by Marco Taboga, PhD
Until now we have used the simplest of all crossvalidation methods, which consists in testing our predictive models on a subset of the data (the test set) that has not been used for training or selecting the predictive models. This simple crossvalidation method is sometimes called the holdout method.
There are more sophisticated crossvalidation methods that allow us to obtain better predictive models, together with accurate estimates of an upper bound on the expected loss. In these methods, we perform multiple different partitions of the data into training, validation and test sets, we build a different predictive model for each partition, and finally we average the predictions made by the various models (socalled ensembling).
Here we introduce the most popular of these methods, called Kfold crossvalidation.
Table of contents
Folds
Ensembling
Advantages and disadvantages
Python example
Import the data
Run the Kfold crossvalidation on LightGBM boosted trees
Put the model in production
Folds
The data is divided into subsets, called folds. Each fold contains (approximately) the same number of observations.
Then, for , we use the th fold (denoted by ) as the test set and use the remaining folds to train a predictive model .
For each fold, we compute the estimate of the expected loss where is a vector of inputs, is the loss incurred by using as a forecast of the observed output , and is the number of observations in the th fold.
Remark: the folds used to train a predictive model can be divided into training and validation sets if we need a validation set for model selection.
Ensembling
After training the models , we use their ensemble average as our final prediction
We then compute the average loss
As previously discussed, this average is an estimate of an upper bound on the expected loss of the ensemble average (remember that the expected loss of the ensemble average equals the average expected loss of the models in the ensemble minus a correction term that measures the diversity of the models in the ensemble).
Advantages and disadvantages
Kfold cross validation is straightforward to implement: once we have a routine for training a predictive model, we just run it times on the different partitions of the data. The only real disadvantage is the computational cost.
As a reward for facing an increased computational cost, we have two main advantages:

our final model (the ensemble average) has been trained on all the data (no data have been "wasted") and it enjoys some benefits from ensembling;

although we no longer have an unbiased estimate of the expected loss of the final model, is an estimate of an upper bound to it, which uses all the data in the sample and should therefore be pretty precise.
Python example
Let us use Kfold crossvalidation to improve on the simpler holdout crossvalidation performed when we built a single boosted tree to predict the output variable in an artificiallygenerated data set.
Import the data
# Import the packages used to load and manipulate the dataimport numpy as np # Numpy is a Matlablike package for array manipulation and linear algebraimport pandas as pd # Pandas is a dataanalysis and tablemanipulation toolimport urllib.request # Urlib will be used to download the dataset# Import the function that performs sample splits from scikitlearnfrom sklearn.model_selection import train_test_split# Load the output variable with pandas (download with urllib if not downloaded previously)remoteAddress = 'https://www.statlect.com/mlassets/y_artificial.csv'localAddress = './y_artificial.csv'try: y = pd.read_csv(localAddress, header=None)except: urllib.request.urlretrieve(remoteAddress, localAddress) y = pd.read_csv(localAddress, header=None)y = y.values # Transform y into a numpy array# Print some information about the output variableprint('Class and dimension of output variable:')print(type(y))print(y.shape)# Load the input variables with pandas remoteAddress = 'https://www.statlect.com/mlassets/x_artificial.csv'localAddress = './x_artificial.csv'try: x = pd.read_csv(localAddress, header=None)except: urllib.request.urlretrieve(remoteAddress, localAddress) x = pd.read_csv(localAddress, header=None)x = x.values# Print some information about the input variablesprint('Class and dimension of input variables:')print(type(x))print(x.shape)
The output is:
Class and dimension of output variable:class 'numpy.ndarray'(500, 1)Class and dimension of input variables:class 'numpy.ndarray'(500, 300)
Run the Kfold crossvalidation on LightGBMboosted trees
We create 5 folds using the KFold class provided by the scikitlearn package.
Then, we use LightGBM to make predictions on each fold.
