From a7a5995813bbed06cf34bb10c9eaf5615f02ffcc Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 14:30:31 -0700 Subject: [PATCH 01/11] a baseline tree-based feature reduction class --- matbench/preprocessing/feature_selection.py | 56 +++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 matbench/preprocessing/feature_selection.py diff --git a/matbench/preprocessing/feature_selection.py b/matbench/preprocessing/feature_selection.py new file mode 100644 index 00000000..e6d78e2a --- /dev/null +++ b/matbench/preprocessing/feature_selection.py @@ -0,0 +1,56 @@ +from matbench.utils.utils import setup_custom_logger, MatbenchError +from sklearn.ensemble import RandomForestRegressor + + +class TreeBasedFeatureReduction(object): + """ + Provides different methods for feature selection/reduction mainly before + the production model is fit hence being under preprocessing. + + Args: + importance_percentile (float): the selected percentile of the features + sorted (descending) based on their importance. + """ + def __init__(self, importance_percentile=0.95, loglevel=None, logpath='.'): + self.logger = setup_custom_logger(filepath=logpath, level=loglevel) + self.importance_percentile = importance_percentile + self.selected_features = None + + def get_top_features(self, feat_importance): + selected_feats = [] + frac = 0.0 + for feat in feat_importance: + selected_feats.append(feat[0]) + frac += feat[1] + if frac >= self.importance_percentile: + break + return selected_feats + + def fit(self, X, y, tree='rf', recursive=True): + m0 = len(X.columns) # initial number of features + if isinstance(tree, str): + if tree=='rf': + tree = RandomForestRegressor() + else: + raise MatbenchError('Unsupported tree_type {}!'.format(tree)) + m_curr = 0 # current number of top/important features + m_prev = len(X.columns) + while m_curr < m_prev: + tree.fit(X, y) + fimportance = sorted(zip(X.columns, tree.feature_importances_), + key=lambda x: x[1], reverse=True) + tfeats = self.get_top_features(fimportance) + m_curr = len(tfeats) + m_prev = len(X.columns) + self.logger.debug('nfeatures: {}->{}'.format(len(X.columns), m_curr)) + X = X[tfeats] + if not recursive: + break + self.logger.info('Finished one_tree_reduction reducing the number of ' + 'features from {} to {}'.format(m0, len(tfeats))) + self.selected_features = tfeats + + def transform(self, X, y=None): + if self.selected_features is None: + raise MatbenchError('Please call fit first') + return X[self.selected_features] \ No newline at end of file From 24187336ac10ff8400e1d9da6ce7be063c36457c Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 14:37:20 -0700 Subject: [PATCH 02/11] better handling of the "tree" input arg --- matbench/preprocessing/feature_selection.py | 31 +++++++++++++++++---- 1 file changed, 26 insertions(+), 5 deletions(-) diff --git a/matbench/preprocessing/feature_selection.py b/matbench/preprocessing/feature_selection.py index e6d78e2a..fe8ec168 100644 --- a/matbench/preprocessing/feature_selection.py +++ b/matbench/preprocessing/feature_selection.py @@ -1,5 +1,6 @@ from matbench.utils.utils import setup_custom_logger, MatbenchError -from sklearn.ensemble import RandomForestRegressor +from sklearn.ensemble import RandomForestRegressor, RandomForestClassifier, \ + GradientBoostingClassifier, GradientBoostingRegressor class TreeBasedFeatureReduction(object): @@ -11,7 +12,8 @@ class TreeBasedFeatureReduction(object): importance_percentile (float): the selected percentile of the features sorted (descending) based on their importance. """ - def __init__(self, importance_percentile=0.95, loglevel=None, logpath='.'): + def __init__(self, mode, importance_percentile=0.95, loglevel=None, logpath='.'): + self.mode = mode self.logger = setup_custom_logger(filepath=logpath, level=loglevel) self.importance_percentile = importance_percentile self.selected_features = None @@ -27,10 +29,29 @@ def get_top_features(self, feat_importance): return selected_feats def fit(self, X, y, tree='rf', recursive=True): - m0 = len(X.columns) # initial number of features + """ + + Args: + X (pandas.DataFrame): + y: + tree: + recursive: + + Returns: + + """ + m0 = len(X.columns) if isinstance(tree, str): - if tree=='rf': - tree = RandomForestRegressor() + if tree.lower() in ['rf', 'random forest', 'randomforest']: + if self.mode.lower() in ['classification', 'classifier']: + tree = RandomForestClassifier() + else: + tree = RandomForestRegressor() + elif tree.lower() in ['gb', 'gbt', 'gradiet boosting']: + if self.mode.lower() in ['classification', 'classifier']: + tree = GradientBoostingClassifier() + else: + tree = GradientBoostingRegressor() else: raise MatbenchError('Unsupported tree_type {}!'.format(tree)) m_curr = 0 # current number of top/important features From 8866101f70b8b1653fb353daafe138992890fc02 Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 14:42:37 -0700 Subject: [PATCH 03/11] add docs to fit --- matbench/preprocessing/feature_selection.py | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/matbench/preprocessing/feature_selection.py b/matbench/preprocessing/feature_selection.py index fe8ec168..7bf08fa5 100644 --- a/matbench/preprocessing/feature_selection.py +++ b/matbench/preprocessing/feature_selection.py @@ -32,13 +32,17 @@ def fit(self, X, y, tree='rf', recursive=True): """ Args: - X (pandas.DataFrame): - y: - tree: - recursive: - - Returns: + X (pandas.DataFrame): input data, note that numpy matrix is NOT + accepted since the X.columns is used for feature names + y (pandas.Series or np.ndarray): list of outputs used for fitting + the tree model + tree (str or instantiated sklearn tree-based model): if a model is + directly fed, it must have the .feature_importances_ attribute + recursive (bool): whether to recursively reduce the features (True) + or just do it once (False) + Returns (None): + sets the class attribute .selected_features """ m0 = len(X.columns) if isinstance(tree, str): @@ -54,6 +58,7 @@ def fit(self, X, y, tree='rf', recursive=True): tree = GradientBoostingRegressor() else: raise MatbenchError('Unsupported tree_type {}!'.format(tree)) + m_curr = 0 # current number of top/important features m_prev = len(X.columns) while m_curr < m_prev: From a495b11a59e7741a6d45fc500c1983fa081d0a9b Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 14:52:16 -0700 Subject: [PATCH 04/11] separate get_reduced_features to start implementing cross-validation --- matbench/preprocessing/feature_selection.py | 44 ++++++++++++--------- 1 file changed, 26 insertions(+), 18 deletions(-) diff --git a/matbench/preprocessing/feature_selection.py b/matbench/preprocessing/feature_selection.py index 7bf08fa5..865f1538 100644 --- a/matbench/preprocessing/feature_selection.py +++ b/matbench/preprocessing/feature_selection.py @@ -12,11 +12,13 @@ class TreeBasedFeatureReduction(object): importance_percentile (float): the selected percentile of the features sorted (descending) based on their importance. """ - def __init__(self, mode, importance_percentile=0.95, loglevel=None, logpath='.'): + def __init__(self, mode, importance_percentile=0.95, loglevel=None, + logpath='.', random_state=0): self.mode = mode self.logger = setup_custom_logger(filepath=logpath, level=loglevel) self.importance_percentile = importance_percentile self.selected_features = None + self.rs = random_state def get_top_features(self, feat_importance): selected_feats = [] @@ -28,8 +30,26 @@ def get_top_features(self, feat_importance): break