How can I implement incremental training for xgboost?

There is now (version 0.6?) a process_update parameter that might help. Here's an experiment with it:

import pandas as pd
import xgboost as xgb
from sklearn.model_selection import ShuffleSplit
from sklearn.datasets import load_boston
from sklearn.metrics import mean_squared_error as mse

boston = load_boston()
features = boston.feature_names
X = boston.data
y = boston.target

X=pd.DataFrame(X,columns=features)
y = pd.Series(y,index=X.index)

# split data into training and testing sets
rs = ShuffleSplit(test_size=0.3, n_splits=1, random_state=0)
for train_idx,test_idx in rs.split(X):  # this looks silly
    pass

train_split = round(len(train_idx) / 2)
train1_idx = train_idx[:train_split]
train2_idx = train_idx[train_split:]
X_train = X.loc[train_idx]
X_train_1 = X.loc[train1_idx]
X_train_2 = X.loc[train2_idx]
X_test = X.loc[test_idx]
y_train = y.loc[train_idx]
y_train_1 = y.loc[train1_idx]
y_train_2 = y.loc[train2_idx]
y_test = y.loc[test_idx]

xg_train_0 = xgb.DMatrix(X_train, label=y_train)
xg_train_1 = xgb.DMatrix(X_train_1, label=y_train_1)
xg_train_2 = xgb.DMatrix(X_train_2, label=y_train_2)
xg_test = xgb.DMatrix(X_test, label=y_test)

params = {'objective': 'reg:linear', 'verbose': False}
model_0 = xgb.train(params, xg_train_0, 30)
model_1 = xgb.train(params, xg_train_1, 30)
model_1.save_model('model_1.model')
model_2_v1 = xgb.train(params, xg_train_2, 30)
model_2_v2 = xgb.train(params, xg_train_2, 30, xgb_model=model_1)

params.update({'process_type': 'update',
               'updater'     : 'refresh',
               'refresh_leaf': True})
model_2_v2_update = xgb.train(params, xg_train_2, 30, xgb_model=model_1)

print('full train\t',mse(model_0.predict(xg_test), y_test)) # benchmark
print('model 1 \t',mse(model_1.predict(xg_test), y_test))  
print('model 2 \t',mse(model_2_v1.predict(xg_test), y_test))  # "before"
print('model 1+2\t',mse(model_2_v2.predict(xg_test), y_test))  # "after"
print('model 1+update2\t',mse(model_2_v2_update.predict(xg_test), y_test))  # "after"

Output:

full train   17.8364309709
model 1      24.2542132108
model 2      25.6967017352
model 1+2    22.8846455135
model 1+update2  14.2816257268

Try saving your model after you train on the first batch. Then, on successive runs, provide the xgb.train method with the filepath of the saved model.

Here's a small experiment that I ran to convince myself that it works:

First, split the boston dataset into training and testing sets. Then split the training set into halves. Fit a model with the first half and get a score that will serve as a benchmark. Then fit two models with the second half; one model will have the additional parameter xgb_model. If passing in the extra parameter didn't make a difference, then we would expect their scores to be similar.. But, fortunately, the new model seems to perform much better than the first.

import xgboost as xgb
from sklearn.cross_validation import train_test_split as ttsplit
from sklearn.datasets import load_boston
from sklearn.metrics import mean_squared_error as mse

X = load_boston()['data']
y = load_boston()['target']

# split data into training and testing sets
# then split training set in half
X_train, X_test, y_train, y_test = ttsplit(X, y, test_size=0.1, random_state=0)
X_train_1, X_train_2, y_train_1, y_train_2 = ttsplit(X_train, 
                                                     y_train, 
                                                     test_size=0.5,
                                                     random_state=0)

xg_train_1 = xgb.DMatrix(X_train_1, label=y_train_1)
xg_train_2 = xgb.DMatrix(X_train_2, label=y_train_2)
xg_test = xgb.DMatrix(X_test, label=y_test)

params = {'objective': 'reg:linear', 'verbose': False}
model_1 = xgb.train(params, xg_train_1, 30)
model_1.save_model('model_1.model')

# ================= train two versions of the model =====================#
model_2_v1 = xgb.train(params, xg_train_2, 30)
model_2_v2 = xgb.train(params, xg_train_2, 30, xgb_model='model_1.model')

print(mse(model_1.predict(xg_test), y_test))     # benchmark
print(mse(model_2_v1.predict(xg_test), y_test))  # "before"
print(mse(model_2_v2.predict(xg_test), y_test))  # "after"

# 23.0475232194
# 39.6776876084
# 27.2053239482

reference: https://github.com/dmlc/xgboost/blob/master/python-package/xgboost/training.py