Encode

Sequence Convolution

Spatial Convolution

Self-Interaction

Trans. Sequence Convolution

Decode

\(\oplus\)

Linear

Tensor Square

MLP

Node Position \(\mathbf X\in\mathbb R^3\)

Node Features \(\mathbf V^{l=0:l_{\max}}\)

Node Position \(\mathbf X\in\mathbb R^3\)

Node Features \(\mathbf V^{l=0:l_{\max}}\)

Norm

\(\cdot\)

\(+\)

\(\mathbf V^{l=0}\)

Node Position \(\mathbf X_{1:K}\)

Node Features \(\mathbf V^{l=0:l_{\max}}_{1:K}\)

Node Position \(\mathbf X\in\mathbb R^3\)

Node Features \(\mathbf V^{l=0:l_{\max}}\)

Norm

Linear

Average

Linear

\(+\)

Average

Node Position \(\mathbf X_{1:N}\)

Node Features \(\mathbf V^{l=0:l_{\max}}_{1:N}\)

Node Position \(\mathbf X\in\mathbb R^3\)

Node Features \(\mathbf V^{l=0:l_{\max}}\)

k-NN

Embed

MLP

Tensor Product

\(\cdot\)

Linear

Norm

\(\oplus\)

Linear

\(+\)

\(\oplus\)

Node Features \(\mathbf V^{l=0:2}\)

Node Position \(\mathbf X\in\mathbb R^3\)

Heavy Atom Relative Positions \(\mathbf X^\ast \in \mathbb R ^{n \times 3}\)

Residue Label \(\mathbf R \in \mathcal R\)

\(C_\alpha\) Position \(\mathbf X^\alpha\in\mathbb R^3\)

Unordenable

Embed

Ordenable

\(\mathbf V^{l=1}\)

\(\mathbf V^{l=1:2}\)

\(\mathbf V^{l=0}\)

Node Position \(\mathbf X\in\mathbb R^3\)

\(C_\alpha\) Position \(\mathbf X^\alpha\in\mathbb R^3\)

Residue Label \(\mathbf R \in \mathcal R\)

Softmax

Node Features \(\mathbf V^{l=0:2}\)

Unordenable

Ordenable

\(\oplus\)

Heavy Atom Relative Positions \(\mathbf X^\ast \in \mathbb R ^{n \times 3}\)

Node Position \(\mathbf X_{1:K}\)

Node Features \(\mathbf V^{l=0:l_{\max}}_{1:K}\)

Node Position \(\mathbf X\in\mathbb R^3\)

MLP

Softmax

\(\mathbf V^{l=0}_{1:K}\)

\(\sum w_k \mathbf X_k\)

\(\oplus\)

Relative Vectors

Node Features \(\mathbf V^{l=0:l_{\max}}\)

Linear

Sequence Convolution

Sequence Convolution

Spatial Convolution

Self-Interaction

Sequence Convolution

Spatial Convolution

Self-Interaction

Sequence Convolution

Trans. Sequence Convolution

Spatial Convolution

Self-Interaction

Sequence Convolution

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By Mario Geiger

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