Merge pull request #250 from Starlitnightly/main

Optimized `SCC` Implementation and Removed `TensorFlow` Dependencies

requirements.txt

@@ -1,7 +1,7 @@
 adjustText
 anndata>=0.8.0
 colorcet>=2.0.1
-cvxopt>=1.2.3
+# cvxopt>=1.2.3
 csbdeep>=0.6.3
 descartes
 dynamo-release>=1.4.1
@@ -21,9 +21,9 @@ networkx>=2.6.3
 numba>=0.46.0
 numpy>=1.18.1
 opencv-python>=4.5.4.60
-pandana
+# pandana
 pandas>=0.25.1
-paste-bio>=1.4.0
+# paste-bio>=1.4.0
 plotly>=5.1.0
 POT>=0.8.1
 psutil>=5.6.3
@@ -39,7 +39,7 @@ seaborn>=0.9.0
 setuptools>=58.0.4
 Shapely>=1.8.0
 statsmodels>=0.9.0
-tensorflow
+# tensorflow
 tqdm>=4.62.3
 torch
 trame>=2.2.5

spateo/external/CAST/CAST_Mark.py

@@ -0,0 +1,117 @@
+from collections import OrderedDict
+from timeit import default_timer as timer
+
+import matplotlib.pyplot as plt
+import networkx as nx
+import numpy as np
+import torch
+from tqdm import trange
+
+from .model.aug import random_aug
+from .utils import coords2adjacentmat
+
+
+def train_seq(graphs, args, dump_epoch_list, out_prefix, model):
+    """The CAST MARK training function
+
+    Args:
+        graphs (List[Tuple(str, dgl.Graph, torch.Tensor)]): List of 3-member tuples, each tuple represents one tissue sample, containing sample name, a DGL graph object, and a feature matrix in the torch.Tensor format
+        args (model_GCNII.Args): the Args object contains training parameters
+        dump_epoch_list (List): A list of epoch id you hope training snapshots to be dumped, for debug use, empty by default
+        out_prefix (str): file name prefix for the snapshot files
+        model (model_GCNII.CCA_SSG): the GNN model
+
+    Returns:
+        Tuple(Dict, List, CCA_SSG): returns a 3-member tuple, a dictionary containing the graph embeddings for each sample, a list of every loss value, and the trained model object
+    """
+    model = model.to(args.device)
+
+    optimizer = torch.optim.Adam(model.parameters(), lr=args.lr1, weight_decay=args.wd1)
+
+    loss_log = []
+    time_now = timer()
+
+    t = trange(args.epochs, desc="", leave=True)
+    for epoch in t:
+
+        with torch.no_grad():
+            if epoch in dump_epoch_list:
+                model.eval()
+                dump_embedding = OrderedDict()
+                for name, graph, feat in graphs:
+                    # graph = graph.to(args.device)
+                    # feat = feat.to(args.device)
+                    dump_embedding[name] = model.get_embedding(graph, feat)
+                torch.save(dump_embedding, f"{out_prefix}_embed_dict_epoch{epoch}.pt")
+                torch.save(loss_log, f"{out_prefix}_loss_log_epoch{epoch}.pt")
+                print(f"Successfully dumped epoch {epoch}")
+
+        losses = dict()
+        model.train()
+        optimizer.zero_grad()
+        # print(f'Epoch: {epoch}')
+
+        for name_, graph_, feat_ in graphs:
+            with torch.no_grad():
+                N = graph_.number_of_nodes()
+                graph1, feat1 = random_aug(graph_, feat_, args.dfr, args.der)
+                graph2, feat2 = random_aug(graph_, feat_, args.dfr, args.der)
+
+                graph1 = graph1.add_self_loop()
+                graph2 = graph2.add_self_loop()
+
+            z1, z2 = model(graph1, feat1, graph2, feat2)
+
+            c = torch.mm(z1.T, z2)
+            c1 = torch.mm(z1.T, z1)
+            c2 = torch.mm(z2.T, z2)
+
+            c = c / N
+            c1 = c1 / N
+            c2 = c2 / N
+
+            loss_inv = -torch.diagonal(c).sum()
+            iden = torch.eye(c.size(0), device=args.device)
+            loss_dec1 = (iden - c1).pow(2).sum()
+            loss_dec2 = (iden - c2).pow(2).sum()
+            loss = loss_inv + args.lambd * (loss_dec1 + loss_dec2)
+            loss.backward()
+            optimizer.step()
+
+        # del graph1, feat1, graph2, feat2
+        loss_log.append(loss.item())
+        time_step = timer() - time_now
+        time_now += time_step
+        # print(f'Loss: {loss.item()} step time={time_step:.3f}s')
+        t.set_description(f"Loss: {loss.item():.3f} step time={time_step:.3f}s")
+        t.refresh()
+
+    model.eval()
+    with torch.no_grad():
+        dump_embedding = OrderedDict()
+        for name, graph, feat in graphs:
+            dump_embedding[name] = model.get_embedding(graph, feat)
+    return dump_embedding, loss_log, model
+
+
+# graph construction tools
+def delaunay_dgl(sample_name, df, output_path, if_plot=True, strategy_t="convex"):
+    coords = np.column_stack((np.array(df)[:, 0], np.array(df)[:, 1]))
+    delaunay_graph = coords2adjacentmat(coords, output_mode="raw", strategy_t=strategy_t)
+    if if_plot:
+        positions = dict(zip(delaunay_graph.nodes, coords[delaunay_graph.nodes, :]))
+        _, ax = plt.subplots(nrows=1, ncols=1, figsize=(10, 10))
+        nx.draw(
+            delaunay_graph,
+            positions,
+            ax=ax,
+            node_size=1,
+            node_color="#000000",
+            edge_color="#5A98AF",
+            alpha=0.6,
+        )
+        plt.axis("equal")
+        plt.savefig(f"{output_path}/delaunay_{sample_name}.png")
+    import dgl
+
+    return dgl.from_networkx(delaunay_graph)