Updateing benchmarks

FreyrS · Mar 9, 2021 · ac480ec · ac480ec
1 parent df1f018
commit ac480ec
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Showing 6 changed files with 24 additions and 25 deletions.
diff --git a/benchmark_models.py b/benchmark_models.py
@@ -191,7 +191,6 @@ def __init__(self, args, in_channels, out_channels):
         self.radius = args.radius
         self.k = 10000  # We don't restrict the number of points in a patch
         self.n_layers = args.n_layers
-        self.point_matching = args.point_matching
 
         # self.sa1_module = SAModule(1.0, self.radius, MLP([self.I+3, self.O, self.O]),self.k)
         self.layers = nn.ModuleList(
@@ -207,13 +206,13 @@ def __init__(self, args, in_channels, out_channels):
                 nn.Sequential(
                     nn.Linear(self.O, self.O), nn.ReLU(), nn.Linear(self.O, self.O)
                 )
-                for i in range(n_layers)
+                for i in range(self.n_layers)
             ]
         )
 
         self.linear_transform = nn.ModuleList(
             [nn.Linear(self.I, self.O)]
-            + [nn.Linear(self.O, self.O) for i in range(n_layers - 1)]
+            + [nn.Linear(self.O, self.O) for i in range(self.n_layers - 1)]
         )
 
     def forward(self, positions, features, batch_indices):

diff --git a/benchmark_scripts/DGCNN_site.sh b/benchmark_scripts/DGCNN_site.sh
@@ -1,6 +1,6 @@
 # Load environment
-python -u main_training.py --experiment_name DGCNN_site_1layer_k200 --batch_size 64 --embedding_layer DGCNN --site True --single_protein True --device cuda:0 --n_layers 1 --random_rotation True --k 200
-python -u main_training.py --experiment_name DGCNN_site_1layer_k100 --batch_size 64 --embedding_layer DGCNN --site True --single_protein True --device cuda:0 --n_layers 1 --random_rotation True --k 100
+python -W ignore -u main_training.py --experiment_name DGCNN_site_1layer_k200 --batch_size 64 --embedding_layer DGCNN --site True --single_protein True --device cuda:0 --n_layers 1 --random_rotation True --k 200
+python -W ignore -u main_training.py --experiment_name DGCNN_site_1layer_k100 --batch_size 64 --embedding_layer DGCNN --site True --single_protein True --device cuda:0 --n_layers 1 --random_rotation True --k 100
 
-python -u main_training.py --experiment_name DGCNN_site_3layer_k200 --batch_size 64 --embedding_layer DGCNN --site True --single_protein True --device cuda:0 --n_layers 3 --random_rotation True --k 200
-python -u main_training.py --experiment_name DGCNN_site_3layer_k100 --batch_size 64 --embedding_layer DGCNN --site True --single_protein True --device cuda:0 --n_layers 3 --random_rotation True --k 100
+python -W ignore -u main_training.py --experiment_name DGCNN_site_3layer_k200 --batch_size 64 --embedding_layer DGCNN --site True --single_protein True --device cuda:0 --n_layers 3 --random_rotation True --k 200
+python -W ignore -u main_training.py --experiment_name DGCNN_site_3layer_k100 --batch_size 64 --embedding_layer DGCNN --site True --single_protein True --device cuda:0 --n_layers 3 --random_rotation True --k 100
diff --git a/benchmark_scripts/Pointnet_site.sh b/benchmark_scripts/Pointnet_site.sh
@@ -1,8 +1,8 @@
 # Load environment
-python -u main_training.py --experiment_name PointNet_site_3layer_15A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 15.0 --n_layers 3
-python -u main_training.py --experiment_name PointNet_site_3layer_5A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 5.0 --n_layers 3
-python -u main_training.py --experiment_name PointNet_site_3layer_9A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 9.0 --n_layers 3
+python -W ignore -u main_training.py --experiment_name PointNet_site_3layer_15A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 15.0 --n_layers 3
+python -W ignore -u main_training.py --experiment_name PointNet_site_3layer_5A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 5.0 --n_layers 3
+python -W ignore -u main_training.py --experiment_name PointNet_site_3layer_9A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 9.0 --n_layers 3
 
