diff --git a/.gitignore b/.gitignore index c1513498..ede20d2f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ + # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] @@ -111,6 +112,7 @@ venv.bak/ ~*.xlsx *.DS_STORE .vscode/ +.idea/ # TSEMO .TSEMO_DATA diff --git a/README.md b/README.md index 1dd9fd0b..c66c93a2 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,7 @@ Summit is a set of tools for optimising chemical processes. We’ve started by targeting reactions. + ## What is Summit? Currently, reaction optimisation in the fine chemicals industry is done by intuition or design of experiments. Both scale poorly with the complexity of the problem. diff --git a/docs/source/Tutorial_MIT_kin.ipynb b/docs/source/Tutorial_MIT_kin.ipynb deleted file mode 100644 index d85fdc24..00000000 --- a/docs/source/Tutorial_MIT_kin.ipynb +++ /dev/null @@ -1,295 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Tutorial - MIT kinetic model" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "In this workbook, the 'Tutorial' IPNB has been modified to show how to run the MIT_kin_n (e.g. MIT_kin_1) files.\n", - "\n", - "Summit introduces two key concepts: **benchmarks** and **strategies**. Benchmarks are simulations of reactions, and strategies are ML algorithms used to choose experiments. Two benchmarks are already implemented, and it is easy to add more. We are going to optimise a reaction network with simulated kinetic constants. The reaction network & accompanying kinetic constants come from the following paper out of MIT:\n", - "\n", - "React. Chem. Eng., 2018, 3,301\n", - "Optimum catalyst selection over continuous and\n", - "discrete process variables with a single droplet\n", - "microfluidic reaction platform (Jensen et al.)\n", - "DOI: 10.1039/c8re00032h\n", - "\n", - "Summit provides access to six different optimisation strategies. And, it gives a common interface, so you can easily switch between strategies. We'll see that soon.\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Google Colab\n", - "\n", - "If you would like to follow along with this tutorial, you can open it in Google Colab using the button below." - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "%load_ext autoreload\n", - "%autoreload 2" - ] - }, - { - "cell_type": "raw", - "metadata": { - "raw_mimetype": "text/restructuredtext" - }, - "source": [ - "|colab_badge|" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "You will need to run the following cell to make sure Summit and all its dependencies are installed. If prompted, restart the runtime." - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Kinetic model\n", - "\n", - "\n", - "![Image from Jensen et al.](kinetic_model.png)\n", - "\n", - "\n", - "Below, we start importing the needed packages and setting up the `MIT_kin_n` benchmark." - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "from summit.domain import *\n", - "from summit import Runner\n", - "from summit.strategies import Random, SOBO, MultitoSingleObjective\n", - "from summit.benchmarks import SnarBenchmark\n", - "from summit.utils.dataset import DataSet\n", - "import matplotlib.pyplot as plt\n", - "import numpy as np\n", - "import matplotlib.pyplot as plt\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [], - "source": [ - "from summit.benchmarks import MIT_case1\n", - "from summit.benchmarks import MIT_case2\n", - "from summit.benchmarks import MIT_case3\n", - "from summit.benchmarks import MIT_case4\n", - "from summit.benchmarks import MIT_case5\n", - "\n", - "exp1 = MIT_case1()\n", - "exp2 = MIT_case2()\n", - "exp3 = MIT_case3()\n", - "exp4 = MIT_case4()\n", - "exp5 = MIT_case5()" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
NameTypeDescriptionValues
conc_catcontinuous, inputcatalyst concentration[0.000835,0.004175]
tcontinuous, inputreaction time[60,600]
cat_indexcategorical, inputChoice of catalyst8 levels
temperaturecontinuous, inputReactor temperature in degress celsius[30,110]
ycontinuous, maximize objectiveyield (%)[0,100]
" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "exp1.domain" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "We print out the `domain` which describes the optimisation problem associated with `MIT_kin_1`. The objective is to maximize yield (y), defined as the concentration of product dividen by the initial concentration of the limiting reagent (We can do this because the stoichiometry is 1:1).\n", - "\n", - "We optimize the reactions by changing the catalyst concentration, reaction time, choice of catalyst, and temperature. " - ] - }, - { - "cell_type": "code", - "execution_count": 32, - "metadata": {}, - "outputs": [ - { - "data": { - "image/png": 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\n", - "text/plain": [ - "
" - ] - }, - "metadata": { - "needs_background": "light" - }, - "output_type": "display_data" - } - ], - "source": [ - "#Case 1\n", - "y, res = exp1._integrate_equations(8*10**-3, 4000, 0, 90)\n", - "for i in range(5):\n", - " plt.plot(res.y[i])" - ] - }, - { - "cell_type": "code", - "execution_count": 33, - "metadata": { - "scrolled": true - }, - "outputs": [ - { - "data": { - "image/png": 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\n", - "text/plain": [ - "
" - ] - }, - "metadata": { - "needs_background": "light" - }, - "output_type": "display_data" - } - ], - "source": [ - "#Case 2\n", - "y, res = exp2._integrate_equations(8*10**-3, 4000, 0, 90)\n", - "for i in range(5):\n", - " plt.plot(res.y[i])" - ] - }, - { - "cell_type": "code", - "execution_count": 34, - "metadata": {}, - "outputs": [ - { - "data": { - "image/png": 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\n", - "text/plain": [ - "
" - ] - }, - "metadata": { - "needs_background": "light" - }, - "output_type": "display_data" - } - ], - "source": [ - "#Case 3\n", - "y, res = exp3._integrate_equations(8*10**-3, 4000, 0, 90)\n", - "for i in range(5):\n", - " plt.plot(res.y[i])" - ] - }, - { - "cell_type": "code", - "execution_count": 35, - "metadata": {}, - "outputs": [ - { - "data": { - "image/png": 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\n", - "text/plain": [ - "
" - ] - }, - "metadata": { - "needs_background": "light" - }, - "output_type": "display_data" - } - ], - "source": [ - "#Case 4\n", - "y, res = exp4._integrate_equations(8*10**-3, 4000, 0, 90)\n", - "for i in range(5):\n", - " plt.plot(res.y[i])" - ] - }, - { - "cell_type": "code", - "execution_count": 37, - "metadata": {}, - "outputs": [ - { - "data": { - "image/png": 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\n", - "text/plain": [ - "
" - ] - }, - "metadata": { - "needs_background": "light" - }, - "output_type": "display_data" - } - ], - "source": [ - "#Case 5\n", - "y, res = exp5._integrate_equations(8*10**-3, 4000, 0, 90)\n", - "for i in range(5):\n", - " plt.plot(res.y[i])" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "summit1", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.7.4" - }, - "toc-autonumbering": false, - "toc-showcode": false, - "toc-showmarkdowntxt": false - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/docs/source/experiments_benchmarks/new_benchmarks.ipynb b/docs/source/experiments_benchmarks/new_benchmarks.ipynb index c82ed8d6..dde60e9d 100644 --- a/docs/source/experiments_benchmarks/new_benchmarks.ipynb +++ b/docs/source/experiments_benchmarks/new_benchmarks.ipynb @@ -60,7 +60,10 @@ "source": [ "from summit.benchmarks import ExperimentalEmulator\n", "from summit.domain import *\n", - "from summit.utils.dataset import DataSet" + "from summit.utils.dataset import DataSet\n", + "import pkg_resources\n", + "import pathlib\n", + "import pprint" ] }, { @@ -97,7 +100,7 @@ "
NameTypeDescriptionValues
catalystcategorical, inputCatalyst type - different ligands8 levels
t_rescontinuous, inputResidence time in seconds (s)[60,600]
temperaturecontinuous, inputReactor temperature in degrees Celsius (ºC)[30,110]
catalyst_loadingcontinuous, inputCatalyst loading in mol%[0.5,2.5]
toncontinuous, maximize objectiveTurnover number - moles product generated divided by moles catalyst used[0,200]
yieldcontinuous, maximize objectiveYield[0,100]
" ], "text/plain": [ - "" + "" ] }, "execution_count": 3, @@ -173,7 +176,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "If you are running this yourself, uncomment the second line." + "Here, we import the data that we already have in the Summit package, but you could use your own data. Change verbose to 1 if you want streaming updates of the training." ] }, { @@ -182,19 +185,10 @@ "metadata": {}, "outputs": [], "source": [ - "import pathlib \n", - "FOLDER = pathlib.Path(\"../_static/\") # When using this in the context of docs\n", - "# FOLDER = pathlib.Path(\".\")" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "emul = ExperimentalEmulator(domain=domain, model_name='my_reizman')\n", - "emul.train(csv_dataset=FOLDER / \"reizman_suzuki_case1_train_test.csv\", cv_fold=2, test_size=0.25)" + "DATA_PATH = pathlib.Path(pkg_resources.resource_filename(\"summit\", \"benchmarks/data\"))\n", + "ds = DataSet.read_csv(DATA_PATH / \"reizman_suzuki_case_1.csv\",)\n", + "emul = ExperimentalEmulator(model_name='my_reizman', domain=domain, dataset=ds)\n", + "res = emul.train(max_epochs=100, cv_fold=2, test_size=0.25, verbose=0)" ] }, { @@ -206,7 +200,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 5, "metadata": {}, "outputs": [ { @@ -215,10 +209,10 @@ "
NameTypeDescriptionValues
catalystcategorical, inputCatalyst type - different ligands8 levels
t_rescontinuous, inputResidence time in seconds (s)[60,600]
temperaturecontinuous, inputReactor temperature in degrees Celsius (ºC)[30,110]
catalyst_loadingcontinuous, inputCatalyst loading in mol%[0.5,2.5]
toncontinuous, maximize objectiveTurnover number - moles product generated divided by moles catalyst used[0,200]
yieldcontinuous, maximize objectiveYield[0,100]
" ], "text/plain": [ - "" + "" ] }, - "execution_count": 7, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -229,7 +223,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 6, "metadata": {}, "outputs": [ { @@ -271,10 +265,10 @@ " 60\n", " 100\n", " 1.0\n", - " 29.972519\n", - " 43.924999\n", + " 23.364954\n", + " 33.13002\n", " 0.0\n", - " 0.063283\n", + " 0.058378\n", " NaN\n", " \n", " \n", @@ -282,16 +276,16 @@ "" ], "text/plain": [ - "NAME catalyst t_res temperature catalyst_loading ton yield \\\n", - "TYPE DATA DATA DATA DATA DATA DATA \n", - "0 P1-L1 60 100 1.0 29.972519 43.924999 \n", + "NAME catalyst t_res temperature catalyst_loading ton yield \\\n", + "TYPE DATA DATA DATA DATA DATA DATA \n", + "0 P1-L1 60 100 1.0 23.364954 33.13002 \n", "\n", "NAME computation_t experiment_t strategy \n", "TYPE METADATA METADATA METADATA \n", - "0 0.0 0.063283 NaN " + "0 0.0 0.058378 NaN " ] }, - "execution_count": 8, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } diff --git a/docs/source/kinetic_model.png b/docs/source/kinetic_model.png deleted file mode 100644 index 27f88dd4..00000000 Binary files a/docs/source/kinetic_model.png and /dev/null differ diff --git a/poetry.lock b/poetry.lock index d37ea2cb..004bdd4f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,3 @@ -[[package]] -category = "main" -description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py." -name = "absl-py" -optional = false -python-versions = "*" -version = "0.11.0" - -[package.dependencies] -six = "*" - [[package]] category = "main" description = "A configurable sidebar-enabled Sphinx theme" @@ -21,7 +10,7 @@ version = "0.7.12" category = "main" description = "Altair: A declarative statistical visualization library for Python." name = "altair" -optional = false +optional = true python-versions = ">=3.6" version = "4.1.0" @@ -74,22 +63,10 @@ tests = ["coverage (>=5.0.2)", "hypothesis", "pytest"] category = "main" description = "Read/rewrite/write Python ASTs" name = "astor" -optional = false +optional = true python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" version = "0.8.1" -[[package]] -category = "main" -description = "An AST unparser for Python" -name = "astunparse" -optional = false -python-versions = "*" -version = "1.6.3" - -[package.dependencies] -six = ">=1.6.1,<2.0" -wheel = ">=0.23.0,<1.0" - [[package]] category = "main" description = "Async generators and context managers for Python 3.5+" @@ -156,7 +133,7 @@ version = "0.2.0" category = "main" description = "Base58 and Base58Check implementation." name = "base58" -optional = false +optional = true python-versions = ">=3.5" version = "2.1.0" @@ -235,7 +212,7 @@ webencodings = "*" category = "main" description = "Fast, simple object-to-object and broadcast signaling" name = "blinker" -optional = false +optional = true python-versions = "*" version = "1.4" @@ -243,7 +220,7 @@ version = "1.4" category = "main" description = "A simple and extensible library to create Bayesian Neural Network Layers on PyTorch without trouble and with full integration with nn.Module and nn.Sequential." name = "blitz-bayesian-pytorch" -optional = false +optional = true python-versions = "*" version = "0.2.5" @@ -262,12 +239,12 @@ url = "https://github.com/sustainable-processes/blitz-bayesian-deep-learning.git category = "main" description = "The AWS SDK for Python" name = "boto3" -optional = false +optional = true python-versions = ">= 2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" -version = "1.17.5" +version = "1.17.11" [package.dependencies] -botocore = ">=1.20.5,<1.21.0" +botocore = ">=1.20.11,<1.21.0" jmespath = ">=0.7.1,<1.0.0" s3transfer = ">=0.3.0,<0.4.0" @@ -275,9 +252,9 @@ s3transfer = ">=0.3.0,<0.4.0" category = "main" description = "Low-level, data-driven core of boto 3." name = "botocore" -optional = false +optional = true python-versions = ">= 2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" -version = "1.20.5" +version = "1.20.11" [package.dependencies] jmespath = ">=0.7.1,<1.0.0" @@ -355,11 +332,20 @@ optional = true python-versions = "*" version = "1.0.9" +[[package]] +category = "main" +description = "A decorator for caching properties in classes." +marker = "python_version < \"3.8\"" +name = "cached-property" +optional = false +python-versions = "*" +version = "1.5.2" + [[package]] category = "main" description = "Extensible memoizing collections and decorators" name = "cachetools" -optional = false +optional = true python-versions = "~=3.5" version = "4.2.1" @@ -367,7 +353,7 @@ version = "4.2.1" category = "main" description = "Python package for providing Mozilla's CA Bundle." name = "certifi" -optional = false +optional = true python-versions = "*" version = "2020.12.5" @@ -377,7 +363,7 @@ description = "Foreign Function Interface for Python calling C code." name = "cffi" optional = false python-versions = "*" -version = "1.14.4" +version = "1.14.5" [package.dependencies] pycparser = "*" @@ -386,7 +372,7 @@ pycparser = "*" category = "main" description = "Universal encoding detector for Python 2 and 3" name = "chardet" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" version = "4.0.0" @@ -398,14 +384,6 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" version = "7.1.2" -[[package]] -category = "main" -description = "Extended pickling support for Python objects" -name = "cloudpickle" -optional = false -python-versions = ">=3.5" -version = "1.6.0" - [[package]] category = "main" description = "CMA-ES, Covariance Matrix Adaptation Evolution Strategy for non-linear numerical optimization in Python" @@ -429,7 +407,7 @@ description = "cryptography is a package which provides cryptographic recipes an name = "cryptography" optional = true python-versions = ">=3.6" -version = "3.4.4" +version = "3.4.6" [package.dependencies] cffi = ">=1.12" @@ -477,17 +455,6 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" version = "0.6.0" -[[package]] -category = "main" -description = "Tree is a library for working with nested data structures." -name = "dm-tree" -optional = false -python-versions = "*" -version = "0.1.5" - -[package.dependencies] -six = ">=1.12.0" - [[package]] category = "main" description = "Docutils -- Python Documentation Utilities" @@ -522,7 +489,7 @@ version = "0.3" category = "main" description = "enum/enum34 compatibility package" name = "enum-compat" -optional = false +optional = true python-versions = "*" version = "0.0.3" @@ -559,20 +526,12 @@ description = "Compress responses in your Flask app with gzip, deflate or brotli name = "flask-compress" optional = true python-versions = "*" -version = "1.8.0" +version = "1.9.0" [package.dependencies] brotli = "*" flask = "*" -[[package]] -category = "main" -description = "The FlatBuffers serialization format for Python" -name = "flatbuffers" -optional = false -python-versions = "*" -version = "1.12" - [[package]] category = "main" description = "Clean single-source support for Python 3 and 2" @@ -581,14 +540,6 @@ optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" version = "0.18.2" -[[package]] -category = "main" -description = "Python AST that abstracts the underlying Python version" -name = "gast" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "0.3.3" - [[package]] category = "main" description = "Git Object Database" @@ -611,53 +562,6 @@ version = "3.1.13" [package.dependencies] gitdb = ">=4.0.1,<5" -[[package]] -category = "main" -description = "Google Authentication Library" -name = "google-auth" -optional = false -python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*" -version = "1.26.0" - -[package.dependencies] -cachetools = ">=2.0.0,<5.0" -pyasn1-modules = ">=0.2.1" -setuptools = ">=40.3.0" -six = ">=1.9.0" - -[package.dependencies.rsa] -python = ">=3.6" -version = ">=3.1.4,<5" - -[package.extras] -aiohttp = ["aiohttp (>=3.6.2,<4.0.0dev)"] - -[[package]] -category = "main" -description = "Google Authentication Library" -name = "google-auth-oauthlib" -optional = false -python-versions = ">=3.6" -version = "0.4.2" - -[package.dependencies] -google-auth = "*" -requests-oauthlib = ">=0.7.0" - -[package.extras] -tool = ["click"] - -[[package]] -category = "main" -description = "pasta is an AST-based Python refactoring library" -name = "google-pasta" -optional = false -python-versions = "*" -version = "0.2.0" - -[package.dependencies] -six = "*" - [[package]] category = "main" description = "The Gaussian Process Toolbox" @@ -713,44 +617,28 @@ test = ["flake8", "flake8-print", "pytest", "nbval"] [[package]] category = "main" -description = "HTTP/2-based RPC framework" -name = "grpcio" -optional = false -python-versions = "*" -version = "1.32.0" - -[package.dependencies] -six = ">=1.5.2" - -[package.extras] -protobuf = ["grpcio-tools (>=1.32.0)"] - -[[package]] -category = "main" -description = "Bayesian optimization for categorical variables" -name = "gryffin" +description = "Read and write HDF5 files from Python" +name = "h5py" optional = false python-versions = ">=3.6" -version = "0.1.1" +version = "3.1.0" [package.dependencies] -Cython = "*" -numpy = "*" -sqlalchemy = "*" -tensorflow = ">=2.2.0,<3.0.0" -tensorflow-probability = ">=0.10.1git,<1.0.0" +[[package.dependencies.numpy]] +python = ">=3.7,<3.8" +version = ">=1.14.5" -[[package]] -category = "main" -description = "Read and write HDF5 files from Python" -name = "h5py" -optional = false -python-versions = "*" -version = "2.10.0" +[[package.dependencies.numpy]] +python = ">=3.8,<3.9" +version = ">=1.17.5" -[package.dependencies] -numpy = ">=1.7" -six = "*" +[[package.dependencies.numpy]] +python = ">=3.9" +version = ">=1.19.3" + +[package.dependencies.cached-property] +python = "<3.8" +version = "*" [[package]] category = "main" @@ -773,7 +661,7 @@ dev = ["pytest", "mypy", "ipykernel", "wheel", "selenium", "sphinx", "twine", "g category = "main" description = "Internationalized Domain Names in Applications (IDNA)" name = "idna" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" version = "2.10" @@ -945,7 +833,7 @@ i18n = ["Babel (>=0.8)"] category = "main" description = "JSON Matching Expressions" name = "jmespath" -optional = false +optional = true python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" version = "0.10.0" @@ -1038,23 +926,6 @@ optional = false python-versions = ">=3.6" version = "1.0.0" -[[package]] -category = "main" -description = "Easy data preprocessing and data augmentation for deep learning models" -name = "keras-preprocessing" -optional = false -python-versions = "*" -version = "1.1.2" - -[package.dependencies] -numpy = ">=1.9.1" -six = ">=1.9.0" - -[package.extras] -image = ["scipy (>=0.14)", "Pillow (>=5.2.0)"] -pep8 = ["flake8"] -tests = ["pandas", "pillow", "tensorflow", "keras", "pytest", "pytest-xdist", "pytest-cov"] - [[package]] category = "main" description = "A fast implementation of the Cassowary constraint solver" @@ -1087,19 +958,11 @@ version = "0.35.0rc3" [[package]] category = "main" -description = "Python implementation of Markdown." -name = "markdown" +description = "lightweight wrapper around basic LLVM functionality" +name = "llvmlite" optional = false python-versions = ">=3.6" -version = "3.3.3" - -[package.dependencies] -[package.dependencies.importlib-metadata] -python = "<3.8" -version = "*" - -[package.extras] -testing = ["coverage", "pyyaml"] +version = "0.35.0" [[package]] category = "main" @@ -1322,19 +1185,32 @@ llvmlite = ">=0.34.0.dev0,<0.35" numpy = ">=1.15" setuptools = "*" +[[package]] +category = "main" +description = "compiling Python code using LLVM" +name = "numba" +optional = false +python-versions = ">=3.6,<3.9" +version = "0.52.0" + +[package.dependencies] +llvmlite = ">=0.35.0,<0.36" +numpy = ">=1.15" +setuptools = "*" + [[package]] category = "main" description = "NumPy is the fundamental package for array computing with Python." name = "numpy" optional = false -python-versions = ">=3.6" -version = "1.19.5" +python-versions = ">=3.7" +version = "1.20.1" [[package]] category = "main" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" name = "oauthlib" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" version = "3.1.0" @@ -1351,21 +1227,6 @@ optional = true python-versions = ">=3.6" version = "4.5.1.48" -[[package]] -category = "main" -description = "Optimizing numpys einsum function" -name = "opt-einsum" -optional = false -python-versions = ">=3.5" -version = "3.3.0" - -[package.dependencies] -numpy = ">=1.7" - -[package.extras] -docs = ["sphinx (1.2.3)", "sphinxcontrib-napoleon", "sphinx-rtd-theme", "numpydoc"] -tests = ["pytest", "pytest-cov", "pytest-pep8"] - [[package]] category = "main" description = "Core utilities for Python packages" @@ -1393,6 +1254,22 @@ pytz = ">=2017.2" [package.extras] test = ["pytest (>=4.0.2)", "pytest-xdist", "hypothesis (>=3.58)"] +[[package]] +category = "main" +description = "Powerful data structures for data analysis, time series, and statistics" +name = "pandas" +optional = false +python-versions = ">=3.7.1" +version = "1.2.2" + +[package.dependencies] +numpy = ">=1.16.5" +python-dateutil = ">=2.7.3" +pytz = ">=2017.3" + +[package.extras] +test = ["pytest (>=5.0.1)", "pytest-xdist", "hypothesis (>=3.58)"] + [[package]] category = "main" description = "Utilities for writing pandoc filters in python" @@ -1523,7 +1400,7 @@ marker = "python_version >= \"3.4\"" name = "prompt-toolkit" optional = false python-versions = ">=3.6.1" -version = "3.0.15" +version = "3.0.16" [package.dependencies] wcwidth = "*" @@ -1532,9 +1409,9 @@ wcwidth = "*" category = "main" description = "Protocol Buffers" name = "protobuf" -optional = false +optional = true python-versions = "*" -version = "3.14.0" +version = "3.15.0" [package.dependencies] six = ">=1.9" @@ -1560,32 +1437,13 @@ version = "1.10.0" category = "main" description = "Python library for Apache Arrow" name = "pyarrow" -optional = false +optional = true python-versions = ">=3.6" version = "3.0.0" [package.dependencies] numpy = ">=1.16.6" -[[package]] -category = "main" -description = "ASN.1 types and codecs" -name = "pyasn1" -optional = false -python-versions = "*" -version = "0.4.8" - -[[package]] -category = "main" -description = "A collection of ASN.1-based protocols modules." -name = "pyasn1-modules" -optional = false -python-versions = "*" -version = "0.2.8" - -[package.dependencies] -pyasn1 = ">=0.4.6,<0.5.0" - [[package]] category = "main" description = "C parser in Python" @@ -1598,9 +1456,9 @@ version = "2.20" category = "main" description = "Widget for deck.gl maps" name = "pydeck" -optional = false +optional = true python-versions = "*" -version = "0.6.0" +version = "0.6.1" [package.dependencies] ipywidgets = ">=7.0.0" @@ -1621,7 +1479,7 @@ description = "Pygments is a syntax highlighting package written in Python." name = "pygments" optional = false python-versions = ">=3.5" -version = "2.7.4" +version = "2.8.0" [[package]] category = "main" @@ -1783,7 +1641,7 @@ description = "Python bindings for 0MQ" name = "pyzmq" optional = false python-versions = ">=3.6" -version = "22.0.2" +version = "22.0.3" [package.dependencies] cffi = "*" @@ -1801,7 +1659,7 @@ version = "2020.11.13" category = "main" description = "Python HTTP for Humans." name = "requests" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" version = "2.25.1" @@ -1819,7 +1677,7 @@ socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7)", "win-inet-pton"] category = "main" description = "OAuthlib authentication support for Requests." name = "requests-oauthlib" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" version = "1.3.0" @@ -1841,23 +1699,11 @@ version = "0.17.0" [package.extras] dev = ["pytest"] -[[package]] -category = "main" -description = "Pure-Python RSA implementation" -marker = "python_version >= \"3.6\"" -name = "rsa" -optional = false -python-versions = ">=3.5, <4" -version = "4.7" - -[package.dependencies] -pyasn1 = ">=0.1.3" - [[package]] category = "main" description = "An Amazon S3 Transfer Manager" name = "s3transfer" -optional = false +optional = true python-versions = "*" version = "0.3.4" @@ -1870,7 +1716,7 @@ description = "A set of python modules for machine learning and data mining" name = "scikit-learn" optional = false python-versions = ">=3.6" -version = "0.23.2" +version = "0.24.1" [package.dependencies] joblib = ">=0.11" @@ -1879,7 +1725,10 @@ scipy = ">=0.19.1" threadpoolctl = ">=2.0.0" [package.extras] -alldeps = ["numpy (>=1.13.3)", "scipy (>=0.19.1)"] +benchmark = ["matplotlib (>=2.1.1)", "pandas (>=0.25.0)", "memory-profiler (>=0.57.0)"] +docs = ["matplotlib (>=2.1.1)", "scikit-image (>=0.13)", "pandas (>=0.25.0)", "seaborn (>=0.9.0)", "memory-profiler (>=0.57.0)", "sphinx (>=3.2.0)", "sphinx-gallery (>=0.7.0)", "numpydoc (>=1.0.0)", "Pillow (>=7.1.2)", "sphinx-prompt (>=1.3.0)"] +examples = ["matplotlib (>=2.1.1)", "scikit-image (>=0.13)", "pandas (>=0.25.0)", "seaborn (>=0.9.0)"] +tests = ["matplotlib (>=2.1.1)", "scikit-image (>=0.13)", "pandas (>=0.25.0)", "pytest (>=5.0.1)", "pytest-cov (>=2.9.0)", "flake8 (>=3.8.2)", "mypy (>=0.770)", "pyamg (>=4.0.0)"] [[package]] category = "main" @@ -1887,7 +1736,7 @@ description = "SciPy: Scientific Library for Python" name = "scipy" optional = false python-versions = ">=3.7" -version = "1.6.0" +version = "1.6.1" [package.dependencies] numpy = ">=1.16.5" @@ -1916,6 +1765,25 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" version = "1.15.0" +[[package]] +category = "main" +description = "scikit-learn compatible neural network library for pytorch" +name = "skorch" +optional = false +python-versions = "*" +version = "0.9.0" + +[package.dependencies] +numpy = ">=1.13.3" +scikit-learn = ">=0.19.1" +scipy = ">=1.1.0" +tabulate = ">=0.7.7" +tqdm = ">=4.14.0" + +[package.extras] +docs = ["sphinx", "sphinx-rtd-theme", "numpydoc"] +testing = ["pytest", "pytest-cov"] + [[package]] category = "main" description = "A pure Python implementation of a sliding window memory map manager" @@ -1947,7 +1815,7 @@ description = "Python documentation generator" name = "sphinx" optional = true python-versions = ">=3.5" -version = "3.4.3" +version = "3.5.1" [package.dependencies] Jinja2 = ">=2.3" @@ -1970,7 +1838,7 @@ sphinxcontrib-serializinghtml = "*" [package.extras] docs = ["sphinxcontrib-websupport"] -lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.790)", "docutils-stubs"] +lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.800)", "docutils-stubs"] test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"] [[package]] @@ -2069,26 +1937,6 @@ version = "0.3.2" [package.dependencies] numpy = "*" -[[package]] -category = "main" -description = "Database Abstraction Library" -name = "sqlalchemy" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "1.3.23" - -[package.extras] -mssql = ["pyodbc"] -mssql_pymssql = ["pymssql"] -mssql_pyodbc = ["pyodbc"] -mysql = ["mysqlclient"] -oracle = ["cx-oracle"] -postgresql = ["psycopg2"] -postgresql_pg8000 = ["pg8000 (<1.16.6)"] -postgresql_psycopg2binary = ["psycopg2-binary"] -postgresql_psycopg2cffi = ["psycopg2cffi"] -pymysql = ["pymysql (<1)", "pymysql"] - [[package]] category = "main" description = "SnobFit - Stable Noisy Optimization by Branch and FIT" @@ -2105,7 +1953,7 @@ numpy = "*" category = "main" description = "The fastest way to build data apps in Python" name = "streamlit" -optional = false +optional = true python-versions = ">=3.6" version = "0.67.1" @@ -2149,101 +1997,14 @@ six = "*" [[package]] category = "main" -description = "TensorBoard lets you watch Tensors Flow" -name = "tensorboard" -optional = false -python-versions = ">= 2.7, != 3.0.*, != 3.1.*" -version = "2.4.1" - -[package.dependencies] -absl-py = ">=0.4" -google-auth = ">=1.6.3,<2" -google-auth-oauthlib = ">=0.4.1,<0.5" -grpcio = ">=1.24.3" -markdown = ">=2.6.8" -numpy = ">=1.12.0" -protobuf = ">=3.6.0" -requests = ">=2.21.0,<3" -setuptools = ">=41.0.0" -six = ">=1.10.0" -tensorboard-plugin-wit = ">=1.6.0" -werkzeug = ">=0.11.15" - -[package.dependencies.wheel] -python = ">=3" -version = ">=0.26" - -[[package]] -category = "main" -description = "What-If Tool TensorBoard plugin." -name = "tensorboard-plugin-wit" +description = "Pretty-print tabular data" +name = "tabulate" optional = false python-versions = "*" -version = "1.8.0" - -[[package]] -category = "main" -description = "TensorFlow is an open source machine learning framework for everyone." -name = "tensorflow" -optional = false -python-versions = "*" -version = "2.4.0" - -[package.dependencies] -absl-py = ">=0.10,<1.0" -astunparse = ">=1.6.3,<1.7.0" -flatbuffers = ">=1.12.0,<1.13.0" -gast = "0.3.3" -google-pasta = ">=0.2,<1.0" -grpcio = ">=1.32.0,<1.33.0" -h5py = ">=2.10.0,<2.11.0" -keras-preprocessing = ">=1.1.2,<1.2.0" -numpy = ">=1.19.2,<1.20.0" -opt-einsum = ">=3.3.0,<3.4.0" -protobuf = ">=3.9.2" -six = ">=1.15.0,<1.16.0" -tensorboard = ">=2.4,<3.0" -tensorflow-estimator = ">=2.4.0rc0,<2.5.0" -termcolor = ">=1.1.0,<1.2.0" -typing-extensions = ">=3.7.4,<3.8.0" -wheel = ">=0.35,<1.0" -wrapt = ">=1.12.1,<1.13.0" - -[[package]] -category = "main" -description = "TensorFlow Estimator." -name = "tensorflow-estimator" -optional = false -python-versions = "*" -version = "2.4.0" - -[[package]] -category = "main" -description = "Probabilistic modeling and statistical inference in TensorFlow" -name = "tensorflow-probability" -optional = false -python-versions = "*" -version = "0.12.1" - -[package.dependencies] -cloudpickle = ">=1.3" -decorator = "*" -dm-tree = "*" -gast = ">=0.3.2" -numpy = ">=1.13.3" -six = ">=1.10.0" +version = "0.8.8" [package.extras] -jax = ["jax", "jaxlib"] -tfds = ["tensorflow-datasets (>=2.2.0)"] - -[[package]] -category = "main" -description = "ANSII Color formatting for output in terminal." -name = "termcolor" -optional = false -python-versions = "*" -version = "1.1.0" +widechars = ["wcwidth"] [[package]] category = "main" @@ -2289,7 +2050,7 @@ version = "0.10.2" category = "main" description = "List processing tools and functional utilities" name = "toolz" -optional = false +optional = true python-versions = ">=3.5" version = "0.11.1" @@ -2309,7 +2070,7 @@ typing-extensions = "*" category = "main" description = "image and video datasets and models for torch deep learning" name = "torchvision" -optional = false +optional = true python-versions = "*" version = "0.8.2" @@ -2329,6 +2090,18 @@ optional = false python-versions = ">= 3.5" version = "6.1" +[[package]] +category = "main" +description = "Fast, Extensible Progress Meter" +name = "tqdm" +optional = false +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" +version = "4.57.0" + +[package.extras] +dev = ["py-make (>=0.1.0)", "twine", "wheel"] +telegram = ["requests"] + [[package]] category = "main" description = "Traitlets Python configuration system" @@ -2363,7 +2136,7 @@ version = "3.7.4.3" category = "main" description = "tzinfo object for the local timezone" name = "tzlocal" -optional = false +optional = true python-versions = "*" version = "2.1" @@ -2374,7 +2147,7 @@ pytz = "*" category = "main" description = "HTTP library with thread-safe connection pooling, file post, and more." name = "urllib3" -optional = false +optional = true python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" version = "1.26.3" @@ -2387,7 +2160,7 @@ socks = ["PySocks (>=1.5.6,<1.5.7 || >1.5.7,<2.0)"] category = "main" 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-pandas = "^1.1.0" +# Core dependencies python = "^3.7" -GPy = "^1.9" -numpy = "^1.18.0" -pyrff = "^2.0.1" -SQSnobFit = "^0.4.3" +pandas = "^1.1.0" fastprogress = "^0.2.3" ipywidgets = "^7.5.1" matplotlib = "^3.2.2" -pymoo = "^0.4.1" -gpyopt = "^1.2.6" +scikit-learn = "^0.24.1" torch = "^1.4.0" +skorch = "^0.9.0" +cython = "^0.29.21" + +# Dependencies for TSEMO and SOBO +GPy = "^1.9" +gpyopt = "^1.2.6" +numpy = "^1.18.0" +pyrff = "^2.0.1" +pymoo = "^0.4.1" + +# Dependencies for Snobfit +SQSnobFit = "^0.4.3" + +# Dependencies for MTBO + botorch = "*" # Temporary fix https://github.com/pytorch/botorch/issues/668 -gpytorch = "1.3.0" -ipykernel = "^5.3.4" -scikit-learn = "^0.23.2" -blitz-bayesian-pytorch = {git = "https://github.com/sustainable-processes/blitz-bayesian-deep-learning.git"} +gpytorch = "1.3.0" + +# Dependencies for emulator +blitz-bayesian-pytorch = {git = "https://github.com/sustainable-processes/blitz-bayesian-deep-learning.git", optional=true} + +# Optinal dependencies +ipykernel = {version="^5.3.4", optional=true} xlrd = {version="^1.2.0", optional=true} -cython = "^0.29.21" -streamlit = {"^0.67.1", optional=true} +streamlit = {version="^0.67.1", optional=true} neptune-client = {version= "^0.4.115", optional = true} hiplot = {version= "^0.1.12", optional = true} paramiko = {version="^2.7.1", optional=true} @@ -41,9 +54,11 @@ pyrecorder = {version="^0.1.8", optional=true} entmoot = {version="^0.1.4", optional=true} [tool.poetry.extras] +bnn = ["blitz-bayesian-pytorch"] +entmoot = ["entmoot"] experiments = ["neptune-client", "hiplot", "paramiko", "pyrecorder", "xlrd", "streamlit"] docs = ["sphinx", "nbsphinx", "sphinx-rtd-theme"] -entmoot = ["entmoot"] + [tool.poetry.dev-dependencies] pytest = "^3.0" diff --git a/scripts/train_emulators/README.md b/scripts/train_emulators/README.md new file mode 100644 index 00000000..e320f0ca --- /dev/null +++ b/scripts/train_emulators/README.md @@ -0,0 +1,16 @@ +# Train Emulators + +The `train_emulators.py` script will train emulators and create this report. +## Reizman Suzuki Cross coupling +This is the data from training of the reizman suzuki benchmark for 1000 epochs with 5 cross-validation folds. +| case | avg_fit_time | avg_val_r2 | avg_val_RMSE | avg_test_r2 | avg_test_RMSE | +|:-------|---------------:|-------------:|---------------:|--------------:|----------------:| +| case_1 | 10.35 | 0.83 | 10.82 | 0.93 | 7.5 | +| case_2 | 8.93 | 0.62 | 5.4 | 0.67 | 4.91 | +| case_3 | 10.12 | 0.74 | 13.79 | 0.84 | 12.07 | +| case_4 | 9.6 | 0.7 | 15.9 | 0.74 | 13.98 | +## Baumgartner C-N Cross Cross Coupling +This is the data from training of the Baumgartner C-N aniline cross-coupling benchmark for 1000 epochs with 5 cross-validation folds. +| case | avg_fit_time | avg_val_r2 | avg_val_RMSE | avg_test_r2 | avg_test_RMSE | +|:--------|---------------:|-------------:|---------------:|--------------:|----------------:| +| one-hot | 8.43 | 0.81 | 0.17 | 0.88 | 0.13 | diff --git a/scripts/train_emulators/results/baumgartner_aniline_cn_crosscoupling.png b/scripts/train_emulators/results/baumgartner_aniline_cn_crosscoupling.png new file mode 100644 index 00000000..acb90128 Binary files /dev/null and b/scripts/train_emulators/results/baumgartner_aniline_cn_crosscoupling.png differ diff --git a/scripts/train_emulators/results/baumgartner_aniline_cn_crosscoupling_scores.csv b/scripts/train_emulators/results/baumgartner_aniline_cn_crosscoupling_scores.csv new file mode 100644 index 00000000..9fd6bccf --- /dev/null +++ b/scripts/train_emulators/results/baumgartner_aniline_cn_crosscoupling_scores.csv @@ -0,0 +1,2 @@ +case,avg_fit_time,avg_score_time,avg_val_r2,avg_val_neg_root_mean_squared_error,avg_test_r2,avg_test_neg_root_mean_squared_error +one-hot,8.43237853050232,0.0061893463134765625,0.8130802170821865,-0.17386471927165986,0.8788791513272004,-0.13320153332761886 diff --git a/scripts/train_emulators/results/reizman_suzuki_case_1.png b/scripts/train_emulators/results/reizman_suzuki_case_1.png new file mode 100644 index 00000000..fc25a806 Binary files /dev/null and b/scripts/train_emulators/results/reizman_suzuki_case_1.png differ diff --git a/scripts/train_emulators/results/reizman_suzuki_case_2.png b/scripts/train_emulators/results/reizman_suzuki_case_2.png new file mode 100644 index 00000000..2acd0cde Binary files /dev/null and b/scripts/train_emulators/results/reizman_suzuki_case_2.png differ diff --git a/scripts/train_emulators/results/reizman_suzuki_case_3.png b/scripts/train_emulators/results/reizman_suzuki_case_3.png new file mode 100644 index 00000000..6e5b0864 Binary files /dev/null and b/scripts/train_emulators/results/reizman_suzuki_case_3.png differ diff --git a/scripts/train_emulators/results/reizman_suzuki_case_4.png b/scripts/train_emulators/results/reizman_suzuki_case_4.png new file mode 100644 index 00000000..f9a862ff Binary files /dev/null and b/scripts/train_emulators/results/reizman_suzuki_case_4.png differ diff --git a/scripts/train_emulators/results/reizman_suzuki_scores.csv b/scripts/train_emulators/results/reizman_suzuki_scores.csv new file mode 100644 index 00000000..da869f97 --- /dev/null +++ b/scripts/train_emulators/results/reizman_suzuki_scores.csv @@ -0,0 +1,5 @@ +case,avg_fit_time,avg_score_time,avg_val_r2,avg_val_neg_root_mean_squared_error,avg_test_r2,avg_test_neg_root_mean_squared_error +case_1,10.348453617095947,0.00654149055480957,0.8295508810399357,-10.816744422912597,0.9307952086976204,-7.498236728819775 +case_2,8.928261852264404,0.005949831008911133,0.6182039897632764,-5.401305246353149,0.6746129777462376,-4.910729931080706 +case_3,10.123983812332153,0.005974340438842774,0.7380188495373521,-13.788355827331543,0.8379006941956488,-12.066490239891527 +case_4,9.60025577545166,0.007497835159301758,0.7013988693185367,-15.903024101257325,0.736780456428538,-13.980203005904974 diff --git a/scripts/train_emulators/train_emulators.py b/scripts/train_emulators/train_emulators.py new file mode 100644 index 00000000..c3f62e7d --- /dev/null +++ b/scripts/train_emulators/train_emulators.py @@ -0,0 +1,182 @@ +from summit.benchmarks.experimental_emulator import * +from summit.utils.dataset import DataSet + +import pandas as pd +import matplotlib.pyplot as plt +import logging +import pkg_resources +import pathlib +from tqdm import trange +import argparse + +DATA_PATH = pathlib.Path(pkg_resources.resource_filename("summit", "benchmarks/data")) +MODELS_PATH = pathlib.Path( + pkg_resources.resource_filename("summit", "benchmarks/models") +) +SUMMARY_FILE = "README.md" +MAX_EPOCHS = 1000 +CV_FOLDS = 5 + + +def train_reizman(show_plots=False): + results = [ + train_one_reizman(i, show_plots=show_plots) + for i in trange(1, 5, desc="Reizman") + ] + + # Average scores from cross validation + results_average = [ + {f"avg_{score_name}": scores.mean() for score_name, scores in result.items()} + for result in results + ] + index = [f"case_{i}" for i in range(1, 5)] + + results_df = pd.DataFrame.from_records(results_average, index=index) + results_df.index.rename("case", inplace=True) + results_df.to_csv(f"results/reizman_suzuki_scores.csv") + + +def train_one_reizman(case, show_plots=False, save_plots=True): + # Setup + model_name = f"reizman_suzuki_case_{case}" + domain = ReizmanSuzukiEmulator.setup_domain() + ds = DataSet.read_csv(DATA_PATH / f"{model_name}.csv") + + # Create emulator and train + exp = ExperimentalEmulator( + model_name, + domain, + dataset=ds, + regressor=ANNRegressor, + ) + res = exp.train( + max_epochs=MAX_EPOCHS, cv_folds=CV_FOLDS, random_state=100, test_size=0.2 + ) + + # Run test + res_test = exp.test() + res.update(res_test) + + # Save emulator + model_path = pathlib.Path(MODELS_PATH / model_name) + model_path.mkdir(exist_ok=True) + exp.save(model_path) + + # Make plot for posteriority sake + fig, ax = exp.parity_plot(include_test=True) + if save_plots: + fig.savefig(f"results/{model_name}.png", dpi=100) + if show_plots: + plt.show() + + return res + + +def train_baumgartner(show_plots=False): + # Train model using one-hot encoding for categorical + print("Training Baumgartner model") + result = train_baumgartner_no_descriptors() + results_average = [ + {f"avg_{score_name}": scores.mean() for score_name, scores in result.items()} + ] + + index = ["one-hot"] + results_df = pd.DataFrame.from_records(results_average, index=index) + results_df.index.rename("case", inplace=True) + results_df.to_csv(f"results/baumgartner_aniline_cn_crosscoupling_scores.csv") + + +def train_baumgartner_no_descriptors(show_plots=False, save_plots=True): + # Setup + model_name = f"baumgartner_aniline_cn_crosscoupling" + domain = BaumgartnerCrossCouplingEmulator.setup_domain() + ds = DataSet.read_csv(DATA_PATH / f"{model_name}.csv") + + # Create emulator and train + exp = ExperimentalEmulator( + model_name, + domain, + dataset=ds, + regressor=ANNRegressor, + output_variable_names=["yield"], + ) + res = exp.train( + max_epochs=MAX_EPOCHS, cv_folds=CV_FOLDS, random_state=100, test_size=0.2 + ) + + # # Run test + res_test = exp.test() + res.update(res_test) + + # Save emulator + model_path = pathlib.Path(MODELS_PATH / model_name) + model_path.mkdir(exist_ok=True) + exp.save(model_path) + + # Make plot for posteriority sake + fig, ax = exp.parity_plot(include_test=True) + if save_plots: + fig.savefig(f"results/{model_name}.png", dpi=100) + if show_plots: + plt.show() + + return res + + +def create_markdown(): + """Create markdown report""" + md = ( + "# Train Emulators\n" + "\n" + "The `train_emulators.py` script will train emulators and create this report.\n" + ) + + # Reizman + reizman_text = ( + "## Reizman Suzuki Cross coupling \n" + "This is the data from training of the reizman suzuki benchmark " + f"for {MAX_EPOCHS} epochs with {CV_FOLDS} cross-validation folds.\n" + ) + baumgartner_text = ( + "## Baumgartner C-N Cross Cross Coupling \n" + "This is the data from training of the Baumgartner C-N aniline cross-coupling benchmark " + f"for {MAX_EPOCHS} epochs with {CV_FOLDS} cross-validation folds.\n" + ) + texts = [reizman_text, baumgartner_text] + df_reizman = pd.read_csv("results/reizman_suzuki_scores.csv") + df_baumgartner = pd.read_csv( + "results/baumgartner_aniline_cn_crosscoupling_scores.csv" + ) + dfs = [df_reizman, df_baumgartner] + + for text, df in zip(texts, dfs): + rename = dict() + for column in df.columns: + mse_substring = "neg_root_mean_squared_error" + if mse_substring in column: + rename[column] = column.replace(mse_substring, "RMSE") + df[column] = -1.0 * df[column] + df = df.rename(columns=rename) + df = df.drop(columns="avg_score_time") + md += text + md += df.round(2).to_markdown(index=False) + md += "\n" + + return md + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(allow_abbrev=False) + parser.add_argument("--bypass_training", action="store_true") + args = parser.parse_args() + + # Training + if not args.bypass_training: + train_reizman() + train_baumgartner() + + # Create report + md = create_markdown() + with open("README.md", "w") as f: + f.write(md) diff --git a/summit/benchmarks/MIT_kin_case1.py b/summit/benchmarks/MIT/MIT_kin_case1.py similarity index 100% rename from summit/benchmarks/MIT_kin_case1.py rename to summit/benchmarks/MIT/MIT_kin_case1.py diff --git a/summit/benchmarks/MIT_kin_case2.py b/summit/benchmarks/MIT/MIT_kin_case2.py similarity index 100% rename from summit/benchmarks/MIT_kin_case2.py rename to summit/benchmarks/MIT/MIT_kin_case2.py diff --git a/summit/benchmarks/MIT_kin_case3.py b/summit/benchmarks/MIT/MIT_kin_case3.py similarity index 100% rename from summit/benchmarks/MIT_kin_case3.py rename to summit/benchmarks/MIT/MIT_kin_case3.py diff --git a/summit/benchmarks/MIT_kin_case4.py b/summit/benchmarks/MIT/MIT_kin_case4.py similarity index 100% rename from summit/benchmarks/MIT_kin_case4.py rename to summit/benchmarks/MIT/MIT_kin_case4.py diff --git a/summit/benchmarks/MIT_kin_case5.py b/summit/benchmarks/MIT/MIT_kin_case5.py similarity index 100% rename from summit/benchmarks/MIT_kin_case5.py rename to summit/benchmarks/MIT/MIT_kin_case5.py diff --git a/summit/benchmarks/MIT/__init__.py b/summit/benchmarks/MIT/__init__.py new file mode 100644 index 00000000..a5fc8972 --- /dev/null +++ b/summit/benchmarks/MIT/__init__.py @@ -0,0 +1,7 @@ +from .MIT_kin_case1 import MIT_case1 +from .MIT_kin_case2 import MIT_case2 +from .MIT_kin_case3 import MIT_case3 +from .MIT_kin_case4 import MIT_case4 +from .MIT_kin_case5 import MIT_case5 + +__all__ = [f"MIT_case{i}" for i in range(1, 6)] diff --git a/summit/benchmarks/__init__.py b/summit/benchmarks/__init__.py index a44caac7..2ec5c9bc 100644 --- a/summit/benchmarks/__init__.py +++ b/summit/benchmarks/__init__.py @@ -1,15 +1,4 @@ from .snar import SnarBenchmark from .test_functions import Himmelblau, Hartmann3D, ThreeHumpCamel, DTLZ2, VLMOP2 - -# from .experimental_emulator import ( -# ExperimentalEmulator, -# ReizmanSuzukiEmulator, -# BaumgartnerCrossCouplingEmulator, -# BaumgartnerCrossCouplingDescriptorEmulator, -# BaumgartnerCrossCouplingEmulator_Yield_Cost, -# ) -# from .MIT_kin_case1 import MIT_case1 -# from .MIT_kin_case2 import MIT_case2 -# from .MIT_kin_case3 import MIT_case3 -# from .MIT_kin_case4 import MIT_case4 -# from .MIT_kin_case5 import MIT_case5 \ No newline at end of file +from .experimental_emulator import * +from .MIT import * diff --git a/summit/benchmarks/experiment_emulator/data/README.md b/summit/benchmarks/data/README.md similarity index 100% rename from summit/benchmarks/experiment_emulator/data/README.md rename to summit/benchmarks/data/README.md diff --git a/summit/benchmarks/experiment_emulator/data/baumgartenter_benzamide_cross_coupling.csv b/summit/benchmarks/data/baumgartenter_benzamide_cross_coupling.csv similarity index 100% rename from summit/benchmarks/experiment_emulator/data/baumgartenter_benzamide_cross_coupling.csv rename to summit/benchmarks/data/baumgartenter_benzamide_cross_coupling.csv diff --git a/summit/benchmarks/data/baumgartner_aniline_cn_crosscoupling.csv b/summit/benchmarks/data/baumgartner_aniline_cn_crosscoupling.csv new file mode 100644 index 00000000..a68d48ea --- /dev/null +++ b/summit/benchmarks/data/baumgartner_aniline_cn_crosscoupling.csv @@ -0,0 +1,98 @@ +,catalyst,base,base_equivalents,temperature,t_res,yield +TYPE,DATA,DATA,DATA,DATA,DATA,DATA +0,tBuXPhos,DBU,2.183015499,30,328.7178016,0.042832638 +1,tBuXPhos,BTMG,2.190881556,100,73.33119392,0.959689589 +2,tBuXPhos,TMG,1.093138191,47.5,75.12129688,0.03157943 +3,tBuXPhos,TMG,2.186276382,100,673.2595081,0.766767923 +4,tBuXPhos,TEA,1.108766571,30,107.541151,0.072298979 +5,tBuXPhos,DBU,2.183015499,100,1088.512259,1.008695766 +6,tBuXPhos,DBU,1.097966375,100,1208.711134,1.001213765 +7,tBuXPhos,TEA,1.108766571,65,1061.645722,0.089740381 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+42,tBuBrettPhos,BTMG,1.64633276,65,320.0973086,0.967285589 +43,tBuBrettPhos,TEA,1.650765753,100,74.52026224,0.022204324 +44,tBuBrettPhos,BTMG,1.100489813,100,75.76033354,1.010162248 +45,tBuBrettPhos,BTMG,1.100489813,30,1292.050901,1.025097628 +46,tBuBrettPhos,TEA,2.158693677,65,1061.794731,0.029545128 +47,tBuBrettPhos,TMG,1.650420244,30,1271.987753,0.075288426 +48,tBuBrettPhos,TEA,2.158693677,30,73.62221098,0.005340242 +49,tBuBrettPhos,TMG,1.100280162,100,326.5346766,0.932317344 +50,tBuBrettPhos,TMG,2.186454169,65,74.14924097,0.039293957 +51,tBuBrettPhos,TEA,2.158693677,100,391.3483839,0.06609534 +52,tBuBrettPhos,DBU,2.189443812,100,477.4873109,1.030315127 +53,tBuBrettPhos,TMG,2.186454169,100,472.8960481,1.003367029 +54,tBuBrettPhos,DBU,1.147978647,100,532.9614835,1.025950003 +55,tBuBrettPhos,TMG,1.988967986,100,476.9942827,1.006211346 +56,tBuBrettPhos,TEA,1.142837829,100,448.6906638,0.056448626 +57,tBuBrettPhos,DBU,1.100639322,57.1,1277.329059,0.421916562 +58,tBuBrettPhos,TMG,2.186454169,62.7,1072.451341,0.353419248 +59,tBuBrettPhos,BTMG,1.681548434,100,386.2370915,0.99815143 +60,tBuBrettPhos,DBU,1.550362916,100,348.0039043,1.026735464 +61,tBuBrettPhos,TMG,1.59399562,100,416.2208061,0.924062878 +62,AlPhos,DBU,1.091453389,30,1257.923949,0.973793101 +63,AlPhos,TMG,1.0995902,65,75.23930359,0.208090937 +64,AlPhos,TEA,1.115310823,65,1071.112264,0.073308686 +65,AlPhos,BTMG,2.19414691,100,1263.449265,0.942713469 +66,AlPhos,DBU,2.19590027,100,73.54120636,0.97934425 +67,AlPhos,BTMG,1.101906378,30,75.11629629,0.929228974 +68,AlPhos,TEA,2.230621646,100,319.7722898,0.232825163 +69,AlPhos,TEA,2.230621646,30,1365.507102,0.14622501 +70,AlPhos,DBU,2.19590027,65,1070.650238,0.986319856 +71,AlPhos,TMG,2.1991804,30,381.7698359,0.045453974 +72,AlPhos,TEA,1.115310823,100,75.66132784,0.056712653 +73,AlPhos,TMG,2.1991804,65,75.43531466,0.156546245 +74,AlPhos,DBU,1.650173576,30,89.51111984,0.567666469 +75,AlPhos,BTMG,2.19414691,30,75.04729271,0.959137709 +76,AlPhos,BTMG,1.101906378,100,1279.138163,0.964080978 +77,AlPhos,TMG,1.0995902,30,327.6697416,0.063736927 +78,AlPhos,TMG,1.641641707,100,1180.186503,0.994961147 +79,AlPhos,DBU,1.507245156,100,1214.58247,0.996941489 +80,AlPhos,TMG,1.626154521,100,1300.974411,0.98961563 +81,AlPhos,BTMG,1.585198648,100,1215.877544,0.947352946 +82,AlPhos,BTMG,1.594864494,100,1275.07693,0.971831102 +83,AlPhos,TMG,2.1991804,30,1369.512331,0.08429262 +84,AlPhos,DBU,1.702147547,100,1308.539844,0.994908646 +85,AlPhos,BTMG,1.101906378,88.5,1092.52949,0.927005687 +86,AlPhos,TMG,1.0995902,88.5,1393.362696,0.939708298 +87,tBuXPhos,TMG,2.186276382,63.1,1242.849087,0.315366703 +88,tBuXPhos,DBU,1.097966375,30,377.9346166,0.093450375 +89,AlPhos,TEA,2.091207793,100,1350.932269,0.207359999 +90,AlPhos,BTMG,1.643193721,65,341.4145279,0.945804957 +91,tBuBrettPhos,BTMG,1.100489813,100,526.4841132,1.000808176 +92,tBuBrettPhos,TEA,1.142837829,30,75.30730724,0.005499146 +93,tBuBrettPhos,BTMG,2.192175707,30,1240.719965,1.019671511 +94,AlPhos,DBU,1.091453389,100,321.2633753,0.95902087 +95,tBuBrettPhos,TMG,1.100280162,47.5,65.77076197,0.043402107 \ No newline at end of file diff --git a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case1_train_test.csv b/summit/benchmarks/data/reizman_suzuki_case_1.csv similarity index 100% rename from summit/benchmarks/experiment_emulator/data/reizman_suzuki_case1_train_test.csv rename to summit/benchmarks/data/reizman_suzuki_case_1.csv diff --git a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case2_train_test.csv b/summit/benchmarks/data/reizman_suzuki_case_2.csv similarity index 100% rename from summit/benchmarks/experiment_emulator/data/reizman_suzuki_case2_train_test.csv rename to summit/benchmarks/data/reizman_suzuki_case_2.csv diff --git a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case3_train_test.csv b/summit/benchmarks/data/reizman_suzuki_case_3.csv similarity index 100% rename from summit/benchmarks/experiment_emulator/data/reizman_suzuki_case3_train_test.csv rename to summit/benchmarks/data/reizman_suzuki_case_3.csv diff --git a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case4_train_test.csv b/summit/benchmarks/data/reizman_suzuki_case_4.csv similarity index 100% rename from summit/benchmarks/experiment_emulator/data/reizman_suzuki_case4_train_test.csv rename to summit/benchmarks/data/reizman_suzuki_case_4.csv diff --git a/summit/benchmarks/experiment_emulator/__init__.py b/summit/benchmarks/experiment_emulator/__init__.py deleted file mode 100644 index cf3af26e..00000000 --- a/summit/benchmarks/experiment_emulator/__init__.py +++ /dev/null @@ -1,6 +0,0 @@ -import os, sys - -sys.path.append(os.path.dirname(os.path.realpath(__file__))) - -# from .emulator import Emulator -# from .bnn_emulator import BNNEmulator diff --git a/summit/benchmarks/experiment_emulator/bnn_emulator.py b/summit/benchmarks/experiment_emulator/bnn_emulator.py deleted file mode 100644 index c271b908..00000000 --- a/summit/benchmarks/experiment_emulator/bnn_emulator.py +++ /dev/null @@ -1,578 +0,0 @@ -# import os -# import os.path as osp - -# import numpy as np - -# from summit.benchmarks.experiment_emulator.emulator import Emulator - -# import torch -# import torch.nn as nn -# import torch.nn.functional as F -# import torch.optim as optim - -# from blitz.modules import BayesianLinear -# from blitz.utils import variational_estimator - -# from sklearn.metrics import r2_score - -# # ======================================================================= - - -# class BNNEmulator(Emulator): -# """BNN Emulator - -# A Bayesian Neural Network (BNN) emulator. - -# Parameters -# --------- -# domain: summit.domain.Domain -# The domain of the experiment -# dataset: class:~summit.utils.dataset.DataSet, optional -# A DataSet with data for training where the data columns correspond to the domain and the data rows correspond to the training points. -# By default: None -# model_name: string, optional -# Name of the model that is used for saving model parameters. Should be unique. -# By default: "dataset_emulator_model_name" -# """ - -# # ======================================================================= - -# def __init__(self, domain, dataset, model_name, kwargs={}): -# super().__init__(domain, dataset, model_name, kwargs) -# self._model = self._setup_model() - -# # Set model name for saving -# self.save_path = kwargs.get( -# "save_path", -# osp.join(osp.dirname(osp.realpath(__file__)), "trained_models/BNN"), -# ) - -# # Set up training hyperparameters -# self.set_training_hyperparameters() - -# # ======================================================================= - -# def _setup_model(self, **kwargs): -# """ Setup the BNN model """ - -# @variational_estimator -# class BayesianRegressor(nn.Module): -# def __init__(self, input_dim): -# super().__init__() - -# self.blinear1 = BayesianLinear(input_dim, 24) -# self.blinear2 = BayesianLinear(24, 24) -# self.blinear3 = BayesianLinear(24, 24) -# self.blinear4 = BayesianLinear(24, 1) - -# def forward(self, x): -# x = F.leaky_relu(self.blinear1(x)) -# x = F.leaky_relu(self.blinear2(x)) -# x = F.dropout(x, p=0.1, training=self.training) -# x = F.leaky_relu(self.blinear3(x)) -# x = F.dropout(x, p=0.1, training=self.training) -# x = F.relu(self.blinear4(x)) -# y = x -# return y.view(-1) - -# # Training of model on given dataloader -# def _train(self, regressor, device, optimizer, criterion, X_train, loader): -# regressor.train() - -# for i, (datapoints, labels) in enumerate(loader): -# optimizer.zero_grad() -# loss = regressor.sample_elbo( -# inputs=datapoints.to(device), -# labels=labels.to(device), -# criterion=criterion, -# sample_nbr=3, -# complexity_cost_weight=1 / X_train.shape[0], -# ) -# loss.backward() -# optimizer.step() - -# # Evaluate model for given dataloader -# def _evaluate_regression( -# self, -# regressor, -# device, -# loader, -# fun_untransform_data, -# out_transform, -# get_predictions=False, -# ): -# regressor.eval() -# regressor.freeze_() - -# mae = 0 -# pred_data = [] -# real_data = [] -# for i, (datapoints, labels) in enumerate(loader): -# data = datapoints.to(device) -# pred = regressor(data) -# tmp_pred_data = fun_untransform_data( -# data=pred, reduce=out_transform[0], divide=out_transform[1] -# ) -# tmp_real_data = fun_untransform_data( -# data=labels, reduce=out_transform[0], divide=out_transform[1] -# ) -# mae += (tmp_pred_data - tmp_real_data).abs().sum(0).item() - -# if get_predictions: -# pred_data.extend(tmp_pred_data.tolist()) -# real_data.extend(tmp_real_data.tolist()) - -# if get_predictions: -# return pred_data, real_data - -# regressor.unfreeze_() - -# return mae / len(loader.dataset) - -# regression_model = BayesianRegressor(self.input_dim) -# return regression_model - -# # ======================================================================= - -# def set_training_hyperparameters(self, kwargs={}): -# # Setter method for hyperparameters of training -# self.epochs = kwargs.get( -# "epochs", 300 -# ) # number of max epochs the model is trained -# self.initial_lr = kwargs.get("initial_lr", 0.001) # initial learning rate -# self.min_lr = kwargs.get("min_lr", 0.00001) -# self.lr_decay = kwargs.get("lr_decay", 0.7) # learning rate decay -# self.lr_decay_patience = kwargs.get( -# "lr_decay_patience", 3 -# ) # number of epochs before learning rate is reduced by lr_decay -# self.early_stopping_epochs = kwargs.get( -# "early_stopping_epochs", 30 -# ) # number of epochs before early stopping -# self.batch_size_train = kwargs.get("batch_size_train", 4) -# self.transform_input = kwargs.get("transform_input", "standardize") -# self.transform_output = kwargs.get("transform_output", "standardize") -# self.test_size = kwargs.get("test_size", 0.1) -# self.shuffle = kwargs.get("shuffle", False) - -# # ======================================================================= - -# def train_model(self, dataset=None, verbose=True, kwargs={}): -# # Manual call of training -> overwrite dataset with new dataset for training -# if dataset is not None: -# self._dataset = dataset - -# # #-fold cross-validation -# cv_fold = kwargs.get("cv_fold", 10) - -# # Data preprocess -# train_dataset, test_dataset = self._data_preprocess( -# transform_input=self.transform_input, -# transform_output=self.transform_output, -# test_size=self.test_size, -# shuffle=self.shuffle, -# ) - -# X_train_init, y_train_init = ( -# torch.tensor(train_dataset[0]).float(), -# torch.tensor(train_dataset[1]).float(), -# ) -# X_test, y_test = ( -# torch.tensor(test_dataset[0]).float(), -# torch.tensor(test_dataset[1]).float(), -# ) - -# shuffle_train = kwargs.get("shuffle_train", False) -# if shuffle_train: -# perm = torch.randperm(len(y_train_init)) -# train_data = torch.cat([X_train_init, y_train_init], axis=1)[perm] -# X_train, y_train = ( -# train_data[:, : -self.output_dim], -# train_data[:, -self.output_dim :], -# ) -# else: -# X_train, y_train = X_train_init, y_train_init - -# if verbose: -# print("\n<---- Start training of BNN model ---->") -# print(" --- Length of train dataset: {} ---".format(X_train.shape[0])) -# print(" --- Length of test dataset: {} ---".format(X_test.shape[0])) -# for i, k in enumerate(self.output_models): -# if verbose: -# print( -# "\n <-- Start {}-fold cross-validation training of BNN regressor on objective: {} -->\n".format( -# cv_fold, k -# ) -# ) - -# train_acc, val_acc, test_acc = [], [], [] -# y_train_pred_l, y_train_real_l, y_test_pred_l, y_test_real_l = ( -# [], -# [], -# [], -# [], -# ) -# for j in range(cv_fold): -# if verbose: -# print(" ---------------- Split {} ----------------".format(j + 1)) - -# # Set training details -# device = torch.device("cuda" if torch.cuda.is_available() else "cpu") -# regressor = self._setup_model().to(device) -# optimizer = optim.Adam(regressor.parameters(), lr=self.initial_lr) -# scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau( -# optimizer, -# factor=self.lr_decay, -# patience=self.lr_decay_patience, -# min_lr=self.min_lr, -# ) -# criterion = torch.nn.MSELoss() -# model_save_name = ( -# self.model_name + "_" + str(k) + "_" + str(j + 1) + "_BNN_model.pt" -# ) -# model_save_dir = osp.join(self.save_path, model_save_name) -# storable = self._check_file_path(model_save_dir) -# if not storable: -# self.output_models[k] = self._load_model(self.model_name)[k] -# continue - -# # Setup train and val dataset for cross-validation -# if cv_fold <= 1: -# raise ValueError( -# "{}-fold Cross-Validation not possible. Increase cv_fold.".format( -# cv_fold -# ) -# ) -# if len(X_train) < cv_fold: -# raise ValueError( -# "Too few data points ({}) for training provided. Decrease cv_fold.".format( -# len(X_train) -# ) -# ) -# n = len(X_train) // cv_fold -# r = len(X_train) % cv_fold -# val_mask = torch.zeros(len(X_train), dtype=torch.uint8) -# # make sure every data point is included in the validation set once -# if j < r: -# val_mask[j * (n + 1) : (j + 1) * (n + 1)] = 1 -# else: -# val_mask[j * n + r : (j + 1) * n + r] = 1 -# X_val_cv, y_val_cv = X_train[val_mask], y_train[val_mask] -# X_train_cv, y_train_cv = X_train[1 - val_mask], y_train[1 - val_mask] - -# out_transform = self.data_transformation_dict[k] -# y_train_obj, y_val_obj, y_test_obj = ( -# y_train_cv[:, i], -# y_val_cv[:, i], -# y_test[:, i], -# ) -# ds_train = torch.utils.data.TensorDataset(X_train_cv, y_train_obj) -# dataloader_train = torch.utils.data.DataLoader( -# ds_train, batch_size=self.batch_size_train, shuffle=True -# ) -# ds_val = torch.utils.data.TensorDataset(X_val_cv, y_val_obj) -# dataloader_val = torch.utils.data.DataLoader( -# ds_val, batch_size=16, shuffle=False -# ) -# ds_test = torch.utils.data.TensorDataset(X_test, y_test_obj) -# dataloader_test = torch.utils.data.DataLoader( -# ds_test, batch_size=16, shuffle=False -# ) - -# max_iter_stop = ( -# self.early_stopping_epochs -# ) # maximum number of consecutive iteration w/o improvement after which training is stopped -# tmp_iter_stop = 0 -# best_train_mae, best_val_mae, best_test_mae = ( -# float("inf"), -# float("inf"), -# float("inf"), -# ) -# for epoch in range(self.epochs): - -# lr = scheduler.optimizer.param_groups[0]["lr"] - -# # train model -# self._model._train( -# regressor, -# device, -# optimizer, -# criterion, -# X_train_cv, -# dataloader_train, -# ) - -# train_mae = self._model._evaluate_regression( -# regressor, -# device, -# dataloader_train, -# self._untransform_data, -# out_transform, -# ) -# val_mae = self._model._evaluate_regression( -# regressor, -# device, -# dataloader_val, -# self._untransform_data, -# out_transform, -# ) -# scheduler.step(val_mae) - -# if verbose: -# print( -# " -- Epoch: {:03d}, LR: {:7f}, Train MAE: {:4f}, Val MAE: {:4f}".format( -# epoch, lr, train_mae, val_mae -# ) -# ) - -# # if prediction accuracy was improved in current epoch, reset and save model -# if best_val_mae > val_mae: -# best_val_mae = val_mae -# tmp_iter_stop = 0 -# torch.save(regressor.state_dict(), model_save_dir) -# test_mae = self._model._evaluate_regression( -# regressor, -# device, -# dataloader_test, -# self._untransform_data, -# out_transform, -# ) -# best_train_mae, best_test_mae = train_mae, test_mae -# if verbose: -# print( -# " -> Val MAE improved, current Test MAE: {:4f}".format( -# test_mae -# ) -# ) -# # if prediction accuracy was not imporved in current epoch, increase and stop training if is reached -# else: -# tmp_iter_stop += 1 -# if tmp_iter_stop >= max_iter_stop: -# break - -# train_acc.append(best_train_mae) -# val_acc.append(best_val_mae) -# test_acc.append(best_test_mae) - -# y_train_obj = y_train_init[:, i] -# ds_train_all = torch.utils.data.TensorDataset(X_train_init, y_train_obj) - -# # load final model from epoch with lowest prediction accuracy -# regressor.load_state_dict(torch.load(model_save_dir)) - -# # get final model predictions for training and test data -# y_train_pred, y_train_real = self._model._evaluate_regression( -# regressor=regressor, -# device=device, -# loader=torch.utils.data.DataLoader(ds_train_all, shuffle=False), -# fun_untransform_data=self._untransform_data, -# out_transform=out_transform, -# get_predictions=True, -# ) -# y_test_pred, y_test_real = self._model._evaluate_regression( -# regressor=regressor, -# device=device, -# loader=torch.utils.data.DataLoader(ds_test, shuffle=False), -# fun_untransform_data=self._untransform_data, -# out_transform=out_transform, -# get_predictions=True, -# ) -# y_train_pred_l.append(y_train_pred), y_train_real_l.append(y_train_real) -# y_test_pred_l.append(y_test_pred), y_test_real_l.append(y_test_real) - -# train_acc, val_acc, test_acc = ( -# torch.tensor(train_acc), -# torch.tensor(val_acc), -# torch.tensor(test_acc), -# ) -# y_train_pred_l, y_train_real_l, y_test_pred_l, y_test_real_l = ( -# torch.tensor(y_train_pred_l), -# torch.tensor(y_train_real_l), -# torch.tensor(y_test_pred_l), -# torch.tensor(y_test_real_l), -# ) - -# X_train_final = np.asarray(X_train_init.tolist()) -# X_test_final = np.asarray(X_test.tolist()) -# for ind, inp_var in enumerate(self.input_names_transformable): -# tmp_inp_transform = self.data_transformation_dict[inp_var] -# X_train_final[:, ind] = self._untransform_data( -# data=X_train_final[:, ind], -# reduce=tmp_inp_transform[0], -# divide=tmp_inp_transform[1], -# ) -# X_test_final[:, ind] = self._untransform_data( -# data=X_test_final[:, ind], -# reduce=tmp_inp_transform[0], -# divide=tmp_inp_transform[1], -# ) - -# self.output_models[k] = { -# "model_save_dirs": [ -# self.model_name + "_" + str(k) + "_" + str(j + 1) -# for j in range(cv_fold) -# ], -# "Final train MAE": train_acc.mean().tolist(), -# "Final validation MAE": val_acc.mean().tolist(), -# "Final test MAE": test_acc.mean().tolist(), -# "data_transformation_dict": self.data_transformation_dict, -# "X variable names": self.input_names, -# "X_train": X_train_final.tolist(), -# "y_train_real": y_train_real_l.mean(axis=0).tolist(), -# "y_train_pred_average": y_train_pred_l.mean(axis=0).tolist(), -# "X_test": X_test_final.tolist(), -# "y_test_real": y_test_real_l.mean(axis=0).tolist(), -# "y_test_pred_average": y_test_pred_l.mean(axis=0).tolist(), -# } - -# if verbose: -# print( -# "\n <-- Finished training of BNN model on objective: {} -->\n" -# " -- Final Train MAE: {:4f}, Final Val MAE: {:4f}, Final Test MAE: {:4f} --\n" -# " -- Model saved at: {} --\n".format( -# k, -# train_acc.mean(), -# val_acc.mean(), -# test_acc.mean(), -# model_save_dir, -# ) -# ) - -# self._save_model() - -# if verbose: -# print("<---- End training of BNN regressor ---->\n") - -# # ======================================================================= - -# def validate_model( -# self, dataset=None, parity_plots=False, get_pred=False, kwargs={} -# ): -# self.output_models = self._load_model(self.model_name) - -# self._model.freeze_() # freeze the model, in order to predict using only their weight distribution means -# self._model.eval() # set to evaluation mode (may be redundant) - -# val_dict = {} -# lst_parity_plots = None -# if parity_plots: -# lst_parity_plots = [] - -# if dataset is not None: -# for i, (k, v) in enumerate(self.output_models.items()): -# model_load_dirs = v["model_save_dirs"] -# self.data_transformation_dict = v["data_transformation_dict"] -# out_transform = self.data_transformation_dict[k] - -# X_val = self._data_preprocess( -# inference=True, infer_dataset=dataset, validate=True -# ) -# X_val = torch.tensor(X_val).float() -# y_val = torch.tensor(dataset[(k, "DATA")].to_numpy()).float() - -# device = torch.device("cuda" if torch.cuda.is_available() else "cpu") -# prediction_l = [] -# for m in model_load_dirs: -# model_load_dir = osp.join(self.save_path, m + "_BNN_model.pt") -# self._model.load_state_dict( -# torch.load(model_load_dir, map_location=torch.device(device)) -# ) -# data = X_val.to(device) -# predictions = self._model(data).detach() -# predictions = self._untransform_data( -# data=predictions, -# reduce=out_transform[0], -# divide=out_transform[1], -# ) -# prediction_l.append(predictions) -# prediction_l = torch.tensor(prediction_l) -# predictions = prediction_l.mean(axis=0) -# val_dict[k] = { -# "MAE": (predictions - y_val).abs().mean().item(), -# "RMSE": ((((predictions - y_val) ** 2).mean()) ** (1 / 2)).item(), -# "r2": r2_score(y_val, predictions) -# if y_val.shape[0] > 1 -# else "Too few data points to calculate r2.", -# } - -# if parity_plots: -# parity_plot = self.create_parity_plot( -# datasets_pred=[predictions], -# datasets_real=[y_val], -# kwargs=kwargs, -# ) -# lst_parity_plots.append(parity_plot) -# else: -# for i, (k, v) in enumerate(self.output_models.items()): -# y_train_real, y_train_pred, y_test_real, y_test_pred = ( -# torch.tensor(v["y_train_real"]).float(), -# torch.tensor(v["y_train_pred_average"]).float(), -# torch.tensor(v["y_test_real"]).float(), -# torch.tensor(v["y_test_pred_average"]).float(), -# ) -# val_dict[k] = { -# "Train": { -# "MAE": (y_train_real - y_train_pred).abs().mean().item(), -# "RMSE": ( -# (((y_train_real - y_train_pred) ** 2).mean()) ** (1 / 2) -# ).item(), -# "r2": r2_score(y_train_real, y_train_pred) -# if y_train_pred.shape[0] > 1 -# else "Too few data points to calculate r2.", -# }, -# "Test": { -# "MAE": (y_test_real - y_test_pred).abs().mean().item(), -# "RMSE": ( -# (((y_test_real - y_test_pred) ** 2).mean()) ** (1 / 2) -# ).item(), -# "r2": r2_score(y_test_real, y_test_pred) -# if y_test_pred.shape[0] > 1 -# else "Too few data points to calculate r2.", -# }, -# } -# if parity_plots: -# parity_plot = self.create_parity_plot( -# datasets_pred=[y_train_pred, y_test_pred], -# datasets_real=[y_train_real, y_test_real], -# kwargs=kwargs, -# ) -# lst_parity_plots.append(parity_plot) -# if get_pred: -# return predictions -# return val_dict, lst_parity_plots - -# # ======================================================================= - -# def infer_model(self, dataset): - -# self.output_models = self._load_model(self.model_name) - -# self._model.eval() # set to evaluation mode (may be redundant) -# self._model.freeze_() # freeze the model, in order to predict using only their weight distribution means - -# infer_dict = {} -# for i, (k, v) in enumerate(self.output_models.items()): -# model_load_dirs = v["model_save_dirs"] -# self.data_transformation_dict = v["data_transformation_dict"] -# out_transform = self.data_transformation_dict[k] - -# X_infer = self._data_preprocess(inference=True, infer_dataset=dataset) -# X_infer = torch.tensor(X_infer).float() - -# device = torch.device("cuda" if torch.cuda.is_available() else "cpu") -# prediction_l = [] -# for m in model_load_dirs: -# model_load_dir = osp.join(self.save_path, m + "_BNN_model.pt") -# self._model.load_state_dict( -# torch.load(model_load_dir, map_location=torch.device(device)) -# ) -# data = X_infer.to(device) -# predictions = self._model(data).item() -# predictions = self._untransform_data( -# data=predictions, reduce=out_transform[0], divide=out_transform[1] -# ) -# prediction_l.append(predictions) -# prediction_l = torch.tensor(prediction_l) -# predictions = prediction_l.mean(axis=0).item() -# infer_dict[k] = predictions - -# return infer_dict diff --git a/summit/benchmarks/experiment_emulator/data/baumgartner_aniline_cn_crosscoupling.csv b/summit/benchmarks/experiment_emulator/data/baumgartner_aniline_cn_crosscoupling.csv deleted file mode 100644 index 53a7b3be..00000000 --- a/summit/benchmarks/experiment_emulator/data/baumgartner_aniline_cn_crosscoupling.csv +++ /dev/null @@ -1,98 +0,0 @@ -catalyst,base,base_equivalents,temperature,t_res,yield -DATA,DATA,DATA,DATA,DATA,DATA -tBuXPhos,DBU,2.18301549894049,30,328.717801570892,0.042832637648038 -tBuXPhos,BTMG,2.19088155603542,100,73.3311939239501,0.95968958853156 -tBuXPhos,TMG,1.09313819095541,47.5,75.1212968826293,0.031579429501285 -tBuXPhos,TMG,2.18627638191082,100,673.259508132934,0.766767922957078 -tBuXPhos,TEA,1.10876657088889,30,107.541151046752,0.072298978989668 -tBuXPhos,DBU,2.18301549894049,100,1088.51225948333,1.00869576600246 -tBuXPhos,DBU,1.09796637520676,100,1208.71113443374,1.0012137649806 -tBuXPhos,TEA,1.10876657088889,65,1061.64572238922,0.089740380763736 -tBuXPhos,BTMG,1.64316116702656,65,325.582622528076,0.91544691571872 -tBuXPhos,TEA,1.66314985633333,100,74.2942495346069,0.034514933659981 -tBuXPhos,BTMG,2.19088155603542,30,1290.76382732391,0.85455167620384 -tBuXPhos,BTMG,1.09544077801771,100,74.5662651062011,0.916912821722727 -tBuXPhos,BTMG,1.09544077801771,30,1256.02684068679,0.844733710048249 -tBuXPhos,TEA,2.21753314177777,65,1278.54612874984,0.087103149507884 -tBuXPhos,TMG,1.64740544270745,30,1119.23001670837,0.072638335760068 -tBuXPhos,TEA,2.21753314177777,30,74.0462350845336,0.011725953659552 -tBuXPhos,TMG,1.09313819095541,100,320.116309642791,0.25665356147935 -tBuXPhos,TMG,2.18627638191082,65,75.6613273620605,0.103883459712673 -tBuXPhos,DBU,1.09796637520676,100,1275.49295377731,1.02720318199391 -tBuXPhos,TEA,1.10876657088889,100,1065.21892690658,0.129264494933606 -tBuXPhos,TMG,2.18627638191082,100,1218.13267326354,0.89505248003316 -tBuXPhos,BTMG,2.19088155603542,100,1250.71853733062,1.00429073048366 -tBuXPhos,TMG,2.18627638191082,100,1290.1377916336,0.857250109532139 -tBuXPhos,DBU,1.09796637520676,100,1427.9566745758,1.02467154125893 -tBuXPhos,BTMG,1.09544077801771,100,1178.9814338684,1.00604039759223 -tBuXPhos,TEA,1.10876657088889,100,1400.80012130737,0.121821068910021 -tBuXPhos,BTMG,2.19088155603542,63.1,1163.43954467773,0.950525899329829 -tBuXPhos,DBU,2.18462989478322,63.1,1322.17462396621,0.833077140654568 -tBuXPhos,BTMG,1.57706267596803,100,503.98282623291,0.984074395272132 -tBuXPhos,DBU,1.53828968922606,100,493.421221733093,0.988433340519029 -tBuXPhos,TMG,2.06463160113265,100,551.720556735992,0.968792781124083 -tBuXPhos,TMG,2.18789318925998,100,456.421105861663,0.799241630269048 -tBuXPhos,DBU,1.09877834944718,100,460.241323947906,0.983315173979014 -tBuXPhos,BTMG,2.19250176902873,100,454.191978454589,0.988162074228893 -tBuBrettPhos,DBU,2.18944381215695,30,369.07010936737,0.366718886194757 -tBuBrettPhos,BTMG,2.19217570734463,100,74.5392632484436,1.03160028485775 -tBuBrettPhos,TMG,2.1864541690596,100,682.144016742706,0.979220428380853 -tBuBrettPhos,DBU,2.18944381215695,100,1250.1225028038,0.991085896376093 -tBuBrettPhos,TEA,1.14283782885996,30,73.8412232398986,0.170684679751242 -tBuBrettPhos,DBU,1.10063932178701,100,1273.82285833358,1.02399265478708 -tBuBrettPhos,TEA,1.14283782885996,65,1250.9315495491,0.023792025741625 -tBuBrettPhos,DBU,1.10063932178701,30,357.990475654602,0.514844459552494 -tBuBrettPhos,BTMG,1.64633276013432,65,320.097308635711,0.96728558881148 -tBuBrettPhos,TEA,1.65076575279773,100,74.5202622413635,0.02220432435262 -tBuBrettPhos,BTMG,1.10048981292401,100,75.7603335380554,1.01016224766721 -tBuBrettPhos,BTMG,1.10048981292401,30,1292.05090093612,1.02509762796796 -tBuBrettPhos,TEA,2.15869367673549,65,1061.79473114013,0.029545128286587 -tBuBrettPhos,TMG,1.65042024374177,30,1271.98775339126,0.075288426185652 -tBuBrettPhos,TEA,2.15869367673549,30,73.6222109794616,0.005340242004793 -tBuBrettPhos,TMG,1.10028016249451,100,326.534676551818,0.932317343758291 -tBuBrettPhos,TMG,2.1864541690596,65,74.1492409706115,0.039293957067321 -tBuBrettPhos,TEA,2.15869367673549,100,391.348383903503,0.066095339846277 -tBuBrettPhos,DBU,2.18944381215695,100,477.487310886383,1.03031512703677 -tBuBrettPhos,TMG,2.1864541690596,100,472.896048069,1.00336702855683 -tBuBrettPhos,DBU,1.14797864745526,100,532.961483478546,1.0259500031919 -tBuBrettPhos,TMG,1.98896798604777,100,476.994282722473,1.00621134623021 -tBuBrettPhos,TEA,1.14283782885996,100,448.690663814544,0.056448625545936 -tBuBrettPhos,DBU,1.10063932178701,57.1,1277.32905912399,0.421916561848111 -tBuBrettPhos,TMG,2.1864541690596,62.7,1072.45134067535,0.353419248066313 -tBuBrettPhos,BTMG,1.68154843414789,100,386.23709154129,0.998151429939476 -tBuBrettPhos,DBU,1.55036291563546,100,348.003904342651,1.02673546415045 -tBuBrettPhos,TMG,1.5939956200241,100,416.220806121826,0.924062878206402 -AlPhos,DBU,1.09145338882669,30,1257.92394924163,0.973793101036851 -AlPhos,TMG,1.09959019999812,65,75.2393035888671,0.208090936691246 -AlPhos,TEA,1.11531082302537,65,1071.11226415634,0.073308685966617 -AlPhos,BTMG,2.19414690973636,100,1263.4492650032,0.9427134690009 -AlPhos,DBU,2.19590027037751,100,73.5412063598632,0.979344250290655 -AlPhos,BTMG,1.10190637757685,30,75.1162962913513,0.929228973867738 -AlPhos,TEA,2.23062164605073,100,319.77228975296,0.232825162787732 -AlPhos,TEA,2.23062164605073,30,1365.50710248947,0.146225010098877 -AlPhos,DBU,2.19590027037751,65,1070.6502380371,0.986319855502312 -AlPhos,TMG,2.19918039999623,30,381.769835948944,0.04545397407633 -AlPhos,TEA,1.11531082302537,100,75.6613278388977,0.056712652877236 -AlPhos,TMG,2.19918039999623,65,75.4353146553039,0.156546245418694 -AlPhos,DBU,1.65017357596417,30,89.5111198425292,0.567666468585633 -AlPhos,BTMG,2.19414690973636,30,75.0472927093505,0.959137709355724 -AlPhos,BTMG,1.10190637757685,100,1279.13816261291,0.96408097822914 -AlPhos,TMG,1.09959019999812,30,327.669741630554,0.063736927306224 -AlPhos,TMG,1.64164170703944,100,1180.1865029335,0.994961147142112 -AlPhos,DBU,1.50724515599877,100,1214.58246994018,0.996941489366245 -AlPhos,TMG,1.62615452112397,100,1300.97441148757,0.989615629596472 -AlPhos,BTMG,1.58519864844389,100,1215.87754392623,0.94735294578709 -AlPhos,BTMG,1.59486449386123,100,1275.07693004608,0.971831102069182 -AlPhos,TMG,2.19918039999623,30,1369.51233148574,0.084292620472884 -AlPhos,DBU,1.70214754686067,100,1308.5398440361,0.99490864634812 -AlPhos,BTMG,1.10190637757685,88.5,1092.52948951721,0.927005687007816 -AlPhos,TMG,1.09959019999812,88.5,1393.36269569396,0.939708297977867 -tBuXPhos,TMG,2.18627638191082,63.1,1242.84908723831,0.31536670318976 -tBuXPhos,DBU,1.09796637520676,30,377.934616565704,0.093450374738737 -AlPhos,TEA,2.09120779317256,100,1350.93226861953,0.207359998748906 -AlPhos,BTMG,1.64319372094794,65,341.414527893066,0.9458049572347 -tBuBrettPhos,BTMG,1.10048981292401,100,526.4841132164,1.00080817597436 -tBuBrettPhos,TEA,1.14283782885996,30,75.3073072433471,0.005499146204924 -tBuBrettPhos,BTMG,2.19217570734463,30,1240.71996498107,1.01967151097374 -AlPhos,DBU,1.09145338882669,100,321.263375282287,0.959020869551022 -tBuBrettPhos,TMG,1.10028016249451,47.5,65.7707619667053,0.043402107312367 diff --git a/summit/benchmarks/experiment_emulator/data/baumgartner_aniline_cn_crosscoupling_descriptors.csv b/summit/benchmarks/experiment_emulator/data/baumgartner_aniline_cn_crosscoupling_descriptors.csv deleted file mode 100644 index 53a7b3be..00000000 --- a/summit/benchmarks/experiment_emulator/data/baumgartner_aniline_cn_crosscoupling_descriptors.csv +++ /dev/null @@ -1,98 +0,0 @@ -catalyst,base,base_equivalents,temperature,t_res,yield -DATA,DATA,DATA,DATA,DATA,DATA -tBuXPhos,DBU,2.18301549894049,30,328.717801570892,0.042832637648038 -tBuXPhos,BTMG,2.19088155603542,100,73.3311939239501,0.95968958853156 -tBuXPhos,TMG,1.09313819095541,47.5,75.1212968826293,0.031579429501285 -tBuXPhos,TMG,2.18627638191082,100,673.259508132934,0.766767922957078 -tBuXPhos,TEA,1.10876657088889,30,107.541151046752,0.072298978989668 -tBuXPhos,DBU,2.18301549894049,100,1088.51225948333,1.00869576600246 -tBuXPhos,DBU,1.09796637520676,100,1208.71113443374,1.0012137649806 -tBuXPhos,TEA,1.10876657088889,65,1061.64572238922,0.089740380763736 -tBuXPhos,BTMG,1.64316116702656,65,325.582622528076,0.91544691571872 -tBuXPhos,TEA,1.66314985633333,100,74.2942495346069,0.034514933659981 -tBuXPhos,BTMG,2.19088155603542,30,1290.76382732391,0.85455167620384 -tBuXPhos,BTMG,1.09544077801771,100,74.5662651062011,0.916912821722727 -tBuXPhos,BTMG,1.09544077801771,30,1256.02684068679,0.844733710048249 -tBuXPhos,TEA,2.21753314177777,65,1278.54612874984,0.087103149507884 -tBuXPhos,TMG,1.64740544270745,30,1119.23001670837,0.072638335760068 -tBuXPhos,TEA,2.21753314177777,30,74.0462350845336,0.011725953659552 -tBuXPhos,TMG,1.09313819095541,100,320.116309642791,0.25665356147935 -tBuXPhos,TMG,2.18627638191082,65,75.6613273620605,0.103883459712673 -tBuXPhos,DBU,1.09796637520676,100,1275.49295377731,1.02720318199391 -tBuXPhos,TEA,1.10876657088889,100,1065.21892690658,0.129264494933606 -tBuXPhos,TMG,2.18627638191082,100,1218.13267326354,0.89505248003316 -tBuXPhos,BTMG,2.19088155603542,100,1250.71853733062,1.00429073048366 -tBuXPhos,TMG,2.18627638191082,100,1290.1377916336,0.857250109532139 -tBuXPhos,DBU,1.09796637520676,100,1427.9566745758,1.02467154125893 -tBuXPhos,BTMG,1.09544077801771,100,1178.9814338684,1.00604039759223 -tBuXPhos,TEA,1.10876657088889,100,1400.80012130737,0.121821068910021 -tBuXPhos,BTMG,2.19088155603542,63.1,1163.43954467773,0.950525899329829 -tBuXPhos,DBU,2.18462989478322,63.1,1322.17462396621,0.833077140654568 -tBuXPhos,BTMG,1.57706267596803,100,503.98282623291,0.984074395272132 -tBuXPhos,DBU,1.53828968922606,100,493.421221733093,0.988433340519029 -tBuXPhos,TMG,2.06463160113265,100,551.720556735992,0.968792781124083 -tBuXPhos,TMG,2.18789318925998,100,456.421105861663,0.799241630269048 -tBuXPhos,DBU,1.09877834944718,100,460.241323947906,0.983315173979014 -tBuXPhos,BTMG,2.19250176902873,100,454.191978454589,0.988162074228893 -tBuBrettPhos,DBU,2.18944381215695,30,369.07010936737,0.366718886194757 -tBuBrettPhos,BTMG,2.19217570734463,100,74.5392632484436,1.03160028485775 -tBuBrettPhos,TMG,2.1864541690596,100,682.144016742706,0.979220428380853 -tBuBrettPhos,DBU,2.18944381215695,100,1250.1225028038,0.991085896376093 -tBuBrettPhos,TEA,1.14283782885996,30,73.8412232398986,0.170684679751242 -tBuBrettPhos,DBU,1.10063932178701,100,1273.82285833358,1.02399265478708 -tBuBrettPhos,TEA,1.14283782885996,65,1250.9315495491,0.023792025741625 -tBuBrettPhos,DBU,1.10063932178701,30,357.990475654602,0.514844459552494 -tBuBrettPhos,BTMG,1.64633276013432,65,320.097308635711,0.96728558881148 -tBuBrettPhos,TEA,1.65076575279773,100,74.5202622413635,0.02220432435262 -tBuBrettPhos,BTMG,1.10048981292401,100,75.7603335380554,1.01016224766721 -tBuBrettPhos,BTMG,1.10048981292401,30,1292.05090093612,1.02509762796796 -tBuBrettPhos,TEA,2.15869367673549,65,1061.79473114013,0.029545128286587 -tBuBrettPhos,TMG,1.65042024374177,30,1271.98775339126,0.075288426185652 -tBuBrettPhos,TEA,2.15869367673549,30,73.6222109794616,0.005340242004793 -tBuBrettPhos,TMG,1.10028016249451,100,326.534676551818,0.932317343758291 -tBuBrettPhos,TMG,2.1864541690596,65,74.1492409706115,0.039293957067321 -tBuBrettPhos,TEA,2.15869367673549,100,391.348383903503,0.066095339846277 -tBuBrettPhos,DBU,2.18944381215695,100,477.487310886383,1.03031512703677 -tBuBrettPhos,TMG,2.1864541690596,100,472.896048069,1.00336702855683 -tBuBrettPhos,DBU,1.14797864745526,100,532.961483478546,1.0259500031919 -tBuBrettPhos,TMG,1.98896798604777,100,476.994282722473,1.00621134623021 -tBuBrettPhos,TEA,1.14283782885996,100,448.690663814544,0.056448625545936 -tBuBrettPhos,DBU,1.10063932178701,57.1,1277.32905912399,0.421916561848111 -tBuBrettPhos,TMG,2.1864541690596,62.7,1072.45134067535,0.353419248066313 -tBuBrettPhos,BTMG,1.68154843414789,100,386.23709154129,0.998151429939476 -tBuBrettPhos,DBU,1.55036291563546,100,348.003904342651,1.02673546415045 -tBuBrettPhos,TMG,1.5939956200241,100,416.220806121826,0.924062878206402 -AlPhos,DBU,1.09145338882669,30,1257.92394924163,0.973793101036851 -AlPhos,TMG,1.09959019999812,65,75.2393035888671,0.208090936691246 -AlPhos,TEA,1.11531082302537,65,1071.11226415634,0.073308685966617 -AlPhos,BTMG,2.19414690973636,100,1263.4492650032,0.9427134690009 -AlPhos,DBU,2.19590027037751,100,73.5412063598632,0.979344250290655 -AlPhos,BTMG,1.10190637757685,30,75.1162962913513,0.929228973867738 -AlPhos,TEA,2.23062164605073,100,319.77228975296,0.232825162787732 -AlPhos,TEA,2.23062164605073,30,1365.50710248947,0.146225010098877 -AlPhos,DBU,2.19590027037751,65,1070.6502380371,0.986319855502312 -AlPhos,TMG,2.19918039999623,30,381.769835948944,0.04545397407633 -AlPhos,TEA,1.11531082302537,100,75.6613278388977,0.056712652877236 -AlPhos,TMG,2.19918039999623,65,75.4353146553039,0.156546245418694 -AlPhos,DBU,1.65017357596417,30,89.5111198425292,0.567666468585633 -AlPhos,BTMG,2.19414690973636,30,75.0472927093505,0.959137709355724 -AlPhos,BTMG,1.10190637757685,100,1279.13816261291,0.96408097822914 -AlPhos,TMG,1.09959019999812,30,327.669741630554,0.063736927306224 -AlPhos,TMG,1.64164170703944,100,1180.1865029335,0.994961147142112 -AlPhos,DBU,1.50724515599877,100,1214.58246994018,0.996941489366245 -AlPhos,TMG,1.62615452112397,100,1300.97441148757,0.989615629596472 -AlPhos,BTMG,1.58519864844389,100,1215.87754392623,0.94735294578709 -AlPhos,BTMG,1.59486449386123,100,1275.07693004608,0.971831102069182 -AlPhos,TMG,2.19918039999623,30,1369.51233148574,0.084292620472884 -AlPhos,DBU,1.70214754686067,100,1308.5398440361,0.99490864634812 -AlPhos,BTMG,1.10190637757685,88.5,1092.52948951721,0.927005687007816 -AlPhos,TMG,1.09959019999812,88.5,1393.36269569396,0.939708297977867 -tBuXPhos,TMG,2.18627638191082,63.1,1242.84908723831,0.31536670318976 -tBuXPhos,DBU,1.09796637520676,30,377.934616565704,0.093450374738737 -AlPhos,TEA,2.09120779317256,100,1350.93226861953,0.207359998748906 -AlPhos,BTMG,1.64319372094794,65,341.414527893066,0.9458049572347 -tBuBrettPhos,BTMG,1.10048981292401,100,526.4841132164,1.00080817597436 -tBuBrettPhos,TEA,1.14283782885996,30,75.3073072433471,0.005499146204924 -tBuBrettPhos,BTMG,2.19217570734463,30,1240.71996498107,1.01967151097374 -AlPhos,DBU,1.09145338882669,100,321.263375282287,0.959020869551022 -tBuBrettPhos,TMG,1.10028016249451,47.5,65.7707619667053,0.043402107312367 diff --git a/summit/benchmarks/experiment_emulator/data/reizman_2016_suzuki.xlsx b/summit/benchmarks/experiment_emulator/data/reizman_2016_suzuki.xlsx deleted file mode 100644 index db45a9dd..00000000 Binary files a/summit/benchmarks/experiment_emulator/data/reizman_2016_suzuki.xlsx and /dev/null differ diff --git a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case1.csv b/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case1.csv deleted file mode 100644 index 8e621c48..00000000 --- a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case1.csv +++ /dev/null @@ -1,98 +0,0 @@ -96,4,,,, - Catalyst, tres (s), T (ºC),Cat. Loading (mol%),TON,Yield (%) -P1-L3,600,30,0.498,1.1,0.6 -P1-L6,600,30,2.515,0.2,0.6 -P1-L4,60,30,2.508,0.2,0.6 -P1-L1,60,30,0.513,1.1,0.6 -P1-L2,600,30,2.513,0.2,0.6 -P1-L5,60,30,0.508,1.1,0.6 -P1-L7,600,30,0.506,1.1,0.6 -P2-L1,60,30,2.509,0.2,0.6 -P2-L1,600,110,0.496,8.5,4.3 -P1-L4,600,110,0.512,84.7,43.4 -P1-L6,60,110,0.498,1.1,0.6 -P1-L1,600,110,2.509,24,60.2 -P1-L5,600,110,2.512,16.7,42 -P1-L7,60,110,2.499,33.8,84.6 -P1-L2,60,110,0.508,16.9,8.5 -P1-L3,60,110,2.489,21.8,54.4 -P1-L7,189.7,65.3,1.123,0.5,0.6 -P1-L1,189.7,65.3,1.106,22.5,24.9 -P1-L6,600,65.3,2.515,0.2,0.6 -P2-L1,189.7,65.3,2.509,8.4,21.1 -P1-L4,189.7,65.3,2.508,21.2,53.1 -P1-L5,189.7,65.3,1.106,0.5,0.6 -P1-L3,600,65.3,1.106,5.1,5.6 -P1-L2,600,65.3,1.129,6.7,7.5 -P1-L4,600,110,1.106,82.6,91.3 -P1-L1,600,110,2.509,27.4,68.6 -P1-L2,189.7,110,2.513,21.1,52.9 -P1-L6,189.7,110,1.127,6.6,7.4 -P1-L7,600,110,2.499,30,75 -P1-L3,189.7,110,2.489,21.6,53.8 -P1-L5,600,110,2.512,18.9,47.6 -P2-L1,600,110,1.131,15,17 -P1-L4,600,30,0.512,1.1,0.6 -P1-L5,600,30,0.508,1.1,0.6 -P1-L1,600,30,0.513,1.1,0.6 -P2-L1,600,30,0.496,1.1,0.6 -P1-L2,60,110,2.513,16.6,41.9 -P1-L3,60,110,2.489,31.2,77.5 -P1-L6,60,110,2.515,3.4,8.5 -P1-L7,60,110,2.499,34.2,85.4 -P1-L4,60,67.5,2.508,13.4,33.4 -P1-L5,60,66.7,2.512,0.2,0.6 -P1-L3,60,67,2.489,9.8,24.4 -P1-L7,60,66.8,2.499,1.4,3.6 -P1-L1,60,66.3,2.509,4.9,12.4 -P2-L1,60,67,2.509,4.5,11.2 -P1-L7,155.6,110,2.499,32.5,81.3 -P1-L5,109.3,110,2.482,15.8,39.1 -P2-L1,104.5,110,2.509,11.3,28.4 -P1-L1,109.2,110,2.482,29.8,74.1 -P1-L3,166.5,110,2.489,24.5,60.9 -P1-L4,60,110,0.512,20.1,10.3 -P1-L7,60,110,0.506,1.1,0.6 -P1-L3,60,110,0.498,43.7,21.7 -P1-L1,60,110,0.513,40,20.5 -P1-L4,60,110,0.512,17,8.7 -P1-L3,600,110,0.968,24.5,23.7 -P1-L1,600,110,0.971,42.6,41.4 -P1-L5,600,110,0.957,40.6,38.8 -P1-L4,600,110,1.268,72.4,91.8 -P1-L7,600,110,0.814,46.6,38 -P1-L4,161.7,110,2.104,39.9,84 -P1-L1,146.1,110,2.509,27.7,69.6 -P1-L3,185.5,110,2.489,25.2,62.8 -P1-L7,176.5,110,2.499,27.5,68.6 -P1-L1,60,110,2.266,37.1,83.9 -P1-L4,60,110,1.915,34.4,65.7 -P1-L7,60,110,2.303,35,80.7 -P1-L3,60,110,2.323,27.7,64.4 -P1-L4,600,110,2.508,30.8,82.1 -P1-L4,600,110,2.508,31.9,80 -P1-L4,600,67.3,1.214,24.4,29.6 -P1-L4,600,68.7,1.268,16.1,20.4 -P1-L4,199.3,110,1.241,57.8,71.6 -P1-L1,202.8,110,1.592,44.6,70.9 -P1-L4,600,110,1.16,65.1,75.5 -P1-L4,600,110,1.16,71.4,82.7 -P1-L4,600,110,1.106,65.3,72.2 -P1-L4,600,110,1.106,83.9,92.8 -P1-L4,600,110,1.187,60.7,72.1 -P1-L4,600,110,1.106,73,80.7 -P1-L4,600,66.3,0.998,20.2,20.1 -P1-L4,600,67.6,0.998,18,17.9 -P1-L4,600,110,1.241,70.5,87.5 -P1-L4,600,110,1.268,63.2,80.2 -P1-L4,600,110,1.187,65.8,78.1 -P1-L4,189.1,110,2.508,39.4,98.7 -P1-L4,600,110,1.268,65.6,83.1 -P1-L4,199.8,110,2.508,33.5,83.9 -P1-L4,199.6,110,2.508,33.2,83.2 -P1-L4,600,110,1.241,62,76.9 -P1-L4,600,110,1.025,73.3,75 -P1-L4,600,110,1.079,81.2,87.6 -P1-L4,600,110,1.133,67,75.9 -P1-L4,600,110,1.052,65.4,68.7 -P1-L4,600,110,1.106,71.2,78.7 diff --git a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case2.csv b/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case2.csv deleted file mode 100644 index 24d2a7d9..00000000 --- a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case2.csv +++ /dev/null @@ -1,98 +0,0 @@ -96,4,,,, - Catalyst, tres (s), T (ºC),Cat. Loading (mol%),TON,Yield (%) -P1-L6,600,110,2.49,0,0.1 -P1-L5,60,110,0.51,0.2,0.1 -P1-L4,60,110,0.498,0.2,0.1 -P1-L7,600,110,2.489,2.3,5.7 -P1-L1,60,110,2.516,2.5,6.4 -P1-L2,60,110,2.516,4.4,11 -P1-L3,600,110,0.512,0.2,0.1 -P2-L1,600,110,0.507,0.2,0.1 -P1-L5,600,30,2.492,0,0.1 -P1-L4,600,30,2.516,0.2,0.5 -P1-L7,60,30,0.509,0.2,0.1 -P1-L6,60,30,0.492,0.2,0.1 -P1-L1,600,30,0.509,0.2,0.1 -P1-L3,60,30,2.505,0,0.1 -P2-L1,60,30,2.509,0,0.1 -P1-L2,600,30,0.492,0.2,0.1 -P2-L1,60,65.3,1.121,0.3,0.4 -P1-L4,189.7,65.3,2.516,0.4,1 -P1-L5,60,65.3,2.492,0,0.1 -P1-L1,189.7,65.3,1.131,5.2,5.9 -P1-L6,60,65.3,1.122,0.1,0.1 -P1-L2,189.7,65.3,1.128,7.8,8.9 -P1-L7,60,65.3,1.131,0.1,0.1 -P1-L3,60,65.3,2.505,4.7,11.8 -P1-L6,189.7,110,2.49,0,0.1 -P1-L5,189.7,110,1.111,7.2,8.2 -P1-L2,60,110,2.516,4.6,11.5 -P1-L3,189.7,110,1.131,9.2,10.5 -P2-L1,189.7,110,2.509,2.1,5.2 -P1-L1,60,110,2.516,5.4,13.5 -P1-L4,60,110,1.106,0.3,0.4 -P1-L7,189.7,110,2.489,4.6,11.7 -P1-L2,339.6,110,2.516,6.4,16.1 -P1-L4,351.3,110,2.516,1,2.4 -P1-L5,370.2,110,2.492,11.1,28 -P1-L1,340.3,110,2.516,6.5,16.3 -P1-L7,600,33.8,2.489,0,0.1 -P2-L1,600,33.4,2.509,0.5,1.2 -P1-L3,600,30,2.047,0.1,0.1 -P1-L6,600,30,2.49,0,0.1 -P1-L7,149,110,2.489,11.2,28.1 -P1-L5,156.7,110,2.492,6.5,16.4 -P1-L3,162.3,110,2.505,6.7,16.9 -P1-L1,172.3,107.8,2.516,7.9,19.9 -P1-L2,177.6,95.1,2.516,5.2,13 -P1-L1,222.1,110,0.792,10.9,8.5 -P1-L2,192.5,110,2.169,5.4,11.6 -P1-L7,155.6,110,1.923,2.8,5.4 -P1-L5,184.7,110,2.011,9.1,18.6 -P1-L3,262.1,56.1,0.754,7,5.5 -P1-L3,203.4,81.9,2.505,7.2,18 -P1-L2,190,93.8,2.516,5.6,14.2 -P1-L5,184.5,110,2.492,7.2,18.1 -P1-L1,213.2,110,2.516,9.8,24.6 -P1-L7,157.7,110,2.489,2.7,6.8 -P1-L1,261,110,2.516,10.3,26 -P1-L5,206.5,110,2.492,9.7,24.5 -P1-L7,166.9,110,2.489,4.3,10.8 -P1-L3,198.4,100.7,2.505,6.9,17.3 -P1-L2,600,110,1.938,8.3,15.9 -P1-L3,600,110,1.993,9.4,18.5 -P1-L1,600,110,1.781,13.3,24 -P1-L5,600,110,1.951,15.5,30.6 -P1-L5,600,110,1.951,15.3,30.2 -P1-L1,600,110,1.385,14.7,20.2 -P1-L3,375.4,97.2,1.94,8.8,16.9 -P1-L3,600,103.3,2.505,8.9,22.3 -P1-L1,600,110,2.516,13,32.6 -P1-L5,600,110,2.011,19.7,40.1 -P1-L5,600,110,2.492,16.7,42 -P1-L1,60,30,2.516,0,0.1 -P1-L1,60,30,2.516,0.2,0.4 -P1-L5,600,110,2.492,18.9,47.6 -P1-L1,600,47.1,2.516,16.6,41.9 -P1-L5,600,71,2.492,0,0.1 -P1-L5,600,110,2.492,16.7,42 -P1-L2,600,39.8,2.516,0.4,1.1 -P1-L3,600,38.1,2.505,1.8,4.6 -P1-L1,600,61,2.516,5.6,14.2 -P1-L3,600,69.4,2.505,9.7,24.4 -P1-L1,600,63,2.516,6.3,15.7 -P1-L1,600,110,2.516,5.6,14 -P1-L5,600,110,2.492,18.1,45.4 -P1-L5,600,110,2.492,15.2,38.4 -P1-L3,600,110,2.505,10,25 -P1-L5,600,110,1.711,15.1,26.2 -P1-L1,600,110,2.516,6.8,17.2 -P1-L5,600,110,2.492,16.3,41.1 -P1-L1,600,110,2.516,6.8,17.1 -P1-L1,600,110,2.516,7,17.7 -P1-L5,600,110,2.492,18,45.2 -P1-L5,600,110,1.771,19.4,34.8 -P1-L1,600,30,2.488,1,2.5 -P1-L1,600,30,2.488,1.3,3.2 -P1-L5,600,110,2.492,17.5,44 -P1-L5,600,110,1.921,20.3,38.9 diff --git a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case3.csv b/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case3.csv deleted file mode 100644 index e611e44b..00000000 --- a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case3.csv +++ /dev/null @@ -1,98 +0,0 @@ -96,4,,,, - Catalyst, tres (s), T (ºC),Cat. Loading (mol%),TON,Yield (%) -P1-L4,60,30,2.513,0.1,0.2 -P1-L2,600,30,2.494,0.1,0.2 -P1-L1,60,30,0.51,0.3,0.2 -P1-L5,600,30,2.511,0.1,0.2 -P1-L6,60,30,0.499,0.3,0.2 -P1-L7,600,30,0.501,0.3,0.2 -P1-L3,60,30,2.512,0.1,0.2 -P2-L1,600,30,0.509,0.3,0.2 -P2-L1,60,110,2.515,32.8,82.6 -P1-L5,60,110,0.508,0.3,0.2 -P1-L4,600,110,0.514,0.3,0.2 -P1-L6,600,110,2.496,0.1,0.2 -P1-L3,600,110,0.503,50.6,25.4 -P1-L7,60,110,2.504,16.9,42.2 -P1-L2,60,110,0.51,46.3,23.6 -P1-L1,600,110,2.493,36.6,91.3 -P1-L3,189.7,110,1.117,77.4,86.5 -P2-L1,189.7,110,2.515,34.3,86.4 -P1-L6,189.7,110,2.496,0.1,0.2 -P1-L5,60,110,1.106,4,4.4 -P1-L1,189.7,110,2.493,31.6,78.8 -P1-L4,189.7,110,1.114,2.6,2.9 -P1-L2,60,110,2.494,34.7,86.7 -P1-L6,60,65.3,1.109,0.1,0.2 -P1-L7,60,110,2.504,19.9,49.9 -P1-L2,189.7,65.3,1.106,3.9,4.3 -P1-L5,189.7,65.3,2.511,2,5.1 -P1-L1,60,65.3,1.105,6.9,7.6 -P1-L3,60,65.3,2.512,8.8,22.1 -P1-L7,189.7,65.3,1.113,0.7,0.8 -P1-L4,60,65.3,2.513,0.3,0.7 -P2-L1,60,65.3,1.13,6.1,6.9 -P1-L4,600,105.1,2.513,1.6,4.1 -P1-L1,600,110,2.352,32.6,76.6 -P1-L2,600,110,2.438,33,80.3 -P1-L3,600,110,2.317,37.7,87.4 -P2-L1,600,110,2.345,34.3,80.3 -P1-L7,600,110,2.393,20.9,49.9 -P1-L5,600,71.7,1.196,0.1,0.2 -P1-L5,600,48.3,0.748,0.2,0.2 -P1-L7,124.3,110,1.113,9.8,10.9 -P1-L2,202.9,110,1.219,51.4,62.6 -P2-L1,160.9,110,1.074,55.6,59.7 -P1-L1,123.2,110,1.105,77.6,85.8 -P1-L3,600,83.8,1.061,48.6,51.7 -P2-L1,60,110,1.413,31.1,43.9 -P1-L7,60,110,1.419,24.8,35.1 -P1-L2,60,110,1.672,53.1,88.8 -P1-L3,60,110,1.312,59.8,78.4 -P1-L1,60,110,1.417,61.8,87.5 -P1-L2,186.8,110,2.494,30.3,75.4 -P1-L1,149.9,110,2.493,32,79.8 -P2-L1,186.8,103.6,2.515,33.2,83.4 -P1-L3,179.9,110,2.512,34.4,86.5 -P1-L1,60,110,1.502,56.6,85 -P1-L2,60,110,1.927,43.6,84.2 -P1-L3,137.9,110,1.312,60.6,79.4 -P1-L3,60,110,1.647,49.5,81.4 -P1-L1,177.6,110,1.048,77.4,81.1 -P1-L2,188.8,110,1.446,49.5,71.5 -P1-L3,211.9,110,1.368,59.9,82 -P1-L2,239.7,110,1.332,51.2,68.2 -P1-L1,253.3,110,1.048,83,87 -P1-L1,108.9,110,1.275,65.3,83.3 -P1-L3,92.2,110,1.787,50.5,90.2 -P1-L2,66.6,110,2.409,35.8,86.4 -P1-L3,192.1,110,1.731,48.1,83.3 -P1-L1,221.3,110,1.077,75.9,81.7 -P1-L2,192.7,110,1.871,41.5,77.7 -P1-L1,180.1,110,1.303,65.1,84.9 -P1-L2,144,110,1.899,44.5,84.6 -P1-L3,146.6,110,2.038,43,87.7 -P1-L1,60,110,2.493,34.4,85.9 -P1-L3,101.5,110,1.926,46.9,90.4 -P1-L2,60,110,2.126,38.3,81.4 -P1-L1,218.5,110,1.105,80.8,89.4 -P1-L2,135.7,110,1.814,40.5,73.5 -P1-L1,600,110,0.935,85.6,79.9 -P1-L3,147.9,110,1.591,52.1,82.9 -P1-L2,162.9,110,1.701,40,68 -P1-L3,162.1,110,1.675,53.8,90.1 -P1-L1,600,110,1.218,74.3,90.6 -P1-L3,600,110,1.424,49.3,70.1 -P1-L2,600,110,1.417,66.4,94.1 -P1-L3,60,110,1.926,45.4,87.6 -P1-L1,600,110,1.09,80.1,87.3 -P1-L2,60,110,1.757,44.3,77.9 -P1-L3,600,110,1.787,45.3,81 -P1-L2,600,110,1.616,52.3,84.5 -P1-L1,600,110,1.303,64.4,84 -P1-L1,600,110,1.218,65.4,79.6 -P1-L2,600,110,1.587,47.2,75 -P1-L3,600,110,1.787,43.6,78 -P1-L3,60,40.2,0.503,0.3,0.2 -P1-L3,60,40.1,0.503,0.3,0.2 -P1-L3,229.2,110,1.619,49.6,80.1 diff --git a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case4.csv b/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case4.csv deleted file mode 100644 index f1a79c40..00000000 --- a/summit/benchmarks/experiment_emulator/data/reizman_suzuki_case4.csv +++ /dev/null @@ -1,99 +0,0 @@ -97,4,,,, - Catalyst, tres (s), T (ºC),Cat. Loading (mol%),TON,Yield (%) -P1-L6,600,110,2.504,11.7,29.4 -P1-L5,600,110,2.499,21.4,53.6 -P1-L7,60,110,2.491,9.5,23.7 -P1-L3,60,110,0.502,129.2,64.8 -P2-L1,600,110,0.506,99.3,50.3 -P1-L2,600,110,0.511,107.8,55.1 -P1-L4,60,110,0.489,32.4,15.8 -P1-L1,60,110,2.501,37.6,94.1 -P1-L1,600,30,0.5,2.9,1.5 -P1-L6,60,30,0.501,0.2,0.1 -P2-L1,60,30,2.508,1.6,4 -P1-L7,600,30,0.503,0.2,0.1 -P1-L5,60,30,0.5,0.2,0.1 -P1-L4,600,30,2.492,4.6,11.5 -P1-L2,60,30,2.507,0,0.1 -P1-L3,600,30,2.51,2.7,6.9 -P2-L1,600,65.3,2.508,38.1,95.5 -P1-L1,600,65.3,1.12,65.3,73.1 -P1-L6,189.7,65.3,1.127,1.3,1.4 -P1-L4,600,65.3,2.492,29.7,74.1 -P1-L2,189.7,65.3,2.507,36.4,91.3 -P1-L7,600,65.3,1.126,0.7,0.8 -P1-L3,189.7,65.3,1.123,60.8,68.3 -P1-L5,189.7,65.3,1.131,1.3,1.5 -P1-L1,189.7,110,2.501,34.9,87.2 -P1-L4,189.7,110,1.124,50.6,56.9 -P1-L6,600,110,2.504,16.1,40.4 -P1-L3,600,110,2.51,32.8,82.2 -P1-L7,189.7,110,2.491,11.6,28.8 -P1-L2,600,110,1.12,72.2,80.9 -P1-L5,600,110,2.499,25.7,64.3 -P2-L1,189.7,110,1.109,80.6,89.4 -P1-L5,114.7,110,1.079,31.4,33.9 -P1-L6,114.7,110,1.077,21.4,23 -P1-L7,250.1,110,0.982,26.8,26.3 -P2-L1,150.3,71.6,1.037,27.7,28.7 -P1-L2,145.8,81.2,1.071,74.9,80.2 -P1-L4,226.1,69.5,1.148,8.1,9.2 -P1-L3,326.4,109.2,0.932,96.1,89.6 -P1-L1,168.9,89.8,0.858,100.7,86.4 -P1-L1,600,61.9,2.501,37.8,94.4 -P1-L2,227.6,101.6,2.507,33.6,84.1 -P1-L4,600,83.7,2.492,35.9,89.4 -P1-L5,60,108.5,2.499,19.4,48.4 -P1-L3,600,75.7,2.51,36.1,90.5 -P2-L1,182.6,104,2.508,34.1,85.5 -P1-L2,600,61.5,1.387,59.5,82.6 -P1-L1,600,106.8,1.215,72.5,88.1 -P1-L3,600,84.7,1.793,48.3,86.5 -P2-L1,600,96.5,1.977,41.3,81.8 -P1-L5,600,110,1.236,34.8,43 -P1-L2,600,73.7,2.507,35.1,88 -P1-L3,134.4,110,1.53,55.8,85.3 -P2-L1,196.1,91.7,2.05,42.1,86.2 -P1-L1,227.9,106.5,0.786,108.5,85.3 -P2-L1,260.4,88.2,2.098,40,83.9 -P1-L2,600,80.8,1.996,47.6,95 -P1-L3,169.1,98.5,2.056,39.4,81 -P1-L1,236.9,105.3,0.739,106.8,78.9 -P1-L1,60,70.4,1.715,39.1,67 -P1-L3,60,82.1,2.295,40,91.8 -P1-L2,60,85.6,2.507,34.5,86.6 -P1-L1,600,97.7,0.715,115.4,82.5 -P1-L2,600,72.8,1.314,66.2,87 -P1-L3,319.6,94.9,1.171,71.4,83.6 -P1-L1,299.9,73.5,2.501,39.9,99.8 -P1-L3,237.1,95.6,1.554,51.4,79.9 -P1-L2,600,87,1.801,46.9,84.6 -P1-L2,196,110,1.412,59.9,84.5 -P1-L1,202.8,108.8,1.358,49.5,67.3 -P1-L2,205.1,76.3,1.655,50,82.7 -P1-L1,222.9,74.7,1.572,51.9,81.6 -P1-L1,167.6,73.2,2.287,38.4,87.9 -P1-L2,200.4,75.8,1.947,50.7,98.7 -P1-L2,600,84.2,2.507,35.5,88.9 -P1-L3,600,98.2,2.51,33,82.8 -P1-L1,600,97.7,2.501,33.5,83.8 -P1-L2,600,70.7,1.144,69.3,79.3 -P1-L3,149.9,93,2.51,33.6,84.2 -P1-L1,600,96.7,0.739,105.3,77.8 -P1-L3,216.2,105.7,1.386,61.7,85.6 -P1-L1,600,97.3,0.715,118.5,84.7 -P1-L1,600,88.6,0.977,87.6,85.6 -P1-L2,600,77.4,1.193,66.2,78.9 -P1-L2,600,77.2,1.314,67.3,88.4 -P1-L3,126.4,97.6,2.51,28.9,72.6 -P1-L2,276.4,69.3,2.507,39.7,99.5 -P1-L1,60,110,0.643,129.4,83.2 -P1-L1,60,110,0.667,105.1,70.1 -P1-L2,258.2,71.6,2.507,33.7,84.5 -P1-L2,211.7,104.7,1.193,65.2,77.8 -P1-L1,113.3,110,1.12,81.4,91.1 -P1-L2,600,58.7,2.507,34.4,86.3 -P1-L1,60,110,1.096,86.3,94.5 -P1-L1,154.1,110,1.096,80.9,88.6 -P1-L2,600,72.4,2.507,33.7,84.4 -P1-L1,60,110,0.977,55.5,54.2 diff --git a/summit/benchmarks/experiment_emulator/emulator.py b/summit/benchmarks/experiment_emulator/emulator.py deleted file mode 100644 index cefa3f6d..00000000 --- a/summit/benchmarks/experiment_emulator/emulator.py +++ /dev/null @@ -1,366 +0,0 @@ -from abc import ABC, abstractmethod - -import os -import os.path as osp -import numpy as np -import json - -from sklearn.model_selection import train_test_split as sklearn_train_test_split -import sklearn.preprocessing - -import matplotlib.pyplot as plt - -class Emulator(ABC): - """Base class for emulator training - - Parameters - --------- - domain: summit.domain.Domain - The domain of the experiment - dataset: summit.utils.dataset.Dataset - The data points obtained from an experiment the emulator - is trained on. - model_name: string, optional - Name of the model that is used for saving model parameters. Should be unique. - By default: "dataset_emulator_model_name" - - Notes - ----- - Developers that subclass `Experiment` need to implement - `_run`, which runs the experiments. - - """ - - def __init__(self, domain, dataset, model_name, kwargs={}): - - self._domain = domain - self._dataset = dataset - self.model_name = str(model_name) - self._cat_to_descr = kwargs.get("cat_to_descr", False) - - self._domain_preprocess() - - @property - def domain(self): - """The domain for the experiment""" - return self._domain - - @property - def dataset(self): - """Dataset of all experiments trained on""" - return self._dataset - - @property - def model(self): - """Model that is trained""" - return self._model - - @abstractmethod - def _setup_model(self, **kwargs): - """ Setup model structure. - - Arguments - --------- - - Returns - ------- - model - Should return a regression model that can be trained on experimental data. - """ - - raise NotImplementedError("_steup_model be implemented by subclasses of Emulator") - - @abstractmethod - def train_model(self, verbose=True, parity_plot=False): - """ Train model on a given Summit Dataset. - - Arguments - --------- - - Returns - ------- - model - Should return a regression model that is trained on experimental data. - """ - - raise NotImplementedError("_train_model be implemented by subclasses of Emulator") - - @abstractmethod - def validate_model(self): - """ Validate a model on a given Summit Dataset. - - Arguments - --------- - - Returns - ------- - model - Should return evaluation values w.r.t. the accuracy of the - regression model. - """ - - raise NotImplementedError("_validate_model be implemented by subclasses of Emulator") - - @abstractmethod - def infer_model(self): - raise NotImplementedError("_infer_model be implemented by subclasses of Emulator") - - @abstractmethod - def _save_model(self, **kwargs): - raise NotImplementedError("_save_model be implemented by subclasses of Emulator") - - def _domain_preprocess(self, **kwargs): - - self.input_dim = 0 - self.output_dim = 0 - self.out_mean = np.asarray([]) - self.output_models = {} - input_names_continuous, input_names_categorical, input_names_descriptors = [], [], [] - - for i, v in enumerate(self._domain.variables): - if not v.is_objective: - if v.variable_type == "continuous": - self.input_dim += 1 - input_names_continuous.append(v.name) - elif v.variable_type == "descriptors" or (v.variable_type == "categorical" and self._cat_to_descr == True): - if v.ds is None: - raise ValueError("No descriptors are defined for categorical variable {}".format(v.name)) - self.input_dim += v.num_descriptors - input_names_descriptors.extend(v.ds.data_columns) - elif v.variable_type == "categorical": - self.input_dim += len(v.levels) - input_names_categorical.append(v.name) - # create one-hot tensor for categorical inputs - else: - raise TypeError("Unknown variable type: {}.".format(v.variable_type)) - else: - if v.variable_type == "continuous": - self.output_dim += 1 - self.output_models[v.name] = "" - elif v.variable_type == "categorical": - raise TypeError( - "{} is a categorical variable. BNN regressor not trainable for categorical outputs.".format(v.name)) - elif v.variable_type == "descriptors": - raise TypeError( - "{} is a descriptor variable. BNN regressor not trainable for descriptor outputs.".format( - v.name)) - else: - raise TypeError("Unknown variable type: {}.".format(v.variable_type)) - self.input_names = [] - self.input_names_transformable = input_names_continuous + input_names_descriptors - self.input_names = self.input_names_transformable + input_names_categorical - - def _data_preprocess( - self, inference=False, infer_dataset=None, validate=False, transform_input="standardize", - transform_output="standardize", test_size=0.1, shuffle=False, kwargs={} - ): - if not inference: - np_dataset = self._dataset.data_to_numpy() - data_column_names = self._dataset.data_columns - else: - np_dataset = infer_dataset.data_to_numpy() - if not validate: - data_column_names = [c[0] for c in infer_dataset.data_columns] - else: - data_column_names = infer_dataset.data_columns - - self.input_data_continuous = [] - self.input_data_categorical = [] - self.input_data_descriptors = [] - self.output_data = [] - if not inference: - self.data_transformation_dict = {} - - # this loop makes sure that the inputs are always in the same order and only - # data with the same column names as in the domain is considered - for v in self._domain.variables: - v_in_dataset = False - for i, c_name in enumerate(data_column_names): - if c_name == v.name: - v_in_dataset = True - if not v.is_objective: - if v.variable_type == "continuous": - # Standardize continuous inputs - tmp_cont_inp = np.asarray(np_dataset[:, i], dtype=float) - if not inference: - tmp_cont_inp, _reduce, _divide = self._transform_data(data=tmp_cont_inp, transformation_type=transform_input) - self.data_transformation_dict[v.name] = [_reduce, _divide] - else: - tmp_cont_inp, _, _ = self._transform_data(data=tmp_cont_inp, reduce=self.data_transformation_dict[v.name][0], divide=self.data_transformation_dict[v.name][1]) - self.input_data_continuous.append(tmp_cont_inp) - elif v.variable_type == "descriptors" or (v.variable_type == "categorical" and self._cat_to_descr == True): - tmp_descr_inp = [] - for ent in np_dataset[:, i]: - tmp_descr_inp.append(v.ds.loc[[ent], :].values[0].tolist()) - tmp_descr_inp = np.asarray(tmp_descr_inp) - for i in range(len(tmp_descr_inp[0])): - if not inference: - tmp_descr_inp[:, i], _reduce, _divide = self._transform_data(data=tmp_descr_inp[:, i], transformation_type=transform_input) - self.data_transformation_dict[v.ds.data_columns[i]] = [_reduce, _divide] - else: - tmp_descr_inp[:, i], _, _ = self._transform_data(data=tmp_descr_inp[:, i], reduce=self.data_transformation_dict[v.ds.data_columns[i]][0], divide=self.data_transformation_dict[v.ds.data_columns[i]][1]) - self.input_data_descriptors.append(np.asarray(tmp_descr_inp)) - elif v.variable_type == "categorical": - # create one-hot tensor for categorical inputs - one_hot_enc = sklearn.preprocessing.OneHotEncoder(categories=[v.levels]) - tmp_disc_inp_one_hot = one_hot_enc.fit_transform(np_dataset[:, i].reshape(-1, 1)).toarray() - self.input_data_categorical.append(np.asarray(tmp_disc_inp_one_hot)) - else: - raise TypeError("Unknown variable type: {}.".format(v.variable_type)) - elif not inference: - if v.variable_type == "continuous": - tmp_cont_out = np.asarray(np_dataset[:, i], dtype=float) - if not inference: - tmp_cont_out, _reduce, _divide = self._transform_data(data=tmp_cont_out, transformation_type=transform_output) - self.data_transformation_dict[v.name] = [_reduce, _divide] - self.output_data.append(tmp_cont_out) - elif v.variable_type == "categorical": - raise TypeError( - "{} is a categorical variable. Regressor not trainable for categorical outputs.".format( - v.name)) - elif v.variable_type == "descriptors": - raise TypeError( - "{} is a descriptor variable. Regressor not trainable for descriptor outputs.".format( - v.name)) - else: - raise TypeError("Unknown variable type: {}.".format(v.variable_type)) - elif inference and v.is_objective: - v_in_dataset = True - if v_in_dataset == False: - raise ValueError("Variable {} defined in the domain is missing in the given dataset.".format(v.name)) - - self.input_data_continuous = np.asarray(self.input_data_continuous).transpose() - if len(self.input_data_categorical) != 0: - self.input_data_categorical = np.concatenate([one_hot for one_hot in self.input_data_categorical], axis=1) - if len(self.input_data_descriptors) != 0: - self.input_data_descriptors = np.concatenate([d for d in self.input_data_descriptors], axis=1) - self.output_data = np.asarray(self.output_data).transpose() - - # Set up training and test data - if not inference: - final_np_dataset = np.concatenate([inp for inp in [self.input_data_continuous, self.input_data_descriptors, - self.input_data_categorical, self.output_data] if len(inp) != 0], axis=1) - X, y = final_np_dataset[:, :-self.output_dim], final_np_dataset[:, -self.output_dim:] - X_train, X_test, y_train, y_test = sklearn_train_test_split(X, y, test_size=test_size, shuffle=shuffle) - return [X_train.astype(dtype=float), y_train.astype(dtype=float)], [X_test.astype(dtype=float), - y_test.astype(dtype=float)] - else: - X = np.concatenate([inp for inp in [self.input_data_continuous, self.input_data_descriptors, self.input_data_categorical] if len(inp) != 0], axis=1) - return X.astype(dtype=float) - - def _transform_data(self, data, transformation_type=None, reduce=None, divide=None, infer=False, kwargs={}): - """ Transform data according to transformation type (standardize, normalize)""" - if not infer: - if transformation_type == "standardize": - tmp_reduce = data.mean() - tmp_divide = data.std() - elif transformation_type == "normalize": - tmp_reduce = np.float64(0) - tmp_divide = data.mean() - elif transformation_type == "min_max": - min, max = kwargs.get("min", 0), kwargs.get("max", 1) - tmp_reduce = np.float64(min) - tmp_divide = np.float64(max - min) - else: - tmp_reduce = reduce if reduce else np.float64(0) - tmp_divide = divide if divide else np.float64(1) - else: - tmp_reduce, tmp_divide = reduce, divide - if tmp_divide == 0: - tmp_divide = 1 - print("Warning: denumerator in data transformation is 0, hence it is ignored and set to 1.") - transf_data = (data - tmp_reduce) / tmp_divide - return transf_data, tmp_reduce, tmp_divide - - def _untransform_data(self, data, reduce=None, divide=None): - """ Untransform data -> revert _transform_data""" - tmp_reduce, tmp_divide = reduce, divide - untransf_data = data * tmp_divide + tmp_reduce - return untransf_data - - def _save_model(self): - filename = osp.join(self.save_path, self.model_name + ".json") - """Save a strategy to a JSON file""" - with open(filename, "w") as f: - json.dump(self.output_models, f) - - def _load_model(self, model_name): - filename = osp.join(self.save_path, model_name + ".json") - """Load a strategy from a JSON file""" - with open(filename, "r") as f: - output_model = json.load(f) - return output_model - - def _check_file_path(self, file_path): - """ Check whether a file with the path already exist. If yes, it asks the user, whether the existing file should be overwritten. """ - if osp.isfile(file_path): - print("Warning: The file {} already exist.".format(file_path)) - valid_input = False - while not valid_input: - tmp_input = str(input("Do you want to overwrite this file? If yes, type \'y\' or \'yes\', else type \'n\' or \'no\': ")) - if tmp_input in ["y", "yes"]: - overwrite = True - valid_input = True - elif tmp_input in ["n", "no"]: - overwrite = False - valid_input = True - if not overwrite: - return False - return True - - - def create_parity_plot(self, datasets_real=None, datasets_pred=None, **kwargs): - """ Make a parity plot of the training and test dataset - - Parameters - ---------- - ax: `matplotlib.pyplot.axes`, optional - An existing axis to apply the plot to - y_pred: np-array, optional - Prediction values for y. - y_real: np-array, optional (required if y_pred != None) - Real values for y. - - Returns - ------- - if ax is None returns a tuple with the first component - as the a new figure and the second component the axis - - if ax is a matplotlib axis, returns only the axis - - Raises - ------ - ValueError - If there are no points to plot - """ - if datasets_pred == None or datasets_real == None: - raise ValueError("No points to plot.") - if (len(datasets_pred) != len(datasets_real)): - raise ValueError("Number of datasets with real points does not correspond to number of datasets with prediction points.") - - - ax = kwargs.get("ax", None) - - if ax is None: - fig, ax = plt.subplots(1) - return_fig = True - else: - return_fig = False - - marker_symbols = ["o", "x", "s", "p", "h", "+", "8"] - for i in range(len(datasets_pred)): - y_pred, y_real = datasets_pred[i], datasets_real[i] - if len(y_pred) != len(y_real): - raise ValueError("Number of real data points does not correspond to number of prediction data points.") - marker_symbol = marker_symbols[i] if i < len(marker_symbols) else marker_symbols[0] - ax.scatter(np.asarray(y_real), np.asarray(y_pred), marker=marker_symbol) - - ax.set_xlabel("Experimental y", fontsize=16) - ax.set_ylabel("Predicted y", fontsize=16) - x = np.linspace(*ax.get_xlim()) - ax.plot(x,x, c="black", linestyle="--", label="_nolegend_", zorder=0) - - if return_fig: - return fig, ax - else: - return ax \ No newline at end of file diff --git a/summit/benchmarks/experiment_emulator/trained_models/BNN/baumgartner_aniline_cn_crosscoupling.json b/summit/benchmarks/experiment_emulator/trained_models/BNN/baumgartner_aniline_cn_crosscoupling.json deleted file mode 100644 index 57a086e8..00000000 --- a/summit/benchmarks/experiment_emulator/trained_models/BNN/baumgartner_aniline_cn_crosscoupling.json +++ /dev/null @@ -1 +0,0 @@ -{"yld": {"model_save_dirs": ["baumgartner_aniline_cn_crosscoupling_yield_1", "baumgartner_aniline_cn_crosscoupling_yield_2", "baumgartner_aniline_cn_crosscoupling_yield_3", "baumgartner_aniline_cn_crosscoupling_yield_4", "baumgartner_aniline_cn_crosscoupling_yield_5", "baumgartner_aniline_cn_crosscoupling_yield_6", "baumgartner_aniline_cn_crosscoupling_yield_7", "baumgartner_aniline_cn_crosscoupling_yield_8", "baumgartner_aniline_cn_crosscoupling_yield_9", "baumgartner_aniline_cn_crosscoupling_yield_10"], "Final train MAE": 0.05946772173047066, "Final 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b/summit/benchmarks/experimental_emulator.py @@ -1,160 +1,1205 @@ -import os -import os.path as osp - -from summit.experiment import Experiment - -import numpy as np - -# from summit.benchmarks.experiment_emulator.bnn_emulator import BNNEmulator from summit.utils.dataset import DataSet from summit.domain import * +from summit.experiment import Experiment +from summit import get_summit_config_path from summit.utils import jsonify_dict, unjsonify_dict +import torch +import torch.nn.functional as F +from skorch import NeuralNetRegressor +from skorch.utils import to_device + +from sklearn.compose import ColumnTransformer, TransformedTargetRegressor +from sklearn.pipeline import Pipeline +from sklearn.preprocessing import StandardScaler, OneHotEncoder, FunctionTransformer +from sklearn.model_selection import ( + train_test_split, + cross_validate, + GridSearchCV, + ParameterGrid, +) +from sklearn.model_selection._search import BaseSearchCV, _check_param_grid +from sklearn.base import BaseEstimator, RegressorMixin, is_classifier, clone +from sklearn.model_selection._split import check_cv +from sklearn.model_selection._validation import ( + _fit_and_score, + _score, + _aggregate_score_dicts, +) +from sklearn.metrics import r2_score +from sklearn.utils.validation import ( + _deprecate_positional_args, + indexable, + check_is_fitted, + _check_fit_params, +) +from sklearn.utils import check_array, _safe_indexing +from sklearn.utils.fixes import delayed +from sklearn.metrics._scorer import _check_multimetric_scoring + +from tqdm.auto import tqdm +from joblib import Parallel +import pathlib +import numpy as np +from numpy.random import default_rng +import pandas as pd +from copy import deepcopy +from itertools import product +from collections import defaultdict +from copy import deepcopy +import pkg_resources +import time +import json +import types +import warnings + +__all__ = [ + "ExperimentalEmulator", + "ANNRegressor", + "get_bnn", + "RegressorRegistry", + "registry", + "get_pretrained_reizman_suzuki_emulator", + "get_pretrained_baumgartner_cc_emulator", + "ReizmanSuzukiEmulator", + "BaumgartnerCrossCouplingEmulator", +] + class ExperimentalEmulator(Experiment): """Experimental Emulator - Parameters - --------- - domain: summit.domain.Domain - The domain of the experiment - dataset: class:~summit.utils.dataset.DataSet, optional - A DataSet with data for training where the data columns correspond to the domain and the data rows correspond to the training points. - By default: None - csv_dataset: string, optional - Path to csv_file with data for training where columns correspond to the domain and the rows correspond to the training points. - Note that the first row should exactly match the variable names of the domain and the second row should only have "DATA" as entry. - By default: None - model_name: string, optional - Name of the model that is used for saving model parameters. Should be unique. - By default: "dataset_emulator_model_name" - regressor_type: string, optional - Type of the regressor that is used within the emulator (available: "BNN"). - By default: "BNN" - cat_to_descr: Boolean, optional - If True, transform categorical variable to one or more continuous variable(s) - corresponding to the descriptors of the categorical variable (else do nothing). - By default: False + Train a machine learning model based on experimental data. + The model acts a benchmark for testing optimisation strategies. - Examples - -------- - >>> test_domain = ReizmanSuzukiEmulator().domain - >>> e = ExperimentalEmulator(domain=test_domain, model_name="Pytest") - No trained model for Pytest. Train this model with ExperimentalEmulator.train() in order to use this Emulator as an virtual Experiment. - >>> columns = [v.name for v in e.domain.variables] - >>> train_values = {("catalyst", "DATA"): ["P1-L2", "P1-L7", "P1-L3", "P1-L3"], ("t_res", "DATA"): [60, 120, 110, 250], ("temperature", "DATA"): [110, 30, 70, 80], ("catalyst_loading", "DATA"): [0.508, 0.6, 1.4, 1.3], ("yield", "DATA"): [20, 40, 60, 34], ("ton", "DATA"): [33, 34, 21, 22]} - >>> train_dataset = DataSet(train_values, columns=columns) - >>> e.train(train_dataset, verbose=False, cv_fold=2, test_size=0.25) - >>> columns = [v.name for v in e.domain.variables] - >>> values = [float(v.bounds[0] + 0.6 * (v.bounds[1] - v.bounds[0])) if v.variable_type == 'continuous' else v.levels[-1] for v in e.domain.variables] - >>> values = np.array(values) - >>> values = np.atleast_2d(values) - >>> conditions = DataSet(values, columns=columns) - >>> results = e.run_experiments(conditions) + Parameters + ---------- + model_name : str + Name of the model, ideally with no spaces + domain : :class:`~summit.domain.Domain` + The domain of the emulator + dataset : :class:`~summit.dataset.Dataset`, optional + Dataset used for training/validation + regressor : :classs:`torch.nn.Module`, optional + Pytorch LightningModule class. Defaults to the ANNRegressor + output_variable_names : str or list, optional + The names of the variables that should be trained by the predictor. + Defaults to all objectives in the domain. + clip : bool or list + Whether to clip predictions to the limits of + the objectives in the domain. True (default) means + clipping is activated for all outputs and False means + it is not activated at all. A list of specific outputs to clip + can also be passed. """ - def __init__( - self, + def __init__(self, model_name, domain, **kwargs): + super().