def __init__(self, in_channels: int, hidden_channels: int,
out_channels: int, edge_dim: int, num_layers: int,
num_timesteps: int, dropout: float = 0.0):
super(AttentiveFP, self).__init__()
self.num_layers = num_layers
self.num_timesteps = num_timesteps
self.dropout = dropout
self.lin1 = Linear(in_channels, hidden_channels)
conv = GATEConv(hidden_channels, hidden_channels, edge_dim, dropout)
gru = GRUCell(hidden_channels, hidden_channels)
self.atom_convs = torch.nn.ModuleList([conv])
self.atom_grus = torch.nn.ModuleList([gru])
for _ in range(num_layers - 1):
conv = GATConv(hidden_channels, hidden_channels, dropout=dropout,
add_self_loops=False, negative_slope=0.01)
self.atom_convs.append(conv)
self.atom_grus.append(GRUCell(hidden_channels, hidden_channels))
self.mol_conv = GATConv(hidden_channels, hidden_channels,
dropout=dropout, add_self_loops=False,
negative_slope=0.01)
self.mol_gru = GRUCell(hidden_channels, hidden_channels)
self.lin2 = Linear(hidden_channels, out_channels)
self.reset_parameters()
def __init__(self,
word_vec_dim,
hidden_size,
sesssion_num_layers=2,
user_num_layers=2,
dropout_p=0.1):
super(HierarchicalRNNCell, self).__init__()
self.word_vec_dim = word_vec_dim
self.hidden_size = hidden_size
self.session_num_layers = sesssion_num_layers
self.user_num_layers = user_num_layers
self.dropout_p = dropout_p
self.session_rnn_cells = [
GRUCell(input_size=word_vec_dim, hidden_size=hidden_size)
]
self.session_rnn_cells = self.session_rnn_cells + [
GRUCell(input_size=hidden_size, hidden_size=hidden_size)
for _ in range(sesssion_num_layers - 1)
]
self.session_rnn_cells = ListModule(*self.session_rnn_cells)
self.user_rnn_cells = [
GRUCell(input_size=hidden_size, hidden_size=hidden_size)
for _ in range(user_num_layers)
]
self.user_rnn_cells = ListModule(*self.user_rnn_cells)
self.dropout = nn.Dropout(p=dropout_p)
def __init__(self,
node_in_channels,
node_out_channels,
edge_in_channels,
edge_out_channels,
heads=5,
dropout=0.1,
parameter_efficient=True,
attention_channels=None,
principal_neighbourhood_aggregation=False,
deg=None,
aggr='add'):
super().__init__()
self.conv = GATEConv(node_in_channels=node_in_channels,
node_out_channels=node_out_channels,
edge_in_channels=edge_in_channels,
edge_out_channels=edge_out_channels,
heads=heads,
concat=True,
attention_channels=attention_channels,
parameter_efficient=parameter_efficient,
principal_neighbourhood_aggregation=
principal_neighbourhood_aggregation,
deg=deg,
aggr=aggr)
self.node_norm = BatchNorm(node_in_channels)
self.edge_norm = BatchNorm(edge_in_channels)
self.node_aggr = GRUCell(node_in_channels, node_out_channels)
self.edge_aggr = GRUCell(edge_in_channels, edge_out_channels)
self.dropout = dropout
self.edge_channels = edge_in_channels
def __init__(self, num_nodes: int, raw_msg_dim: int, memory_dim: int,
time_dim: int, message_module: Callable,
aggregator_module: Callable):
super().__init__()
self.num_nodes = num_nodes
self.raw_msg_dim = raw_msg_dim
self.memory_dim = memory_dim
self.time_dim = time_dim
self.msg_s_module = message_module
self.msg_d_module = copy.deepcopy(message_module)
self.aggr_module = aggregator_module
self.time_enc = TimeEncoder(time_dim)
self.gru = GRUCell(message_module.out_channels, memory_dim)
self.register_buffer('memory', torch.empty(num_nodes, memory_dim))
last_update = torch.empty(self.num_nodes, dtype=torch.long)
self.register_buffer('last_update', last_update)
self.register_buffer('__assoc__',
torch.empty(num_nodes, dtype=torch.long))
self.msg_s_store = {}
self.msg_d_store = {}
self.reset_parameters()
def __init__(self, in_features, memory_dim, r, eps=0):
super(Decoder, self).__init__()
self.max_decoder_steps = 200
self.memory_dim = memory_dim
self.eps = eps
self.r = r
self.prenet = Prenet(in_features=(self.memory_dim * self.r), out_features=[256, 128])
self.attention_rnn = AttentionRNN(out_dim=256, annot_dim=in_features, memory_dim=128)
self.project_to_decoder_in = Linear(in_features=(256 + in_features), out_features=256)
# 2-layer residual GRU (256 cells)
self.decoder_rnns = ModuleList(
[GRUCell(input_size=256, hidden_size=256), GRUCell(input_size=256, hidden_size=256)])
self.proj_to_mel = Linear(in_features=256, out_features=(self.memory_dim * self.r))
def __init__(self,
c_dim: int,
m_dim: int,
p_dim: int,
radius=2,
use_cuda=False,
dropout=0.,
use_gru=True):
super(AlignAttendPooling, self).__init__()
self.use_cuda = use_cuda
self.use_gru = use_gru
self.radius = radius
self.map = Linear(c_dim, m_dim)
self.relu = LeakyReLU()
self.relu1 = LeakyReLU()
if use_gru:
self.gru = GRUCell(c_dim, m_dim)
else:
self.linear = Linear(c_dim + m_dim, m_dim)
self.attend = Linear(c_dim + p_dim, c_dim)
self.align = Linear(m_dim + c_dim + p_dim, 1)
self.softmax = Softmax(dim=1)
self.elu = ELU()
self.relu2 = ReLU()
self.dropout = Dropout(p=dropout)
def __init__(self,
input_dim,
contxt_dim,
hidden_dim,
att_module,
pointer_gen_module,
cat_contx_to_inp=True,
pass_extra_feat_to_pg=False,
copy_prob=None,
**kwargs):
"""
:param pass_extra_feat_to_pg: whether to pass (concatenated) extra
features to the pointer-generator network
or just embeddings.
