.025216666666666665, "[0, 1, 2, 3, 3, 4]": 0.028766666666666663, "[0, 1, 1, 2]": 0.018366666666666663, "[0, 1, 2, 3, 3, 1]": 0.03356666666666666, "[0, 1, 2, 2, 3, 4]": 0.026366666666666663, "[0, 1, 2, 3, 2, 1]": 0.03506666666666666, "[0, 1, 1, 2, 2, 3]": 0.033666666666666664, "[0, 1, 2, 1, 2, 2]": 0.029416666666666664, "[0, 1, 2, 3, 4, 2]": 0.033466666666666665, "[0, 1, 2, 2, 3, 1]": 0.030766666666666664, "[0, 1, 2, 3, 2, 3]": 0.03256666666666666, "[0, 1, 1, 2, 2]": 0.026016666666666664, "[0, 1, 2, 2]": 0.014916666666666665, "[0, 1, 2, 3, 1, 2]": 0.034216666666666666, "[0, 1, 2, 3, 4, 1]": 0.032516666666666666, "[0, 1, 1, 2, 3]": 0.026966666666666667, "[0, 1, 2, 1, 2, 3]": 0.033666666666666664, "[0, 1, 2, 3, 3, 2]": 0.029266666666666663, "[0, 1, 1]": 0.012866666666666665, "[0, 1, 2, 3, 3]": 0.021866666666666663, "[0, 1, 2, 3, 2]": 0.030616666666666664, "[0, 1, 2, 3, 4, 3]": 0.032016666666666665, "[0, 1, 2, 1, 2]": 0.03281666666666666, "[0, 1, 2, 2, 3]": 0.026566666666666662, "[0, 1, 2, 3, 4]": 0.028466666666666664, "[0, 1, 2, 2, 1]": 0.026866666666666664, "[0, 1, 1, 2, 3, 3]": 0.021866666666666663, "[0, 1, 1, 2, 3, 2]": 0.031466666666666664, "[0, 1, 1, 2, 3, 4]": 0.028766666666666663, "[0, 1, 2, 2, 3, 3]": 0.024866666666666665, "[0, 1, 2, 3, 4, 4]": 0.023266666666666665, "[0, 1, 2, 2, 1, 2]": 0.025516666666666663}, "functions": {"log": 0.11468674789410348, "exp": 0.11322014139590852, "sqrt": 0.11070998796630566, "abs": 0.11206377858002406, "acos": 0.1089895457280385, "sin": 0.11082280385078218, "cos": 0.1097510529482551, "asin": 0.11133047533092658, "tan": 0.10842546630565583}, "operators": {"^": 0.11614890979362648, "max": 0.15966601035513744, "*": 0.13720557135564793, "-": 0.13894965847492646, "/": 0.14490507790660928, "min": 0.159878703906269, "+": 0.14324606820778335}, "features": {"constants": 0.5949710398087709, "variables": 0.4050289601912292}}} \ No newline at end of file diff --git a/src/equation_tree/defaults.py b/src/equation_tree/defaults.py index dd8fc48..a2a9237 100644 --- a/src/equation_tree/defaults.py +++ b/src/equation_tree/defaults.py @@ -11,9 +11,17 @@ function_space = DEFAULT_FUNCTION_SPACE operators_prior = DEFAULT_PRIOR_OPERATORS functions_prior = DEFAULT_PRIOR_FUNCTIONS +features_prior = {'constants': 0.5, 'variables': 0.5} structure_prior_from_depth = structure_prior_from_depth structure_prior_from_leaves = structure_prior_from_max_depth +DEFAULT_PRIOR = { + 'structures': structure_prior_from_max_depth(6), + 'functions': functions_prior, + 'operators': operators_prior, + 'features': features_prior +} + def is_operator(a): return a.lower() in operator_space diff --git a/src/equation_tree/prior.py b/src/equation_tree/prior.py index df14878..5f8a9a3 100644 --- a/src/equation_tree/prior.py +++ b/src/equation_tree/prior.py @@ -23,6 +23,8 @@ DEFAULT_PRIOR_OPERATORS = priors_from_space(DEFAULT_OPERATOR_SPACE) + + def prior_from_space(space): """ Uniform prior from a list of strings diff --git a/src/equation_tree/sample.py b/src/equation_tree/sample.py index 976227d..cf58355 100644 --- a/src/equation_tree/sample.py +++ b/src/equation_tree/sample.py @@ -1,3 +1,4 @@ +import copy from typing import Dict, List, Optional, Union from tqdm import tqdm @@ -19,6 +20,9 @@ from equation_tree.util.priors import priors_from_space from equation_tree.util.type_check import is_constant_formatted, is_variable_formatted +from equation_tree.defaults import DEFAULT_PRIOR, structure_prior_from_max_depth, \ + structure_prior_from_depth + PriorType = Union[List, Dict] MAX_ITER = 10_000 @@ -29,8 +33,21 @@ def sample_fast(n, prior, tree_depth, max_num_variables, file=None): return sample_trees_fast(n, adjusted_prior, tree_depth, max_num_variables) -def sample(n, prior, max_num_variables, file=None): - adjusted_prior = load(prior, max_num_variables, file) +def sample(n=1, + prior=DEFAULT_PRIOR, + max_num_variables=1, + file=None, + max_depth=None, + depth=None): + _prior = copy.deepcopy(prior) + if max_depth is not None and depth is not None: + raise Exception("Both depth and max depth are defined. Please only define one of both") + elif max_depth is not None: + _prior['structures'] = structure_prior_from_max_depth(max_depth) + elif depth is not None: + _prior['structures'] = structure_prior_from_depth(depth) + + adjusted_prior = load(_prior, max_num_variables, file) return sample_trees(n, adjusted_prior, max_num_variables) diff --git a/src/equation_tree/src/__init__.py b/src/equation_tree/src/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/equation_tree/tree.py b/src/equation_tree/tree.py index 6b0dfde..6e4e8f5 100644 --- a/src/equation_tree/tree.py +++ b/src/equation_tree/tree.py @@ -186,6 +186,9 @@ def __init__(self, node: TreeNode): self._build() + def __repr__(self): + return str(self.sympy_expr) + @classmethod def from_prefix( cls, @@ -350,6 +353,8 @@ def from_prior(cls, prior: Dict, max_variables_unique: int): root = sample_tree_full(prior, max_variables_unique) return cls(root) + + @classmethod def from_priors( cls, @@ -625,6 +630,14 @@ def has_valid_value(self): ev = self.evaluation[0, :] return np.any(np.isfinite(ev) & ~np.isnan(ev)) + @property + def depth(self): + return max(self.structure) + + @property + def n_nodes(self): + return len(self.structure) + @property def info(self): """ diff --git a/src/equation_tree/util/__init__.py b/src/equation_tree/util/__init__.py new file mode 100644 index 0000000..e69de29