Publications

@article{Yin_2026,
  title={MapsTorch: automatic differentiation for X-ray fluorescence data analysis},
  volume={33},
  ISSN={1600-5775},
  url={http://dx.doi.org/10.1107/s160057752501032x},
  DOI={10.1107/s160057752501032x},
  number={1},
  journal={Journal of Synchrotron Radiation},
  publisher={International Union of Crystallography (IUCr)},
  author={Yin, Xiangyu and Di, Zichao and Antipova, Olga and Chen, Si and Jiang, Yi and Glowacki, Arthur},
  year={2026}, month=Jan,
  pages={235–245}
}

@article{Pratiush_2025,
  title={Mic-hackathon 2024: hackathon on machine learning for electron and scanning probe microscopy},
  volume={6},
  ISSN={2632-2153},
  url={http://dx.doi.org/10.1088/2632-2153/ae1f5d},
  DOI={10.1088/2632-2153/ae1f5d},
  number={4},
  journal={Machine Learning: Science and Technology},
  publisher={IOP Publishing},
  author={Pratiush, Utkarsh and Houston, Austin and Barakati, Kamyar and Raghavan, Aditya and Bulanadi, Ralph and Yin, Xiangyu and Welborn, Samuel S and Yoon, Dasol and K P, Harikrishnan and Baraissov, Zhaslan and Ma, Desheng and Jakowski, Mikolaj and Barhorst, Shawn-Patrick and Pattison, Alexander J and Manganaris, Panayotis and Madugula, Sita Sirisha and Gayathri Ayyagari, Sai Venkata and Kennedy, Vishal and Wang, Michelle and Pang, Kieran J and Addison-Smith, Ian and Menacho, Willy and Guzman, Horacio V and Kiefer, Alexander and Furth, Nicholas and Kolev, Nikola L and Petrov, Mikhail and Liu, Viktoriia and Ilyev, Sergey and Rairao, Srikar and Rodani, Tommaso and Pinto-Huguet, Ivan and Chen, Xuli and Cruañes, Josep and Torrens, Marta and Pomar, Jovan and Su, Fanzhi and Vedanti, Pawan and Lyu, Zhiheng and Wang, Xingzhi and Yao, Lehan and Taqieddin, Amir and Laskowski, Forrest and Shao, Yu-Tsun and Fein-Ashley, Benjamin and Jiang, Yi and Kumar, Vineet and Mishra, Himanshu and Paul, Yogesh and Bazgir, Adib and Praneeth Madugula, Rama Chandra and Zhang, Yuwen and Omprakash, Pravan and Huang, Jian and Montufar-Morales, Eric and Chawla, Vivek and Sethi, Harshit and Huang, Jie and Kurki, Lauri and Guinan, Grace and Salvador, Addison and Ter-Petrosyan, Arman and Van Winkle, Madeline and Spurgeon, Steven R and Narasimha, Ganesh and Wu, Zijie and Liu, Richard and Liu, Yongtao and Slautin, Boris and Lupini, Andrew R and Vasudevan, Rama and Duscher, Gerd and Kalinin, Sergei V},
  year={2025}, month=Dec,
  pages={040701}
}

@article{Yin_2022,
  title={Search methods for inorganic materials crystal structure prediction},
  volume={35},
  ISSN={2211-3398},
  url={http://dx.doi.org/10.1016/j.coche.2021.100726},
  DOI={10.1016/j.coche.2021.100726},
  journal={Current Opinion in Chemical Engineering},
  publisher={Elsevier BV},
  author={Yin, Xiangyu and Gounaris, Chrysanthos E},
  year={2022}, month=Mar,
  pages={100726}
}

@article{Yin_2022,
  title={Computational discovery of Metal–Organic Frameworks for sustainable energy systems: Open challenges},
  volume={167},
  ISSN={0098-1354},
  url={http://dx.doi.org/10.1016/j.compchemeng.2022.108022},
  DOI={10.1016/j.compchemeng.2022.108022},
  journal={Computers & Chemical Engineering},
  publisher={Elsevier BV},
  author={Yin, Xiangyu and Gounaris, Chrysanthos E.},
  year={2022}, month=Nov,
  pages={108022}
}

@article{Hanselman_2022,
  title={MatOpt: A Python Package for Nanomaterials Design Using Discrete Optimization},
  volume={62},
  ISSN={1549-960X},
  url={http://dx.doi.org/10.1021/acs.jcim.1c00984},
  DOI={10.1021/acs.jcim.1c00984},
  number={2},
  journal={Journal of Chemical Information and Modeling},
  publisher={American Chemical Society (ACS)},
  author={Hanselman, Christopher L. and Yin, Xiangyu and Miller, David C. and Gounaris, Chrysanthos E.},
  year={2022}, month=Jan,
  pages={295–308}
}

