Yu Li

117 papers A* 13B 4Journal 83Unranked 16
YearRankTypeTitle / Venue / Authors
2026 J jnl
ChartVerse: Scaling Chart Reasoning via Reliable Programmatic Synthesis from Scratch.
CoRR
Zheng Liu, Honglin Lin, Chonghan Qin, Xiaoyang Wang, Xin Gao, Yu Li, Mengzhang Cai, Yun Zhu, Zhanping Zhong, Qizhi Pei, Zhuoshi Pan, Xiaoran Shang, Bin Cui, Conghui He, Wentao Zhang, Lijun Wu
2026 A* conf
DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Design.
AAAI
Yanting Li, Zikang Wang, Jiyue Jiang, Ziqian Lin, Dongchen He, Yuheng Shan, Yanruisheng Shao, Jiayi Li, Xiangyu Shi, Jiuming Wang, Yanyu Chen, Yimin Fan, Han Li, Yu Li
2026 J jnl
Predicting drug responses of unseen cell types through transfer learning with foundation models.
Nat. Comput. Sci.
Yixuan Wang, Xinyuan Liu, Yimin Fan, Binghui Xie, James Cheng, Kam Chung Wong, Pak Hang Peter Cheung, Irwin King, Yu Li
2026 J jnl
Scientific Image Synthesis: Benchmarking, Methodologies, and Downstream Utility.
CoRR
Honglin Lin, Chonghan Qin, Zheng Liu, Qizhi Pei, Yu Li, Zhanping Zhong, Xin Gao, Yanfeng Wang, Conghui He, Lijun Wu
2025 J jnl
A Strategic Coordination Framework of Small LLMs Matches Large LLMs in Data Synthesis.
CoRR
Xin Gao, Qizhi Pei, Zinan Tang, Yu Li, Honglin Lin, Jiang Wu, Lijun Wu, Conghui He
2025 — conf
A Strategic Coordination Framework of Small LMs Matches Large LMs in Data Synthesis.
ACL (1)
Xin Gao, Qizhi Pei, Zinan Tang, Yu Li, Honglin Lin, Jiang Wu, Lijun Wu, Conghui He
2025 J jnl
AlgoFormer: An Efficient Transformer Framework with Algorithmic Structures.
Trans. Mach. Learn. Res.
Yihang Gao, Chuanyang Zheng, Enze Xie, Han Shi, Tianyang Hu, Yu Li, Michael Ng, Zhenguo Li, Zhaoqiang Liu
2025 J jnl
An effective encoding of human medical conditions in disease space provides a versatile framework for deciphering disease associations.
Quant. Biol.
Tianxin Xu, Yu Li, Xin Gao, Andrey Rzhetsky, Gengjie Jia
2025 J jnl
Artificial intelligence in bioinformatics: a survey.
Briefings Bioinform.
Jiyue Jiang, Yunke Li, Shiwei Cao, Yuheng Shan, Yuexing Liu, Tianyi Fei, Yule Yu, Yi Feng, Yu Li, Yixue Li, Jiao Yuan
2025 J jnl
Benchmarking Large Language Models on Multiple Tasks in Bioinformatics NLP with Prompting.
CoRR
Jiyue Jiang, Pengan Chen, Jiuming Wang, Dongchen He, Ziqin Wei, Liang Hong, Licheng Zong, Sheng Wang, Qinze Yu, Zixian Ma, Yanyu Chen, Yimin Fan, Xiangyu Shi, Jiawei Sun, Chuan Wu, Yu Li
2025 J jnl
Biological Sequence with Language Model Prompting: A Survey.
CoRR
Jiyue Jiang, Zikang Wang, Yuheng Shan, Heyan Chai, Jiayi Li, Zixian Ma, Xinrui Zhang, Yu Li
2025 J jnl
Can One Domain Help Others? A Data-Centric Study on Multi-Domain Reasoning via Reinforcement Learning.
CoRR
Yu Li, Zhuoshi Pan, Honglin Lin, Mengyuan Sun, Conghui He, Lijun Wu
2025 — conf
CipherBank: Exploring the Boundary of LLM Reasoning Capabilities through Cryptography Challenge.
