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Figure 1: CoarsenConf architecture.
<!– (I) The encoder $q_phi(z| X, mathcal{R})$ takes the fine-grained (FG) ground truth conformer $X$, RDKit approximate conformer $mathcal{R}$ , and coarse-grained (CG) conformer $mathcal{C}$ as inputs (derived from $X$ and a predefined CG strategy), and outputs a variable-length equivariant CG representation via equivariant message passing and point convolutions.
(II) Equivariant MLPs are applied to learn the mean and log variance of both the posterior and prior distributions.
(III) The posterior (training) or prior (inference) is sampled and fed into the Channel Selection module, where an attention layer is used to learn the optimal pathway from CG to FG structure.
(IV) Given the FG latent vector and the RDKit approximation, the decoder $p_theta(X |mathcal{R}, z)$ learns to recover the low-energy FG structure through autoregressive equivariant message passing. The entire model can be trained end-to-end by optimizing the KL divergence of latent distributions and reconstruction error of generated conformers. –>
Molecular conformer generation is a fundamental task in computational chemistry. The objective is to predict stable low-energy 3D molecular structures, known as conformers, given the 2D molecule. Accurate molecular conformations are crucial for various applications that depend on precise spatial and geometric qualities, including drug discovery and protein docking.
We introduce CoarsenConf, an SE(3)-equivariant hierarchical variational autoencoder (VAE) that pools information from fine-grain atomic coordinates to a coarse-grain subgraph level representation for efficient autoregressive conformer generation.
Read More »Generating 3D Molecular Conformers via Equivariant Coarse-Graining and Aggregated Attention The Berkeley Artificial Intelligence Research Blog
