(†: equal contribution, ~: corresponding author)

Journal Paper

• Toward Automatic Inference of Glycan Linkages Using MSn and Machine Learning─Proof of Concept Using Sialic Acid Linkages
  Xinyi Ni, Nathan B Murray, Stephanie Archer-Hartmann, Lauren E Pepi, Richard F Helm, Parastoo Azadi, Pengyu Hong
  Journal of the American Society for Mass Spectrometry.
  

Preprints

• Doc2Agent: Scalable Generation of Tool-Using Agents from API Documentation
  Xinyi Ni, Haonan Jian, Qiuyang Wang, Vedanshi Chetan Shah, Pengyu Hong
  

• ToolFactory: Automating Tool Generation by Leveraging LLM to Understand REST API Documentations
  Xinyi Ni, Qiuyang Wang, Yukun Zhang, Haonan Jian, Pengyu Hong
  

• Multiple Abstraction Level Retrieve Augment Generation
  Zheng Zheng, Xinyi Ni, Pengyu Hong
  

• Reflections from the 2024 large language model (llm) hackathon for applications in materials science and chemistry
  Yoel Zimmermann et al.