Module Import alias identifier Import alias Import alias identifier ImportFrom alias Import alias ImportFrom alias Import alias identifier ImportFrom alias Import alias Import alias identifier ImportFrom alias ImportFrom alias ImportFrom alias FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr Return SubscriptLoad Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Call AttributeLoad NameLoad attr Index Num decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults NameLoad body Expr Str If CompareEq SubscriptLoad NameLoad Index Str Str body If UnaryOpNot SubscriptLoad NameLoad Index Str body If UnaryOpNot NameLoad body Assign NameStore Call AttributeLoad NameLoad attr keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str keyword Num keyword Num keyword Num keyword SubscriptLoad NameLoad Index Str keyword NameLoad keyword NameLoad keyword NameLoad keyword Num keyword NameLoad keyword NameLoad orelse Assign NameStore Call AttributeLoad NameLoad attr keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str keyword Num keyword Num keyword Num keyword SubscriptLoad NameLoad Index Str keyword NameLoad keyword NameLoad keyword NameLoad keyword Num keyword NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad ExtSlice Slice Index NameLoad orelse If CompareEq SubscriptLoad NameLoad Index Str Str body Print ImportFrom alias alias alias alias FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad SubscriptLoad AttributeLoad SubscriptLoad NameLoad Index Str attr Index NameLoad attr Index Num keyword Num keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr keyword Num keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str Assign NameStore Call NameLoad NameLoad SubscriptLoad NameLoad Index NameLoad Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr keyword NameLoad keyword Num Return Call AttributeLoad NameLoad attr NameLoad decorator_list Assign NameStore Dict Str Str Str Str Call AttributeLoad NameLoad attr Str Num Num Call AttributeLoad NameLoad attr Str Num Num Num Call AttributeLoad NameLoad attr Str Num Num Num Call AttributeLoad NameLoad attr Str Num Num Assign NameStore Call NameLoad NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword Num keyword Num Print NameLoad Assign NameStore Call AttributeLoad NameLoad attr keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr orelse If CompareEq SubscriptLoad NameLoad Index Str Str body Assert UnaryOpNot NameLoad Str Assign NameStore Num Print Str ImportFrom alias Assign NameStore Dict Str Str Str Str ListLoad Num Num ListLoad Num Num ListLoad Num Num ListLoad Num Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad SubscriptLoad NameLoad Index Str attr Index NameLoad Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad SubscriptLoad NameLoad Index Str attr Index NameLoad Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad keyword NameLoad keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr keyword SubscriptLoad NameLoad Index Str keyword SubscriptLoad NameLoad Index Str Assign NameStore Call AttributeLoad Call NameLoad NameLoad NameLoad keyword NameLoad keyword Num keyword NameLoad keyword NameLoad keyword NameLoad attr SubscriptLoad NameLoad Index NameLoad Call AttributeLoad SubscriptLoad NameLoad Index NameLoad attr Print AttributeLoad NameLoad attr orelse Raise Call NameLoad Str Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad ExtSlice Slice Index NameLoad orelse Raise NameLoad Return TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults body Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr NameLoad Index Num Assign NameStore BinOpMult Call NameLoad NameLoad Num Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign NameStore SubscriptLoad NameLoad Slice NameLoad Assign NameStore SubscriptLoad NameLoad Slice NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad keyword NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad Assign SubscriptStore NameLoad Index NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr TupleLoad Call NameLoad NameLoad Call NameLoad Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr TupleLoad Call AttributeLoad NameLoad attr Call NameLoad Call AttributeLoad NameLoad attr For TupleStore NameStore NameStore Call NameLoad Call AttributeLoad NameLoad attr body Assign NameStore AttributeLoad SubscriptLoad