Commit 47be8a55 authored by evanfeinberg's avatar evanfeinberg
Browse files

solved some bugs

parent 34925328
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+2 −1
Original line number Diff line number Diff line
@@ -36,6 +36,7 @@ class DockingDNN(Model):
                          axis_length, axis_length, axis_length)

      learning_rate = model_params["learning_rate"]
      print("learning rate = %f" % learning_rate)
      loss_function = model_params["loss_function"]

         # number of convolutional filters to use at each layer
+5 −1
Original line number Diff line number Diff line
@@ -51,7 +51,7 @@ def compute_y_pred(model, data_dir, csv_out, split):

  split_df = metadata_df.loc[metadata_df['split'] == split]
  nb_batch = split_df.shape[0]
  MAX_GPU_RAM = float(691007488/50)
  MAX_GPU_RAM = float(691007488/100)

  for i, row in split_df.iterrows():
    print("Evaluating on %s batch %d out of %d" % (split, i+1, nb_batch))
@@ -106,7 +106,11 @@ def compute_model_performance(pred_y_df, task_names, task_type, stats_file, outp
  performance_df = pd.DataFrame(columns=colnames)

  y_means = pred_y_df.iterrows().next()[1]["y_means"]
  print("y_means")
  print(y_means)
  y_stds = pred_y_df.iterrows().next()[1]["y_stds"]
  print("y_stds")
  print(y_stds)

  for i, task_name in enumerate(task_names):
    y = pred_y_df[task_name]
+23 −21
Original line number Diff line number Diff line
@@ -17,7 +17,7 @@ def get_task_names(metadata_df):
  _, row = metadata_df.iterrows().next()
  return row['task_names']

def fit_model(model_name, model_params, model_dir, data_dir):
def fit_model(model_name, model_params, model_dir, data_dir, nb_epoch=25):
  """Builds model from featurized data."""
  task_type = get_task_type(model_name)
  metadata_filename = get_metadata_filename(data_dir)
@@ -38,8 +38,9 @@ def fit_model(model_name, model_params, model_dir, data_dir):
  print(model)

  train_metadata = metadata_df.loc[metadata_df['split'] =="train"]
  for epoch in range(0, nb_epoch):
    nb_batch = train_metadata.shape[0]
  MAX_GPU_RAM = float(691007488/50)
    MAX_GPU_RAM = float(691007488/100)
    for i, row in train_metadata.iterrows():
      print("Training on batch %d out of %d" % (i+1, nb_batch))
      X = load_sharded_dataset(row['X-transformed'])
@@ -58,5 +59,6 @@ def fit_model(model_name, model_params, model_dir, data_dir):
          model.fit_on_batch(X_batch, y_batch, w_batch)
      else:
        model.fit_on_batch(X, y, w)
    print("Completed fitting epoch %d" % epoch)

  save_model(model, model_name, model_dir)
+3 −2
Original line number Diff line number Diff line
@@ -299,8 +299,8 @@ def transform_data(metadata_df, input_transforms, output_transforms):

def undo_normalization(y, y_means, y_stds):
  """Undo the applied normalization transform."""
  y = y * y_means + y_stds
  return y * y_means + y_stds
  y = y * y_stds + y_means
  return y

def undo_transform(y, y_means, y_stds, output_transforms):
  """Undo transforms on y_pred, W_pred."""
@@ -312,6 +312,7 @@ def undo_transform(y, y_means, y_stds, output_transforms):
  elif output_transforms == ["log"]:
    return np.exp(y)
  elif output_transforms == ["normalize"]:
    print("Undoing normalization.")
    return undo_normalization(y, y_means, y_stds)
  elif output_transforms == ["log", "normalize"]:
    return np.exp(undo_normalization(y, y_means, y_stds))