Commit c6b5ccaa authored by joegomes's avatar joegomes
Browse files

Move _add_user_specified_features into _standardize_df. Cleaned up some prints

parent 0fa8c2dc
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+4 −4
Original line number Diff line number Diff line
@@ -136,11 +136,9 @@ class DataFeaturizer(object):
        0, nb_sample, np.ceil(float(nb_sample)/shard_size)+1, dtype=int)
    shard_files = []
    for j in range(len(interval_points)-1):
      #log("Sharding and standardizing into shard-%s / %s shards" % (str(j+1), len(interval_points)-1), self.verbose)
      log("Sharding and standardizing into shard-%s / %s shards" % (str(j+1), len(interval_points)-1), self.verbose)
      raw_df_shard = raw_df.iloc[range(interval_points[j], interval_points[j+1])]
      df = self._standardize_df(raw_df_shard)
      #log("Aggregating User-Specified Features", self.verbose)
      self._add_user_specified_features(df)

      for compound_featurizer in self.compound_featurizers:
        log("Currently featurizing feature_type: %s"
@@ -199,6 +197,9 @@ class DataFeaturizer(object):
      df["ligand_pdb"] = ori_df[[self.ligand_pdb_field]]
    if self.ligand_mol2_field is not None:
      df["ligand_mol2"] = ori_df[[self.ligand_mol2_field]]
    if self.user_specified_features is not None:
      log("Aggregating User-Specified Features", self.verbose)
      self._add_user_specified_features(df)
    return df

  def _featurize_complexes(self, df, featurizer):
@@ -343,7 +344,6 @@ class FeaturizedSamples(object):
    """Returns size of internal dataset."""
    return self.num_samples

    irint("feature types %s" % self.feature_types)
  def itersamples(self):
    """Iterates over samples in this object."""
    compound_ids = set(list(self.compounds_df["mol_id"]))
+0 −3
Original line number Diff line number Diff line
@@ -77,9 +77,6 @@ class Model(object):
    """
    Factory method that initializes model of requested type.
    """
    print(model_instance.__class__)
    print(task_types)
    print(model_params)
    if model_instance.__class__ in Model.non_sklearn_models:
      model = model_instance(task_types, model_params, initialize_raw_model)
    else:
+0 −1
Original line number Diff line number Diff line
@@ -96,7 +96,6 @@ def nnscore_hyperparam_search(train_dataset, test_dataset,
                  "decay": 1e-4, "batch_size": 5,
                  "nb_epoch": 10}
  model_name = "singletask_deep_regressor"
  #model_name = "SingleTaskDNN"
  nb_hidden_vals = [10, 100]
  learning_rate_vals = [.01, .001]
  init_vals = ["glorot_uniform"]