Bo Li 李波: multimodal virtual cell modeling and agent systems
Hi, I’m Bo Li (李波), a Ph.D. student in the Department of Artificial Intelligence, University of Macau, advised by Prof. Bob Zhang (University of Macau) and co-advised by Prof. Qianqian Song (Purdue University). Since June 2026 I have been a visiting student at the School of Computing, National University of Singapore, hosted by Prof. Yang Zhang.
I build multimodal virtual cell models: systems that learn how cells respond to drugs across morphology, transcriptomics, and molecular structure, together with the agent systems that turn such models into automated scientific discovery. My work has moved along one continuous line, from perceiving cell phenotypes in images, to aligning them with molecular readouts, to benchmarking and orchestrating virtual cell models end to end.
📫 Contact: Boom985426@gmail.com · WeChat: BoomLi5426
🔥 News
- 2026.06: 🇸🇬 Started a one-year visit to the School of Computing, National University of Singapore, hosted by Prof. Yang Zhang.
- 2026.05: 📄 CellScientist preprint released on arXiv (co-author).
- 2026.04: 🧬 MVCBench preprint released on bioRxiv.
- 2026.01: 🎉 One paper accepted at ICLR 2026 (co-author).
- 2025.12: 🎉 PhenoProfiler published in Nature Communications.
- 2025.08: 🎉 SpaIM published in Nature Communications.
📝 Selected Publications
Five representative works below, cited times in total. The complete list is one click below, and on Google Scholar.
MVCBench: A Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes
Bo Li, Qing Wang, Shihang Wang, Bob Zhang, Yuzhong Peng, Pinxian Zeng, Chengliang Liu, Mengran Li, Ziyang Tang, Xiaojun Yao, Chuxia Deng, Qianqian Song
bioRxiv 2026 · Preprint
TL;DR: A systematic benchmark of 24 drug-molecular and gene representation methods across ~1.1M drug-induced profiles. It exposes a modality-dependent asymmetry: advanced molecular representations substantially help morphological phenotype prediction but barely beat classical fingerprints for transcriptomic response, where task-specific gene representations outperform general-purpose foundation models.
PhenoProfiler: Advancing Phenotypic Learning for Image-based Drug Discovery
Bo Li, Bob Zhang, Chengyang Zhang, Minghao Zhou, Weiliang Huang, Shihang Wang, Qing Wang, Mengran Li, Yong Zhang, Qianqian Song
Nature Communications 17, 793 (2026) · Paper · Code · arXiv
TL;DR: The first end-to-end encoder for image-based phenotypic drug discovery. It replaces the conventional multi-step segmentation-and-feature-extraction pipeline with a single model, evaluated on ~400K high-content images and 8.42M single-cell images, improving accuracy and robustness by up to 20% over prior methods while cutting inference time by roughly 40×.
SpaIM: Single-cell Spatial Transcriptomics Imputation via Style Transfer
Bo Li, Ziyang Tang, Aishwarya Budhkar, Xiang Liu, Tonglin Zhang, Baijian Yang, Jing Su, Qianqian Song
Nature Communications 16, 7861 (2025) · Paper · Code
TL;DR: Recasts cross-modal imputation as style transfer, separating data-agnostic gene-expression “content” from platform-specific “style” to predict unmeasured genes in spatial transcriptomics from scRNA-seq. Across 53 datasets spanning sequencing- and imaging-based platforms, it consistently outperforms 12 state-of-the-art methods in gene coverage and expression accuracy.
Gene Expression Prediction from Histology Images via Hypergraph Neural Networks
Bo Li, Yong Zhang, Qing Wang, Chengyang Zhang, Mengran Li, Guangyu Wang, Qianqian Song
Briefings in Bioinformatics 25(6), bbae500 (2024) · Paper · Code
TL;DR: Builds a hypergraph over image patches using Euclidean distance and adjacent-position weighting, so that higher-order local correlations in whole-slide images can be exploited to predict spot-level gene expression.
Multi-scale Hypergraph-based Feature Alignment Network for Cell Localization
Bo Li, Yong Zhang, Chengyang Zhang, Xinglin Piao, Yongli Hu, Baocai Yin
Pattern Recognition 149, 110260 (2024) · Paper · Code
TL;DR: Reframes cell localization as a feature-alignment problem and introduces a multi-scale hypergraph module that adaptively aggregates multi-level features, substantially improving localization accuracy in dense tissue.
Full publication list
Every journal paper and preprint, newest first, 26 in total. Bo Li in bold; first-author work therefore opens the author line. Compiled from the ORCID and Crossref records.
2026
- Adaptive Prototype-Guided Personalized Propagation for Heterophilic Graphs With Missing Data
Mengran Li, Wenbin Xing, Zelin Zang, Bo Li, Chengyang Zhang, Yong Zhang, et al.
