chainer_chemistry.models.NFP

class chainer_chemistry.models.NFP(out_dim, hidden_dim=16, n_layers=4, max_degree=6, n_atom_types=117, concat_hidden=False)[source]

Neural Finger Print (NFP)

See: David K Duvenaud, Dougal Maclaurin, Jorge Iparraguirre, Rafael
Bombarell, Timothy Hirzel, Alan Aspuru-Guzik, and Ryan P Adams (2015). Convolutional networks on graphs for learning molecular fingerprints. Advances in Neural Information Processing Systems (NIPS) 28,
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
  • max_degree (int) – max degree of atoms when molecules are regarded as graphs
  • 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
__init__(out_dim, hidden_dim=16, n_layers=4, max_degree=6, n_atom_types=117, concat_hidden=False)[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.
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.