def __init__(self, net_params):
super().__init__()
in_dim = net_params['in_dim']
hidden_dim = net_params['hidden_dim']
out_dim = net_params['out_dim']
n_classes = net_params['n_classes']
num_heads = net_params['n_heads']
in_feat_dropout = net_params['in_feat_dropout']
dropout = net_params['dropout']
n_layers = net_params['L']
self.readout = net_params['readout']
self.graph_norm = net_params['graph_norm']
self.batch_norm = net_params['batch_norm']
self.residual = net_params['residual']
self.dropout = dropout
self.embedding_h = nn.Linear(in_dim, hidden_dim * num_heads)
self.in_feat_dropout = nn.Dropout(in_feat_dropout)
self.layers = nn.ModuleList([
GATLayer(hidden_dim * num_heads, hidden_dim, num_heads, dropout,
self.graph_norm, self.batch_norm, self.residual)
for _ in range(n_layers - 1)
])
self.layers.append(
GATLayer(hidden_dim * num_heads, out_dim, 1, dropout,
self.graph_norm, self.batch_norm, self.residual))
self.MLP_layer = MLPReadout(out_dim, n_classes)
def __init__(self, net_params):
super().__init__()
in_dim_node = net_params['in_dim'] # node_dim (feat is an integer)
hidden_dim = net_params['hidden_dim']
out_dim = net_params['out_dim']
n_classes = net_params['n_classes']
num_heads = net_params['n_heads']
in_feat_dropout = net_params['in_feat_dropout']
dropout = net_params['dropout']
n_layers = net_params['L']
self.readout = net_params['readout']
self.norm = net_params['norm']
self.residual = net_params['residual']
self.dropout = dropout
self.n_classes = n_classes
self.device = net_params['device']
self.embedding_h = nn.Embedding(in_dim_node, hidden_dim *
num_heads) # node feat is an integer
self.in_feat_dropout = nn.Dropout(in_feat_dropout)
self.layers = nn.ModuleList([
GATLayer(hidden_dim * num_heads, hidden_dim, num_heads, dropout,
self.norm, self.residual) for _ in range(n_layers - 1)
])
self.layers.append(
GATLayer(hidden_dim * num_heads, out_dim, 1, dropout, self.norm,
self.residual))
self.MLP_layer = MLPReadout(out_dim, n_classes)
def __init__(self,
num_feats,
num_classes,
num_hidden,
num_layers,
num_heads,
merge='cat',
activation=F.elu,
graph_norm=False,
batch_norm=False,
residual=False,
dropout=0):
super(ResGATNet, self).__init__()
self.num_layers = num_layers
self.layers = nn.ModuleList()
self.layers.append(
GATLayer(num_feats, num_hidden, num_heads, merge, activation,
graph_norm, batch_norm, residual, dropout))
for i in range(1, num_layers - 1):
self.layers.append(
GATLayer(num_hidden * num_heads, num_hidden, num_heads, merge,
activation, graph_norm, batch_norm, residual,
dropout))
self.layers.append(
GATLayer(num_hidden * num_heads, num_classes, 1, 'mean',
activation, graph_norm, batch_norm, residual, dropout))
def __init__(self):
super().__init__()
self.L = 4
self.out_dim = 152
self.residual = True
self.readout = "mean"
self.in_dim = 32
self.hidden_dim = 19
self.n_heads = 8
self.n_classes = 10
self.in_feat_dropout = 0.0
self.dropout = 0.0
self.graph_norm = True
self.batch_norm = True
self.embedding_h = nn.Linear(self.in_dim,
self.hidden_dim * self.n_heads)
self.in_feat_dropout = nn.Dropout(self.in_feat_dropout)
self.layers = nn.ModuleList([
GATLayer(self.hidden_dim * self.n_heads, self.hidden_dim,
self.n_heads, self.dropout, self.graph_norm,
