import torch from torch.nn import Linear, ReLU, SiLU, Sequential from torch_geometric.nn import MessagePassing from torch_scatter import scatter from models_cifm.mlp_and_gnn import MLPBiasFree class EGNNLayer(MessagePassing): """E(n) Equivariant GNN Layer Paper: E(n) Equivariant Graph Neural Networks, Satorras et al. """ def __init__(self, emb_dim, num_mlp_layers, aggr="add"): """ Args: emb_dim: (int) - hidden dimension `d` activation: (str) - non-linearity within MLPs (swish/relu) norm: (str) - normalisation layer (layer/batch) aggr: (str) - aggregation function `\oplus` (sum/mean/max) """ # Set the aggregation function super().__init__(aggr=aggr) self.emb_dim = emb_dim self.dist_embedding = Linear(1, emb_dim, bias=False) self.innerprod_embedding = MLPBiasFree(in_dim=1, out_dim=1, hidden_dim=emb_dim, num_layer=num_mlp_layers) self.mlp_msg = MLPBiasFree(in_dim=3*emb_dim, out_dim=emb_dim, hidden_dim=emb_dim, num_layer=num_mlp_layers) self.mlp_pos = MLPBiasFree(in_dim=emb_dim, out_dim=1, hidden_dim=emb_dim, num_layer=num_mlp_layers) self.mlp_upd = MLPBiasFree(in_dim=emb_dim, out_dim=emb_dim, hidden_dim=emb_dim, num_layer=num_mlp_layers) def forward(self, h, pos, edge_index): """ Args: h: (n, d) - initial node features pos: (n, 3) - initial node coordinates edge_index: (e, 2) - pairs of edges (i, j) Returns: out: [(n, d),(n,3)] - updated node features """ out = self.propagate(edge_index, h=h, pos=pos) return out def message(self, h_i, h_j, pos_i, pos_j): # Compute messages pos_diff = pos_i - pos_j dists = torch.exp(- torch.norm(pos_diff, dim=-1).unsqueeze(1) / 30 ) # reference distances: 30um inner_prod = torch.mean(h_i * h_j, dim=-1).unsqueeze(1) msg = torch.cat([h_i, h_j, self.dist_embedding(dists)], dim=-1) * self.innerprod_embedding(inner_prod) msg = self.mlp_msg(msg) # Scale magnitude of displacement vector pos_diff = pos_diff * self.mlp_pos(msg) # NOTE: some papers divide pos_diff by (dists + 1) to stabilise model. return msg, pos_diff, inner_prod def aggregate(self, inputs, index): msgs, pos_diffs, inner_prod = inputs # Aggregate messages msg_aggr = scatter(msgs, index, dim=self.node_dim, reduce="add") # Aggregate displacement vectors pos_aggr = scatter(pos_diffs, index, dim=self.node_dim, reduce="add") counts = torch.ones_like(inner_prod) counts[inner_prod==0] = 0 counts = scatter(counts, index, dim=0, reduce="add") counts[counts==0] = 1 pos_aggr = pos_aggr / counts return msg_aggr, pos_aggr def update(self, aggr_out, h, pos): msg_aggr, pos_aggr = aggr_out upd_out = self.mlp_upd(msg_aggr) upd_pos = pos + pos_aggr return upd_out, upd_pos def __repr__(self) -> str: return f"{self.__class__.__name__}(emb_dim={self.emb_dim}, aggr={self.aggr})"