@article{wang2026large,
	title = {Making Large Language Models Reliable Data Science Programming Copilots for Biomedical Research},
	author = {Zifeng Wang and Benjamin Danek and Ziwei Yang and Zheng Chen and Jimeng Sun},
	journal = {Nature Biomedical Engineering},
	year = {2026},
	pages = {1--15},
	publisher = {Nature Publishing Group UK},
	url = {https://www.nature.com/articles/s41551-025-01587-2},
	doi = {10.1038/s41551-025-01587-2}
}


@article{wang2026empowering,
	title = {Empowering Biomedical Evidence Exploration and Synthesis with Deep Knowledge Graph Research},
	author = {Zifeng Wang and Zheng Chen and Ziwei Yang and Xuan Wang and Qiao Jin and Yifan Peng and Zhiyong Lu and Jimeng Sun},
	journal = {Nature Machine Intelligence},
	year = {2026},
	pages = {1--15},
	publisher = {Nature Publishing Group UK},
	url = {https://www.nature.com/articles/s42256-026-01266-0},
	doi = {10.1038/s42256-026-01266-0}
}


@article{yang2026graphgdel,
	title = {{GraphGDel}: Constructing and Learning Graph Representations of Genome-Scale Metabolic Models for Growth-Coupled Gene Deletion Prediction},
	author = {Ziwei Yang and Takeyuki Tamura},
	journal = {IEEE Transactions on Computational Biology and Bioinformatics},
	year = {2026},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/abstract/document/11614164/}
}


@inproceedings{kotoge2026targeted,
	title = {Targeted Pathway Inference for Biological Knowledge Bases via Graph Learning and Explanation},
	author = {Rikuto Kotoge and Ziwei Yang and Zheng Chen and Yushun Dong and Yasuko Matsubara and Jimeng Sun and Yasushi Sakurai},
	booktitle = {Proceedings of the AAAI Conference on Artificial Intelligence},
	year = {2026},
	volume = {40},
	number = {1},
	pages = {534--542},
	url = {https://ojs.aaai.org/index.php/AAAI/article/view/37017},
	doi = {10.1609/aaai.v40i1.37017}
}


@article{yang2025mlomics,
	title = {{MLOmics}: Cancer Multi-Omics Database for Machine Learning},
	author = {Ziwei Yang and Rikuto Kotoge and Xihao Piao and Zheng Chen and Lingwei Zhu and Peng Gao and Yasuko Matsubara and Yasushi Sakurai and Jimeng Sun},
	journal = {Scientific Data},
	year = {2025},
	volume = {12},
	number = {1},
	pages = {913},
	publisher = {Nature Publishing Group UK},
	url = {https://www.nature.com/articles/s41597-025-05235-x},
	doi = {10.1038/s41597-025-05235-x}
}


@inproceedings{yang2025gesubnet,
	title = {{GeSubNet}: Gene Interaction Inference for Disease Subtype Network Generation},
	author = {Ziwei Yang and Zheng Chen and Xin Liu and Rikuto Kotoge and Peng Chen and Yasuko Matsubara and Yasushi Sakurai and Jimeng Sun},
	booktitle = {International Conference on Learning Representations (ICLR)},
	year = {2025},
	url = {https://proceedings.iclr.cc/paper_files/paper/2025/hash/a924b7178e5975dfed1de235f0b72973-Abstract-Conference.html}
}


@article{yang2025dbgdel,
	title = {{DBgDel}: Database-Enhanced Gene Deletion Framework for Growth-Coupled Production in Genome-Scale Metabolic Models},
	author = {Ziwei Yang and Takeyuki Tamura},
	journal = {IEEE Transactions on Computational Biology and Bioinformatics},
	year = {2025},
	volume = {22},
	number = {4},
	pages = {1415--1427},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/document/10945660}
}


