Biography

I am a Postdoc Research Fellow at ZhangLab/DeepMed, supervised by Prof. Yang Zhang. Previously, I completed my PhD at the NExT++ lab at NUS, where I was supervised by Prof. Tat-Seng Chua and co-supervised by Prof. Kenji Kawaguchi. I was also fortunate to be mentored by Prof. Xiang Wang at the University of Science and Technology of China (USTC). Before my PhD, I spent nine wonderful months at THUNLP, where I was supervised by Prof. Zhiyuan Liu. Yes, my first supervisor's name spells the same as mine! My research primarily focuses on AI for Science, particularly Multi-modal Generative Modeling for emerging scientific modalities such as proteins, RNAs, single-cell, and small molecules. Additionally, I have a keen interest in Diffusion Models, Language Models, Natural Language Processing, and Geometric Deep Learning.

Prospective Collaborations

I am always looking for passionate and motivated graduate and undergraduate students to collaborate with me on AI for Science. Feel free to shoot me an Email if you’re interested in having a chat over coffee at the Coffee Bean & Tea Leaf at the School of Computing of NUS.

News

Selected Publications (Google Scholar)

KDD'26	Language-Enhanced Representation Learning for Single-Cell Transcriptomics. [Paper; Code] Jiaqi Yang, Zhiyuan Liu†, Yaorui Shi, Qingchuan Zhang, Changhao Nai, Junfeng Fang, Yahui Long†, Yang Zhang, Xiang Wang†.
NeurIPS'25	Towards Unified and Lossless Latent Space for 3D Molecular Latent Diffusion Modeling. [Paper; Code] Yanchen Luo, Zhiyuan Liu†, Yi Zhao, Sihang Li, Hengxing Cai, Kenji Kawaguchi, Tat-Seng Chua, Yang Zhang, Xiang Wang†.
NeurIPS'25	EnzyControl: Adding Functional and Substrate-Specific Control for Enzyme Backbone Generation. [Paper; Code] Chao Song*, Zhiyuan Liu*, Han Huang, Liang Wang, Qiong Wang, Jian-Yu Shi, Hui Yu, Yihang Zhou, Yang Zhang
NeurIPS'25	3D-GSRD: 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding. [Paper; Code] Chang Wu*, Zhiyuan Liu*, Wen Shu, Liang Wang, Yanchen Luo, Wenqiang Lei, Yatao Bian, Junfeng Fang, Xiang Wang
NeurIPS'25	Learning 3D Anisotropic Noise Distributions Improves Molecular Force Fields. [Paper; Code] Xixian Liu, Rui Jiao, Zhiyuan Liu†, Yurou Liu, Yang Liu, Ziheng Lu, Wenbing Huang†, Yang Zhang, Yixin Cao
NeurIPS'25	PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs. [Paper; Code] Xinzhe Zheng, Hao Du, Fanding Xu, Jinzhe Li, Zhiyuan Liu†, Wenkang Wang, Tao Chen, Wanli Ouyang, Stan Z. Li, Yan Lu†, Nanqing Dong†, Yang Zhang†.
ICLR'25	NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation. [Paper; Code] Zhiyuan Liu*, Yanchen Luo*, Han Huang, Enzhi Zhang, Sihang Li, Junfeng Fang, Yaorui Shi, Xiang Wang, Kenji Kawaguchi, Tat-Seng Chua.
ACL'24	ProtT3: Protein-to-Text Generation for Text-based Protein Understanding. [Paper; Code] Zhiyuan Liu, An Zhang, Hao Fei, Enzhi Zhang, Xiang Wang, Kenji Kawaguchi, Tat-Seng Chua.
ACL Findings'24	ReactXT: Understanding Molecular “Reaction-ship” via Reaction-Contextualized Molecule-Text Pretraining. [Paper; Code; Demo; Website] Zhiyuan Liu*, Yaorui Shi*, An Zhang, Sihang Li, Enzhi Zhang, Xiang Wang, Kenji Kawaguchi, Tat-Seng Chua.
ICLR'24	Towards 3D Molecule-Text Interpretation in Language Models. [Paper; Code] Sihang Li*, Zhiyuan Liu*, Yanchen Luo, Xiang Wang, Xiangnan He, Kenji Kawaguchi, Tat-Seng Chua, Qi Tian.
EMNLP'23	MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter. [Paper; Code; Website] Zhiyuan Liu, Sihang Li, Yanchen Luo, Hao Fei, Yixin Cao, Kenji Kawaguchi, Xiang Wang, and Tat-Seng Chua.
NeurIPS'23	Rethinking Tokenizer and Decoder in Masked Graph Modeling for Molecules. [Paper; Code] Zhiyuan Liu, Yaorui Shi, An Zhang, Enzhi Zhang, Kenji Kawaguchi, Xiang Wang, and Tat-Seng Chua
EMNLP'20	Exploring and Evaluating Attributes, Values, and Structures for Entity Alignment. [Paper; Code] Zhiyuan Liu, Yixin Cao, Liangming Pan, Juanzi Li, Zhiyuan Liu, and Tat-Seng Chua.
ACL'19	Multi-Channel Graph Neural Network for Entity Alignment. [Paper; Code] Yixin Cao, Zhiyuan Liu, Chengjiang Li, Zhiyuan Liu, Juanzi Li, and Tat-Seng Chua.