return selected_feats + def get_reduced_features(self, tree_model, X, y, recursive=True): + m_curr = 0 # current number of top/important features + m_prev = len(X.columns) + while m_curr < m_prev: + tree_model.fit(X, y) + fimportance = sorted(zip(X.columns, tree_model.feature_importances_), + key=lambda x: x[1], reverse=True) + tfeats = self.get_top_features(fimportance) + m_curr = len(tfeats) + m_prev = len(X.columns) + self.logger.debug( + 'nfeatures: {}->{}'.format(len(X.columns), m_curr)) + X = X[tfeats] + if not recursive: + break + return tfeats + def fit(self, X, y, tree='rf', recursive=True): """ + Fits to the data (X) and target (y) to determine the selected_features. Args: X (pandas.DataFrame): input data, note that numpy matrix is NOT @@ -48,30 +68,18 @@ def fit(self, X, y, tree='rf', recursive=True): if isinstance(tree, str): if tree.lower() in ['rf', 'random forest', 'randomforest']: if self.mode.lower() in ['classification', 'classifier']: - tree = RandomForestClassifier() + tree = RandomForestClassifier(random_state=self.rs) else: - tree = RandomForestRegressor() + tree = RandomForestRegressor(random_state=self.rs) elif tree.lower() in ['gb', 'gbt', 'gradiet boosting']: if self.mode.lower() in ['classification', 'classifier']: - tree = GradientBoostingClassifier() + tree = GradientBoostingClassifier(random_state=self.rs) else: - tree = GradientBoostingRegressor() + tree = GradientBoostingRegressor(random_state=self.rs) else: raise MatbenchError('Unsupported tree_type {}!'.format(tree)) - m_curr = 0 # current number of top/important features - m_prev = len(X.columns) - while m_curr < m_prev: - tree.fit(X, y) - fimportance = sorted(zip(X.columns, tree.feature_importances_), - key=lambda x: x[1], reverse=True) - tfeats = self.get_top_features(fimportance) - m_curr = len(tfeats) - m_prev = len(X.columns) - self.logger.debug('nfeatures: {}->{}'.format(len(X.columns), m_curr)) - X = X[tfeats] - if not recursive: - break + tfeats = self.get_reduced_features(tree, X, y, recursive=recursive) self.logger.info('Finished one_tree_reduction reducing the number of ' 'features from {} to {}'.format(m0, len(tfeats))) self.selected_features = tfeats From 973f92346be4db12cfa8aadd9840cf6b348faa85 Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 15:15:51 -0700 Subject: [PATCH 05/11] implement cross-validation in tree-based feature selection --- matbench/preprocessing/feature_selection.py | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/matbench/preprocessing/feature_selection.py b/matbench/preprocessing/feature_selection.py index 865f1538..04899979 100644 --- a/matbench/preprocessing/feature_selection.py +++ b/matbench/preprocessing/feature_selection.py @@ -1,7 +1,9 @@ +import pandas as pd from matbench.utils.utils import setup_custom_logger, MatbenchError +from sklearn.base import is_classifier from sklearn.ensemble import RandomForestRegressor, RandomForestClassifier, \ GradientBoostingClassifier, GradientBoostingRegressor - +from sklearn.model_selection import RandomizedSearchCV, check_cv class TreeBasedFeatureReduction(object): """ @@ -47,7 +49,7 @@ def get_reduced_features(self, tree_model, X, y, recursive=True): break return tfeats - def fit(self, X, y, tree='rf', recursive=True): + def fit(self, X, y, tree='rf', recursive=True, cv=5): """ Fits to the data (X) and target (y) to determine the selected_features. @@ -79,10 +81,16 @@ def fit(self, X, y, tree='rf', recursive=True): else: raise MatbenchError('Unsupported tree_type {}!'