Yu Li

Orcid: 0000-0002-3664-6722

Affiliations:

Chinese University of Hong Kong, Department of Computer Science and Engineering, China
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia (former)

According to our database¹, Yu Li authored at least 64 papers between 2006 and 2024.

Collaborative distances:

Dijkstra number² of four.
Erdős number³ of four.

Timeline

Legend:

Book

In proceedings

Article

PhD thesis

Dataset

Other

Bibliography

2024

Meta-Learning Without Data via Unconditional Diffusion Models.

[BibT_eX]

[DOI]

IEEE Trans. Circuits Syst. Video Technol., November, 2024

Deep generative design of RNA aptamers using structural predictions.

[BibT_eX]

[DOI]

Nat. Comput. Sci., November, 2024

ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles.

[BibT_eX]

[DOI]

Database J. Biol. Databases Curation, January, 2024

Lyra: Orchestrating Dual Correction in Automated Theorem Proving.

[BibT_eX]

[DOI]

Trans. Mach. Learn. Res., 2024

Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model.

[BibT_eX]

[DOI]

Nat. Comput. Sci., 2024

Data Augmentation of Multi-turn Psychological Dialogue via Knowledge-driven Progressive Thought Prompting.

[BibT_eX]

[DOI]

CoRR, 2024

Enhancing Biomedical Knowledge Retrieval-Augmented Generation with Self-Rewarding Tree Search and Proximal Policy Optimization.

[BibT_eX]

[DOI]

CoRR, 2024

Progress and Opportunities of Foundation Models in Bioinformatics.

[BibT_eX]

[DOI]

CoRR, 2024

Developing ChatGPT for Biology and Medicine: A Complete Review of Biomedical Question Answering.

[BibT_eX]

[DOI]

Qing Li

Lei Li

Yu Li

CoRR, 2024

RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models.

[BibT_eX]

[DOI]

Bioinform., 2024

Learning meaningful representation of single-neuron morphology via large-scale pre-training.

[BibT_eX]

[DOI]

Bioinform., 2024

ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

Progress and opportunities of foundation models in bioinformatics.

[BibT_eX]

[DOI]

Briefings Bioinform., 2024

GFETM: Genome Foundation-Based Embedded Topic Model for scATAC-seq Modeling.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2024

Task Groupings Regularization: Data-Free Meta-Learning with Heterogeneous Pre-trained Models.

[BibT_eX]

[DOI]

Proceedings of the Forty-first International Conference on Machine Learning, 2024

SeRTS: Self-Rewarding Tree Search for Biomedical Retrieval-Augmented Generation.

[BibT_eX]

[DOI]

Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2024, 2024

Enhancing Biomedical Question Answering with Parameter-Efficient Fine-Tuning and Hierarchical Retrieval Augmented Generation.

[BibT_eX]

[DOI]

Yichen Gao

Licheng Zong

Yu Li

Proceedings of the Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2024), 2024

2023

AcrNET: predicting anti-CRISPR with deep learning.

[BibT_eX]

[DOI]

Bioinform., May, 2023

Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration.

[BibT_eX]

[DOI]

Bioinform., April, 2023

Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci.

[BibT_eX]

[DOI]

Nat. Comput. Sci., 2023

The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci.

[BibT_eX]

[DOI]

Nat. Comput. Sci., 2023

Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model.

[BibT_eX]

[DOI]

CoRR, 2023

Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation.

[BibT_eX]

[DOI]

CoRR, 2023

Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning.

[BibT_eX]

[DOI]

CoRR, 2023

2022

DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning.

[BibT_eX]

[DOI]

Genom. Proteom. Bioinform., 2022

E2Efold-3D: End-to-End Deep Learning Method for accurate de novo RNA 3D Structure Prediction.

[BibT_eX]

[DOI]

CoRR, 2022

Deep learning identifies and quantifies recombination hotspot determinants.

[BibT_eX]

[DOI]

Yu Li

Siyuan Chen

Trisevgeni Rapakoulia

Hiroyuki Kuwahara

Kevin Y. Yip

Xin Gao

Bioinform., 2022

Protein-RNA interaction prediction with deep learning: structure matters.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis.

[BibT_eX]

[DOI]

Briefings Bioinform., 2022

Understanding Dropout for Graph Neural Networks.

[BibT_eX]

[DOI]

Proceedings of the Companion of The Web Conference 2022, Virtual Event / Lyon, France, April 25, 2022

CLMB: Deep Contrastive Learning for Robust Metagenomic Binning.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2022

Contact-Distil: Boosting Low Homologous Protein Contact Map Prediction by Self-Supervised Distillation.