NameLoad Index NameLoad attr Assign TupleStore NameStore NameStore Call NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Assign SubscriptStore NameLoad ExtSlice Slice Index NameLoad Call AttributeLoad Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad attr Assign SubscriptStore NameLoad ExtSlice Slice Index NameLoad Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad Expr Call AttributeLoad NameLoad attr NameLoad SubscriptLoad NameLoad Index NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Return TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr keyword NameLoad Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad SubscriptLoad SubscriptLoad NameLoad Index NameLoad ExtSlice Slice Index Num Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad ExtSlice Slice Index NameLoad Return TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad SubscriptLoad SubscriptLoad NameLoad Index NameLoad ExtSlice Slice Index Num Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index NameLoad ExtSlice Slice Index NameLoad Return TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Return Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad For NameStore Call NameLoad NameLoad body For NameStore Call NameLoad NameLoad body If CompareEq NameLoad NameLoad body Continue Assign SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad CompareGt Call AttributeLoad CompareGt SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad attr BinOpDiv SubscriptLoad AttributeLoad NameLoad attr Index Num Num Return BinOpDiv Call AttributeLoad NameLoad attr Num Call AttributeLoad Call AttributeLoad NameLoad attr Num attr decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad NameLoad attr NameLoad keyword Num decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Dict Str Str Str Str ListLoad Num Num Num ListLoad Num Num Num Num ListLoad Num Num Num ListLoad Num Num Num Num Assign NameStore Call AttributeLoad NameLoad attr keyword Str keyword Num Assign NameStore Call AttributeLoad Call NameLoad NameLoad NameLoad keyword Num keyword Num keyword Num keyword NameLoad attr NameLoad Call AttributeLoad NameLoad attr Return Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Import alias Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad keyword Num keyword Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index Num Expr Call AttributeLoad NameLoad attr Str keyword Num Assign NameStore SubscriptLoad Call AttributeLoad NameLoad attr NameLoad Index Num Return Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Assign NameStore Dict Str Str Str TupleLoad Str Str Call AttributeLoad NameLoad attr Num Num Num Call AttributeLoad NameLoad attr Num Num Num Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad NameLoad NameLoad keyword Num keyword Num keyword Num keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr Return Call AttributeLoad NameLoad attr NameLoad decorator_list
N/A N/A numpy np N/A sklearn.linear_model N/A sklearn.ensemble en sklearn.grid_search GridSearchCV N/A sklearn sklearn.linear_model LinearRegression N/A scipy sp regression linreg_on_fold N/A sklearn N/A sklearn.tree tree sklearn svm sklearn.grid_search GridSearchCV sklearn.cross_validation cross_val_score spearman_scoring N/A N/A clf X y N/A N/A N/A y_pred N/A N/A N/A N/A clf predict X flatten N/A N/A N/A N/A N/A sp stats spearmanr y_pred N/A N/A y flatten N/A 0 N/A adaboost_on_fold N/A N/A feature_sets train test y y_all X dim dimsum learn_options classification N/A False N/A N/A 
    AdaBoostRegressor/Classifier from scikitlearn.
     N/A N/A N/A learn_options N/A adaboost_version python N/A N/A N/A N/A learn_options N/A adaboost_CV N/A N/A N/A classification N/A N/A clf N/A N/A en GradientBoostingRegressor loss N/A learn_options N/A adaboost_loss learning_rate N/A learn_options N/A adaboost_learning_rate n_estimators N/A learn_options N/A adaboost_n_estimators alpha N/A learn_options N/A adaboost_alpha subsample 1.0 min_samples_split 2 min_samples_leaf 1 max_depth N/A learn_options N/A adaboost_max_depth init None random_state None max_features None verbose 0 max_leaf_nodes None warm_start False N/A N/A clf N/A N/A en GradientBoostingClassifier learning_rate N/A learn_options N/A adaboost_learning_rate n_estimators N/A learn_options N/A adaboost_n_estimators subsample 