MAterials Simulation Toolkit for Machine Learning (MAST-ML)
latest
Acknowledgements
MAST-ML version 3.x
New changes to MAST-ML
Installing MAST-ML
Hardware and Data Requirements
Hardware
Data
Terminal installation (Linux or linux-like terminal environment e.g. Mac)
Install Python3
Create a conda environment (if using Anaconda)
Create a virtualenv environment (if not using Anaconda)
Install the MAST-ML package via PyPi
Install the MAST-ML package via Git
Set up Juptyer notebooks
Imports that don’t work
Windows installation
Install Python3
Create a conda environment
Set up the Spyder IDE and Jupyter notebooks
Install the MAST-ML package
Imports that don’t work
Windows 10 install: step-by-step guide (credit Joe Kern)
Getting Started with MAST-ML
Installing MAST-ML
Performing your first MAST-ML run
Overview of MAST-ML tutorials and examples
MAST-ML tutorials
Code Documentation: Data Cleaning
mastml.data_cleaning Module
Classes
DataCleaning
DataUtilities
PPCA
Class Inheritance Diagram
Code Documentation: Data Splitters
mastml.data_splitters Module
Classes
BaseSplitter
Bootstrap
JustEachGroup
LeaveCloseCompositionsOut
LeaveMultiGroupOut
LeaveOutClusterCV
LeaveOutPercent
LeaveOutTwinCV
NoSplit
SklearnDataSplitter
Class Inheritance Diagram
Code Documentation: Datasets
mastml.datasets Module
Classes
FigshareDatasets
FoundryDatasets
LocalDatasets
MatminerDatasets
SklearnDatasets
Class Inheritance Diagram
Code Documentation: Error Analysis
mastml.error_analysis Module
Classes
CorrectionFactors
ErrorUtils
Class Inheritance Diagram
Code Documentation: Feature Generators
mastml.feature_generators Module
Classes
BaseGenerator
DataframeUtilities
ElementalFeatureGenerator
ElementalFractionGenerator
MaterialsProjectFeatureGenerator
MatminerFeatureGenerator
OneHotElementEncoder
OneHotGroupGenerator
PolynomialFeatureGenerator
Class Inheritance Diagram
Code Documentation: Feature Selectors
mastml.feature_selectors Module
Functions
selected_features_correlation
Classes
BaseSelector
EnsembleModelFeatureSelector
MASTMLFeatureSelector
NoSelect
PearsonSelector
ShapFeatureSelector
SklearnFeatureSelector
Class Inheritance Diagram
Code Documentation: Hyperparameter Optimization
mastml.hyper_opt Module
Classes
BayesianSearch
GridSearch
HyperOptUtils
RandomizedSearch
Class Inheritance Diagram
Code Documentation: Learning Curve
mastml.learning_curve Module
Classes
LearningCurve
Class Inheritance Diagram
Code Documentation: Mastml
mastml.mastml Module
Functions
parallel
write_requirements
Classes
Mastml
Class Inheritance Diagram
Code Documentation: Metrics
mastml.metrics Module
Functions
r2_score_adjusted
r2_score_fitted
r2_score_noint
rmse_over_stdev
root_mean_squared_error
Classes
Metrics
Class Inheritance Diagram
Code Documentation: Models
mastml.models Module
Classes
EnsembleModel
SklearnModel
Class Inheritance Diagram
Code Documentation: Plots
mastml.plots Module
Functions
check_dimensions
get_divisor
make_axis_same
make_fig_ax
make_fig_ax_square
make_plots
nice_mean
nice_names
nice_range
nice_std
plot_avg_score_vs_occurrence
plot_feature_occurrence
plot_stats
recursive_max
recursive_max_and_min
recursive_min
reset_index
round_down
round_up
rounder
stat_to_string
trim_array
Classes
Classification
Error
Histogram
Line
Scatter
Class Inheritance Diagram
Code Documentation: Preprocessing
mastml.preprocessing Module
Classes
BasePreprocessor
MeanStdevScaler
NoPreprocessor
SklearnPreprocessor
Class Inheritance Diagram
Code Documentation: Baseline Tests
mastml.baseline_tests Module
Classes
Baseline_tests
Class Inheritance Diagram
Code Documentation: MAST-ML Predictor
mastml.mastml_predictor Module
Functions
make_prediction
make_prediction_dlhub
MAterials Simulation Toolkit for Machine Learning (MAST-ML)
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Index
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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W
A
array_to_dataframe() (mastml.feature_generators.DataframeUtilities class method)
assign_columns_as_features() (mastml.feature_generators.DataframeUtilities class method)
B
BaseGenerator (class in mastml.feature_generators)
Baseline_tests (class in mastml.baseline_tests)
BasePreprocessor (class in mastml.preprocessing)