@article{yang2025deepgdel,
	title = {{DeepGDel}: Deep Learning-Based Gene Deletion Prediction Framework for Growth-Coupled Production in Genome-Scale Metabolic Models},
	author = {Ziwei Yang and Takeyuki Tamura},
	journal = {IEEE Transactions on Computational Biology and Bioinformatics},
	year = {2025},
	volume = {22},
	number = {5},
	pages = {2252--2266},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/abstract/document/11082676/},
	doi = {10.1109/TCBBIO.2025.3590141}
}


@article{zhang2024strategic,
	title = {Strategic Multi-Omics Data Integration via Multi-Level Feature Contrasting and Matching},
	author = {Jinli Zhang and Hongwei Ren and Zongli Jiang and Zheng Chen and Ziwei Yang and Yasuko Matsubara and Yasushi Sakurai},
	journal = {IEEE Transactions on NanoBioscience},
	year = {2024},
	volume = {23},
	number = {4},
	pages = {579--590},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/abstract/document/10672554/}
}


@article{chen2023sleep,
	title = {Automated Sleep Staging via Parallel Frequency-Cut Attention},
	author = {Zheng Chen and Ziwei Yang and Lingwei Zhu and Wei Chen and Toshiyo Tamura and Naoaki Ono and Md Altaf-Ul-Amin and Shigehiko Kanaya and Ming Huang},
	journal = {IEEE Transactions on Neural Systems and Rehabilitation Engineering},
	year = {2023},
	volume = {31},
	pages = {1974--1985},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/document/10041186/}
}


@article{yang2023vector,
	title = {Learning Vector Quantized Representation for Cancer Subtypes Identification},
	author = {Ziwei Yang and Zheng Chen and Lingwei Zhu and Peng Gao and Takashi Matsubara and Shigehiko Kanaya and Md Altaf-Ul-Amin},
	journal = {Computer Methods and Programs in Biomedicine},
	year = {2023},
	volume = {236},
	pages = {107543},
	publisher = {Elsevier},
	url = {https://www.sciencedirect.com/science/article/pii/S0169260723002080},
	doi = {10.1016/j.cmpb.2023.107543}
}


@inproceedings{chen2023cancer,
	title = {Automated Cancer Subtyping via Vector Quantization Mutual Information Maximization},
	author = {Zheng Chen and Lingwei Zhu and Ziwei Yang and Takashi Matsubara},
	booktitle = {Joint European Conference on Machine Learning and Knowledge Discovery in Databases (ECML-PKDD)},
	year = {2022},
	pages = {88--103},
	publisher = {Springer International Publishing},
	url = {https://link.springer.com/chapter/10.1007/978-3-031-26387-3_6},
	doi = {10.1007/978-3-031-26387-3_6}
}


@inproceedings{yang2023moclim,
	title = {{MoCLIM}: Towards Accurate Cancer Subtyping via Multi-Omics Contrastive Learning with Omics-Inference Modeling},
	author = {Ziwei Yang and Zheng Chen and Yasuko Matsubara and Yasushi Sakurai},
	booktitle = {ACM International Conference on Information and Knowledge Management (CIKM)},
	year = {2023},
	pages = {2895--2905},
	url = {https://dl.acm.org/doi/abs/10.1145/3583780.3614970},
	doi = {10.1145/3583780.3614970}
}


@article{chen2023sleep2,
	title = {Sleep Staging Framework with Physiologically Harmonized Sub-Networks},
	author = {Zheng Chen and Ziwei Yang and Dong Wang and Xin Zhu and Naoaki Ono and Md Altaf-Ul-Amin and Shigehiko Kanaya and Ming Huang},
	journal = {Methods},
	year = {2023},
	volume = {209},
	pages = {18--28},
	publisher = {Academic Press},
	url = {https://www.sciencedirect.com/science/article/pii/S1046202322002420},
	doi = {10.1016/j.ymeth.2022.11.003}
}