1.0 min_samples_split 2 min_samples_leaf 1 max_depth N/A learn_options N/A adaboost_max_depth init None random_state None max_features None verbose 0 max_leaf_nodes None warm_start False N/A N/A N/A clf fit N/A X N/A train N/A N/A N/A y N/A train flatten N/A y_pred N/A N/A N/A clf predict N/A X N/A test N/A N/A N/A None N/A N/A N/A N/A learn_options N/A algorithm_hyperparam_search bo N/A N/A hyperopt hp fmin tpe rand adaboost_scoring_bo N/A N/A params N/A N/A N/A cv N/A N/A N/A sklearn cross_validation KFold N/A N/A N/A N/A N/A y_all N/A Target gene values N/A train shape N/A 0 n_folds 20 shuffle True N/A est N/A N/A en GradientBoostingRegressor n_estimators 1000 learning_rate N/A params N/A learning_rate max_depth N/A params N/A max_depth min_samples_leaf N/A params N/A min_samples_leaf max_features N/A params N/A max_features N/A scorer N/A cross_val_score est N/A X N/A train N/A N/A N/A y N/A train flatten cv cv n_jobs 20 N/A N/A N/A np median scorer N/A N/A space N/A learning_rate max_depth min_samples_leaf max_features N/A N/A hp uniform learning_rate 0.001 0.1 N/A N/A hp quniform max_depth 1 8 1 N/A N/A hp quniform min_samples_leaf 3 20 1 N/A N/A hp uniform max_features 0.05 1.0 N/A best N/A fmin adaboost_scoring_bo space algo N/A tpe suggest max_evals 50 verbose 1 N/A best N/A clf N/A N/A en GradientBoostingRegressor n_estimators N/A learn_options N/A adaboost_n_estimators learning_rate N/A best N/A learning_rate max_depth N/A best N/A max_depth min_samples_leaf N/A best N/A min_samples_leaf max_features N/A best N/A max_features N/A N/A N/A clf fit N/A X N/A train N/A N/A N/A y N/A train flatten N/A N/A N/A N/A learn_options N/A algorithm_hyperparam_search grid N/A N/A N/A classification need to tweak code below to do classificaton, as above N/A n_jobs 20 N/A Adaboost with GridSearch sklearn.grid_search GridSearchCV N/A param_grid N/A learning_rate max_depth min_samples_leaf max_features N/A 0.1 0.01 N/A 4 7 N/A 5 15 N/A 1.0 0.1 N/A label_encoder N/A N/A N/A sklearn preprocessing LabelEncoder N/A N/A N/A label_encoder fit N/A N/A N/A y_all N/A Target gene values N/A train N/A gene_classes N/A N/A label_encoder transform N/A N/A N/A y_all N/A Target gene values N/A train N/A n_folds N/A len N/A N/A np unique gene_classes N/A cv N/A N/A N/A sklearn cross_validation StratifiedKFold gene_classes n_folds n_folds shuffle True N/A est N/A N/A en GradientBoostingRegressor loss N/A learn_options N/A adaboost_loss n_estimators N/A learn_options N/A adaboost_n_estimators N/A clf N/A N/A N/A GridSearchCV est param_grid n_jobs n_jobs verbose 1 cv cv scoring spearman_scoring iid False fit N/A X N/A train N/A N/A N/A y N/A train flatten N/A N/A clf best_params_ N/A N/A N/A Exception if using adaboost_CV then need to specify grid (grid search) or bo (bayesian optimization) N/A y_pred N/A N/A N/A clf predict N/A X N/A test N/A N/A N/A None N/A N/A NotImplementedError N/A N/A y_pred clf N/A LASSOs_ensemble_on_fold N/A N/A feature_sets train test y y_all X dim dimsum learn_options N/A N/A N/A train_indices N/A N/A N/A np where train N/A 0 N/A sel N/A N/A len train_indices 0.1 N/A permuted_ind N/A N/A N/A np random permutation train_indices N/A valid_indices N/A permuted_ind N/A sel N/A train_indices N/A permuted_ind N/A sel N/A train_sub N/A N/A np zeros_like train dtype bool N/A valid_sub N/A N/A np zeros_like train dtype bool N/A N/A train_sub N/A train_indices True N/A N/A valid_sub N/A valid_indices True N/A validations N/A N/A np zeros N/A N/A len valid_indices N/A len N/A N/A feature_sets keys N/A predictions N/A N/A np zeros N/A N/A N/A test sum N/A len N/A N/A feature_sets keys N/A N/A i feature_name N/A enumerate N/A N/A feature_sets keys N/A N/A X_feature N/A N/A feature_sets N/A feature_name values N/A N/A y_pred m N/A linreg_on_fold feature_sets train_sub valid_sub y y_all X_feature dim dimsum learn_options N/A N/A predictions N/A N/A N/A i N/A N/A N/A N/A m predict N/A X_feature N/A test flatten N/A N/A validations N/A N/A N/A i N/A N/A y_pred flatten N/A clf N/A LinearRegression N/A N/A N/A clf fit validations N/A y N/A valid_sub N/A y_pred N/A N/A clf predict predictions N/A N/A y_pred None N/A randomforest_on_fold N/A N/A feature_sets train test y y_all X dim dimsum learn_options N/A N/A N/A 
    RandomForestRegressor from scikitlearn.
