PhD student at NUS
NExT++ Research Center
NUS Institute of Data Science
NUS School of Computing

Email: acharkq at gmail.com
• Google Scholar Page • GitHub Page • Twitter/X

Biography

I am a PhD student at NExT++, where I am supervised by Prof. Chua Tat-Seng and co-supervised by Prof. Kawaguchi Kenji. I am also fortunate to be mentored by Prof. Wang Xiang at the University of Science and Technology of China (USTC). My research primarily focuses on AI for Science, particularly Multi-modal Generative Modeling for emerging scientific modalities such as molecules and proteins. Additionally, I have a keen interest in Graph Neural Networks and Natural Language Processing.

News

  • [New!] 2024/08 I am invited to speak as a panelist for the AI for Science BoF sesion at the ACL 2024 conference.
  • [New!] 2024/01 Three papers are accepted by ACL 2024! Many thanks to Yaorui, Junfeng and other collaborators!
         ReactXT: Understanding Molecular “Reaction-ship” via Reaction-Contextualized Molecule-Text Pretraining.
         ProtT3: Protein-to-Text Generation for Text-based Protein Understanding.
         MolTC: Towards Molecular Relational Modeling In Language Models.

  • [New!] 2024/01 One paper is accepted by ICLR 2024!
         Towards 3D Molecule-Text Interpretation in Language Models.

  • [New!] 2023/10 Two papers are accepted by EMNLP 2023, one for the EMNLP main conference and one for the EMNLP Findings!
         MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter.
         ReLM: Leveraging Language Models for Enhanced Chemical Reaction Prediction.

  • [New!] 2023/09 One paper is accepted by NeurIPS'23!
         Rethinking Tokenizer and Decoder in Masked Graph Modeling for Molecules.


    • Selected Publications (Google Scholar)

    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.

    * denotes equal contribution.

    Academic Service

    I am serving as an Action Editor (Area Chair) for ACL2024 (ARR Feburary 2024), EMNLP 2024 (ARR June 2024), and NAACL2024 (ARR December 2023). I have also served as a Reviewer for ICLR2024, NeurIPS 2024, NeurIPS2023, NeurIPS2022, NeurIPS2021, ICML2024, ICML2023, ICML2022, COLM 2024 etc. I am also reviewing top journals like TPAMI and TKDE.

    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

  • PhD student in Computer Science, NExT++, National University of Singapore, 2020-Present
         Supervisor: Prof. Chua Tat-Seng; Co-supervisor: Prof. Kawaguchi Kenji; Mentor: Prof. Wang Xiang
  • Bachelor in Physics, Xi'an Jiaotong University, 2015-2019