ACL (Findings)
Yu Li, Qizhi Pei, Mengyuan Sun, Honglin Lin, Chenlin Ming, Xin Gao, Jiang Wu, Conghui He, Lijun Wu
2025 — conf
DAPE V2: Process Attention Score as Feature Map for Length Extrapolation.
ACL (1)
Chuanyang Zheng, Yihang Gao, Han Shi, Jing Xiong, Jiankai Sun, Jingyao Li, Minbin Huang, Xiaozhe Ren, Michael Ng, Xin Jiang, Zhenguo Li, Yu Li
2025 J jnl
DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Design.
CoRR
Yanting Li, Jiyue Jiang, Zikang Wang, Ziqian Lin, Dongchen He, Yuheng Shan, Yanruisheng Shao, Jiayi Li, Xiangyu Shi, Jiuming Wang, Yanyu Chen, Yimin Fan, Han Li, Yu Li
2025 J jnl
Developing and Utilizing a Large-Scale Cantonese Dataset for Multi-Tasking in Large Language Models.
CoRR
Jiyue Jiang, Alfred Kar Yin Truong, Yanyu Chen, Qinghang Bao, Sheng Wang, Pengan Chen, Jiuming Wang, Lingpeng Kong, Yu Li, Chuan Wu
2025 J jnl
GS-DTI: a graph-structure-aware framework leveraging large language models for drug-target interaction prediction.
Bioinform.
Qinze Yu, Chang Zhou, Jiyue Jiang, Xiangyu Shi, Yu Li
2025 J jnl
Hierarchical affinity landscape navigation through learning a shared pocket-ligand space.
Patterns
Bin Feng, Zijing Liu, Hao Li, Mingjun Yang, Junjie Zou, He Cao, Yu Li, Lei Zhang, Sheng Wang
2025 — conf
How Well Do LLMs Handle Cantonese? Benchmarking Cantonese Capabilities of Large Language Models.
NAACL (Findings)
Jiyue Jiang, Pengan Chen, Liheng Chen, Sheng Wang, Qinghang Bao, Lingpeng Kong, Yu Li, Chuan Wu
2025 — conf
LEMMA: Learning from Errors for MatheMatical Advancement in LLMs.
ACL (Findings)
Zhuoshi Pan, Yu Li, Honglin Lin, Qizhi Pei, Zinan Tang, Wei Wu, Chenlin Ming, H. Vicky Zhao, Conghui He, Lijun Wu
2025 J jnl
LEMMA: Learning from Errors for MatheMatical Advancement in LLMs.
CoRR
Zhuoshi Pan, Yu Li, Honglin Lin, Qizhi Pei, Zinan Tang, Wei Wu, Chenlin Ming, H. Vicky Zhao, Conghui He, Lijun Wu
2025 — conf
Large Language Models in Bioinformatics: A Survey.
ACL (Findings)
Zhenyu Wang, Zikang Wang, Jiyue Jiang, Pengan Chen, Xiangyu Shi, Yu Li
2025 J jnl
Large Language Models in Bioinformatics: A Survey.
CoRR
Zhenyu Wang, Zikang Wang, Jiyue Jiang, Pengan Chen, Xiangyu Shi, Yu Li
2025 J jnl
MathFusion: Enhancing Mathematic Problem-solving of LLM through Instruction Fusion.
CoRR
Qizhi Pei, Lijun Wu, Zhuoshi Pan, Yu Li, Honglin Lin, Chenlin Ming, Xin Gao, Conghui He, Rui Yan
2025 — conf
MathFusion: Enhancing Mathematical Problem-solving of LLM through Instruction Fusion.
ACL (1)
Qizhi Pei, Lijun Wu, Zhuoshi Pan, Yu Li, Honglin Lin, Chenlin Ming, Xin Gao, Conghui He, Rui Yan
2025 — conf
MetaLadder: Ascending Mathematical Solution Quality via Analogical-Problem Reasoning Transfer.
EMNLP (Findings)
Honglin Lin, Zhuoshi Pan, Qizhi Pei, Xin Gao, Yu Li, Mengzhang Cai, Conghui He, Lijun Wu
2025 J jnl
OpenDataArena: A Fair and Open Arena for Benchmarking Post-Training Dataset Value.
