gsMap 1.71.1__py3-none-any.whl → 1.72.3__py3-none-any.whl

gsMap/GNN/adjacency_matrix.py

@@ -1,75 +1,73 @@
-import numpy as np
-import pandas as pd
-import scipy.sparse as sp
-from sklearn.neighbors import NearestNeighbors
-import torch
-
-def cal_spatial_net(adata, n_neighbors=5, verbose=True):
-    """Construct the spatial neighbor network."""
-    if verbose:
-        print('------Calculating spatial graph...')
-    coor = pd.DataFrame(adata.obsm['spatial'], index=adata.obs.index)
-    nbrs = NearestNeighbors(n_neighbors=n_neighbors).fit(coor)
-    distances, indices = nbrs.kneighbors(coor)
-    n_cells, n_neighbors = indices.shape
-    cell_indices = np.arange(n_cells)
-    cell1 = np.repeat(cell_indices, n_neighbors)
-    cell2 = indices.flatten()
-    distance = distances.flatten()
-    knn_df = pd.DataFrame({'Cell1': cell1, 'Cell2': cell2, 'Distance': distance})
-    knn_df = knn_df[knn_df['Distance'] > 0].copy()
-    cell_id_map = dict(zip(cell_indices, coor.index))
-    knn_df['Cell1'] = knn_df['Cell1'].map(cell_id_map)
-    knn_df['Cell2'] = knn_df['Cell2'].map(cell_id_map)
-    return knn_df
-
-def sparse_mx_to_torch_sparse_tensor(sparse_mx):
-    """Convert a scipy sparse matrix to a torch sparse tensor."""
-    sparse_mx = sparse_mx.tocoo().astype(np.float32)
-    indices = torch.from_numpy(
-        np.vstack((sparse_mx.row, sparse_mx.col)).astype(np.int64)
-    )
-    values = torch.from_numpy(sparse_mx.data)
-    shape = torch.Size(sparse_mx.shape)
-    return  torch.sparse_coo_tensor(indices, values, shape)
-
-def preprocess_graph(adj):
-    """Symmetrically normalize the adjacency matrix."""
-    adj = sp.coo_matrix(adj)
-    adj_ = adj + sp.eye(adj.shape[0])
-    rowsum = np.array(adj_.sum(1)).flatten()
-    degree_mat_inv_sqrt = sp.diags(np.power(rowsum, -0.5))
-    adj_normalized = adj_.dot(degree_mat_inv_sqrt).transpose().dot(degree_mat_inv_sqrt).tocoo()
-    return sparse_mx_to_torch_sparse_tensor(adj_normalized)
-
-def construct_adjacency_matrix(adata, params, verbose=True):
-    """Construct the adjacency matrix from spatial data."""
-    spatial_net = cal_spatial_net(adata, n_neighbors=params.n_neighbors, verbose=verbose)
-    if verbose:
-        num_edges = spatial_net.shape[0]
-        num_cells = adata.n_obs
-        print(f'The graph contains {num_edges} edges, {num_cells} cells.')
-        print(f'{num_edges / num_cells:.2f} neighbors per cell on average.')
-    cell_ids = {cell: idx for idx, cell in enumerate(adata.obs.index)}
-    spatial_net['Cell1'] = spatial_net['Cell1'].map(cell_ids)
-    spatial_net['Cell2'] = spatial_net['Cell2'].map(cell_ids)
-    if params.weighted_adj:
-        distance_normalized = spatial_net['Distance'] / (spatial_net['Distance'].max() + 1)
-        weights = np.exp(-0.5 * distance_normalized ** 2)
-        adj_org = sp.coo_matrix(
-            (weights, (spatial_net['Cell1'], spatial_net['Cell2'])),
-            shape=(adata.n_obs, adata.n_obs)
-        )
-    else:
-        adj_org = sp.coo_matrix(
-            (np.ones(spatial_net.shape[0]), (spatial_net['Cell1'], spatial_net['Cell2'])),
-            shape=(adata.n_obs, adata.n_obs)
-        )
-    adj_norm = preprocess_graph(adj_org)
-    norm_value = adj_org.shape[0] ** 2 / ((adj_org.shape[0] ** 2 - adj_org.sum()) * 2)
-    graph_dict = {
-        "adj_org": adj_org,
-        "adj_norm": adj_norm,