     N/A clf N/A N/A en RandomForestRegressor oob_score True N/A N/A N/A clf fit N/A X N/A train N/A N/A y N/A train N/A N/A N/A 0 N/A y_pred N/A N/A N/A clf predict N/A X N/A test N/A N/A N/A None N/A N/A y_pred clf N/A decisiontree_on_fold N/A N/A feature_sets train test y y_all X dim dimsum learn_options N/A N/A N/A 
    DecisionTreeRegressor from scikitlearn.
     N/A clf N/A N/A tree DecisionTreeRegressor N/A N/A N/A clf fit N/A X N/A train N/A N/A y N/A train N/A N/A N/A 0 N/A y_pred N/A N/A N/A clf predict N/A X N/A test N/A N/A N/A None N/A N/A y_pred clf N/A linear_stacking N/A N/A y_train X_train X_test N/A N/A N/A clf N/A N/A N/A sklearn linear_model LinearRegression N/A N/A N/A clf fit X_train y_train N/A y_pred N/A N/A clf predict X_test N/A N/A N/A y_pred flatten N/A pairwise_majority_voting N/A N/A y N/A N/A N/A N N/A N/A y shape N/A 0 N/A y_pred N/A N/A np zeros N/A N N N/A i N/A range N N/A N/A j N/A range N N/A N/A N/A i j N/A N/A N/A N/A y_pred N/A N/A i j N/A N/A N/A N/A N/A y N/A i N/A y N/A j sum N/A N/A N/A y shape N/A 1 2 N/A N/A N/A N/A y_pred sum 1 N/A N/A N/A N/A y_pred sum 1 max N/A median N/A N/A y N/A N/A N/A N/A N/A np median y axis 1 N/A GBR_stacking N/A N/A y_train X_train X_test N/A N/A N/A param_grid N/A learning_rate max_depth min_samples_leaf max_features N/A 0.1 0.05 0.01 N/A 2 3 4 5 N/A 1 2 3 N/A 1.0 0.5 0.3 0.1 N/A est N/A N/A en GradientBoostingRegressor loss ls n_estimators 100 N/A clf N/A N/A N/A GridSearchCV est param_grid n_jobs 3 verbose 1 cv 20 scoring spearman_scoring fit X_train N/A N/A y_train flatten N/A N/A N/A clf predict X_test N/A GP_stacking N/A N/A y_train X_train X_test N/A N/A N/A GPy N/A m N/A N/A N/A GPy models SparseGPRegression X_train y_train num_inducing 20 kernel N/A N/A N/A GPy kern RBF N/A N/A X_train shape N/A 1 N/A N/A N/A m optimize bfgs messages 0 N/A y_pred N/A N/A N/A m predict X_test N/A 0 N/A N/A N/A y_pred flatten N/A SVM_stacking N/A N/A y_train X_train X_test N/A N/A N/A parameters N/A kernel C gamma N/A linear rbf N/A N/A np linspace 1 10 10 N/A N/A np linspace 0.001 1.0 10 N/A svr N/A N/A svm SVR N/A clf N/A GridSearchCV svr parameters n_jobs 3 verbose 1 cv 10 scoring spearman_scoring N/A N/A N/A clf fit X_train N/A N/A y_train flatten N/A N/A N/A clf predict X_test N/A