.format(tree)) - tfeats = self.get_reduced_features(tree, X, y, recursive=recursive) - self.logger.info('Finished one_tree_reduction reducing the number of ' - 'features from {} to {}'.format(m0, len(tfeats))) - self.selected_features = tfeats + cv = check_cv(cv=cv, y=y, classifier=is_classifier(tree)) + all_feats = [] + for train, test in cv.split(X, y, groups=None): + Xtrn = X.iloc[train] + ytrn = y[train] + all_feats += self.get_reduced_features(tree, Xtrn, ytrn, recursive) + # take the union of selected features of each fold + self.selected_features = list(set(all_feats)) + self.logger.info('Finished tree-based feature reduction of {} intial ' + 'features to {}'.format(m0, len(self.selected_features))) def transform(self, X, y=None): if self.selected_features is None: From 47b62469ec20d0bb71389d1a1c177148a52e1dfb Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 15:27:00 -0700 Subject: [PATCH 06/11] complete docs for methods --- matbench/preprocessing/feature_selection.py | 41 +++++++++++++++++++-- 1 file changed, 38 insertions(+), 3 deletions(-) diff --git a/matbench/preprocessing/feature_selection.py b/matbench/preprocessing/feature_selection.py index 04899979..24802069 100644 --- a/matbench/preprocessing/feature_selection.py +++ b/matbench/preprocessing/feature_selection.py @@ -1,9 +1,8 @@ -import pandas as pd from matbench.utils.utils import setup_custom_logger, MatbenchError from sklearn.base import is_classifier from sklearn.ensemble import RandomForestRegressor, RandomForestClassifier, \ GradientBoostingClassifier, GradientBoostingRegressor -from sklearn.model_selection import RandomizedSearchCV, check_cv +from sklearn.model_selection import check_cv class TreeBasedFeatureReduction(object): """ @@ -23,6 +22,18 @@ def __init__(self, mode, importance_percentile=0.95, loglevel=None, self.rs = random_state def get_top_features(self, feat_importance): + """ + Simple function to through a sorted list of features and select top + percentiles. + + Args: + feat_importance ([(str, float)]): a sorted list of + (feature, importance) tuples + + Returns ([str]): list of the top * percentile of features. * determined + by importance_percentile argument. + + """ selected_feats = [] frac = 0.0 for feat in feat_importance: @@ -33,6 +44,19 @@ def get_top_features(self, feat_importance): return selected_feats def get_reduced_features(self, tree_model, X, y, recursive=True): + """ + Gives a reduced list of feature names given a tree-based model that + has the .feature_importances_ attribute. + + Args: + tree_model (instantiated sklearn tree-based model): + X (pandas.dataframe): + y (pandas.Series or numpy.ndarray): the target column + recursive (bool): + + Returns ([str]): list of the top * percentile of features. * determined + by importance_percentile argument. + """ m_curr = 0 # current number of top/important features m_prev = len(X.columns) while m_curr < m_prev: @@ -93,6 +117,17 @@ def fit(self, X, y, tree='rf', recursive=True, cv=5): 'features to {}'.format(m0, len(self.selected_features))) def transform(self, X, y=None): + """ + Transforms the data with the subset of features determined after + calling the fit method on the data. + + Args: + X (pandas.DataFrame): input data, note that numpy matrix is NOT + accepted since the X.columns is used for feature names + y (placeholder): ignored input (for consistency in notation) + + Returns (pandas.DataFrame): the data with reduced number of features. + """ if self.selected_features is None: - raise MatbenchError('Please call fit first') + raise MatbenchError('The fit method should be called first!') return X[self.selected_features] \ No newline at end of file From 8fbc505d693912689448a11130c67f9071ed5f19 Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 16:01:55 -0700 Subject: [PATCH 07/11] add a test file for preprocessing tests --- .../tests/test_featurized_df.csv | 201 ++++++++++++++++++ 1 file changed, 201 insertions(+) create mode 100644 