Commit 019dd9b8 authored by Bharath Ramsundar's avatar Bharath Ramsundar
Browse files

Fixing up docstring to have defaults

parent aa4add51
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+21 −18
Original line number Diff line number Diff line
@@ -111,47 +111,48 @@ class WeaveModel(KerasModel):
    ----------
    n_tasks: int
      Number of tasks
    n_atom_feat: int, optional
      Number of features per atom.
    n_pair_feat: int, optional
    n_atom_feat: int, optional (default 75)
      Number of features per atom. Note this is 75 by default and should be 78
      if chirality is used by `WeaveFeaturizer`.
    n_pair_feat: int, optional (default 14)
      Number of features per pair of atoms.
    n_hidden: int, optional
    n_hidden: int, optional (default 50)
      Number of units(convolution depths) in corresponding hidden layer
    n_graph_feat: int, optional
    n_graph_feat: int, optional (default 128)
      Number of output features for each molecule(graph)
    n_weave: int, optional
    n_weave: int, optional (default 2)
      The number of weave layers in this model.
    fully_connected_layer_sizes: list
    fully_connected_layer_sizes: list (default `[2000, 100]`)
      The size of each dense layer in the network.  The length of
      this list determines the number of layers.
    conv_weight_init_stddevs: list or float
    conv_weight_init_stddevs: list or float (default 0.03)
      The standard deviation of the distribution to use for weight
      initialization of each convolutional layer. The length of this lisst
      should equal `n_weave`. Alternatively, this may be a single value instead
      of a list, in which case the same value is used for each layer.
    weight_init_stddevs: list or float
    weight_init_stddevs: list or float (default 0.01)
      The standard deviation of the distribution to use for weight
      initialization of each fully connected layer.  The length of this list
      should equal len(layer_sizes).  Alternatively this may be a single value
      instead of a list, in which case the same value is used for every layer.
    bias_init_consts: list or float
    bias_init_consts: list or float (default 0.0)
      The value to initialize the biases in each fully connected layer.  The
      length of this list should equal len(layer_sizes).
      Alternatively this may be a single value instead of a list, in
      which case the same value is used for every layer.
    weight_decay_penalty: float
    weight_decay_penalty: float (default 0.0)
      The magnitude of the weight decay penalty to use
    weight_decay_penalty_type: str
    weight_decay_penalty_type: str (default "l2")
      The type of penalty to use for weight decay, either 'l1' or 'l2'
    dropouts: list or float
    dropouts: list or float (default 0.25)
      The dropout probablity to use for each fully connected layer.  The length of this list
      should equal len(layer_sizes).  Alternatively this may be a single value
      instead of a list, in which case the same value is used for every layer.
    final_conv_activation_fn: Optional[KerasActivationFn]
    final_conv_activation_fn: Optional[KerasActivationFn] (default `tf.nn.tanh`)
      The Tensorflow activation funcntion to apply to the final
      convolution at the end of the weave convolutions. If `None`, then no
      convolution (linear) is applied.
    activation_fns: list or object
      activate is applied (hence linear).
    activation_fns: list or object (default `tf.nn.relu`)
      The Tensorflow activation function to apply to each fully connected layer.  The length
      of this list should equal len(layer_sizes).  Alternatively this may be a
      single value instead of a list, in which case the same value is used for
@@ -170,10 +171,12 @@ class WeaveModel(KerasModel):
    compress_post_gaussian_expansion: bool, optional (default False)
      If True, compress the results of the Gaussian expansion back to the
      original dimensions of the input.
    mode: str
    mode: str (default "classification")
      Either "classification" or "regression" for type of model.
    n_classes: int
    n_classes: int (default 2)
      Number of classes to predict (only used in classification mode)
    batch_size: int (default 100)
      Batch size used by this model for training.
    """
    if mode not in ['classification', 'regression']:
      raise ValueError("mode must be either 'classification' or 'regression'")