@@ -88,75 +88,31 @@ python -m chebai fit --trainer=configs/training/default_trainer.yml --trainer.lo
8888
8989To use a GAT-based model, choose ** one** of the following configs:
9090
91- - ** Atom–Motif–Graph Node Pooling**
92- ``` bash
93- --model=../python-chebai-graph/configs/model/gat_aug_amgpool.yml
94- ```
95-
96- - ** Atom-Augmented Node Pooling**
97- ``` bash
98- --model=../python-chebai-graph/configs/model/gat_aug_aagpool.yml
99- ```
100-
101- - ** Standard Pooling**
102- ``` bash
103- --model=../python-chebai-graph/configs/model/gat.yml
104- ```
91+ - ** Atom–Motif–Graph Node Pooling** : ` --model=../python-chebai-graph/configs/model/gat_aug_amgpool.yml `
92+ - ** Atom-Augmented Node Pooling** : ` --model=../python-chebai-graph/configs/model/gat_aug_aagpool.yml `
93+ - ** Standard Pooling** : ` --model=../python-chebai-graph/configs/model/gat.yml `
10594
10695#### GAT-specific hyperparameters
10796
108- - ** Number of message-passing layers**
109- ``` bash
110- --model.config.num_layers=5 # Default: 4
111- ```
112-
113- - ** Attention heads**
114- ``` bash
115- --model.config.heads=4 # Default: 8
116- ```
117- * Note: The number of heads should be divisible by the output channels (or hidden channels if output channels are not specified).*
118-
119- - ** Use GATv2**
120- ``` bash
121- --model.config.v2=True # Default: False
122- ```
123-
97+ - ** Number of message-passing layers** : ` --model.config.num_layers=5 ` (default: 4)
98+ - ** Attention heads** : ` --model.config.heads=4 ` (Default: 8)
99+ > Note: The number of heads should be divisible by the output channels (or hidden channels if output channels are not specified).
100+ - ** Use GATv2** : ` --model.config.v2=True ` (default: False)
124101
125102#### ** ResGated Architecture**
126103
127104To use a ResGated GNN model, choose ** one** of the following configs:
128105
129- - ** Atom–Motif–Graph Node Pooling**
130- ``` bash
131- --model=../python-chebai-graph/configs/model/res_aug_amgpool.yml
132- ```
133-
134- - ** Atom-Augmented Node Pooling**
135- ``` bash
136- --model=../python-chebai-graph/configs/model/res_aug_aagpool.yml
137- ```
138-
139- - ** Standard Pooling**
140- ``` bash
141- --model=../python-chebai-graph/configs/model/resgated.yml
142- ```
143-
106+ - ** Atom–Motif–Graph Node Pooling** : ` --model=../python-chebai-graph/configs/model/res_aug_amgpool.yml `
107+ - ** Atom-Augmented Node Pooling** : ` --model=../python-chebai-graph/configs/model/res_aug_aagpool.yml `
108+ - ** Standard Pooling** : ` --model=../python-chebai-graph/configs/model/resgated.yml `
144109
145110#### ** Common Hyperparameters**
146111
147112These can be used for both GAT and ResGated architectures:
148113
149- - ** Dropout**
150- ``` bash
151- --model.config.dropout=0.1 # Default: 0
152- ```
153-
154- - ** Number of final linear layers**
155- ``` bash
156- --model.n_linear_layers=2 # Default: 1
157- ```
158-
159-
114+ - ** Dropout** : ` --model.config.dropout=0.1 ` (default: 0)
115+ - ** Number of final linear layers** : ` --model.n_linear_layers=2 ` (default: 1)
160116
161117# Random Node Initialization
162118
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