Python Package Introduction

This document gives a basic walkthrough of xgboost python package.

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Install XGBoost

To install XGBoost, do the following:

  • Run make in the root directory of the project
  • In the python-package directory, run
python setup.py install

To verify your installation, try to import xgboost in Python.

import xgboost as xgb

Data Interface

The XGBoost python module is able to load data from:

  • libsvm txt format file
  • Numpy 2D array, and
  • xgboost binary buffer file.

The data is stored in a DMatrix object.

  • To load a libsvm text file or a XGBoost binary file into DMatrix:
dtrain = xgb.DMatrix('train.svm.txt')
dtest = xgb.DMatrix('test.svm.buffer')
  • To load a numpy array into DMatrix:
data = np.random.rand(5, 10)  # 5 entities, each contains 10 features
label = np.random.randint(2, size=5)  # binary target
dtrain = xgb.DMatrix(data, label=label)
  • To load a scpiy.sparse array into DMatrix:
csr = scipy.sparse.csr_matrix((dat, (row, col)))
dtrain = xgb.DMatrix(csr)
  • Saving DMatrix into a XGBoost binary file will make loading faster:
dtrain = xgb.DMatrix('train.svm.txt')
dtrain.save_binary('train.buffer')
  • Missing values can be replaced by a default value in the DMatrix constructor:
dtrain = xgb.DMatrix(data, label=label, missing=-999.0)
  • Weights can be set when needed:
w = np.random.rand(5, 1)
dtrain = xgb.DMatrix(data, label=label, missing=-999.0, weight=w)

Setting Parameters

XGBoost can use either a list of pairs or a dictionary to set parameters. For instance:

  • Booster parameters
param = {'max_depth': 2, 'eta': 1, 'silent': 1, 'objective': 'binary:logistic'}
param['nthread'] = 4
param['eval_metric'] = 'auc'
  • You can also specify multiple eval metrics:
param['eval_metric'] = ['auc', 'ams@0']

# alternatively:
# plst = param.items()
# plst += [('eval_metric', 'ams@0')]
  • Specify validations set to watch performance
evallist = [(dtest, 'eval'), (dtrain, 'train')]

Training

Training a model requires a parameter list and data set.

num_round = 10
bst = xgb.train(plst, dtrain, num_round, evallist)

After training, the model can be saved.

bst.save_model('0001.model')

The model and its feature map can also be dumped to a text file.

# dump model
bst.dump_model('dump.raw.txt')
# dump model with feature map
bst.dump_model('dump.raw.txt', 'featmap.txt')

A saved model can be loaded as follows:

bst = xgb.Booster({'nthread': 4})  # init model
bst.load_model('model.bin')  # load data

Early Stopping

If you have a validation set, you can use early stopping to find the optimal number of boosting rounds. Early stopping requires at least one set in evals. If there’s more than one, it will use the last.

train(..., evals=evals, early_stopping_rounds=10)

The model will train until the validation score stops improving. Validation error needs to decrease at least every early_stopping_rounds to continue training.

If early stopping occurs, the model will have three additional fields: bst.best_score, bst.best_iteration and bst.best_ntree_limit. Note that train() will return a model from the last iteration, not the best one.

This works with both metrics to minimize (RMSE, log loss, etc.) and to maximize (MAP, NDCG, AUC). Note that if you specify more than one evaluation metric the last one in param['eval_metric'] is used for early stopping.

Prediction

A model that has been trained or loaded can perform predictions on data sets.

# 7 entities, each contains 10 features
data = np.random.rand(7, 10)
dtest = xgb.DMatrix(data)
ypred = bst.predict(dtest)

If early stopping is enabled during training, you can get predictions from the best iteration with bst.best_ntree_limit:

ypred = bst.predict(dtest, ntree_limit=bst.best_ntree_limit)

Plotting

You can use plotting module to plot importance and output tree.

To plot importance, use plot_importance. This function requires matplotlib to be installed.

xgb.plot_importance(bst)

To plot the output tree via matplotlib, use plot_tree, specifying the ordinal number of the target tree. This function requires graphviz and matplotlib.

xgb.plot_tree(bst, num_trees=2)

When you use IPython, you can use the to_graphviz function, which converts the target tree to a graphviz instance. The graphviz instance is automatically rendered in IPython.

xgb.to_graphviz(bst, num_trees=2)