"""Implementation of the Uni-mol+ model with alterations to the original model.""" from typing import Any, Optional, Tuple import torch import torch.nn.functional as f from torch import nn from transformers.modeling_utils import PreTrainedModel from .configuration_atomformer import AtomformerConfig ATOM_METADATA = [ [ 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.106761565836299, 0.4573170731707318, 0.46896368424867707, 0.0, 0.0, 0.0027383806383189145, 0.0, 1.0, 0.0, 0.0, ], [ 0.008547008547008548, 0.010187317385107808, 0.011235955056179775, 0.008547008547008548, 0.008547008547008548, 0.0, 1.0, 0.0, -1.0, 0.9999999999999999, 2.1731754967921256e-06, -1.0, 0.0, 0.010000000000000002, 0.3588318085855031, 0.0, -1.0, ], [ 0.017094017094017096, 0.02018415404448405, 0.02247191011235955, 0.017094017094017096, 0.017094017094017096, 0.16666666666666666, 0.0, 0.5729537366548044, 0.08536585365853658, 0.0723802160098582, 0.01302222611458848, 0.1117635470484688, 0.2746530986669577, 0.010000000000000002, 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torch.exp(-0.5 * (((x - mean) / std) ** 2)) / (a * std) return output class GaussianLayer(nn.Module): """Gaussian pairwise positional embedding layer.""" def __init__(self, k: int = 128, edge_types: int = 1024): super().__init__() self.k = k self.means = nn.Embedding(1, k) self.stds = nn.Embedding(1, k) self.mul = nn.Embedding(edge_types, 1) self.bias = nn.Embedding(edge_types, 1) nn.init.uniform_(self.means.weight, 0, 3) nn.init.uniform_(self.stds.weight, 0, 3) nn.init.constant_(self.bias.weight, 0) nn.init.constant_(self.mul.weight, 1) def forward(self, x: torch.Tensor, edge_types: int) -> torch.Tensor: """Forward pass to compute the Gaussian pos. embeddings.""" mul = self.mul(edge_types) bias = self.bias(edge_types) x = mul * x.unsqueeze(-1) + bias x = x.expand(-1, -1, -1, self.k) mean = self.means.weight.float().view(-1) std = self.stds.weight.float().view(-1).abs() + 1e-5 output: torch.Tensor = gaussian(x.float(), mean, std).type_as(self.means.weight) return output class ParallelBlock(nn.Module): """Parallel transformer block (MLP & Attention in parallel). Based on: 'Scaling Vision Atomformers to 22 Billion Parameters` - https://arxiv.org/abs/2302.05442 Adapted from TIMM implementation. """ def __init__( self, dim: int, num_heads: int, mlp_ratio: int = 4, dropout: float = 0.0, k: int = 128, gradient_checkpointing: bool = False, ): super().__init__() assert ( dim % num_heads == 0 ), f"dim {dim} should be divisible by num_heads {num_heads}" self.num_heads = num_heads self.head_dim = dim // num_heads self.scale = self.head_dim**-0.5 self.mlp_hidden_dim = int(mlp_ratio * dim) self.proj_drop = nn.Dropout(dropout) self.attn_drop = nn.Dropout(dropout) self.gradient_checkpointing = gradient_checkpointing self.in_proj_in_dim = dim self.in_proj_out_dim = self.mlp_hidden_dim + 3 * dim self.out_proj_in_dim = self.mlp_hidden_dim + dim self.out_proj_out_dim = 2 * dim self.in_split = [self.mlp_hidden_dim] + [dim] * 3 self.out_split = [dim] * 2 self.in_norm = nn.LayerNorm(dim) self.q_norm = nn.LayerNorm(self.head_dim) self.k_norm = nn.LayerNorm(self.head_dim) self.in_proj = nn.Linear(self.in_proj_in_dim, self.in_proj_out_dim, bias=False) self.act_fn = nn.GELU() self.out_proj = nn.Linear( self.out_proj_in_dim, self.out_proj_out_dim, bias=False ) self.gaussian_proj = nn.Linear(k, 1) self.pos_embed_ff_norm = nn.LayerNorm(k) def forward( self, x: torch.Tensor, pos_embed: torch.Tensor, attention_mask: Optional[torch.Tensor] = None, ) -> Tuple[torch.Tensor, torch.Tensor]: """Forward pass for the parallel block.""" b, n, c = x.shape res = x # Combined MLP fc1 & qkv projections x = self.in_proj(self.in_norm(x)) x, q, k, v = torch.split(x, self.in_split, dim=-1) x = self.act_fn(x) x = self.proj_drop(x) # Dot product attention q = self.q_norm(q.view(b, n, self.num_heads, self.head_dim).transpose(1, 2)) k = self.k_norm(k.view(b, n, self.num_heads, self.head_dim).transpose(1, 2)) v = v.view(b, n, self.num_heads, self.head_dim).transpose(1, 2) x_attn = ( f.scaled_dot_product_attention( q, k, v, attn_mask=attention_mask + self.gaussian_proj(self.pos_embed_ff_norm(pos_embed)).permute( 0, 3, 1, 2 ), is_causal=False, ) .transpose(1, 2) .reshape(b, n, c) ) # Combined MLP fc2 & attn_output projection x_mlp, x_attn = self.out_proj(torch.cat([x, x_attn], dim=-1)).split( self.out_split, dim=-1 ) # Residual connections x = x_mlp + x_attn + res del x_mlp, x_attn, res return x, pos_embed class AtomformerEncoder(nn.Module): """Atomformer encoder. The transformer encoder consists of a series of parallel blocks, each containing a multi-head self-attention mechanism and a feed-forward network. """ def __init__(self, config: AtomformerConfig): super().__init__() self.vocab_size = config.vocab_size self.dim = config.dim self.num_heads = config.num_heads self.depth = config.depth self.mlp_ratio = config.mlp_ratio self.dropout = config.dropout self.k = config.k self.gradient_checkpointing = config.gradient_checkpointing self.metadata_vocab = nn.Embedding(self.vocab_size, 17) self.metadata_vocab.weight.requires_grad = False self.metadata_vocab.weight.fill_(-1) self.metadata_vocab.weight[1:-4] = torch.tensor( ATOM_METADATA, dtype=torch.float32 ) self.embed_metadata = nn.Linear(17, self.dim) self.gaussian_embed = GaussianLayer( k=self.k, edge_types=(self.vocab_size + 1) ** 2 ) self.embed_tokens = nn.Embedding(config.vocab_size, config.dim) nn.init.normal_(self.embed_tokens.weight, std=0.02) self.blocks = nn.ModuleList() for _ in range(self.depth): self.blocks.append( ParallelBlock( self.dim, self.num_heads, self.mlp_ratio, self.dropout, self.k, self.gradient_checkpointing, ) ) def _expand_mask( self, mask: torch.Tensor, dtype: torch.dtype, device: torch.device, tgt_len: Optional[int] = None, ) -> torch.Tensor: """ Expand attention mask. Expands attention_mask from `[bsz, seq_len]` to `[bsz, 1, tgt_seq_len, src_seq_len]`. """ bsz, src_len = mask.size() tgt_len = tgt_len if tgt_len is not None else src_len expanded_mask = ( mask[:, None, None, :].expand(bsz, 1, tgt_len, src_len).to(dtype) ) inverted_mask: torch.Tensor = 1.0 - expanded_mask return inverted_mask.masked_fill( inverted_mask.to(torch.bool), torch.finfo(dtype).min ).to(device) def forward( self, input_ids: torch.Tensor, coords: torch.Tensor, attention_mask: Optional[torch.Tensor] = None, ) -> Tuple[torch.Tensor, torch.Tensor]: """Forward pass for the transformer encoder.""" # pad coords by zeros for graph token coords_center = torch.sum(coords, dim=1, keepdim=True) / coords.shape[1] coords = torch.cat([coords_center, coords], dim=1) r_ij = torch.cdist(coords, coords, p=2) # [B, N, N] # pad input_ids by graph token input_ids = torch.cat( [ torch.zeros( input_ids.size(0), 1, dtype=torch.long, device=input_ids.device ).fill_(122), input_ids, ], dim=1, ) edge_type = input_ids.unsqueeze(-1) * self.vocab_size + input_ids.unsqueeze( -2 ) # [B, N, N] pos_embeds = self.gaussian_embed(r_ij, edge_type) # [B, N, N, K] input_embeds = self.embed_tokens(input_ids) atom_metadata = self.metadata_vocab(input_ids) input_embeds = input_embeds + self.embed_metadata(atom_metadata) # [B, N, C] attention_mask = ( torch.cat( [ torch.ones( attention_mask.size(0), 1, dtype=torch.bool, device=attention_mask.device, ), attention_mask.bool(), ], dim=1, ) if attention_mask is not None else None ) attention_mask = ( self._expand_mask(attention_mask, input_embeds.dtype, input_embeds.device) if