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

torch_molecule/generator/graph_dit/modeling_graph_dit.py

@@ -0,0 +1,581 @@
+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 .transformer import Transformer
+from .utils import PlaceHolder, to_dense, compute_dataset_info
+from .diffusion import NoiseScheduleDiscrete, MarginalTransition, sample_discrete_features, sample_discrete_feature_noise, reverse_diffusion
+
+from ...base import BaseMolecularGenerator
+from ...utils import graph_from_smiles, graph_to_smiles
+
+@dataclass
+class GraphDITMolecularGenerator(BaseMolecularGenerator):
+    """
+    This generator implements the graph diffusion transformer for (multi-conditional and unconditional) molecular generation.
+
+    References
+    ----------
+    - Graph Diffusion Transformers for Multi-Conditional Molecular Generation. NeurIPS 2024.
+      https://openreview.net/forum?id=cfrDLD1wfO
+    - Implementation: https://github.com/liugangcode/Graph-DiT
+
+    Parameters
+    ----------
+    num_layer : int, default=6
+        Number of transformer layers
+    hidden_size : int, default=1152
+        Dimension of hidden layers
+    dropout : float, default=0.0
+        Dropout rate for transformer layers
+    drop_condition : float, default=0.0
+        Dropout rate for condition embedding
+    num_head : int, default=16
+        Number of attention heads in transformer
+    mlp_ratio : float, default=4
+        Ratio of MLP hidden dimension to transformer hidden dimension
+    task_type : List[str], default=[]
+        List specifying type of each task ('regression' or 'classification')
+    timesteps : int, default=500
+        Number of diffusion timesteps
+    batch_size : int, default=128
+        Batch size for training
+    epochs : int, default=10000
+        Number of training epochs
+    learning_rate : float, default=0.0002
+        Learning rate for optimization
+    grad_clip_value : Optional[float], default=None
+        Value for gradient clipping (None = no clipping)
+    weight_decay : float, default=0.0
+        Weight decay for optimization
+    lw_X : float, default=1
+        Loss weight for node reconstruction
+    lw_E : float, default=5
+        Loss weight for edge reconstruction
+    guide_scale : float, default=2.0
+        Scale factor for classifier-free guidance during sampling
+    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 on plateau
+    scheduler_patience : int, default=5
+        Number of epochs with no improvement after which learning rate will be reduced
+    verbose : bool, default=False
+        Whether to display progress bars and logs
+    """
+    
+    # Model parameters
+    num_layer: int = 6
+    hidden_size: int = 1152
+    dropout: float = 0.
+    drop_condition: float = 0.
+    num_head: int = 16
+    mlp_ratio: float = 4
+    task_type: List[str] = field(default_factory=list)
+
+    # Diffusion parameters
+    timesteps: int = 500
+    
+    # Training parameters
+    batch_size: int = 128
+    epochs: int = 10000
+    learning_rate: float = 0.0002
+    grad_clip_value: Optional[float] = None
+    weight_decay: float = 0.0
+    lw_X: float = 1
+    lw_E: float = 5
+    # Sampling parameters
+    guide_scale: float = 2.