matbench/preprocessing/tests/test_featurized_df.csv diff --git a/matbench/preprocessing/tests/test_featurized_df.csv b/matbench/preprocessing/tests/test_featurized_df.csv new file mode 100644 index 00000000..d2e6e27c --- /dev/null +++ b/matbench/preprocessing/tests/test_featurized_df.csv @@ -0,0 +1,201 @@ +formula,HOMO_energy,LUMO_energy,gap_AO,minimum X,maximum X,range X,mean X,std_dev X,minimum row,maximum row,range row,mean row,std_dev row,minimum group,maximum group,range group,mean group,std_dev group,minimum block,maximum block,range block,mean block,std_dev block,minimum atomic_mass,maximum atomic_mass,range atomic_mass,mean atomic_mass,std_dev atomic_mass,minimum atomic_radius,maximum atomic_radius,range atomic_radius,mean atomic_radius,std_dev atomic_radius,minimum mendeleev_no,maximum mendeleev_no,range mendeleev_no,mean mendeleev_no,std_dev mendeleev_no,minimum thermal_conductivity,maximum thermal_conductivity,range thermal_conductivity,mean thermal_conductivity,std_dev thermal_conductivity,minimum melting_point,maximum melting_point,range melting_point,mean melting_point,std_dev melting_point,minimum Number,maximum Number,range Number,mean Number,avg_dev Number,mode Number,minimum MendeleevNumber,maximum MendeleevNumber,range MendeleevNumber,mean MendeleevNumber,avg_dev MendeleevNumber,mode MendeleevNumber,minimum AtomicWeight,maximum AtomicWeight,range AtomicWeight,mean AtomicWeight,avg_dev AtomicWeight,mode AtomicWeight,minimum MeltingT,maximum MeltingT,range MeltingT,mean MeltingT,avg_dev MeltingT,mode MeltingT,minimum Column,maximum Column,range Column,mean Column,avg_dev Column,mode Column,minimum Row,maximum Row,range Row,mean Row,avg_dev Row,mode Row,minimum CovalentRadius,maximum CovalentRadius,range CovalentRadius,mean CovalentRadius,avg_dev CovalentRadius,mode CovalentRadius,minimum Electronegativity,maximum Electronegativity,range Electronegativity,mean Electronegativity,avg_dev Electronegativity,mode Electronegativity,minimum NsValence,maximum NsValence,range NsValence,mean NsValence,avg_dev NsValence,mode NsValence,minimum NpValence,maximum NpValence,range NpValence,mean NpValence,avg_dev NpValence,mode NpValence,minimum NdValence,maximum NdValence,range NdValence,mean NdValence,avg_dev NdValence,mode NdValence,minimum NfValence,maximum NfValence,range NfValence,mean NfValence,avg_dev NfValence,mode NfValence,minimum NValence,maximum NValence,range NValence,mean NValence,avg_dev NValence,mode NValence,minimum NsUnfilled,maximum NsUnfilled,range NsUnfilled,mean NsUnfilled,avg_dev NsUnfilled,mode NsUnfilled,minimum NpUnfilled,maximum NpUnfilled,range NpUnfilled,mean NpUnfilled,avg_dev NpUnfilled,mode NpUnfilled,minimum NdUnfilled,maximum NdUnfilled,range NdUnfilled,mean NdUnfilled,avg_dev NdUnfilled,mode NdUnfilled,minimum NfUnfilled,maximum NfUnfilled,range NfUnfilled,mean NfUnfilled,avg_dev NfUnfilled,mode NfUnfilled,minimum NUnfilled,maximum NUnfilled,range NUnfilled,mean NUnfilled,avg_dev NUnfilled,mode NUnfilled,minimum GSvolume_pa,maximum GSvolume_pa,range GSvolume_pa,mean GSvolume_pa,avg_dev GSvolume_pa,mode GSvolume_pa,minimum GSbandgap,maximum GSbandgap,range GSbandgap,mean GSbandgap,avg_dev GSbandgap,mode GSbandgap,minimum GSmagmom,maximum GSmagmom,range GSmagmom,mean GSmagmom,avg_dev GSmagmom,mode GSmagmom,minimum SpaceGroupNumber,maximum SpaceGroupNumber,range SpaceGroupNumber,mean SpaceGroupNumber,avg_dev SpaceGroupNumber,mode SpaceGroupNumber,H,He,Li,Be,B,C,N,O,F,Ne,Na,Mg,Al,Si,P,S,Cl,Ar,K,Ca,Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Ga,Ge,As,Se,Br,Kr,Rb,Sr,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd,In,Sn,Sb,Te,I,Xe,Cs,Ba,La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu,Hf,Ta,W,Re,Os,Ir,Pt,Au,Hg,Tl,Pb,Bi,Po,At,Rn,Fr,Ra,Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr,0-norm,2-norm,3-norm,5-norm,7-norm,10-norm,transition