attention_mask is not None else None ) for blk in self.blocks: input_embeds, pos_embeds = blk(input_embeds, pos_embeds, attention_mask) return input_embeds, pos_embeds class AtomformerPreTrainedModel(PreTrainedModel): # type: ignore """Base class for all transformer models.""" config_class = AtomformerConfig base_model_prefix = "model" supports_gradient_checkpointing = True _no_split_modules = ["ParallelBlock"] def _set_gradient_checkpointing( self, module: nn.Module, value: bool = False ) -> None: if isinstance(module, (AtomformerEncoder)): module.gradient_checkpointing = value class AtomformerModel(AtomformerPreTrainedModel): """Atomformer model for atom modeling.""" def __init__(self, config: AtomformerConfig): super().__init__(config) self.config = config self.encoder = AtomformerEncoder(config) def forward( self, input_ids: torch.Tensor, coords: torch.Tensor, attention_mask: Optional[torch.Tensor] = None, ) -> torch.Tensor: """Forward function call for the transformer model.""" output: torch.Tensor = self.encoder(input_ids, coords, attention_mask) return output class AtomformerForMaskedAM(AtomformerPreTrainedModel): """Atomformer with an atom modeling head on top for masked atom modeling.""" def __init__(self, config: AtomformerConfig): super().__init__(config) self.config = config self.encoder = AtomformerEncoder(config) self.am_head = nn.Linear(config.dim, config.vocab_size, bias=False) def forward( self, input_ids: torch.Tensor, coords: torch.Tensor, labels: Optional[torch.Tensor] = None, fixed: Optional[torch.Tensor] = None, attention_mask: Optional[torch.Tensor] = None, ) -> Tuple[Optional[torch.Tensor], torch.Tensor]: """Forward function call for the masked atom modeling model.""" hidden_states = self.encoder(input_ids, coords, attention_mask) logits = self.am_head(hidden_states) loss = None if labels is not None: loss_fct = nn.CrossEntropyLoss() logits, labels = logits.view(-1, self.config.vocab_size), labels.view(-1) loss = loss_fct(logits, labels) return loss, logits class AtomformerForCoordinateAM(AtomformerPreTrainedModel): """Atomformer with an atom coordinate head on top for coordinate denoising.""" def __init__(self, config: AtomformerConfig): super().__init__(config) self.config = config self.encoder = AtomformerEncoder(config) self.coords_head = nn.Linear(config.dim, 3) def forward( self, input_ids: torch.Tensor, coords: torch.Tensor, labels_coords: Optional[torch.Tensor] = None, fixed: Optional[torch.Tensor] = None, attention_mask: Optional[torch.Tensor] = None, ) -> Tuple[Optional[torch.Tensor], torch.Tensor]: """Forward function call for the coordinate atom modeling model.""" hidden_states = self.encoder(input_ids, coords, attention_mask) coords_pred = self.coords_head(hidden_states) loss = None if labels_coords is not None: labels_coords = labels_coords.to(coords_pred.device) loss_fct = nn.L1Loss() loss = loss_fct(coords_pred, labels_coords) return loss, coords_pred class InitialStructure2RelaxedStructure(AtomformerPreTrainedModel): """Atomformer with an coordinate head on top for relaxed structure prediction.""" def __init__(self, config: AtomformerConfig): super().__init__(config) self.config = config self.encoder = AtomformerEncoder(config) self.coords_head = nn.Linear(config.dim, 3) def forward( self, input_ids: torch.Tensor, coords: torch.Tensor, labels_coords: Optional[torch.Tensor] = None, fixed: Optional[torch.Tensor] = None, attention_mask: Optional[torch.Tensor] = None, ) -> Tuple[Optional[torch.Tensor], torch.Tensor]: """Forward function call. Initial structure to relaxed structure model. """ hidden_states = self.encoder(input_ids, coords, attention_mask) coords_pred = self.coords_head(hidden_states) loss = None if labels_coords is not None: labels_coords = labels_coords.to(coords_pred.device) loss_fct = nn.L1Loss() loss = loss_fct(coords_pred, labels_coords) return loss, coords_pred class InitialStructure2RelaxedEnergy(AtomformerPreTrainedModel): """Atomformer with an energy head on top for relaxed energy prediction.""" def __init__(self, config: AtomformerConfig): super().