-        "norm_value": norm_value
-    }
-    return graph_dict
+import numpy as np
+import pandas as pd
+import scipy.sparse as sp
+import torch
+from sklearn.neighbors import NearestNeighbors
+
+
+def cal_spatial_net(adata, n_neighbors=5, verbose=True):
+    """Construct the spatial neighbor network."""
+    if verbose:
+        print("------Calculating spatial graph...")
+    coor = pd.DataFrame(adata.obsm["spatial"], index=adata.obs.index)
+    nbrs = NearestNeighbors(n_neighbors=n_neighbors).fit(coor)
+    distances, indices = nbrs.kneighbors(coor)
+    n_cells, n_neighbors = indices.shape
+    cell_indices = np.arange(n_cells)
+    cell1 = np.repeat(cell_indices, n_neighbors)
+    cell2 = indices.flatten()
+    distance = distances.flatten()
+    knn_df = pd.DataFrame({"Cell1": cell1, "Cell2": cell2, "Distance": distance})
+    knn_df = knn_df[knn_df["Distance"] > 0].copy()
+    cell_id_map = dict(zip(cell_indices, coor.index, strict=False))
+    knn_df["Cell1"] = knn_df["Cell1"].map(cell_id_map)
+    knn_df["Cell2"] = knn_df["Cell2"].map(cell_id_map)
+    return knn_df
+
+
+def sparse_mx_to_torch_sparse_tensor(sparse_mx):
+    """Convert a scipy sparse matrix to a torch sparse tensor."""
+    sparse_mx = sparse_mx.tocoo().astype(np.float32)
+    indices = torch.from_numpy(np.vstack((sparse_mx.row, sparse_mx.col)).astype(np.int64))
+    values = torch.from_numpy(sparse_mx.data)
+    shape = torch.Size(sparse_mx.shape)
+    return torch.sparse_coo_tensor(indices, values, shape)
+
+
+def preprocess_graph(adj):
+    """Symmetrically normalize the adjacency matrix."""
+    adj = sp.coo_matrix(adj)
+    adj_ = adj + sp.eye(adj.shape[0])
+    rowsum = np.array(adj_.sum(1)).flatten()
+    degree_mat_inv_sqrt = sp.diags(np.power(rowsum, -0.5))
+    adj_normalized = adj_.dot(degree_mat_inv_sqrt).transpose().dot(degree_mat_inv_sqrt).tocoo()
+    return sparse_mx_to_torch_sparse_tensor(adj_normalized)
+
+
+def construct_adjacency_matrix(adata, params, verbose=True):
+    """Construct the adjacency matrix from spatial data."""
+    spatial_net = cal_spatial_net(adata, n_neighbors=params.n_neighbors, verbose=verbose)
+    if verbose:
+        num_edges = spatial_net.shape[0]
+        num_cells = adata.n_obs
+        print(f"The graph contains {num_edges} edges, {num_cells} cells.")
+        print(f"{num_edges / num_cells:.2f} neighbors per cell on average.")
+    cell_ids = {cell: idx for idx, cell in enumerate(adata.obs.index)}
+    spatial_net["Cell1"] = spatial_net["Cell1"].map(cell_ids)
+    spatial_net["Cell2"] = spatial_net["Cell2"].map(cell_ids)
+    if params.weighted_adj:
+        distance_normalized = spatial_net["Distance"] / (spatial_net["Distance"].max() + 1)
+        weights = np.exp(-0.5 * distance_normalized**2)
+        adj_org = sp.coo_matrix(
+            (weights, (spatial_net["Cell1"], spatial_net["Cell2"])),
+            shape=(adata.n_obs, adata.n_obs),
+        )
+    else:
+        adj_org = sp.coo_matrix(
+            (np.ones(spatial_net.shape[0]), (spatial_net["Cell1"], spatial_net["Cell2"])),
+            shape=(adata.n_obs, adata.n_obs),
+        )
+    adj_norm = preprocess_graph(adj_org)
+    norm_value = adj_org.shape[0] ** 2 / ((adj_org.shape[0] ** 2 - adj_org.sum()) * 2)
+    graph_dict = {"adj_org": adj_org, "adj_norm": adj_norm, "norm_value": norm_value}
+    return graph_dict