BaseSelector (class in mastml.feature_selectors)
BaseSplitter (class in mastml.data_splitters)
BayesianSearch (class in mastml.hyper_opt)
Bootstrap (class in mastml.data_splitters)
C
check_dimensions() (in module mastml.plots)
check_dummy_ranking() (mastml.feature_selectors.EnsembleModelFeatureSelector method)
Classification (class in mastml.plots)
clean_dataframe() (mastml.feature_generators.DataframeUtilities class method)
concatenate_arrays() (mastml.feature_generators.DataframeUtilities class method)
CorrectionFactors (class in mastml.error_analysis)
create_dummy_variable() (mastml.feature_selectors.EnsembleModelFeatureSelector method)
createClassificationReport() (mastml.plots.Classification method)
D
data_learning_curve() (mastml.learning_curve.LearningCurve method)
DataCleaning (class in mastml.data_cleaning)
dataframe_to_array() (mastml.feature_generators.DataframeUtilities class method)
DataframeUtilities (class in mastml.feature_generators)
DataUtilities (class in mastml.data_cleaning)
doProba() (mastml.plots.Classification class method)
download_data() (mastml.datasets.FigshareDatasets method)
(mastml.datasets.FoundryDatasets method)
(mastml.datasets.MatminerDatasets method)
E
ElementalFeatureGenerator (class in mastml.feature_generators)
ElementalFractionGenerator (class in mastml.feature_generators)
EnsembleModel (class in mastml.models)
EnsembleModelFeatureSelector (class in mastml.feature_selectors)
Error (class in mastml.plots)
ErrorUtils (class in mastml.error_analysis)
evaluate() (mastml.data_cleaning.DataCleaning method)
(mastml.data_splitters.BaseSplitter method)
(mastml.feature_generators.BaseGenerator method)
(mastml.feature_selectors.BaseSelector method)
(mastml.learning_curve.LearningCurve method)
(mastml.metrics.Metrics method)
(mastml.preprocessing.BasePreprocessor method)
F
feature_learning_curve() (mastml.learning_curve.LearningCurve method)
FigshareDatasets (class in mastml.datasets)
fit() (mastml.data_cleaning.PPCA method)
(mastml.feature_generators.ElementalFeatureGenerator method)
(mastml.feature_generators.ElementalFractionGenerator method)
(mastml.feature_generators.MaterialsProjectFeatureGenerator method)
(mastml.feature_generators.MatminerFeatureGenerator method)
(mastml.feature_generators.OneHotElementEncoder method)
(mastml.feature_generators.OneHotGroupGenerator method)
(mastml.feature_generators.PolynomialFeatureGenerator method)
(mastml.feature_selectors.BaseSelector method)
(mastml.feature_selectors.EnsembleModelFeatureSelector method)
(mastml.feature_selectors.MASTMLFeatureSelector method)
(mastml.feature_selectors.PearsonSelector method)
(mastml.feature_selectors.ShapFeatureSelector method)
(mastml.feature_selectors.SklearnFeatureSelector method)
(mastml.hyper_opt.BayesianSearch method)
(mastml.hyper_opt.GridSearch method)
(mastml.hyper_opt.RandomizedSearch method)
(mastml.models.EnsembleModel method)
(mastml.models.SklearnModel method)
(mastml.preprocessing.BasePreprocessor method)
(mastml.preprocessing.NoPreprocessor method)
fit_transform() (mastml.preprocessing.BasePreprocessor method)
(mastml.preprocessing.MeanStdevScaler method)
(mastml.preprocessing.NoPreprocessor method)
flag_columns_with_strings() (mastml.data_cleaning.DataUtilities class method)
flag_outliers() (mastml.data_cleaning.DataUtilities class method)
FoundryDatasets (class in mastml.datasets)
G
generate_elementfraction_features() (mastml.feature_generators.ElementalFractionGenerator method)
generate_magpie_features() (mastml.feature_generators.ElementalFeatureGenerator method)
generate_materialsproject_features() (mastml.feature_generators.MaterialsProjectFeatureGenerator method)
generate_matminer_features() (mastml.feature_generators.MatminerFeatureGenerator method)
get_available_datasets() (mastml.datasets.MatminerDatasets method)
get_dataframe_statistics() (mastml.feature_generators.DataframeUtilities class method)
get_divisor() (in module mastml.plots)
get_mastml_metadata (mastml.mastml.Mastml attribute)
get_n_splits() (mastml.data_splitters.Bootstrap method)
(mastml.data_splitters.JustEachGroup method)
(mastml.data_splitters.LeaveCloseCompositionsOut method)
(mastml.data_splitters.LeaveMultiGroupOut method)
(mastml.data_splitters.LeaveOutClusterCV method)
