torch-molecule 0.1.0.dev2__py3-none-any.whl

torch_molecule/generator/gdss/modeling_gdss.py

@@ -0,0 +1,474 @@
+import numpy as np
+from tqdm import tqdm
+from typing import Optional, Union, Dict, Any, Tuple, List, Type
+from dataclasses import dataclass, field
+
+import torch
+import torch.nn.functional as F
+from torch_geometric.loader import DataLoader
+from torch_geometric.data import Data
+
+from .sde import load_sde
+from .solver import get_pc_sampler
+from .model import GDSSModel, get_sde_loss_fn
+from .utils import compute_dataset_info, to_dense, quantize_mol
+
+from ...base import BaseMolecularGenerator
+from ...utils import graph_from_smiles, graph_to_smiles
+
+@dataclass
+class GDSSMolecularGenerator(BaseMolecularGenerator):
+    """ This generator implements "Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations"
+
+    References
+    ----------
+    - Paper: https://arxiv.org/abs/2202.02514
+    - Official Implementation: https://github.com/harryjo97/GDSS
+
+    
+    Parameters
+    ----------
+    num_layer : int, default=3
+        Number of layers in the score networks.
+    hidden_size_adj : float, default=8
+        Hidden dimension size for the adjacency in the adjacency score network.
+    hidden_size : int, default=16
+        Hidden dimension size latent representation.
+    attention_dim : int, default=16
+        Dimension of attention layers.
+    num_head : int, default=4
+        Number of attention heads.
+    sde_type_x : str, default='VE'
+        SDE type for node features. One of 'VP', 'VE', 'subVP'.
+    sde_beta_min_x : float, default=0.1
+        Minimum noise level for node features.
+    sde_beta_max_x : float, default=1
+        Maximum noise level for node features.
+    sde_num_scales_x : int, default=1000
+        Number of noise scales for node features.
+    sde_type_adj : str, default='VE'
+        SDE type for adjacency matrix. One of 'VP', 'VE', 'subVP'.
+    sde_beta_min_adj : float, default=0.1
+        Minimum noise level for adjacency matrix.
+    sde_beta_max_adj : float, default=1
+        Maximum noise level for adjacency matrix.
+    sde_num_scales_adj : int, default=1000
+        Number of noise scales for adjacency matrix.
+    batch_size : int, default=128
+        Batch size for training.
+    epochs : int, default=500
+        Number of training epochs.
+    learning_rate : float, default=0.005
+        Learning rate for optimizer.
+    grad_clip_value : Optional[float], default=1
+        Value for gradient clipping. None means no clipping.
+    weight_decay : float, default=1e-4
+        Weight decay for optimizer.
+    use_loss_reduce_mean : bool, default=False
+        Whether to use mean reduction for loss calculation.
+    use_lr_scheduler : bool, default=False
+        Whether to use learning rate scheduler.
+    scheduler_factor : float, default=0.5
+        Factor by which to reduce learning rate when using scheduler (only used if use_lr_scheduler is True).
+    scheduler_patience : int, default=5
+        Number of epochs with no improvement after which learning rate will be reduced (only used if use_lr_scheduler is True).
+    sampler_predictor : str, default='Reverse'
+        Predictor method for sampling. One of 'Euler', 'Reverse'.
+    sampler_corrector : str, default='Langevin'
+        Corrector method for sampling. One of 'Langevin', 'None'.
+    sampler_snr : float, default=0.2
+        Signal-to-noise ratio for corrector.
+    sampler_scale_eps : float, default=0.7
+        Scale factor for noise level in corrector.
+    sampler_n_steps : int, default=1
+        Number of corrector steps per predictor step.
+    sampler_probability_flow : bool, default=False
+        Whether to use probability flow ODE for sampling.
+    sampler_noise_removal : bool, default=True
+        Whether to remove noise in the final step of sampling.
