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--ninput_edges should be the maximum number of edges in the entire dataset. Any meshes which have less than that will be padded automatically.
Pooling Resolution
This is a hyper parameter of the network. For example setting --pool_res 600 450 will create two mesh_pooling layers in the network, where the first one pools meshes to 600 edges, and the second one pools to 450 edges. If using meshes with larger resolutions than the examples from this repo, be sure to increase the pooling resolution.