Shikui Tu  (涂仕奎) Department of Computer Science and Engineering Center for Cognitive Machines and Computational Health (CMaCH) Shanghai Jiao Tong University Shanghai, China. 200240. Office: Room 541, SEIEE Building#3, Minhang Campus Email: tushikui@sjtu.edu.cn

Looking for Ph.D. students, graduate students. Send your CV to tushikui@sjtu.edu.cn
实验室常年招收博士生、硕士生，也欢迎本科生来实习。发送简历到 tushikui@sjtu.edu.cn.

Biography

I am a tenured associate professor (长聘副教授) at Department of Computer Science and Engineering, Shanghai Jiao Tong University (SJTU). I am also an academic assistant to the department head, and to the head of Center for Cognitive Machines and Computational Health (CMaCH，电信学院认知机器与计算健康研究中心), School of Electronic Information and Electrical Engineering (SEIEE), SJTU. I obtained my B.Sc. from School of Mathematical Sciences, Peking University (PKU), in 2006, and Ph.D. from Department of Computer Science and Engineering, The Chinese University of Hong Kong (CUHK) in 2012, under the supervision of Professor Lei Xu. I worked as postdoctoral associate in Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, between 2012 and 2017, under Professor Zhiping Weng and also Professor Craig Mello who won the Nobel Prize in Physiology or Medicine 2006.

Research Interests

My research interests include machine learning, bioinformatics, and also neural combinatorial optimization, drug discovery, causal discovery and reasoning, computational finance. I have published more than 80 academic papers in top conferences, e.g., NeurIPS/ICML/AAAI/IJCAI, and the journals with high impact factors, including Science, Cell, Nature Communications, Nature Structural and Molecular Biology, and so on.