CoRR
Mengzhang Cai, Xin Gao, Yu Li, Honglin Lin, Zheng Liu, Zhuoshi Pan, Qizhi Pei, Xiaoran Shang, Mengyuan Sun, Zinan Tang, Xiaoyang Wang, Zhanping Zhong, Yun Zhu, Dahua Lin, Conghui He, Lijun Wu
2025 A* conf
RBPtool: A Deep Language Model Framework for Multi-Resolution RBP-RNA Binding Prediction and RNA Molecule Design.
EMNLP
Jiyue Jiang, Yitao Xu, Zikang Wang, Yihan Ye, Yanruisheng Shao, Yuheng Shan, Jiuming Wang, Xiaodan Fan, Jiao Yuan, Yu Li
2025 J jnl
REST: Stress Testing Large Reasoning Models by Asking Multiple Problems at Once.
CoRR
Zhuoshi Pan, Qizhi Pei, Yu Li, Qiyao Sun, Zinan Tang, H. Vicky Zhao, Conghui He, Lijun Wu
2025 A* conf
Rethinking Text-based Protein Understanding: Retrieval or LLM?
EMNLP
Juntong Wu, Zijing Liu, He Cao, Li Hao, Bin Feng, Zishan Shu, Ke Yu, Li Yuan, Yu Li
2025 J jnl
ScaleDiff: Scaling Difficult Problems for Advanced Mathematical Reasoning.
CoRR
Qizhi Pei, Zhuoshi Pan, Honglin Lin, Xin Gao, Yu Li, Zinan Tang, Conghui He, Rui Yan, Lijun Wu
2025 J jnl
Scaling Code-Assisted Chain-of-Thoughts and Instructions for Model Reasoning.
CoRR
Honglin Lin, Qizhi Pei, Xin Gao, Zhuoshi Pan, Yu Li, Juntao Li, Conghui He, Lijun Wu
2025 A* conf
Self-Adjust Softmax.
EMNLP
Chuanyang Zheng, Yihang Gao, Guoxuan Chen, Han Shi, Jing Xiong, Xiaozhe Ren, Chao Huang, Zhenguo Li, Yu Li
2025 J jnl
Self-Adjust Softmax.
CoRR
Chuanyang Zheng, Yihang Gao, Guoxuan Chen, Han Shi, Jing Xiong, Xiaozhe Ren, Chao Huang, Xin Jiang, Zhenguo Li, Yu Li
2025 — conf
Visual-Semantic Dual Calibration Network for Zero-Shot Learning.
ICIC (9)
Qingyang Hao, Lei Li, Yu Li, Chun Yuan
2025 B conf
cfDecon: Accurate and Interpretable Methylation-Based Cell Type Deconvolution for Cell-Free DNA.
RECOMB
Yixuan Wang, Jiayi Li, Jingqi Li, Shen Yang, Yuhan Huang, Xinyuan Liu, Yimin Fan, Irwin King, Yumei Li, Yu Li
2024 J jnl
CAPE: Context-Adaptive Positional Encoding for Length Extrapolation.
CoRR
Chuanyang Zheng, Yihang Gao, Han Shi, Minbin Huang, Jingyao Li, Jing Xiong, Xiaozhe Ren, Michael K. Ng, Xin Jiang, Zhenguo Li, Yu Li
2024 J jnl
DAPE V2: Process Attention Score as Feature Map for Length Extrapolation.
CoRR
Chuanyang Zheng, Yihang Gao, Han Shi, Jing Xiong, Jiankai Sun, Jingyao Li, Minbin Huang, Xiaozhe Ren, Michael K. Ng, Xin Jiang, Zhenguo Li, Yu Li
2024 A* conf
DAPE: Data-Adaptive Positional Encoding for Length Extrapolation.
NeurIPS
Chuanyang Zheng, Yihang Gao, Han Shi, Minbin Huang, Jingyao Li, Jing Xiong, Xiaozhe Ren, Michael K. Ng, Xin Jiang, Zhenguo Li, Yu Li
2024 J jnl
Data Augmentation of Multi-turn Psychological Dialogue via Knowledge-driven Progressive Thought Prompting.