__init__(config) self.config = config self.encoder = AtomformerEncoder(config) self.energy_norm = nn.LayerNorm(config.dim) self.energy_head = nn.Linear(config.dim, 1, bias=False) def forward( self, input_ids: torch.Tensor, coords: torch.Tensor, labels_energy: Optional[torch.Tensor] = None, fixed: Optional[torch.Tensor] = None, attention_mask: Optional[torch.Tensor] = None, ) -> Tuple[Optional[torch.Tensor], torch.Tensor]: """Forward function call for the relaxed energy prediction model.""" hidden_states = self.encoder(input_ids, coords, attention_mask) energy = self.energy_head(self.energy_norm(hidden_states[:, 0])).squeeze(-1) loss = None if labels_energy is not None: loss_fct = nn.L1Loss() loss = loss_fct(energy, labels_energy) return loss, energy class InitialStructure2RelaxedStructureAndEnergy(AtomformerPreTrainedModel): """Atomformer with an coordinate and energy head.""" def __init__(self, config: AtomformerConfig): super().__init__(config) self.config = config self.encoder = AtomformerEncoder(config) self.energy_norm = nn.LayerNorm(config.dim) self.energy_head = nn.Linear(config.dim, 1, bias=False) self.coords_head = nn.Linear(config.dim, 3) def forward( self, input_ids: torch.Tensor, coords: torch.Tensor, labels_coords: Optional[torch.Tensor] = None, forces: Optional[torch.Tensor] = None, total_energy: Optional[torch.Tensor] = None, formation_energy: Optional[torch.Tensor] = None, has_formation_energy: Optional[torch.Tensor] = None, attention_mask: Optional[torch.Tensor] = None, ) -> Tuple[torch.Tensor, Tuple[torch.Tensor, torch.Tensor]]: """Forward function call for the relaxed structure and energy model.""" atom_hidden_states, pos_hidden_states = self.encoder( input_ids, coords, attention_mask ) formation_energy_pred = self.formation_energy_head( self.energy_norm(atom_hidden_states[:, 0]) ).squeeze(-1) loss_formation_energy = None if formation_energy is not None: loss_fct = nn.L1Loss() loss_formation_energy = loss_fct( formation_energy_pred[has_formation_energy], formation_energy[has_formation_energy], ) coords_pred = self.coords_head(atom_hidden_states[:, 1:]) loss_coords = None if labels_coords is not None: loss_fct = nn.L1Loss() loss_coords = loss_fct(coords_pred, labels_coords) loss = torch.Tensor(0).to(coords.device) loss = ( loss + loss_formation_energy if loss_formation_energy is not None else loss ) loss = loss + loss_coords if loss_coords is not None else loss return loss, (formation_energy_pred, coords_pred) class Structure2Energy(AtomformerPreTrainedModel): """Atomformer with an atom modeling head on top for masked atom modeling.""" def __init__(self, config: AtomformerConfig): super().__init__(config) self.config = config self.encoder = AtomformerEncoder(config) self.energy_norm = nn.LayerNorm(config.dim) self.formation_energy_head = nn.Linear(config.dim, 1, bias=False) def forward( self, input_ids: torch.Tensor, coords: torch.Tensor, forces: Optional[torch.Tensor] = None, total_energy: Optional[torch.Tensor] = None, formation_energy: Optional[torch.Tensor] = None, has_formation_energy: Optional[torch.Tensor] = None, attention_mask: Optional[torch.Tensor] = None, ) -> Tuple[Optional[torch.Tensor], Tuple[torch.Tensor, Optional[torch.Tensor]]]: """Forward function call for the structure to energy model.""" atom_hidden_states, pos_hidden_states = self.encoder( input_ids, coords, attention_mask ) formation_energy_pred: torch.Tensor = self.formation_energy_head( self.energy_norm(atom_hidden_states[:, 0]) ).squeeze(-1) loss = torch.Tensor(0).to(coords.device) if formation_energy is not None: loss_fct = nn.L1Loss() loss = loss_fct( formation_energy_pred[has_formation_energy], formation_energy[has_formation_energy], ) return loss, ( formation_energy_pred, attention_mask.bool() if attention_mask is not None else None, ) class Structure2Forces(AtomformerPreTrainedModel): """Atomformer with a forces head on top for forces prediction.""" def __init__(self, config: AtomformerConfig): super().__init__(config) self.config = config self.encoder = AtomformerEncoder(config) self.force_norm = nn.LayerNorm(config.dim) self.force_head = nn.Linear(config.dim, 3) self.energy_norm = nn.LayerNorm(config.dim) self.formation_energy_head = nn.Linear(config.dim, 1, bias=False) def forward( self, input_ids: torch.Tensor, coords: torch.Tensor, forces: Optional[torch.Tensor] = None, total_energy: Optional[torch.Tensor] = None, formation_energy: Optional[torch.Tensor] = None, has_formation_energy: Optional[torch.Tensor] = None, attention_mask: Optional[torch.Tensor] = None, ) -> Tuple[torch.Tensor, Tuple[torch.Tensor, Optional[torch.Tensor]]]: """Forward function call for the structure to forces model.""" atom_hidden_states, pos_hidden_states = self.encoder( input_ids, coords, attention_mask ) attention_mask = attention_mask.bool() if attention_mask is not None else None forces_pred: torch.Tensor = self.force_head( self.force_norm(atom_hidden_states[:, 1:]) ) loss = torch.Tensor(0).to(coords.device) if forces is not None: loss_fct = nn.L1Loss() loss = loss_fct(forces_pred[attention_mask], forces[attention_mask]) return loss, ( forces_pred, attention_mask if attention_mask is not None else None, ) class Structure2EnergyAndForces(AtomformerPreTrainedModel): """Atomformer with an energy and forces head for energy and forces prediction.""" def __init__(self, config: AtomformerConfig): super().__init__(config) self.config = config self.encoder = AtomformerEncoder(config) self.force_norm = nn.LayerNorm(config.dim) self.force_head = nn.Linear(config.dim, 3) self.energy_norm = nn.LayerNorm(config.dim) self.formation_energy_head = nn.Linear(config.dim, 1, bias=False) def forward( self, input_ids: torch.Tensor, coords: torch.Tensor, forces: Optional[torch.Tensor] = None, total_energy: Optional[torch.Tensor] = None, formation_energy: Optional[torch.Tensor] = None, has_formation_energy: Optional[torch.Tensor] = None, attention_mask: Optional[torch.Tensor] = None, ) -> Tuple[torch.Tensor, Tuple[torch.Tensor, torch.Tensor, Optional[torch.Tensor]]]: """Forward function call for the structure to energy and forces model.""" atom_hidden_states, pos_hidden_states = self.encoder( input_ids, coords, attention_mask ) formation_energy_pred: torch.Tensor = self.formation_energy_head( self.energy_norm(atom_hidden_states[:, 0]) ).squeeze(-1) loss_formation_energy = None if formation_energy is not None: loss_fct = nn.L1Loss() loss_formation_energy = loss_fct( formation_energy_pred[has_formation_energy], formation_energy[has_formation_energy], ) attention_mask = attention_mask.bool() if attention_mask is not None else None forces_pred: torch.Tensor = self.force_head( self.force_norm(atom_hidden_states[:, 1:]) ) loss_forces = None if forces is not None: loss_fct = nn.L1Loss() loss_forces = loss_fct(forces_pred[attention_mask], forces[attention_mask]) loss = torch.Tensor(0).to(coords.device) loss = ( loss + loss_formation_energy if loss_formation_energy is not None else loss ) loss = loss + loss_forces if loss_forces is not None else loss return loss, (formation_energy_pred, forces_pred, attention_mask)