refactor conf

geometric-intelligence · May 15, 2024 · 8173c96 · 8173c96
1 parent 3b87ee9
commit 8173c96
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Showing 23 changed files with 475 additions and 30 deletions.
diff --git a/configs/dataset/transforms/graph2cell_lifting/cell_cycles.yaml b/configs/dataset/transforms/graph2cell_lifting/cell_cycles.yaml
@@ -1,7 +1,6 @@
 _target_: topobenchmarkx.transforms.data_transform.DataTransform
 transform_type: 'lifting'
 transform_name: "CellCyclesLifting"
-k_value: 1
 complex_dim: ${oc.select:dataset.parameters.max_dim_if_lifted,3}
 max_cell_length: 6
 preserve_edge_attr: ${oc.select:dataset.parameters.preserve_edge_attr_if_lifted,False}
diff --git a/configs/model/cell/can.yaml b/configs/model/cell/can.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: can
 model_domain: cell
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
   selected_dimensions:
     - 0
     - 1

diff --git a/configs/model/cell/cccn.yaml b/configs/model/cell/cccn.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: cwn_dcm
 model_domain: cell
@@ -8,15 +8,15 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
-  proj_dropout: 0.0
+  proj_dropout: 0.
   selected_dimensions:
     - 0
     - 1
 
 backbone:
   _target_: custom_models.cell.cccn.CCCN
   in_channels: ${model.feature_encoder.out_channels}
-  n_layers: 1
+  n_layers: 4
   dropout: 0.0
 
 backbone_wrapper:

diff --git a/configs/model/cell/ccxn.yaml b/configs/model/cell/ccxn.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: ccxn
 model_domain: cell
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
 
 backbone:
   _target_: topomodelx.nn.cell.ccxn.CCXN

diff --git a/configs/model/cell/cwn.yaml b/configs/model/cell/cwn.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: cwn
 model_domain: cell
@@ -7,7 +7,7 @@ feature_encoder:
   _target_: topobenchmarkx.models.encoders.${model.feature_encoder.encoder_name}
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
-  out_channels: 32
+  out_channels: 64
   proj_dropout: 0.0
 
 backbone:
@@ -16,7 +16,7 @@ backbone:
   in_channels_1: ${model.feature_encoder.out_channels}
   in_channels_2: ${model.feature_encoder.out_channels}
   hid_channels: ${model.feature_encoder.out_channels}
-  n_layers: 1
+  n_layers: 4
 
 backbone_wrapper:
   _target_: topobenchmarkx.models.wrappers.CWNWrapper
@@ -27,7 +27,7 @@ backbone_wrapper:
 
 readout:
   _target_: topobenchmarkx.models.readouts.${model.readout.readout_name}
-  readout_name: PropagateSignalDown #  Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
+  readout_name: NoReadOut #  Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
   hidden_dim: ${model.feature_encoder.out_channels}
   num_cell_dimensions: ${infere_list_length:${model.feature_encoder.in_channels}}
 

diff --git a/configs/model/graph/gat.yaml b/configs/model/graph/gat.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: gat
 model_domain: graph
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} 
   out_channels: 32
+  proj_dropout: 0.0
 
 backbone:
   _target_: torch_geometric.nn.models.GAT

diff --git a/configs/model/graph/gcn.yaml b/configs/model/graph/gcn.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: gcn
 model_domain: graph
@@ -7,13 +7,14 @@ feature_encoder:
   _target_: topobenchmarkx.models.encoders.${model.feature_encoder.encoder_name}
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
-  out_channels: 64
+  out_channels: 32
+  proj_dropout: 0.0
 
 backbone:
   _target_: torch_geometric.nn.models.GCN
   in_channels: ${model.feature_encoder.out_channels}
   hidden_channels: ${model.feature_encoder.out_channels}
-  num_layers: 1
+  num_layers: 2
   dropout: 0.0
   act: relu
 

diff --git a/configs/model/graph/gin.yaml b/configs/model/graph/gin.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: gin
 model_domain: graph
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
 
 backbone:
   _target_: torch_geometric.nn.models.GIN

diff --git a/configs/model/hypergraph/alldeepset.yaml b/configs/model/hypergraph/alldeepset.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: alldeepset
 model_domain: hypergraph
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
 