CoRR
Jiyue Jiang, Liheng Chen, Sheng Wang, Lingpeng Kong, Yu Li, Chuan Wu
2024 J jnl
Deep generative design of RNA aptamers using structural predictions.
Nat. Comput. Sci.
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
2024 J jnl
Developing ChatGPT for Biology and Medicine: A Complete Review of Biomedical Question Answering.
CoRR
Qing Li, Lei Li, Yu Li
2024 J jnl
Enhancing Biomedical Knowledge Retrieval-Augmented Generation with Self-Rewarding Tree Search and Proximal Policy Optimization.
CoRR
Minda Hu, Licheng Zong, Hongru Wang, Jingyan Zhou, Jingjing Li, Yichen Gao, Kam-Fai Wong, Yu Li, Irwin King
2024 — conf
Enhancing Biomedical Question Answering with Parameter-Efficient Fine-Tuning and Hierarchical Retrieval Augmented Generation.
CLEF (Working Notes)
Yichen Gao, Licheng Zong, Yu Li
2024 B conf
GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling.
RECOMB
Yimin Fan, Yu Li, Jun Ding, Yue Li
2024 J jnl
How Far Can Cantonese NLP Go? Benchmarking Cantonese Capabilities of Large Language Models.
CoRR
Jiyue Jiang, Liheng Chen, Pengan Chen, Sheng Wang, Qinghang Bao, Lingpeng Kong, Yu Li, Chuan Wu
2024 J jnl
Learning meaningful representation of single-neuron morphology via large-scale pre-training.
Bioinform.
Yimin Fan, Yaxuan Li, Yunhua Zhong, Liang Hong, Lei Li, Yu Li
2024 J jnl
Lyra: Orchestrating Dual Correction in Automated Theorem Proving.
Trans. Mach. Learn. Res.
Chuanyang Zheng, Haiming Wang, Enze Xie, Zhengying Liu, Jiankai Sun, Huajian Xin, Jianhao Shen, Zhenguo Li, Yu Li
2024 A* conf
MSA Generation with Seqs2Seqs Pretraining: Advancing Protein Structure Predictions.
NeurIPS
Le Zhang, Jiayang Chen, Tao Shen, Yu Li, Siqi Sun
2024 J jnl
Meta-Learning Without Data via Unconditional Diffusion Models.
IEEE Trans. Circuits Syst. Video Technol.
Yongxian Wei, Zixuan Hu, Li Shen, Zhenyi Wang, Lei Li, Yu Li, Chun Yuan
2024 J jnl
On the Expressive Power of a Variant of the Looped Transformer.
CoRR
Yihang Gao, Chuanyang Zheng, Enze Xie, Han Shi, Tianyang Hu, Yu Li, Michael K. Ng, Zhenguo Li, Zhaoqiang Liu
2024 J jnl
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles.
Database J. Biol. Databases Curation
Junkang Wei, Jin Xiao, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li
2024 J jnl
Progress and Opportunities of Foundation Models in Bioinformatics.
CoRR
Qing Li, Zhihang Hu, Yixuan Wang, Lei Li, Yimin Fan, Irwin King, Le Song, Yu Li
2024 J jnl
Progress and opportunities of foundation models in bioinformatics.
Briefings Bioinform.
Qing Li, Zhihang Hu, Yixuan Wang, Lei Li, Yimin Fan, Irwin King, Gengjie Jia, Sheng Wang, Le Song, Yu Li
2024 J jnl
RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models.
Bioinform.
Han Huang, Ziqian Lin, Dongchen He, Liang Hong, Yu Li
2024 — conf
SeRTS: Self-Rewarding Tree Search for Biomedical Retrieval-Augmented Generation.
EMNLP (Findings)
Minda Hu, Licheng Zong, Hongru Wang, Jingyan Zhou, Jingjing Li, Yichen Gao, Kam-Fai Wong, Yu Li, Irwin King
2024 A* conf
Task Groupings Regularization: Data-Free Meta-Learning with Heterogeneous Pre-trained Models.