#Import the lightGBM packageimport lightgbm as lgb# Import the functions that performs sample splits from scikitlearnfrom sklearn.model_selection import train_test_split, KFold# Import modelevaluation metrics from scikitlearnfrom sklearn.metrics import mean_squared_error, r2_score# Set number of folds and ensemble variablesn_folds = 5ensemble = []mses_single_models = []mses_constant_predictions = []r_squareds_single_models = []# Initialize k_fold splitterK_fold = KFold(n_splits=n_folds, random_state=0, shuffle=True)# Iterate over foldsfor train_val_index, test_index in K_fold.split(x): # Get train_val (K1 folds) and test (1 fold) x_train_val, x_test = x[train_val_index], x[test_index] y_train_val, y_test = y[train_val_index], y[test_index] # Partition the train_val set x_train, x_val, y_train, y_val = train_test_split(x_train_val, y_train_val, test_size=0.25, random_state=0) # Prepare dataset in LightGMB format y_train = np.squeeze(y_train) y_val = np.squeeze(y_val) train_set = lgb.Dataset(x_train, y_train, silent=True) valid_set = lgb.Dataset(x_val, y_val, silent=True) # Set algorithm parameters params = { 'objective': 'regression', 'learning_rate': 0.10, 'metric': 'mse', 'nthread': 8, 'min_data_in_leaf': 10, 'max_depth': 2, 'verbose': 1 } # Train the model boosted_tree = lgb.train( params = params, train_set = train_set, valid_sets = valid_set, num_boost_round = 10000, early_stopping_rounds = 20, verbose_eval = False, ) # Save the model in the ensemble list ensemble.append(boosted_tree) # Make predictions on test and compute performance metrics y_test_pred = boosted_tree.predict(x_test) mses_single_models.append(mean_squared_error(y_test, y_test_pred)) mses_constant_predictions.append(mean_squared_error(y_test, 0*y_test + np.mean(y_train))) r_squareds_single_models.append(r2_score(y_test, y_test_pred))# Print performance metrics on test sampleprint('Test MSEs of models in the ensemble:')print(mses_single_models)print('Test MSEs of constant predictions equal to sample mean on training set:')print(mses_constant_predictions)print('Average test MSE of models in the ensemble:')print(np.mean(mses_single_models))print('')print('Test R squareds of models in the ensemble:')print(r_squareds_single_models)print('Average test R squared of models in the ensemble:')print(np.mean(r_squareds_single_models))
The output is:
Test MSEs of models in the ensemble:[74.57708434382333, 37.439965145009516, 16.801894170417487, 54.55429632149937, 30.007456926513534]Test MSEs of constant predictions equal to sample mean on training set:[293.2026939915153, 167.6726253022108, 104.80130552664033, 213.67954000052373, 131.20844137862687]Average test MSE of models in the ensemble:42.67613938145264Test R squareds of models in the ensemble:[0.7414010556669601, 0.7762513029977958, 0.8356878267813256, 0.7416211645498416, 0.7712684886703587]Average test R squared of models in the ensemble:0.7732459677332564
There is significant variation in test mean squared errors (MSEs) across the folds, although it is mostly due to differences in variance (test MSEs of constant predictions). The R squareds are more homogeneous, that is, the proportion of variance explained by the predictions is more stable across folds.
Anyway, the variability in test MSEs reveals that it was probably a good idea to run a Kfold crossvalidation.
At this stage, it is not possible to say anything more precise about the benefits from using Kfold crossvalidation instead of the simple holdout method (although there are good theoretical guarantees about them). The benefits are likely to become apparent when we put the model in production, which we simulate below.
Put the model in production
We now see how our predictive model performs in production, on new data that becomes available after we have completed the training.
# Load the input and output variables with pandas y_production = pd.read_csv('./assets/y_artificial_production.csv', header=None)y_production = y_production.valuesy_production = np.squeeze(y_production)x_production = pd.read_csv('./assets/x_artificial_production.csv', header=None)x_production = x_production.values# Initialize ensemble variables on production datasety_production_pred_ensemble = 0production_mses_single_models = []production_r_squareds_single_models = []# Make predictions with all models in the ensemble and compute ensemble averagefor model in ensemble: y_production_pred = model.predict(x_production) production_mses_single_models.append(mean_squared_error(y_production, y_production_pred)) production_r_squareds_single_models.append(r2_score(y_production, y_production_pred)) y_production_pred_ensemble += y_production_pred/n_folds# Print MSEs print('Production MSEs of models in the ensemble:')print(production_mses_single_models)print('Average production MSE of models in the ensemble:')print(np.mean(production_mses_single_models))print('Production MSE of ensemble average:')print(mean_squared_error(y_production, y_production_pred_ensemble))print('')# Print R squaredsprint('Production R squareds of models in the ensemble:')print(production_r_squareds_single_models)print('Average production R squared of models in the ensemble:')print(np.mean(production_r_squareds_single_models))print('Production R squared of ensemble average:')print(r2_score(y_production, y_production_pred_ensemble))
The output is:
Production MSEs of models in the ensemble:[39.64176656361246, 32.90628594145072, 37.6388748646386, 44.169307277678485, 43.86534683792454]Average production MSE of models in the ensemble:39.64431629706096Production MSE of ensemble average:33.64136466519085Production R squareds of models in the ensemble:[0.7639469310457051, 0.8040543987387033, 0.7758734614027009, 0.736986985185174, 0.73879696493291]Average production R squared of models in the ensemble:0.7639317482610387Production R squared of ensemble average:0.7996772580685613
This is an excellent result! The performance of the ensemble average is significantly better than the average performance of the models in the ensemble.
How to cite
Please cite as:
Taboga, Marco (2021). "Kfold crossvalidation", Lectures on machine learning. https://www.statlect.com/machinelearning/kfoldcrossvalidation.