 backbone:
   _target_: topomodelx.nn.hypergraph.allset.AllSet

diff --git a/configs/model/hypergraph/allsettransformer.yaml b/configs/model/hypergraph/allsettransformer.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: allsettransformer
 model_domain: hypergraph
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
 
 backbone:
   _target_: topomodelx.nn.hypergraph.allset_transformer.AllSetTransformer

diff --git a/configs/model/hypergraph/edgnn.yaml b/configs/model/hypergraph/edgnn.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: edgnn
 model_domain: hypergraph
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 16
+  proj_dropout: 0.0
 
 backbone:
   _target_: custom_models.hypergraph.edgnn.EDGNN

diff --git a/configs/model/hypergraph/unignn.yaml b/configs/model/hypergraph/unignn.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: unignn2
 mode_domain: hypergraph
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
 
 backbone:
   _target_: topomodelx.nn.hypergraph.unigcn.UniGCN

diff --git a/configs/model/hypergraph/unignn2.yaml b/configs/model/hypergraph/unignn2.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: unignn2
 mode_domain: hypergraph
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
 
 backbone:
   _target_: topomodelx.nn.hypergraph.unigcnii.UniGCNII

diff --git a/configs/model/simplicial/san.yaml b/configs/model/simplicial/san.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: san
 model_domain: simplicial
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 64
+  proj_dropout: 0.0
   selected_dimensions:
     - 0
     - 1

diff --git a/configs/model/simplicial/sccn.yaml b/configs/model/simplicial/sccn.yaml
@@ -1,12 +1,14 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: sccnn
 model_domain: simplicial
+
 feature_encoder:
   _target_: topobenchmarkx.models.encoders.${model.feature_encoder.encoder_name}
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} # ${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
 
 backbone:
   _target_: topomodelx.nn.simplicial.sccn.SCCN

diff --git a/configs/model/simplicial/sccnn.yaml b/configs/model/simplicial/sccnn.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: sccnn 
 model_domain: simplicial
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
   selected_dimensions:
     - 0
     - 1

diff --git a/configs/model/simplicial/sccnn_custom.yaml b/configs/model/simplicial/sccnn_custom.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 model_name: sccnn_custom
 model_domain: simplicial
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
   selected_dimensions:
     - 0
     - 1

diff --git a/configs/model/simplicial/scn.yaml b/configs/model/simplicial/scn.yaml
@@ -1,4 +1,4 @@
-_target_: topobenchmarkx.models.network_module.NetworkModule
+_target_: topobenchmarkx.models.TopologicalNetworkModule
 
 mdoel_name: scn 
 model_type: simplicial
@@ -8,6 +8,7 @@ feature_encoder:
   encoder_name: AllCellFeatureEncoder
   in_channels: ${infer_in_channels:${dataset}} #${dataset.parameters.num_features}
   out_channels: 32
+  proj_dropout: 0.0
   selected_dimensions:
     - 0
     - 1

diff --git a/configs/train.yaml b/configs/train.yaml
@@ -4,7 +4,7 @@
 # order of defaults determines the order in which configs override each other
 defaults:
   - _self_
-  - dataset: IMDB-BINARY #us_country_demos
+  - dataset: REDDIT-BINARY #us_country_demos
   - model: simplicial/sccnn_custom #hypergraph/unignn2 #allsettransformer
   - evaluator: default
   - callbacks: default

diff --git a/custom_models/cell/cin.py b/custom_models/cell/cin.py
@@ -4,7 +4,6 @@
 import torch.nn as nn
 import torch.nn.functional as F
 from topomodelx.base.conv import Conv
-from topomodelx.nn.cell.cwn_layer import CWNLayer
 from torch_geometric.nn.models import MLP
 
 

diff --git a/custom_models/simplicial/sccnn.py b/custom_models/simplicial/sccnn.py
@@ -1,7 +1,6 @@
 """SCCNN implementation for complex classification."""
 
 import torch
-from topomodelx.nn.simplicial.sccnn_layer import SCCNNLayer
 from torch.nn.parameter import Parameter