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

torch_molecule/encoder/infograph/modeling_infograph.py

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+import numpy as np
+from tqdm import tqdm
+from typing import Optional, Union, Dict, Any, Tuple, List, Literal, Type
+
+from dataclasses import dataclass, field
+
+import torch
+from torch_geometric.loader import DataLoader
+from torch_geometric.data import Data
+
+from .model import GNN
+from ..constant import GNN_ENCODER_MODELS, GNN_ENCODER_READOUTS, GNN_ENCODER_PARAMS
+from ...base import BaseMolecularEncoder
+from ...utils import graph_from_smiles
+
+ALLOWABLE_ENCODER_MODELS = GNN_ENCODER_MODELS
+ALLOWABLE_ENCODER_READOUTS = GNN_ENCODER_READOUTS
+
+@dataclass
+class InfoGraphMolecularEncoder(BaseMolecularEncoder):
+    """This encoder implements a InfoGraph for molecular representation learning.
+
+    InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization (ICLR 2020)
+
+    References
+    ----------
+    - Paper: https://arxiv.org/abs/1908.01000 
+    - Code: https://github.com/sunfanyunn/InfoGraph/tree/master/unsupervised
+
+    Parameters
+    ----------
+    lw_prior : float, default=0.
+        Weight for prior loss term.
+    embedding_dim : int, default=160
+        Dimension of final graph embedding. Must be divisible by num_layer.
+    num_layer : int, default=5
+        Number of GNN layers.
+    drop_ratio : float, default=0.5
+        Dropout probability.
+    norm_layer : str, default="batch_norm"
+        Type of normalization layer to use. One of ["batch_norm", "layer_norm", "instance_norm", "graph_norm", "size_norm", "pair_norm"].
+    encoder_type : str, default="gin-virtual"
+        Type of GNN architecture to use. One of ["gin-virtual", "gcn-virtual", "gin", "gcn"].
+    readout : str, default="sum"
+        Method for aggregating node features to obtain graph-level representations. One of ["sum", "mean", "max"].
+    batch_size : int, default=128
+        Number of samples per batch for training.
+    epochs : int, default=500
+        Maximum number of training epochs.
+    learning_rate : float, default=0.001
+        Learning rate for optimizer.
+    grad_clip_value : float, optional
+        Maximum norm of gradients for gradient clipping.
+    weight_decay : float, default=0.0
+        L2 regularization strength.
+    use_lr_scheduler : bool, default=False
+        Whether to use a learning rate scheduler.
+    scheduler_factor : float, default=0.5
+        Factor by which to reduce the learning rate when plateau is detected.
+    scheduler_patience : int, default=5
+        Number of epochs with no improvement after which learning rate will be reduced.
+    verbose : bool, default=False
+        Whether to print progress information during training.
+    model_name : str, default="InfographMolecularEncoder"
+        Name of the encoder model.
+    """
+    # Task related parameters
+    lw_prior : float = 0.
+    embedding_dim: int = 160
+
+    # Model parameters
+    num_layer: int = 5
+    drop_ratio: float = 0.5
+    norm_layer: str = "batch_norm"
+    encoder_type: str = "gin-virtual"
+    readout: str = "sum"
+    
+    # Training parameters
+    batch_size: int = 128
+    epochs: int = 500
+    learning_rate: float = 0.001
+    grad_clip_value: Optional[float] = None
+    weight_decay: float = 0.0
+    
+    # Scheduler parameters
+    use_lr_scheduler: bool = False
+    scheduler_factor: float = 0.5
+    scheduler_patience: int = 5
+    
+    # Other parameters
+    verbose: bool = False
+    model_name: str = "InfographMolecularEncoder"
+    
+    # Non-init fields
+    fitting_loss: List[float] = field(default_factory=list, init=False)
+    fitting_epoch: int = field(default=0, init=False)
+    model_class: Type[GNN] = field(default=GNN, init=False)
+    
+    def __post_init__(self):
+        """Initialize the model after dataclass initialization."""
+        super().__post_init__()
+        if self.encoder_type not in ALLOWABLE_ENCODER_MODELS:
+            raise ValueError(f"Invalid encoder_model: {self.encoder_type}. Currently only {ALLOWABLE_ENCODER_MODELS} are supported.")
+        if self.readout not in ALLOWABLE_ENCODER_READOUTS:
+            raise ValueError(f"Invalid encoder_readout: {self.readout}. Currently only {ALLOWABLE_ENCODER_READOUTS} are supported.")
+
+        if self.lw_prior == 0:
+            self.use_prior = False
+        else:
+            self.use_prior = True
+        
+        assert self.embedding_dim % self.num_layer == 0, "embedding_dim must be divisible by num_layer for InfographMolecularEncoder"
+
