Yu Li

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 41

Top Topics

Regulatory Elements

Bayesian Inference

Dimensional Data

Top Venues

Briefings Bioinform.

Publications

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 (2024)
Yichen Gao, Licheng Zong, Yu Li
Enhancing Biomedical Question Answering with Parameter-Efficient Fine-Tuning and Hierarchical Retrieval Augmented Generation. CLEF (Working Notes) (2024)
Yimin Fan, Yu Li, Jun Ding, Yue Li
GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling. RECOMB (2024)
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) (2024)
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)
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)
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 (2023)
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)
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 (2023)
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) (2022)
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)
Yu Li, Siyuan Chen, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Kevin Y. Yip, Xin Gao
Deep learning identifies and quantifies recombination hotspot determinants. Bioinform. 38 (10) (2022)
Junkang Wei, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li
Protein-RNA interaction prediction with deep learning: structure matters. Briefings Bioinform. 23 (1) (2022)
Junkang Wei, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li
Protein-RNA interaction prediction with deep learning: Structure matters. CoRR (2021)
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)
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)
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 (2021)
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) (2020)
Xinshi Chen, Hanjun Dai, Yu Li, Xin Gao, Le Song
Learning to Stop While Learning to Predict. CoRR (2020)
Xinshi Chen, Yu Li, Ramzan Umarov, Xin Gao, Le Song
RNA Secondary Structure Prediction By Learning Unrolled Algorithms. ICLR (2020)
Xinshi Chen, Yu Li, Ramzan Umarov, Xin Gao, Le Song
RNA Secondary Structure Prediction By Learning Unrolled Algorithms. CoRR (2020)
Xinshi Chen, Hanjun Dai, Yu Li, Xin Gao, Le Song
Learning To Stop While Learning To Predict. ICML (2020)
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 (2019)
Yu Li, Tao Zhang, Shuyu Sun, Xin Gao
Accelerating flash calculation through deep learning methods. J. Comput. Phys. 394 (2019)
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) (2019)
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) (2019)
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)
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)
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)
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) (2019)
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) (2019)
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 (2018)
Yu Li, Renmin Han, Chongwei Bi, Mo Li, Sheng Wang, Xin Gao
DeepSimulator: a deep simulator for Nanopore sequencing. Bioinform. 34 (17) (2018)
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) (2018)
Yu Li, Tao Zhang, Shuyu Sun, Xin Gao
Accelerating Flash Calculation through Deep Learning Methods. CoRR (2018)
Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Xin Gao, Victor V. Solovyev
PromID: human promoter prediction by deep learning. CoRR (2018)
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) (2018)
Yu Li, Lizhong Ding, Xin Gao
On the Decision Boundary of Deep Neural Networks. CoRR (2018)
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 (2018)
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) (2018)
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) (2017)