(mastml.data_splitters.LeaveOutPercent method)
(mastml.data_splitters.LeaveOutTwinCV method)
(mastml.data_splitters.NoSplit method)
(mastml.data_splitters.SklearnDataSplitter method)
get_params() (mastml.models.EnsembleModel method)
(mastml.models.SklearnModel method)
get_savepath (mastml.mastml.Mastml attribute)
GridSearch (class in mastml.hyper_opt)
H
help() (mastml.data_splitters.BaseSplitter method)
(mastml.models.SklearnModel method)
(mastml.preprocessing.BasePreprocessor method)
Histogram (class in mastml.plots)
HyperOptUtils (class in mastml.hyper_opt)
I
imputation() (mastml.data_cleaning.DataCleaning method)
indices (mastml.data_splitters.Bootstrap attribute)
inverse_transform() (mastml.preprocessing.BasePreprocessor method)
J
JustEachGroup (class in mastml.data_splitters)
L
labels() (mastml.data_splitters.LeaveOutClusterCV method)
LearningCurve (class in mastml.learning_curve)
LeaveCloseCompositionsOut (class in mastml.data_splitters)
LeaveMultiGroupOut (class in mastml.data_splitters)
LeaveOutClusterCV (class in mastml.data_splitters)
LeaveOutPercent (class in mastml.data_splitters)
LeaveOutTwinCV (class in mastml.data_splitters)
Line (class in mastml.plots)
load() (mastml.data_cleaning.PPCA method)
load_boston() (mastml.datasets.SklearnDatasets method)
load_breast_cancer() (mastml.datasets.SklearnDatasets method)
load_data() (mastml.datasets.LocalDatasets method)
load_diabetes() (mastml.datasets.SklearnDatasets method)
load_digits() (mastml.datasets.SklearnDatasets method)
load_friedman() (mastml.datasets.SklearnDatasets method)
load_iris() (mastml.datasets.SklearnDatasets method)
load_linnerud() (mastml.datasets.SklearnDatasets method)
load_wine() (mastml.datasets.SklearnDatasets method)
LocalDatasets (class in mastml.datasets)
M
make_axis_same() (in module mastml.plots)
make_fig_ax() (in module mastml.plots)
make_fig_ax_square() (in module mastml.plots)
make_plots() (in module mastml.plots)
make_prediction() (in module mastml.mastml_predictor)
make_prediction_dlhub() (in module mastml.mastml_predictor)
Mastml (class in mastml.mastml)
mastml.baseline_tests
module
mastml.data_cleaning
module
mastml.data_splitters
module
mastml.datasets
module
mastml.error_analysis
module
mastml.feature_generators
module
mastml.feature_selectors
module
mastml.hyper_opt
module
mastml.learning_curve
module
mastml.mastml
module
mastml.mastml_predictor
module
mastml.metrics
module
mastml.models
module
mastml.plots
module
mastml.preprocessing
module
MASTMLFeatureSelector (class in mastml.feature_selectors)
MaterialsProjectFeatureGenerator (class in mastml.feature_generators)
MatminerDatasets (class in mastml.datasets)
MatminerFeatureGenerator (class in mastml.feature_generators)
MeanStdevScaler (class in mastml.preprocessing)
merge_dataframe_columns() (mastml.feature_generators.DataframeUtilities class method)
merge_dataframe_rows() (mastml.feature_generators.DataframeUtilities class method)
Metrics (class in mastml.metrics)
module
mastml.baseline_tests
mastml.data_cleaning
mastml.data_splitters
mastml.datasets
mastml.error_analysis
mastml.feature_generators
mastml.feature_selectors
mastml.hyper_opt
mastml.learning_curve
mastml.mastml
mastml.mastml_predictor
mastml.metrics
mastml.models
mastml.plots
mastml.preprocessing
N
nice_mean() (in module mastml.plots)
nice_names() (in module mastml.plots)
nice_range() (in module mastml.plots)
nice_std() (in module mastml.plots)
nll() (mastml.error_analysis.CorrectionFactors method)
NoPreprocessor (class in mastml.preprocessing)
NoSelect (class in mastml.feature_selectors)
NoSplit (class in mastml.data_splitters)
O
OneHotElementEncoder (class in mastml.feature_generators)
OneHotGroupGenerator (class in mastml.feature_generators)
P
parallel() (in module mastml.mastml)
PearsonSelector (class in mastml.feature_selectors)
plot_avg_score_vs_occurrence() (in module mastml.plots)
plot_best_worst_per_point() (mastml.plots.Scatter class method)
plot_best_worst_split() (mastml.plots.Scatter class method)
plot_classification_report() (mastml.plots.Classification class method)
plot_cumulative_normalized_error() (mastml.plots.Error class method)
plot_feature_occurrence() (in module mastml.plots)
plot_histogram() (mastml.plots.Histogram class method)