ICML
Yongxian Wei, Zixuan Hu, Li Shen, Zhenyi Wang, Yu Li, Chun Yuan, Dacheng Tao
2024 J jnl
Task Groupings Regularization: Data-Free Meta-Learning with Heterogeneous Pre-trained Models.
CoRR
Yongxian Wei, Zixuan Hu, Li Shen, Zhenyi Wang, Yu Li, Chun Yuan, Dacheng Tao
2024 J jnl
Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model.
Nat. Comput. Sci.
Junbo Shen, Qinze Yu, Shenyang Chen, Qingxiong Tan, Jingchen Li, Yu Li
2024 J jnl
ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers.
Briefings Bioinform.
Qingxiong Tan, Jin Xiao, Jiayang Chen, Yixuan Wang, Zeliang Zhang, Tiancheng Zhao, Yu Li
2024 J jnl
scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics.
Briefings Bioinform.
Chuanyang Zheng, Yixuan Wang, Yuqi Cheng, Xuesong Wang, Hongxin Wei, Irwin King, Yu Li
2023 J jnl
AcrNET: predicting anti-CRISPR with deep learning.
Bioinform.
Yunxiang Li, Yumeng Wei, Sheng Xu, Qingxiong Tan, Licheng Zong, Jiuming Wang, Yixuan Wang, Jiayang Chen, Liang Hong, Yu Li
2023 J jnl
Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci.
Nat. Comput. Sci.
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
2023 J jnl
Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration.
Bioinform.
Xuesong Wang, Zhihang Hu, Tingyang Yu, Yixuan Wang, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li
2023 J jnl
Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning.
CoRR
Zhihang Hu, Qinze Yu, Yucheng Guo, Taifeng Wang, Irwin King, Xin Gao, Le Song, Yu Li
2023 J jnl
Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation.
CoRR
Le Zhang, Jiayang Chen, Tao Shen, Yu Li, Siqi Sun
2023 J jnl
Lyra: Orchestrating Dual Correction in Automated Theorem Proving.
CoRR
Chuanyang Zheng, Haiming Wang, Enze Xie, Zhengying Liu, Jiankai Sun, Huajian Xin, Jianhao Shen, Zhenguo Li, Yu Li
2023 J jnl
Progressive-Hint Prompting Improves Reasoning in Large Language Models.
CoRR
Chuanyang Zheng, Zhengying Liu, Enze Xie, Zhenguo Li, Yu Li
2023 J jnl
The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci.
Nat. Comput. Sci.
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
2023 J jnl
Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model.
CoRR
Junbo Shen, Qinze Yu, Shenyang Chen, Qingxiong Tan, Jingcheng Li, Yu Li
2022 B conf
CLMB: Deep Contrastive Learning for Robust Metagenomic Binning.
RECOMB
Pengfei Zhang, Zhengyuan Jiang, Yixuan Wang, Yu Li
2022 A* conf
Contact-Distil: Boosting Low Homologous Protein Contact Map Prediction by Self-Supervised Distillation.
AAAI
Qin Wang, Jiayang Chen, Yuzhe Zhou, Yu Li, Liangzhen Zheng, Sheng Wang, Zhen Li, Shuguang Cui
2022 J jnl
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning.
Genom. Proteom. Bioinform.
Zhongxiao Li, Yisheng Li, Bin Zhang, Yu Li, Yongkang Long, Juexiao Zhou, Xudong Zou, Min Zhang, Yuhui Hu, Wei Chen, Xin Gao
2022 J jnl
Deep learning identifies and quantifies recombination hotspot determinants.
Bioinform.
Yu Li, Siyuan Chen, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Kevin Y. Yip, Xin Gao
2022 J jnl
E2Efold-3D: End-to-End Deep Learning Method for accurate de novo RNA 3D Structure Prediction.
CoRR
Tao Shen, Zhihang Hu, Zhangzhi Peng, Jiayang Chen, Peng Xiong, Liang Hong, Liangzhen Zheng, Yixuan Wang, Irwin King, Sheng Wang, Siqi Sun, Yu Li
2022 J jnl
Protein-RNA interaction prediction with deep learning: structure matters.
