Zelin Xu

Wenchong He, Zhe Jiang, Tingsong Xiao et al.

Transformers are widely used deep learning architectures. Existing transformers are mostly designed for sequences (texts or time series), images or videos, and graphs. This paper proposes a novel transformer model for massive (up to a million) point samples in continuous space. Such data are ubiquitous in environment sciences (e.g., sensor observations), numerical simulations (e.g., particle-laden flow, astrophysics), and location-based services (e.g., POIs and trajectories). However, designing a transformer for massive spatial points is non-trivial due to several challenges, including implicit long-range and multi-scale dependency on irregular points in continuous space, a non-uniform point distribution, the potential high computational costs of calculating all-pair attention across massive points, and the risks of over-confident predictions due to varying point density. To address these challenges, we propose a new hierarchical spatial transformer model, which includes multi-resolution representation learning within a quad-tree hierarchy and efficient spatial attention via coarse approximation. We also design an uncertainty quantification branch to estimate prediction confidence related to input feature noise and point sparsity. We provide a theoretical analysis of computational time complexity and memory costs. Extensive experiments on both real-world and synthetic datasets show that our method outperforms multiple baselines in prediction accuracy and our model can scale up to one million points on one NVIDIA A100 GPU. The code is available at \url{https://github.com/spatialdatasciencegroup/HST}.

Jinqing Zhang, Zehua Fu, Zelin Xu et al.

The comprehensive understanding capabilities of world models for driving scenarios have significantly improved the planning accuracy of end-to-end autonomous driving frameworks. However, the redundant modeling of static regions and the lack of deep interaction with trajectories hinder world models from exerting their full effectiveness. In this paper, we propose Temporal Residual World Model (TR-World), which focuses on dynamic object modeling. By calculating the temporal residuals of scene representations, the information of dynamic objects can be extracted without relying on detection and tracking. TR-World takes only temporal residuals as input, thus predicting the future spatial distribution of dynamic objects more precisely. By combining the prediction with the static object information contained in the current BEV features, accurate future BEV features can be obtained. Furthermore, we propose Future-Guided Trajectory Refinement (FGTR) module, which conducts interaction between prior trajectories (predicted from the current scene representation) and the future BEV features. This module can not only utilize future road conditions to refine trajectories, but also provides sparse spatial-temporal supervision on future BEV features to prevent world model collapse. Comprehensive experiments conducted on the nuScenes and NAVSIM datasets demonstrate that our method, namely ResWorld, achieves state-of-the-art planning performance. The code is available at https://github.com/mengtan00/ResWorld.git.

Zibo Liu, Zhe Jiang, Zelin Xu et al.

Traffic forecasting uses recent measurements by sensors installed at chosen locations to forecast the future road traffic. Existing work either assumes all locations are equipped with sensors or focuses on short-term forecast. This paper studies partial sensing forecast of long-term traffic, assuming sensors are available only at some locations. The problem is challenging due to the unknown data distribution at unsensed locations, the intricate spatio-temporal correlation in long-term forecasting, as well as noise to traffic patterns. We propose a Spatio-temporal Long-term Partial sensing Forecast model (SLPF) for traffic prediction, with several novel contributions, including a rank-based embedding technique to reduce the impact of noise in data, a spatial transfer matrix to overcome the spatial distribution shift from sensed locations to unsensed locations, and a multi-step training process that utilizes all available data to successively refine the model parameters for better accuracy. Extensive experiments on several real-world traffic datasets demonstrate its superior performance. Our source code is at https://github.com/zbliu98/SLPF

Zelin Xu, Yupu Zhang, Saugat Adhikari et al.

Benchmarking spatial reasoning in multimodal large language models (MLLMs) has attracted growing interest in computer vision due to its importance for embodied AI and other agentic systems that require precise interaction with the physical world. However, spatial reasoning on Earth imagery has lagged behind, as it uniquely involves grounding objects in georeferenced images and quantitatively reasoning about distances, directions, and topological relations using both visual cues and vector geometry coordinates (e.g., 2D bounding boxes, polylines, and polygons). Existing benchmarks for Earth imagery primarily focus on 2D spatial grounding, image captioning, and coarse spatial relations (e.g., simple directional or proximity cues). They lack support for quantitative direction and distance reasoning, systematic topological relations, and complex object geometries beyond bounding boxes. To fill this gap, we propose \textbf{EarthSpatialBench}, a comprehensive benchmark for evaluating spatial reasoning in MLLMs on Earth imagery. The benchmark contains over 325K question-answer pairs spanning: (1) qualitative and quantitative reasoning about spatial distance and direction; (2) systematic topological relations; (3) single-object queries, object-pair queries, and compositional aggregate group queries; and (4) object references expressed via textual descriptions, visual overlays, and explicit geometry coordinates, including 2D bounding boxes, polylines, and polygons. We conducted extensive experiments on both open-source and proprietary models to identify limitations in the spatial reasoning of MLLMs.

Yupu Zhang, Zelin Xu, Tingsong Xiao et al.

Predicting the binding affinity of protein-ligand complexes plays a vital role in drug discovery. Unfortunately, progress has been hindered by the lack of large-scale and high-quality binding affinity labels. The widely used PDBbind dataset has fewer than 20K labeled complexes. Self-supervised learning, especially graph contrastive learning (GCL), provides a unique opportunity to break the barrier by pre-training graph neural network models based on vast unlabeled complexes and fine-tuning the models on much fewer labeled complexes. However, the problem faces unique challenges, including a lack of a comprehensive unlabeled dataset with well-defined positive/negative complex pairs and the need to design GCL algorithms that incorporate the unique characteristics of such data. To fill the gap, we propose DecoyDB, a large-scale, structure-aware dataset specifically designed for self-supervised GCL on protein-ligand complexes. DecoyDB consists of high-resolution ground truth complexes (less than 2.5 Angstrom) and diverse decoy structures with computationally generated binding poses that range from realistic to suboptimal (negative pairs). Each decoy is annotated with a Root Mean Squared Deviation (RMSD) from the native pose. We further design a customized GCL framework to pre-train graph neural networks based on DecoyDB and fine-tune the models with labels from PDBbind. Extensive experiments confirm that models pre-trained with DecoyDB achieve superior accuracy, label efficiency, and generalizability.