Selected Honors and Awards

Selected Recent Publications | Full Publications

• Qin Ma, Shikui Tu*, Lei Xu*. "Cauchy-Schwarz bounded trade-off weighting for causal inference with small sample sizes", International Journal of Approximate Reasoning (IJAR), Volume 176, 109311, January 2025 (first online: 29 October 2024) [codes]
• Dengwei Zhao, Shikui Tu*, Lei Xu*. "SeeA*: Efficient Exploration-Enhanced A* Search by Selective Sampling", Thirty-eighth Conference on Neural Information Processing Systems (NeurIPS 2024), Dec. 10-15, 2024 (Oral paper: 144/15671=0.92%) (CCF-A会议) [codes]
• Wenjing Huang, Shikui Tu*, Lei Xu*. "PFB-Diff: Progressive Feature Blending diffusion for text-driven image editing", (Neural Networks), Volume 181, 106777, January 2025 (first online: 09 October, 2024) [codes]
• Dengwei Zhao, Jingyuan Zhou, Shikui Tu* and Lei Xu*. "De Novo Drug Design by Multi-Objective Path Consistency Learning with Beam A∗ Search," IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 09 October 2024 [codes]
• Xin Wang, Tengjie Li, Sicong Zang, Shikui Tu*, Lei Xu*. "Self-Supervised Learning for Enhancing Spatial Awareness in Free-Hand Sketches", in Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence (IJCAI), Main Track, Pages 5117-5125, August 2024 (CCF-A会议) [codes]
• Tengjie Li, Shikui Tu*, Lei Xu*. "SketchEdit: Editing Freehand Sketches at the Stroke-Level", in Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence (IJCAI), Main Track, Pages 4461-4469, August 2024 (CCF-A会议) [codes]
• Yupei Yang, Biwei Huang*, Shikui Tu*, Lei Xu. "Boosting Efficiency in Task-Agnostic Exploration through Causal Knowledge", in Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence (IJCAI), Main Track, Pages 5344-5352, August 2024 (CCF-A会议) [codes]
• Zhousan Xie, Shikui Tu*, Lei Xu*. "Multilevel Attention Network with Semi-supervised Domain Adaptation for Drug-Target Prediction", in Proceedings of the AAAI Conference on Artificial Intelligence (AAAI 2024), 38(1), 329-337, 2024 (CCF-A会议) [codes]
• Dengwei Zhao, Shikui Tu*, Lei Xu*. "Efficient retrosynthetic planning with MCTS exploration enhanced A* search.", Communications Chemistry 7, 52 (2024) [codes]
• Tengjie Li, Sicong Zang, Shikui Tu*, and Lei Xu*. "Lmser-pix2seq: Learning stable sketch representations for sketch healing", Computer Vision and Image Understanding (CVIU), Volume 240, 2024, 103931 [codes]
• Hao Qian, Wenjing Huang, Shikui Tu*, and Lei Xu*. "KGDiff: towards explainable target-aware molecule generation with knowledge guidance", Briefings in Bioinformatics (BIB), Volume 25, Issue 1, bbad435, January 2024 [codes]
• Hao Qian, Jingyuan Zhou, Shikui Tu*, and Lei Xu*. "DrugGen: a database of de novo-generated molecular binders for specified target proteins, Database, Volume 2023, 2023, baad090 [DrugGen's website]
• Dengwei Zhao, Shikui Tu* and Lei Xu*. "Generalized Weighted Path Consistency for Mastering Atari Games", Thirty-seventh Conference on Neural Information Processing Systems (NeurIPS), Dec.12-14, 2023 (CCF-A会议)[codes] [poster]
• Zhiqing Li, Zhenzhen Li, Yuqi Zhang, Lunni Zhou, Qikui Xu, Lili Li, Lin Zeng, Junchao Xue, Huilin Niu, Jing Zhong, Qilu Yu, Dengfeng Li, Miao Gui, Yongping Huang, Shikui Tu, ZZ Zhao Zhang, Chun-Qing Song*, Jianping Wu*, En-Zhi Shen*, “Mammalian PIWI-piRNA-target complexes reveal features for broad and efficient target-silencing”, Nature Structural and Molecular Biology, 2023 (In press) (JCR 1区, IF: 18.361)
• Peiying Li, Yongchang Liu, Shikui Tu*, Lei Xu*. "GLPocket: A Multi-Scale Representation Learning Approach for Protein Binding Site Prediction", in Proceedings of the Thirty-Second International Joint Conference on Artificial Intelligence (IJCAI), Main Track, Pages 4821-4828, 19th-25th August 2023 Macao, S.A.R (CCF-A会议)[codes]