__init__(domain, **kwargs) + self.model_name = model_name + + # Data + self.ds = kwargs.get("dataset") + if self.ds is not None: + self.n_features = self._caclulate_input_dimensions(self.domain) + self.n_examples = self.ds.shape[0] + + self.output_variable_names = kwargs.get( + "output_variable_names", + [v.name for v in self.domain.output_variables], + ) + + # Create the regressor + self.regressor = kwargs.get("regressor", ANNRegressor) + self.predictors = kwargs.get("predictors") + self.clip = kwargs.get("clip", True) + + def _run(self, conditions, **kwargs): + input_columns = [v.name for v in self.domain.input_variables] + X = conditions[input_columns].to_numpy() + if X.shape[0] == len(input_columns): + X = X[np.newaxis, :] + X = pd.DataFrame(X, columns=input_columns) + y_pred, y_pred_std = self._predict(X) + return_std = kwargs.get("return_std", False) + for i, name in enumerate(self.output_variable_names): + if type(conditions) == pd.Series: + y = y_pred[0, i] + y_std = y_pred_std[0, i] + else: + y = y_pred[:, i] + y_std = y_pred_std[:, i] + conditions.at[(name, "DATA")] = y + if return_std: + conditions.at[(f"{name}_std", "METADATA")] = y_std + return conditions, {} + + def _predict(self, X, **kwargs): + """Get a prediction + + Parameters + ---------- + X : pd.DataFrame + A pandas dataframe with inputs to the predictor + + Returns + ------- + mean, std + Numpy arrays with the average and standard deviation of the ensemble + + """ + y_pred = np.array( + [estimator.predict(X, **kwargs) for estimator in self.predictors] + ) + if self.clip: + for i, v in enumerate(self.domain.output_variables): + if type(self.clip) == list: + if v.name not in self.clip: + continue + y_pred[:, :, i] = np.clip(y_pred[:, :, i], v.lower_bound, v.upper_bound) + + return y_pred.mean(axis=0), y_pred.std(axis=0) + + def train(self, **kwargs): + """Train the model on the dataset + + Parameters + --------- + test_size : float, optional + The size of the test as a fraction of the total dataset. Defaults to 0.1. + cv_folds : int, optional + The number of cross validation folds. Defaults to 5. + max_epochs : int, optional + The max number of epochs for each CV fold. Defaults to 100. + scoring : str or list, optional + A list of scoring functions or names of them. Defaults to R2 and MSE. + See here for more https://scikit-learn.org/stable/modules/model_evaluation.html#scoring-parameter + regressor_kwargs : dict, optional + You can pass extra arguments to the regressor here. + callbacks : None, "disable" or list of Callbacks + Skorch callbacks passed to skorch.net. See: https://skorch.readthedocs.io/en/latest/net.html + verbose : int + 0 for no logging, 1 for logging + + Notes + ------ + If predictor was set in the initialization, it will not be overwritten. + + Returns + ------- + A dictionary containing the results of the training. + """ + if self.ds is None: + raise ValueError("Dataset is required for training.") + + # Create predictor + predictor = self._create_predictor( + self.regressor, + self.domain, + self.n_features, + self.n_examples, + output_variable_names=self.output_variable_names, + **kwargs, + ) + + # Get data + input_columns = [v.name for v in self.domain.input_variables] + X = self.ds[input_columns].to_numpy() + y = self.ds[self.output_variable_names].to_numpy().astype(float) + # Sklearn columntransformer expects a pandas dataframe not a dataset + X = pd.DataFrame(X, columns=input_columns) + + # Train-test split + test_size = kwargs.get("test_size", 0.1) + random_state = kwargs.get("random_state") + self.X_train, self.X_test, self.y_train, self.y_test = train_test_split( + X, y, test_size=test_size, random_state=random_state + ) + y_train, y_test = ( + torch.tensor(self.y_train).float(), + torch.tensor(self.y_test).float(), + ) + + # Training + scoring = kwargs.get("scoring", ["r2", "neg_root_mean_squared_error"]) + folds = kwargs.get("cv_folds", 5) + search_params = kwargs.get("search_params", {}) + # Run grid search if requested + if search_params: + self.logger.info("Starting grid search.") + gs = ProgressGridSearchCV( + predictor, search_params, refit="r2", cv=folds, scoring=scoring + ) + gs.fit(self.X_train, y_train) + best_params = gs.best_params_ + params = {} + for param in search_params.keys(): + params[param] = best_params[param] + predictor.set_params(**params) + + # Run final training using cross validation + initializing = kwargs.get("initializing", False) + + if not initializing: + self.logger.info("Starting training.") + res = cross_validate( + predictor, + self.X_train, + y_train, + scoring=scoring, + cv=folds, + return_estimator=True, + ) + + self.predictors = res.pop("estimator") + # Rename from test to validation + for name in scoring: + scores = res.pop(f"test_{name}") + res[f"val_{name}"] = scores + return res + + def test(self, **kwargs): + scoring = kwargs.get("scoring", ["r2", "neg_root_mean_squared_error"]) + scores_list = [] + for predictor in self.predictors: + if callable(scoring): + scorers = scoring + elif scoring is None or isinstance(scoring, str): + scorers = check_scoring(predictor, scoring) + else: + scorers = _check_multimetric_scoring(predictor, scoring) + scores_list.append(_score(predictor, self.X_test, self.y_test, scorers)) + scores_dict = _aggregate_score_dicts(scores_list) + for name in scoring: + scores = scores_dict.pop(name) + scores_dict[f"test_{name}"] = scores + return scores_dict + + @classmethod + def _create_predictor( + cls, + regressor, domain, - dataset=None, - csv_dataset=None, - model_name="dataset_name_emulator_bnn", - regressor_type="BNN", - cat_to_descr=False, - **kwargs + input_dimensions, + num_examples, + output_variable_names, + **kwargs, ): - super().__init__(domain) - dataset = self._check_datasets(dataset, csv_dataset) + # Preprocessors + output_variable_names = kwargs.get( + "output_variable_names", [v.name for v in domain.output_variables] + ) + X_preprocessor = cls._create_input_preprocessor(domain) + y_preprocessor = cls._create_output_preprocessor(output_variable_names) + + # Create network + regressor_kwargs = kwargs.get("regressor_kwargs", {}) + regressor_kwargs.update( + dict( + module__input_dim=input_dimensions, + module__output_dim=len(output_variable_names), + module__n_examples=num_examples, + ) + ) + verbose = kwargs.get("verbose", 0) + net = NeuralNetRegressor( + regressor, + train_split=None, + max_epochs=kwargs.get("max_epochs", 100), + callbacks=kwargs.get("callbacks"), + verbose=verbose, + **regressor_kwargs, + ) + + # Create predictor + # TODO: also create an inverse function + ds_to_tensor = FunctionTransformer(numpy_to_tensor, check_inverse=False) + pipe = Pipeline( + steps=[ + ("preprocessor", X_preprocessor), + ("dst", ds_to_tensor), + ("net", net), + ] + ) - kwargs["cat_to_descr"] = cat_to_descr + # output_pipeline = Pipeline( + # steps=[("scaler", StandardScaler()), ("dst", ds_to_tensor)] + # ) - if regressor_type == "BNN": - self.emulator = BNNEmulator( - domain=domain, dataset=dataset, model_name=model_name, kwargs=kwargs + return UpdatedTransformedTargetRegressor( + regressor=pipe, transformer=StandardScaler(), check_inverse=False + ) + + @staticmethod + def _caclulate_input_dimensions(domain): + num_dimensions = 0 + for v in domain.input_variables: + if v.variable_type == "continuous": + num_dimensions += 1 + elif v.variable_type == "categorical": + num_dimensions += len(v.levels) + return num_dimensions + + @staticmethod + def _create_input_preprocessor(domain): + """Create feature preprocessors """ + transformers = [] + # Numeric transforms + numeric_features = [ + v.name for v in domain.input_variables if v.variable_type == "continuous" + ] + if len(numeric_features) > 0: + transformers.append(("num", StandardScaler(), numeric_features)) + + # Categorical transforms + categorical_features = [ + v.name for v in domain.input_variables if v.variable_type == "categorical" + ] + categories = [ + v.levels for v in domain.input_variables if v.variable_type == "categorical" + ] + if len(categorical_features) > 0: + transformers.append( + ("cat", OneHotEncoder(categories=categories), categorical_features) ) - try: - self.extras = [self.emulator._load_model(model_name)] - except: - print( - "No trained model for {}. Train this model with ExperimentalEmulator.train() in order to use this Emulator as an virtual Experiment.".format( - self.emulator.model_name + + # Create preprocessor + if len(numeric_features) == 0 and len(categorical_features) > 0: + raise DomainError( + "With only categorical features, you can do a simple lookup." + ) + elif len(numeric_features) > 0 or len(categorical_features) > 0: + preprocessor = ColumnTransformer(transformers=transformers) + else: + raise DomainError( + "No continuous or categorical features were found in the dataset." + ) + return preprocessor + + @staticmethod + def _create_output_preprocessor(output_variable_names): + """"Create target preprocessors""" + transformers = [ + ("scale", StandardScaler(), output_variable_names), + ("dst", FunctionTransformer(numpy_to_tensor), output_variable_names), + ] + return ColumnTransformer(transformers=transformers) + + def to_dict(self, **experiment_params): + """Convert emulator parameters to dictionary + + Notes + ------ + This does not save the weights and biases of the regressor. + You need to use save_regressor method. + + """ + # Predictors + predictors = [ + self._create_predictor_dict(predictor) for predictor in self.predictors + ] + + # Update experiment_params + experiment_params.update( + { + "model_name": self.model_name, + "regressor_name": str(self.regressor.__name__), + "n_features": self.n_features, + "n_examples": self.n_examples, + "output_variable_names": self.output_variable_names, + "predictors": predictors, + } + ) + return super().to_dict(**experiment_params) + + @staticmethod + def _create_predictor_dict(predictor): + num = predictor.regressor_.named_steps.preprocessor.named_transformers_.num + cat = predictor.regressor_.named_steps.preprocessor.named_transformers_.cat + input_preprocessor = { + # Numerical + "num": { + "mean_": num.mean_, + "var_": num.var_, + "scale_": num.scale_, + "n_samples_seen_": num.n_samples_seen_, + } + # Categorical is automatic from the domain + } + out = predictor.transformer_ + output_preprocessor = { + "mean_": out.mean_, + "var_": out.var_, + "scale_": out.scale_, + "n_samples_seen_": out.n_samples_seen_, + } + return jsonify_dict( + { + "input_preprocessor": input_preprocessor, + "output_preprocessor": output_preprocessor, + } + ) + + @classmethod + def from_dict(cls, d, **kwargs): + """Create ExperimentalEmulator from a dictionary + + Notes + ----- + This does not load the regressor weights and biases. + After calling from_dict, call load_regressor to load the + weights and biases. + + """ + params = d["experiment_params"] + domain = Domain.from_dict(d["domain"]) + + # Load regressor + regressor = registry[params["regressor_name"]] + d["experiment_params"]["regressor"] = regressor + + # Load predictors + predictors_params = params["predictors"] + predictors = [ + cls._create_predictor( + regressor, + domain, + params["n_features"], + params["n_examples"], + output_variable_names=params["output_variable_names"], + ) + for predictor_params in predictors_params + ] + d["experiment_params"]["predictor"] = predictors + + # Dataset + dataset = kwargs.get("dataset") + d["experiment_params"]["dataset"] = dataset + + # Instantiate the class + exp = super().from_dict(d) + + # Set runtime parameters + exp.n_features = params["n_features"] + exp.n_examples = params["n_examples"] + + # One round of training to initialize all variables + if exp.ds is None: + exp.ds = generate_data(domain, params["n_features"] + 1) + exp.train(max_epochs=1, verbose=0, initializing=True) + + # Set parameters on predictors + for predictor, predictor_params in zip(exp.predictors, predictors_params): + exp.set_predictor_params(predictor, unjsonify_dict(predictor_params)) + + return exp + + @staticmethod + def set_predictor_params(predictor, predictor_params): + # Input transforms + num = predictor.regressor_.named_steps.preprocessor.named_transformers_.num + cat = predictor.regressor_.named_steps.preprocessor.named_transformers_.cat + input_preprocessor = RecursiveNamespace( + **predictor_params["input_preprocessor"] + ) + num.mean_ = input_preprocessor.num.mean_ + num.var_ = input_preprocessor.num.var_ + num.scale_ = input_preprocessor.num.scale_ + num.n_samples_seen_ = input_preprocessor.num.n_samples_seen_ + + # Output transforms + out = predictor.transformer_ + output_preprocessor = RecursiveNamespace( + **predictor_params["output_preprocessor"] + ) + out.mean_ = output_preprocessor.mean_ + out.var_ = output_preprocessor.var_ + out.scale_ = output_preprocessor.scale_ + out.n_samples_seen_ = output_preprocessor.n_samples_seen_ + + def save_regressor(self, save_dir): + """Save the weights and biases of the regressor to disk + + Parameters + ---------- + save_dir : str or pathlib.Path + The directory used for saving emulator files. + + """ + save_dir = pathlib.Path(save_dir) + if self.predictors is None: + raise ValueError( + "No predictors available. First, run training using the train method." + ) + for i, predictor in enumerate(self.predictors): + predictor.regressor_.named_steps.net.save_params( + f_params=save_dir / f"{self.model_name}_predictor_{i}.pt" + ) + + def load_regressor(self, save_dir): + """Load the weights and biases of the regressor from disk + + Parameters + ---------- + save_dir : str or pathlib.Path + The directory used for saving emulator files. + + """ + save_dir = pathlib.Path(save_dir) + for i, predictor in enumerate(self.predictors): + net = predictor.regressor_.named_steps.net + net.initialize() + net.load_params(f_params=save_dir / f"{self.model_name}_predictor_{i}.pt") + + def save(self, save_dir): + """Save all the essential parameters of the ExperimentalEmulator to disk + + Parameters + ---------- + save_dir : str or pathlib.Path + The directory used for saving emulator files. + + """ + save_dir = pathlib.Path(save_dir) + if not save_dir.exists(): + save_dir.mkdir() + with open(save_dir / f"{self.model_name}.json", "w") as f: + json.dump(self.to_dict(), f) + self.save_regressor(save_dir) + + @classmethod + def load(cls, model_name, save_dir, **kwargs): + """Load all the essential parameters of the ExperimentalEmulator to disk + + Parameters + ---------- + save_dir : str or pathlib.Path + The directory from which to load emulator files. + + """ + save_dir = pathlib.Path(save_dir) + with open(save_dir / f"{model_name}.json", "r") as f: + d = json.load(f) + exp = ExperimentalEmulator.from_dict(d, **kwargs) + exp.load_regressor(save_dir) + return exp + + def parity_plot(self, **kwargs): + """Produce a parity plot based for the trained model using matplotlib + + Parameters + --------- + output_variable_names : str or list, optional + The output variables to plot. Defaults to all. + include_test : bool, optional + Include the performance of the model on the test set. + Defaults to False. + train_color : str, optional + Hex string for the train points. Defaults to "#6f3666" + test_color : str, optional + Hex string for the train points. Defaults to "#3c328c" + + """ + import matplotlib.pyplot as plt + + include_test = kwargs.get("include_test", False) + train_color = kwargs.get("train_color", "#6f3666") + test_color = kwargs.get("test_color", "#3c328c") + clip = kwargs.get("clip") + vars = kwargs.get("output_variable_names", self.output_variable_names) + if type(vars) == str: + vars = [vars] + + fig, axes = plt.subplots(1, len(vars)) + if len(vars) > 1: + fig.subplots_adjust(wspace=0.2) + if type(axes) != np.ndarray: + axes = np.array([axes]) + + # Do predictions + with torch.no_grad(): + y_train_pred, y_train_pred_std = self._predict(self.X_train) + if include_test: + y_test_pred, y_train_pred_std = self._predict(self.X_test) + + plots = 0 + for i, v in enumerate(self.output_variable_names): + if v in vars: + if include_test: + kwargs = dict( + y_test=self.y_test[:, i], y_test_pred=y_test_pred[:, i] ) + else: + kwargs = {} + make_parity_plot( + self.y_train[:, i], + y_train_pred[:, i], + ax=axes[plots], + train_color=train_color, + test_color=test_color, + title=v, + **kwargs, ) + plots += 1 + + return fig, axes + + +def generate_data(domain, n_examples, random_state=None): + data = {} + random = default_rng(random_state) + for v in domain.input_variables: + if v.variable_type == "continuous": + data[v.name] = random.normal(size=n_examples) + elif v.variable_type == "categorical": + data[v.name] = random.choice(v.levels, size=n_examples) + for v in domain.output_variables: + if v.variable_type == "continuous": + data[v.name] = random.normal(size=n_examples) + return pd.DataFrame(data) + + +def make_parity_plot( + y_train, + y_train_pred, + y_test=None, + y_test_pred=None, + ax=None, + train_color="#6f3666", + test_color="#3c328c", + title=None, +): + import matplotlib.pyplot as plt + import matplotlib.patches as mpatches + + if ax is None: + fig, ax = plt.subplots(1) + ax.scatter(y_train, y_train_pred, color=train_color, alpha=0.5) + # Test + if y_test is not None: + ax.scatter(y_test, y_test_pred, color=test_color, alpha=0.5) + + # Parity line + min = np.min(np.concatenate([y_train, y_train_pred])) + max = np.max(np.concatenate([y_train, y_train_pred])) + ax.plot([min, max], [min, max], c="#747378") + # Scores + handles = [] + r2_train = r2_score(y_train, y_train_pred) + r2_train_patch = mpatches.Patch( + label=f"Train R2 = {r2_train:.2f}", color=train_color + ) + handles.append(r2_train_patch) + if y_test is not None: + r2_test = r2_score(y_test, y_test_pred) + r2_test_patch = mpatches.Patch( + label=f"Test R2 = {r2_test:.2f}", color=test_color + ) + handles.append(r2_test_patch) + + # Formatting + ax.legend(handles=handles, fontsize=12) + ax.set_xlim(min, max) + ax.set_ylim(min, max) + ax.set_xlabel("Measured") + ax.set_ylabel("Predicted") + if title is not None: + ax.set_title(title) + ax.tick_params(direction="in") + return ax + + +def numpy_to_tensor(X): + """Convert datasets into """ + return torch.tensor(X).float() + + +class UpdatedTransformedTargetRegressor(TransformedTargetRegressor): + def fit(self, X, y, **fit_params): + """Fit the model according to the given training data. + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training vector, where n_samples is the number of samples and + n_features is the number of features. + y : array-like of shape (n_samples,) + Target values. + **fit_params : dict + Parameters passed to the ``fit`` method of the underlying + regressor. + Returns + ------- + self : object + """ + y = check_array( + y, + accept_sparse=False, + force_all_finite=True, + ensure_2d=False, + dtype="numeric", + ) + + # store the number of dimension of the target to predict an array of + # similar shape at predict + self._training_dim = y.ndim + + # transformers are designed to modify X which is 2d dimensional, we + # need to modify y accordingly. + if y.ndim == 1: + y_2d = y.reshape(-1, 1) else: - raise NotImplementedError( - "Regressor type <{}> not implemented yet".format(str(regressor_type)) - ) + y_2d = y + self._fit_transformer(y_2d) + + # transform y and convert back to 1d array if needed + y_trans = self.transformer_.transform(y_2d) + # Remove this stupid line + # FIXME: a FunctionTransformer can return a 1D array even when validate + # is set to True. Therefore, we need to check the number of dimension + # first. + # if y_trans.ndim == 2 and y_trans.shape[1] == 1: + # y_trans = y_trans.squeeze(axis=1) + + if self.regressor is None: + from ..linear_model import LinearRegression + + self.regressor_ = LinearRegression() + else: + self.regressor_ = clone(self.regressor) - def _run(self, conditions, **kwargs): - condition = DataSet.from_df(conditions.to_frame().T) - infer_dict = self.emulator.infer_model(dataset=condition) - for k, v in infer_dict.items(): - conditions[(k, "DATA")] = v - return conditions, None - - def train(self, dataset=None, csv_dataset=None, verbose=True, **kwargs): - dataset = self._check_datasets(dataset, csv_dataset) - self.emulator.set_training_hyperparameters(kwargs=kwargs) - self.emulator.train_model(dataset=dataset, verbose=verbose, kwargs=kwargs) - self.extras = [self.emulator.output_models] - - def validate( + self.regressor_.fit(X, y_trans, **fit_params) + + return self + + +class RecursiveNamespace(types.SimpleNamespace): + # def __init__(self, /, **kwargs): # better, but Python 3.8+ + def __init__(self, **kwargs): + """Create a SimpleNamespace recursively""" + self.__dict__.update({k: self.__elt(v) for k, v in kwargs.items()}) + + def __elt(self, elt): + """Recurse into elt to create leaf namepace objects""" + if type(elt) is dict: + return type(self)(**elt) + if type(elt) in (list, tuple): + return [self.__elt(i) for i in elt] + return elt + + +class ProgressParallel(Parallel): + def __init__(self, use_tqdm=True, total=None, *args, **kwargs): + self._use_tqdm = use_tqdm + self._total = total + super().__init__(*args, **kwargs) + + def __call__(self, *args, **kwargs): + with tqdm(disable=not self._use_tqdm, total=self._total) as self._pbar: + return Parallel.__call__(self, *args, **kwargs) + + @property + def total(self): + return self._total + + @total.setter + def total(self, val): + self._total = val + + def print_progress(self): + if self._total is None: + self._pbar.total = self.n_dispatched_tasks + self._pbar.n = self.n_completed_tasks + self._pbar.refresh() + + +class ProgressGridSearchCV(BaseSearchCV): + @_deprecate_positional_args + def __init__( self, - dataset=None, - csv_dataset=None, - parity_plots=False, - get_pred=False, - **kwargs + estimator, + param_grid, + *, + scoring=None, + n_jobs=None, + refit=True, + cv=None, + verbose=0, + pre_dispatch="2*n_jobs", + error_score=np.nan, + return_train_score=False, ): - dataset = self._check_datasets(dataset, csv_dataset) - if dataset is not None: - return self.emulator.validate_model( - dataset=dataset, - parity_plots=parity_plots, - get_pred=get_pred, - kwargs=kwargs, - ) + super().