Commit 71868b05 authored by haozhenWu's avatar haozhenWu
Browse files

update doc

parent f47210f7
Loading
Loading
Loading
Loading
+11 −7
Original line number Diff line number Diff line
@@ -11,13 +11,15 @@ Giving classification performances of:
    Random forest(rf), MultitaskDNN(tf),
    RobustMultitaskDNN(tf_robust),
    Logistic regression(logreg), IRV(irv)
    Graph convolution(graphconv)
    Graph convolution(graphconv),
    Xgboost classifier(xgb_classifier)
on datasets: muv, pcba, tox21, sider, toxcast, clintox, hiv

Giving regression performances of:
    MultitaskDNN(tf_regression),
    Random forest(rf_regression),
    Graph convolution regression(graphconvreg)
    Graph convolution regression(graphconvreg),
    Xgboost regression(xgb_regression)
on datasets: delaney(ESOL), nci, kaggle, pdbbind,
             qm7, qm7b, qm9, chembl, sampl(FreeSolv)

@@ -79,7 +81,8 @@ def benchmark_loading_datasets(hyper_parameters,
      qm7, qm7b, qm9, sampl
  model: string,  optional (default='tf')
      choice of which model to use, should be: rf, tf, tf_robust, logreg,
      irv, graphconv, tf_regression, rf_regression, graphconvreg
      irv, graphconv, xgb_classifier, tf_regression, rf_regression, 
      graphconvreg, xgb_regression
  split: string,  optional (default=None)
      choice of splitter function, None = using the default splitter
  out_path: string, optional(default='.')
@@ -101,7 +104,8 @@ def benchmark_loading_datasets(hyper_parameters,
    featurizer = 'GraphConv'
    n_features = 75
  elif model in [
      'tf', 'tf_robust', 'logreg', 'rf', 'irv', 'tf_regression', 'rf_regression'
      'tf', 'tf_robust', 'logreg', 'rf', 'irv', 'tf_regression', 'rf_regression',
      'xgb_classifier', 'xgb_regression'
  ]:
    featurizer = 'ECFP'
    n_features = 1024
@@ -290,7 +294,7 @@ def benchmark_classification(train_dataset,
      number of features, or length of binary fingerprints
  model: string,  optional (default='tf')
      choice of which model to use, should be: rf, tf, tf_robust, logreg,
      irv, graphconv
      irv, graphconv, xgb_classifier
  test: boolean
      whether to calculate test_set performance

@@ -658,7 +662,7 @@ def benchmark_regression(train_dataset,
      number of features, or length of binary fingerprints
  model: string,  optional (default='tf_regression')
      choice of which model to use, should be: tf_regression, graphconvreg,
      rf_regression
      rf_regression, xgb_regression
  test: boolean
      whether to calculate test_set performance

@@ -871,7 +875,7 @@ def benchmark_regression(train_dataset,
    model_xgb = dc.models.multitask.SingletaskToMultitask(tasks, model_builder)

    print('-------------------------------------')
    print('Start fitting by xgoost')
    print('Start fitting by xgboost')
    model_xgb.fit(train_dataset)

    # Evaluating xgboost classification model