+    # Scheduler parameters
+    use_lr_scheduler: bool = False
+    scheduler_factor: float = 0.5
+    scheduler_patience: int = 5
+
+    verbose: bool = False
+
+    # Attributes
+    model_name: str = "GraphDITMolecularGenerator"
+    fitting_loss: List[float] = field(default_factory=list, init=False)
+    fitting_epoch: int = field(default=0, init=False)
+    dataset_info: Dict[str, Any] = field(default_factory=dict, init=False)
+    model_class: Type[Transformer] = field(default=Transformer, 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_E = None
+        self.input_dim_y = len(self.task_type)
+
+    @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", "hidden_size", "num_layer", "num_head",
+            "mlp_ratio", "dropout", "drop_condition", "input_dim_X", "input_dim_E", "input_dim_y",
+            "task_type",
+            # Diffusion parameters  
+            "timesteps", "dataset_info",
+            # Training Parameters
+            "batch_size", "epochs", "learning_rate", "grad_clip_value", 
+            "weight_decay", "lw_X", "lw_E",
+            # Scheduler Parameters
+            "use_lr_scheduler", "scheduler_factor", "scheduler_patience",
+            # Sampling Parameters
+            "guide_scale",
+            # Other Parameters
+            "fitting_epoch", "fitting_loss", "device", "verbose", "model_name"
+        ]
+    
+    def _get_model_params(self, checkpoint: Optional[Dict] = None) -> Dict[str, Any]:
+        params = ["max_node", "hidden_size", "num_layer", "num_head", "mlp_ratio", 
+                 "dropout", "drop_condition", "input_dim_X", "input_dim_E", "input_dim_y", "task_type"]
+        
+        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"]
+            timesteps = X["hyperparameters"]["timesteps"] 
+            max_node = X["hyperparameters"]["max_node"]
+        else:
+            assert isinstance(X, list)
+            dataset_info = compute_dataset_info(X)
+            timesteps = self.timesteps
+            max_node = dataset_info["max_node"]
+
+        self.input_dim_X = dataset_info["x_margins"].shape[0]
+        self.input_dim_E = dataset_info["e_margins"].shape[0]
+        self.dataset_info = dataset_info
+        self.timesteps = timesteps
+        self.max_node = max_node
+
+        x_limit = dataset_info["x_margins"].to(self.device)
+        e_limit = dataset_info["e_margins"].to(self.device)
+        xe_conditions = dataset_info["xe_conditions"].to(self.device)
+        ex_conditions = dataset_info["ex_conditions"].to(self.device)
+
+        self.transition_model = MarginalTransition(x_limit, e_limit, xe_conditions, ex_conditions, self.max_node)
+        self.limit_dist = PlaceHolder(X=x_limit, E=e_limit, y=None)
+        self.noise_schedule = NoiseScheduleDiscrete(timesteps=self.timesteps).to(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],
+        y_train: Optional[Union[List, np.ndarray]] = None,
+    ) -> "GraphDITMolecularGenerator":
+        num_task = len(self.task_type)
+        X_train, y_train = self._validate_inputs(X_train, y_train, num_task=num_task)
+        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, y_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 = F.one_hot(batched_data.edge_attr, num_classes=5).float()
+            dense_data, node_mask = to_dense(data_x, batched_data.edge_index, data_edge_attr, batched_data.batch, self.max_node)
+            dense_data = dense_data.mask(node_mask)
+            X, E = dense_data.X, dense_data.E
+            noisy_data = self.apply_noise(X, E, batched_data.y, node_mask)
+
+            loss, loss_X, loss_E = self.model.compute_loss(noisy_data, true_X=X, true_E=E, lw_X=self.lw_X, lw_E=self.lw_E)
+            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_E": f"{loss_E.item():.4f}"})
+            
+        return losses
+
+    def apply_noise(self, X, E, y, node_mask) -> Dict[str, Any]:
+        t_int = torch.randint(0, self.timesteps + 1, size=(X.size(0), 1), device=X.device).float()  # (bs, 1)
+        s_int = t_int - 1
+
+        t_float = t_int / self.timesteps
+        s_float = s_int / self.timesteps
+
+        # beta_t and alpha_s_bar are used for denoising/loss computation
+        beta_t = self.noise_schedule(t_normalized=t_float)                         # (bs, 1)
+        alpha_s_bar = self.noise_schedule.get_alpha_bar(t_normalized=s_float)      # (bs, 1)
+        alpha_t_bar = self.noise_schedule.get_alpha_bar(t_normalized=t_float)      # (bs, 1)
+
+        Qtb = self.transition_model.get_Qt_bar(alpha_t_bar, self.device)  # (bs, dx_in, dx_out), (bs, de_in, de_out)
+        
+        bs, n, _ = X.shape
+        X_all = torch.cat([X, E.reshape(bs, n, -1)], dim=-1)
+        prob_all = X_all @ Qtb.X
+        probX = prob_all[:, :, :self.input_dim_X]
+        probE = prob_all[:, :, self.input_dim_X:].reshape(bs, n, n, -1)
+
+        # check whether X_all/prob_all/probX/probE contain nan
+        
+        sampled_t = sample_discrete_features(probX=probX, probE=probE, node_mask=node_mask)
+
+        X_t = F.one_hot(sampled_t.X, num_classes=self.input_dim_X)
+        E_t = F.one_hot(sampled_t.E, num_classes=self.input_dim_E)
+        assert (X.shape == X_t.shape) and (E.shape == E_t.shape)
+
+        z_t = PlaceHolder(X=X_t, E=E_t, y=y).type_as(X_t).mask(node_mask)
+
+        noisy_data = {'t': t_float * self.timesteps, 'beta_t': beta_t, 'alpha_s_bar': alpha_s_bar,
+                      'alpha_t_bar': alpha_t_bar, 'X_t': z_t.X, 'E_t': z_t.E, 'y_t': z_t.y, 'node_mask': node_mask}
+        
+        return noisy_data
+
+    @torch.no_grad()
+    def generate(self, labels: Optional[Union[List[List], np.ndarray, torch.Tensor]] = None, num_nodes: Optional[Union[List[List], np.ndarray, torch.Tensor]] = None, batch_size: int = 32) -> List[str]:
+        """Generate molecules with specified properties and optional node counts.
