Yu Li
Assistant Professor
Develops machine learning for bioinformatics and healthcare, such as antibiotic resistance gene detection and RNA structure prediction.
Yu Li's lab at CUHK works on genomics & computational biology, medical imaging & healthcare AI and recognition, detection & segmentation. 68 papers since 2023, 6 at top venues, mostly Bioinformatics and Nature Communications. 12 PhD students. 3 alumni. Applications close .
At a glance
- papers, 2023–2026
- 18/ year
- at T1 venues
- 9%
- PhD students
- 12
- MS students
- 0
- alumni listed
- 3
Papers by yearfrom the lab homepage, 2023–2026
- 19 papers2026 · T1 2 · collecting
- 21 papers2025 · T1 2
- 22 papers2024 · T1 2
- 6 papers2023 · T1 0
T1 venuesOtherVenues: Bioinformatics, Nature Communications, TMLR, Briefings in Bioinformatics, Nature Methods
Research focuspaper titles that use each topic's words
- rna12 papers
- Genomics & computational biology8 papers
- Recognition, detection & segmentation4 papers
- Medical imaging & healthcare AI2 papers
- structure prediction2 papers
Paper list
From the lab homepage.
202619 papers
- Computers and Electronics in AgricultureA self-supervised learning based method for fish disease diagnosis utilizing extremely limited samples
- Molecular CellAI empowers scalable and programmable RNA design
- Neural NetworksAn end-to-end dual backbone framework for UAV fish disease detection using optimized GateHCO feature fusion mechanism
- EMNLP- FindingsCONDUIT: A Unified Residual-Stream Restoration Framework for KV Cache Reuse in Vision-Language Models
- BioinformaticsDiscovering Reference-missing Cell Types from Bulk Transcriptomics
- AAAI-26DS-ProGen: A Dual-Structure Deep Language Model for Functional Protein Design
- Cell SystemsGFETM: Genome Foundation-based Embedded Topic Model for scATAC-seq Modeling
- npj Digital MedicineHuman–large language model collaboration in clinical medicine: a systematic review and meta-analysis
- RECOMBIntegrative Multi-Scale Sequence–Structure Modeling for Antimicrobial Peptide Prediction and Design
- AAAI-26Investigating Data Pruning for Pretraining Biological Foundation Models at Scale
- KDD-26LC-ERD: Mining Latent Logic for Self-Evolving Reasoning via Consistency-Regulated Reward Decomposition
- Nature Communications (T1)Nucleotide flipping correlates with fluorescence activation in the RhoBAST imaging platform (opens in a new tab)
202521 papers
- ACM Computing SurveysA Survey of Reasoning with Foundation Models: Concepts, Methodologies, and Outlook
- TMLR (T1)AlgoFormer: An Efficient Transformer Framework with Algorithmic Structures
- Quantitative BiologyAn effective encoding of human medical conditions in disease space provides a versatile framework for deciphering disease associations
- Briefings in BioinformaticsArtificial intelligence in bioinformatics: a survey (opens in a new tab)
- RECOMB-25cfDecon: Accurate and Interpretable methylation-based cell type deconvolution for cell-free DNA
- ACL-25DAPE V2: Process Attention Score as Feature Map for Length Extrapolation
- Current Opinion in Structural BiologyDeep Learning for RNA Structure Prediction (opens in a new tab)
- EMNLP-25 FindingsDeveloping and Utilizing a Large-Scale Cantonese Dataset for Multi-Tasking in Large Language Models
- Cell Host & MicrobeExploring functional insights into the human gut microbiome via the structural proteome (opens in a new tab)
- Chemistry AfricaFrom 2015 to 2023: How Machine Learning Aids Natural Product Analysis
- BioinformaticsGS-DTI: A Graph-Structure-Aware Framework Leveraging Large Language Models for Drug–Target Interaction Prediction (opens in a new tab)
- NAACL-25 FindingsHow Well Do LLMs Handle Cantonese? Benchmarking Cantonese Capabilities of Large Language Models
202422 papers
- Genome ResearchA fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
- The Journal of Infectious DiseasesA machine learning-based risk score for prediction of infective endocarditis among patients with Staphylococcus aureus bacteraemia (opens in a new tab)
- Nature Methods (T1)Accurate RNA 3D structure prediction using a language model-based deep learning approach (opens in a new tab)
- NeurIPS-24DAPE: Data-Adaptive Positional Encoding for Length Extrapolation
- Nature Computational ScienceDeep generative design of RNA aptamers using structural predictions (opens in a new tab)
- Biophysics ReportsDeveloping ChatGPT for Biology and Medicine: A Complete Review of Biomedical Question Answering (opens in a new tab)
- EMNLP- FindingsEnhancing Biomedical Knowledge Retrieval-Augmented Generation with Self-Rewarding Tree Search and Proximal Policy Optimization (opens in a new tab)
- Nature BiotechnologyFast, sensitive detection of protein homologs using deep dense retrieval (opens in a new tab)
- NeurIPS-24HORSE: Hierarchical Representation for Large-Scale Neural Subset Selection
- Briefing in BioinformaticsifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers (opens in a new tab)
- BioinformaticsLearning Meaningful Representation of Single-Neuron Morphology via Large-scale Pre-training
- TMLR (T1)Lyra: Orchestrating Dual Correction in Automated Theorem Proving (opens in a new tab)
20236 papers
- Communications BiologyA scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data (opens in a new tab)
- BioinformaticsAcrNET: Predicting anti-CRISPR with Deep Learning (opens in a new tab)
- BioinformaticsCon-AAE: Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration (opens in a new tab)
- RECOMB-23Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning
- Nature Computational ScienceThe High-dimensional Space of Human Diseases Built from Diagnosis Records and Mapped to Genetic Loci (opens in a new tab)
- Nature Computational ScienceUSPNet: unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model (opens in a new tab)
Where alumni went3 listed, 0% to industry
Industry 0Academia 2
Apply to CUHKFall 2027
Computer Science and Engineering MPhil/PhD
- Round
- HKPFS / main round
- Opens
- —
- GRE
- See program page
- English
- Interview in English
- Fee
- See program page
Not yet confirmed for this intake.
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