• Sicong Zang, Shikui Tu* and Lei Xu*. "Self-Organizing a Latent Hierarchy of Sketch Patterns for Controllable Sketch Synthesis," in IEEE Transactions on Neural Networks and Learning Systems (TNNLS), 06 June 2023 (CCF-B期刊, JCR 1区, IF: 14.255) [codes]
• Yongchang Liu, Peiying Li, Shikui Tu*, and Lei Xu*. "RefinePocket: An Attention-Enhanced and Mask-Guided Deep Learning Approach for Protein Binding Site Prediction," in IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 20, no. 5, pp. 3314-3321, 1 Sept.-Oct. 2023 (CCF-B期刊) [codes]
• Peiying Li, Yongchang Liu, Jiafeng Zhou, Shikui Tu*, Bing Zhao, Jieqing Wan, Yunjun Yang*, and Lei Xu*. “A deep learning method for end-to-end prediction of intracranial aneurysm rupture risk”. Patterns 4, 100709, May 12, 2023 [codes]
• Peng Zhang, Shikui Tu*. "MGAE-DC: Predicting the synergistic effects of drug combinations through multi-channel graph autoencoders". PLOS Computational Biology 19(3): e1010951, March 03, 2023 (CCF-B期刊) [codes]
• Yao Zhou, Ruidan Su, Shikui Tu* and Lei Xu*. "A Deep Temporal Factor Analysis Method for Large Scale Financial Portfolio Selection," ICASSP 2023 - 2023 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Rhodes Island, Greece, 04-10 June 2023, pp. 1-5 (CCF-B会议) [codes]
• Dengwei Zhao, Shuai Yuan, Yanan Sun*, Shikui Tu*, and Lei Xu. "DeepTH: Chip Placement with Deep Reinforcement Learning Using a Three-Head Policy Network." In 2023 Design, Automation and Test in Europe Conference and Exhibition (DATE), pp. 1-2. IEEE, 2023. (CCF-B会议) [codes]
• Sicong Zang, Shikui Tu*, and Lei Xu*, “Linking Sketch Patches by Learning Synonymous Proximity for Graphic Sketch Representation,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, AAAI-23, Feb.07-14, 2023, Washington, DC, USA. (CCF-A会议) [codes] [arXiv]
• Wenqi Guo, Lin Zhang, Shikui Tu*, and Lei Xu*, “Self-Supervised Bidirectional Learning for Graph Matching,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, AAAI-23, Feb.07-14, 2023, Washington, DC, USA. (CCF-A会议) [codes]
• Wenjing Huang, Shikui Tu*, and Lei Xu*. "IA-FaceS: A bidirectional method for semantic face editing." Neural Networks, Volume 158, Pages 272-292, January, 2023. (CCF-B期刊, JCR 1区, IF: 9.657）[codes] [arXiv]
• Tianxiang Qin, Shikui Tu*, and Lei Xu*. "IA-NGM: A bidirectional learning method for neural graph matching with feature fusion." Machine Learning, Volume 113, pages 1743–1769, (2024) (Published: November 01, 2022) (CCF-B期刊）[codes]
• Wenjing Huang, Shikui Tu*, and Lei Xu*, "Box-FaceS: A Bidirectional Method for Box-Guided Face Component Editing." In Proceedings of the 30th ACM International Conference on Multimedia (MM2022), pp. 6061-6071, October 10–14, 2022, Lisboa, Portugal. (CCF-A会议) [codes] [presentation]
• Shuai Yuan, Yanan Sun, Weifeng He, Qianrong Gu, Shi Xu, Zhigang Mao, Shikui Tu. "MSLM-RF: A Spatial Feature Enhanced Random Forest for On-Board Hyperspectral Image Classification." IEEE Transactions on Geoscience and Remote Sensing (TGARS), vol. 60, pp. 1-17, 26 July 2022. (CCF-B期刊)
• Dengwei Zhao, Shikui Tu*, and Lei Xu*, "Efficient Learning for AlphaZero via Path Consistency". In Proceedings of the 39th International Conference on Machine Learning (ICML), Baltimore, Maryland, USA, PMLR 162:26971-26981, 2022 (CCF-A会议) [codes] [presentation]
• 臧思聪, 涂仕奎*, 徐雷*. “IA-pix2seq：一个实现简笔画可控生成的深度双向学习方法”, 计算机学报, 第46卷第3期，2023年03月 [codes]
• Qin Ma, Lin Zeng, Shikui Tu*, Lei Xu*. "Kernel Mean Matching with Mahalanobis Distance for Causal Inference of Time-to-event Outcome". 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 509-514, Las Vegas, NV, USA, December 06-08, 2022 (CCF-B会议) [codes]