__init__( + estimator=estimator, + scoring=scoring, + n_jobs=n_jobs, + refit=refit, + cv=cv, + verbose=verbose, + pre_dispatch=pre_dispatch, + error_score=error_score, + return_train_score=return_train_score, + ) + self.param_grid = param_grid + _check_param_grid(param_grid) + + def _run_search(self, evaluate_candidates): + """Search all candidates in param_grid""" + evaluate_candidates(ParameterGrid(self.param_grid)) + + @_deprecate_positional_args + def fit(self, X, y=None, *, groups=None, **fit_params): + """Run fit with all sets of parameters. + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training vector, where n_samples is the number of samples and + n_features is the number of features. + y : array-like of shape (n_samples, n_output) \ + or (n_samples,), default=None + Target relative to X for classification or regression; + None for unsupervised learning. + groups : array-like of shape (n_samples,), default=None + Group labels for the samples used while splitting the dataset into + train/test set. Only used in conjunction with a "Group" :term:`cv` + instance (e.g., :class:`~sklearn.model_selection.GroupKFold`). + **fit_params : dict of str -> object + Parameters passed to the ``fit`` method of the estimator + """ + estimator = self.estimator + refit_metric = "score" + + if callable(self.scoring): + scorers = self.scoring + elif self.scoring is None or isinstance(self.scoring, str): + scorers = check_scoring(self.estimator, self.scoring) else: - try: - print("Evaluation based on training and test set.") - return self.emulator.validate_model(parity_plots=parity_plots) - except: - raise ValueError("No dataset to evaluate.") - - def _check_datasets(self, dataset=None, csv_dataset=None): - if csv_dataset: - if dataset: - print( - "Dataset and csv.dataset are given, hence dataset will be overwritten by csv.data." + scorers = _check_multimetric_scoring(self.estimator, self.scoring) + # self._check_refit_for_multimetric(scorers) + refit_metric = self.refit + + X, y, groups = indexable(X, y, groups) + fit_params = _check_fit_params(X, fit_params) + + cv_orig = check_cv(self.cv, y, classifier=is_classifier(estimator)) + n_splits = cv_orig.get_n_splits(X, y, groups) + + base_estimator = clone(self.estimator) + + parallel = ProgressParallel(n_jobs=self.n_jobs, pre_dispatch=self.pre_dispatch) + + fit_and_score_kwargs = dict( + scorer=scorers, + fit_params=fit_params, + return_train_score=self.return_train_score, + return_n_test_samples=True, + return_times=True, + return_parameters=False, + error_score=self.error_score, + verbose=self.verbose, + ) + results = {} + with parallel: + all_candidate_params = [] + all_out = [] + all_more_results = defaultdict(list) + + def evaluate_candidates(candidate_params, cv=None, more_results=None): + cv = cv or cv_orig + candidate_params = list(candidate_params) + n_candidates = len(candidate_params) + + if self.verbose > 0: + print( + "Fitting {0} folds for each of {1} candidates," + " totalling {2} fits".format( + n_splits, n_candidates, n_candidates * n_splits + ) + ) + runs = product( + enumerate(candidate_params), enumerate(cv.split(X, y, groups)) + ) + parallel.total = len(list(deepcopy(runs))) + out = parallel( + delayed(_fit_and_score)( + clone(base_estimator), + X, + y, + train=train, + test=test, + parameters=parameters, + split_progress=(split_idx, n_splits), + candidate_progress=(cand_idx, n_candidates), + **fit_and_score_kwargs, + ) + for (cand_idx, parameters), (split_idx, (train, test)) in runs ) - dataset = DataSet.read_csv(csv_dataset, index_col=None) - return dataset - def to_dict(self, **kwargs): - """Serialize the class to a dictionary + if len(out) < 1: + raise ValueError( + "No fits were performed. " + "Was the CV iterator empty? " + "Were there no candidates?" + ) + elif len(out) != n_candidates * n_splits: + raise ValueError( + "cv.split and cv.get_n_splits returned " + "inconsistent results. Expected {} " + "splits, got {}".format(n_splits, len(out) // n_candidates) + ) - Subclasses can add a experiment_params dictionary - key with custom parameters for the experiment - """ - kwargs.update( - dict( - model_name=self.emulator.model_name, - dataset=self.emulator._dataset.to_dict() - if self.emulator._dataset is not None - else None, - output_models=self.emulator.output_models, + # For callable self.scoring, the return type is only know after + # calling. If the return type is a dictionary, the error scores + # can now be inserted with the correct key. The type checking + # of out will be done in `_insert_error_scores`. + if callable(self.scoring): + _insert_error_scores(out, self.error_score) + all_candidate_params.extend(candidate_params) + all_out.extend(out) + if more_results is not None: + for key, value in more_results.items(): + all_more_results[key].extend(value) + + nonlocal results + results = self._format_results( + all_candidate_params, n_splits, all_out, all_more_results + ) + + return results + + self._run_search(evaluate_candidates) + + # multimetric is determined here because in the case of a callable + # self.scoring the return type is only known after calling + first_test_score = all_out[0]["test_scores"] + self.multimetric_ = isinstance(first_test_score, dict) + + # check refit_metric now for a callabe scorer that is multimetric + if callable(self.scoring) and self.multimetric_: + self._check_refit_for_multimetric(first_test_score) + refit_metric = self.refit + + # For multi-metric evaluation, store the best_index_, best_params_ and + # best_score_ iff refit is one of the scorer names + # In single metric evaluation, refit_metric is "score" + if self.refit or not self.multimetric_: + # If callable, refit is expected to return the index of the best + # parameter set. + if callable(self.refit): + self.best_index_ = self.refit(results) + if not isinstance(self.best_index_, numbers.Integral): + raise TypeError("best_index_ returned is not an integer") + if self.best_index_ < 0 or self.best_index_ >= len(results["params"]): + raise IndexError("best_index_ index out of range") + else: + self.best_index_ = results["rank_test_%s" % refit_metric].argmin() + self.best_score_ = results["mean_test_%s" % refit_metric][ + self.best_index_ + ] + self.best_params_ = results["params"][self.best_index_] + + if self.refit: + # we clone again after setting params in case some + # of the params are estimators as well. + self.best_estimator_ = clone( + clone(base_estimator).set_params(**self.best_params_) ) + refit_start_time = time.time() + if y is not None: + self.best_estimator_.fit(X, y, **fit_params) + else: + self.best_estimator_.fit(X, **fit_params) + refit_end_time = time.time() + self.refit_time_ = refit_end_time - refit_start_time + + # Store the only scorer not as a dict for single metric evaluation + self.scorer_ = scorers + + self.cv_results_ = results + self.n_splits_ = n_splits + + return self + + def _check_refit_for_multimetric(self, scores): + """Check `refit` is compatible with `scores` is valid""" + multimetric_refit_msg = ( + "For multi-metric scoring, the parameter refit must be set to a " + "scorer key or a callable to refit an estimator with the best " + "parameter setting on the whole data and make the best_* " + "attributes available for that metric. If this is not needed, " + f"refit should be set to False explicitly. {self.refit!r} was " + "passed." ) - return super().to_dict(**kwargs) - @classmethod - def from_dict(cls, d): - dataset = d["experiment_params"]["dataset"] - d["experiment_params"]["dataset"] = DataSet.from_dict(dataset) - exp = super().from_dict(d) - exp.emulator.output_models = d["experiment_params"]["output_models"] - return exp + valid_refit_dict = isinstance(self.refit, str) and self.refit in scores + + if ( + self.refit is not False + and not valid_refit_dict + and not callable(self.refit) + ): + raise ValueError(multimetric_refit_msg) + + +def get_bnn(): + from blitz.modules import BayesianLinear + from blitz.utils import variational_estimator + + @variational_estimator + class BNNRegressor(torch.nn.Module): + """A Bayesian Neural Network pytorch lightining module""" + + val_str = "CI acc: {:.2f}, CI upper acc: {:.2f}, CI lower acc: {:.2f}" + + def __init__( + self, input_dim, output_dim, n_examples=100, hidden_units=512, **kwargs + ): + super().__init__() + self.blinear1 = BayesianLinear(input_dim, hidden_units) + self.blinear2 = BayesianLinear(hidden_units, output_dim) + self.n_examples = n_examples + self.n_samples = kwargs.get("n_samples", 50) + self.criterion = torch.nn.MSELoss() + + def forward(self, x): + # for layer in self.layers[:-1]: + # x = layer(x) + # x = F.relu(x) + # return self.layers[-1](x) + x = self.blinear1(x) + x = F.relu(x) + return self.blinear2(x) + + def evaluate_regression(self, batch, samples=100, std_multiplier=1.96): + """Evaluate Bayesian Neural Network + + This answers the question "How many correction predictions + are in the confidence interval (CI)?" It also spits out the CI. + + Parameters + ---------- + batch : tuple + The batch being evaluatd + samples : int, optional + The number of samples of the BNN for calculating the CI + std_multiplier : float, optional + The Z-score corresponding with the desired CI. Default is + 1.96, which corresponds with a 95% CI. + + Returns + ------- + tuple of ic_acc, over_ci_lower, under_ci_upper + + icc_acc is the percentage within the CI. + + """ + + X, y = batch + + # Sample + preds = torch.tensor([self(X) for i in range(samples)]) + preds = torch.stack(preds) + means = preds.mean(axis=0) + stds = preds.std(axis=0) + + # Calculate CI + ci_upper, ci_lower = self._calc_ci(means, stds, std_multiplier) + ic_acc = (ci_lower <= y) * (ci_upper >= y) + ic_acc = ic_acc.float().mean() + + under_ci_upper = (ci_upper >= y).float().mean() + over_ci_lower = (ci_lower <= y).float().mean() + + ic_acc = (ci_lower <= y) * (ci_upper >= y) + ic_acc = ic_acc.float().mean() + + return ic_acc, over_ci_lower, under_ci_upper + + def _calc_ci(self, means, stds, std_multiplier=1.96): + ci_upper = means + (std_multiplier * stds) + ci_lower = means - (std_multiplier * stds) + return ci_lower, ci_upper + + +class ANNRegressor(torch.nn.Module): + """Artificial Neural Network Regressor + + Parameters + ----------- + input_dim : int + The number of features in the input + output_dim : int + The number of outputs in the targets + hidden_units : int, optional + The number of hidden units. Default is 512. + + """ + + def __init__(self, input_dim, output_dim, hidden_units=512, **kwargs): + super().__init__() + + self.num_hidden_layers = 1 + self.input_layer = torch.nn.Linear(input_dim, hidden_units) + self.output_layer = torch.nn.Linear(hidden_units, output_dim) + + def forward(self, x, **kwargs): + x_ = F.relu(self.input_layer(x)) + if self.num_hidden_layers > 1: + x_ = self.hidden_layers(x_) + x_ = F.relu(x_) + return self.output_layer(x_) + + +class RegressorRegistry: + """Registry for Regressors + + Models registered using the register method + are saved as the class name. + + """ + + regressors = {} + + def __getitem__(self, key): + reg = self.regressors.get(key) + if reg is not None: + return reg + else: + raise KeyError( + f"{key} is not in the §. Register using the register method." + ) + + def __setitem__(self, key, value): + reg = self.regressors.get(key) + if reg is not None: + self.regressors[key] = value + + def register(self, regressor): + key = regressor.__name__ + self.regressors[key] = regressor + + +# Create global regressor registry +registry = RegressorRegistry() +registry.register(ANNRegressor) + + +def get_data_path(): + return pathlib.Path(pkg_resources.resource_filename("summit", "benchmarks/data")) + + +def get_model_path(): + return pathlib.Path(pkg_resources.resource_filename("summit", "benchmarks/models")) + + +def get_pretrained_reizman_suzuki_emulator(case=1): + model_name = f"reizman_suzuki_case_{case}" + model_path = get_model_path() / model_name + if not model_path.exists(): + raise NotADirectoryError("Could not initialize from expected path.") + exp = ReizmanSuzukiEmulator.load(model_path, case=case) + data_path = get_data_path() + exp.ds = DataSet.read_csv(data_path / f"{model_name}.csv") + return exp class ReizmanSuzukiEmulator(ExperimentalEmulator): @@ -168,8 +1213,8 @@ class ReizmanSuzukiEmulator(ExperimentalEmulator): ---------- case: int, optional, default=1 Reizman et al. (2016) reported experimental data for 4 different - cases. The case number refers to the cases they reported. - Please see their paper for more information on the cases. + cases. Each case was has a different set of substrates but the + same possible catalysts. Please see their paper for more information on the cases. Examples -------- @@ -187,15 +1232,15 @@ class ReizmanSuzukiEmulator(ExperimentalEmulator): """ def __init__(self, case=1, **kwargs): - model_name = "reizman_suzuki_case" + str(case) - domain = self.setup_domain() - dataset_file = osp.join( - osp.dirname(osp.realpath(__file__)), - "experiment_emulator/data/" + model_name + "_train_test.csv", - ) - super().__init__(domain=domain, model_name=model_name) + # Initialization + model_name = kwargs.get("model_name", f"reizman_suzuki_case_{case}") + domain = kwargs.pop("domain", self.setup_domain()) + data_path = get_data_path() + ds = DataSet.read_csv(data_path / f"{model_name}.csv") + super().__init__(model_name, domain, dataset=ds, **kwargs) - def setup_domain(self): + @staticmethod + def setup_domain(): domain = Domain() # Decision variables @@ -251,14 +1296,32 @@ def setup_domain(self): return domain + @classmethod + def load(cls, save_dir, case=1): + model_name = f"reizman_suzuki_case_{case}" + return super().load(model_name, save_dir) + + @classmethod def to_dict(self): """Serialize the class to a dictionary""" experiment_params = dict( - case=self.emulator.model_name[-1], + case=self.model_name[-1], ) return super().to_dict(**experiment_params) +def get_pretrained_baumgartner_cc_emulator(include_cost=False): + model_name = "baumgartner_aniline_cn_crosscoupling" + model_path = get_model_path() / model_name + if not model_path.exists(): + raise NotADirectoryError("Could not initialize from expected path.") + data_path = get_data_path() + ds = DataSet.read_csv(data_path / f"{model_name}.csv") + exp = BaumgartnerCrossCouplingEmulator.load(model_path, dataset=ds) + + return exp + + class BaumgartnerCrossCouplingEmulator(ExperimentalEmulator): """Baumgartner Cross Coupling Emulator @@ -272,9 +1335,16 @@ class BaumgartnerCrossCouplingEmulator(ExperimentalEmulator): The categorical variables (catalyst and base) contain descriptors calculated using COSMO-RS. Specifically, the descriptors are the first two sigma moments. + Parameters + ---------- + include_cost : bool, optional + Include minimization of cost as an extra objective. Cost is calculated + as a deterministic function of the inputs (i.e., no model is trained). + Defaults to False. + Examples -------- - >>> bemul = BaumgartnerCrossCouplingDescriptorEmulator() + >>> bemul = BaumgartnerCrossCouplingEmulator() Notes ----- @@ -288,19 +1358,16 @@ class BaumgartnerCrossCouplingEmulator(ExperimentalEmulator): """ - def __init__(self, **kwargs): - model_name = kwargs.get("model_name", "baumgartner_aniline_cn_crosscoupling") - dataset_file = kwargs.get( - "dataset_file", "baumgartner_aniline_cn_crosscoupling.csv" - ) - domain = self.setup_domain() - dataset_file = osp.join( - osp.dirname(osp.realpath(__file__)), - "experiment_emulator/data/" + dataset_file, - ) - super().__init__(domain=domain, csv_dataset=dataset_file, model_name=model_name) + def __init__(self, include_cost=False, **kwargs): + # TODO: make it possible to select model based on one-hot encoding or descriptors + model_name = kwargs.pop("model_name", "baumgartner_aniline_cn_crosscoupling") + self.include_cost = include_cost + domain = kwargs.pop("domain", self.setup_domain(self.include_cost)) + data_path = get_data_path() + super().__init__(model_name, domain, **kwargs) - def setup_domain(self): + @staticmethod + def setup_domain(include_cost=False): domain = Domain() # Decision variables @@ -358,115 +1425,6 @@ def setup_domain(self): des_5 = "residence time in seconds (s)" domain += ContinuousVariable(name="t_res", description=des_5, bounds=[60, 1800]) - des_6 = "Yield" - domain += ContinuousVariable( - name="yld", - description=des_6, - bounds=[0.0, 1.0], - is_objective=True, - maximize=True, - ) - - return domain - - -class BaumgartnerCrossCouplingDescriptorEmulator(ExperimentalEmulator): - """Baumgartner Cross Coupling Emulator - - Virtual experiments representing the Aniline Cross-Coupling reaction - similar to Baumgartner et al. (2019). Experimental outcomes are based on an - emulator that is trained on the experimental data published by Baumgartner et al. - - The difference with this model is that it uses descriptors for the catalyst and base - instead of one-hot encoding the options. The descriptors are the first two - sigma moments from COSMO-RS. - - - Parameters - ---------- - - Examples - -------- - >>> bemul = BaumgartnerCrossCouplingDescriptorEmulator() - - Notes - ----- - This benchmark is based on data from [Baumgartner]_ et al. - - References - ---------- - - .. [Baumgartner] L. M. Baumgartner et al., Org. Process Res. Dev., 2019, 23, 1594–1601 - DOI: `10.1021/acs.oprd.9b00236 `_ - - """ - - def __init__(self, **kwargs): - model_name = kwargs.get( - "model_name", "baumgartner_aniline_cn_crosscoupling_descriptors" - ) - dataset_file = kwargs.get( - "dataset_file", "baumgartner_aniline_cn_crosscoupling_descriptors.csv" - ) - domain = self.setup_domain() - dataset_file = osp.join( - osp.dirname(osp.realpath(__file__)), - "experiment_emulator/data/" + dataset_file, - ) - super().__init__(domain=domain, csv_dataset=dataset_file, model_name=model_name) - - def setup_domain(self): - domain = Domain() - - # Decision variables - des_1 = "Catalyst type with descriptors" - catalyst_df = DataSet( - [ - [460.7543, 67.2057, 30.8413, 2.3043, 0], # , 424.64, 421.25040226], - [518.8408, 89.8738, 39.4424, 2.5548, 0], # , 487.7, 781.11247064], - [819.933, 129.0808, 83.2017, 4.2959, 0], # , 815.06, 880.74916884], - ], - index=["tBuXPhos", "tBuBrettPhos", "AlPhos"], - columns=[ - "area_cat", - "M2_cat", - "M3_cat", - "Macc3_cat", - "Mdon3_cat", - ], # ,'mol_weight', 'sol'] - ) - domain += CategoricalVariable( - name="catalyst", description=des_1, descriptors=catalyst_df - ) - - des_2 = "Base type with descriptors" - base_df = DataSet( - [ - [162.2992, 25.8165, 40.9469, 3.0278, 0], # 101.19, 642.2973283], - [165.5447, 81.4847, 107.0287, 10.215, 0.0169], # 115.18, 534.01544123], - [227.3523, 30.554, 14.3676, 1.1196, 0.0127], # 171.28, 839.81215], - [192.4693, 59.8367, 82.0661, 7.42, 0], # 152.24, 1055.82799], - ], - index=["TEA", "TMG", "BTMG", "DBU"], - columns=["area", "M2", "M3", "Macc3", "Mdon3"], # 'mol_weight', 'sol'] - ) - domain += CategoricalVariable( - name="base", description=des_2, descriptors=base_df - ) - - des_3 = "Base equivalents" - domain += ContinuousVariable( - name="base_equivalents", description=des_3, bounds=[1.0, 2.5] - ) - - des_4 = "Temperature in degrees Celsius (ºC)" - domain += ContinuousVariable( - name="temperature", description=des_4, bounds=[30, 100] - ) - - des_5 = "residence time in seconds (s)" - domain += ContinuousVariable(name="t_res", description=des_5, bounds=[60, 1800]) - des_6 = "Yield" domain += ContinuousVariable( name="yield", @@ -476,60 +1434,39 @@ def setup_domain(self): maximize=True, ) - return domain - - -class BaumgartnerCrossCouplingEmulator_Yield_Cost(BaumgartnerCrossCouplingEmulator): - """Baumgartner Cross Coupling Emulator - - Virtual experiments representing the Aniline Cross-Coupling reaction - similar to Baumgartner et al. (2019). Experimental outcomes are based on an - emulator that is trained on the experimental data published by Baumgartner et al. - - This is a multiobjective version for optimizing yield and cost simultaneously. - - Parameters - ---------- - - Examples - -------- - >>> bemul = BaumgartnerCrossCouplingDescriptorEmulator() - - Notes - ----- - This benchmark is based on data from [Baumgartner]_ et al. + if include_cost: + domain += ContinuousVariable( + name="cost", + description="cost in USD of 40 uL reaction", + bounds=[0.0, 1.0], + is_objective=True, + maximize=False, + ) - References - ---------- + return domain - .. [Baumgartner] L. M. Baumgartner et al., Org. Process Res. Dev., 2019, 23, 1594–1601 - DOI: `10.1021/acs.oprd.9b00236 `_ + @classmethod + def load(cls, save_dir, **kwargs): + """Load all the essential parameters of the BaumgartnerCrossCouplingEmulator + from disc - """ + Parameters + ---------- + save_dir : str or pathlib.Path + The directory from which to load emulator files. - def __init__(self, **kwargs): - super().__init__() - self.init_domain = self._domain - self.mod_domain = self._domain + ContinuousVariable( - name="cost", - description="cost in USD of 40 uL reaction", - bounds=[0.0, 1.0], - is_objective=True, - maximize=False, - ) - self._domain = self.mod_domain + """ + model_name = "baumgartner_aniline_cn_crosscoupling" + return super().load(model_name, save_dir, **kwargs) def _run(self, conditions, **kwargs): - # Change to original domain for running predictive model - self._domain = self.init_domain conditions, _ = super()._run(conditions=conditions, **kwargs) # Calculate costs - costs = self._calculate_costs(conditions) - conditions[("cost", "DATA")] = costs + if self.include_cost: + costs = self._calculate_costs(conditions) + conditions[("cost", "DATA")] = costs - # Change back to modified domain - self._domain = self.mod_domain return conditions, {} @classmethod diff --git a/summit/benchmarks/models/baumgartner_aniline_cn_crosscoupling/baumgartner_aniline_cn_crosscoupling.json b/summit/benchmarks/models/baumgartner_aniline_cn_crosscoupling/baumgartner_aniline_cn_crosscoupling.json new file mode 100644 index 00000000..9a0c7f2f --- /dev/null +++ b/summit/benchmarks/models/baumgartner_aniline_cn_crosscoupling/baumgartner_aniline_cn_crosscoupling.json @@ -0,0 +1 @@ +{"domain": [{"type": "CategoricalVariable", "is_objective": false, "name": "catalyst", "description": "Catalyst type", "units": null, "levels": ["tBuXPhos", "tBuBrettPhos", "AlPhos"], "ds": {"index": ["tBuXPhos", "tBuBrettPhos", "AlPhos"], "columns": [["area_cat", "DATA"], ["M2_cat", "DATA"]], "data": [[460.7543, 67.2057], [518.8408, 89.8738], 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a/summit/benchmarks/models/reizman_suzuki_case_4/reizman_suzuki_case_4_predictor_4.pt b/summit/benchmarks/models/reizman_suzuki_case_4/reizman_suzuki_case_4_predictor_4.pt new file mode 100644 index 00000000..baefd629 Binary files /dev/null and b/summit/benchmarks/models/reizman_suzuki_case_4/reizman_suzuki_case_4_predictor_4.pt differ diff --git a/summit/experiment.py b/summit/experiment.py index a15c4db6..31c8f000 100644 --- a/summit/experiment.py +++ b/summit/experiment.py @@ -9,6 +9,7 @@ import pandas as pd import numpy as np import time +import logging COLORS = [ (165, 0, 38), @@ -44,6 +45,7 @@ class Experiment(ABC): """ def __init__(self, domain, **kwargs): + self.logger = kwargs.get("logger", logging.getLogger(__name__)) self._domain = domain self.reset() @@ -148,7 +150,7 @@ def to_dict(self, **experiment_params): return dict( domain=self.domain.to_dict(), - name=self.__class__.__name__, + name=str(self.__class__.__name__), data=self.data.to_dict(), experiment_params=experiment_params, extras=extras, diff --git a/summit/run.py b/summit/run.py index 4ce98ebd..a0f99dbe 100644 --- a/summit/run.py +++ b/summit/run.py @@ -11,6 +11,7 @@ import uuid import json import logging +import pkg_resources __all__ = ["experiment_from_dict", "Runner", "NeptuneRunner"] @@ -45,11 +46,17 @@ def experiment_from_dict(d): elif d["name"] == "BaumgartnerCrossCouplingEmulator": return BaumgartnerCrossCouplingEmulator.from_dict(d) elif d["name"] == "BaumgartnerCrossCouplingDescriptorEmulator": - BaumgartnerCrossCouplingDescriptorEmulator.from_dict(d) + raise NotImplementedError( + "BaumgartnerCrossCouplingDescriptorEmulator has been deprecated." + ) elif d["name"] == "BaumgartnerCrossCouplingEmulator_Yield_Cost": - return BaumgartnerCrossCouplingEmulator_Yield_Cost.from_dict(d) + raise NotImplementedError( + "BaumgartnerCrossCouplingEmulator_Yield_Cost has been deprecated." + ) elif d["name"] == "BaumgartnerCrossCouplingBenchmark": - return BaumgartnerCrossCouplingEmulator.from_dict(d) + raise NotImplementedError( + "BaumgartnerCrossCouplingBenchmark has been deprecated." + ) else: raise ValueError(f"""Experiment {d["name"]} not found.""") diff --git a/summit/strategies/__init__.py b/summit/strategies/__init__.py index f9d3926c..799b4c59 100644 --- a/summit/strategies/__init__.py +++ b/summit/strategies/__init__.py @@ -7,7 +7,6 @@ from .snobfit import SNOBFIT from .sobo import SOBO from .multitask import MTBO, STBO -from .gryffin import GRYFFIN from .deep_reaction_optimizer import DRO from .entmoot import ENTMOOT @@ -21,7 +20,6 @@ "MTBO", "STBO", "SOBO", - "GRYFFIN", "DRO", "strategy_from_dict", ] + base_all @@ -35,7 +33,7 @@ def strategy_from_dict(d): elif d["name"] == "TSEMO": return TSEMO.from_dict(d) elif d["name"] == "GRYFFIN": - return GRYFFIN.from_dict(d) + raise ValueError("Gryffin is now deprecated.") elif d["name"] == "SOBO": return SOBO.from_dict(d) elif d["name"] == "SNOBFIT": diff --git a/summit/strategies/base.py b/summit/strategies/base.py index 7d2b08a9..1a8b6801 100644 --- a/summit/strategies/base.py +++ b/summit/strategies/base.py @@ -64,6 +64,7 @@ def transform_inputs_outputs(self, ds: DataSet, **kwargs): Datasets with the input and output datasets """ from sklearn.preprocessing import OneHotEncoder + copy = kwargs.get("copy", True) categorical_method = kwargs.get("categorical_method", "one-hot") standardize_inputs = kwargs.get("standardize_inputs", False) @@ -200,6 +201,7 @@ def un_transform(self, ds, **kwargs): """ from sklearn.preprocessing import OneHotEncoder + categorical_method = kwargs.get("categorical_method") standardize_inputs = kwargs.get("standardize_inputs", False) standardize_outputs = kwargs.get("standardize_outputs", False) @@ -811,7 +813,7 @@ def to_dict(self, **strategy_params): # You can pass in as keyword arguments any custom parameters # for a strategy, which will be stored under the key strategy_params. return dict( - name=self.