"""
super(GruPointerDecoder, self).__init__()
self.input_dim = input_dim
self.contxt_dim = contxt_dim
self.hidden_dim = hidden_dim
self.att = att_module
self.cat_conxt_to_inp = cat_contx_to_inp
cell_inp_dim = input_dim + contxt_dim if cat_contx_to_inp else input_dim
self.gru_cell = GRUCell(cell_inp_dim, hidden_dim, **kwargs)
self.pgn = pointer_gen_module
self.copy_prob = copy_prob
self.pass_extra_feat_to_pg = pass_extra_feat_to_pg
def __init__(self, cnn_channels, cnn_dropout, rnn_in_dim,
rnn_out_dim, rnn_dropout, nb_classes):
"""The CRNN model.
:param cnn_channels: The amount of CNN channels.
:type cnn_channels: int
:param cnn_dropout: The dropout to be applied to the CNNs.
:type cnn_dropout: float
:param rnn_in_dim: The input dimensionality of the RNN.
:type rnn_in_dim: int
:param rnn_out_dim: The output dimensionality of the RNN.
:type rnn_out_dim: int
:param rnn_dropout: The dropout to be applied to the RNN.
:type rnn_dropout: float
:param nb_classes: The amount of classes to be predicted.
:type nb_classes: int
"""
super(CRNN, self).__init__()
self.dnn_output_features = cnn_channels
self.rnn_hh_size = rnn_out_dim
self.nb_classes = nb_classes
self.dnn = Sequential(
dnn.DNN(cnn_channels=cnn_channels, cnn_dropout=cnn_dropout),
Dropout(rnn_dropout)
)
self.rnn = GRUCell(rnn_in_dim, self.rnn_hh_size, bias=True)
self.classifier = Linear(self.rnn_hh_size, self.nb_classes, bias=True)
def __init__(self,
cnn_channels: int,
cnn_dropout: float,
rnn_in_dim: int,
rnn_out_dim: int,
nb_classes: int) \
-> None:
"""The DESSED model.
:param cnn_channels: Amount of CNN channels.
:type cnn_channels: int
:param cnn_dropout: Dropout to be applied to the CNNs.
:type cnn_dropout: float
:param rnn_in_dim: Input dimensionality of the RNN.
:type rnn_in_dim: int
:param rnn_out_dim: Output dimensionality of the RNN.
:type rnn_out_dim: int
:param nb_classes: Amount of classes to be predicted.
