I work at the intersection of computational biology and artificial intelligence, developing AI systems for understanding, modeling, and engineering biological systems.
My research connects two directions:
Mechanistic Biological Modeling — combining genome-scale models, biological knowledge, and data-driven learning to model and engineer complex biological systems.
AI Agents for Scientific Discovery — developing intelligent agents that integrate multimodal biological data, reason over scientific knowledge, and assist with biomedical research.
Current Focus
Building AI systems that bridge data-driven learning and mechanistic modeling for metabolic engineering and biomedical discovery.
Zifeng Wang, Benjamin Danek, Ziwei Yang, Zheng Chen, Jimeng Sun
Nature Biomedical Engineering
Benchmarking 16 LLMs on 293 coding tasks from 39 biomedical studies shows overall accuracy below 40%; an agent that first drafts and iteratively refines an analysis plan reaches 74%.
@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}
}
An open cancer multi-omics database for machine learning: 8,314 patients across 32 cancer types with four omics types, stratified feature versions and baseline benchmarks.
@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}
}
@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}
}
International Joint Conference on Artificial Intelligence (IJCAI)
A multi-tier platform chaining a spiking neural network and a Transformer for EEG sleep staging, reaching 87% overall accuracy from EEG alone on datasets of up to 42,560 hours from 5,793 subjects.
@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}
}
@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/}
}
2023
IEEE TNSRE
Automated Sleep Staging via Parallel Frequency-Cut AttentionZheng Chen, Ziwei Yang, Lingwei Zhu, Wei Chen, Toshiyo Tamura, Naoaki Ono, Md Altaf-Ul-Amin, Shigehiko Kanaya, Ming HuangIEEE Transactions on Neural Systems and Rehabilitation Engineering, 2023
@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{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{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{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/}
}
CrossGapFilling, a context-aware hypergraph neural network for cross-species metabolic network gap-filling (from my previous internship at Chugai Pharmaceutical), presented at ISCB-AI 2026.
Co-authored paper on deep knowledge graph research for biomedical evidence exploration and synthesis published in Nature Machine Intelligence.
Joined Keiji AI as a Bioinformatics Scientist.
Received my Ph.D. in Informatics from Kyoto University.
Paper on targeted pathway inference for biological knowledge bases published in the AAAI 2026 proceedings.
Co-authored paper on making LLMs reliable data-science programming copilots published in Nature Biomedical Engineering.
Gene-deletion prediction frameworks DBgDel, DeepGDel and GraphGDel published in IEEE/ACM TCBB.
MLOmics, a cancer multi-omics database for machine learning, published in Scientific Data.