__class__.__name__, + name=str(self.__class__.__name__), transform=self.transform.to_dict(), strategy_params=strategy_params, ) diff --git a/summit/strategies/deep_reaction_optimizer.py b/summit/strategies/deep_reaction_optimizer.py index 06cc3b82..3faf7665 100644 --- a/summit/strategies/deep_reaction_optimizer.py +++ b/summit/strategies/deep_reaction_optimizer.py @@ -16,10 +16,6 @@ from collections import namedtuple from copy import deepcopy -IGNORE_CHEMOPT = ( - True # Global variable to ignore issues with tensorflow just for sake of analysis -) - class DRO(Strategy): """Deep Reaction Optimizer (DRO) @@ -105,13 +101,6 @@ def __init__( ): Strategy.__init__(self, domain, transform) - import tensorflow as tf - - if tf.__version__ != "1.13.1" and not IGNORE_CHEMOPT: - raise ImportError( - "Tensorflow version 1.13.1 needed for DRO, which is different than the versions needed for other strategies. We suggest using the docker container marcosfelt/summit:dro." - ) - # Create directories to store temporary files summit_config_path = get_summit_config_path() self.uuid_val = uuid.uuid4() # Unique identifier for this run @@ -146,16 +135,15 @@ def suggest_experiments(self, prev_res: DataSet = None, **kwargs): """ - - # if tf.__version__ != "1.13.1": - # raise ImportError( - # """Tensorflow version 1.13.1 needed for DRO, which is different than the versions - # needed for other strategies. We suggest using the docker container marcosfelt/summit:dro. - # """ - # ) - import tensorflow as tf + if tf.__version__ != "1.13.1": + raise ImportError( + """Tensorflow version 1.13.1 needed for DRO, which is different than the versions + needed for other strategies. We suggest using the docker container marcosfelt/summit:dro. + """ + ) + # Extract dimension of input domain self.dim = self.domain.num_continuous_dimensions() diff --git a/summit/strategies/tsemo.py b/summit/strategies/tsemo.py index e9868d72..95eaeab4 100644 --- a/summit/strategies/tsemo.py +++ b/summit/strategies/tsemo.py @@ -145,7 +145,7 @@ def suggest_experiments(self, num_experiments, prev_res: DataSet = None, **kwarg A Dataset object with the suggested experiments """ from GPy.models import GPRegression as gpr - from GPy.priors import LogGaussian + from GPy.core.parameterization.priors import LogGaussian from GPy.kern import Exponential, Matern32, Matern52, RBF import pyrff from pymoo.algorithms.nsga2 import NSGA2 diff --git a/summit/utils/__init__.py b/summit/utils/__init__.py index d9f7507c..005dbe5b 100644 --- a/summit/utils/__init__.py +++ b/summit/utils/__init__.py @@ -1,5 +1,6 @@ import numpy as np from copy import deepcopy +import numpy as np def jsonify_dict(d, copy=True): @@ -13,6 +14,10 @@ def jsonify_dict(d, copy=True): d[k] = jsonify_list(v) elif type(v) == dict: d[k] = jsonify_dict(v) + elif type(v) in (np.int64, np.int32, np.int8): + d[k] = int(v) + elif type(v) in (np.float16, np.float32, np.float64, np.float128): + d[k] = float(v) elif type(v) in [str, int, float, bool, tuple] or v is None: pass else: diff --git a/summit/utils/data.py b/summit/utils/data.py deleted file mode 100644 index 7b7e9453..00000000 --- a/summit/utils/data.py +++ /dev/null @@ -1,21 +0,0 @@ -# import summit -# from .dataset import DataSet -# import pandas as pd - -# #Constants -# DATA_PATH = summit.__path__[0] + '/data/' -# SOLVENT_DESCRIPTOR_DATA_FILE = DATA_PATH + 'solvent_descriptors.csv' -# SOLVENT_INDEX = 'cas_number' -# SOLVENT_METADATA_VARIABLES = ['stenutz_name', 'cosmo_name', 'chemical_formula'] -# UCB_PHARMA_APPROVED_LIST = DATA_PATH + 'ucb_pharma_approved_list.csv' - - -# #Load solvent descriptor dataset -# _solvent_candidates = pd.read_csv(SOLVENT_DESCRIPTOR_DATA_FILE) -# _solvent_candidates = _solvent_candidates.set_index(SOLVENT_INDEX) -# solvent_ds = DataSet.from_df(_solvent_candidates, metadata_columns=SOLVENT_METADATA_VARIABLES) - -# #Load UCB Pharma approved list -# ucb_list = pd.read_csv(UCB_PHARMA_APPROVED_LIST) -# ucb_list = ucb_list.set_index('cas_number') -# ucb_ds = DataSet.from_df(ucb_list, metadata_columns=['solvent_class', 'solvent_name']) diff --git a/summit/utils/lhs.py b/summit/utils/lhs.py deleted file mode 100644 index 7a2d6c05..00000000 --- a/summit/utils/lhs.py +++ /dev/null @@ -1,234 +0,0 @@ -import numpy as np -""" -The lhs code was copied from pyDoE and was originally published by -the following individuals for use with Scilab: - Copyright (C) 2012 - 2013 - Michael Baudin - Copyright (C) 2012 - Maria Christopoulou - Copyright (C) 2010 - 2011 - INRIA - Michael Baudin - Copyright (C) 2009 - Yann Collette - Copyright (C) 2009 - CEA - Jean-Marc Martinez - - website: forge.scilab.org/index.php/p/scidoe/sourcetree/master/macros -Much thanks goes to these individuals. It has been converted to Python by -Abraham Lee. - -""" -def lhs(n, samples=None, criterion=None, iterations=None, random_state=None): - """ - Generate a latin-hypercube design - - Parameters - ---------- - n : int - The number of factors to generate samples for - - Optional - -------- - samples : int - The number of samples to generate for each factor (Default: n) - criterion : str - Allowable values are "center" or "c", "maximin" or "m", - "centermaximin" or "cm", and "correlation" or "corr". If no value - given, the design is simply randomized. - iterations : int - The number of iterations in the maximin and correlations algorithms - (Default: 5). - - Returns - ------- - H : 2d-array - An n-by-samples design matrix that has been normalized so factor values - are uniformly spaced between zero and one. - - Example - ------- - >>> import numpy as np - - A 3-factor design (defaults to 3 samples):: - - >>> lhs(3, random_state=np.random.RandomState(3)) - array([[0.5036092 , 0.73574763, 0.6320977 ], - [0.70852844, 0.63098232, 0.09696825], - [0.1835993 , 0.23604927, 0.6838224 ]]) - - A 4-factor design with 6 samples:: - - >>> lhs(4, samples=6, random_state=np.random.RandomState(3)) - array([[0.3419112 , 0.54641455, 0.3383127 , 0.59847714], - [0.88058751, 0.11802464, 0.61270915, 0.4094722 ], - [0.09179965, 0.40680164, 0.18759755, 0.20120715], - [0.67066365, 0.94885632, 0.90674229, 0.85947796], - [0.60819067, 0.31604885, 0.04848412, 0.08513793], - [0.31549116, 0.75980901, 0.70987541, 0.7358502 ]]) - - A 2-factor design with 5 centered samples:: - - >>> lhs(2, samples=5, criterion='center', random_state=np.random.RandomState(3)) - array([[0.7, 0.7], - [0.1, 0.1], - [0.5, 0.9], - [0.3, 0.3], - [0.9, 0.5]]) - - A 3-factor design with 4 samples where the minimum distance between - all samples has been maximized:: - - >>> lhs(3, samples=4, criterion='maximin', random_state=np.random.RandomState(3)) - array([[0.07987376, 0.37639351, 0.92316265], - [0.25650657, 0.7314332 , 0.12061145], - [0.55174153, 0.00530644, 0.56933076], - [0.79401553, 0.9975753 , 0.47950751]]) - - A 4-factor design with 5 samples where the samples are as uncorrelated - as possible (within 10 iterations):: - - >>> lhs(4, samples=5, criterion='correlation', iterations=10, random_state=np.random.RandomState(3)) - array([[0.72982881, 0.91177082, 0.73525098, 0.71817256], - [0.37858939, 0.48816197, 0.40597524, 0.10216552], - [0.80479638, 0.37925862, 0.85185049, 0.49136664], - [0.11015958, 0.65569746, 0.22511706, 0.88302024], - [0.41029344, 0.14162956, 0.05818095, 0.24144858]]) - """ - H = None - random_state = random_state if random_state else np.random.RandomState() - - if samples is None: - samples = n - - if criterion is not None: - assert criterion.lower() in ('center', 'c', 'maximin', 'm', - 'centermaximin', 'cm', 'correlation', - 'corr'), 'Invalid value for "criterion": {}'.format(criterion) - else: - H = _lhsclassic(n, samples, random_state) - - if criterion is None: - criterion = 'center' - - if iterations is None: - iterations = 5 - - if H is None: - if criterion.lower() in ('center', 'c'): - H = _lhscentered(n, samples, random_state) - elif criterion.lower() in ('maximin', 'm'): - H = _lhsmaximin(n, samples, iterations, 'maximin', random_state) - elif criterion.lower() in ('centermaximin', 'cm'): - H = _lhsmaximin(n, samples, iterations, 'centermaximin', random_state) - elif criterion.lower() in ('correlation', 'corr'): - H = _lhscorrelate(n, samples, iterations, random_state) - - return H - -################################################################################ - -def _lhsclassic(n, samples, random_state): - # Generate the intervals - cut = np.linspace(0, 1, samples + 1) - - # Fill points uniformly in each interval - u = random_state.rand(samples, n) - a = cut[:samples] - b = cut[1:samples + 1] - rdpoints = np.zeros_like(u) - for j in range(n): - rdpoints[:, j] = u[:, j]*(b-a) + a - - # Make the random pairings - H = np.zeros_like(rdpoints) - for j in range(n): - order = random_state.permutation(range(samples)) - H[:, j] = rdpoints[order, j] - - return H - -################################################################################ - -def _lhscentered(n, samples, random_state): - # Generate the intervals - cut = np.linspace(0, 1, samples + 1) - - # Fill points uniformly in each interval - u = random_state.rand(samples, n) - a = cut[:samples] - b = cut[1:samples + 1] - _center = (a + b)/2 - - # Make the random pairings - H = np.zeros_like(u) - for j in range(n): - H[:, j] = random_state.permutation(_center) - - return H - -################################################################################ - -def _lhsmaximin(n, samples, iterations, lhstype, - random_state): - maxdist = 0 - - # Maximize the minimum distance between points - for i in range(iterations): - if lhstype=='maximin': - Hcandidate = _lhsclassic(n, samples, random_state) - else: - Hcandidate = _lhscentered(n, samples, random_state) - - d = _pdist(Hcandidate) - if maxdist 1: - raise ValueError("Y must be 1D") - - # Spectral sampling. Clip values to match Matlab implementation - noise = self._model.Gaussian_noise.variance.values[0] - sampled_f = None - for i in range(n_retries): - try: - sampled_f = pyrff.sample_rff( - lengthscales=self._model.kern.lengthscale.values, - scaling=np.sqrt(self._model.kern.variance.values[0]), - noise=noise, - kernel_nu=matern_nu, - X=X, - Y=y[:,0], - M=n_spectral_points, - ) - break - except np.linalg.LinAlgError as e: - self.logger.error(e) - except ValueError as e: - self.logger.error(e) - - if sampled_f is None: - raise RuntimeError(f"Spectral sampling failed after {n_retries} retries.") - - # Define function wrapper - def f(x_new): - y_s = sampled_f(x_new) - return np.atleast_2d(y_s).T - self.sampled_f = f - return self.sampled_f - - @property - def hyperparameters(self): - """Returns a tuple for the form legnthscales, variance, noise""" - lengthscales = self._model.kern.lengthscale.values - variance = self._model.kern.variance.values[0] - noise = self._model.Gaussian_noise.variance.values[0] - return lengthscales, variance, noise - - def to_dict(self): - _model = self._model.to_dict() if self._model is not None else self._model - return dict( - name="GPyModel", - _model=_model, - kernel=self._kernel.to_dict(), - noise_var=self._noise_var, - input_mean=list(self.input_mean), - input_std=list(self.input_std), - output_mean=list(self.output_mean), - output_std=list(self.output_std), - ) - - @classmethod - def from_dict(cls, d): - kernel = GPy.kern.Kern.from_dict(d["kernel"]) - m = cls(kernel=kernel, noise_var=d["noise_var"]) - if d["_model"] is not None: - m._model = GPRegression.from_dict(d["_model"]) - m.input_mean = np.array(d["input_mean"]) - m.input_std = np.array(d["input_std"]) - m.output_mean = np.array(d["output_mean"]) - m.output_std = np.array(d["output_std"]) - return m - -def spectral_sample(lengthscales, scaling, noise, kernel_nu, X, Y, M): - # Get variables from problem structure - n, D = np.shape(X) - ell = np.array(lengthscales) - sf2 = scaling**2 - sn2 = noise - - # Monte carlo samples of W and b - sW = lhs(D, M, criterion='maximin') - p = matlib.repmat(np.divide(1, ell), M, 1) - if kernel_nu != np.inf: - inv = chi2.ppf(sW, kernel_nu) - q = np.sqrt(np.divide(kernel_nu, inv)+1e-7) - W = np.multiply(p, norm.ppf(sW)) - W = np.multiply(W, q) - else: - raise NotImplementedError("RBF not implemented yet!") - - b = 2*np.pi*lhs(1, M) - - # Calculate phi - phi = np.sqrt(2*sf2/M)*np.cos(W@X.T + matlib.repmat(b, 1, n)) - - #Sampling of theta according to phi - #For the matrix inverses, I defualt to Cholesky when possible - A = phi@phi.T + sn2*np.identity(M) - try: - c = np.linalg.inv(np.linalg.cholesky(A)) - invA = np.dot(c.T,c) - except np.linalg.LinAlgError: - u,s, vh = np.linalg.svd(A) - invA = vh.T@np.diag(1/s)@u.T - if isinstance(Y, DataSet): - Y = Y.data_to_numpy() - mu_theta = invA@phi@Y - cov_theta = sn2*invA - #Add some noise to covariance to prevent issues - cov_theta = 0.5*(cov_theta+cov_theta.T)+1e-4*np.identity(M) - rng = default_rng() - try: - theta = rng.multivariate_normal(mu_theta, cov_theta, - method='cholesky') - except np.linalg.LinAlgError: - theta = rng.multivariate_normal(mu_theta, cov_theta, - method='svd') - - #Posterior sample according to theta - def f(x): - inputs, _ = np.shape(x) - bprime = matlib.repmat(b, 1, inputs) - output = (theta.T*np.sqrt(2*sf2/M))@np.cos(W@x.T+bprime) - return output - return f - -class AnalyticalModel(Model): - """ An analytical model instead of statistical model - - Use this for an objective that is a - known analytical function of the inputs - - Parameters - ---------- - function: callable - An an analytical function that takes an input - array and returns the output - """ - - def __init__(self, function: callable): - self._function = function - - def fit(self, X, Y, **kwargs): - """This method is here because it is required. - No fitting actually occurs""" - pass - - def predict(self, X, **kwargs): - """Predict using the analytical function - - Parameters - ---------- - X : array-like, shape = (n_samples, n_features) - Query points where the GP is evaluated - """ - - return self.function(X, **kwargs) - - @property - def function(self) -> callable: - return self._function -''' diff --git a/tests/test_benchmarks.py b/tests/test_benchmarks.py index afa70087..de541fef 100644 --- a/tests/test_benchmarks.py +++ b/tests/test_benchmarks.py @@ -1,18 +1,15 @@ import pytest -from summit.strategies import Strategy -from summit.experiment import Experiment -from summit.benchmarks import ( - SnarBenchmark, - DTLZ2, - Hartmann3D, - Himmelblau, - ThreeHumpCamel, - ReizmanSuzukiEmulator, - BaumgartnerCrossCouplingEmulator, -) +from summit.benchmarks import * from summit.utils.dataset import DataSet import numpy as np +import pandas as pd import os +import pathlib +import shutil +import pkg_resources +import matplotlib.pyplot as plt + +DATA_PATH = pathlib.Path(pkg_resources.resource_filename("summit", "benchmarks/data")) @pytest.mark.parametrize("noise_level", [0.0, 2.5]) @@ -46,31 +43,89 @@ def test_snar_benchmark(noise_level): return results -def test_baumgartner_CC_emulator(): - """ Test the Baumgartner Cross Coupling emulator""" - b = BaumgartnerCrossCouplingEmulator() +def test_train_experimental_emulator(): + model_name = f"reizman_suzuki_case_1" + domain = ReizmanSuzukiEmulator.setup_domain() + ds = DataSet.read_csv(DATA_PATH / f"{model_name}.csv") + exp = ExperimentalEmulator(model_name, domain, dataset=ds, regressor=ANNRegressor) + + # Test grid search cross validation and training + params = { + "regressor__net__max_epochs": [1, 1000], + } + exp.train(cv_folds=5, random_state=100, search_params=params, verbose=0) + + # Testing + res = exp.test() + r2 = res["test_r2"].mean() + assert r2 > 0.8 + + # Test plotting + fig, ax = exp.parity_plot(output_variables="yield", include_test=True) + + # Test saving/loading + exp.save("test_ee") + exp_2 = ExperimentalEmulator.load(model_name, "test_ee") + shutil.rmtree("test_ee") + + +def test_reizman_emulator(show_plots=False): + b = get_pretrained_reizman_suzuki_emulator(case=1) + b.parity_plot(include_test=True) + if show_plots: + plt.show() columns = [v.name for v in b.domain.variables] values = { - ("catalyst", "DATA"): "tBuXPhos", - ("base", "DATA"): "DBU", - ("t_res", "DATA"): 328.717801570892, - ("temperature", "DATA"): 30, - ("base_equivalents", "DATA"): 2.18301549894049, - ("yield", "DATA"): 0.19, + "catalyst": ["P1-L3"], + "t_res": [600], + "temperature": [30], + "catalyst_loading": [0.498], } - conditions = DataSet([values], columns=columns) - results = b.run_experiments(conditions) + conditions = pd.DataFrame(values) + conditions = DataSet.from_df(conditions) + results = b.run_experiments(conditions, return_std=True) - assert str(results["catalyst", "DATA"].iloc[0]) == values["catalyst", "DATA"] - assert str(results["base", "DATA"].iloc[0]) == values["base", "DATA"] - assert float(results["t_res"]) == values["t_res", "DATA"] - assert float(results["temperature"]) == values["temperature", "DATA"] - assert np.isclose(float(results["yld"]), 0.173581) + for name, value in values.items(): + if type(value[0]) == str: + assert str(results[name].iloc[0]) == value[0] + else: + assert float(results[name].iloc[0]) == value[0] + assert np.isclose(float(results["yield"]), 0.6, atol=15) + assert np.isclose(float(results["ton"]), 1.1, atol=15) # Test serialization d = b.to_dict() exp = BaumgartnerCrossCouplingEmulator.from_dict(d) + return results + +def test_baumgartner_CC_emulator(show_plots=False): + """ Test the Baumgartner Cross Coupling emulator""" + b = get_pretrained_baumgartner_cc_emulator() + b.parity_plot(include_test=True) + if show_plots: + plt.show() + columns = [v.name for v in b.domain.variables] + values = { + "catalyst": ["tBuXPhos"], + "base": ["DBU"], + "t_res": [328.717801570892], + "temperature": [30], + "base_equivalents": [2.18301549894049], + } + conditions = pd.DataFrame(values) + conditions = DataSet.from_df(conditions) + results = b.run_experiments(conditions, return_std=True) + + assert str(results["catalyst"].iloc[0]) == values["catalyst"][0] + assert str(results["base"].iloc[0]) == values["base"][0] + assert float(results["t_res"]) == values["t_res"][0] + assert float(results["temperature"]) == values["temperature"][0] + assert np.isclose(float(results["yield"]), 0.042832638, atol=0.15) + + # Test serialization + d = b.to_dict() + exp = BaumgartnerCrossCouplingEmulator.from_dict(d) return results @@ -84,4 +139,3 @@ def test_dltz2_benchmark(num_inputs): data = b.data assert np.isclose(data["y_0"].iloc[0], 0.7071) assert np.isclose(data["y_1"].iloc[0], 0.7071) - diff --git a/tests/test_models.py b/tests/test_models.py deleted file mode 100644 index fa1922c9..00000000 --- a/tests/test_models.py +++ /dev/null @@ -1,20 +0,0 @@ -# import pytest -# from summit.utils.models import GPyModel -# import matplotlib.pyplot as plt -# import numpy as np - -# Add back in once fixed GPyModel - -# def test_gpy_model(): -# X = np.random.uniform(-3.,3.,(20,1)) -# Y = np.sin(X) + np.random.randn(20,1)*0.05 -# m = GPyModel(input_dim=1) -# m.fit(X, Y) -# sampled_f = m.spectral_sample(X, Y) -# predict_Y = m.predict(X) -# sample_Y = sampled_f(X) -# mae_sample = np.mean(np.abs(sample_Y[:,0]-Y[:,0])) -# mae_pred = np.mean(np.abs(predict_Y[:,0]-Y[:,0])) -# assert mae_sample < 0.1 -# assert mae_pred < 0.1 - diff --git a/tests/test_runner.py b/tests/test_runner.py index a664858a..89b31f41 100644 --- a/tests/test_runner.py +++ b/tests/test_runner.py @@ -78,13 +78,22 @@ def stop(self): assert r.experiment.data.shape[0] == int(batch_size * iterations) -@pytest.mark.parametrize("strategy", [SOBO, SNOBFIT, GRYFFIN, NelderMead, Random, LHS]) +@pytest.mark.parametrize("strategy", [SOBO, SNOBFIT, NelderMead, Random, LHS]) @pytest.mark.parametrize( "experiment", - [Himmelblau, Hartmann3D, ThreeHumpCamel, BaumgartnerCrossCouplingEmulator,], + [ + Himmelblau, + Hartmann3D, + ThreeHumpCamel, + get_pretrained_baumgartner_cc_emulator(include_cost=True), + ], ) def test_runner_so_integration(strategy, experiment): - exp = experiment() + if not isinstance(experiment, ExperimentalEmulator): + exp = experiment() + else: + exp = experiment + s = strategy(exp.domain) r = Runner(strategy=s, experiment=exp, max_iterations=1, batch_size=1) @@ -96,23 +105,23 @@ def test_runner_so_integration(strategy, experiment): os.remove("test_save.json") -@pytest.mark.parametrize( - "strategy", [SOBO, SNOBFIT, GRYFFIN, NelderMead, Random, LHS, TSEMO] -) +@pytest.mark.parametrize("strategy", [SOBO, SNOBFIT, NelderMead, Random, LHS, TSEMO]) @pytest.mark.parametrize( "experiment", [ SnarBenchmark, - ReizmanSuzukiEmulator, - BaumgartnerCrossCouplingEmulator_Yield_Cost, + get_pretrained_baumgartner_cc_emulator(include_cost=True), DTLZ2, VLMOP2, ], ) def test_runner_mo_integration(strategy, experiment): - exp = experiment() + if not isinstance(experiment, ExperimentalEmulator): + exp = experiment() + else: + exp = experiment - if experiment == ReizmanSuzukiEmulator and strategy not in [SOBO, GRYFFIN]: + if experiment == ReizmanSuzukiEmulator and strategy not in [SOBO]: # only run on strategies that work with categorical variables deireclty return elif strategy == TSEMO: @@ -129,6 +138,6 @@ def test_runner_mo_integration(strategy, experiment): r.run() # Try saving and loading - r.save("test_save.json") - r.load("test_save.json") - os.remove("test_save.json") + # r.save("test_save.json") + # r.load("test_save.json") + # os.remove("test_save.json") diff --git a/tests/test_utils.py b/tests/test_utils.py deleted file mode 100644 index 4564eb65..00000000 --- a/tests/test_utils.py +++ /dev/null @@ -1,57 +0,0 @@ -# import pytest - -# from summit.utils.models import GPyModel - -# import numpy as np -# import matplotlib.pyplot as plt -# import warnings - -# @pytest.mark.parametrize('n_dim', [1,6]) -# def test_gpy_model(n_dim, n_points=100, n_repeats=5, plot=False): -# noisy_fun = lambda x: np.mean(np.sin(x), axis=1) + np.random.randn(x.shape[0])*0.05 - -# for i in range(n_repeats): -# X_train = np.random.uniform(-3.,3.,(n_points,n_dim)) -# Y_train = noisy_fun(X_train) - -# #Scaling -# X_min = np.min(X_train, axis=0) -# X_max = np.max(X_train, axis=0) -# X_train_scaled = (X_train-X_min)/(X_max-X_min) - -# Y_mean = np.mean(Y_train) -# Y_std = np.std(Y_train) -# Y_train_scaled = (Y_train-Y_mean)/Y_std -# Y_train_scaled = np.atleast_2d(Y_train_scaled).T - -# # Fit model -# warnings.filterwarnings('ignore', category=DeprecationWarning) -# m = GPyModel(input_dim=n_dim) -# m.fit(X_train_scaled, Y_train_scaled, spectral_sample=True) -# Y_train_pred_scaled = m.predict(X_train_scaled, use_spectral_sample=True) -# Y_train_pred = Y_train_pred_scaled[:,0]*Y_std + Y_mean -# square_error = (Y_train_pred-Y_train)**2 -# train_rmse = np.sqrt(np.mean(square_error)) -# print("Training root mean squared error:", train_rmse) -# assert train_rmse < 0.1 - -# # Model validation -# X_valid = np.random.uniform(-3, 3, (n_points,n_dim)) -# Y_valid = noisy_fun(X_valid) -# X_valid_scaled = (X_valid-X_min)/(X_max-X_min) - -# Y_valid_pred_scaled = m.predict(X_valid_scaled, use_spectral_sample=True) -# Y_valid_pred = Y_valid_pred_scaled[:,0]*Y_std+Y_mean - -# square_error = (Y_valid-Y_valid_pred)**2 -# valid_rmse = np.sqrt(np.mean(square_error)) -# print("Validation root mean squared error:",valid_rmse) - -# assert valid_rmse < 0.3 - -# if plot and n_dim == 1: -# fig, ax, = plt.subplots(1) -# ax.scatter(X_valid[:,0], Y_valid_pred, label="Prediction") -# ax.scatter(X_valid[:,0], Y_valid, label="True") -# ax.legend() -# plt.show()