:type nb_classes: int
"""
super().__init__()
self.rnn_hh_size: int = rnn_out_dim
self.nb_classes: int = nb_classes
self.dnn: Module = DepthWiseSeparableDNN(cnn_channels=cnn_channels,
cnn_dropout=cnn_dropout)
self.rnn: Module = GRUCell(input_size=rnn_in_dim,
hidden_size=self.rnn_hh_size,
bias=True)
self.classifier: Module = Linear(in_features=self.rnn_hh_size,
out_features=self.nb_classes,
bias=True)
def __init__(self, arch: dict):
super().__init__()
self.ldim = arch['latent_dim']
self.defaultSteps = arch['std_T']
self.Cinit = torch.nn.Parameter(torch.FloatTensor(self.ldim))
torch.nn.init.normal_(self.Cinit)
self.Linit = torch.nn.Parameter(torch.FloatTensor(self.ldim))
torch.nn.init.normal_(self.Linit)
self.rec_block = arch['recurrent_block']
if self.rec_block == 'test':
# self.block = BiPartialTestBlock(self.ldim, self.ldim, 2 * self.ldim, 2)
Ldim, Cdim, Hdim, Dpth = self.ldim, self.ldim, 2 * self.ldim, 2
self.Cmsg = batchMLP(Cdim, Hdim, Cdim, Dpth, False)
self.Lmsg = batchMLP(Ldim, Hdim, Ldim, Dpth, False)
self.Cu = batchMLP(Cdim * 2, Hdim, Cdim, Dpth, False)
self.Lu = batchMLP(Ldim * 3, Hdim, Ldim, Dpth, False)
elif self.rec_block in ['std_lstm', 'ln_lstm', 'gru']:
Ldim, Cdim, Hdim, Dpth = self.ldim, self.ldim, self.ldim, 4
self.Cmsg = batchMLP(Cdim, Hdim, Cdim, Dpth, False)
self.Lmsg = batchMLP(Ldim, Hdim, Ldim, Dpth, False)
if self.rec_block == 'std_lstm':
self.Cu = LSTMCell(self.ldim, self.ldim, True)
self.Lu = LSTMCell(self.ldim * 2, self.ldim, True)
elif self.rec_block == 'ln_lstm':
self.Cu = ln_LSTMCell(self.ldim, self.ldim, True)
self.Lu = ln_LSTMCell(self.ldim * 2, self.ldim, True)
elif self.rec_block == 'gru':
self.Cu = GRUCell(self.ldim, self.ldim, True)
self.Lu = GRUCell(self.ldim * 2, self.ldim, True)
self.cl = arch['classifier']
if self.cl == 'NeuroSAT':
self.Lvote = batchMLP(self.ldim, 2 * self.ldim, 1, 2, False)
elif self.cl == 'CircuitSAT-like':
self.tnormf = arch['tnorm']
if 'tnorm_train' in arch:
self.train_tnorm = arch['tnorm_train']
else:
self.train_tnorm = self.tnormf
self.tnorm_tmp = arch['tnorm_temperature']
self.train_temp = arch['temp_train']
self.test_temp = arch['temp_test']
self.Lvote = batchMLP(self.ldim, 2 * self.ldim, 1, 2, False)
def __init__(self, num_L):
super(DrBC, self).__init__()
self.num_L = num_L
self.data_in = Sequential(Linear(3, 128), ReLU())
self.Aggregation = GCNConv(128, 128)
self.Combine = GRUCell(128, 128, bias=False)
self.data_out = Sequential(Linear(128, 64), ReLU(), Linear(64,1), ReLU())
def __init__(self, input_dim, hidden_dim, dropout_prob=0., hidden_norm=False,
**kwargs):
super(GruMaskedEncoder, self).__init__()
self.input_dim = input_dim
self.hidden_dim = hidden_dim
self.dropout_prob = dropout_prob
self.gru_cell = GRUCell(input_dim, hidden_dim, **kwargs)
self.dropout_layer = Dropout(dropout_prob)
self.hidden_norm = LayerNorm(hidden_dim) if hidden_norm else None
def get_pytorch_gru(input_size, used_gru):
"""Load in a PyTorch GRU that is a copy of the currently used GRU."""
gru = PytorchGRU(input_size, 1)
if type(used_gru) == GRUBerkeley:
gru.bias_hh[:] = tensor(zeros((3,)), dtype=float64)[:]
gru.bias_ih[:] = tensor(used_gru.bias, dtype=float64)[:]
gru.weight_hh[:] = tensor(used_gru.weight_hh, dtype=float64)[:]
gru.weight_ih[:] = tensor(used_gru.weight_xh, dtype=float64)[:]
elif type(used_gru) == GRUPyTorch:
gru.bias_hh[:] = tensor(used_gru.bias_hh, dtype=float64)[:]
gru.bias_ih[:] = tensor(used_gru.bias_ih, dtype=float64)[:]
gru.weight_hh[:] = tensor(used_gru.weight_hh, dtype=float64)[:]
gru.weight_ih[:] = tensor(used_gru.weight_ih, dtype=float64)[:]
else:
raise Exception(f"Invalid input for used_gru: {used_gru}")
return gru
def __init__(self,params:configargparse.Namespace,att: torch.nn.Module=None):
"""
Neural Network Module for the Sequence to Sequence LAS Model
:params configargparse.Namespace params: The training options
:params torch.nn.Module att: The attention module
"""
super(Speller,self).__init__()
## Embedding Layer
self.embed = Embedding(params.odim,params.demb_dim)
## Decoder with LSTM Cells
self.decoder = ModuleList()
self.dropout_dec = ModuleList()
self.dtype = params.dtype
self.dunits = params.dhiddens
self.dlayers = params.dlayers
self.decoder += [
LSTMCell(params.eprojs + params.demb_dim, params.dhiddens)
if self.dtype == "lstm"
else GRUCell(params.eprojs + params.demb_dim, params.dhiddens)
]
self.dropout_dec += [Dropout(p=params.ddropout)]
self.dropout_emb = Dropout(p=params.ddropout)
## Other decoder layers if > 1 decoder layer
for i in range(1,params.dlayers):
self.decoder += [
LSTMCell(params.dhiddens, params.dhiddens)
if self.dtype == "lstm"
else GRUCell(params.dhiddens, params.dhiddens)
]
self.dropout_dec += [LockedDropout(p=params.ddropout)] # Dropout
## Project to Softmax Space- Output
self.projections = Linear(params.dhiddens, params.odim)
## Attention Module
self.att = att
## Scheduled Sampling
self.sampling_probability = params.ssprob
## Initialize EOS, SOS
self.eos = len(params.char_list) -1
self.sos = self.eos
self.ignore_id = params.text_pad
def __init__(self, input_dim, context_length, debug):
"""The RNN encoder of the Masker.
