chainer_chemistry.models.GGNN¶
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class
chainer_chemistry.models.
GGNN
(out_dim, hidden_dim=16, n_layers=4, n_atom_types=117, concat_hidden=False, weight_tying=True, activation=<function identity>, num_edge_type=4)[source]¶ Gated Graph Neural Networks (GGNN)
See: Li, Y., Tarlow, D., Brockschmidt, M., & Zemel, R. (2015). Gated graph sequence neural networks. arXiv:1511.05493
Parameters: - out_dim (int) – dimension of output feature vector
- hidden_dim (int) – dimension of feature vector associated to each atom
- n_layers (int) – number of layers
- n_atom_types (int) – number of types of atoms
- concat_hidden (bool) – If set to True, readout is executed in each layer and the result is concatenated
- weight_tying (bool) – enable weight_tying or not
- activation (Function or FunctionNode) – activate function
- num_edge_type (int) – number of edge type. Defaults to 4 for single, double, triple and aromatic bond.
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__init__
(out_dim, hidden_dim=16, n_layers=4, n_atom_types=117, concat_hidden=False, weight_tying=True, activation=<function identity>, num_edge_type=4)[source]¶ Initialize self. See help(type(self)) for accurate signature.
Methods
__init__
(out_dim[, hidden_dim, n_layers, …])Initialize self. add_hook
(hook[, name])Registers a link hook. add_link
(name, link)Registers a child link to this chain. add_param
(name[, shape, dtype, initializer])Registers a parameter to the link. add_persistent
(name, value)Registers a persistent value to the link. addgrads
(link)Accumulates gradient values from given link. children
()Returns a generator of all child links. cleargrads
()Clears all gradient arrays. copy
([mode])Copies the link hierarchy to new one. copyparams
(link[, copy_persistent])Copies all parameters from given link. count_params
()Counts the total number of parameters. delete_hook
(name)Unregisters the link hook. disable_update
()Disables update rules of all parameters under the link hierarchy. enable_update
()Enables update rules of all parameters under the link hierarchy. init_scope
()Creates an initialization scope. links
([skipself])Returns a generator of all links under the hierarchy. namedlinks
([skipself])Returns a generator of all (path, link) pairs under the hierarchy. namedparams
([include_uninit])Returns a generator of all (path, param) pairs under the hierarchy. params
([include_uninit])Returns a generator of all parameters under the link hierarchy. register_persistent
(name)Registers an attribute of a given name as a persistent value. repeat
(n_repeat[, mode])Repeats this link multiple times to make a Sequential
.reset_state
()serialize
(serializer)Serializes the link object. to_cpu
()Copies parameter variables and persistent values to CPU. to_gpu
([device])Copies parameter variables and persistent values to GPU. to_intel64
()Copies parameter variables and persistent values to CPU. zerograds
()Initializes all gradient arrays by zero. Attributes
local_link_hooks
Ordered dictionary of registered link hooks. update_enabled
True
if at least one parameter has an update rule enabled.within_init_scope
True if the current code is inside of an initialization scope. xp
Array module for this link.