import torch import torch.nn as nn import torch import torch.nn as nn import torch.nn.functional as F from torch.nn import Linear, ReLU, Dropout, Sequential, BatchNorm1d from torch_geometric.nn import GCNConv, GINConv, GATv2Conv, TransformerConv, GATConv from torch_geometric.nn.norm import GraphNorm, LayerNorm, BatchNorm, PairNorm, DiffGroupNorm from torch_geometric.nn.pool import global_add_pool, global_mean_pool, global_max_pool from torch_geometric.nn.aggr import MultiAggregation, DeepSetsAggregation, GraphMultisetTransformer, AttentionalAggregation class EGNN(nn.Module): def __init__(self, num_node_features=960, num_layers=3, hidden_dim=64, num_attn_heads=1, norm_type='graph', aggr_type='attentional'): super(EGNN, self).__init__() self.num_layers = num_layers self.layers = nn.ModuleDict() if num_node_features != hidden_dim: self.layers['embedding_in'] = Linear(num_node_features, hidden_dim) for i in range(num_layers): self.layers[f'gl{i+1}'] = E_GCL(hidden_dim, hidden_dim, hidden_dim) self.layers[f'n{i+1}'] = construct_norm(norm_type, hidden_dim) self.layers['aggr'] = MultiAttentionAggr(hidden_dim, num_heads=num_attn_heads) self.out_dim = hidden_dim * num_attn_heads def forward(self, data): x, edge_index, pos, batch = data.x, data.edge_index, data.pos, data.batch if 'embedding_in' in self.layers: x = self.layers['embedding_in'](x) for i in range(self.num_layers): x, pos, _ = self.layers[f'gl{i+1}'](x=x, edge_index=edge_index, pos=pos) x = self.layers[f'n{i+1}'](x) x = F.relu(x) return self.layers['aggr'](x, batch) class GCN(nn.Module): def __init__(self, num_node_features=960, num_layers=3, hidden_dim=128, num_attn_heads=1, norm_type='graph', aggr_type='attentional'): super(GCN, self).__init__() self.num_layers = num_layers self.layers = nn.ModuleDict() if num_node_features != hidden_dim: self.layers['embedding_in'] = Linear(num_node_features, hidden_dim) for i in range(num_layers): self.layers[f'gl{i+1}'] = GCNConv(hidden_dim, hidden_dim) self.layers[f'n{i+1}'] = construct_norm(norm_type, hidden_dim) self.layers['aggr'] = MultiAttentionAggr(hidden_dim, num_heads=num_attn_heads) self.out_dim = hidden_dim * num_attn_heads def forward(self, data): x, edge_index, batch = data.x, data.edge_index, data.batch if 'embedding_in' in self.layers: x = self.layers['embedding_in'](x) for i in range(self.num_layers): x = self.layers[f'gl{i+1}'](x=x, edge_index=edge_index) x = self.layers[f'n{i+1}'](x) x = F.relu(x) return self.layers['aggr'](x, batch) class GAT(nn.Module): def __init__(self, num_node_features=960, num_layers=3, hidden_dims=[128, 64, 32], num_attn_heads=1, heads=4, norm_type='graph', aggr_type='attentional'): super(GAT, self).__init__() assert len(hidden_dims) == num_layers, "Length of hidden_dims must match num_layers" self.num_layers = num_layers self.layers = nn.ModuleDict() dims = [num_node_features] + [dim * heads for dim in hidden_dims] for i in range(num_layers): self.layers[f'gl{i+1}'] = GATv2Conv(dims[i], hidden_dims[i], heads=heads) self.layers[f'n{i+1}'] = construct_norm(norm_type, dims[i+1]) self.layers['aggr'] = MultiAttentionAggr(dims[-1], num_heads=num_attn_heads) self.out_dim = dims[-1] * num_attn_heads def forward(self, data): x, edge_index, batch = data.x, data.edge_index, data.batch for i in range(self.num_layers): x = self.layers[f'gl{i+1}'](x=x, edge_index=edge_index) x = self.layers[f'n{i+1}'](x) x = F.relu(x) return self.layers['aggr'](x, batch) class GIN(nn.Module): def __init__(self, num_node_features=960, num_layers=3, hidden_dims=[128, 64, 32], num_attn_heads=1, norm_type='graph', aggr_type='attentional'): super(GIN, self).