:param input_dim: The input dimensionality.
:type input_dim: int
:param context_length: The context length.
:type context_length: int
:param debug: Flag to indicate debug
:type debug: bool
"""
super(RNNEnc, self).__init__()
self._input_dim = input_dim
self._context_length = context_length
self.gru_enc_f = GRUCell(self._input_dim, self._input_dim)
self.gru_enc_b = GRUCell(self._input_dim, self._input_dim)
self._debug = debug
self.initialize_encoder()
def __init__(
self,
input_size: int,
hidden_size: int,
) -> None:
super().__init__()
# We'll use an LSTM cell as the recurrent cell that produces a hidden state
# for the decoder at each time step.
self._generator = GRUCell(input_size, hidden_size)
self._projection = nn.Linear(2*hidden_size, hidden_size)
def __init__(self, inp_size, hid_size, out_size, rnn_type="raw_rnn", single_loss=True): super().__init__() allow_rnn_types = ["raw_rnn","lstm","gru"] assert rnn_type in allow_rnn_types self.rnn_type = rnn_type self.single_loss = single_loss self.inp_size = inp_size self.hid_size = hid_size self.out_size = out_size if rnn_type == "raw_rnn": self.lstm = RNNCell(inp_size, hid_size) if rnn_type == "lstm": self.lstm = LSTMCell(inp_size, hid_size) if rnn_type == "gru": self.lstm = GRUCell(inp_size, hid_size) self.fc1 = nn.Linear(hid_size, out_size) self.criterion = nn.CrossEntropyLoss()
def __init__(self,
num_timesteps=4,
emb_dim=300,
num_layers=5,
drop_ratio=0,
num_tasks=1,
**args):
super(AttentiveFP, self).__init__()
self.num_layers = num_layers
self.num_timesteps = num_timesteps
self.drop_ratio = drop_ratio
self.atom_encoder = AtomEncoder(emb_dim)
self.bond_encoder = BondEncoder(emb_dim=emb_dim)
conv = GATEConv(emb_dim, emb_dim, emb_dim, drop_ratio)
gru = GRUCell(emb_dim, emb_dim)
self.atom_convs = torch.nn.ModuleList([conv])
self.atom_grus = torch.nn.ModuleList([gru])
for _ in range(num_layers - 1):
conv = GATConv(emb_dim,
emb_dim,
dropout=drop_ratio,
add_self_loops=False,
negative_slope=0.01)
self.atom_convs.append(conv)
self.atom_grus.append(GRUCell(emb_dim, emb_dim))
self.mol_conv = GATConv(emb_dim,
emb_dim,
dropout=drop_ratio,
add_self_loops=False,
negative_slope=0.01)
self.mol_gru = GRUCell(emb_dim, emb_dim)
self.graph_pred_linear = Linear(emb_dim, num_tasks)
self.reset_parameters()
def __init__(self, voc_size, hidden_size, device, num_layers=2):
super().__init__()
self.encoder = Encoder(voc_size, hidden_size, num_layers)
self.gru = GRU(input_size=hidden_size,
hidden_size=hidden_size,
num_layers=num_layers)
self.grucell_list = [
GRUCell(input_size=hidden_size, hidden_size=hidden_size).to(device)
for i in range(num_layers)
]
self.score = Linear(in_features=hidden_size * num_layers,
out_features=1)
self.num_layers = num_layers
self.hidden_size = hidden_size
self.device = device
def __init__(self, input_dim, debug):
"""The RNN dec of the Masker.
:param input_dim: The input dimensionality.
:type input_dim: int
:param debug: Flag to indicate debug
:type debug: bool
"""
super(RNNDec, self).__init__()
self._input_dim = input_dim
self.gru_dec = GRUCell(self._input_dim, self._input_dim)
self._debug = debug
self.initialize_decoder()
def __init__(self, cnn_channels, cnn_dropout, rnn_in_dim, rnn_out_dim,
rnn_dropout, nb_classes, batch_counter, gamma_factor,
mul_factor, min_prob, max_prob):
"""The Sound Event Detection (SED) model with teacher forcing and\
scheduled sampling.
:param cnn_channels: The amount of CNN channels for the SED model.
:type cnn_channels: int
:param cnn_dropout: The dropout percentage for the CNNs dropout.
:type cnn_dropout: float
:param rnn_in_dim: The input dimensionality for the RNNs.
:type rnn_in_dim: int
:param rnn_out_dim: The output dimensionality for the RNNs.