self.batch_norm, self.residual) for _ in range(self.L - 1)
])
self.layers.append(
GATLayer(self.hidden_dim * self.n_heads, self.out_dim, 1,
self.dropout, self.graph_norm, self.batch_norm,
self.residual))
self.readout_mlp = MLPReadout(self.out_dim, self.n_classes)
pass
def __init__(self, net_params):
super().__init__()
num_atom_type = net_params['num_atom_type']
num_bond_type = net_params['num_bond_type']
hidden_dim = net_params['hidden_dim']
num_heads = net_params['n_heads']
out_dim = net_params['out_dim']
in_feat_dropout = net_params['in_feat_dropout']
dropout = net_params['dropout']
n_layers = net_params['L']
self.readout = net_params['readout']
self.batch_norm = net_params['batch_norm']
self.residual = net_params['residual']
self.dropout = dropout
self.embedding_h = nn.Embedding(num_atom_type, hidden_dim * num_heads)
self.in_feat_dropout = nn.Dropout(in_feat_dropout)
self.layers = nn.ModuleList([
GATLayer(hidden_dim * num_heads, hidden_dim, num_heads, dropout,
self.batch_norm, self.residual)
for _ in range(n_layers - 1)
])
self.layers.append(
GATLayer(hidden_dim * num_heads, out_dim, 1, dropout,
self.batch_norm, self.residual))
self.MLP_layer = MLPReadout(out_dim,
1) # 1 out dim since regression problem
def __init__(self, net_params):
super().__init__()
in_dim = net_params['in_dim']
hidden_dim = net_params['hidden_dim']
out_dim = net_params['out_dim']
n_classes = net_params['n_classes']
num_heads = net_params['n_heads']
dropout = net_params['dropout']
n_layers = net_params['L']
self.graph_norm = net_params['graph_norm']
self.batch_norm = net_params['batch_norm']
self.residual = net_params['residual']
self.dropout = dropout
self.n_classes = n_classes
self.device = net_params['device']
self.dgl_builtin = net_params['builtin']
feat_drop = dropout
attn_drop = dropout
negative_slope = 0.2
residual = False
self.layers = nn.ModuleList()
self.activation = F.elu
# input projection (no residual)
self.layers.append(
GATLayer(in_dim,
hidden_dim,
num_heads,
dropout,
self.graph_norm,
self.batch_norm,
self.residual,
activation=self.activation,
dgl_builtin=self.dgl_builtin))
# hidden layers
for l in range(1, n_layers):
# due to multi-head, the in_dim = hidden_dim * num_heads
self.layers.append(
GATLayer(hidden_dim * num_heads,
hidden_dim,
num_heads,
dropout,
self.graph_norm,
self.batch_norm,
self.residual,
activation=self.activation,
dgl_builtin=self.dgl_builtin))
# output projection
self.layers.append(
GATLayer(hidden_dim * num_heads,
n_classes,
1,
dropout,
self.graph_norm,
self.batch_norm,
self.residual,
activation=None,
dgl_builtin=self.dgl_builtin))
def __init__(self, in_dim=64, hidden_dims=[19, 19]):
super().__init__()
self.n_heads = 8
self.embedding_h = nn.Linear(in_dim, hidden_dims[0] * self.n_heads)
self.gcn_list = nn.ModuleList()
for hidden_dim in hidden_dims[:-1]:
self.gcn_list.append(GATLayer(hidden_dim * self.n_heads, hidden_dim, self.n_heads, 0.0, True, True, True))
pass
self.gcn_list.append(GATLayer(hidden_dims[-2] * self.n_heads,
hidden_dims[-1] * self.n_heads, 1, 0.0, True, True, True))
pass
def __init__(self, in_dim=19, hidden_dims=[19, 19, 19, 19], n_classes=10):
super().__init__()
self.n_heads = 8
self.embedding_h = nn.Linear(in_dim * self.n_heads,
hidden_dims[0] * self.n_heads)
