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ORCIDYu Li 0006
李煜
Person information
- unicode name: 李煜
- affiliation: Chinese University of Hong Kong, Department of Computer Science and Engineering, China
- affiliation (former): King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
Other persons with the same name
- Yu Li — disambiguation page
- Yu Li 0001 — Tsinghua University, Department of Automation, Beijing, China
- Yu Li 0002
![[0000-0003-3955-189X]](https://dblp.uni-trier.de./img/orcid-mark.12x12.png "0000-0003-3955-189X")
— Liaoning Technical University, School of Geomatics, Institute for Remote Sensing Science and Application, Fuxin, China (and 1 more) - Yu Li 0003 — University of Illinois at Urbana-Champaign, IL, USA (and 3 more)
- Yu Li 0004 — University of Science and Technology of China, Department of Electronic Science and Technology, Hefei, China
- Yu Li 0005 — A*STAR, Institute of Microelectronics, Singapore
- Yu Li 0007 — Chinese University of Hong Kong, CURE, Hong Kong (and 1 more)
- Yu Li 0008 — Wright State University, Department of Computer Science and Engineering, Dayton, OH, USA
- Yu Li 0009 — Beijing University of Technology, Faculty of Information Technology, China (and 2 more)
- Yu Li 0010 — Polytechnic University of Milan, Italy
- Yu Li 0011 — School of Computing and Information Technology, Institute of Cybersecurity and Cryptology, University of Wollongong, Wollongong, NSW, Australia (and 1 more)
- Yu Li 0012 — University of Picardie Jules Verne, LaRIA, Amiens, France
- Yu Li 0013 — Columbia University, Natural Language Processing Group, New York, NY, USA (and 1 more)
- Yu Li 0014 — Henan University, School of Business, Institute of Management Science and Engineering, Kaifeng, China
- Yu Li 0015 — Hangzhou Dianzi University, Department of Computing, Hangzhou, China (and 1 more)
- Yu Li 0016 — Chinese Academy of Sciences, Institute of Computing Technology, Key Laboratory of Intelligent Information Processing, Beijing, China (and 1 more)
- Yu Li 0017 — Northeast Forestry University, Department of Mathematics, Harbin, China
- Yu Li 0018 — University of Queensland, School of Information Technology and Electrical Engineering, Brisbane, Australia
- Yu Li 0019 — University of Texas at Austin, Center for Transportation Research, Austin, TX, USA (and 1 more)
- Yu Li 0020 — Luxembourg Institute of Science and Technology (LIST), Department of Environmental Research and Innovation (ERIN), Esch-sur-Alzette, Luxembourg (and 2 more)
- Yu Li 0021 — Southeast University, School of Computer Science and Engineering, Nanjing, China (and 1 more)
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2020 – today
- 2024
[j32]Qingxiong Tan, Jin Xiao, Jiayang Chen, Yixuan Wang, Zeliang Zhang, Tiancheng Zhao, Yu Li:
ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers. Briefings Bioinform. 25(4) (2024)- [j31]Qing Li, Zhihang Hu, Yixuan Wang, Lei Li, Yimin Fan, Irwin King, Gengjie Jia, Sheng Wang, Le Song, Yu Li:
Progress and opportunities of foundation models in bioinformatics. Briefings Bioinform. 25(6) (2024) - [j30]Junkang Wei, Jin Xiao, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li:
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles. Database J. Biol. Databases Curation 2024 (2024) - [j29]Han Huang, Ziqian Lin, Dongchen He, Liang Hong, Yu Li:
RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models. Bioinform. 40(Supplement_1): i347-i356 (2024) - [j28]Yimin Fan, Yaxuan Li, Yunhua Zhong, Liang Hong, Lei Li, Yu Li:
Learning meaningful representation of single-neuron morphology via large-scale pre-training. Bioinform. 40(Supplement_2): ii128-ii136 (2024) - [j27]Junbo Shen, Qinze Yu, Shenyang Chen, Qingxiong Tan, Jingchen Li, Yu Li:
Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model. Nat. Comput. Sci. 4(1): 29-42 (2024) - [j26]Felix Wong, Dongchen He, Aarti Krishnan, Liang Hong, Alexander Z. Wang, Jiuming Wang, Zhihang Hu, Satotaka Omori, Alicia Li, Jiahua Rao, Qinze Yu, Wengong Jin, Tianqing Zhang, Katherine Ilia, Jack X. Chen, Shuangjia Zheng, Irwin King, Yu Li, James J. Collins:
Deep generative design of RNA aptamers using structural predictions. Nat. Comput. Sci. 4(11): 829-839 (2024) - [j25]Yongxian Wei, Zixuan Hu, Li Shen, Zhenyi Wang, Lei Li, Yu Li, Chun Yuan:
Meta-Learning Without Data via Unconditional Diffusion Models. IEEE Trans. Circuits Syst. Video Technol. 34(11): 11874-11885 (2024) - [j24]Chuanyang Zheng, Haiming Wang, Enze Xie, Zhengying Liu, Jiankai Sun, Huajian Xin, Jianhao Shen, Zhenguo Li, Yu Li:
Lyra: Orchestrating Dual Correction in Automated Theorem Proving. Trans. Mach. Learn. Res. 2024 (2024) - [c16]Yichen Gao, Licheng Zong, Yu Li:
Enhancing Biomedical Question Answering with Parameter-Efficient Fine-Tuning and Hierarchical Retrieval Augmented Generation. CLEF (Working Notes) 2024: 117-129 - [c15]Minda Hu, Licheng Zong, Hongru Wang, Jingyan Zhou, Jingjing Li, Yichen Gao, Kam-Fai Wong, Yu Li, Irwin King:
SeRTS: Self-Rewarding Tree Search for Biomedical Retrieval-Augmented Generation. EMNLP (Findings) 2024: 1321-1335 - [c14]Yongxian Wei, Zixuan Hu, Li Shen, Zhenyi Wang, Yu Li, Chun Yuan, Dacheng Tao:
Task Groupings Regularization: Data-Free Meta-Learning with Heterogeneous Pre-trained Models. ICML 2024 - [c13]Yimin Fan, Yu Li, Jun Ding, Yue Li:
GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling. RECOMB 2024: 314-319 - [i22]Qing Li, Lei Li, Yu Li:
Developing ChatGPT for Biology and Medicine: A Complete Review of Biomedical Question Answering. CoRR abs/2401.07510 (2024) - [i21]Qing Li, Zhihang Hu, Yixuan Wang, Lei Li, Yimin Fan, Irwin King, Le Song, Yu Li:
Progress and Opportunities of Foundation Models in Bioinformatics. CoRR abs/2402.04286 (2024) - [i20]Yongxian Wei, Zixuan Hu, Li Shen, Zhenyi Wang, Yu Li, Chun Yuan, Dacheng Tao:
Task Groupings Regularization: Data-Free Meta-Learning with Heterogeneous Pre-trained Models. CoRR abs/2405.16560 (2024) - [i19]Minda Hu, Licheng Zong, Hongru Wang, Jingyan Zhou, Jingjing Li, Yichen Gao, Kam-Fai Wong, Yu Li, Irwin King:
Enhancing Biomedical Knowledge Retrieval-Augmented Generation with Self-Rewarding Tree Search and Proximal Policy Optimization. CoRR abs/2406.11258 (2024) - [i18]Jiyue Jiang, Liheng Chen, Sheng Wang, Lingpeng Kong, Yu Li, Chuan Wu:
Data Augmentation of Multi-turn Psychological Dialogue via Knowledge-driven Progressive Thought Prompting. CoRR abs/2406.16567 (2024) - 2023
- [j23]Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li:
Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration. Bioinform. 39(4) (2023) - [j22]Yunxiang Li, Yumeng Wei, Sheng Xu, Qingxiong Tan, Licheng Zong, Jiuming Wang, Yixuan Wang, Jiayang Chen, Liang Hong, Yu Li:
AcrNET: predicting anti-CRISPR with deep learning. Bioinform. 39(5) (2023) - [j21]Gengjie Jia, Yu Li, Xue Zhong, Kanix Wang, Milton Pividori, Rabab Alomairy, Aniello Esposito, Hatem Ltaief, Chikashi Terao, Masato Akiyama, Koichi Matsuda, David E. Keyes, Hae Kyung Im, Takashi Gojobori, Yoichiro Kamatani, Michiaki Kubo, Nancy J. Cox, James A. Evans, Xin Gao, Andrey Rzhetsky:
The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. Nat. Comput. Sci. 3(5): 403-417 (2023) - [j20]Gengjie Jia, Yu Li, Xue Zhong, Kanix Wang, Milton Pividori, Rabab Alomairy, Aniello Esposito, Hatem Ltaief, Chikashi Terao, Masato Akiyama, Koichi Matsuda, David E. Keyes, Hae Kyung Im, Takashi Gojobori, Yoichiro Kamatani, Michiaki Kubo, Nancy J. Cox, James A. Evans, Xin Gao, Andrey Rzhetsky:
Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. Nat. Comput. Sci. 3(7): 658 (2023) - [i17]Zhihang Hu, Qinze Yu, Yucheng Guo, Taifeng Wang, Irwin King, Xin Gao, Le Song, Yu Li:
Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning. CoRR abs/2301.05931 (2023) - [i16]Le Zhang, Jiayang Chen, Tao Shen, Yu Li, Siqi Sun:
Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation. CoRR abs/2306.01824 (2023) - [i15]Chuanyang Zheng, Haiming Wang, Enze Xie, Zhengying Liu, Jiankai Sun, Huajian Xin, Jianhao Shen, Zhenguo Li, Yu Li:
Lyra: Orchestrating Dual Correction in Automated Theorem Proving. CoRR abs/2309.15806 (2023) - [i14]Junbo Shen, Qinze Yu, Shenyang Chen, Qingxiong Tan, Jingcheng Li, Yu Li:
Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model. CoRR abs/2312.08987 (2023) - 2022
- [j19]Junkang Wei, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li:
Protein-RNA interaction prediction with deep learning: structure matters. Briefings Bioinform. 23(1) (2022) - [j18]Wenkai Han, Yuqi Cheng, Jiayang Chen, Huawen Zhong, Zhihang Hu, Siyuan Chen, Licheng Zong, Liang Hong, Ting-Fung Chan, Irwin King, Xin Gao, Yu Li:
Self-supervised contrastive learning for integrative single cell RNA-seq data analysis. Briefings Bioinform. 23(5) (2022) - [j17]Yu Li, Siyuan Chen, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Kevin Y. Yip, Xin Gao:
Deep learning identifies and quantifies recombination hotspot determinants. Bioinform. 38(10): 2683-2691 (2022) - [j16]Zhongxiao Li, Yisheng Li, Bin Zhang, Yu Li, Yongkang Long, Juexiao Zhou, Xudong Zou, Min Zhang, Yuhui Hu, Wei Chen, Xin Gao:
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning. Genom. Proteom. Bioinform. 20(3): 483-495 (2022) - [c12]Qin Wang, Jiayang Chen, Yuzhe Zhou, Yu Li, Liangzhen Zheng, Sheng Wang, Zhen Li, Shuguang Cui:
Contact-Distil: Boosting Low Homologous Protein Contact Map Prediction by Self-Supervised Distillation. AAAI 2022: 4620-4627 - [c11]Pengfei Zhang, Zhengyuan Jiang, Yixuan Wang, Yu Li:
CLMB: Deep Contrastive Learning for Robust Metagenomic Binning. RECOMB 2022: 326-348 - [c10]Juan Shu, Bowei Xi, Yu Li, Fan Wu, Charles A. Kamhoua, Jianzhu Ma:
Understanding Dropout for Graph Neural Networks. WWW (Companion Volume) 2022: 1128-1138 - [i13]Tao Shen, Zhihang Hu, Zhangzhi Peng, Jiayang Chen, Peng Xiong, Liang Hong, Liangzhen Zheng, Yixuan Wang, Irwin King, Sheng Wang, Siqi Sun, Yu Li:
E2Efold-3D: End-to-End Deep Learning Method for accurate de novo RNA 3D Structure Prediction. CoRR abs/2207.01586 (2022) - 2021
- [j15]Juan Shu, Yu Li, Sheng Wang, Bowei Xi, Jianzhu Ma:
Disease gene prediction with privileged information and heteroscedastic dropout. Bioinform. 37(Supplement): 410-417 (2021) - [j14]Ramzan Umarov, Yu Li, Takahiro Arakawa, Satoshi Takizawa, Xin Gao, Erik Arner:
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation. PLoS Comput. Biol. 17(9) (2021) - [j13]Ramzan Umarov, Yu Li, Erik Arner:
DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment. PLoS Comput. Biol. 17(10) (2021) - [c9]Zhihang Hu, Bhaavanaa Thumu, Yuren Qin, ZhiSheng Tao, Yijian Lu, Omar Kan, Yu Li, Irwin King:
DeepCURATER: Deep Learning for CoURse And Teaching Evaluation and Review. TALE 2021: 646-653 - [i12]Junkang Wei, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li:
Protein-RNA interaction prediction with deep learning: Structure matters. CoRR abs/2107.12243 (2021) - [i11]Qinze Yu, Zhihang Dong, Xingyu Fan, Licheng Zong, Yu Li:
HMD-AMP: Protein Language-Powered Hierarchical Multi-label Deep Forest for Annotating Antimicrobial Peptides. CoRR abs/2111.06023 (2021) - [i10]Xuesong Wang, Zhihang Hu, Tingyang Yu, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li:
Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration. CoRR abs/2112.03266 (2021) - 2020
- [b1]Yu Li:
Towards Structured Prediction in Bioinformatics with Deep Learning. King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, 2020 - [j12]Yu Li, Sheng Wang, Chongwei Bi, Zhaowen Qiu, Mo Li, Xin Gao:
DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing. Bioinform. 36(8): 2578-2580 (2020) - [c8]Xinshi Chen, Yu Li, Ramzan Umarov, Xin Gao, Le Song:
RNA Secondary Structure Prediction By Learning Unrolled Algorithms. ICLR 2020 - [c7]Xinshi Chen, Hanjun Dai, Yu Li, Xin Gao, Le Song:
Learning To Stop While Learning To Predict. ICML 2020: 1520-1530 - [i9]Xinshi Chen, Yu Li, Ramzan Umarov, Xin Gao, Le Song:
RNA Secondary Structure Prediction By Learning Unrolled Algorithms. CoRR abs/2002.05810 (2020) - [i8]Xinshi Chen, Hanjun Dai, Yu Li, Xin Gao, Le Song:
Learning to Stop While Learning to Predict. CoRR abs/2006.05082 (2020) - [i7]Yu Li:
Towards Structured Prediction in Bioinformatics with Deep Learning. CoRR abs/2008.11546 (2020)
2010 – 2019
- 2019
- [j11]Renmin Han, Xiaohua Wan, Lun Li, Albert F. Lawrence, Peng Yang, Yu Li, Sheng Wang, Fei Sun, Zhiyong Liu, Xin Gao, Fa Zhang:
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. Bioinform. 35(2): 319-328 (2019) - [j10]Sheng Wang, Shiyang Fei, Zongan Wang, Yu Li, Jinbo Xu, Feng Zhao, Xin Gao:
PredMP: a web server for de novo prediction and visualization of membrane proteins. Bioinform. 35(4): 691-693 (2019) - [j9]Zhihao Xia, Yu Li, Bin Zhang, Zhongxiao Li, Yuhui Hu, Wei Chen, Xin Gao:
DeeReCT-PolyA: a robust and generic deep learning method for PAS identification. Bioinform. 35(14): 2371-2379 (2019) - [j8]Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Xin Gao, Victor V. Solovyev:
Promoter analysis and prediction in the human genome using sequence-based deep learning models. Bioinform. 35(16): 2730-2737 (2019) - [j7]Yu Li, Tao Zhang, Shuyu Sun, Xin Gao:
Accelerating flash calculation through deep learning methods. J. Comput. Phys. 394: 153-165 (2019) - [c6]Lizhong Ding, Zhi Liu, Yu Li, Shizhong Liao, Yong Liu, Peng Yang, Ge Yu, Ling Shao, Xin Gao:
Linear Kernel Tests via Empirical Likelihood for High-Dimensional Data. AAAI 2019: 3454-3461 - [c5]Lizhong Ding, Yong Liu, Shizhong Liao, Yu Li, Peng Yang, Yijie Pan, Chao Huang, Ling Shao, Xin Gao:
Approximate Kernel Selection with Strong Approximate Consistency. AAAI 2019: 3462-3469 - [c4]Lizhong Ding, Mengyang Yu, Li Liu, Fan Zhu, Yong Liu, Yu Li, Ling Shao:
Two Generator Game: Learning to Sample via Linear Goodness-of-Fit Test. NeurIPS 2019: 11257-11268 - [i6]Yu Li, Chao Huang, Lizhong Ding, Zhongxiao Li, Yijie Pan, Xin Gao:
Deep learning in bioinformatics: introduction, application, and perspective in big data era. CoRR abs/1903.00342 (2019) - 2018
- [j6]Yu Li, Sheng Wang, Ramzan Umarov, Bingqing Xie, Ming Fan, Lihua Li, Xin Gao:
DEEPre: sequence-based enzyme EC number prediction by deep learning. Bioinform. 34(5): 760-769 (2018) - [j5]Yu Li, Fan Xu, Fa Zhang, Pingyong Xu, Mingshu Zhang, Ming Fan, Lihua Li, Xin Gao, Renmin Han:
DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy. Bioinform. 34(13): i284-i294 (2018) - [j4]Yu Li, Renmin Han, Chongwei Bi, Mo Li, Sheng Wang, Xin Gao:
DeepSimulator: a deep simulator for Nanopore sequencing. Bioinform. 34(17): 2899-2908 (2018) - [j3]Renmin Han, Yu Li, Xin Gao, Sheng Wang:
An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing. Bioinform. 34(17): i722-i731 (2018) - [i5]Yu Li, Fan Xu, Fa Zhang, Pingyong Xu, Mingshu Zhang, Ming Fan, Lihua Li, Xin Gao, Renmin Han:
DLBI: Deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy. CoRR abs/1805.07777 (2018) - [i4]Yu Li, Zhongxiao Li, Lizhong Ding, Peng Yang, Yuhui Hu, Wei Chen, Xin Gao:
SupportNet: solving catastrophic forgetting in class incremental learning with support data. CoRR abs/1806.02942 (2018) - [i3]Yu Li, Lizhong Ding, Xin Gao:
On the Decision Boundary of Deep Neural Networks. CoRR abs/1808.05385 (2018) - [i2]Yu Li, Tao Zhang, Shuyu Sun, Xin Gao:
Accelerating Flash Calculation through Deep Learning Methods. CoRR abs/1809.07311 (2018) - [i1]Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Xin Gao, Victor V. Solovyev:
PromID: human promoter prediction by deep learning. CoRR abs/1810.01414 (2018) - 2017
- [j2]Hanjun Dai, Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Le Song, Xin Gao:
Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape. Bioinform. 33(22): 3575-3583 (2017)
2000 – 2009
- 2008
- [j1]Liping Wang, Qing Li, Guozhu Dong, Yu Li:
Semantic knowledge facilities for a web-based recipe database system supporting personalization. Concurr. Comput. Pract. Exp. 20(7): 753-782 (2008) - 2006
- [c3]Liping Wang, Qing Li, Yu Li, Xiaofeng Meng:
Dish_Master: an Intelligent and Adaptive Manager for a Web-based Recipe Database System. SKG 2006: 6 - [c2]Yu Li, Xiaofeng Meng, Liping Wang, Qing Li:
RecipeCrawler: Collecting Recipe Data from WWW Incrementally. WAIM 2006: 263-274 - [c1]Yu Li, Xiaofeng Meng, Qing Li, Liping Wang:
Hybrid Method for Automated News Content Extraction from the Web. WISE 2006: 327-338
Coauthor Index
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