+    verbose : bool, default=False
+        Whether to display progress bars and logs.
+        
+    """
+    
+    # Model parameters
+    num_layer: int = 3
+    hidden_size_adj: float = 8
+    hidden_size: int = 16
+    attention_dim: int = 16
+    num_head: int = 4
+
+    # Diffusion parameters
+    sde_type_x: str = 'VE' # One of 'VP', 'VE', 'subVP'
+    sde_beta_min_x: float = 0.1
+    sde_beta_max_x: float = 1
+    sde_num_scales_x: int = 1000
+    sde_type_adj: str = 'VE' # One of 'VP', 'VE', 'subVP'
+    sde_beta_min_adj: float = 0.1
+    sde_beta_max_adj: float = 1
+    sde_num_scales_adj: int = 1000
+
+    # Training parameters
+    batch_size: int = 128
+    epochs: int = 500
+    learning_rate: float = 0.005
+    grad_clip_value: Optional[float] = 1.0
+    weight_decay: float = 1e-4
+    use_loss_reduce_mean: bool = False
+
+    # Scheduler parameters
+    use_lr_scheduler: bool = False
+    scheduler_factor: float = 0.5
+    scheduler_patience: int = 5
+
+    # Sampling parameters
+    sampler_predictor: str = 'Reverse'  # One of 'Euler', 'Reverse', others will be treated as 'Euler'
+    sampler_corrector: str = 'Langevin' # One of 'Langevin', 'None', others will be treated as 'None'
+    sampler_snr: float = 0.2
+    sampler_scale_eps: float = 0.7
+    sampler_n_steps: int = 1
+    sampler_probability_flow: bool = False
+    sampler_noise_removal: bool = True
+
+    verbose: bool = False
+    # Attributes
+    model_name: str = "GDSSMolecularGenerator"
+    fitting_loss: List[float] = field(default_factory=list, init=False)
+    fitting_epoch: int = field(default=0, init=False)
+    model_class: Type[GDSSModel] = field(default=GDSSModel, init=False)
+    # dataset_info: Dict[str, Any] = field(default_factory=dict, init=False)
+    def __post_init__(self):
+        """Initialize the model after dataclass initialization."""
+        super().__post_init__()
+        self.max_node = None
+        self.input_dim_X = None
+        self.input_dim_adj = None
+        self.conv = 'GCN'
+        self.sampler_eps = 1e-4
+        self.train_eps = 1e-5
+        self.dataset_info = None
+        self.loss_fn = None
+        self.sampling_fn = None
+
+    @staticmethod
+    def _get_param_names() -> List[str]:
+        """Get parameter names for the estimator.
+
+        Returns
+        -------
+        List[str]
+            List of parameter names that can be used for model configuration.
+        """
+
+        return [
+            # Model Hyperparameters
+            "max_node", "num_layer", "num_head", "input_dim_X", "input_dim_adj", "hidden_size_adj", "hidden_size", "attention_dim",
+            # Diffusion parameters  
+            "dataset_info", "sde_type_x", "sde_beta_min_x", "sde_beta_max_x", "sde_num_scales_x", 
+            "sde_type_adj", "sde_beta_min_adj", "sde_beta_max_adj", "sde_num_scales_adj",
+            # Training Parameters
+            "batch_size", "epochs", "learning_rate", "grad_clip_value", 
+            "weight_decay", "use_loss_reduce_mean", "train_eps", "conv",
+            # Scheduler Parameters
+            "use_lr_scheduler", "scheduler_factor", "scheduler_patience",
+            # Sampling Parameters
+            "sampler_predictor", "sampler_corrector", "sampler_snr", "sampler_scale_eps", 
+            "sampler_n_steps", "sampler_probability_flow", "sampler_noise_removal", "sampler_eps",
+            # Other Parameters
+            "fitting_epoch", "fitting_loss", "device", "verbose", "model_name"
+        ]
+    
+    def _get_model_params(self, checkpoint: Optional[Dict] = None) -> Dict[str, Any]:
+        params = ["input_dim_X", "max_node", "hidden_size", "num_layer", "input_dim_adj", "hidden_size_adj", "attention_dim", "num_head"]
+
+        if checkpoint is not None:
+            if "hyperparameters" not in checkpoint:
+                raise ValueError("Checkpoint missing 'hyperparameters' key")
+            return {k: checkpoint["hyperparameters"][k] for k in params}
+        
+        return {k: getattr(self, k) for k in params}
+        
+    def _convert_to_pytorch_data(self, X, y=None):
+        """Convert numpy arrays to PyTorch Geometric data format.