+    @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.
+        """
+        params = GNN_ENCODER_PARAMS.copy()
+        params.remove("hidden_size")
+        params = params + ["embedding_dim", 'use_prior', 'lw_prior']
+        return params
+    
+
+    def _get_model_params(self, checkpoint: Optional[Dict] = None) -> Dict[str, Any]:
+        params = [
+            "num_layer", "embedding_dim", "drop_ratio", "norm_layer", "encoder_type", "readout", "use_prior",
+        ]        
+        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):
+        """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:
+            graph = graph_from_smiles(smiles_or_mol, None)
+            g = Data()
+            g.num_nodes = graph["num_nodes"]
+            g.edge_index = torch.from_numpy(graph["edge_index"])
+
+            del graph["num_nodes"]
+            del graph["edge_index"]
+
+            if graph["edge_feat"] is not None:
+                g.edge_attr = torch.from_numpy(graph["edge_feat"])
+                del graph["edge_feat"]
+
+            if graph["node_feat"] is not None:
+                g.x = torch.from_numpy(graph["node_feat"])
+                del graph["node_feat"]
+
+            pyg_graph_list.append(g)
+
+        return pyg_graph_list
+    
+    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],
+    ) -> "InfographMolecularEncoder":
+        """Fit the model to the training data with optional validation set.
+
+        Parameters
+        ----------
+        X_train : List[str]
+            Training set input molecular structures as SMILES strings
+        Returns
+        -------
+        self : InfographMolecularEncoder
+            Fitted estimator
+        """
+        
+        self._initialize_model(self.model_class)
+        self.model.initialize_parameters()
+        optimizer, scheduler = self._setup_optimizers()
+        
+        # Prepare datasets and loaders
+        X_train, _ = self._validate_inputs(X_train, return_rdkit_mol=True)
+        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 = []
+
+        for epoch in range(self.epochs):
+            # Training phase
+            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):
+        """Training logic for one epoch.
+
+        Args:
+            train_loader: DataLoader containing training data
+            optimizer: Optimizer instance for model parameter updates
+
+        Returns:
+            list: List of loss values for each training step
+        """
+        self.model.train()
+        losses = []
+
+        iterator = (
+            tqdm(train_loader, desc="Training", leave=False)
+            if self.verbose
+            else train_loader
+        )
+
+        for batch in iterator:
+            batch = batch.to(self.device)
+            optimizer.zero_grad()
+            local_global_loss, prior_loss = self.model.compute_loss(batch, self.lw_prior)
+            loss = local_global_loss + prior_loss
+            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": f"{epoch}", "Loss": f"{loss.item():.4f}", "Local/Global": f"{local_global_loss.item():.4f}", "Prior": f"{prior_loss.item():.4f}"})
+
+        return losses
+
+    def encode(self, X: List[str], return_type: Literal["np", "pt"] = "pt") -> Union[np.ndarray, torch.Tensor]:
+        """Encode molecules into vector representations.
+
+        Parameters
+        ----------
+        X : List[str]
+            List of SMILES strings
+        return_type : Literal["np", "pt"], default="pt"
+            Return type of the representations
+
+        Returns
+        -------
+        representations : ndarray or torch.Tensor
+            Molecular representations
+        """
+        self._check_is_fitted()
+
+        # Convert to PyTorch Geometric format and create loader
+        X, _ = self._validate_inputs(X, return_rdkit_mol=True)
+        dataset = self._convert_to_pytorch_data(X)
+        loader = DataLoader(dataset, batch_size=self.batch_size, shuffle=False)
+
+        if self.model is None:
+            raise RuntimeError("Model not initialized")
+
+        # Generate encodings
+        self.model = self.model.to(self.device)
+        self.model.eval()
+        encodings = []
+        with torch.no_grad():
+            for batch in tqdm(loader, disable=not self.verbose):
+                batch = batch.to(self.device)
+                out = self.model(batch)
+                encodings.append(out["graph"].cpu())
+
+        # Concatenate and convert to requested format
+        encodings = torch.cat(encodings, dim=0)
+        return encodings if return_type == "pt" else encodings.numpy()