[BibT_eX]

[DOI]

Proceedings of the Thirty-Sixth AAAI Conference on Artificial Intelligence, 2022

2021

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2021

DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment.

[BibT_eX]

[DOI]

Ramzan Umarov

Yu Li

Erik Arner

PLoS Comput. Biol., 2021

Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration.

[BibT_eX]

[DOI]

CoRR, 2021

HMD-AMP: Protein Language-Powered Hierarchical Multi-label Deep Forest for Annotating Antimicrobial Peptides.

[BibT_eX]

[DOI]

CoRR, 2021

Disease gene prediction with privileged information and heteroscedastic dropout.

[BibT_eX]

[DOI]

Bioinform., 2021

DeepCURATER: Deep Learning for CoURse And Teaching Evaluation and Review.

[BibT_eX]

[DOI]

Proceedings of the 2021 IEEE International Conference on Engineering, 2021

2020

Towards Structured Prediction in Bioinformatics with Deep Learning.

[BibT_eX]

[DOI]

Yu Li

PhD thesis, 2020

Towards Structured Prediction in Bioinformatics with Deep Learning.

[BibT_eX]

[DOI]

Yu Li

CoRR, 2020

DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing.

[BibT_eX]

[DOI]

Bioinform., 2020

Learning To Stop While Learning To Predict.

[BibT_eX]

[DOI]

Proceedings of the 37th International Conference on Machine Learning, 2020

RNA Secondary Structure Prediction By Learning Unrolled Algorithms.

[BibT_eX]

[DOI]

Proceedings of the 8th International Conference on Learning Representations, 2020

2019

Accelerating flash calculation through deep learning methods.

[BibT_eX]

[DOI]

J. Comput. Phys., 2019

Deep learning in bioinformatics: introduction, application, and perspective in big data era.

[BibT_eX]

[DOI]

CoRR, 2019

DeeReCT-PolyA: a robust and generic deep learning method for PAS identification.

[BibT_eX]

[DOI]

Bioinform., 2019

PredMP: a web server for de novo prediction and visualization of membrane proteins.

[BibT_eX]

[DOI]

Bioinform., 2019

Promoter analysis and prediction in the human genome using sequence-based deep learning models.

[BibT_eX]

[DOI]

Bioinform., 2019

AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction.

[BibT_eX]

[DOI]

Bioinform., 2019

Two Generator Game: Learning to Sample via Linear Goodness-of-Fit Test.

[BibT_eX]

[DOI]

Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019

Approximate Kernel Selection with Strong Approximate Consistency.

[BibT_eX]

[DOI]

Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019

Linear Kernel Tests via Empirical Likelihood for High-Dimensional Data.

[BibT_eX]

[DOI]

Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019

2018

PromID: human promoter prediction by deep learning.

[BibT_eX]

[DOI]

CoRR, 2018

On the Decision Boundary of Deep Neural Networks.

[BibT_eX]

[DOI]

Yu Li

Lizhong Ding

Xin Gao

CoRR, 2018

SupportNet: solving catastrophic forgetting in class incremental learning with support data.

[BibT_eX]

[DOI]

CoRR, 2018

DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy.

[BibT_eX]

[DOI]

Bioinform., 2018

DEEPre: sequence-based enzyme EC number prediction by deep learning.

[BibT_eX]

[DOI]

Bioinform., 2018

DeepSimulator: a deep simulator for Nanopore sequencing.

[BibT_eX]

[DOI]

Bioinform., 2018

An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing.

[BibT_eX]

[DOI]

Bioinform., 2018

2017

Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape.

[BibT_eX]

[DOI]

Bioinform., 2017

2008

Semantic knowledge facilities for a web-based recipe database system supporting personalization.

[BibT_eX]

[DOI]

Concurr. Comput. Pract. Exp., 2008

2006

Hybrid Method for Automated News Content Extraction from the Web.

[BibT_eX]

[DOI]

Proceedings of the Web Information Systems, 2006

<i>RecipeCrawler: </i> Collecting Recipe Data from WWW Incrementally.

[BibT_eX]

[DOI]

Proceedings of the Advances in Web-Age Information Management, 2006

Dish_Master: an Intelligent and Adaptive Manager for a Web-based Recipe Database System.

[BibT_eX]

[DOI]

Proceedings of the 2006 International Conference on Semantics, 2006

Yu Li

Timeline

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Online presence:

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