:type rnn_out_dim: int
:param rnn_dropout: The dropout percentage for the RNN dropout.
:type rnn_dropout: float
:param nb_classes: The amount of output classes.
:type nb_classes: int
:param batch_counter: The amount of batches in one full epoch.
:type batch_counter: int
:param gamma_factor: The gamma factor for scheduled sampling.
:type gamma_factor: float
:param mul_factor: The multiplication factor for scheduled sampling.
:type mul_factor: float
:param min_prob: The minimum probability for selecting predictions.
:type min_prob: float
:param max_prob: The maximum probability for selecting predictions.
:type max_prob: float
"""
super(TFCRNN, self).__init__()
self.dnn_output_features = cnn_channels
self.rnn_hh_size = rnn_out_dim
self.nb_classes = nb_classes
self.batch_counter = batch_counter
self.gamma_factor = gamma_factor / mul_factor
self._min_prob = 1 - min_prob
self.max_prob = max_prob
self.iteration = 0
self.dnn = dnn.DNN(cnn_channels=cnn_channels, cnn_dropout=cnn_dropout)
self.rnn_dropout = Dropout(rnn_dropout)
self.rnn = GRUCell(rnn_in_dim + self.nb_classes,
self.rnn_hh_size,
bias=True)
self.classifier = Linear(self.rnn_hh_size, self.nb_classes, bias=True)
def __init__(self, is_training, batch_size, message_size, scaler, adj_mx,
**model_kwargs):
# Scaler for data normalization.
super(MPNNModel, self).__init__()
self._scaler = scaler
self._horizon = int(model_kwargs.get('horizon', 1))
self._num_nodes = int(model_kwargs.get('num_nodes', 1))
self._rnn_units = int(model_kwargs.get('rnn_units'))
self._input_dim = int(model_kwargs.get('input_dim', 1))
self._output_dim = int(model_kwargs.get('output_dim', 1))
self._message_size = message_size
self._batch_size = batch_size
self._adj_mx = adj_mx
self._cell = GRUCell((self._input_dim + self._message_size),
self._rnn_units)
self._M_t = Linear(self._rnn_units, self._message_size)
self._R_t = Linear(self._rnn_units, self._output_dim * self._horizon)
def __init__(
self,
in_feats: int,
out_feats: int,
n_steps: int,
n_etypes: int,
bias: bool = True,
) -> None:
"""Construct a GGNN layer."""
super().__init__()
self.in_feats = in_feats
self.out_feats = out_feats
self.n_steps = n_steps
self.n_etypes = n_etypes
self._linears = ModuleList(
[Linear(out_feats, out_feats) for _n in range(n_etypes)]
)
self._gru = GRUCell(input_size=out_feats, hidden_size=out_feats, bias=bias)
def __init__(self, input_dim, debug):
"""The RNN dec of the Masker.
:param input_dim: The input dimensionality.
:type input_dim: int
:param debug: Flag to indicate debug
:type debug: bool
"""
super(RNNDec, self).__init__()
self._input_dim = input_dim
self.gru_dec = GRUCell(self._input_dim, self._input_dim)
self._debug = debug
self._device = 'cuda' if not self._debug and torch.cuda.is_available(
) else 'cpu'
self.initialize_decoder()
def __init__(self,
input_dim,
contxt_dim,
hidden_dim,
att_module,
input_norm=False,
hidden_norm=False,
cat_contx_to_inp=True,
**kwargs):
"""
:param input_dim: usually embeddings dim.
:param hidden_dim: dimensionality of the hidden layer.
:param att_module: module to attend over some external values.
:param input_norm: if set to True will use layer normalization to
normalize inputs to the decoder.
:param hidden_norm: if set to True will use layer normalization over
produced hidden states.
:param cat_contx_to_inp: whether to concatenated context vector to the
input word embeddings.
:param kwargs:
"""
super(GruAttDecoder, self).__init__()
self.input_dim = input_dim
self.contxt_dim = contxt_dim
self.hidden_dim = hidden_dim
self.att = att_module
self.input_norm = input_norm
self.hidden_norm = hidden_norm
self.cat_conxt_to_inp = cat_contx_to_inp
cell_inp_dim = input_dim + contxt_dim if cat_contx_to_inp else input_dim
self.gru_cell = GRUCell(cell_inp_dim, hidden_dim, **kwargs)
if self.input_norm:
self.inp_norm_layer = LayerNorm(input_dim + contxt_dim)
if self.hidden_norm:
self.hidden_norm_layer = LayerNorm(hidden_dim)
def __init__(self,
input_dim: int,
output_dim: int,
nb_classes: int,
dropout_p: float,
max_out_t_steps: Optional[int] = 22,
attention_dropout: Optional[float] = .25,
attention_dim: Optional[Union[List[int], None]] = None) \
-> None:
"""Attention decoder for the baseline audio captioning method.
:param input_dim: Input dimensionality for the RNN.
:type input_dim: int
:param output_dim: Output dimensionality for the RNN.