+
+        Parameters
+        ----------
+        labels : Optional[Union[List[List], np.ndarray, torch.Tensor]], default=None
+            Target properties for the generated molecules. Can be provided as:
+            - A list of lists for multiple properties 
+            - A numpy array of shape (batch_size, n_properties)
+            - A torch tensor of shape (batch_size, n_properties)
+            For single label (properties values), can also be provided as 1D array/tensor.
+            If None, generates unconditional samples.
+            
+        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. Only used if labels is None.
+
+        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 self.input_dim_X is None or self.input_dim_E is None or self.max_node is None:
+            raise ValueError(f"Model may not be fitted correctly as one of below attributes is not set: input_dim_X={self.input_dim_X}, input_dim_E={self.input_dim_E}, max_node={self.max_node}")
+        
+        if len(self.task_type) > 0 and labels is None:
+            raise ValueError(f"labels must be provided if task_type is not empty: {self.task_type}")
+
+        if labels is not None and num_nodes is not None:
+            assert len(labels) == len(num_nodes), "labels and num_nodes must have the same batch size"
+        
+        if labels is not None:
+            if num_nodes is not None:
+                assert len(labels) == len(num_nodes), "labels and num_nodes must have the same batch size"
+            batch_size = len(labels)
+        elif num_nodes is not None:
+            batch_size = len(num_nodes)
+
+        # Convert properties to 2D tensor if needed
+        if isinstance(labels, list):
+            labels = torch.tensor(labels)
+        elif isinstance(labels, np.ndarray):
+            labels = torch.from_numpy(labels)
+        if labels is not None and labels.dim() == 1:
+            labels = labels.unsqueeze(-1)
+        
+        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, 'limit_dist') or self.limit_dist is None:
+            raise ValueError("Limit distribution not found. Please call setup_diffusion_params first.")
+        if not hasattr(self, 'dataset_info') or self.dataset_info is None:
+            raise ValueError("Dataset info not found. Please call setup_diffusion_params first.")
+        
+        z_T = sample_discrete_feature_noise(
+            limit_dist=self.limit_dist, node_mask=node_mask
+        )
+        X, E = z_T.X, z_T.E
+
+        assert (E == torch.transpose(E, 1, 2)).all()
+
+        # Iteratively sample p(z_s | z_t) for t = 1, ..., T, with s = t - 1.
+        if labels is not None:
+            y = labels.to(self.device).float()
+        else:
+            y = None
+
+        self.model.eval()
+        for s_int in reversed(range(0, self.timesteps)):
+            s_array = s_int * torch.ones((batch_size, 1)).float().to(self.device)
+            t_array = s_array + 1
+            s_norm = s_array / self.timesteps
+            t_norm = t_array / self.timesteps
+
+            # Sample z_s
+            sampled_s = self.sample_p_zs_given_zt(s_norm, t_norm, X, E, y, node_mask)
+            X, E, y = sampled_s.X, sampled_s.E, sampled_s.y
+
+        # Sample
+        sampled_s = sampled_s.mask(node_mask, collapse=True)
+        X, E, y = sampled_s.X, sampled_s.E, sampled_s.y
+
+        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
+
+    def sample_p_zs_given_zt(
+        self, s, t, X_t, E_t, properties, node_mask
+    ):
+        """Samples from zs ~ p(zs | zt). Only used during sampling.