plot_learning_curve() (mastml.plots.Line class method)
plot_metric_vs_group() (mastml.plots.Scatter class method)
plot_normalized_error() (mastml.plots.Error class method)
plot_predicted_vs_true() (mastml.plots.Scatter class method)
plot_predicted_vs_true_bars() (mastml.plots.Scatter class method)
plot_real_vs_predicted_error() (mastml.plots.Error class method)
plot_real_vs_predicted_error_uncal_cal_overlay() (mastml.plots.Error class method)
plot_residuals_histogram() (mastml.plots.Histogram class method)
plot_rstat() (mastml.plots.Error class method)
plot_rstat_uncal_cal_overlay() (mastml.plots.Error class method)
plot_stats() (in module mastml.plots)
PolynomialFeatureGenerator (class in mastml.feature_generators)
PPCA (class in mastml.data_cleaning)
ppca() (mastml.data_cleaning.DataCleaning method)
predict() (mastml.models.EnsembleModel method)
(mastml.models.SklearnModel method)
R
r2_score_adjusted() (in module mastml.metrics)
r2_score_fitted() (in module mastml.metrics)
r2_score_noint() (in module mastml.metrics)
RandomizedSearch (class in mastml.hyper_opt)
recursive_max() (in module mastml.plots)
recursive_max_and_min() (in module mastml.plots)
recursive_min() (in module mastml.plots)
remove() (mastml.data_cleaning.DataCleaning method)
remove_constant_columns() (mastml.feature_generators.DataframeUtilities class method)
reset_index() (in module mastml.plots)
rmse_over_stdev() (in module mastml.metrics)
root_mean_squared_error() (in module mastml.metrics)
round_down() (in module mastml.plots)
round_up() (in module mastml.plots)
rounder() (in module mastml.plots)
S
save() (mastml.data_cleaning.PPCA method)
save_all_dataframe_statistics() (mastml.feature_generators.DataframeUtilities class method)
Scatter (class in mastml.plots)
selected_features_correlation() (in module mastml.feature_selectors)
ShapFeatureSelector (class in mastml.feature_selectors)
SklearnDatasets (class in mastml.datasets)
SklearnDataSplitter (class in mastml.data_splitters)
SklearnFeatureSelector (class in mastml.feature_selectors)
SklearnModel (class in mastml.models)
SklearnPreprocessor (class in mastml.preprocessing)
split() (mastml.data_splitters.Bootstrap method)
(mastml.data_splitters.JustEachGroup method)
(mastml.data_splitters.LeaveCloseCompositionsOut method)
(mastml.data_splitters.LeaveMultiGroupOut method)
(mastml.data_splitters.LeaveOutClusterCV method)
(mastml.data_splitters.LeaveOutPercent method)
(mastml.data_splitters.LeaveOutTwinCV method)
(mastml.data_splitters.NoSplit method)
(mastml.data_splitters.SklearnDataSplitter method)
split_asframe() (mastml.data_splitters.BaseSplitter method)
stat_to_string() (in module mastml.plots)
T
test_classifier_dominant() (mastml.baseline_tests.Baseline_tests method)
test_classifier_random() (mastml.baseline_tests.Baseline_tests method)
test_mean() (mastml.baseline_tests.Baseline_tests method)
test_nearest_neighbour_cdist() (mastml.baseline_tests.Baseline_tests method)
test_nearest_neighbour_kdtree() (mastml.baseline_tests.Baseline_tests method)
test_permuted() (mastml.baseline_tests.Baseline_tests method)
to_excel() (mastml.baseline_tests.Baseline_tests method)
transform() (mastml.data_cleaning.PPCA method)
(mastml.feature_generators.ElementalFeatureGenerator method)
(mastml.feature_generators.ElementalFractionGenerator method)
(mastml.feature_generators.MaterialsProjectFeatureGenerator method)
(mastml.feature_generators.MatminerFeatureGenerator method)
(mastml.feature_generators.OneHotElementEncoder method)
(mastml.feature_generators.OneHotGroupGenerator method)
(mastml.feature_generators.PolynomialFeatureGenerator method)
(mastml.feature_selectors.BaseSelector method)
(mastml.feature_selectors.EnsembleModelFeatureSelector method)
(mastml.feature_selectors.MASTMLFeatureSelector method)
(mastml.feature_selectors.PearsonSelector method)
(mastml.feature_selectors.ShapFeatureSelector method)
(mastml.feature_selectors.SklearnFeatureSelector method)
(mastml.preprocessing.BasePreprocessor method)
(mastml.preprocessing.NoPreprocessor method)
trim_array() (in module mastml.plots)
W
write_requirements() (in module mastml.mastml)
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version_2.0
dev_ryan_2020-12-21
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