Xingtong Yu
Publications
GraphReAct: Reasoning and Acting for Multi-step Graph Inference
Reasoning-acting frameworks enhance large language models (LLMs) by interleaving reasoning with actions for dynamic information acquisition. However, extending this paradigm to graph learning remains underexplored. Graph data is inherently structured, with information distributed across nodes and edges and encoded through both topology and latent representations. As a result, effective reasoning over graphs requires not only retrieving informative evidence from the graph, but also progressively refining the accumulated context during multi-step inference. In this work, we propose GraphReAct, a graph reasoning-acting framework that enables step-by-step inference over graph-structured data. Specifically, we design a graph-based action space with two complementary retrieval actions: topological retrieval, which captures local structural dependencies, and semantic retrieval, which accesses non-local but relevant evidence in the representation space. These actions dynamically expand the reasoning context. To further support multi-step reasoning, we introduce another type of action, context refinement, which distills and reorganizes accumulated information into a compact representation. By interleaving reasoning with both retrieval and refinement actions, our framework enables a progressive transition from context expansion to compression. Extensive experiments on six benchmark datasets demonstrate that GraphReAct consistently outperforms state-of-the-art methods, validating the effectiveness of reasoning-acting for graph learning.
Learning Multi-Relational Graph Representations for DNA Methylation-Based Biological Age Estimation
Aging clocks aim to estimate biological age, a measure of physiological state distinct from chronological age, from observable biomarkers, and are widely used for health assessment and disease analysis. DNA methylation is a particularly informative biomarker due to its stability and strong association with aging, and recent learning-based approaches have improved predictive performance. However, most existing methods treat CpG sites as independent features, overlooking the complex and heterogeneous biological relationships among them. We propose RelAge-GNN, a multi-relational graph neural network framework for DNA methylation-based age prediction. Our method constructs three complementary graphs capturing co-methylation patterns, genomic co-localization, and gene-level associations among CpG sites. Each graph is modeled by an independent GNN branch, and a learnable gating mechanism adaptively fuses the resulting representations. Experiments on large-scale datasets show that RelAge-GNN achieves competitive accuracy and stronger correlation with chronological age compared to state-of-the-art methods. Moreover, the model exhibits improved sensitivity in detecting age acceleration across diverse disease cohorts, highlighting its potential utility for disease characterization. Finally, through post hoc interpretability analyses, we quantify the contributions of different relational structures and CpG sites, providing biologically meaningful insights and suggesting potential directions for aging-related research. Our code is available at: https://anonymous.4open.science/r/RelAge-GNN-F1E3/.
UrbanGraphEmbeddings: Learning and Evaluating Spatially Grounded Multimodal Embeddings for Urban Science
Learning transferable multimodal embeddings for urban environments is challenging because urban understanding is inherently spatial, yet existing datasets and benchmarks lack explicit alignment between street-view images and urban structure. We introduce UGData, a spatially grounded dataset that anchors street-view images to structured spatial graphs and provides graph-aligned supervision via spatial reasoning paths and spatial context captions, exposing distance, directionality, connectivity, and neighborhood context beyond image content. Building on UGData, we propose UGE, a two-stage training strategy that progressively and stably aligns images, text, and spatial structures by combining instruction-guided contrastive learning with graph-based spatial encoding. We finally introduce UGBench, a comprehensive benchmark to evaluate how spatially grounded embeddings support diverse urban understanding tasks -- including geolocation ranking, image retrieval, urban perception, and spatial grounding. We develop UGE on multiple state-of-the-art VLM backbones, including Qwen2-VL, Qwen2.5-VL, Phi-3-Vision, and LLaVA1.6-Mistral, and train fixed-dimensional spatial embeddings with LoRA tuning. UGE built upon Qwen2.5-VL-7B backbone achieves up to 44% improvement in image retrieval and 30% in geolocation ranking on training cities, and over 30% and 22% gains respectively on held-out cities, demonstrating the effectiveness of explicit spatial grounding for spatially intensive urban tasks.