+        if last_step, return the graph prediction as well"""
+        bs, n, _ = X_t.shape
+        beta_t = self.noise_schedule(t_normalized=t)  # (bs, 1)
+        alpha_s_bar = self.noise_schedule.get_alpha_bar(t_normalized=s)
+        alpha_t_bar = self.noise_schedule.get_alpha_bar(t_normalized=t)
+
+        # Neural net predictions
+        noisy_data = {
+            "X_t": X_t,
+            "E_t": E_t,
+            "y_t": properties,
+            "t": t,
+            "node_mask": node_mask,
+        }
+
+        def get_prob(noisy_data, unconditioned=False):
+            pred = self.model(noisy_data, unconditioned=unconditioned)
+
+            # Normalize predictions
+            pred_X = F.softmax(pred.X, dim=-1)  # bs, n, d0
+            pred_E = F.softmax(pred.E, dim=-1)  # bs, n, n, d0
+
+            device = pred_X.device
+            # Retrieve transitions matrix
+            Qtb = self.transition_model.get_Qt_bar(alpha_t_bar, device)
+            Qsb = self.transition_model.get_Qt_bar(alpha_s_bar, device)
+            Qt = self.transition_model.get_Qt(beta_t, device)
+
+            Xt_all = torch.cat([X_t, E_t.reshape(bs, n, -1)], dim=-1)
+            predX_all = torch.cat([pred_X, pred_E.reshape(bs, n, -1)], dim=-1)
+
+            # raise ValueError('stop here')
+            unnormalized_probX_all = reverse_diffusion(
+                predX_0=predX_all, X_t=Xt_all, Qt=Qt.X, Qsb=Qsb.X, Qtb=Qtb.X
+            )
+
+            unnormalized_prob_X = unnormalized_probX_all[:, :, : self.input_dim_X]
+            unnormalized_prob_E = unnormalized_probX_all[
+                :, :, self.input_dim_X :
+            ].reshape(bs, n * n, -1)
+
+            unnormalized_prob_X[torch.sum(unnormalized_prob_X, dim=-1) == 0] = 1e-5
+            unnormalized_prob_E[torch.sum(unnormalized_prob_E, dim=-1) == 0] = 1e-5
+
+            prob_X = unnormalized_prob_X / torch.sum(
+                unnormalized_prob_X, dim=-1, keepdim=True
+            )  # bs, n, d_t-1
+            prob_E = unnormalized_prob_E / torch.sum(
+                unnormalized_prob_E, dim=-1, keepdim=True
+            )  # bs, n, d_t-1
+            prob_E = prob_E.reshape(bs, n, n, pred_E.shape[-1])
+
+            return prob_X, prob_E
+
+        prob_X, prob_E = get_prob(noisy_data)
+
+        ### Guidance
+        if self.guide_scale is not None and self.guide_scale != 1:
+            uncon_prob_X, uncon_prob_E = get_prob(noisy_data, unconditioned=True)
+            prob_X = (
+                uncon_prob_X
+                * (prob_X / uncon_prob_X.clamp_min(1e-5)) ** self.guide_scale
+            )
+            prob_E = (
+                uncon_prob_E
+                * (prob_E / uncon_prob_E.clamp_min(1e-5)) ** self.guide_scale
+            )
+            prob_X = prob_X / prob_X.sum(dim=-1, keepdim=True).clamp_min(1e-5)
+            prob_E = prob_E / prob_E.sum(dim=-1, keepdim=True).clamp_min(1e-5)
+
+        sampled_s = sample_discrete_features(prob_X, prob_E, node_mask=node_mask)
+
+        X_s = F.one_hot(sampled_s.X, num_classes=self.input_dim_X).to(self.device).float()
+        E_s = F.one_hot(sampled_s.E, num_classes=self.input_dim_E).to(self.device).float()
+
+        assert (E_s == torch.transpose(E_s, 1, 2)).all()
+        assert (X_t.shape == X_s.shape) and (E_t.shape == E_s.shape)
+
+        out_one_hot = PlaceHolder(X=X_s, E=E_s, y=properties)
+
+        return out_one_hot.mask(node_mask)