The ability to capture rich representations of combinatorial structures has enabled the application of machine learning to tasks such as analysis and generation of floorplans, terrains, images, and animations. Recent work has primarily focused on understanding structures with well-defined features, neighborhoods, or underlying distance metrics, while those lacking such characteristics remain largely unstudied. Examples of these combinatorial structures can be found in polygons, where a small change in the vertex locations causes a significant rearrangement of the combinatorial structure, expressed as a visibility or triangulation graphs. Current representation learning approaches fail to capture structures without well-defined features and distance metrics. In this paper, we study the open problem of Visibility Reconstruction: Given a visibility graph G, construct a polygon P whose visibility graph is G.

We propose a novel neural network-based approach to modeling protein dynamics using an implicit representation of a protein's surface in 3D and time. Our method utilizes the zero-level set of signed distance functions (SDFs) to represent protein surfaces, enabling temporally and spatially continuous representations of protein dynamics. Our experimental results demonstrate that our model accurately captures protein dynamic trajectories and can interpolate and extrapolate in 3D and time. Importantly, this is the first study to introduce this method and successfully model large-scale protein dynamics. This approach offers a promising alternative to current methods, overcoming the limitations of first-principles-based and deep learning methods, and provides a more scalable and efficient approach to modeling protein dynamics. Additionally, our surface representation approach simplifies calculations and allows identifying movement trends and amplitudes of protein domains, making it a useful tool for protein dynamics research. Codes are available at https://github.com/Sundw-818/DSR,

Our motivation is grounded in a fundamental observation: aligning the gradient and the Hessian of the SDF provides a more efficient mechanism to govern gradient directions.

Thesecond stage then introduces unlabeled data withdisjoint classesin a semi-supervised scheme to diversify these priors and achieve generalization. We assess our method on both synthetic data and real collected point clouds.

We propose a novel neural network-based approach to modeling protein dynamics using an implicit representation of a protein's surface in 3D and time.