• Peng Zhang, Shikui Tu*. "A knowledge graph embedding-based method for predicting the synergistic effects of drug combinations". 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 1974-1981, Las Vegas, NV, USA, December 06-08, 2022 (CCF-B会议) [codes]
• Peiying Li, Boheng Cao, Shikui Tu*, Lei Xu*. "RecurPocket: Recurrent Lmser Network with Gating Mechanism for Protein Binding Site Detection". 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 334-339, Las Vegas, NV, USA, December 06-08, 2022 (CCF-B会议) [codes]
• 涂仕奎. "AI与药物分子生成." 中国人工智能学会通讯, 第12卷，第11期，2022年11月
• 《2022 中国人工智能系列白皮书--人工智能与药物发现》, 其中第三章“人工智能与药物从头设计”主要由本实验室（林铖、钱浩、涂仕奎）完成。
• Hao Qian, Cheng Lin, Dengwei Zhao, Shikui Tu*, Lei Xu*. "AlphaDrug: Protein target specific de novo molecular generation." PNAS Nexus, 1(4), pgac227, 07 October 2022 [codes]
• Peng Zhang, Shikui Tu*, Wen Zhang*, Lei Xu. "Predicting cell line-specific synergistic drug combinations through a relational graph convolutional network with attention mechanism." Briefings in Bioinformatics (BIB), vol. 23, issue 6, 22 Sep. 2022, bbac403 (CCF-B期刊) [codes]
• Wenjun Chen, Jordan S. Brown, Tao He, Wei-Sheng Wu, Shikui Tu, Zhiping Weng, Donglei Zhang, Heng-Chi Lee. "GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance." Nature Communications 13, 5306 (2022). (IF: 17.694)
• 盛庆杰, 苏锐丹, 涂仕奎, 徐雷. “基于Lmser-in-Lmser双向网络的人脸素描图像生成方法"[J]. 模式识别与人工智能, 2022, 35(7): 589-601 [codes]
• Peiying Li, Shikui Tu*, and Lei Xu*, “Deep Rival Penalized Competitive Learning for Low-resolution Face Recognition”, Neural Networks, vol. 148, pp. 183-193, April 2022, doi: 10.1016/j.neunet.2022.01.009. (CCF-B期刊) [codes]
• Sicong Zang, Shikui Tu*, and Lei Xu*, “Controllable stroke-based sketch synthesis from a self-organized latent space,” Neural Networks, vol. 137, pp. 138–150, May 2021, doi: 10.1016/j.neunet.2021.01.006. (CCF-B期刊) [codes]
• Kaixuan Zhao, Shikui Tu*, and Lei Xu*, “IA-GM: A deep bidirectional learning method for graph matching,” in Proceedings of the 35th AAAI Conference on Artificial Intelligence, AAAI-21, 2021, Feb.02-09 (CCF-A会议) [codes]
• Zhicheng Wang, Biwei Huang, Shikui Tu*, Kun Zhang, and Lei Xu*, “DeepTrader: A Deep Reinforcement Learning Approach to Risk-Return Balanced Portfolio Management with Market Conditions Embedding,” in Proceedings of the 35th AAAI Conference on Artificial Intelligence, AAAI-21, 2021, Feb.02-09 (CCF-A会议) [codes]
• Zhihao Xing, Shikui Tu*, “A Graph Neural Network Assisted Monte Carlo Tree Search Approach to Traveling Salesman Problem,” IEEE Access, vol. 8, pp. 108418–108428, 2020 [codes]
• Wenjing Huang, Shikui Tu, and Lei Xu, “Deep CNN Based Lmser and Strengths of Two Built-In Dualities,” Neural Processing Letters, vol. 8, pp. 108418–108428, 2020 [codes]
• Fucheng Deng, Shikui Tu*, and Lei Xu*. “Multi-source unsupervised domain adaptation for ECG classification,” in 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 854-859, 9-12 Dec. 2021 (CCF-B会议) [codes]
• Haodong Nie, Shikui Tu*, and Lei Xu*. “RecSleepNet: An Automatic Sleep Staging Model Based on Feature Reconstruction,” in 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 1458-1461, 9-12 Dec. 2021 (CCF-B会议) [codes]
• Jinxiong Lv, Shikui Tu*, Lei Xu*. "Detection of Phenotype-related Mutations of COVID-19 via the Whole Genomic Data." IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) vol. 18, issue 4, pp. 1242-1249, 01 July-Aug. 2021 (CCF-B期刊)
• Qingsong Xie, Shikui Tu*, Guoxing Wang, Yong Lian, and Lei Xu*, “Discrete Biorthogonal Wavelet Transform Based Convolutional Neural Network for Atrial Fibrillation Diagnosis from Electrocardiogram,” in Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, IJCAI-20, 2020, pp. 4403–4409 (CCF-A会议)
• Peiying Li, Shikui Tu, and Lei Xu, "GAN Flexible Lmser for Super-resolution." In Proceedings of the 27th ACM International Conference on Multimedia (MM2019), pp. 756-764. ACM, 2019 (CCF-A会议) [codes]
