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1. Geometry-complete diffusion for 3D molecule generation and optimization

   https://doi.org/10.1038/s42004-024-01233-z  

   Morehead, Alex; Cheng, Jianlin (July 2024, Communications Chemistry)

   Abstract Generative deep learning methods have recently been proposed for generating 3D molecules using equivariant graph neural networks (GNNs) within a denoising diffusion framework. However, such methods are unable to learn important geometric properties of 3D molecules, as they adopt molecule-agnostic and non-geometric GNNs as their 3D graph denoising networks, which notably hinders their ability to generate valid large 3D molecules. In this work, we address these gaps by introducing the Geometry-Complete Diffusion Model (GCDM) for 3D molecule generation, which outperforms existing 3D molecular diffusion models by significant margins across conditional and unconditional settings for the QM9 dataset and the larger GEOM-Drugs dataset, respectively. Importantly, we demonstrate that GCDM’s generative denoising process enables the model to generate a significant proportion of valid and energetically-stable large molecules at the scale of GEOM-Drugs, whereas previous methods fail to do so with the features they learn. Additionally, we show that extensions of GCDM can not only effectively design 3D molecules for specific protein pockets but can be repurposed to consistently optimize the geometry and chemical composition of existing 3D molecules for molecular stability and property specificity, demonstrating new versatility of molecular diffusion models. Code and data are freely available onGitHub. 

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2. GlobalMapper: Arbitrary-Shaped Urban Layout Generation

   He, Liu; Aliaga, Daniel (October 2023, IEEE International Conference on Computer Vision)

   Modeling and designing urban building layouts is of significant interest in computer vision, computer graphics, and urban applications. A building layout consists of a set of buildings in city blocks defined by a network of roads. We observe that building layouts are discrete structures, consisting of multiple rows of buildings of various shapes, and are amenable to skeletonization for mapping arbitrary city block shapes to a canonical form. Hence, we propose a fully automatic approach to building layout generation using graph attention networks. Our method generates realistic urban layouts given arbitrary road networks, and enables conditional generation based on learned priors. Our results, including user study, demonstrate superior performance as compared to prior layout generation networks, support arbitrary city block and varying building shapes as demonstrated by generating layouts for 28 large cities. 

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3. GlobalMapper: Arbitrary-Shaped Urban Layout Generation

   He, Liu; Aliaga, Daniel (October 2023, IEEE)

   Modeling and designing urban building layouts is of significant interest in computer vision, computer graphics, and urban applications. A building layout consists of a set of buildings in city blocks defined by a network of roads. We observe that building layouts are discrete structures, consisting of multiple rows of buildings of various shapes, and are amenable to skeletonization for mapping arbitrary city block shapes to a canonical form. Hence, we propose a fully automatic approach to building layout generation using graph attention networks. Our method generates realistic urban layouts given arbitrary road networks, and enables conditional generation based on learned priors. Our results, including user study, demonstrate superior performance as compared to prior layout generation networks, support arbitrary city block and varying building shapes as demonstrated by generating layouts for 28 large cities. 

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4. Drawing Transforms: A Unifying Interaction Primitive to Procedurally Manipulate Graphics across Style, Space, and Time

   https://doi.org/10.1145/3544548.3580642  

   Hashim, Sonia; Höllerer, Tobias; Jacobs, Jennifer (April 2023, ACM)

   Procedural functionality enables visual creators to rapidly edit, explore alternatives, and fine-tune artwork in many domains including illustration, motion graphics, and interactive animation. Symbolic procedural tools, such as textual programming languages, are highly expressive but often limit directly manipulating concrete artwork; whereas direct manipulation tools support some procedural expression but limit creators to pre-defined behaviors and inputs. Inspired by visions of using geometric input to create procedural relationships, we identify an opportunity to use vector geometry from artwork to specify expressive user-defined procedural functions. We present Drawing Transforms (DTs), a technique that enables the use of any drawing to procedurally transform the stylistic, spatial, and temporal properties of target artwork. We apply DTs in a prototype motion graphics system to author continuous and discrete transformations, modify multiple elements in a composition simultaneously, create animations, and control fine-grained procedural instantiation. We discuss how DTs can unify procedural authoring through direct manipulation across visual media domains. 

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5. E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction

   https://doi.org/10.1371/journal.pcbi.1011435  

   Roche, Rahmatullah; Moussad, Bernard; Shuvo, Md Hossain; Bhattacharya, Debswapna (August 2023, PLOS Computational Biology)

   Li, Jinyan (Ed.)

   Artificial intelligence-powered protein structure prediction methods have led to a paradigm-shift in computational structural biology, yet contemporary approaches for predicting the interfacial residues (i.e., sites) of protein-protein interaction (PPI) still rely on experimental structures. Recent studies have demonstrated benefits of employing graph convolution for PPI site prediction, but ignore symmetries naturally occurring in 3-dimensional space and act only on experimental coordinates. Here we present EquiPPIS, an E(3) equivariant graph neural network approach for PPI site prediction. EquiPPIS employs symmetry-aware graph convolutions that transform equivariantly with translation, rotation, and reflection in 3D space, providing richer representations for molecular data compared to invariant convolutions. EquiPPIS substantially outperforms state-of-the-art approaches based on the same experimental input, and exhibits remarkable robustness by attaining better accuracy with predicted structural models from AlphaFold2 than what existing methods can achieve even with experimental structures. Freely available athttps://github.com/Bhattacharya-Lab/EquiPPIS, EquiPPIS enables accurate PPI site prediction at scale. 

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