__init__() assert len(hidden_dims) == num_layers, "Length of hidden_dims must match num_layers" self.num_layers = num_layers self.layers = nn.ModuleDict() dims = [num_node_features] + hidden_dims for i in range(num_layers): nn_conv = Sequential( Linear(dims[i], dims[i+1]), ReLU(), Linear(dims[i+1], dims[i+1]) ) self.layers[f'gl{i+1}'] = GINConv(nn_conv) self.layers[f'n{i+1}'] = construct_norm(norm_type, dims[i+1]) self.layers['aggr'] = MultiAttentionAggr(hidden_dims[-1], num_heads=num_attn_heads) self.out_dim = hidden_dims[-1] * num_attn_heads def forward(self, data): x, edge_index, batch = data.x, data.edge_index, data.batch for i in range(self.num_layers): x = self.layers[f'gl{i+1}'](x=x, edge_index=edge_index) x = self.layers[f'n{i+1}'](x) x = F.relu(x) return self.layers['aggr'](x, batch) class GT(nn.Module): def __init__(self, num_node_features=960, num_layers=3, hidden_dims=[128, 64, 32], num_attn_heads=1, heads=4, norm_type='graph', aggr_type='attentional'): super(GT, self).__init__() assert len(hidden_dims) == num_layers, "Length of hidden_dims must match num_layers" self.num_layers = num_layers self.layers = nn.ModuleDict() dims = [num_node_features] + [dim * heads for dim in hidden_dims] for i in range(num_layers): self.layers[f'gl{i+1}'] = TransformerConv(dims[i], hidden_dims[i], heads=heads) self.layers[f'n{i+1}'] = construct_norm(norm_type, dims[i+1]) self.layers['aggr'] = MultiAttentionAggr(dims[-1], num_heads=num_attn_heads) self.out_dim = dims[-1] * num_attn_heads def forward(self, data): x, edge_index, batch = data.x, data.edge_index, data.batch for i in range(self.num_layers): x = self.layers[f'gl{i+1}'](x=x, edge_index=edge_index) x = self.layers[f'n{i+1}'](x) x = F.relu(x) return self.layers['aggr'](x, batch) # Residual Block class ResidualBlock(nn.Module): def __init__(self, input_dim, hidden_dim, dropout_rate=0.3): super(ResidualBlock, self).__init__() self.fc1 = nn.Linear(input_dim, hidden_dim) self.fc2 = nn.Linear(hidden_dim, input_dim) # Output same size as input for residual self.relu = nn.ReLU() self.dropout = nn.Dropout(dropout_rate) def forward(self, x): residual = x out = self.fc1(x) out = self.relu(out) out = self.dropout(out) out = self.fc2(out) return self.relu(out + residual) # Apply activation after residual addition class MultiAttentionAggr(nn.Module): def __init__(self, in_dim, num_heads=4): super().__init__() self.heads = nn.ModuleList([construct_aggr('attentional', in_dim) for _ in range(num_heads)]) def forward(self, x, batch): outs = [h(x, batch) for h in self.heads] return torch.cat(outs, dim=-1) def construct_norm(norm_type, dim): norm_map = { 'batch': BatchNorm, 'layer': LayerNorm, 'graph': GraphNorm } if norm_type in norm_map: return norm_map[norm_type](dim) elif norm_type == 'pair': return PairNorm() elif norm_type == 'diffgroup': return DiffGroupNorm(dim, 30) else: raise Exception('Unsupported norm type: %s' % norm_type) def construct_aggr(aggr_type, dim): aggr_map = { 'add': global_add_pool, 'mean': global_mean_pool, 'max': global_max_pool } if aggr_type in ['add', 'mean', 'max']: return aggr_map[aggr_type] elif aggr_type == 'multi': return MultiAggregation(['mean', 'max', 'min', 'std']) elif aggr_type == 'deepset': return DeepSetsAggregation(Linear(dim, dim), Linear(dim, dim)) elif aggr_type == 'gmt': return GraphMultisetTransformer(channels=dim, k=4, num_encoder_blocks=1, heads=4, layer_norm=True, dropout=0.1) elif aggr_type == 'attentional': return AttentionalAggregation(gate_nn=Sequential(Linear(dim, min(128, dim)), ReLU(), Linear(min(128, dim), 1))) else: raise Exception('Unsupported aggr type: %s' % aggr_type) class GCN_GAT_GINE_FIXED_OUT_DIM(torch.nn.Module): def __init__(self, num_node_features, num_classes): super(GCN_GAT_GINE_FIXED_OUT_DIM, self).__init__() self.num_classes = num_classes # GCN-representation self.conv1 = GCNConv(num_node_features, 128, cached=False) self.bn01 = BatchNorm1d(128, track_running_stats=False) self.conv2 = GCNConv(128, 64, cached=False) self.bn02 = BatchNorm1d(64, track_running_stats=False) self.conv3 = GCNConv(64, 32, cached=False) self.bn03 = BatchNorm1d(32, track_running_stats=False) # GAT-representation self.gat1 = GATConv(num_node_features, 128, heads=8) self.bn11 = BatchNorm1d(128 * 8, track_running_stats=False) self.gat2 = GATConv(128 * 8, 64, heads=8) self.bn12 = BatchNorm1d(64 * 8, track_running_stats=False) self.gat3 = GATConv(64 * 8, 32, heads=8) self.bn13 = BatchNorm1d(32 * 8, track_running_stats=False) # GIN-representation fc_gin1 = Sequential(Linear(num_node_features, 128), ReLU(), Linear(128, 128)) self.gin1 = GINConv(fc_gin1) self.bn21 = BatchNorm1d(128, track_running_stats=False) fc_gin2 = Sequential(Linear(128, 64), ReLU(), Linear(64, 64)) self.gin2 = GINConv(fc_gin2) self.bn22 = BatchNorm1d(64, track_running_stats=False) fc_gin3 = Sequential(Linear(64, 32), ReLU(), Linear(32, 32)) self.gin3 = GINConv(fc_gin3) self.bn23 = BatchNorm1d(32, track_running_stats=False) # Fully connected layers for concatenating outputs self.fc1 = Linear(32 + 32 * 8 + 32, 128) # Adjusted input size to match concatenated size self.dropout1 = Dropout(p=0.2) self.res_block10 = ResidualBlock(128, 256, dropout_rate=0.3) self.res_block20 = ResidualBlock(128, 256, dropout_rate=0.3) self.res_block30 = ResidualBlock(128, 256, dropout_rate=0.3) self.res_block11 = ResidualBlock(128, 256, dropout_rate=0.3) self.res_block21 = ResidualBlock(128, 256, dropout_rate=0.3) self.res_block31 = ResidualBlock(128, 256, dropout_rate=0.3) # Dense connection: 128 + 128 + 128 + 128 + 128 + 128 + 128 = 896 self.fc2 = Linear(896, 96) # Updated from 128 to 896 def forward(self, data): x, edge_index, edge_w, batch = data.x, data.edge_index, data.edge_attr, data.batch y = x z = x # GCN-representation x = F.relu(self.conv1(x, edge_index)) x = self.bn01(x) x = F.relu(self.conv2(x, edge_index)) x = self.bn02(x) x = F.relu(self.conv3(x, edge_index)) x = self.bn03(x) x = global_add_pool(x, batch) # GAT-representation y = F.relu(self.gat1(y, edge_index)) y = self.bn11(y) y = F.relu(self.gat2(y, edge_index)) y = self.bn12(y) y = F.relu(self.gat3(y, edge_index)) y = self.bn13(y) y = global_add_pool(y, batch) # GIN-representation