Publications

Publications and preprints on scientific generation, structured learning, and LLM reasoning.

2026

  1. ACL
    AOT*: Efficient Synthesis Planning via LLM-Empowered AND-OR Tree Search
    Xiaozhuang Song, Xuanhao Pan, Xinjian Zhao, and
    4 more authors Hangting Ye, Shufei Zhang, Jian Tang, Tianshu Yu
    In Findings of the Association for Computational Linguistics: ACL 2026, 2026
  2. Preprint
    Calibrating Tabular Anomaly Detection via Optimal Transport
    Hangting Ye, He Zhao, Wei Fan, and
    4 more authors Xiaozhuang Song, Dandan Guo, Yi Chang, Hongyuan Zha
    arXiv preprint, 2026
  3. Preprint
    ChemOPD: Multi-Teacher On-Policy Distillation for Multi-Task Chemical Reasoning
    Yaoyao Xu, Xinjian Zhao, Xiaozhuang Song, and
    2 more authors Xuemin Chen, Tianshu Yu
    arXiv preprint, 2026
  4. Preprint
    Closed-Loop Bayesian Molecular Inverse Design with Semantic LLM Surrogates
    Yaoyao Xu, Xinjian Zhao, Xiaozhuang Song, and
    2 more authors Lei Bai, Tianshu Yu
    arXiv preprint, 2026
  5. Preprint
    Coverage Before Control: Route-Instruction Grounding and Steering for Controllable Retrosynthesis
    Xuemin Chen, Xiaozhuang Song, Xinjian Zhao, and
    2 more authors Yaoyao Xu, Tianshu Yu
    arXiv preprint arXiv:2609.39955, 2026
  6. TPAMI
    Deep Tabular Representation Corrector
    Hangting Ye, Peng Wang, Wei Fan, and
    4 more authors Xiaozhuang Song, He Zhao, Dandan Guo, Yi Chang
    IEEE Transactions on Pattern Analysis and Machine Intelligence, 2026
  7. Preprint
    Latent JEPA: Abstract Future Prediction for Latent Reasoning in Chemistry
    Xinjian Zhao, Yaoyao Xu, Xiaozhuang Song, and
    2 more authors Xuemin Chen, Tianshu Yu
    arXiv preprint arXiv:2610.01947, 2026
  8. ICML
    MolEmb: Multimodal Large Language Models Can Be Strong Molecular Embedding Models
    Xinjian Zhao, Xiangru Jian, Yaoyao Xu, and
    4 more authors Xiaozhuang Song, Wei Pang, Lei Bai, Tianshu Yu
    In ICML 2026 Workshop on Foundation Models for Life Sciences, 2026
  9. AAAI
    Physically-Informed Flow Matching with Graph Neural Networks for Complex Fluid Dynamics
    Xiaozhuang Song, and Tianshu Yu
    In Proceedings of the AAAI Conference on Artificial Intelligence, 2026
  10. Preprint
    RetroGEF: Dynamic Graph Edit Flow for Single-Step Retrosynthesis
    Xiaozhuang Song, Xuemin Chen, Xinjian Zhao, and
    2 more authors Yaoyao Xu, Tianshu Yu
    arXiv preprint arXiv:2609.38484, 2026
  11. IJCAI
    When Vision Meets Graphs: A Survey on Graph Reasoning and Learning
    Xinjian Zhao, Wei Pang, Zhixuan Yu, and
    8 more authors Xiangru Jian, Xiaozhuang Song, Yaoyao Xu, Zhongkai Xue, Dingshuo Chen, Shu Wu, Philip Torr, Tianshu Yu
    Proceedings of the International Joint Conference on Artificial Intelligence, 2026
    Survey Track

2025

  1. AAAI
    Enhancing Generalizability in Molecular Conformation Generation with Metrization-Informed Geometric Diffusion Pretraining
    Xiaozhuang Song, Yuzhao Tu, Hangting Ye, and
    4 more authors Wei Fan, Qingquan Zhang, Xiaoxue Wang, Tianshu Yu
    In Proceedings of the AAAI Conference on Artificial Intelligence, 2025
  2. TMLR
    Enhancing Molecular Conformer Generation via Fragment-Augmented Diffusion Pretraining
    Xiaozhuang Song, Yuzhao Tu, and Tianshu Yu
    Transactions on Machine Learning Research, 2025
  3. WWW
    MedGNN: Towards Multi-resolution Spatiotemporal Graph Learning for Medical Time Series Classification
    Wei Fan, Jingru Fei, Dingyu Guo, and
    5 more authors Kun Yi, Xiaozhuang Song, Haolong Xiang, Hangting Ye, Min Li
    In Proceedings of the ACM Web Conference, 2025
  4. Inf. Fusion
    Medvia: Empowering Medical Time Series Classification with Vision Augmentation and Multimodal Fusion
    Wei Fan, Jingru Fei, Junwen Han, and
    6 more authors Jinglan Lian, Hangting Ye, Xiaozhuang Song, Xiaoling Lv, Kun Yi, Min Li
    Information Fusion, 2025
  5. ACL
    ReKG-MCTS: Reinforcing LLM Reasoning on Knowledge Graphs via Training-Free Monte Carlo Tree Search
    Xiaozhuang Song, Shufei Zhang, and Tianshu Yu
    In Findings of the Association for Computational Linguistics: ACL 2025, 2025
  6. NeurIPS
    The Underappreciated Power of Vision Models for Graph Structural Understanding
    Xinjian Zhao, Wei Pang, Zhongkai Xue, and
    6 more authors Xiangru Jian, Lei Zhang, Yaoyao Xu, Xiaozhuang Song, Shu Wu, Tianshu Yu
    In Advances in Neural Information Processing Systems, 2025