@inproceedings{jiang2023mfhcc,
	title = {{MFHCC}: Multi-View Feature Hierarchical Contrastive Clustering Model for Multi-Omics Data},
	author = {Zongli Jiang and Hongwei Ren and Ziwei Yang and Jinli Zhang and Zheng Chen},
	booktitle = {IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
	year = {2023},
	pages = {1182--1187},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/abstract/document/10385651/}
}


@inproceedings{chen2022multi,
	title = {Multi-Tier Platform for Cognizing Massive Electroencephalogram},
	author = {Zheng Chen and Lingwei Zhu and Ziwei Yang and Renyuan Zhang},
	booktitle = {International Joint Conference on Artificial Intelligence (IJCAI)},
	year = {2022},
	pages = {2464--2470},
	url = {https://arxiv.org/abs/2204.09840},
	doi = {10.24963/ijcai.2022/342}
}


@inproceedings{jia2022sleep,
	title = {Automatic Sleep Staging via Frequency-Wise Spiking Neural Networks},
	author = {Haohui Jia and Ziwei Yang and Pei Gao and Man Wu and Chen Li and Yirong Kan and Renyuan Zhang},
	booktitle = {IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
	year = {2022},
	pages = {1028--1033},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/abstract/document/9995710/}
}


@inproceedings{zhu2022adaptive,
	title = {Adaptive Spike-Like Representation of {EEG} Signals for Sleep Stages Scoring},
	author = {Lingwei Zhu and Ziwei Yang and Koki Odani and Guang Shi and Yirong Kan and Zheng Chen and Renyuan Zhang},
	booktitle = {International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC)},
	year = {2022},
	pages = {4453--4456},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/abstract/document/9871250/}
}


@inproceedings{yang2022hierarchical,
	title = {Hierarchical Categorical Generative Modeling for Multi-omics Cancer Subtyping},
	author = {Ziwei Yang and Lingwei Zhu and Chen Li and Zheng Chen and Naoki Ono and Md Altaf-Ul-Amin and Shigehiko Kanaya},
	booktitle = {IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
	year = {2022},
	pages = {1350--1355},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/abstract/document/9994928/},
	doi = {10.1109/BIBM55620.2022.9994928}
}


@inproceedings{yang2022cancer,
	title = {Cancer Subtyping via Embedded Unsupervised Learning on Transcriptomics Data},
	author = {Ziwei Yang and Lingwei Zhu and Zheng Chen and Ming Huang and Naoaki Ono and Md Altaf-Ul-Amin and Shigehiko Kanaya},
	booktitle = {International Conference of the IEEE Engineering in Medicine \& Biology Society (EMBC)},
	year = {2022},
	pages = {1113--1116},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/abstract/document/9870903/}
}


@inproceedings{shu2022feasibility,
	title = {Exploring the Feasibility of Transformer Based Models on Question Relatedness},
	author = {Honglin Shu and Pei Gao and Ziwei Yang and Chen Li and Man Wu},
	booktitle = {IEEE International Conference on High Performance Computing \& Communications (HPCC)},
	year = {2022},
	pages = {831--838},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/abstract/document/10074888/}
}


@inproceedings{chen2021end,
	title = {An End-to-End Sleep Staging Simulator Based on Mixed Deep Neural Networks},
	author = {Zheng Chen and Ziwei Yang and Dong Wang and Ming Huang and Naoaki Ono and Md Altaf-Ul-Amin and Shigehiko Kanaya},
	booktitle = {IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
	year = {2021},
	pages = {848--853},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/abstract/document/9669384/}
}


@inproceedings{yang2021feasibility,
	title = {Exploring Feasibility of Truth-Involved Automatic Sleep Staging Combined with Transformer},
	author = {Ziwei Yang and Dong Wang and Zheng Chen and Ming Huang and Naoaki Ono and Md Altaf-Ul-Amin and Shigehiko Kanaya},
	booktitle = {IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
	year = {2021},
	pages = {2920--2923},
	publisher = {IEEE},
	url = {https://ieeexplore.ieee.org/document/9669456/}
}