compute_f1_score

examples/train_gcn.py

@@ -5,7 +5,7 @@ from torch_geometric.nn.conv.gcn_conv import gcn_norm
 
 from torch_geometric_autoscale.models import GCN
 from torch_geometric_autoscale import metis, permute, SubgraphLoader
-from torch_geometric_autoscale import get_data, compute_acc
+from torch_geometric_autoscale import get_data, compute_micro_f1
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--root', type=str, required=True,
@@ -67,9 +67,9 @@ def test(model, data):
 
     # Full-batch inference since the graph is small
     out = model(data.x.to(model.device), data.adj_t.to(model.device)).cpu()
-    train_acc = compute_acc(out, data.y, data.train_mask)
-    val_acc = compute_acc(out, data.y, data.val_mask)
-    test_acc = compute_acc(out, data.y, data.test_mask)
+    train_acc = compute_micro_f1(out, data.y, data.train_mask)
+    val_acc = compute_micro_f1(out, data.y, data.val_mask)
+    test_acc = compute_micro_f1(out, data.y, data.test_mask)
 
     return train_acc, val_acc, test_acc
 

examples/train_gcn2.py

@@ -5,7 +5,7 @@ from torch_geometric.nn.conv.gcn_conv import gcn_norm
 
 from torch_geometric_autoscale.models import GCN2
 from torch_geometric_autoscale import metis, permute, SubgraphLoader
-from torch_geometric_autoscale import get_data, compute_acc
+from torch_geometric_autoscale import get_data, compute_micro_f1
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--root', type=str, required=True,
@@ -69,9 +69,9 @@ def test(model, data):
 
     # Full-batch inference since the graph is small
     out = model(data.x.to(model.device), data.adj_t.to(model.device)).cpu()
-    train_acc = compute_acc(out, data.y, data.train_mask)
-    val_acc = compute_acc(out, data.y, data.val_mask)
-    test_acc = compute_acc(out, data.y, data.test_mask)
+    train_acc = compute_micro_f1(out, data.y, data.train_mask)
+    val_acc = compute_micro_f1(out, data.y, data.val_mask)
+    test_acc = compute_micro_f1(out, data.y, data.test_mask)
 
     return train_acc, val_acc, test_acc
 

large_benchmark/main.py

@@ -7,7 +7,7 @@ from torch_geometric.nn.conv.gcn_conv import gcn_norm
 
 from torch_geometric_autoscale import (get_data, metis, permute,
                                        SubgraphLoader, EvalSubgraphLoader,
-                                       models, compute_acc)
+                                       models, compute_micro_f1)
 from torch_geometric_autoscale.data import get_ppi
 
 torch.manual_seed(123)
@@ -144,16 +144,16 @@ def main(conf):
         loss = mini_train(model, train_loader, criterion, optimizer,
                           params.max_steps, grad_norm)
         out = mini_test(model, eval_loader)
-        train_acc = compute_acc(out, data.y, data.train_mask)
+        train_acc = compute_micro_f1(out, data.y, data.train_mask)
 
         if conf.dataset.name != 'ppi':
-            val_acc = compute_acc(out, data.y, data.val_mask)
-            tmp_test_acc = compute_acc(out, data.y, data.test_mask)
+            val_acc = compute_micro_f1(out, data.y, data.val_mask)
+            tmp_test_acc = compute_micro_f1(out, data.y, data.test_mask)
         else:
             # We need to perform inference on a different graph as PPI is an
             # inductive dataset.
-            val_acc = compute_acc(full_test(model, val_data), val_data.y)
-            tmp_test_acc = compute_acc(full_test(model, test_data),
+            val_acc = compute_micro_f1(full_test(model, val_data), val_data.y)
+            tmp_test_acc = compute_micro_f1(full_test(model, test_data),
                                             test_data.y)
 
         if val_acc > best_val_acc:

small_benchmark/main.py

@@ -5,8 +5,8 @@ from omegaconf import OmegaConf
 import torch
 from torch_geometric.nn.conv.gcn_conv import gcn_norm
 
-from torch_geometric_autoscale import (get_data, metis, permute,
-                                       SubgraphLoader, models, compute_acc)
+from torch_geometric_autoscale import (get_data, metis, permute, models,
+                                       SubgraphLoader, compute_micro_f1)
 
 torch.manual_seed(123)
 criterion = torch.nn.CrossEntropyLoss()
@@ -50,8 +50,8 @@ def test(run, model, data):
     test_mask = test_mask[:, run] if test_mask.dim() == 2 else test_mask
 
     out = model(data.x, data.adj_t)
-    val_acc = compute_acc(out, data.y, val_mask)
-    test_acc = compute_acc(out, data.y, test_mask)
+    val_acc = compute_micro_f1(out, data.y, val_mask)
+    test_acc = compute_micro_f1(out, data.y, test_mask)
 
     return val_acc, test_acc
 

torch_geometric_autoscale/__init__.py

@@ -13,7 +13,7 @@ from .data import get_data  # noqa
 from .history import History  # noqa
 from .pool import AsyncIOPool  # noqa
 from .metis import metis, permute  # noqa
-from .utils import compute_acc  # noqa
+from .utils import compute_micro_f1  # noqa
 from .loader import SubgraphLoader, EvalSubgraphLoader  # noqa
 
 __all__ = [
@@ -22,7 +22,7 @@ __all__ = [
     'AsyncIOPool',
     'metis',
     'permute',
-    'compute_acc',
+    'compute_micro_f1',
     'SubgraphLoader',
     'EvalSubgraphLoader',
     '__version__',

torch_geometric_autoscale/utils.py

@@ -10,7 +10,7 @@ def index2mask(idx: Tensor, size: int) -> Tensor:
     return mask
 
 
-def compute_acc(logits: Tensor, y: Tensor,
+def compute_micro_f1(logits: Tensor, y: Tensor,
                      mask: Optional[Tensor] = None) -> float:
     if mask is not None:
         logits, y = logits[mask], y[mask]
@@ -24,9 +24,12 @@ def compute_acc(logits: Tensor, y: Tensor,
         tp = int((y_true & y_pred).sum())
         fp = int((~y_true & y_pred).sum())
         fn = int((y_true & ~y_pred).sum())
-        precision = tp / (tp + fp)
-        recall = tp / (tp + fn)
+        precision = tp / (tp + fp) if (tp + fp) > 0 else 0.
+        recall = tp / (tp + fn) if (tp + fn) > 0 else 0.
+        if precision + recall > 0:
             return 2 * (precision * recall) / (precision + recall)
+        else:
+            return 0.
 
 
 def gen_masks(y: Tensor, train_per_class: int = 20, val_per_class: int = 30,