-python -u main_training.py --experiment_name PointNet_site_1layer_15A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 15.0 --n_layers 1
-python -u main_training.py --experiment_name PointNet_site_1layer_5A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 5.0 --n_layers 1
-python -u main_training.py --experiment_name PointNet_site_1layer_9A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 9.0 --n_layers 1
+python -W ignore -u main_training.py --experiment_name PointNet_site_1layer_15A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 15.0 --n_layers 1
+python -W ignore -u main_training.py --experiment_name PointNet_site_1layer_5A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 5.0 --n_layers 1
+python -W ignore -u main_training.py --experiment_name PointNet_site_1layer_9A --batch_size 64 --embedding_layer PointNet++ --site True --single_protein True --device cuda:0 --random_rotation True --radius 9.0 --n_layers 1
diff --git a/benchmark_scripts/dMaSIF_search.sh b/benchmark_scripts/dMaSIF_search.sh
@@ -1,3 +1,3 @@
 # Load environment
-python -u main_training.py --experiment_name dMaSIF_site_1layer_12A --batch_size 64 --embedding_layer dMaSIF --search True --device cuda:0 --random_rotation True --radius 12.0 --n_layers 1
-python -u main_training.py --experiment_name dMaSIF_site_3layer_12A --batch_size 64 --embedding_layer dMaSIF --search True --device cuda:0 --random_rotation True --radius 12.0 --n_layers 3
+python -W ignore -u main_training.py --experiment_name dMaSIF_site_1layer_12A --batch_size 64 --embedding_layer dMaSIF --search True --device cuda:0 --random_rotation True --radius 12.0 --n_layers 1
+python -W ignore -u main_training.py --experiment_name dMaSIF_site_3layer_12A --batch_size 64 --embedding_layer dMaSIF --search True --device cuda:0 --random_rotation True --radius 12.0 --n_layers 3
diff --git a/benchmark_scripts/dMaSIF_site.sh b/benchmark_scripts/dMaSIF_site.sh
@@ -1,8 +1,8 @@
 # Load environment
-python -u main_training.py --experiment_name dMaSIF_site_1layer_15A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 15.0 --n_layers 1
-python -u main_training.py --experiment_name dMaSIF_site_1layer_5A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 5.0 --n_layers 1
-python -u main_training.py --experiment_name dMaSIF_site_1layer_9A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 9.0 --n_layers 1
+python -W ignore -u main_training.py --experiment_name dMaSIF_site_1layer_15A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 15.0 --n_layers 1
+python -W ignore -u main_training.py --experiment_name dMaSIF_site_1layer_5A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 5.0 --n_layers 1
+python -W ignore -u main_training.py --experiment_name dMaSIF_site_1layer_9A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 9.0 --n_layers 1
 
-python -u main_training.py --experiment_name dMaSIF_site_3layer_15A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 15.0 --n_layers 3
-python -u main_training.py --experiment_name dMaSIF_site_3layer_5A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 5.0 --n_layers 3
-python -u main_training.py --experiment_name dMaSIF_site_3layer_9A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 9.0 --n_layers 3
+python -W ignore -u main_training.py --experiment_name dMaSIF_site_3layer_15A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 15.0 --n_layers 3
+python -W ignore -u main_training.py --experiment_name dMaSIF_site_3layer_5A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 5.0 --n_layers 3
+python -W ignore -u main_training.py --experiment_name dMaSIF_site_3layer_9A --batch_size 64 --embedding_layer dMaSIF --site True --single_protein True --device cuda:0 --random_rotation True --radius 9.0 --n_layers 3
diff --git a/model.py b/model.py
@@ -218,9 +218,9 @@ def __init__(self, args):
                 )
 
         elif args.embedding_layer == "DGCNN":
-            self.conv = DGCNN(I + 3, E)
+            self.conv = DGCNN_seg(I + 3, E,self.args.n_layers,self.args.k)
             if args.search:
-                self.conv2 = DGCNN(I + 3, E)
+                self.conv2 = DGCNN_seg(I + 3, E,self.args.n_layers,self.args.k)
 
         elif args.embedding_layer == "PointNet++":
             self.conv = PointNet2_seg(args, I, E)
@@ -306,10 +306,10 @@ def embed(self, P):
         # First baseline:
         elif self.args.embedding_layer == "DGCNN":
             features = torch.cat([features, P["xyz"]], dim=-1).contiguous()
-            P["embedding_1"] = self.conv(features, features, P["batch"], P["batch"])
+            P["embedding_1"] = self.conv(P["xyz"], features, P["batch"])
             if self.args.search:
                 P["embedding_2"] = self.conv2(
-                    features, features, P["batch"], P["batch"]
+                    P["xyz"], features, P["batch"]
                 )
 
         # Second baseline