+        """
+        if self.verbose:
+            iterator = tqdm(enumerate(X), desc="Converting molecules to graphs", total=len(X))
+        else:
+            iterator = enumerate(X)
+
+        pyg_graph_list = []
+        for idx, smiles_or_mol in iterator:
+            if y is not None:
+                properties = y[idx]
+            else: 
+                properties = None
+            graph = graph_from_smiles(smiles_or_mol, properties)
+            g = Data()
+            
+            # No H, first heavy atom has type 0
+            node_type = torch.from_numpy(graph['node_feat'][:, 0] - 1)
+            
+            # Filter out invalid node types (< 0)
+            valid_mask = node_type >= 0
+            if not valid_mask.all():
+                # Get valid nodes and adjust edge indices
+                valid_indices = torch.where(valid_mask)[0]
+                index_map = -torch.ones(node_type.size(0), dtype=torch.long)
+                index_map[valid_indices] = torch.arange(valid_indices.size(0))
+                
+                # Filter edges that connect to invalid nodes
+                edge_index = torch.from_numpy(graph["edge_index"])
+                valid_edges_mask = valid_mask[edge_index[0]] & valid_mask[edge_index[1]]
+                valid_edge_index = edge_index[:, valid_edges_mask]
+                
+                # Remap edge indices to account for removed nodes
+                remapped_edge_index = index_map[valid_edge_index]
+                
+                # Filter edge attributes
+                edge_attr = torch.from_numpy(graph["edge_feat"])[:, 0] + 1
+                valid_edge_attr = edge_attr[valid_edges_mask]
+                
+                # Update node and edge data
+                node_type = node_type[valid_mask]
+                g.edge_index = remapped_edge_index
+                g.edge_attr = valid_edge_attr.long().squeeze(-1)
+            else:
+                # No invalid nodes, proceed normally
+                g.edge_index = torch.from_numpy(graph["edge_index"])
+                edge_attr = torch.from_numpy(graph["edge_feat"])[:, 0] + 1
+                g.edge_attr = edge_attr.long().squeeze(-1)
+            
+            # * is encoded as "misc" which is 119 - 1 and should be 117
+            node_type[node_type == 118] = 117
+            g.x = node_type.long().squeeze(-1)
+            del graph["node_feat"]
+            del graph["edge_index"]
+            del graph["edge_feat"]
+
+            g.y = torch.from_numpy(graph["y"])
+            del graph["y"]
+
+            pyg_graph_list.append(g)
+
+        return pyg_graph_list
+
+    def _setup_diffusion_params(self, X: Union[List, Dict]) -> None:
+        # Extract dataset info from X if it's a dict (from checkpoint), otherwise compute it
+        if isinstance(X, dict):
+            dataset_info = X["hyperparameters"]["dataset_info"]
+            max_node = X["hyperparameters"]["max_node"]
+        else:
+            assert isinstance(X, list)
+            dataset_info = compute_dataset_info(X)
+            max_node = dataset_info["max_node"]
+
+        self.input_dim_X = dataset_info["x_margins"].shape[0]
+        self.input_dim_adj = dataset_info["e_margins"].shape[0]
+        self.dataset_info = dataset_info
+        self.max_node = max_node
+
+        x_sde = load_sde(self.sde_type_x, self.sde_beta_min_x, self.sde_beta_max_x, self.sde_num_scales_x)
+        adj_sde = load_sde(self.sde_type_adj, self.sde_beta_min_adj, self.sde_beta_max_adj, self.sde_num_scales_adj)
+
+        self.loss_fn = get_sde_loss_fn(
+            x_sde,
+            adj_sde,
+            train=True,
+            reduce_mean=self.use_loss_reduce_mean,
