From c365aedf44797667d8c0dd9356d57374fc357ec1 Mon Sep 17 00:00:00 2001 From: Gianmarco Ghiandoni <30413455+ghiander@users.noreply.github.com> Date: Wed, 15 Mar 2023 12:22:34 +0000 Subject: [PATCH] dumped best params into serialisable and fixed optuna to version 2.3.0 (#225) --- .../03-optuna_deltag_fitting_best_params.json | 13 + notebooks/gerber_deltag_validation.ipynb | 10 +- notebooks/guthrie_deltag_validation.ipynb | 11 +- optimisation/02-deltag_fitting.py | 10 +- optimisation/config.py | 1 + optimisation/helpers.py | 28 +- poetry.lock | 611 +++++++++++------- pyproject.toml | 4 +- 8 files changed, 449 insertions(+), 239 deletions(-) create mode 100644 data/optuna_fitting/03-optuna_deltag_fitting_best_params.json diff --git a/data/optuna_fitting/03-optuna_deltag_fitting_best_params.json b/data/optuna_fitting/03-optuna_deltag_fitting_best_params.json new file mode 100644 index 0000000..0c3ca8d --- /dev/null +++ b/data/optuna_fitting/03-optuna_deltag_fitting_best_params.json @@ -0,0 +1,13 @@ +{ + "gd": -0.9076664181509553, + "ga": -16.13143317348325, + "g0": 1.8842791231644282, + "gs": 0.046698073586512054, + "gr": -3.6429426011852524, + "gpi1": -1.6022604035599135, + "gpi2": -1.1740853831959548, + "gi": 4.999560447432514, + "F": 0.5143359987215719, + "expd": 0.5041243951898653, + "expa": 0.3436880638589098 +} \ No newline at end of file diff --git a/notebooks/gerber_deltag_validation.ipynb b/notebooks/gerber_deltag_validation.ipynb index 13b7386..c91956c 100644 --- a/notebooks/gerber_deltag_validation.ipynb +++ b/notebooks/gerber_deltag_validation.ipynb @@ -9,6 +9,7 @@ "import os\n", "import sys\n", "import bz2\n", + "import json\n", "import mpld3\n", "import pandas as pd\n", "import _pickle as cPickle\n", @@ -72,11 +73,10 @@ "input_data = bz2.BZ2File(data_filepath, 'rb')\n", "input_data = cPickle.load(input_data)\n", "\n", - "# Open the study\n", - "study_filepath = os.path.join(optuna_path, config.OPTUNA_DELTAG_STUDY_FILENAME)\n", - "study = bz2.BZ2File(study_filepath, 'rb')\n", - "study = cPickle.load(study)\n", - "best_params = study.best_trial.params\n", + "# Open the parameters\n", + "params_filepath = os.path.join(optuna_path, config.OPTUNA_DELTAG_PARAMETERS_FILENAME)\n", + "with open(params_filepath) as f:\n", + " best_params = json.load(f)\n", "best_params" ] }, diff --git a/notebooks/guthrie_deltag_validation.ipynb b/notebooks/guthrie_deltag_validation.ipynb index 748f42b..d288d70 100644 --- a/notebooks/guthrie_deltag_validation.ipynb +++ b/notebooks/guthrie_deltag_validation.ipynb @@ -9,6 +9,7 @@ "import os\n", "import sys\n", "import bz2\n", + "import json\n", "import mpld3\n", "import pandas as pd\n", "import _pickle as cPickle\n", @@ -64,14 +65,12 @@ "sys.path.insert(0, opt_path)\n", "import config\n", "\n", - "# Open the study\n", + "# Open the parameters\n", "data_path = os.path.abspath(os.path.join(os.getcwd(), '..', config.DATA_PATH))\n", "optuna_path = os.path.join(data_path, config.OPTUNA_DIRNAME)\n", - "study_filepath = os.path.join(optuna_path, config.OPTUNA_DELTAG_STUDY_FILENAME)\n", - "study = bz2.BZ2File(study_filepath, 'rb')\n", - "study = cPickle.load(study)\n", - "\n", - "best_params = study.best_trial.params\n", + "params_filepath = os.path.join(optuna_path, config.OPTUNA_DELTAG_PARAMETERS_FILENAME)\n", + "with open(params_filepath) as f:\n", + " best_params = json.load(f)\n", "best_params" ] }, diff --git a/optimisation/02-deltag_fitting.py b/optimisation/02-deltag_fitting.py index b91f850..1e6c82b 100644 --- a/optimisation/02-deltag_fitting.py +++ b/optimisation/02-deltag_fitting.py @@ -1,6 +1,7 @@ """Parameter fitting of Jazzy using Optuna and sklearn.""" # optimisation/02-deltag_fitting.py import config +from helpers import dump_parameters_to_json from helpers import load_data_configuration from helpers import run_optimisation from sklearn.metrics import mean_absolute_error @@ -106,10 +107,13 @@ def deltag_objective(trial): return loss -# load input/ouput configuration -input_data, study_filepath = load_data_configuration( - config.OPTUNA_DELTAG_STUDY_FILENAME +# load input/output configuration +input_data, study_filepath, params_filepath = load_data_configuration( + config.OPTUNA_DELTAG_STUDY_FILENAME, config.OPTUNA_DELTAG_PARAMETERS_FILENAME ) # run optimisation study = run_optimisation(deltag_objective, study_filepath, verbose=config.VERBOSE) + +# dump best parameters into json +dump_parameters_to_json(study_filepath, params_filepath) diff --git a/optimisation/config.py b/optimisation/config.py index 3a72667..91c863f 100644 --- a/optimisation/config.py +++ b/optimisation/config.py @@ -9,6 +9,7 @@ ORIGINAL_DATA_FILENAME = "03-free_energies_gerber_curated.txt" PRECALCULATED_DATA_FILENAME = "01-precalculated_mol_data.pbz2" OPTUNA_DELTAG_STUDY_FILENAME = "02-optuna_deltag_fitting_study.pbz2" +OPTUNA_DELTAG_PARAMETERS_FILENAME = "03-optuna_deltag_fitting_best_params.json" # logic configuration MINIMISATION_METHOD = "MMFF94" diff --git a/optimisation/helpers.py b/optimisation/helpers.py index f03deba..9103990 100644 --- a/optimisation/helpers.py +++ b/optimisation/helpers.py @@ -2,6 +2,7 @@ # optimisation/helpers.py import _pickle as cpickle import bz2 +import json import os import config @@ -9,11 +10,12 @@ from optuna.samplers import TPESampler -def load_data_configuration(study_filename): +def load_data_configuration(study_filename, params_filename): """Abstraction for input and output loading and configuration setting. - The method only accepts the name of the output study file, whilst - the rest of the parameters must be defined in a config file. + The method only accepts the name of the output study and best parameters + files, whilst the rest of the parameters must be defined in a config file. + """ # load the input data_path = os.path.abspath(os.path.join(os.getcwd(), "..", config.DATA_PATH)) @@ -24,7 +26,8 @@ def load_data_configuration(study_filename): # configure output study_filepath = os.path.join(optuna_path, study_filename) - return input_data, study_filepath + params_filepath = os.path.join(optuna_path, params_filename) + return input_data, study_filepath, params_filepath def run_optimisation(objective, study_filepath, verbose=False): @@ -80,3 +83,20 @@ def early_stopping_opt(study, trial): # write the results out with bz2.BZ2File(study_filepath, "w") as f: cpickle.dump(study, f) + + +def dump_parameters_to_json(study_filepath, params_filepath): + """Helper for dumping the study best parameters. + + Accepts the path to a study file, unpickles it, + and dumps the best parameters into a serialisable. + + """ + # read the parameters + with bz2.BZ2File(study_filepath, "rb") as f: + study = cpickle.load(f) + best_params = study.best_trial.params + + # dump the parameters + with open(params_filepath, "w") as f: + json.dump(best_params, f, indent=4) diff --git a/poetry.lock b/poetry.lock index ef02bdc..7529f02 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. 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"20.19.0" +version = "20.21.0" description = "Virtual Python Environment builder" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.19.0-py3-none-any.whl", hash = "sha256:54eb59e7352b573aa04d53f80fc9736ed0ad5143af445a1e539aada6eb947dd1"}, - {file = "virtualenv-20.19.0.tar.gz", hash = "sha256:37a640ba82ed40b226599c522d411e4be5edb339a0c0de030c0dc7b646d61590"}, + {file = "virtualenv-20.21.0-py3-none-any.whl", hash = "sha256:31712f8f2a17bd06234fa97fdf19609e789dd4e3e4bf108c3da71d710651adbc"}, + {file = "virtualenv-20.21.0.tar.gz", hash = "sha256:f50e3e60f990a0757c9b68333c9fdaa72d7188caa417f96af9e52407831a3b68"}, ] [package.dependencies] @@ -2099,6 +2260,18 @@ platformdirs = ">=2.4,<4" docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"] test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"] +[[package]] +name = "wcwidth" +version = "0.2.6" +description = "Measures the displayed width of unicode strings in a terminal" +category = "main" +optional = true +python-versions = "*" +files = [ + {file = "wcwidth-0.2.6-py2.py3-none-any.whl", hash = "sha256:795b138f6875577cd91bba52baf9e445cd5118fd32723b460e30a0af30ea230e"}, + {file = "wcwidth-0.2.6.tar.gz", hash = "sha256:a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0"}, +] + [[package]] name = "xdoctest" version = "1.1.1" @@ -2131,21 +2304,21 @@ tests-strict = ["codecov (==2.0.15)", "pytest (==4.6.0)", "pytest (==4.6.0)", "p [[package]] name = "zipp" -version = "3.13.0" +version = "3.15.0" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "zipp-3.13.0-py3-none-any.whl", hash = "sha256:e8b2a36ea17df80ffe9e2c4fda3f693c3dad6df1697d3cd3af232db680950b0b"}, - {file = "zipp-3.13.0.tar.gz", hash = "sha256:23f70e964bc11a34cef175bc90ba2914e1e4545ea1e3e2f67c079671883f9cb6"}, + {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"}, + {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"}, ] [package.extras] docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [metadata] lock-version = "2.0" python-versions = "^3.8.0" -content-hash = "6002f780f2fbdfeb4e94830431b11422bcd9350f38e4e1d500a24eb31360b1b5" +content-hash = "b63c827ab0bf47574494b3c3a224cec96fc661285f1a8a63a5079f40807c33cb" diff --git a/pyproject.toml b/pyproject.toml index 31073c8..7baeeab 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "jazzy" -version = "0.0.8" +version = "0.0.9" description = "Jazzy" authors = ["Gian Marco Ghiandoni ", "Eike Caldeweyher "] license = "Apache-2.0" @@ -22,7 +22,7 @@ python = "^3.8.0" click = "8.0.4" rdkit-pypi = "<=2021.9.4" kallisto = "^1.0.9" -optuna = {version = "3.1.0", optional = true} +optuna = {version = "2.3.0", optional = true} [tool.poetry.dev-dependencies] pytest = "^7.2.0"