import torch.nn as nn import torch.nn.functional as F class ElectraDTA(nn.Module): def __init__(self, smilen, seq_len, hidden_dim): super().__init__() self.drug_input = nn.Linear(smilen, hidden_dim) self.prot_input = nn.Linear(seq_len, hidden_dim) self.num_filters = hidden_dim self.filter_length = 3 self.n_layers = 4 self.seblock = True self.encode_smiles = ConvBlock(hidden_dim, self.seblock, self.num_filters, self.filter_length) self.encode_prot = ConvBlock(hidden_dim, self.seblock, self.num_filters, self.filter_length) self.global_pool = nn.AdaptiveMaxPool1d(1) self.concat = nn.Linear(hidden_dim * 4, hidden_dim * 4) self.predictions = FCNet(hidden_dim * 4) # you need to define this function self.interaction_model = nn.Sequential(self.drug_input, self.prot_input, self.encode_smiles, self.encode_prot, self.global_pool, self.concat, self.predictions) def forward(self, x): x = self.interaction_model(x) return x class SEBlock(nn.Module): def __init__(self, channels, r=8): super().__init__() self.squeeze = nn.AdaptiveAvgPool1d(1) self.excitation = nn.Sequential( nn.Linear(channels, channels // r), nn.ReLU(), nn.Linear(channels // r, channels), nn.Sigmoid() ) def forward(self, x): out = self.squeeze(x) out = self.excitation(out) return x * out class ConvBlock(nn.Module): def __init__(self, input_channels, seblock, num_filters, filter_length): super().__init__() self.conv1 = nn.Conv1d(input_channels, num_filters, filter_length, padding='valid', stride=1) self.conv2 = nn.Conv1d(num_filters, num_filters * 2, filter_length, padding='valid', stride=1) self.seblock = seblock if seblock: self.se1 = SEBlock(num_filters) self.se2 = SEBlock(num_filters * 2) def forward(self, x): x = F.relu(self.conv1(x)) if self.seblock: x = self.se1(x) x = F.relu(self.conv2(x)) if self.seblock: x = self.se2(x) return x class Highway(nn.Module): def __init__(self, dim, n_layers, activation=nn.Tanh(), gate_bias=0): super(Highway, self).__init__() self.n_layers = n_layers self.activation = activation self.T_gates = nn.ModuleList([nn.Linear(dim, dim) for _ in range(n_layers)]) self.transforms = nn.ModuleList([nn.Linear(dim, dim) for _ in range(n_layers)]) self.sigmoid = nn.Sigmoid() nn.init.constant_(self.linear.bias, gate_bias) def forward(self, x): for i in range(self.n_layers): T = self.sigmoid(self.gate(x)) C = 1 - T H = self.activation(self.linear(x)) x = T * H + C * x return x class FCNet(nn.Module): def __init__(self, input_dim): super().__init__() self.n_layers = 4 self.highway = Highway(input_dim, self.n_layers, gate_bias=-2) self.fc1 = nn.Linear(input_dim, 1024) self.fc2 = nn.Linear(1024, 1024) self.fc3 = nn.Linear(1024, 512) # self.fc4 = nn.Linear(512, 1) self.dropout = nn.Dropout(0.4) def forward(self, x): x = self.highway(x) x = F.relu(self.fc1(x)) x = self.dropout(x) x = F.relu(self.fc2(x)) x = self.dropout(x) x = F.relu(self.fc3(x)) # x = self.fc4(x) return x