:type output_dim: int
:param nb_classes: Amount of amount classes.
:type nb_classes: int
:param dropout_p: RNN dropout.
:type dropout_p: float
:param max_out_t_steps: Maximum output time steps during inference.
:type max_out_t_steps: int
:param attention_dropout: Dropout for attention, defaults to .25.
:type attention_dropout: float, optional
:param attention_dim: Dimensionality of attention layers, defaults to None.
:type attention_dim: list[int] | None, optional
"""
super().__init__()
self.input_dim = input_dim
self.output_dim = output_dim
self.nb_classes = nb_classes
self.max_out_t_steps = max_out_t_steps
self.dropout: Module = Dropout(p=dropout_p)
self.attention: Attention = Attention(input_dim=self.input_dim,
h_dim=self.output_dim,
dropout_p=attention_dropout,
layers_dim=attention_dim)
self.gru: Module = GRUCell(self.input_dim, self.output_dim)
self.classifier: Module = Linear(self.output_dim, self.nb_classes)
class TGNMemory(torch.nn.Module):
r"""The Temporal Graph Network (TGN) memory model from the
`"Temporal Graph Networks for Deep Learning on Dynamic Graphs"
<https://arxiv.org/abs/2006.10637>`_ paper.
.. note::
For an example of using TGN, see `examples/tgn.py
<https://github.com/pyg-team/pytorch_geometric/blob/master/examples/
tgn.py>`_.
Args:
num_nodes (int): The number of nodes to save memories for.
raw_msg_dim (int): The raw message dimensionality.
memory_dim (int): The hidden memory dimensionality.
time_dim (int): The time encoding dimensionality.
message_module (torch.nn.Module): The message function which
combines source and destination node memory embeddings, the raw
message and the time encoding.
aggregator_module (torch.nn.Module): The message aggregator function
which aggregates messages to the same destination into a single
representation.
"""
def __init__(self, num_nodes: int, raw_msg_dim: int, memory_dim: int,
time_dim: int, message_module: Callable,
aggregator_module: Callable):
super().__init__()
self.num_nodes = num_nodes
self.raw_msg_dim = raw_msg_dim
self.memory_dim = memory_dim
self.time_dim = time_dim
self.msg_s_module = message_module
self.msg_d_module = copy.deepcopy(message_module)
self.aggr_module = aggregator_module
self.time_enc = TimeEncoder(time_dim)
self.gru = GRUCell(message_module.out_channels, memory_dim)
self.register_buffer('memory', torch.empty(num_nodes, memory_dim))
last_update = torch.empty(self.num_nodes, dtype=torch.long)
self.register_buffer('last_update', last_update)
self.register_buffer('__assoc__',
torch.empty(num_nodes, dtype=torch.long))
self.msg_s_store = {}
self.msg_d_store = {}
self.reset_parameters()
def reset_parameters(self):
if hasattr(self.msg_s_module, 'reset_parameters'):
self.msg_s_module.reset_parameters()
if hasattr(self.msg_d_module, 'reset_parameters'):
self.msg_d_module.reset_parameters()
if hasattr(self.aggr_module, 'reset_parameters'):
self.aggr_module.reset_parameters()
self.time_enc.reset_parameters()
self.gru.reset_parameters()
self.reset_state()
def reset_state(self):
"""Resets the memory to its initial state."""
zeros(self.memory)
zeros(self.last_update)
self.__reset_message_store__()
def detach(self):
"""Detachs the memory from gradient computation."""
self.memory.detach_()
def forward(self, n_id: Tensor) -> Tuple[Tensor, Tensor]:
"""Returns, for all nodes :obj:`n_id`, their current memory and their
last updated timestamp."""
if self.training:
memory, last_update = self.__get_updated_memory__(n_id)
else:
memory, last_update = self.memory[n_id], self.last_update[n_id]
return memory, last_update
def update_state(self, src, dst, t, raw_msg):
"""Updates the memory with newly encountered interactions
:obj:`(src, dst, t, raw_msg)`."""
n_id = torch.cat([src, dst]).unique()
if self.training:
self.__update_memory__(n_id)
self.__update_msg_store__(src, dst, t, raw_msg, self.msg_s_store)
self.__update_msg_store__(dst, src, t, raw_msg, self.msg_d_store)
else:
self.__update_msg_store__(src, dst, t, raw_msg, self.msg_s_store)
self.__update_msg_store__(dst, src, t, raw_msg, self.msg_d_store)
self.__update_memory__(n_id)
def __reset_message_store__(self):
i = self.memory.new_empty((0, ), dtype=torch.long)
msg = self.memory.new_empty((0, self.raw_msg_dim))
# Message store format: (src, dst, t, msg)
self.msg_s_store = {j: (i, i, i, msg) for j in range(self.num_nodes)}
self.msg_d_store = {j: (i, i, i, msg) for j in range(self.num_nodes)}
def __update_memory__(self, n_id):
memory, last_update = self.__get_updated_memory__(n_id)
self.memory[n_id] = memory
self.last_update[n_id] = last_update
def __get_updated_memory__(self, n_id):
self.__assoc__[n_id] = torch.arange(n_id.size(0), device=n_id.device)
