馬劍竹，男，2016年於芝加哥豐田工業研究院獲得博士學位。
現任清華大學智慧型產業研究院副研究員、副教授，博導，海外優青項目入選者。
基本介紹
- 中文名：馬劍竹
- 畢業院校：北京大學信息科學技術學院、豐田工業大學芝加哥分校
- 學位/學歷：博士
- 職稱：清華大學智慧型產業研究院副教授
人物經歷,教育經歷,工作經歷,研究領域,著作論文,
人物經歷
2016年於芝加哥豐田工業研究院獲得博士學位，隨後在加州大學聖地亞哥分校醫學院擔任項目科學家。2020年開始擔任美國普度大學計算機系Walther助理教授，兼任普渡大學生物化學系助理教授，2021年擔任北京大學人工智慧研究院副教授，北京大學公共衛生學院副教授，主要研究領域為人工智慧、系統生物學、生物製藥和智慧醫療。曾獲得生物計算學國際頂級會議RECOMB的最佳論文獎，國際計算生物學會議ISMB的Warren DeLano獎，國際RNA和蛋白質摺疊大會的最佳海報獎，論文曾被Nature Methods，Nature Machine Intelligence評為封面論文。
教育經歷
2010-2016 豐田工業大學芝加哥分校 博士
2007-2010 北京大學信息科學技術學院計算機系 碩士
2003-2007 北京大學信息科學技術學院計算機系 學士
工作經歷
2022-至今 清華大學智慧型產業研究院副教授
2021-2022 北京大學人工智慧研究院 副教授
2021-2022 北京大學醫學部公共衛生學院 副教授
2020-2021 美國普渡大學計算機系 助理教授
2020-2021 美國普渡大學生化系 助理教授
研究領域
人工智慧、系統生物學、生物製藥、智慧醫療
著作論文
Nature Science Cell及子刊生物論文
1. Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma
Qi Xie, Zhilin Long, Chengfang Sun, Min Tang, Yin Wang, Jiayan Ma, Jichuan Yu, Jingchao Wei, Jianzhu Ma , Bohan Wang, and Jiaming Wen，Cell Discovery 2022
2. A multi-scale map of cell structure fusing protein images and interactions
Yue Qin, Edward L. Huttlin, Casper F. Winsnes, Maya L. Gosztyla, Ludivine Wacheul, Marcus R. Kelly, Steven M. Blue, Fan Zheng, Michael Chen, Leah V. Schaffer, Katherine Licon, Anna Bäckström, Laura Pontano Vaites, John J. Lee, Wei Ouyang, Sophie N. Liu, Tian Zhang, Erica Silva, Jisoo Park, Adriana Pitea, Jason F. Kreisberg, Steven P. Gygi, Jianzhu Ma, J. Wade Harper, Gene W. Yeo, Denis L. J. Lafontaine, Emma Lundberg，Trey Ideker，Nature 2021
3. SARS-CoV-2 exacerbates proinflammatory responses in myeloid cells through ACE2-independent interactions via C-type lectin receptors and TTYH2
Qiao Lu, Jia Liu, Shuai Zhao, Maria Florencia Gomez Castro, Maudry Laurent-Rolle, Jianbo Dong, Xiaojuan Ran, Payal Damani-Yokota, Hongzheng Tang, Triantafyllia Karakousi, Juhee Son, Maria E. Kaczmarek, Ze Zhang, Stephen T. Yeung, Broc T. McCune, Rita E. Chen, Fei Tang, Xianwen Ren, Xufeng Chen, Jack C.C. Hsu, Marianna Teplova, Betty Huang, Haijing Deng, Zhilin Long, Tenny Mudianto, Shumin Jin, Peng Lin, Jasper Du, Ruochen Zang, Tina Tianjiao Su, Alberto Herrera, Ming Zhou, Renhong Yan, Jia Cui, James Zhu, Qiang Zhou, Tao Wang, Jianzhu Ma, Sergei B. Koralov, Zemin Zhang, Iannis Aifantis, Leopoldo N. Segal, Michael S. Diamond, Kamal M. Khanna, Kenneth A. Stapleford, Peter Cresswel, Yue Liu, Siyuan Ding, Qi Xie, Jun Wang，Immunity 2021 (Impact Factor=22)
4. Modeling Gene Regulatory Networks Using Neural Network Architectures
Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng, Jianzhu Ma，Nature Computational Science 2021
5. Predicting drug response and synergy using a deep learning model of a cancer cell
Brent Kuenzi, Jisoo Park, Samson H. Fong, Kyle Salinas Sanchez, Jason F. Kreisberg, Jianzhu Ma, Trey Ideker，Cancer Cell 2020
6. A conserved epigenetic progression aligns dog and human age
Tina Wang, Jianzhu Ma, Andrew N. Hogan, Samson Fong, Katherine Licon, Brian Tsui, Jason F. Kreisberg, Peter D. Adams, Anne-Ruxandra Carvunis, Danika L. Bannasch, Elaine A. Ostrander and Trey Ideker，Cell Systems 2020
7. Learning predictive models of drug response that translate across biological contexts
Jianzhu Ma, Samson Fong, Yunan Luo, Christopher Bakkenist, John Paul Shen, Soufiane Mourragui, Lodewyk Wessels, Marc Hafner, Roded Sharan, Jian Peng, Trey Ideker
Nature Cancer 2020
8. DDOT: A Swiss-Army Knife for Investigating Data-Driven Biological Ontologies
Michael Ku Yu, Jianzhu Ma, Keiichiro Ono, Fan Zheng, Samson H. Fong, Aaron Gary, Jing Chen, Barry Demchak, Dexter Pratt, Trey Ideker