z = F.relu(self.gin1(z, edge_index)) z = self.bn21(z) z = F.relu(self.gin2(z, edge_index)) z = self.bn22(z) z = F.relu(self.gin3(z, edge_index)) z = self.bn23(z) z = global_add_pool(z, batch) # Concatenating representations cr = torch.cat((x, y, z), 1) cr = F.relu(self.fc1(cr)) cr = self.dropout1(cr) # Apply residual blocks and collect outputs for dense connections x1 = self.res_block10(cr) x2 = self.res_block11(x1) x3 = self.res_block20(x2) x4 = self.res_block21(x3) x5 = self.res_block30(x4) x6 = self.res_block31(x5) # Dense connection: concatenate all residual block outputs dense_features = torch.cat((cr, x1, x2, x3, x4, x5, x6), dim=1) cr = F.relu(self.fc2(dense_features)) return cr.view(-1, 96) class GAT_L_NO_FIXED_OUTPUT_DIM(torch.nn.Module): def __init__(self, num_node_features, num_classes): super(GAT_L_NO_FIXED_OUTPUT_DIM, self).__init__() self.num_classes = num_classes # GAT-representation self.gat1 = GATConv(num_node_features, 128, heads=3) self.bn11 = BatchNorm1d(128 * 3, track_running_stats=False) self.gat2 = GATConv(128 * 3, 64, heads=3) self.bn12 = BatchNorm1d(64 * 3, track_running_stats=False) self.gat3 = GATConv(64 * 3, 32, heads=3) self.bn13 = BatchNorm1d(32 * 3, track_running_stats=False) # Fully connected layers for concatenating outputs self.fc1 = Linear(32 * 3, 64) # Adjusted input size to match concatenated size self.dropout1 = Dropout(p=0.2) self.res_block1 = ResidualBlock(64, 128, dropout_rate=0.3) self.res_block2 = ResidualBlock(64, 128, dropout_rate=0.3) self.res_block3 = ResidualBlock(64, 128, dropout_rate=0.3) # Dense connection: 64 + 64 + 64 + 64 = 256 self.fc2 = Linear(256, 32) # Updated from 64 to 256 def forward(self, data): x, edge_index, edge_w, batch = data.x, data.edge_index, data.edge_attr, data.batch y = x z = x # GAT-representation y = F.relu(self.gat1(y, edge_index, edge_w)) y = self.bn11(y) y = F.relu(self.gat2(y, edge_index, edge_w)) y = self.bn12(y) y = F.relu(self.gat3(y, edge_index, edge_w)) y = self.bn13(y) y = global_add_pool(y, batch) # Concatenating representations cr = y cr = F.relu(self.fc1(cr)) cr = self.dropout1(cr) # Apply residual blocks and collect outputs for dense connections x1 = self.res_block1(cr) x2 = self.res_block2(x1) x3 = self.res_block3(x2) # Dense connection: concatenate all residual block outputs dense_features = torch.cat((cr, x1, x2, x3), dim=1) cr = F.relu(self.fc2(dense_features)) return cr.view(-1, 32) class E_GCL(nn.Module): """ E(n) Equivariant Convolutional Layer re """ def __init__(self, input_nf, output_nf, hidden_nf, edges_in_d=0, act_fn=nn.SiLU(), residual=True, attention=True, normalize=True, coords_agg='mean', tanh=True): super(E_GCL, self).__init__() input_edge = input_nf * 2 self.residual = residual self.attention = attention self.normalize = normalize self.coords_agg = coords_agg self.tanh = tanh self.epsilon = 1e-8 edge_coords_nf = 1 self.edge_mlp = nn.Sequential( nn.Linear(input_edge + edge_coords_nf + edges_in_d, hidden_nf), act_fn, nn.Linear(hidden_nf, hidden_nf), act_fn) self.node_mlp = nn.Sequential( nn.Linear(hidden_nf + input_nf, hidden_nf), act_fn, nn.Linear(hidden_nf, output_nf)) layer = nn.Linear(hidden_nf, 1, bias=False) torch.nn.init.xavier_uniform_(layer.weight, gain=0.001) coord_mlp = [] coord_mlp.append(nn.Linear(hidden_nf, hidden_nf)) coord_mlp.append(act_fn) coord_mlp.append(layer) if self.tanh: coord_mlp.append(nn.Tanh()) self.coord_mlp = nn.Sequential(*coord_mlp) if self.attention: self.att_mlp = nn.Sequential( nn.Linear(hidden_nf, 1), nn.Sigmoid()) def edge_model(self, source, target, radial, edge_attr): if edge_attr is None: # Unused. out = torch.cat([source, target, radial], dim=1) else: out = torch.cat([source, target, radial, edge_attr], dim=1) out = self.edge_mlp(out) if self.attention: att_val = self.att_mlp(out) out = out * att_val return out def node_model(self, x, edge_index, edge_attr, node_attr): row, col = edge_index agg = unsorted_segment_sum(edge_attr, row, num_segments=x.size(0)) if node_attr is not None: agg = torch.cat([x, agg, node_attr], dim=1) else: agg = torch.cat([x, agg], dim=1) out = self.node_mlp(agg) if self.residual: out = x + out return out, agg def coord_model(self, pos, edge_index, coord_diff, edge_feat): row, col = edge_index trans = coord_diff * self.coord_mlp(edge_feat) if self.coords_agg == 'sum': agg = unsorted_segment_sum(trans, row, num_segments=pos.size(0)) elif self.coords_agg == 'mean': agg = unsorted_segment_mean(trans, row, num_segments=pos.size(0)) else: raise Exception('Wrong coords_agg parameter' % self.coords_agg) pos += agg return pos def coord2radial(self, edge_index, pos): row, col = edge_index coord_diff = pos[row] - pos[col] radial = torch.sum(coord_diff**2, 1).unsqueeze(1) if self.normalize: norm = torch.sqrt(radial).detach() + self.epsilon coord_diff = coord_diff / norm return radial, coord_diff def forward(self, x, edge_index, pos, edge_attr=None, node_attr=None): row, col = edge_index radial, coord_diff = self.coord2radial(edge_index, pos) edge_feat = self.edge_model(x[row], x[col], radial, edge_attr) pos = self.coord_model(pos, edge_index, coord_diff, edge_feat) x, agg = self.node_model(x, edge_index, edge_feat, node_attr) return x, pos, edge_attr def unsorted_segment_sum(data, segment_ids, num_segments): result_shape = (num_segments, data.size(1)) result = data.new_full(result_shape, 0) # Init empty result tensor. segment_ids = segment_ids.unsqueeze(-1).expand(-1, data.size(1)) result.scatter_add_(0, segment_ids, data) return result def unsorted_segment_mean(data, segment_ids, num_segments): result_shape = (num_segments, data.size(1)) segment_ids = segment_ids.unsqueeze(-1).expand(-1, data.size(1)) result = data.new_full(result_shape, 0) # Init empty result tensor. count = data.new_full(result_shape, 0) result.scatter_add_(0, segment_ids, data) count.scatter_add_(0, segment_ids, torch.ones_like(data)) return result / count.clamp(min=1) def get_edges(n_nodes): rows, cols = [], [] for i in range(n_nodes): for j in range(n_nodes): if i != j: rows.append(i) cols.append(j) edges = [rows, cols] return edges def get_edges_batch(n_nodes, batch_size): edges = get_edges(n_nodes) edge_attr = torch.ones(len(edges[0]) * batch_size, 1) edges = [torch.LongTensor(edges[0]), torch.LongTensor(edges[1])] if batch_size == 1: return edges, edge_attr elif batch_size > 1: rows, cols = [], [] for i in range(batch_size): rows.append(edges[0] + n_nodes * i) cols.append(edges[1] + n_nodes * i) edges = [torch.cat(rows), torch.cat(cols)] return edges, edge_attr