Briefings Bioinform.
Junkang Wei, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li
2022 J jnl
Self-supervised contrastive learning for integrative single cell RNA-seq data analysis.
Briefings Bioinform.
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
2022 — conf
Understanding Dropout for Graph Neural Networks.
WWW (Companion Volume)
Juan Shu, Bowei Xi, Yu Li, Fan Wu, Charles A. Kamhoua, Jianzhu Ma
2021 J jnl
Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration.
CoRR
Xuesong Wang, Zhihang Hu, Tingyang Yu, Ruijie Wang, Yumeng Wei, Juan Shu, Jianzhu Ma, Yu Li
2021 — conf
DeepCURATER: Deep Learning for CoURse And Teaching Evaluation and Review.
TALE
Zhihang Hu, Bhaavanaa Thumu, Yuren Qin, ZhiSheng Tao, Yijian Lu, Omar Kan, Yu Li, Irwin King
2021 J jnl
DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment.
PLoS Comput. Biol.
Ramzan Umarov, Yu Li, Erik Arner
2021 J jnl
Disease gene prediction with privileged information and heteroscedastic dropout.
Bioinform.
Juan Shu, Yu Li, Sheng Wang, Bowei Xi, Jianzhu Ma
2021 J jnl
HMD-AMP: Protein Language-Powered Hierarchical Multi-label Deep Forest for Annotating Antimicrobial Peptides.
CoRR
Qinze Yu, Zhihang Dong, Xingyu Fan, Licheng Zong, Yu Li
2021 J jnl
Protein-RNA interaction prediction with deep learning: Structure matters.
CoRR
Junkang Wei, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li
2021 J jnl
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.
PLoS Comput. Biol.
Ramzan Umarov, Yu Li, Takahiro Arakawa, Satoshi Takizawa, Xin Gao, Erik Arner
2020 J jnl
DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing.
Bioinform.
Yu Li, Sheng Wang, Chongwei Bi, Zhaowen Qiu, Mo Li, Xin Gao
2020 A* conf
Learning To Stop While Learning To Predict.
ICML
Xinshi Chen, Hanjun Dai, Yu Li, Xin Gao, Le Song
2020 J jnl
Learning to Stop While Learning to Predict.
CoRR
Xinshi Chen, Hanjun Dai, Yu Li, Xin Gao, Le Song
2020 A* conf
RNA Secondary Structure Prediction By Learning Unrolled Algorithms.
ICLR
Xinshi Chen, Yu Li, Ramzan Umarov, Xin Gao, Le Song
2020 J jnl
RNA Secondary Structure Prediction By Learning Unrolled Algorithms.
CoRR
Xinshi Chen, Yu Li, Ramzan Umarov, Xin Gao, Le Song
2020 J jnl
Towards Structured Prediction in Bioinformatics with Deep Learning.
CoRR
Yu Li
2020 — —
Towards Structured Prediction in Bioinformatics with Deep Learning.
Yu Li
2019 J jnl
Accelerating flash calculation through deep learning methods.
J. Comput. Phys.
Yu Li, Tao Zhang, Shuyu Sun, Xin Gao
2019 A* conf
Approximate Kernel Selection with Strong Approximate Consistency.
AAAI
Lizhong Ding, Yong Liu, Shizhong Liao, Yu Li, Peng Yang, Yijie Pan, Chao Huang, Ling Shao, Xin Gao
2019 J jnl
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction.
Bioinform.
Renmin Han, Xiaohua Wan, Lun Li, Albert F. Lawrence, Peng Yang, Yu Li, Sheng Wang, Fei Sun, Zhiyong Liu, Xin Gao, Fa Zhang
2019 J jnl
DeeReCT-PolyA: a robust and generic deep learning method for PAS identification.
Bioinform.
Zhihao Xia, Yu Li, Bin Zhang, Zhongxiao Li, Yuhui Hu, Wei Chen, Xin Gao
2019 J jnl
Deep learning in bioinformatics: introduction, application, and perspective in big data era.