self.gcn_list = nn.ModuleList()
for hidden_dim in hidden_dims[:-1]:
self.gcn_list.append(
GATLayer(hidden_dim * self.n_heads, hidden_dim, self.n_heads,
0.0, True, True, True))
pass
self.gcn_list.append(
GATLayer(hidden_dims[-2] * self.n_heads,
hidden_dims[-1] * self.n_heads, 1, 0.0, True, True, True))
self.readout_mlp = MLPReadout(hidden_dims[-1] * self.n_heads,
n_classes)
pass
def __init__(self, in_dim, hidden_dims, skip_which, skip_dim=128, n_out=1):
super().__init__()
self.n_heads = 8
self.embedding_h = nn.Linear(in_dim, in_dim)
_in_dim = in_dim
self.gcn_list = nn.ModuleList()
for hidden_dim in hidden_dims[:-1]:
self.gcn_list.append(GATLayer(_in_dim, hidden_dim, self.n_heads, 0.0, True, True, True))
_in_dim = hidden_dim * self.n_heads
pass
self.gcn_list.append(GATLayer(_in_dim, hidden_dims[-1]*self.n_heads, 1, 0.0, True, True, True))
sk_hidden_dims = [in_dim] + [hidden_dims[which-1] * self.n_heads for which in skip_which]
self.skip_connect_index = [0] + skip_which
self.skip_connect_list = nn.ModuleList()
for hidden_dim in sk_hidden_dims:
self.skip_connect_list.append(nn.Linear(hidden_dim, skip_dim, bias=False))
pass
self.readout = nn.Linear(len(self.skip_connect_list) * skip_dim, n_out, bias=False)
pass
def __init__(self, net_params):
super().__init__()
self.readout = net_params.readout
self.embedding_h = nn.Linear(
net_params.in_dim, net_params.hidden_dim * net_params.n_heads)
self.in_feat_dropout = nn.Dropout(net_params.in_feat_dropout)
self.layers = nn.ModuleList([
GATLayer(net_params.hidden_dim * net_params.n_heads,
net_params.hidden_dim, net_params.n_heads,
net_params.dropout, net_params.graph_norm,
net_params.batch_norm, net_params.residual)
for _ in range(net_params.L - 1)
])
self.layers.append(
GATLayer(net_params.hidden_dim * net_params.n_heads,
net_params.out_dim, 1, net_params.dropout,
net_params.graph_norm, net_params.batch_norm,
net_params.residual))
self.readout_mlp = MLPReadout(net_params.out_dim, net_params.n_classes)
pass
def __init__(self, net_params):
super().__init__()
num_atom_type = net_params['num_atom_type']
num_bond_type = net_params['num_bond_type']
hidden_dim = net_params['hidden_dim']
num_heads = net_params['n_heads']
out_dim = net_params['out_dim']
in_feat_dropout = net_params['in_feat_dropout']
dropout = net_params['dropout']
n_layers = net_params['L']
self.readout = net_params['readout']
self.graph_norm = net_params['graph_norm']
self.batch_norm = net_params['batch_norm']
self.layer_norm = net_params['layer_norm']
self.residual = net_params['residual']
self.att_reduce_fn = net_params['att_reduce_fn']
self.task = net_params['task']
if self.task == 'classification':
self.num_classes = net_params['num_classes']
self.dropout = dropout
self.embedding_lin = nn.Linear(num_atom_type, hidden_dim, bias=False)
self.in_feat_dropout = nn.Dropout(in_feat_dropout)
self.layers = nn.ModuleList([
GATLayer(hidden_dim, hidden_dim, num_heads, dropout,
self.graph_norm, self.batch_norm, self.layer_norm, self.att_reduce_fn) for _ in range(n_layers)])
self.linear_ro = nn.Linear(hidden_dim, out_dim, bias=False)
self.linear_predict = nn.Linear(out_dim, 1, bias=True)
# additional parameters for gated gcn
if self.residual == "gated":
self.W_g = nn.Linear(2*hidden_dim, hidden_dim, False)