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Cleaning and typos #127

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merged 4 commits into from
Dec 18, 2024
Merged

Cleaning and typos #127

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a7662a9
Remove karate_club reference (deprecated)
gbg141 Dec 18, 2024
30547f3
Fix typo
gbg141 Dec 18, 2024
ecdd658
Merge branch 'main' of github.com:geometric-intelligence/TopoBenchmar…
gbg141 Dec 18, 2024
58819d6
Remove karate_club config
gbg141 Dec 18, 2024
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24 changes: 0 additions & 24 deletions configs/dataset/simplicial/karate_club.yaml
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4 changes: 2 additions & 2 deletions configs/model/cell/can.yaml
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Expand Up @@ -30,12 +30,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: CANWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/cell/cccn.yaml
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Expand Up @@ -24,12 +24,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: CCCNWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/cell/ccxn.yaml
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Expand Up @@ -26,12 +26,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: CCXNWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/cell/cwn.yaml
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Expand Up @@ -23,12 +23,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: CWNWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/cell/topotune.yaml
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Expand Up @@ -39,12 +39,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: TuneWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/cell/topotune_onehasse.yaml
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Expand Up @@ -38,12 +38,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: TuneWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/graph/gat.yaml
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Expand Up @@ -26,12 +26,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: GNNWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: NoReadOut # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/graph/gcn.yaml
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Expand Up @@ -23,12 +23,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: GNNWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: NoReadOut # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/graph/gcn_dgm.yaml
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Expand Up @@ -26,12 +26,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: GNNWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: NoReadOut # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/graph/gin.yaml
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Expand Up @@ -23,12 +23,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: GNNWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: NoReadOut # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/graph/graph_mlp.yaml
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Expand Up @@ -27,12 +27,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: GraphMLPWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: NoReadOut # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/hypergraph/alldeepset.yaml
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Expand Up @@ -31,12 +31,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: HypergraphWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/hypergraph/allsettransformer.yaml
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Expand Up @@ -25,12 +25,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: HypergraphWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/hypergraph/edgnn.yaml
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Expand Up @@ -26,12 +26,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: HypergraphWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/hypergraph/unignn.yaml
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Expand Up @@ -21,12 +21,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: HypergraphWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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4 changes: 2 additions & 2 deletions configs/model/hypergraph/unignn2.yaml
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Expand Up @@ -25,12 +25,12 @@ backbone_wrapper:
_partial_: true
wrapper_name: HypergraphWrapper
out_channels: ${model.feature_encoder.out_channels}
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}}

readout:
_target_: topobenchmark.nn.readouts.${model.readout.readout_name}
readout_name: PropagateSignalDown # Use <NoReadOut> in case readout is not needed Options: PropagateSignalDown
num_cell_dimensions: ${infere_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
num_cell_dimensions: ${infer_num_cell_dimensions:${oc.select:model.feature_encoder.selected_dimensions,null},${model.feature_encoder.in_channels}} # The highest order of cell dimensions to consider
hidden_dim: ${model.feature_encoder.out_channels}
out_channels: ${dataset.parameters.num_classes}
task_level: ${dataset.parameters.task_level}
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