Understanding the 3D structure of RNA is essential for deciphering its function and developing RNA-based therapeutics. Geometric Graph Neural Networks (GeoGNNs) that conform to the $\mathrm{E}(3)$-symmetry have advanced RNA structure evaluation, a crucial step toward RNA structure prediction. However, existing GeoGNNs are still defective in two aspects: 1. inefficient or incapable of capturing the full geometries of RNA; 2. limited generalization ability when the size of RNA significantly differs between training and test datasets. In this paper, we propose EquiRNA, a novel equivariant GNN model by exploring the three-level hierarchical geometries of RNA. At its core, EquiRNA effectively addresses the size generalization challenge by reusing the representation of nucleotide, the common building block shared across RNAs of varying sizes. Moreover, by adopting a scalarization-based equivariant GNN as the backbone, our model maintains directional information while offering higher computational efficiency compared to existing GeoGNNs. Additionally, we propose a size-insensitive $K$-nearest neighbor sampling strategy to enhance the model's robustness to RNA size shifts. We test our approach on our created benchmark as well as an existing dataset. The results show that our method significantly outperforms other state-of-the-art methods, providing a robust baseline for RNA 3D structure modeling and evaluation.

Accurately predicting 3D structures and dynamics of physical systems is crucial in scientific applications. Existing approaches that rely on geometric Graph Neural Networks (GNNs) effectively enforce $\mathrm{E}(3)$-equivariance, but they often fail in leveraging extensive broader information. While direct application of Large Language Models (LLMs) can incorporate external knowledge, they lack the capability for spatial reasoning with guaranteed equivariance. In this paper, we propose EquiLLM, a novel framework for representing 3D physical systems that seamlessly integrates $\mathrm{E}(3)$-equivariance with LLM capabilities. Specifically, EquiLLM comprises four key components: geometry-aware prompting, an equivariant encoder, an LLM, and an equivariant adapter. Essentially, the LLM guided by the instructive prompt serves as a sophisticated invariant feature processor, while 3D directional information is exclusively handled by the equivariant encoder and adapter modules. Experimental results demonstrate that EquiLLM delivers significant improvements over previous methods across molecular dynamics simulation, human motion simulation, and antibody design, highlighting its promising generalizability.

Abstract Geometric graphs are a special kind of graph with geometric features, which are vital to model many scientific problems. Unlike generic graphs, geometric graphs often exhibit physical symmetries of translations, rotations, and reflections, making them ineffectively processed by current Graph Neural Networks (GNNs). To address this issue, researchers proposed a variety of geometric GNNs equipped with invariant/equivariant properties to better characterize the geometry and topology of geometric graphs. Given the current progress in this field, it is imperative to conduct a comprehensive survey of data structures, models, and applications related to geometric GNNs. In this paper, based on the necessary but concise mathematical preliminaries, we formalize geometric graph as the data structure, on top of which we provide a unified view of existing models from the geometric message passing perspective. Additionally, we summarize the applications as well as the related datasets to facilitate later research for methodology development and experimental evaluation. We also discuss the challenges and future potential directions of geometric GNNs at the end of this survey.

Discovering the underneath causal relations is the fundamental ability for reasoning about the surrounding environment and predicting the future states in the physical world. Counterfactual prediction from visual input, which requires simulating future states based on unrealized situations in the past, is a vital component in causal relation tasks. In this paper, we work on the confounders that have effect on the physical dynamics, including masses, friction coefficients, etc., to bridge relations between the intervened variable and the affected variable whose future state may be altered. We propose a neural network framework combining Global Causal Relation Attention (GCRA) and Confounder Transmission Structure (CTS). The GCRA looks for the latent causal relations between different variables and estimates the confounders by capturing both spatial and temporal information. The CTS integrates and transmits the learnt confounders in a residual way, so that the estimated confounders can be encoded into the network as a constraint for object positions when performing counterfactual prediction. Without any access to ground truth information about confounders, our model outperforms the state-of-the-art method on various benchmarks by fully utilizing the constraints of confounders. Extensive experiments demonstrate that our model can generalize to unseen environments and maintain good performance.

Although the anchor-based detectors have taken a big step forward in pedestrian detection, the overall performance of algorithm still needs further improvement for practical applications, e.g., a good trade-off between the accuracy and efficiency. To this end, this paper proposes a series of systematic optimization strategies for the detection pipeline of one-stage detector, forming a single shot anchor-based detector (SADet) for efficient and accurate pedestrian detection, which includes three main improvements. Firstly, we optimize the sample generation process by assigning soft labels to the outlier samples to generate semi-positive samples with continuous tag value between 0 and 1. Secondly, a novel Center-IoU loss is applied as a new regression loss for bounding box regression, which not only retains the good characteristics of IoU loss, but also solves some defects of it. Thirdly, we also design Cosine-NMS for the post-processing of predicted bounding boxes, and further propose adaptive anchor matching to enable the model to adaptively match the anchor boxes to full or visible bounding boxes according to the degree of occlusion. Though structurally simple, it presents state-of-the-art result and real-time speed of 20 FPS for VGA-resolution images (640×480) tested on one GeForce GTX 1080Ti GPU on challenging pedestrian detection benchmarks, i.e., CityPersons, Caltech, and human detection benchmark CrowdHuman, leading to a new attractive pedestrian detector.