From 7ae41deac054ab4766230359de828584e264ef2b Mon Sep 17 00:00:00 2001 From: Alice0416 <151115442+Alice0416@users.noreply.github.com> Date: Fri, 21 Jun 2024 05:24:29 +0800 Subject: [PATCH 1/3] Add files via upload --- info.json | 55 ++++++++++++++++++++++++++++++++++++ my_python_file.py.py | 66 +++++++++++++++++++++++++++++++++++++++++++ results.json.gz | Bin 0 -> 9184 bytes 3 files changed, 121 insertions(+) create mode 100644 info.json create mode 100644 my_python_file.py.py create mode 100644 results.json.gz diff --git a/info.json b/info.json new file mode 100644 index 00000000..a0842e34 --- /dev/null +++ b/info.json @@ -0,0 +1,55 @@ +{ +"author": "Xinping Song" +"algorithm": "RF-SCM/Magpie v1.0" +"algorithm_long": +"bibtex_refs": ['@article{Dunn2020,\n' + ' doi = {10.1038/s41524-020-00406-3},\n' + ' url = {https://doi.org/10.1038/s41524-020-00406-3},\n' + ' year = {2020},\n' + ' month = sep,\n' + ' publisher = {Springer Science and Business Media {LLC}},\n' + ' volume = {6},\n' + ' number = {1},\n' + ' author = {Alexander Dunn and Qi Wang and Alex Ganose and Daniel Dopp and ' + 'Anubhav Jain},\n' + ' title = {Benchmarking materials property prediction methods: the Matbench ' + 'test set and Automatminer reference algorithm},\n' + ' journal = {npj Computational Materials}\n' + '}', + '@article{Breiman2001,\n' + ' doi = {10.1023/a:1010933404324},\n' + ' url = {https://doi.org/10.1023/a:1010933404324},\n' + ' year = {2001},\n' + ' publisher = {Springer Science and Business Media {LLC}},\n' + ' volume = {45},\n' + ' number = {1},\n' + ' pages = {5--32},\n' + ' author = {Leo Breiman},\n' + ' journal = {Machine Learning}\n' + '}', + '@article{Ward2016,\n' + ' doi = {10.1038/npjcompumats.2016.28},\n' + ' url = {https://doi.org/10.1038/npjcompumats.2016.28},\n' + ' year = {2016},\n' + ' month = aug,\n' + ' publisher = {Springer Science and Business Media {LLC}},\n' + ' volume = {2},\n' + ' number = {1},\n' + ' author = {Logan Ward and Ankit Agrawal and Alok Choudhary and Christopher ' + 'Wolverton},\n' + ' title = {A general-purpose machine learning framework for predicting ' + 'properties of inorganic materials},\n' + ' journal = {npj Computational Materials}\n' + '}', + '@article {QUA:QUA24917,author = {Faber, Felix and Lindmaa, Alexander and von ' + 'Lilienfeld, O. Anatole and Armiento, Rickard},title = {Crystal structure ' + 'representations for machine learning models of formation energies},journal = ' + '{International Journal of Quantum Chemistry},volume = {115},number = ' + '{16},issn = {1097-461X},url = {http://dx.doi.org/10.1002/qua.24917},doi = ' + '{10.1002/qua.24917},pages = {1094--1101},keywords = {machine learning, ' + 'formation energies, representations, crystal structure, periodic ' + 'systems},year = {2015},}'] +"notes": +"requirements":{"python": ["scikit-learn==0.23.2", "numpy==1.22.4", "matbench==0.6.0"]} + +} \ No newline at end of file diff --git a/my_python_file.py.py b/my_python_file.py.py new file mode 100644 index 00000000..15dfeedd --- /dev/null +++ b/my_python_file.py.py @@ -0,0 +1,66 @@ +""" +Code