gsMap/GNN/model.py

@@ -1,90 +1,92 @@
-import torch
-import torch.nn as nn
-import torch.nn.functional as F
-from torch_geometric.nn import GATConv
-
-def full_block(in_features, out_features, p_drop):
-    return nn.Sequential(
-        nn.Linear(in_features, out_features),
-        nn.BatchNorm1d(out_features),
-        nn.ELU(),
-        nn.Dropout(p=p_drop)
-    )
-
-class GATModel(nn.Module):
-    def __init__(self, input_dim, params, num_classes=1):
-        super().__init__()
-        self.var = params.var
-        self.num_classes = num_classes
-        self.params = params
-
-        # Encoder
-        self.encoder = nn.Sequential(
-            full_block(input_dim, params.feat_hidden1, params.p_drop),
-            full_block(params.feat_hidden1, params.feat_hidden2, params.p_drop)
-        )
-
-        # GAT Layers
-        self.gat1 = GATConv(
-            in_channels=params.feat_hidden2,
-            out_channels=params.gat_hidden1,
-            heads=params.nheads,
-            dropout=params.p_drop
-        )
-        self.gat2 = GATConv(
-            in_channels=params.gat_hidden1 * params.nheads,
-            out_channels=params.gat_hidden2,
-            heads=1,
-            concat=False,
-            dropout=params.p_drop
-        )
-        if self.var:
-            self.gat3 = GATConv(
-                in_channels=params.gat_hidden1 * params.nheads,
-                out_channels=params.gat_hidden2,
-                heads=1,
-                concat=False,
-                dropout=params.p_drop
-            )
-
-        # Decoder
-        self.decoder = nn.Sequential(
-            full_block(params.gat_hidden2, params.feat_hidden2, params.p_drop),
-            full_block(params.feat_hidden2, params.feat_hidden1, params.p_drop),
-            nn.Linear(params.feat_hidden1, input_dim)
-        )
-
-        # Clustering Layer
-        self.cluster = nn.Sequential(
-            full_block(params.gat_hidden2, params.feat_hidden2, params.p_drop),
-            nn.Linear(params.feat_hidden2, self.num_classes)
-        )
-
-    def encode(self, x, edge_index):
-        x = self.encoder(x)
-        x = self.gat1(x, edge_index)
-        x = F.relu(x)
-        x = F.dropout(x, p=self.params.p_drop, training=self.training)
-
-        mu = self.gat2(x, edge_index)
-        if self.var:
-            logvar = self.gat3(x, edge_index)
-            return mu, logvar
-        else:
-            return mu, None
-
-    def reparameterize(self, mu, logvar):
-        if self.training and logvar is not None:
-            std = torch.exp(0.5 * logvar)
-            eps = torch.randn_like(std)
-            return eps * std + mu
-        else:
-            return mu
-
-    def forward(self, x, edge_index):
-        mu, logvar = self.encode(x, edge_index)
-        z = self.reparameterize(mu, logvar)
-        x_reconstructed = self.decoder(z)
-        # pred_label = F.softmax(self.cluster(z), dim=1)
-        pred_label = self.cluster(z)
-        return pred_label, x_reconstructed, z, mu, logvar
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+from torch_geometric.nn import GATConv
+
+
+def full_block(in_features, out_features, p_drop):
+    return nn.Sequential(
+        nn.Linear(in_features, out_features),
+        nn.BatchNorm1d(out_features),
+        nn.ELU(),
+        nn.Dropout(p=p_drop),
+    )
+
+
+class GATModel(nn.Module):
+    def __init__(self, input_dim, params, num_classes=1):
+        super().__init__()
+        self.var = params.var
+        self.num_classes = num_classes
+        self.params = params
+
+        # Encoder
+        self.encoder = nn.Sequential(
+            full_block(input_dim, params.feat_hidden1, params.p_drop),
+            full_block(params.feat_hidden1, params.feat_hidden2, params.p_drop),
+        )
+
+        # GAT Layers
+        self.gat1 = GATConv(
+            in_channels=params.feat_hidden2,
+            out_channels=params.gat_hidden1,
+            heads=params.nheads,
+            dropout=params.p_drop,
+        )
+        self.gat2 = GATConv(
+            in_channels=params.gat_hidden1 * params.nheads,
+            out_channels=params.gat_hidden2,
+            heads=1,
+            concat=False,
+            dropout=params.p_drop,
+        )
+        if self.var:
+            self.gat3 = GATConv(
+                in_channels=params.gat_hidden1 * params.nheads,
+                out_channels=params.gat_hidden2,
+                heads=1,
+                concat=False,
+                dropout=params.p_drop,
+            )
+
+        # Decoder
+        self.decoder = nn.Sequential(
+            full_block(params.gat_hidden2, params.feat_hidden2, params.p_drop),
+            full_block(params.feat_hidden2, params.feat_hidden1, params.p_drop),
+            nn.Linear(params.feat_hidden1, input_dim),
+        )
+
+        # Clustering Layer
+        self.cluster = nn.Sequential(
+            full_block(params.gat_hidden2, params.feat_hidden2, params.p_drop),
+            nn.Linear(params.feat_hidden2, self.num_classes),
+        )
+
+    def encode(self, x, edge_index):
+        x = self.encoder(x)
+        x = self.gat1(x, edge_index)
+        x = F.relu(x)
+        x = F.dropout(x, p=self.params.p_drop, training=self.training)
+
+        mu = self.gat2(x, edge_index)
+        if self.var:
+            logvar = self.gat3(x, edge_index)
+            return mu, logvar
+        else:
+            return mu, None
+
+    def reparameterize(self, mu, logvar):
+        if self.training and logvar is not None:
+            std = torch.exp(0.5 * logvar)
+            eps = torch.randn_like(std)
+            return eps * std + mu
+        else:
+            return mu
+
+    def forward(self, x, edge_index):
+        mu, logvar = self.encode(x, edge_index)
+        z = self.reparameterize(mu, logvar)
+        x_reconstructed = self.decoder(z)
+        # pred_label = F.softmax(self.cluster(z), dim=1)
+        pred_label = self.cluster(z)
+        return pred_label, x_reconstructed, z, mu, logvar

