diff --git a/matbench/preprocessing/feature_selection.py b/matbench/preprocessing/feature_selection.py new file mode 100644 index 00000000..dba20aeb --- /dev/null +++ b/matbench/preprocessing/feature_selection.py @@ -0,0 +1,136 @@ +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 check_cv + +class TreeBasedFeatureReduction(object): + """ + 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): + 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): + """ + 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: + selected_feats.append(feat[0]) + frac += feat[1] + if frac >= self.importance_percentile: + break + 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: + 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, cv=5): + """ + 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 + 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): + if tree.lower() in ['rf', 'random forest', 'randomforest']: + if self.mode.lower() in ['classification', 'classifier']: + tree = RandomForestClassifier(random_state=self.rs) + else: + tree = RandomForestRegressor(random_state=self.rs) + elif tree.lower() in ['gb', 'gbt', 'gradiet boosting']: + if self.mode.lower() in ['classification', 'classifier']: + tree = GradientBoostingClassifier(random_state=self.rs) + else: + tree = GradientBoostingRegressor(random_state=self.rs) + else: + raise MatbenchError('Unsupported tree_type {}!'.format(tree)) + + 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): + """ + 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('The fit method should be called first!') + return X[self.selected_features] \ No newline at end of file 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 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diff --git a/matbench/preprocessing/tests/test_preprocess.py b/matbench/preprocessing/tests/test_preprocess.py index ef5b82e9..bb94487c 100644 --- a/matbench/preprocessing/tests/test_preprocess.py +++ b/matbench/preprocessing/tests/test_preprocess.py @@ -1,14 +1,20 @@ +import pandas as pd +import os 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 +test_dir = os.path.dirname(__file__) class TestPreprocess(unittest.TestCase): + def setUp(self): + self.random_state = 12 + # Todo: Add more tests def test_preprocess_basic(self): """ @@ -17,12 +23,24 @@ 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(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', + random_state=self.random_state) + 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)