# Compute messages (src -> dst).
msg_s, t_s, src_s, dst_s = self.__compute_msg__(
n_id, self.msg_s_store, self.msg_s_module)
# Compute messages (dst -> src).
msg_d, t_d, src_d, dst_d = self.__compute_msg__(
n_id, self.msg_d_store, self.msg_d_module)
# Aggregate messages.
idx = torch.cat([src_s, src_d], dim=0)
msg = torch.cat([msg_s, msg_d], dim=0)
t = torch.cat([t_s, t_d], dim=0)
aggr = self.aggr_module(msg, self.__assoc__[idx], t, n_id.size(0))
# Get local copy of updated memory.
memory = self.gru(aggr, self.memory[n_id])
# Get local copy of updated `last_update`.
dim_size = self.last_update.size(0)
last_update = scatter_max(t, idx, dim=0, dim_size=dim_size)[0][n_id]
return memory, last_update
def __update_msg_store__(self, src, dst, t, raw_msg, msg_store):
n_id, perm = src.sort()
n_id, count = n_id.unique_consecutive(return_counts=True)
for i, idx in zip(n_id.tolist(), perm.split(count.tolist())):
msg_store[i] = (src[idx], dst[idx], t[idx], raw_msg[idx])
def __compute_msg__(self, n_id, msg_store, msg_module):
data = [msg_store[i] for i in n_id.tolist()]
src, dst, t, raw_msg = list(zip(*data))
src = torch.cat(src, dim=0)
dst = torch.cat(dst, dim=0)
t = torch.cat(t, dim=0)
raw_msg = torch.cat(raw_msg, dim=0)
t_rel = t - self.last_update[src]
t_enc = self.time_enc(t_rel.to(raw_msg.dtype))
msg = msg_module(self.memory[src], self.memory[dst], raw_msg, t_enc)
return msg, t, src, dst
def train(self, mode: bool = True):
"""Sets the module in training mode."""
if self.training and not mode:
# Flush message store to memory in case we just entered eval mode.
self.__update_memory__(
torch.arange(self.num_nodes, device=self.memory.device))
self.__reset_message_store__()
super().train(mode)
def __init__(self, c_dim, h_dim):
super(GRUAggregation, self).__init__()
self.gru = GRUCell(c_dim, h_dim)
class PlainRNN(BaseModel):
"""
single_loss: single_loss= True, means the loss is
only caculated in the last time step.
"""
def __init__(self, inp_size,
hid_size,
out_size,
rnn_type="raw_rnn",
single_loss=True):
super().__init__()
allow_rnn_types = ["raw_rnn","lstm","gru"]
assert rnn_type in allow_rnn_types
self.rnn_type = rnn_type
self.single_loss = single_loss
self.inp_size = inp_size
self.hid_size = hid_size
self.out_size = out_size
if rnn_type == "raw_rnn":
self.lstm = RNNCell(inp_size, hid_size)
if rnn_type == "lstm":
self.lstm = LSTMCell(inp_size, hid_size)
if rnn_type == "gru":
self.lstm = GRUCell(inp_size, hid_size)
self.fc1 = nn.Linear(hid_size, out_size)
self.criterion = nn.CrossEntropyLoss()
def init_weights(self):
self.lstm.reset_parameters()
self.fc1.reset_parameters()
def init_states(self,batch_size):
if self.rnn_type == "lstm":
self.h = torch.zeros(batch_size, self.hid_size).to(device)
self.c = torch.zeros(batch_size, self.hid_size).to(device)
if self.rnn_type == "raw_rnn" or self.rnn_type == "gru":
self.h = torch.zeros(batch_size, self.hid_size).to(device)
def forward_train(self, x):
assert len(x) == 2
inp_x, inp_y = x
inp_x = inp_x.to(device)
inp_y = inp_y.to(device)
batch, T, _ = inp_x.shape
self.init_states(batch)
dm_states = []
loss = 0
rr = torch.zeros((batch,self.out_size)).to(device)
if self.rnn_type == "lstm":
for i in range(T):
y, (self.h,self.c) = self.lstm(inp_x[:,i],(self.h,self.c))
output = self.fc1(y)
rr.copy_(output)
dm_states.append(rr.cpu().detach().numpy())
if not self.single_loss:
loss += self.criterion(output, inp_y.reshape(-1))
if self.single_loss:
loss += self.criterion(output, inp_y.reshape(-1))
if self.rnn_type == "raw_rnn" or self.rnn_type == "gru":
for i in range(T):
self.h = self.lstm(inp_x[:,i],self.h)
output = self.fc1(self.h)
rr.copy_(output)
dm_states.append(rr.cpu().detach().numpy())
if not self.single_loss:
loss += self.criterion(output, inp_y.reshape(-1))
if self.single_loss:
loss += self.criterion(output, inp_y.reshape(-1))
print("loss is ",loss.cpu().item())
outputs = dict(
loss = loss,
outputs = dm_states
)
return outputs
def forward_test(self,x):