for training and recording the matbench_v0.1 random forest benchmark. + +The ML pipeline is placed within the Automatminer pipeline code infrastructure for convenience. + +All training and inference was done on a single 128-core HPC node. + +Reduce the number of jobs n_jobs for less memory usage on consumer machines. +""" + +if __name__ == '__main__': + from automatminer import MatPipe + from automatminer.automl.adaptors import SinglePipelineAdaptor, TPOTAdaptor + from automatminer.featurization import AutoFeaturizer + from automatminer.preprocessing import DataCleaner, FeatureReducer + from sklearn.ensemble import RandomForestClassifier, RandomForestRegressor + + from matbench.bench import MatbenchBenchmark + from multiprocessing import set_start_method + + set_start_method("spawn", force=True) + + # The learner is a single 500-estimator Random Forest model + learner = SinglePipelineAdaptor( + regressor=RandomForestRegressor(n_estimators=500), + classifier=RandomForestClassifier(n_estimators=500), + ) + pipe_config = { + "learner": learner, + "reducer": FeatureReducer(reducers=[]), + "cleaner": DataCleaner(feature_na_method="mean", max_na_frac=0.01, na_method_fit="drop", na_method_transform="mean"), + "autofeaturizer": AutoFeaturizer(n_jobs=8, preset="debug"), + } + + pipe = MatPipe(**pipe_config) + + mb = MatbenchBenchmark(autoload=False) + + i = 0 + + #for task in mb.tasks: + task = mb.matbench_jdft2d + print(task) + task.load() + for fold in task.folds: + + df_train = task.get_train_and_val_data(fold, as_type="df") + + # Fit the RF with matpipe + pipe.fit(df_train, task.metadata.target) + + df_test = task.get_test_data(fold, include_target=False, as_type="df") + predictions = pipe.predict(df_test)[f"{task.metadata.target} predicted"] + + # A single configuration is used + params = {'note': 'single config; see benchmark user metadata'} + + task.record(fold, predictions, params=params) + + mb.to_file("results_" + str(i) + ".json.gz") + i += 1 + + # Save your results + mb.to_file("results.json.gz") + + diff --git a/results.json.gz b/results.json.gz new file mode 100644 index 0000000000000000000000000000000000000000..10c38bc7b33c8aa3324bc2e2adfb5b03eaab41d5 GIT binary patch literal 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q5AEA`-@d$*??-DttamT(_P0UreEnbl4*&rF{{sLfYTrTqX8-^v)IzcV literal 0 HcmV?d00001 From e7dec77caebd737fcd438a88eba17f1959c07e83 Mon Sep 17 00:00:00 2001 From: Alice0416 <151115442+Alice0416@users.noreply.github.com> Date: Fri, 21 Jun 2024 05:52:12 +0800 Subject: [PATCH 2/3] update new requirements update using python 3.8 --- info.json | 118 +++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 117 insertions(+), 1 deletion(-) diff --git a/info.json b/info.json index a0842e34..3b05fa5d 100644 --- a/info.json +++ b/info.json @@ -50,6 +50,122 @@ 'formation energies, representations, crystal structure, periodic ' 'systems},year = {2015},}'] "notes": -"requirements":{"python": ["scikit-learn==0.23.2", "numpy==1.22.4", "matbench==0.6.0"]} +"requirements":{asttokens==2.0.5 +attrs==21.4.0 +automatminer @ git+https://github.com/noidvan/automatminer.git@ceb81f8537dd66fcaa3fef43396b2e102366cfd2 +backcall==0.2.0 +beniget==0.4.1 +black==21.12b0 +certifi==2021.10.8 +cffi==1.15.0 +charset-normalizer==2.0.10 +click==8.0.3 +cloudpickle==2.0.0 +cycler==0.11.0 +Cython==0.29.26 +daal==2021.5.1 +dask==2022.1.0 +deap==1.4.1 +decorator==5.1.1 +distlib==0.3.4 +dnspython==2.6.1 +emmet-core==0.68.0 +executing==0.8.2 +filelock==3.4.2 +fonttools==4.28.5 +fsspec==2022.1.0 +future==1.0.0 +gast==0.5.3 +hypothesis==6.35.1 +idna==3.3 +importlib_resources==6.4.0 +iniconfig==1.1.1 +intel-openmp==2022.0.1 +ipp==2021.5.1 +ipython==8.0.0 +jedi==0.18.1 +joblib==1.1.0 +kiwisolver==1.3.2 +latexcodec==3.0.0 +line-profiler==3.4.0 +llvmlite==0.38.0 +locket==0.2.1 +matbench @ git+https://github.com/noidvan/matbench@abdb4679b2ee92d0659527d10e7d75e14a87d7a4 +matminer==0.8.0 +matplotlib==3.5.1 +matplotlib-inline==0.1.3 +memory-profiler==0.60.0 +mkl==2022.0.1 +monty==2024.5.24 +mp-api==0.36.1 +mpmath==1.3.0 +msgpack==1.0.8 +mypy-extensions==0.4.3 +networkx==3.2.1 +numba==0.55.0 +numexpr==2.8.1 +numpy==1.22.4 +packaging==21.3 +palettable==3.3.3 +pandas==1.3.5 +parso==0.8.3 +partd==1.2.0 +pathspec==0.9.0 +pexpect==4.8.0 +pickleshare==0.7.5 +Pillow==9.0.0 +platformdirs==2.4.1 +plotly==5.22.0 +pluggy==1.0.0 +ply==3.11 +prompt-toolkit==3.0.24 +psutil==5.9.0 +ptyprocess==0.7.0 +pure-eval==0.2.1 +py==1.11.0 +pybind11==2.9.0 +pybtex==0.24.0 +pycparser==2.21 +pydantic==1.10.16 +Pygments==2.11.2 +pymatgen==2023.8.10 +pymongo==4.7.3 +pyparsing==3.0.6 +pytest==6.2.5 +python-dateutil==2.8.2 +pythran==0.11.0 +pytz==2021.3 +PyYAML==5.3.1 +requests==2.27.1 +ruamel.yaml==0.17.4 +ruamel.yaml.clib==0.2.8 +scikit-learn==0.23.2 +scipy==1.7.3 +six==1.16.0 +skrebate==0.62 +sortedcontainers==2.4.0 +spglib==2.4.0 +stack-data==0.1.4 +stopit==1.1.2 +sympy==1.12.1 +tabulate==0.9.0 +tbb==2021.4.0 +tenacity==8.3.0 +threadpoolctl==3.0.0 +toml==0.10.2 +tomli==1.2.3 +toolz==0.11.2 +TPOT==0.11.7 +tqdm==4.66.4 +traitlets==5.1.1 +typing_extensions==4.12.2 +uncertainties==3.2.1 +update-checker==0.18.0 +urllib3==1.26.8 +virtualenv==20.13.0 +wcwidth==0.2.5 +xgboost==1.5.2 +zipp==3.19.2 +} } \ No newline at end of file From ebc93bb1299ee7b5260817496fc700d1d2018a97 Mon Sep 17 00:00:00 2001 From: Alice0416 <151115442+Alice0416@users.noreply.github.com> Date: Fri, 21 Jun 2024 06:02:22 +0800 Subject: [PATCH 3/3] update python version python == 3.8 --- info.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/info.json b/info.json index 3b05fa5d..97b65c8c 100644 --- a/info.json +++ b/info.json @@ -50,7 +50,8 @@ 'formation energies, representations, crystal structure, periodic ' 'systems},year = {2015},}'] "notes": -"requirements":{asttokens==2.0.5 +"python_version": ">=3.8,<3.9" +"requirements":{"python":[asttokens==2.0.5 attrs==21.4.0 automatminer @ git+https://github.com/noidvan/automatminer.git@ceb81f8537dd66fcaa3fef43396b2e102366cfd2 backcall==0.2.0 @@ -165,7 +166,7 @@ urllib3==1.26.8 virtualenv==20.13.0 wcwidth==0.2.5 xgboost==1.5.2 -zipp==3.19.2 +zipp==3.19.2] } } \ No newline at end of file