+            continuous=True,
+            likelihood_weighting=False,
+            eps=self.train_eps,
+        )
+
+        self.sampling_fn = get_pc_sampler(
+            sde_x=x_sde,
+            sde_adj=adj_sde,
+            predictor=self.sampler_predictor,
+            corrector=self.sampler_corrector,
+            snr=self.sampler_snr,
+            scale_eps=self.sampler_scale_eps,
+            n_steps=self.sampler_n_steps,
+            probability_flow=self.sampler_probability_flow,
+            continuous=True,
+            denoise=self.sampler_noise_removal,
+            eps=self.sampler_eps,
+            device=self.device,
+        )
+
+
+    def _initialize_model(
+        self,
+        model_class: Type[torch.nn.Module],
+        checkpoint: Optional[Dict] = None
+    ) -> torch.nn.Module:
+        """Initialize the model with parameters or a checkpoint."""
+        model_params = self._get_model_params(checkpoint)
+        self.model = model_class(**model_params)
+        self.model = self.model.to(self.device)
+        
+        if checkpoint is not None:
+            self._setup_diffusion_params(checkpoint)
+            self.model.load_state_dict(checkpoint["model_state_dict"])
+        return self.model
+
+    def _setup_optimizers(self) -> Tuple[torch.optim.Optimizer, Optional[Any]]:
+        """Setup optimization components including optimizer and learning rate scheduler.
+        """
+        optimizer = torch.optim.Adam(
+            self.model.parameters(), lr=self.learning_rate, weight_decay=self.weight_decay
+        )
+        scheduler = None
+        if self.use_lr_scheduler:
+            scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(
+                optimizer,
+                mode="min",
+                factor=self.scheduler_factor,
+                patience=self.scheduler_patience,
+                min_lr=1e-6,
+                cooldown=0,
+                eps=1e-8,
+            )
+
+        return optimizer, scheduler
+
+    def fit(
+        self,
+        X_train: List[str],
+    ) -> "GDSSMolecularGenerator":
+        """Fit the model to the training data.
+
+        Parameters
+        ----------
+        X_train : List[str]
+            List of training data in SMILES format.
+
+        Returns
+        -------
+        self : GDSSMolecularGenerator
+            The fitted model.
+        """
+        X_train, _ = self._validate_inputs(X_train)
+        self._setup_diffusion_params(X_train)
+        self._initialize_model(self.model_class)
+        self.model.initialize_parameters()
+
+        optimizer, scheduler = self._setup_optimizers()
+        train_dataset = self._convert_to_pytorch_data(X_train)
+        train_loader = DataLoader(
+            train_dataset,
+            batch_size=self.batch_size,
+            shuffle=True,
+            num_workers=0
+        )
+
+        self.fitting_loss = []
+        self.fitting_epoch = 0
+        for epoch in range(self.epochs):
+            train_losses = self._train_epoch(train_loader, optimizer, epoch)
+            self.fitting_loss.append(np.mean(train_losses).item())
+            if scheduler:
+                scheduler.step(np.mean(train_losses).item())
+
+        self.fitting_epoch = epoch
+        self.is_fitted_ = True
+        return self
+    
+    def _train_epoch(self, train_loader, optimizer, epoch):
+        self.model.train()
+        losses = []
+        iterator = (
+            tqdm(train_loader, desc="Training", leave=False)
+            if self.verbose
+            else train_loader
+        )
+        active_index = self.dataset_info["active_index"]
+        for step, batched_data in enumerate(iterator):