• Yuze Guo, Wenjing Huang, Yajing Chen, and Shikui Tu*. "Regularize Network Skip Connections by Gating Mechanisms for Electron Microscopy Image Segmentation." In 2019 IEEE International Conference on Multimedia and Expo (ICME 2019), pp. 868-873. IEEE, 2019 (CCF-B会议) [codes]
• Yongjie Wang, Lin Zeng, Chao Liang, Rui Zan, Weiping Ji, Zhichang Zhang, Yuxuan Wei, Shikui Tu*, and Yang Dong*. "Integrated analysis of transcriptome-wide m6A methylome of osteosarcoma stem cells enriched by chemotherapy." Epigenomics (2019) Oct. 25.
• Wenjing Huang, Shikui Tu*, and Lei Xu*, “Revisit Lmser from a Deep Learning Perspective,” in Intelligence Science and Big Data Engineering (IScIDE 2019), Cham, 2019, pp. 197–208, doi: 10.1007/978-3-030-36204-1_16.
• Gen Zhang#, Shikui Tu#, Tianxiong Yu, Xiao-Ou Zhang, Swapnil S. Parhad, Zhiping Weng, William E. Theurkauf. “Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin,” Cell Reports, vol. 24, no. 13, pp. 3413–3422.e4, Sep. 2018. (#co-first author) (JCR 1区, IF: 8.8)
• Gregory M Davis#, Shikui Tu#, Joshua WT Anderson#, Rhys N Colson, Menachem J Gunzburg, Michelle A Francisco, Debashish Ray, Sean P Shrubsole, Julia A Sobotka, Uri Seroussi, Robert X Lao, Tuhin Maity, Monica Z Wu, Katherine McJunkin, Quaid D Morris, Timothy R Hughes, Jacqueline A Wilce, Julie M Claycomb, Zhiping Weng, and Peter R Boag. "The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans." eLife 2018; 7:e35478 (#co-first author)
• Enzhi Shen, Hao Chen, Ahmet R. Ozturk, Shikui Tu, Masaki Shirayama, Wen Tang, Yue-He Ding, Si-Yuan Dai, Zhiping Weng, and Craig C. Mello. "Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline." Cell 172(5), 937–951.e18, 22 February 2018 (JCR 1区, IF: 66.85)
• Donglei Zhang#, Shikui Tu#, Michael Stubna, Wei-Sheng Wu, Wei-Che Huang, Zhiping Weng, Heng-Chi Lee. "The rules for piRNA targeting reveal resistance of endogenous genes to piRNA silencing in C. elegans." Science, Vol. 359, Issue 6375, pp. 587-592, 2 February 2018 (#co-first author) (JCR 1区, IF: 63.832)
• Swapnil S. Parhad, Shikui Tu, Zhiping Weng, and William E. Theurkauf. "Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery." Developmental Cell 2017 Oct 9; 43(1):60-70.e5 (JCR 1区, IF: 13.417)
• Yajing Chen, Shikui Tu, Yuqi Yi, Lei Xu. "Sketch-pix2seq: a Model to Generate Sketches of Multiple Categories." arXiv:1709.04121, 2017
• Wen Zhang, Xiang Yue, Feng Liu, Yanlin Chen, Shikui Tu, and Xining Zhang, “A unified frame of predicting side effects of drugs by using linear neighborhood similarity,” BMC Systems Biology, vol. 11, no. 6, pp. 101, Dec.14, 2017.
• Longqiang Luo, Dingfang Li, Wen Zhang, Shikui Tu, Xiaopeng Zhu, and Gang Tian. "Accurate Prediction of Transposon-Derived piRNAs by Integrating Various Sequential and Physicochemical Features." PLoS ONE 11(4): e0153268, 2016
• Wen Tang, Shikui Tu, Heng-Chi Lee, Zhiping Weng, and Craig C. Mello. "The RNase PARN-1 Trims piRNA 3´ Ends to Promote Transcriptome Surveillance in C. elegans." Cell, Vol. 164, Issue 5, pp. 974-984, 25 February 2016 (JCR 1区, IF: 66.85)
• Shikui Tu, Monica Z Wu, Jie Wang, Asher D Cutter, Zhiping Weng, and Julie M Claycomb. "Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes." Nucleic Acids Research, Vol. 43, Issue 1, Pages 208–224, 9 January 2015 (JCR 1区, IF: 19.16)
• Zhao Zhang, Jie Wang, Nadine Schultz, Fan Zhang, Swapnil S Parhad, Shikui Tu, Thom Vreven, Phillip D Zamore, Zhiping Weng, and William E Theurkauf. "The HP1 Homolog Rhino Anchors a Nuclear Complex that Suppresses piRNA Precursor Splicing." Cell, Vol. 157, Issue 6, pp.1353-1363, June 05, 2014 (JCR 1区, IF: 66.85)

*Corresponding author

Papers before 2012

Refer to my Google Scholar page.

Teaching

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