@article{Yin_2021,
  title={Designing stable bimetallic nanoclusters via an iterative two-step optimization approach},
  volume={6},
  ISSN={2058-9689},
  url={http://dx.doi.org/10.1039/d1me00027f},
  DOI={10.1039/d1me00027f},
  number={7},
  journal={Molecular Systems Design & Engineering},
  publisher={Royal Society of Chemistry (RSC)},
  author={Yin, Xiangyu and Isenberg, Natalie M. and Hanselman, Christopher L. and Dean, James R. and Mpourmpakis, Giannis and Gounaris, Chrysanthos E.},
  year={2021},
  pages={545–557}
}

@misc{https://doi.org/10.48550/arxiv.2605.11359, doi = {10.48550/ARXIV.2605.11359}, url = {https://arxiv.org/abs/2605.11359}, author = {Du, Ming and Yin, Xiangyu and Luo, Yanqi and Beniwal, Dishant and Tang, Songyuan and Sharma, Hemant and Cherukara, Mathew J.}, keywords = {Artificial Intelligence (cs.AI), Data Analysis, Statistics and Probability (physics.data-an), FOS: Computer and information sciences, FOS: Computer and information sciences, FOS: Physical sciences, FOS: Physical sciences, I.2.2, 68T42}, title = {CVEvolve: Autonomous Algorithm Discovery for Unstructured Scientific Data Processing}, publisher = {arXiv}, year = {2026}, copyright = {Creative Commons Attribution 4.0 International}
}

@misc{https://doi.org/10.48550/arxiv.2603.23367, doi = {10.48550/ARXIV.2603.23367}, url = {https://arxiv.org/abs/2603.23367}, author = {Andrejevic, Nina and Du, Ming and Sharma, Hemant and Horwath, James P. and Luo, Aileen and Yin, Xiangyu and Prince, Michael and Toby, Brian H. and Cherukara, Mathew J.}, keywords = {Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, FOS: Physical sciences}, title = {AlphaDiffract: Automated Crystallographic Analysis of Powder X-ray Diffraction Data}, publisher = {arXiv}, year = {2026}, copyright = {Creative Commons Attribution Non Commercial Share Alike 4.0 International}
}

@misc{https://doi.org/10.48550/arxiv.2603.05696, doi = {10.48550/ARXIV.2603.05696}, url = {https://arxiv.org/abs/2603.05696}, author = {Yin, Xiangyu and Du, Ming and Deng, Junjing and Yang, Zhi and Han, Yimo and Jiang, Yi}, keywords = {Computational Engineering, Finance, and Science (cs.CE), Artificial Intelligence (cs.AI), Computation and Language (cs.CL), Numerical Analysis (math.NA), FOS: Computer and information sciences, FOS: Computer and information sciences, FOS: Mathematics, FOS: Mathematics}, title = {Autonomous Algorithm Discovery for Ptychography via Evolutionary LLM Reasoning}, publisher = {arXiv}, year = {2026}, copyright = {Creative Commons Attribution 4.0 International}
}

@misc{https://doi.org/10.48550/arxiv.2511.02503, doi = {10.48550/ARXIV.2511.02503}, url = {https://arxiv.org/abs/2511.02503}, author = {Umeike, Robinson and Getty, Neil and Xiangyu, Yin and Jiang, Yi}, keywords = {Computer Vision and Pattern Recognition (cs.CV), FOS: Computer and information sciences, FOS: Computer and information sciences}, title = {Adapting General-Purpose Foundation Models for X-ray Ptychography in Low-Data Regimes}, publisher = {arXiv}, year = {2025}, copyright = {Creative Commons Attribution Non Commercial Share Alike 4.0 International}
}

@misc{https://doi.org/10.48550/arxiv.2410.09034, doi = {10.48550/ARXIV.2410.09034}, url = {https://arxiv.org/abs/2410.09034}, author = {Yin, Xiangyu and Shi, Chuqiao and Han, Yimo and Jiang, Yi}, keywords = {Computational Engineering, Finance, and Science (cs.CE), Artificial Intelligence (cs.AI), Computation and Language (cs.CL), Multiagent Systems (cs.MA), FOS: Computer and information sciences, FOS: Computer and information sciences}, title = {PEAR: A Robust and Flexible Automation Framework for Ptychography Enabled by Multiple Large Language Model Agents}, publisher = {arXiv}, year = {2024}, copyright = {arXiv.org perpetual, non-exclusive license}
}