torch_molecule/encoder/infograph/module.py

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+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+
+class PriorDiscriminator(nn.Module):
+    def __init__(self, input_dim):
+        super().__init__()
+        self.l0 = nn.Linear(input_dim, input_dim)
+        self.l1 = nn.Linear(input_dim, input_dim)
+        self.l2 = nn.Linear(input_dim, 1)
+
+    def forward(self, x):
+        h = F.relu(self.l0(x))
+        h = F.relu(self.l1(h))
+        return torch.sigmoid(self.l2(h))
+
+class FF(nn.Module):
+    def __init__(self, input_dim):
+        super().__init__()
+        self.block = nn.Sequential(
+            nn.Linear(input_dim, input_dim),
+            nn.ReLU(),
+            nn.Linear(input_dim, input_dim),
+            nn.ReLU(),
+            nn.Linear(input_dim, input_dim),
+            nn.ReLU()
+        )
+        self.linear_shortcut = nn.Linear(input_dim, input_dim)
+
+    def forward(self, x):
+        return self.block(x) + self.linear_shortcut(x)

torch_molecule/encoder/moama/__init__.py

@@ -0,0 +1,3 @@
+from .modeling_moama import MoamaMolecularEncoder
+
+__all__ = ['MoamaMolecularEncoder']

torch_molecule/encoder/moama/model.py

@@ -0,0 +1,131 @@
+import torch
+import torch.nn as nn
+from torch_geometric.nn import global_add_pool, global_mean_pool, global_max_pool
+
+from ...nn import GNN_node, GNN_node_Virtualnode, GCNConv, GINConv
+from ...utils import init_weights
+
+from .utils import get_mask_indices, get_fingerprint_loss
+
+class_criterion = torch.nn.CrossEntropyLoss()
+
+class GNN(nn.Module):
+    def __init__(
+        self,
+        num_layer,
+        hidden_size,
+        drop_ratio=0.5,
+        norm_layer="batch_norm",
+        encoder_type="gin-virtual",
+        readout="max",
+        mask_rate=0.15,
+        lw_rec=0.5
+    ):
+        super(GNN, self).__init__()
+        gnn_name = encoder_type.split("-")[0]
+        self.num_atom_type = 119
+        self.hidden_size = hidden_size
+        self.mask_rate = mask_rate
+        self.lw_rec = lw_rec
+
+        encoder_params = {
+            "num_layer": num_layer,
+            "hidden_size": hidden_size,
+            "JK": "last", 
+            "drop_ratio": drop_ratio,
+            "residual": True,
+            "gnn_name": gnn_name,
+            "norm_layer": norm_layer
+        }
+        
+        # Choose encoder type based on encoder_model
+        encoder_class = GNN_node_Virtualnode if "virtual" in encoder_type else GNN_node
+        self.graph_encoder = encoder_class(**encoder_params)
+        pooling_funcs = {
+            "sum": global_add_pool,
+            "mean": global_mean_pool,
+            "max": global_max_pool
+        }
+        self.pool = pooling_funcs.get(readout)
+        if self.pool is None:
+            raise ValueError(f"Invalid graph pooling type {readout}.")
+
+        self.predictor = GNN_Decoder(hidden_size, self.num_atom_type)
+    
+    def initialize_parameters(self, seed=None):
+        """
+        Randomly initialize all model parameters using the init_weights function.
+        
+        Args:
+            seed (int, optional): Random seed for reproducibility. Defaults to None.
+        """
+        if seed is not None:
+            torch.manual_seed(seed)
+        
+        # Initialize the main components
+        init_weights(self.graph_encoder)
+        init_weights(self.predictor)
+        
+        # Reset all parameters using PyTorch Geometric's reset function
+        def reset_parameters(module):
+            if hasattr(module, 'reset_parameters'):
+                module.reset_parameters()
+            elif hasattr(module, 'weight') and hasattr(module.weight, 'data'):
+                init_weights(module)
+        
+        self.apply(reset_parameters)
+
+    def compute_loss(self, batched_data):
+        masked_node_indices = get_mask_indices(batched_data, self.mask_rate)
+        batched_data.masked_node_indices = torch.tensor(masked_node_indices)
+        batched_data.y = batched_data.x[masked_node_indices][:, 0]
+
+        # mask nodes' features
+        for node_idx in masked_node_indices:
+            batched_data.x[node_idx] = torch.tensor([self.num_atom_type - 1] + [0] * (batched_data.x.shape[1] - 1))
+    
+        # generate predictions
+        h_node, _ = self.graph_encoder(batched_data)
+        h_rep = self.pool(h_node, batched_data.batch)
+        batched_data.x = h_node
+        prediction_class = self.predictor(batched_data)[masked_node_indices]
+        
+        # target_class = batched_data.y.to(torch.float32)
+        loss_class = class_criterion(prediction_class.to(torch.float32), batched_data.y.long())
+        
+        fingerprint_loss = get_fingerprint_loss(batched_data.smiles, h_rep)
+                
+        loss = self.lw_rec * loss_class + (1 - self.lw_rec) * fingerprint_loss
+
+        return loss
+
+    def forward(self, batched_data):
+        h_node, _ = self.graph_encoder(batched_data)
+        h_rep = self.pool(h_node, batched_data.batch)
+        return {"graph": h_rep, "node": h_node}
+    
+class GNN_Decoder(torch.nn.Module):
+    def __init__(self, hidden_size, out_dim, JK = "last", gnn_name = "gin"):
+        super().__init__()
+        if gnn_name == 'gin':
+            self.conv = GINConv(hidden_size)
+        elif gnn_name == 'gcn':
+            self.conv = GCNConv(hidden_size)
+        else:
+            raise ValueError('Undefined GNN type called {}'.format(gnn_name))
+        self.dec_token = torch.nn.Parameter(torch.zeros([1, hidden_size]))
+        self.enc_to_dec = torch.nn.Linear(hidden_size, hidden_size, bias=False)    
+        self.activation = torch.nn.PReLU()
+        self.out = torch.nn.Linear(hidden_size, out_dim) 
+
+    def forward(self, batched_data):
+        x, edge_index, edge_attr, batch = batched_data.x, batched_data.edge_index, batched_data.edge_attr, batched_data.batch
+        masked_node_indices = batched_data.masked_node_indices
+
+        x = self.activation(x)
+        x = self.enc_to_dec(x)
+        x[masked_node_indices] = self.dec_token.detach().expand(len(masked_node_indices), -1)
+
+        x = self.conv(x, edge_index, edge_attr)
+        out = self.out(x)
+        return out