CoRR
Yu Li, Chao Huang, Lizhong Ding, Zhongxiao Li, Yijie Pan, Xin Gao
2019 A* conf
Linear Kernel Tests via Empirical Likelihood for High-Dimensional Data.
AAAI
Lizhong Ding, Zhi Liu, Yu Li, Shizhong Liao, Yong Liu, Peng Yang, Ge Yu, Ling Shao, Xin Gao
2019 J jnl
PredMP: a web server for de novo prediction and visualization of membrane proteins.
Bioinform.
Sheng Wang, Shiyang Fei, Zongan Wang, Yu Li, Jinbo Xu, Feng Zhao, Xin Gao
2019 J jnl
Promoter analysis and prediction in the human genome using sequence-based deep learning models.
Bioinform.
Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Xin Gao, Victor V. Solovyev
2019 A* conf
Two Generator Game: Learning to Sample via Linear Goodness-of-Fit Test.
NeurIPS
Lizhong Ding, Mengyang Yu, Li Liu, Fan Zhu, Yong Liu, Yu Li, Ling Shao
2018 J jnl
Accelerating Flash Calculation through Deep Learning Methods.
CoRR
Yu Li, Tao Zhang, Shuyu Sun, Xin Gao
2018 J jnl
An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing.
Bioinform.
Renmin Han, Yu Li, Xin Gao, Sheng Wang
2018 J jnl
DEEPre: sequence-based enzyme EC number prediction by deep learning.
Bioinform.
Yu Li, Sheng Wang, Ramzan Umarov, Bingqing Xie, Ming Fan, Lihua Li, Xin Gao
2018 J jnl
DLBI: Deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy.
CoRR
Yu Li, Fan Xu, Fa Zhang, Pingyong Xu, Mingshu Zhang, Ming Fan, Lihua Li, Xin Gao, Renmin Han
2018 J jnl
DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy.
Bioinform.
Yu Li, Fan Xu, Fa Zhang, Pingyong Xu, Mingshu Zhang, Ming Fan, Lihua Li, Xin Gao, Renmin Han
2018 J jnl
DeepSimulator: a deep simulator for Nanopore sequencing.
Bioinform.
Yu Li, Renmin Han, Chongwei Bi, Mo Li, Sheng Wang, Xin Gao
2018 J jnl
On the Decision Boundary of Deep Neural Networks.
CoRR
Yu Li, Lizhong Ding, Xin Gao
2018 J jnl
PromID: human promoter prediction by deep learning.
CoRR
Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Xin Gao, Victor V. Solovyev
2018 J jnl
SupportNet: solving catastrophic forgetting in class incremental learning with support data.
CoRR
Yu Li, Zhongxiao Li, Lizhong Ding, Peng Yang, Yuhui Hu, Wei Chen, Xin Gao
2017 J jnl
Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape.
Bioinform.
Hanjun Dai, Ramzan Umarov, Hiroyuki Kuwahara, Yu Li, Le Song, Xin Gao
2011 — conf
A finegrained digestion of news webpages through Event Snippet Extraction.
WWW (Companion Volume)
Rui Yan, Liang Kong, Yu Li, Yan Zhang, Xiaoming Li
2010 J jnl
Dynamic memory paravirtualization transparent to guest OS.
Sci. China Inf. Sci.
Xiaolin Wang, Yifeng Sun, Yingwei Luo, Zhenlin Wang, Yu Li, Binbin Zhang, Haogang Chen, Xiaoming Li
2010 — conf
Event Recognition from News Webpages through Latent Ingredients Extraction.
AIRS
Rui Yan, Yu Li, Yan Zhang, Xiaoming Li
2008 J jnl
Semantic knowledge facilities for a web-based recipe database system supporting personalization.
Concurr. Comput. Pract. Exp.
Liping Wang, Qing Li, Guozhu Dong, Yu Li
2006 — conf
Dish_Master: an Intelligent and Adaptive Manager for a Web-based Recipe Database System.
SKG
Liping Wang, Qing Li, Yu Li, Xiaofeng Meng
2006 B conf
Hybrid Method for Automated News Content Extraction from the Web.
WISE
Yu Li, Xiaofeng Meng, Qing Li, Liping Wang