Data

Data description. We use the train.csv from the original task as bioresponse.csv file.

(1) sklearn.ensemble.RandomForestClassifier
and
(2) xgboost.XGBClassifier

from sklearn import ensemble, model_selection, metrics 

import numpy as np
import pandas as pd
import xgboost as xgb

%pylab inline

Data

bioresponce = pd.read_csv("bioresponse.csv", header=0, sep=",")
bioresponce.head()

5 rows × 1777 columns

bioresponce_target = bioresponce.Activity.values
bioresponce_data = bioresponce.iloc[:, 1:]

Now we’ll run algorithms measuring their quality depending on the number of trees

Model RandomForestClassifier

We want to know how does the quality (accuracy) changes from the number of trees.

n_trees = [1] + list(range(10, 55, 5))
n_trees

%%time
scoring = []
for n_tree in n_trees:
    estimator = ensemble.RandomForestClassifier(n_estimators = n_tree, min_samples_split=5, random_state=1)
    score = model_selection.cross_val_score(estimator, bioresponce_data, bioresponce_target, 
                                             scoring = "accuracy", cv = 3)    
    scoring.append(score)
scoring = np.asmatrix(scoring)

The result is the matrix where each line corresponds to the number of trees from the n_trees array

scoring

matrix([[0.66906475, 0.668     , 0.6704    ],
        [0.75859313, 0.7592    , 0.7504    ],
        [0.78097522, 0.7616    , 0.7592    ],
        [0.78417266, 0.7736    , 0.7648    ],
        [0.78257394, 0.7736    , 0.7704    ],
        [0.78816946, 0.7752    , 0.7736    ],
        [0.78816946, 0.7856    , 0.7776    ],
        [0.78896882, 0.78      , 0.7832    ],
        [0.78976819, 0.7856    , 0.7896    ],
        [0.79536371, 0.7816    , 0.7928    ]])

We draw a graph of scoring depending on the number of trees (n_trees).

pylab.plot(n_trees, scoring.mean(axis = 1), marker=".", label="RandomForest")
pylab.grid(True) # adding the grid to the graph
pylab.xlabel("n_trees")
pylab.ylabel("score")
pylab.title("Accuracy score")
pylab.legend(loc="lower right")

Model xgboost.XGBClassifier

Now we build the gradien boosting, xgb.XGBClassifier, and use the same set of max number of trees

Learning curves for trees of greater depth

• max_depth – max tree depth
• n_estimators – max number of trees

%%time
xgb_scoring = []
for n_tree in n_trees:
    estimator = xgb.XGBClassifier(learning_rate=0.1, max_depth=5, n_estimators=n_tree, min_child_weight=3)
    # the object xgb.XGBClassifier() is complient with cross_val_score() function
    score = model_selection.cross_val_score(estimator, bioresponce_data, bioresponce_target, 
                                             scoring = "accuracy", cv = 3)    
    xgb_scoring.append(score)
xgb_scoring = np.asmatrix(xgb_scoring)

matrix([[0.76498801, 0.756     , 0.756     ],
        [0.77617906, 0.7752    , 0.7688    ],
        [0.77857714, 0.7744    , 0.7768    ],
        [0.7873701 , 0.7784    , 0.7768    ],
        [0.79216627, 0.7736    , 0.7832    ],
        [0.79776179, 0.7776    , 0.7824    ],
        [0.79616307, 0.7816    , 0.78      ],
        [0.79296563, 0.7848    , 0.7792    ],
        [0.79856115, 0.7832    , 0.7808    ],
        [0.79936051, 0.7832    , 0.7832    ]])

We draw a grath with both RF and the Gradient boosting for comparison.

pylab.plot(n_trees, scoring.mean(axis = 1), marker=".", label="RandomForest")
pylab.plot(n_trees, xgb_scoring.mean(axis = 1), marker=".", label="XGBoost")
pylab.grid(True)
pylab.xlabel("n_trees")
pylab.ylabel("score")
pylab.title("Accuracy score")
pylab.legend(loc="lower right")

Results comparison

Consclusion

1. Both algorithms are of high quality/accuracy, 0.8.
2. Gradient boosting yields relatively high classification results with a low number of max trees compare to RF.
3. Random Forest algorithm is much faster than that of Gradient boosting, XGBoost. See the results comparison table above.

More of xgboost:

• python api
• Installation