Cell Systems 2019 co-first author
9. Visible Machine Learning for Biomedicine
Michael Ku Yu, Jianzhu Ma, Jasmin Fisher, Jason F. Kreisberg, Benjamin J. Raphael, Trey Ideker
Cell 2018 co-first author
10. Typing tumors using pathways selected by somatic evolution
Sheng Wang, Jianzhu Ma, Wei Zhang, John Shen, Justin Huang, Jian Peng, Trey Ideker
Nature Communications 2018 co-first author
11. Using deep learning to model the hierarchical structure and function of a cell
Jianzhu Ma, Michael Ku Yu, Samson Fong, Keiichiro Ono, Eric Sage, Barry Demchak, Roded Sharan, Trey Ideker
Nature Methods 2018
近期人工智慧會議及期刊論文
1. Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models
Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma，NeurlPS 2022
2. Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation
Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma，NeurlPS 2022
3. MobilePrune: Neural Network Compression via ℓ0 Sparse Group Lasso on the Mobile System
Yubo Shao, Kaikai Zhao, Zhiwen Cao, Zhehao Peng, Xingang Peng, Pan Li, Yijie Wang, Jianzhu Ma，Sensor 2022
4. Multiwave COVID-19 Prediction from Social Awareness using Web Search and Mobility Data
Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma , Satish V. Ukkusuri，KDD 2022 corresponding author Oral presentation
5. Proximal Exploration for Model-guided Biological Sequence Design
Zhizhou Ren, Jiahan Li, Fan Ding, Yuan Zhou, Jianzhu Ma , Jian Peng，ICML 2022 Short presentation
6. Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma，ICML 2022 Short presentation
7. 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design
Yinan Huang, Xingang Peng, Jianzhu Ma , Muhan Zhang，ICML 2022 corresponding author Long presentation
8. Equivariant Point Set Analysis via Learning Orientations for Message Passing
Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma，CVPR 2022 Oral presentation
9. Physics-Guided and Physics-Explainable Recurrent Neural Network for Time Dynamics in Optical Resonances，Yingheng Tang, Jichao Fan, Xinwei Li, Jianzhu Ma , Minghao Qi, Cunxi Yu, Weilu Gao，Nature Computational Science 2022
10. Neural Energy Minimization for Molecular Conformation Optimization
Jiaqi Guan, Wei Qian, Qiang Liu, Wei-ying Ma, Jianzhu Ma, Jian Peng，ICLR 2022
11. Neural Predicting Higher-order Patterns in Temporal Networks
Yuyun Liu, Jianzhu Ma, Pan Li，WWW 2022
12. Quantifying spatial homogeneity of urban road networks via graph neural networks
Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Takahiro Yabe, Satish Ukkusuri, Jianzhu Ma，Nature Machine intelligence 2022 cover paper
13. A 3D Generative Model for Structure-Based Drug Design
Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng，NeurlPS 2021
14. Fast Projection onto the Capped Simplex withApplications to Sparse Regression in Bioinformatics Andersen Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang，NeurlPS 2021
15. XOR-CD: Linearly Convergent Constrained Structure Generation
Fan Ding, Jianzhu Ma, Jinbo Xu, Yexiang Xue，ICML 2021 oral presentation
16. AirSign: Smartphone Authentication by Signing in the Air
Yubo Shao, Tinghan Yang, He Wang, Jianzhu Ma，Sensor 2021
17. PALM: Probabilistic Area Loss Minimization for Protein Sequence Alignment
Fan Ding, Nan Jiang, Jianzhu Ma, Jian Peng, Jinbo Xu, Yexiang Xue，UAI 2021
18. Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns
Susheel Suresh, Vinith Budde, Jennifer Neville, Pan Li, Jianzhu Ma，KDD 2021
19. Causality in machine learning: When causal inference meets deep neural networks
Yunan Luo, Jian Peng, Jianzhu Ma，Nature Machine intelligence 2020