2024

  1. ECML-PKDD
    Boosting Protein Language Models with Negative Sample Mining
    Yaoyao Xu, Xinjian Zhao, Xiaozhuang Song, and
    2 more authors Benyou Wang, Tianshu Yu
    In European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases, 2024
  2. IoT-J
    GT-TTE: Modeling Trajectories as Graphs for Travel Time Estimation
    Yunjie Huang, Xiaozhuang Song, Shiyao Zhang, and
    2 more authors Lei Li, James J. Q. Yu
    IEEE Internet of Things Journal, 2024
  3. ICLR
    PTaRL: Prototype-based Tabular Representation Learning via Space Calibration
    Hangting Ye, Wei Fan, Xiaozhuang Song, and
    4 more authors Shun Zheng, He Zhao, Dandan Guo, Yi Chang
    In International Conference on Learning Representations, 2024
    Spotlight
  4. BIBM
    Single Cell Gene Expression Prediction via Prototype-based Proximal Neural Factorization
    Xiaozhuang Song, Xu Liao, Hangting Ye, and
    4 more authors Yaoyao Xu, Wei Fan, Jin Liu, Tianshu Yu
    In IEEE International Conference on Bioinformatics and Biomedicine, 2024

2023

  1. T-ITS
    Traffic Prediction With Missing Data: A Multi-Task Learning Approach
    Ao Wang, Yongchao Ye, Xiaozhuang Song, and
    2 more authors Shiyao Zhang, JQ James
    IEEE Transactions on Intelligent Transportation Systems, 2023
  2. T-ITS
    Traffic Prediction With Transfer Learning: A Mutual Information-Based Approach
    Yunjie Huang, Xiaozhuang Song, Yuanshao Zhu, and
    2 more authors Shiyao Zhang, JQ James
    IEEE Transactions on Intelligent Transportation Systems, 2023

2022

  1. NeurIPS
    Efficient and effective multi-task grouping via meta learning on task combinations
    Xiaozhuang Song, Shun Zheng, Wei Cao, and
    2 more authors James Yu, Jiang Bian
    NeurIPS, 2022
  2. NeurIPS
    The CityLearn Challenge 2022: Overview, Results, and Lessons Learned
    Kingsley Nweye, Zoltan Nagy, Sharada Mohanty, and
    23 more authors Dipam Chakraborty, Siva Sankaranarayanan, Tianzhen Hong, Sourav Dey, Gregor Henze, Jan Drgona, Fangquan Lin, Wei Jiang, Hanwei Zhang, Zhongkai Yi, Jihai Zhang, Cheng Yang, Matthew Motoki, Sorapong Khongnawang, Michael Ibrahim, Abilmansur Zhumabekov, Daniel May, Zhihu Yang, Xiaozhuang Song, Han Zhang, Xiaoning Dong, Shun Zheng, Jiang Bian
    NeurIPS Competition Track, 2022

2021

  1. TCSS
    Complicating the social networks for better storytelling: An empirical study of Chinese historical text and novel
    Chenhan Zhang, Qingpeng Zhang, Shui Yu, and
    2 more authors JQ James, Xiaozhuang Song
    IEEE Transactions on Computational Social Systems, 2021
  2. ITSC
    Learn travel time distribution with graph deep learning and generative adversarial network
    Xiaozhuang Song, Chenhan Zhang, and JQ James
    In 2021 IEEE International Intelligent Transportation Systems Conference (ITSC), 2021
  3. ICANN
    TSTNet: a sequence to sequence transformer network for spatial-temporal traffic prediction
    Xiaozhuang Song, Ying Wu, and Chenhan Zhang
    In ICANN 2021, 2021
  4. ITSC
    Transfer learning in traffic prediction with graph neural networks
    Yunjie Huang, Xiaozhuang Song, Shiyao Zhang, and
    1 more author JQ James
    In 2021 IEEE International Intelligent Transportation Systems Conference (ITSC), 2021

2020

  1. ITSC
    Multimix: A multi-task deep learning approach for travel mode identification with few gps data
    Xiaozhuang Song, Christos Markos, and JQ James
    In 2020 IEEE 23rd International Conference on Intelligent Transportation Systems (ITSC), 2020