A model-driven algorithm for doublet identification in single-cell RNA-sequencing data.
@article{zhao2023scmodd,
title={scMODD: A model-driven algorithm for doublet identification in single-cell RNA-sequencing data},
author={Zhao, Xinye and Du, Alexander and Qiu, Peng},
journal={Frontiers in Systems Biology},
volume={2},
pages={1082309},
year={2023},
doi={10.3389/fsysb.2022.1082309}
}
Disentangled learning for integration and prediction across multi-batch, multi-condition single-cell RNA-sequencing data.
@article{zhang2024scdisinfact,
title={scDisInFact: Disentangled Learning for the Integration and Prediction of Multi-Batch, Multi-Condition Single-Cell RNA-Sequencing Data},
author={Zhang, Ziqi and Zhao, Xinye and Bindra, Mehak and Qiu, Peng and Zhang, Xiuwei},
journal={Nature Communications},
volume={15},
number={1},
pages={912},
year={2024},
doi={10.1038/s41467-024-45227-w}
}
Efficient KVCache sharing for semantically similar prompts via token-level LSH matching.
@inproceedings{zhao2025semsharekv,
title={SemShareKV: Efficient KVCache Sharing for Semantically Similar Prompts via Token-Level LSH Matching},
author={Zhao, Xinye and Mastorakis, Spyridon},
booktitle={Proceedings of IJCNLP 2025},
year={2025}
}
An empirical study of security-related agentic pull requests on GitHub.
@article{siddiq2026security,
title={Security in the Age of AI Teammates: An Empirical Study of Agentic Pull Requests on GitHub},
author={Siddiq, Mohammed Latif and Zhao, Xinye and Lopes, Vinicius Carvalho and Casey, Beatrice and Santos, Joanna C. S.},
journal={arXiv},
year={2026}
}
A multi-agent assisted static analysis framework for Java vulnerability detection that improves precision through stage-specific reasoning.
@inproceedings{zhao2026trivul,
title={TriVul: Improving Precision of Static Vulnerability Detection through Multi-Agent Reasoning},
author={Zhao, Xinye and Santos, Joanna C. S.},
booktitle={SAS'26: 33rd Static Analysis Symposium},
year={2026},
note={Accepted}
}
A budget-aware approach for early candidate selection in vulnerability analysis workflows.
A static-analysis-guided LLM pipeline for security tactic-aware vulnerability repair in Java programs.
Preprint |
@article{siddiq2026strata,
title={STRATA: A Security Tactic-Aware Framework for LLM-Based Vulnerability Repair},
author={Siddiq, Mohammed Latif and Zhao, Xinye and Santos, Joanna Cecilia da Silva},
journal={SSRN},
year={2026},
note={Preprint, SSRN 6799069},
url={https://papers.ssrn.com/sol3/papers.cfm?abstract_id=6799069}
}
Teaching Assistant, University of Notre Dame, 2025
Teaching Assistant for Computer Networks (CSE 30264) at the University of Notre Dame in Spring 2025.
Teaching Assistant, University of Notre Dame, 2025
Teaching Assistant for Systems Programming (CSE 20289) at the University of Notre Dame in Fall 2025.