+            batched_data = batched_data.to(self.device)
+            optimizer.zero_grad()
+
+            data_x = F.one_hot(batched_data.x, num_classes=118).float()[:, active_index]
+            data_edge_attr = batched_data.edge_attr.float()
+            X, E, node_mask = to_dense(data_x, batched_data.edge_index, data_edge_attr, batched_data.batch, self.max_node)
+            
+            loss_x, loss_adj = self.model.compute_loss(x=X, adj=E, flags=node_mask, loss_fn=self.loss_fn)
+            loss = loss_x + loss_adj
+            loss.backward()
+            if self.grad_clip_value is not None:
+                torch.nn.utils.clip_grad_norm_(self.model.parameters(), self.grad_clip_value)
+
+            optimizer.step()
+            losses.append(loss.item())
+
+            if self.verbose:
+                iterator.set_postfix({"Epoch": epoch, "Loss": f"{loss.item():.4f}", "Loss_x": f"{loss_x.item():.4f}", "Loss_adj": f"{loss_adj.item():.4f}"})
+            
+        return losses
+    
+    @torch.no_grad()
+    def generate(self, num_nodes: Optional[Union[List[List], np.ndarray, torch.Tensor]] = None, batch_size: int = 32) -> List[str]:
+        """Randomly generate molecules with specified node counts.
+
+        Parameters
+        ----------
+        num_nodes : Optional[Union[List[List], np.ndarray, torch.Tensor]], default=None
+            Number of nodes for each molecule in the batch. If None, samples from
+            the training distribution. Can be provided as:
+            - A list of lists
+            - A numpy array of shape (batch_size, 1) 
+            - A torch tensor of shape (batch_size, 1)
+            
+        batch_size : int, default=32
+            Number of molecules to generate.
+
+        Returns
+        -------
+        List[str]
+            List of generated molecules in SMILES format.
+        """
+        if not self.is_fitted_:
+            raise ValueError("Model must be fitted before generating molecules.")
+
+        if num_nodes is not None:
+            batch_size = len(num_nodes)
+
+        if num_nodes is None:
+            num_nodes_dist = self.dataset_info["num_nodes_dist"]
+            num_nodes = num_nodes_dist.sample_n(batch_size, self.device)
+        elif isinstance(num_nodes, list):
+            num_nodes = torch.tensor(num_nodes).to(self.device)
+        elif isinstance(num_nodes, np.ndarray):
+            num_nodes = torch.from_numpy(num_nodes).to(self.device)
+        if num_nodes.dim() == 1:
+            num_nodes = num_nodes.unsqueeze(-1)
+        
+        assert num_nodes.size(0) == batch_size
+        arange = (
+            torch.arange(self.max_node).to(self.device)
+            .unsqueeze(0)
+            .expand(batch_size, -1)
+        )
+        node_mask = arange < num_nodes
+
+        if not hasattr(self, 'dataset_info') or self.dataset_info is None:
+            raise ValueError("Dataset info not found. Please call setup_diffusion_params first.")
+        
+        shape_x = (
+            batch_size,
+            self.max_node,
+            self.input_dim_X,
+        )
+        shape_adj = (batch_size, self.max_node, self.max_node)
+
+        X, E, _ = self.sampling_fn(self.model.score_network_x, self.model.score_network_a, shape_x, shape_adj, node_mask)
+        E = quantize_mol(E)
+        X = X.argmax(dim=-1)
+
+        molecule_list = []
+        for i in range(batch_size):
+            n = num_nodes[i][0].item()
+            atom_types = X[i, :n].cpu()
+            edge_types = E[i, :n, :n].cpu()
+            molecule_list.append([atom_types, edge_types])
+
+        smiles_list = graph_to_smiles(molecule_list, self.dataset_info["atom_decoder"])
+        return smiles_list