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_make.py
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# import keras_core as ks
from ._model import model_disjoint
from kgcnn.models.utils import update_model_kwargs
from kgcnn.layers.scale import get as get_scaler
from kgcnn.layers.modules import Input
from kgcnn.models.casting import (template_cast_output, template_cast_list_input,
template_cast_list_input_docs, template_cast_output_docs)
from keras.backend import backend as backend_to_use
from kgcnn.ops.activ import *
# Keep track of model version from commit date in literature.
# To be updated if model is changed in a significant way.
__model_version__ = "2023-10-12"
# Supported backends
__kgcnn_model_backend_supported__ = ["tensorflow", "torch", "jax"]
if backend_to_use() not in __kgcnn_model_backend_supported__:
raise NotImplementedError("Backend '%s' for model 'rGIN' is not supported." % backend_to_use())
# Implementation of rGIN in `keras` from paper:
# Random Features Strengthen Graph Neural Networks
# Ryoma Sato, Makoto Yamada, Hisashi Kashima
# https://arxiv.org/abs/2002.03155
model_default = {
"name": "rGIN",
"inputs": [
{"shape": (None,), "name": "node_attributes", "dtype": "float32", "ragged": True},
{"shape": (None, 2), "name": "edge_indices", "dtype": "int64", "ragged": True}
],
"input_tensor_type": "padded",
"cast_disjoint_kwargs": {},
"input_embedding": None, # deprecated
"input_node_embedding": {"input_dim": 95, "output_dim": 64},
"gin_mlp": {"units": [64, 64], "use_bias": True, "activation": ["relu", "linear"],
"use_normalization": True, "normalization_technique": "graph_batch"},
"rgin_args": {"random_range": 100},
"depth": 3, "dropout": 0.0, "verbose": 10,
"last_mlp": {"use_bias": [True, True, True], "units": [64, 64, 64],
"activation": ["relu", "relu", "linear"]},
"output_embedding": 'graph',
"output_mlp": {"use_bias": True, "units": 1,
"activation": "softmax"},
"output_to_tensor": None, # deprecated
"output_tensor_type": "padded",
"output_scaling": None,
}
@update_model_kwargs(model_default, update_recursive=0, deprecated=["input_embedding", "output_to_tensor"])
def make_model(inputs: list = None,
input_tensor_type: str = None,
cast_disjoint_kwargs: dict = None,
input_embedding: dict = None,
input_node_embedding: dict = None,
depth: int = None,
rgin_args: dict = None,
gin_mlp: dict = None,
last_mlp: dict = None,
dropout: float = None,
name: str = None,
verbose: int = None,
output_embedding: str = None,
output_to_tensor: bool = None,
output_mlp: dict = None,
output_scaling: dict = None,
output_tensor_type: str = None,
):
r"""Make `rGIN <https://arxiv.org/abs/2002.03155>`__ graph network via functional API.
Default parameters can be found in :obj:`kgcnn.literature.rGIN.model_default` .
**Model inputs**:
Model uses the list template of inputs and standard output template.
The supported inputs are :obj:`[nodes, edge_indices, ...]`
with '...' indicating mask or ID tensors following the template below:
%s
**Model outputs**:
The standard output template:
%s
Args:
inputs (list): List of dictionaries unpacked in :obj:`tf.keras.layers.Input`. Order must match model definition.
input_tensor_type (str): Input type of graph tensor. Default is "padded".
cast_disjoint_kwargs (dict): Dictionary of arguments for castin layers.
input_embedding (dict): Deprecated in favour of input_node_embedding etc.
input_node_embedding (dict): Dictionary of arguments for nodes unpacked in :obj:`Embedding` layers.
depth (int): Number of graph embedding units or depth of the network.
rgin_args (dict): Dictionary of layer arguments unpacked in :obj:`GIN` convolutional layer.
gin_mlp (dict): Dictionary of layer arguments unpacked in :obj:`MLP` for convolutional layer.
last_mlp (dict): Dictionary of layer arguments unpacked in last :obj:`MLP` layer before output or pooling.
dropout (float): Dropout to use.
name (str): Name of the model.
verbose (int): Level of print output.
output_embedding (str): Main embedding task for graph network. Either "node", "edge" or "graph".
output_to_tensor (bool): Deprecated in favour of `output_tensor_type` .
output_mlp (dict): Dictionary of layer arguments unpacked in the final classification :obj:`MLP` layer block.
Defines number of model outputs and activation.
output_scaling (dict): Dictionary of layer arguments unpacked in scaling layers. Default is None.
output_tensor_type (str): Output type of graph tensors such as nodes or edges. Default is "padded".
Returns:
:obj:`keras.models.Model`
"""
# Make input
model_inputs = [Input(**x) for x in inputs]
disjoint_inputs = template_cast_list_input(
model_inputs, input_tensor_type=input_tensor_type, cast_disjoint_kwargs=cast_disjoint_kwargs,
mask_assignment=[0, 1],
index_assignment=[None, 0]
)
n, disjoint_indices, batch_id_node, batch_id_edge, node_id, edge_id, count_nodes, count_edges = disjoint_inputs
# Wrapping disjoint model.
out = model_disjoint(
[n, disjoint_indices, batch_id_node, count_nodes],
use_node_embedding=("int" in inputs[0]['dtype']) if input_node_embedding is not None else False,
input_node_embedding=input_node_embedding,
gin_mlp=gin_mlp,
depth=depth,
rgin_args=rgin_args,
last_mlp=last_mlp,
output_mlp=output_mlp,
output_embedding=output_embedding,
dropout=dropout
)
if output_scaling is not None:
scaler = get_scaler(output_scaling["name"])(**output_scaling)
out = scaler(out)
# Output embedding choice
out = template_cast_output(
[out, batch_id_node, batch_id_edge, node_id, edge_id, count_nodes, count_edges],
output_embedding=output_embedding, output_tensor_type=output_tensor_type,
input_tensor_type=input_tensor_type, cast_disjoint_kwargs=cast_disjoint_kwargs
)
model = ks.models.Model(inputs=model_inputs, outputs=out, name=name)
model.__kgcnn_model_version__ = __model_version__
if output_scaling is not None:
def set_scale(*args, **kwargs):
scaler.set_scale(*args, **kwargs)
setattr(model, "set_scale", set_scale)
return model
make_model.__doc__ = make_model.__doc__ % (template_cast_list_input_docs, template_cast_output_docs)