metal fraction,band center,avg s valence electrons,avg p valence electrons,avg d valence electrons,avg f valence electrons,frac s valence electrons,frac p valence electrons,frac d valence electrons,frac f valence electrons,HOMO_character_d,HOMO_character_f,HOMO_character_p,HOMO_character_s,HOMO_element_Ag,HOMO_element_As,HOMO_element_Au,HOMO_element_B,HOMO_element_Bi,HOMO_element_Br,HOMO_element_C,HOMO_element_Ce,HOMO_element_Cl,HOMO_element_Co,HOMO_element_Cr,HOMO_element_Cu,HOMO_element_Dy,HOMO_element_Eu,HOMO_element_F,HOMO_element_Fe,HOMO_element_Ge,HOMO_element_Hg,HOMO_element_I,HOMO_element_In,HOMO_element_Mn,HOMO_element_Mo,HOMO_element_N,HOMO_element_Nb,HOMO_element_Nd,HOMO_element_O,HOMO_element_P,HOMO_element_Pd,HOMO_element_Pr,HOMO_element_Pt,HOMO_element_Rh,HOMO_element_Ru,HOMO_element_S,HOMO_element_Sb,HOMO_element_Se,HOMO_element_Si,HOMO_element_Sm,HOMO_element_Sn,HOMO_element_Ta,HOMO_element_Tb,HOMO_element_Tc,HOMO_element_Te,HOMO_element_Ti,HOMO_element_Tl,HOMO_element_V,HOMO_element_W,HOMO_element_Zn,HOMO_element_Zr,LUMO_character_d,LUMO_character_f,LUMO_character_p,LUMO_character_s,LUMO_element_Ag,LUMO_element_As,LUMO_element_Au,LUMO_element_B,LUMO_element_Ba,LUMO_element_Bi,LUMO_element_Ca,LUMO_element_Cd,LUMO_element_Ce,LUMO_element_Co,LUMO_element_Cr,LUMO_element_Cs,LUMO_element_Cu,LUMO_element_Dy,LUMO_element_Eu,LUMO_element_Ga,LUMO_element_Ge,LUMO_element_Hf,LUMO_element_Hg,LUMO_element_I,LUMO_element_In,LUMO_element_K,LUMO_element_La,LUMO_element_Li,LUMO_element_Lu,LUMO_element_Mg,LUMO_element_Mn,LUMO_element_Mo,LUMO_element_N,LUMO_element_Na,LUMO_element_Nb,LUMO_element_Nd,LUMO_element_O,LUMO_element_P,LUMO_element_Pb,LUMO_element_Pd,LUMO_element_Pr,LUMO_element_Pt,LUMO_element_Rb,LUMO_element_Rh,LUMO_element_Ru,LUMO_element_S,LUMO_element_Sb,LUMO_element_Sc,LUMO_element_Se,LUMO_element_Si,LUMO_element_Sm,LUMO_element_Sn,LUMO_element_Sr,LUMO_element_Ta,LUMO_element_Tb,LUMO_element_Tc,LUMO_element_Te,LUMO_element_Th,LUMO_element_Ti,LUMO_element_Tl,LUMO_element_V,LUMO_element_W,LUMO_element_Y,LUMO_element_Zn,LUMO_element_Zr,gap expt +Hg0.7Cd0.3Te,-0.226594,-0.205137,0.021456999999999976,1.69,2.1,0.41000000000000014,2.0035,0.17908283322815957,5,6,1,5.35,0.6132153437832746,12,16,4,14.0,2.5712973861329003,2.0,3.0,1.0,2.5,0.6428243465332251,112.411,200.59,88.179,150.86814999999999,47.37468181672081,1.4,1.55,0.15000000000000013,1.4574999999999998,0.07680338749416281,74.0,92.0,18.0,83.15,11.385615108765917,3.0,97.0,94.0,18.955,42.263820664843855,234.32,722.66,488.34,532.4749999999999,286.8200555334273,48.0,80.0,32.0,61.2,13.16,52.0,70.0,90.0,20.0,80.35,9.649999999999999,90.0,112.411,200.59,88.179,150.86814999999999,34.805295,127.6,234.32,722.66,488.34,532.4749999999999,208.70850000000002,722.66,12.0,16.0,4.0,14.0,2.0,16.0,5.0,6.0,1.0,5.35,0.4549999999999999,5.0,132.0,144.0,12.0,136.8,3.3599999999999968,138.0,1.69,2.1,0.41000000000000014,2.0035,0.09650000000000006,2.1,2.0,2.0,0.0,2.0,0.0,2.0,0.0,4.0,4.0,2.0,2.0,4.0,10.0,10.0,0.0,10.0,0.0,10.0,0.0,14.0,14.0,4.8999999999999995,6.37,0.0,12.0,26.0,14.0,18.9,4.969999999999999,16.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,2.0,2.0,1.0,1.0,2.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,2.0,2.0,1.0,1.0,2.0,19.495,34.7633333333,15.268333333299996,29.139071839064997,5.6242614942349975,34.7633333333,0.0,0.464,0.464,0.232,0.23199999999999998,0.464,0.0,0.0,0.0,0.0,0.0,0.0,152.0,194.0,42.0,163.2,11.2,152.