gsMap/GNN/train.py

@@ -23,7 +23,7 @@ def label_loss(pred_label, true_label):
 class ModelTrainer:
     def __init__(self, node_x, graph_dict, params, label=None):
         """Initialize the ModelTrainer with data and hyperparameters."""
-        self.device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
+        self.device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
         self.params = params
         self.epochs = params.epochs
         self.node_x = torch.FloatTensor(node_x).to(self.device)
@@ -38,17 +38,15 @@ class ModelTrainer:
         # Set up the model
         self.model = GATModel(self.params.feat_cell, self.params, self.num_classes).to(self.device)
         self.optimizer = torch.optim.Adam(
-            self.model.parameters(),
-            lr=self.params.gat_lr,
-            weight_decay=self.params.gcn_decay
+            self.model.parameters(), lr=self.params.gat_lr, weight_decay=self.params.gcn_decay
         )
 
     def run_train(self):
         """Train the model."""
         self.model.train()
-        prev_loss = float('inf')
-        logger.info('Start training...')
-        pbar = tqdm(range(self.epochs), desc='GAT-AE model train:', total=self.epochs)
+        prev_loss = float("inf")
+        logger.info("Start training...")
+        pbar = tqdm(range(self.epochs), desc="GAT-AE model train:", total=self.epochs)
         for epoch in range(self.epochs):
             start_time = time.time()
             self.optimizer.zero_grad()
@@ -67,18 +65,17 @@ class ModelTrainer:
             batch_time = time.time() - start_time
             left_time = batch_time * (self.epochs - epoch - 1) / 60  # in minutes
 
-            pbar.set_postfix({'Left time': f'{left_time:.2f} mins', 'Loss': f'{loss.item():.4f}'})
+            pbar.set_postfix({"Left time": f"{left_time:.2f} mins", "Loss": f"{loss.item():.4f}"})
             pbar.update(1)
 
             if abs(loss.item() - prev_loss) <= self.params.convergence_threshold and epoch >= 200:
                 pbar.close()
-                logger.info('Convergence reached. Training stopped.')
+                logger.info("Convergence reached. Training stopped.")
                 break
             prev_loss = loss.item()
         else:
             pbar.close()
-            logger.info('Max epochs reached. Training stopped.')
-
+            logger.info("Max epochs reached. Training stopped.")
 
     def get_latent(self):
         """Retrieve the latent representation from the model."""

gsMap/__init__.py

@@ -1,5 +1,5 @@
-'''
-Genetics-informed pathogenic spatial mapping
-'''
-
-__version__ = '1.71.1'
+"""
+Genetics-informed pathogenic spatial mapping
+"""
+
+__version__ = "1.72.3"

gsMap/__main__.py

@@ -1,3 +1,4 @@
-from .main import main
-if __name__ == '__main__':
-    main()
+from .main import main
+
+if __name__ == "__main__":
+    main()