# x, new_state = self.lstm(x, state)
# x = self.fc1(x
assert len(x) == 2
inp_x, inp_y = x
inp_x = inp_x.to(device)
batch, T, _ = inp_x.shape
self.init_states(batch)
dm_states = []
rr = torch.zeros((batch,self.out_size)).to(device)
if self.rnn_type == "lstm":
for i in range(T):
y, (self.h,self.c) = self.lstm(inp_x[:,i],(self.h,self.c))
output = self.fc1(y)
rr.copy_(output)
dm_states.append(rr.cpu().detach().numpy())
if self.rnn_type == "raw_rnn" or self.rnn_type == "gru":
for i in range(T):
self.h = self.lstm(inp_x[:,i],self.h)
output = self.fc1(self.h)
rr.copy_(output)
dm_states.append(rr.cpu().detach().numpy())
if self.single_loss:
dm_states = (np.array(dm_states)[-1]).reshape(1,batch,-1)
else:
# dm_states = (np.array(dm_states)).reshape(T,batch,-1)
dm_states = np.array(dm_states).reshape(T*batch,-1)
dm_states_ = np.zeros_like(dm_states)
index = np.argmax(dm_states,axis=1)
dm_states_[range(T*batch),index] = 1
dm_states = dm_states_.reshape(T,batch,-1).mean(axis=0).reshape(1,batch,-1)
inp_y = inp_y.view(-1).cpu().numpy()
outputs = dict(
outputs = dm_states,
labels = inp_y
)
return outputs
class AttentiveFP(torch.nn.Module):
r"""The Attentive FP model for molecular representation learning from the
`"Pushing the Boundaries of Molecular Representation for Drug Discovery
with the Graph Attention Mechanism"
<https://pubs.acs.org/doi/10.1021/acs.jmedchem.9b00959>`_ paper, based on
graph attention mechanisms.
Args:
in_channels (int): Size of each input sample.
hidden_channels (int): Hidden node feature dimensionality.
out_channels (int): Size of each output sample.
edge_dim (int): Edge feature dimensionality.
num_layers (int): Number of GNN layers.
num_timesteps (int): Number of iterative refinement steps for global
readout.
dropout (float, optional): Dropout probability. (default: :obj:`0.0`)
"""
def __init__(self,
in_channels: int,
hidden_channels: int,
out_channels: int,
edge_dim: int,
num_layers: int,
num_timesteps: int,
dropout: float = 0.0):
super().__init__()
self.num_layers = num_layers
self.num_timesteps = num_timesteps
self.dropout = dropout
self.lin1 = Linear(in_channels, hidden_channels)
conv = GATEConv(hidden_channels, hidden_channels, edge_dim, dropout)
gru = GRUCell(hidden_channels, hidden_channels)
self.atom_convs = torch.nn.ModuleList([conv])
self.atom_grus = torch.nn.ModuleList([gru])
for _ in range(num_layers - 1):
conv = GATConv(hidden_channels,
hidden_channels,
dropout=dropout,
add_self_loops=False,
negative_slope=0.01)
self.atom_convs.append(conv)
self.atom_grus.append(GRUCell(hidden_channels, hidden_channels))
self.mol_conv = GATConv(hidden_channels,
hidden_channels,
dropout=dropout,
add_self_loops=False,
negative_slope=0.01)
self.mol_gru = GRUCell(hidden_channels, hidden_channels)
self.lin2 = Linear(hidden_channels, out_channels)
self.reset_parameters()
def reset_parameters(self):
self.lin1.reset_parameters()
for conv, gru in zip(self.atom_convs, self.atom_grus):
conv.reset_parameters()
gru.reset_parameters()
self.mol_conv.reset_parameters()
self.mol_gru.reset_parameters()
self.lin2.reset_parameters()
def forward(self, x, edge_index, edge_attr, batch):
""""""
# Atom Embedding:
x = F.leaky_relu_(self.lin1(x))
h = F.elu_(self.atom_convs[0](x, edge_index, edge_attr))
h = F.dropout(h, p=self.dropout, training=self.training)
x = self.atom_grus[0](h, x).relu_()
for conv, gru in zip(self.atom_convs[1:], self.atom_grus[1:]):
h = F.elu_(conv(x, edge_index))
h = F.dropout(h, p=self.dropout, training=self.training)
x = gru(h, x).relu_()
# Molecule Embedding:
row = torch.arange(batch.size(0), device=batch.device)
edge_index = torch.stack([row, batch], dim=0)
out = global_add_pool(x, batch).relu_()
for t in range(self.num_timesteps):
h = F.elu_(self.mol_conv((x, out), edge_index))
h = F.dropout(h, p=self.dropout, training=self.training)
out = self.mol_gru(h, out).relu_()
# Predictor:
out = F.dropout(out, p=self.dropout, training=self.training)
return self.lin2(out)