* Equal contribution.

† Corresponding author.

Mentees (by the time of starting mentorship)

2025	Changhao Nai (HIT Undergraduate -> ); Qingchuan Zhang (USTC Undergraduate -> ); Xinzhe Zheng (NUS Master -> ); Chengxin Hu (NUS Master -> )
2024	Jiaqi Yang (USTC Undergraduate -> USTC Master); Chang Wu (USTC Undergraduate -> USTC Master); Wen Shu (SCU Undergraduate -> SCU PhD); Ze Yuan (USTC Undergraduate -> )
2023	Chao Song (NWPU Master -> Bytedance)
2022	Yaorui Shi (XJTU Undergraduate -> USTC Master -> USTC PhD); Yu Sun (NUS Master -> Bytedance)

Academic Service

Area Chair: ACL2025 (ARR Feburary 2025), ACL2024 (ARR Feburary 2024), EMNLP 2024 (ARR June 2024), and NAACL2024 (ARR December 2023)

Conference Reviewer: ICLR 2026, ICLR 2025, ICLR2024, NeurIPS 2025,NeurIPS 2024, NeurIPS2023, NeurIPS2022, NeurIPS2021, ICML 2025, ICML2024, ICML2023, ICML2022, COLM 2024.

Journal Reviewer: Nature Communications, TPAMI, TKDE.

Guest Lecturer

CS6222, Advanced Topics in Computational Biology, Spring 2024 – 2025

Teaching Assistant

IT1244, Artificial Intelligence: Technology and Impact, Spring 2021 – 2022

CS3244, Machine Learning, Fall 2021 – 2022

CS3245, Information Retrieval, Spring 2020 – 2021

Honors and Awards

Dean's Graduate Research Excellence Award, National University of Singapore 2023

Student Research Award, Institue of Data Science at NUS 2023

Research Achievement Award, National University of Singapore 2021

National Group First Prize, the 7th China Undergraduate Physics Tournament 2016

Background

Postdoc Research Fellow, ZhangLab/DeepMed, National University of Singapore, 2025-Present
     Supervisor: Prof. Zhang Yang

PhD in Computer Science, NExT++, National University of Singapore, 2020-2024
     Supervisor: Prof. Chua Tat-Seng; Co-supervisor: Prof. Kawaguchi Kenji; Mentor: Prof. Wang Xiang

Bachelor in Physics, Xi'an Jiaotong University, 2015-2019