Graph neural networks (GNNs) -- learn graph representations by exploiting the graph's sparsity, connectivity, and symmetries -- have become indispensable for learning geometric data like molecules. However, the most used graphs (e.g., radial cutoff graphs) in molecular modeling lack theoretical guarantees for achieving connectivity and sparsity simultaneously, which are essential for the performance and scalability of GNNs. Furthermore, existing widely used graph construction methods for molecules lack rigidity, limiting GNNs' ability to exploit graph nodes' spatial arrangement. In this paper, we introduce a new hyperparameter-free graph construction of molecules and beyond with sparsity, connectivity, and rigidity guarantees. Remarkably, our method consistently generates connected and sparse graphs with the edge-to-node ratio being bounded above by 3. Our graphs' rigidity guarantees that edge distances and dihedral angles are sufficient to uniquely determine the general spatial arrangements of atoms. We substantiate the effectiveness and efficiency of our proposed graphs in various molecular modeling benchmarks. Code is available at https://github.com/shihhsinwang0214/SCHull.

Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale representations and modeling long-range dependencies efficiently. In this work, we propose an efficient multiscale graph-based learning framework tailored to proteins. Our proposed framework contains two crucial components: (1) It constructs a hierarchical graph representation comprising a collection of fine-grained subgraphs, each corresponding to a secondary structure motif (e.g., $\alpha$-helices, $\beta$-strands, loops), and a single coarse-grained graph that connects these motifs based on their spatial arrangement and relative orientation. (2) It employs two GNNs for feature learning: the first operates within individual secondary motifs to capture local interactions, and the second models higher-level structural relationships across motifs. Our modular framework allows a flexible choice of GNN in each stage. Theoretically, we show that our hierarchical framework preserves the desired maximal expressiveness, ensuring no loss of critical structural information. Empirically, we demonstrate that integrating baseline GNNs into our multiscale framework remarkably improves prediction accuracy and reduces computational cost across various benchmarks.

Theoretical and empirical comparisons have been made to assess the expressive power and performance of invariant and equivariant GNNs. However, there is currently no theoretical result comparing the expressive power of $k$-hop invariant GNNs and equivariant GNNs. Additionally, little is understood about whether the performance of equivariant GNNs, employing steerable features up to type-$L$, increases as $L$ grows -- especially when the feature dimension is held constant. In this study, we introduce a key lemma that allows us to analyze steerable features by examining their corresponding invariant features. The lemma facilitates us in understanding the limitations of $k$-hop invariant GNNs, which fail to capture the global geometric structure due to the loss of geometric information between local structures. Furthermore, we investigate the invariant features associated with different types of steerable features and demonstrate that the expressiveness of steerable features is primarily determined by their dimension -- independent of their irreducible decomposition. This suggests that when the feature dimension is constant, increasing $L$ does not lead to essentially improved performance in equivariant GNNs employing steerable features up to type-$L$. We substantiate our theoretical insights with numerical evidence.

Many real-world datasets are represented as 3D point clouds -- yet they often lack a predefined reference frame, posing a challenge for machine learning or general data analysis. Traditional methods for determining reference frames and normalizing 3D point clouds often struggle with specific inputs, lack theoretical guarantees, or require massive data. We introduce a new algorithm that overcomes these limitations and guarantees both universality and compatibility with any learnable framework for 3D point cloud analysis. Our algorithm works with any input point cloud and performs consistently regardless of input complexities, unlike data-driven methods that are susceptible to biases or limited training data. Empirically, our algorithm outperforms existing methods in effectiveness and generalizability across diverse benchmark datasets. Code is available at https://github.com/Utah-Math-Data-Science/alignment.

Implicit graph neural networks (IGNNs) – that solve a fixed-point equilibrium equation using Picard iteration for representation learning – have shown remarkable performance in learning long-range dependencies (LRD) in the underlying graphs. However, IGNNs suffer from several issues, including 1) their expressivity is limited by their parameterizations for the well-posedness guarantee, 2) IGNNs are unstable in learning LRD, and 3) IGNNs become computationally inefficient when learning LRD. In this paper, we provide a new well-posedness characterization for IGNNs leveraging monotone operator theory, resulting in a much more expressive parameterization than the existing one. We also propose an orthogonal parameterization for IGNN based on Cayley transform to stabilize learning LRD. Furthermore, we leverage Anderson-accelerated operator splitting schemes to efficiently solve for the fixed point of the equilibrium equation of IGNN with monotone or orthogonal parameterization. We verify the computational efficiency and accuracy of the new models over existing IGNNs on various graph learning tasks at both graph and node levels.