@article{Yin_2025,
  title={Nodeology: Creating Graph-based Agentic Workflows for AI-Assisted Electron Microscopy},
  volume={31},
  ISSN={1435-8115},
  url={http://dx.doi.org/10.1093/mam/ozaf048.1108},
  DOI={10.1093/mam/ozaf048.1108},
  number={Supplement_1},
  journal={Microscopy and Microanalysis},
  publisher={Oxford University Press (OUP)},
  author={Yin, Xiangyu and Shi, Chuqiao and Fein-Ashley, Benjamin and Shao, Yu-Tsun and Han, Yimo and Jiang, Yi},
  year={2025}, month=July }

@article{Jiang_2025,
  title={Empowering Electron Ptychography with Generative Artificial Intelligence and Agentic Workflows},
  volume={31},
  ISSN={1435-8115},
  url={http://dx.doi.org/10.1093/mam/ozaf048.1061},
  DOI={10.1093/mam/ozaf048.1061},
  number={Supplement_1},
  journal={Microscopy and Microanalysis},
  publisher={Oxford University Press (OUP)},
  author={Jiang, Yi and Yin, Xiangyu and Shi, Chuqiao and Fein-Ashley, Benjamin and Shao, Yu-Tsun and Han, Yimo},
  year={2025}, month=July }

@article{Yin_2025,
  title={Accelerating Ptychography Algorithm Development with Reasoning Large Language Models},
  volume={31},
  ISSN={1435-8115},
  url={http://dx.doi.org/10.1093/mam/ozaf048.039},
  DOI={10.1093/mam/ozaf048.039},
  number={Supplement_1},
  journal={Microscopy and Microanalysis},
  publisher={Oxford University Press (OUP)},
  author={Yin, Xiangyu and Shi, Chuqiao and Han, Yimo and Jiang, Yi},
  year={2025}, month=July }

@inproceedings{Jiang_2025,
  title={LLM-assisted workflows for x-ray ptychography at the advanced photon source},
  url={http://dx.doi.org/10.1117/12.3065346},
  DOI={10.1117/12.3065346},
  booktitle={X-Ray Nanoimaging: Instruments and Methods VII},
  publisher={SPIE},
  author={Jiang, Yi and Yin, Xiangyu and Luktuke, Amey and Luo, Yanqi and Deng, Junjing},
  editor={Lai, Barry and Chu, Yong S.},
  year={2025}, month=Sept,
  pages={3}
}

@inproceedings{Yin_2025,
  title={Empowering x-ray science with LLMs and agentic workflow},
  url={http://dx.doi.org/10.1117/12.3065753},
  DOI={10.1117/12.3065753},
  booktitle={X-Ray Nanoimaging: Instruments and Methods VII},
  publisher={SPIE},
  author={Yin, Xiangyu and Luktuke, Amey and Luo, Yanqi and Deng, Junjing and Glowacki, Arthur and Jiang, Yi},
  editor={Lai, Barry and Chu, Yong S.},
  year={2025}, month=Sept,
  pages={15}
}

@article{Yin_2024,
  title={PEAR: A Knowledge-guided Autonomous Pipeline for Ptychography Enabled by Large Language Models},
  volume={30},
  ISSN={1435-8115},
  url={http://dx.doi.org/10.1093/mam/ozae044.184},
  DOI={10.1093/mam/ozae044.184},
  number={Supplement_1},
  journal={Microscopy and Microanalysis},
  publisher={Oxford University Press (OUP)},
  author={Yin, Xiangyu and Shi, Chuqiao and Deng, Junjing and Han, Yimo and Jiang, Yi},
  year={2024}, month=July }

@article{Yin_2024,
  title={Automating X-ray Fluorescence Mapping with Differentiable Modeling},
  volume={30},
  ISSN={1435-8115},
  url={http://dx.doi.org/10.1093/mam/ozae044.1017},
  DOI={10.1093/mam/ozae044.1017},
  number={Supplement_1},
  journal={Microscopy and Microanalysis},
  publisher={Oxford University Press (OUP)},
  author={Yin, Xiangyu and Wendy Di, Zichao and Antipova, Olga and Chen, Si and Jiang, Yi and Glowacki, Arthur},
  year={2024}, month=July }

@article{Yin_2024,
  title={Pushing the Limits of Electron Ptychography with Physics-informed Bayesian Optimization},
  volume={30},
  ISSN={1435-8115},
  url={http://dx.doi.org/10.1093/mam/ozae044.906},
  DOI={10.1093/mam/ozae044.906},
  number={Supplement_1},
  journal={Microscopy and Microanalysis},
  publisher={Oxford University Press (OUP)},
  author={Yin, Xiangyu and Yang, Zhi and Han, Yimo and Jiang, Yi},
  year={2024}, month=July }