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

By Mario Geiger

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