Zian Li

Zian Li, Xiyuan Wang, Yinan Huang et al.

Graph Neural Networks (GNNs) are often used for tasks involving the 3D geometry of a given graph, such as molecular dynamics simulation. While incorporating Euclidean distance into Message Passing Neural Networks (referred to as Vanilla DisGNN) is a straightforward way to learn the geometry, it has been demonstrated that Vanilla DisGNN is geometrically incomplete. In this work, we first construct families of novel and symmetric geometric graphs that Vanilla DisGNN cannot distinguish even when considering all-pair distances, which greatly expands the existing counterexample families. Our counterexamples show the inherent limitation of Vanilla DisGNN to capture symmetric geometric structures. We then propose $k$-DisGNNs, which can effectively exploit the rich geometry contained in the distance matrix. We demonstrate the high expressive power of $k$-DisGNNs from three perspectives: 1. They can learn high-order geometric information that cannot be captured by Vanilla DisGNN. 2. They can unify some existing well-designed geometric models. 3. They are universal function approximators from geometric graphs to scalars (when $k\geq 2$) and vectors (when $k\geq 3$). Most importantly, we establish a connection between geometric deep learning (GDL) and traditional graph representation learning (GRL), showing that those highly expressive GNN models originally designed for GRL can also be applied to GDL with impressive performance, and that existing complicated, equivariant models are not the only solution. Experiments verify our theory. Our $k$-DisGNNs achieve many new state-of-the-art results on MD17.

Zian Li, Xiyuan Wang, Shijia Kang et al.

Invariant models, one important class of geometric deep learning models, are capable of generating meaningful geometric representations by leveraging informative geometric features in point clouds. These models are characterized by their simplicity, good experimental results and computational efficiency. However, their theoretical expressive power still remains unclear, restricting a deeper understanding of the potential of such models. In this work, we concentrate on characterizing the theoretical expressiveness of a wide range of invariant models under fully-connected conditions. We first rigorously characterize the expressiveness of the most classic invariant model, message-passing neural networks incorporating distance (DisGNN), restricting its unidentifiable cases to be only highly symmetric point clouds. We then prove that GeoNGNN, the geometric counterpart of one of the simplest subgraph graph neural networks, can effectively break these corner cases' symmetry and thus achieve E(3)-completeness. By leveraging GeoNGNN as a theoretical tool, we further prove that: 1) most subgraph GNNs developed in traditional graph learning can be seamlessly extended to geometric scenarios with E(3)-completeness; 2) DimeNet, GemNet and SphereNet, three well-established invariant models, are also all capable of achieving E(3)-completeness. Our theoretical results fill the gap in the expressive power of invariant models, contributing to a rigorous and comprehensive understanding of their capabilities.

Shaoheng Yan, Zian Li, Muhan Zhang

The pretraining-finetuning paradigm has powered major advances in domains such as natural language processing and computer vision, with representative examples including masked language modeling and next-token prediction. In molecular representation learning, however, pretraining tasks remain largely restricted to node-level denoising, which effectively captures local atomic environments but is often insufficient for encoding the global molecular structure critical to graph-level property prediction tasks such as energy estimation and molecular regression. To address this gap, we introduce GeoRecon, a graph-level pretraining framework that shifts the focus from individual atoms to the molecule as an integrated whole. GeoRecon formulates a graph-level reconstruction task: during pretraining, the model is trained to produce an informative graph representation that guides geometry reconstruction while inducing smoother and more transferable latent spaces. This encourages the learning of coherent, global structural features beyond isolated atomic details. Without relying on external supervision, GeoRecon generally improves over backbone baselines on multiple molecular benchmarks including QM9, MD17, MD22, and 3BPA, demonstrating the effectiveness of graph-level reconstruction for holistic and geometry-aware molecular embeddings.

Zian Li, Muhan Zhang

Masked autoregressive models (MAR) have recently emerged as a powerful paradigm for image and video generation, combining the flexibility of masked modeling with the potential of continuous tokenizer. However, video MAR models suffer from two major limitations: the slow-start problem, caused by the lack of a structured global prior at early sampling stages, and error accumulation across the autoregression in both spatial and temporal dimensions. In this work, we propose CanvasMAR, a novel video MAR model that mitigates these issues by introducing a canvas mechanism--a blurred, global prediction of the next frame, used as the starting point for masked generation. The canvas provides global structure early in sampling, enabling faster and more coherent frame synthesis. Furthermore, we introduce compositional classifier-free guidance that jointly enlarges spatial (canvas) and temporal conditioning, and employ noise-based canvas augmentation to enhance robustness. Experiments on the BAIR and Kinetics-600 benchmarks demonstrate that CanvasMAR produces high-quality videos with fewer autoregressive steps. Our approach achieves remarkable performance among autoregressive models on Kinetics-600 dataset and rivals diffusion-based methods.