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.15,0.0,0.0,0.0,0.5,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0,0.0,0.0,0.0,0.0,0.35,0.0,0.0,0.0,0,0,0,0,0,0,0.0,0,0.0,0,0,0,0,0,0,0,0,0,0,0,3,0.6284902544988268,0.5553202707383361,0.5159935678577735,0.5056994254864157,0.5013950256690175,0.0,-1.998265321394679,2.0,2.0,10.0,4.8999999999999995,0.10582010582010583,0.10582010582010583,0.5291005291005292,0.25925925925925924,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.35 +CuBr,-0.202272,-0.172056,0.03021600000000002,1.9,2.96,1.06,2.4299999999999997,0.7495331880577404,4,4,0,4.0,0.0,11,17,6,14.0,4.242640687119285,2.0,3.0,1.0,2.5,0.7071067811865476,63.546,79.904,16.357999999999997,71.725,11.566852726649541,1.15,1.35,0.20000000000000018,1.25,0.14142135623730964,72.0,98.0,26.0,85.0,18.384776310850235,0.12,400.0,399.88,200.06,282.7578596608766,265.8,1357.77,1091.97,811.785,772.1393918522742,29.0,35.0,6.0,32.0,3.0,29.0,64.0,95.0,31.0,79.5,15.5,64.0,63.546,79.904,16.357999999999997,71.725,8.178999999999998,63.546,265.8,1357.77,1091.97,811.785,545.9849999999999,265.8,11.0,17.0,6.0,14.0,3.0,11.0,4.0,4.0,0.0,4.0,0.0,4.0,120.0,132.0,12.0,126.0,6.0,120.0,1.9,2.96,1.06,2.4299999999999997,0.53,1.9,1.0,2.0,1.0,1.5,0.5,1.0,0.0,5.0,5.0,2.5,2.5,0.0,10.0,10.0,0.0,10.0,0.0,10.0,0.0,0.0,0.0,0.0,0.0,0.0,11.0,17.0,6.0,14.0,3.0,11.0,0.0,1.0,1.0,0.5,0.5,0.0,0.0,1.0,1.0,0.5,0.5,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,0.0,1.0,0.0,1.0,11.07,29.48,18.41,20.275,9.205,11.07,0.0,1.457,1.457,0.7285,0.7285,0.0,0.0,0.0,0.0,0.0,0.0,0.0,64.0,225.0,161.0,144.5,80.5,64.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.5,0.0,0.0,0.0,0.0,0.0,0.5,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0,0,0,0,0,0,0.0,0,0.0,0,0,0,0,0,0,0,0,0,0,0,2,0.7071067811865476,0.6299605249474366,0.5743491774985174,0.5520447568369062,0.5358867312681466,0.5,-2.371497417245062,1.5,2.5,10.0,0.0,0.10714285714285714,0.17857142857142858,0.7142857142857143,0.0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3.08 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From 1a170357549af2ebc672b184c8435dd34611fbaa Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 16:02:13 -0700 Subject: [PATCH 08/11] add test_TreeBasedFeatureReduction --- .../preprocessing/tests/test_preprocess.py | 24 +++++++++++++++---- 1 file changed, 19 insertions(+), 5 deletions(-) diff --git a/matbench/preprocessing/tests/test_preprocess.py b/matbench/preprocessing/tests/test_preprocess.py index ef5b82e9..938fb73a 100644 --- a/matbench/preprocessing/tests/test_preprocess.py +++ b/matbench/preprocessing/tests/test_preprocess.py @@ -1,14 +1,17 @@ +import pandas as pd import unittest from matminer.datasets import load_dataset from matminer.featurizers.structure import GlobalSymmetryFeatures from matbench.featurization.core import Featurization - from matbench.preprocessing.core import Preprocessing - +from matbench.preprocessing.feature_selection import TreeBasedFeatureReduction class TestPreprocess(unittest.TestCase): + def setUp(self): + self.random_seed = 12 + # Todo: Add more tests def test_preprocess_basic(self): """ @@ -17,12 +20,23 @@ def test_preprocess_basic(self): Returns: None """ - df = load_dataset("elastic_tensor_2015")[:5][['K_VRH', 'structure']] + df = load_dataset('elastic_tensor_2015')[:15][['K_VRH', 'structure']] df['K_VRH'] = df['K_VRH'].astype(str) f = Featurization() df = f.featurize_structure(df, featurizers=[GlobalSymmetryFeatures()]) - p = Preprocessing() df = p.preprocess(df, 'K_VRH') self.assertAlmostEqual(df['K_VRH'].iloc[0], 194.26888435900003) - self.assertEqual(df["crystal_system_tetragonal"].iloc[0], 1) \ No newline at end of file + self.assertEqual(df['crystal_system_tetragonal'].iloc[0], 1) + + def test_TreeBasedFeatureReduction(self): + df = pd.read_csv('test_featurized_df.csv').set_index('formula') + X = df.drop('gap expt', axis=1) + y = df['gap expt'] + tbfr = TreeBasedFeatureReduction(mode='regression', + random_state=self.random_seed) + tbfr.fit(X, y, cv=3) + self.assertEqual(len(tbfr.selected_features), 19) + X_reduced = tbfr.transform(X) + self.assertEqual(X_reduced.shape, (len(X), 19)) + self.assertTrue('HOMO_energy' in X_reduced.columns) From eee3a59a2f2c90eba94a1783b3141436c73d28d0 Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 16:03:29 -0700 Subject: [PATCH 09/11] add more docs --- matbench/preprocessing/feature_selection.