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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
portfolio
publications
scMODD: A model-driven algorithm for doublet identification in single-cell RNA-sequencing data
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}
}
scDisInFact: Disentangled Learning for the Integration and Prediction of Multi-Batch, Multi-Condition Single-Cell RNA-Sequencing Data
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}
}
SemShareKV: Efficient KVCache Sharing for Semantically Similar Prompts via Token-Level LSH Matching
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}
}
Security in the Age of AI Teammates: An Empirical Study of Agentic Pull Requests on GitHub
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}
}
TriVul: Improving Precision of Static Vulnerability Detection through Multi-Agent Reasoning
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}
}
Towards Budget-Aware Early Candidate Selection for Vulnerability Analysis
A budget-aware approach for early candidate selection in vulnerability analysis workflows.
STRATA: A Security Tactic-Aware Framework for LLM-Based Vulnerability Repair
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}
}
talks
teaching
Computer Networks (CSE 30264)
Teaching Assistant, University of Notre Dame, 2025
Teaching Assistant for Computer Networks (CSE 30264) at the University of Notre Dame in Spring 2025.
Systems Programming (CSE 20289)
Teaching Assistant, University of Notre Dame, 2025
Teaching Assistant for Systems Programming (CSE 20289) at the University of Notre Dame in Fall 2025.