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/matbench/preprocessing/feature_selection.py b/matbench/preprocessing/feature_selection.py index 24802069..dba20aeb 100644 --- a/matbench/preprocessing/feature_selection.py +++ b/matbench/preprocessing/feature_selection.py @@ -6,12 +6,15 @@ class TreeBasedFeatureReduction(object): """ - Provides different methods for feature selection/reduction mainly before - the production model is fit hence being under preprocessing. + Tree-based feature reduction tools based on sklearn models that have + the .feature_importances_ attribute. Args: + mode (str): "regression" or "classification" importance_percentile (float): the selected percentile of the features sorted (descending) based on their importance. + random_state (int): relevant if non-deterministic algorithms such as + random forest are used. """ def __init__(self, mode, importance_percentile=0.95, loglevel=None, logpath='.', random_state=0): From aa044b390890b90a4ee1c8c528ed7b177c74a405 Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 16:05:08 -0700 Subject: [PATCH 10/11] rename --- matbench/preprocessing/tests/test_preprocess.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/matbench/preprocessing/tests/test_preprocess.py b/matbench/preprocessing/tests/test_preprocess.py index 938fb73a..a55b5804 100644 --- a/matbench/preprocessing/tests/test_preprocess.py +++ b/matbench/preprocessing/tests/test_preprocess.py @@ -10,7 +10,7 @@ class TestPreprocess(unittest.TestCase): def setUp(self): - self.random_seed = 12 + self.random_state = 12 # Todo: Add more tests def test_preprocess_basic(self): @@ -34,7 +34,7 @@ def test_TreeBasedFeatureReduction(self): X = df.drop('gap expt', axis=1) y = df['gap expt'] tbfr = TreeBasedFeatureReduction(mode='regression', - random_state=self.random_seed) + random_state=self.random_state) tbfr.fit(X, y, cv=3) self.assertEqual(len(tbfr.selected_features), 19) X_reduced = tbfr.transform(X) From 1ee3a123c83cb1ff2bc1d67dbb424ca0d9a6066b Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 19 Oct 2018 17:57:59 -0700 Subject: [PATCH 11/11] add the reference for csv test file --- matbench/preprocessing/tests/test_preprocess.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/matbench/preprocessing/tests/test_preprocess.py b/matbench/preprocessing/tests/test_preprocess.py index a55b5804..bb94487c 100644 --- a/matbench/preprocessing/tests/test_preprocess.py +++ b/matbench/preprocessing/tests/test_preprocess.py @@ -1,4 +1,5 @@ import pandas as pd +import os import unittest from matminer.datasets import load_dataset @@ -7,6 +8,8 @@ from matbench.preprocessing.core import Preprocessing from matbench.preprocessing.feature_selection import TreeBasedFeatureReduction +test_dir = os.path.dirname(__file__) + class TestPreprocess(unittest.TestCase): def setUp(self): @@ -30,7 +33,8 @@ def test_preprocess_basic(self): self.assertEqual(df['crystal_system_tetragonal'].iloc[0], 1) def test_TreeBasedFeatureReduction(self): - df = pd.read_csv('test_featurized_df.csv').set_index('formula') + df = pd.read_csv(os.path.join(test_dir, 'test_featurized_df.csv')) + df = df.set_index('formula') X = df.drop('gap expt', axis=1) y = df['gap expt'] tbfr = TreeBasedFeatureReduction(mode='regression',