IEEE Transactions on Neural Networks and Learning Systems, 1-16 (2026) - CellScientist: Dual-Space Hierarchical Orchestration for Closed-Loop Refinement of Virtual Cell Models
Mengran Li, Bo Li, Jiaying Wang, Wenbin Xing, Yixuan Dong, Chengyang Zhang, et al.
arXiv preprint (2026) - DiffCTRG: A Diffusion Model for City-Level Traffic Report Generation
Chengyang Zhang, Yong Zhang, Qitan Shao, Bo Li, Yisheng Lv, Xinglin Piao, et al.
IEEE Transactions on Computational Social Systems, 1-13 (2026) - Hypergraph-driven spatial multimodal fusion for precise domain delineation and tumor microenvironment decoding
Chengyang Zhang, Xulong Li, Bo Li, Chenxun Deng, Mengran Li, Shiqi Zhang, et al.
Communications Biology, 9, 45 (2026) - LocSAM: Modular SAM enhancement for dense object localization in complex scenes
Jingjing Wang, Yong Zhang, Bo Li, Yongli Hu, Bob Zhang, Baocai Yin
Computer Vision and Image Understanding, 271, 104878 (2026) - Mitigating Feature Degradation in Deep Forward-Forward Networks
Weijing Zhao, Bob Zhang, Yuqi Wang, Bo Li, Kangdao Liu
SSRN preprint (2026) - MORSE: Molecular representation learning via structured semantic extraction across hierarchical and asymmetric biological modalities
Ronghui Zhang, Mengran Li, Wenbin Xing, Bo Li, Chengyang Zhang, Wenxuan Tu, et al.
Pattern Recognition, 174, 112975 (2026) - MVCBench: A Multimodal Benchmark for Drug-induced Virtual Cell Phenotypes
Bo Li, Qing Wang, Shihang Wang, Bob Zhang, Yuzhong Peng, Pinxian Zeng, et al.
bioRxiv preprint (2026) - PhenoProfiler: advancing phenotypic learning for image-based drug discovery
Bo Li, Bob Zhang, Chengyang Zhang, Minghao Zhou, Weiliang Huang, Shihang Wang, et al.
Nature Communications, 17, 793 (2026) - PSSD: Progressive Spatial-Semantic Decoupling for Flow-Based Gene Expression Prediction from Histology Images
Chengyang Zhang, Bo Li, Bob Zhang, Yuansong Zeng, Yuhao Yi, Jiancheng Lv
Bioinformatics, btag598 (2026)
2025
- ChatTraffic: Text-to-Traffic Generation via Diffusion Model
Chengyang Zhang, Yong Zhang, Qitan Shao, Bo Li, Yisheng Lv, Xinglin Piao, et al.
IEEE Transactions on Intelligent Transportation Systems, 26, 2656-2668 (2025) - SpaIM: single-cell spatial transcriptomics imputation via style transfer
Bo Li, Ziyang Tang, Aishwarya Budhkar, Xiang Liu, Tonglin Zhang, Baijian Yang, et al.
Nature Communications, 16, 7861 (2025) - TDG-Mamba: Advanced Spatiotemporal Embedding for Temporal Dynamic Graph Learning via Bidirectional Information Propagation
Mengran Li, Junzhou Chen, Bo Li, Yong Zhang, Ronghui Zhang, Siyuan Gong, et al.
IEEE Transactions on Computational Social Systems, 12, 2014-2029 (2025)
2024
- AntiFormer: graph enhanced large language model for binding affinity prediction
Qing Wang, Yuzhou Feng, Yanfei Wang, Bo Li, Jianguo Wen, Xiaobo Zhou, et al.
Briefings in Bioinformatics, 25, bbae403 (2024) - BjTT: A Large-Scale Multimodal Dataset for Traffic Prediction
Chengyang Zhang, Yong Zhang, Qitan Shao, Jiangtao Feng, Bo Li, Yisheng Lv, et al.
IEEE Transactions on Intelligent Transportation Systems, 25, 18992-19003 (2024) - CrowdGraph: Weakly supervised Crowd Counting via Pure Graph Neural Network
Chengyang Zhang, Yong Zhang, Bo Li, Xinglin Piao, Baocai Yin
ACM Transactions on Multimedia Computing, Communications, and Applications, 20, 1-23 (2024) - Deep learning in phenotypic drug discovery: a survey
Bo Li, Weiliang Huang, Weijing Zhao, Caijie Zhao, Jingtao Wang, Yuqi Wang
TechRxiv preprint (2024) - Difference-Deformable Convolution With Pseudo Scale Instance Map for Cell Localization
Chengyang Zhang, Jie Chen, Bo Li, Min Feng, Yongquan Yang, Qikui Zhu, et al.
IEEE Journal of Biomedical and Health Informatics, 28, 355-366 (2024) - Exponential distance transform maps for cell localization
Bo Li, Jie Chen, Hang Yi, Min Feng, Yongquan Yang, Qikui Zhu, et al.
Engineering Applications of Artificial Intelligence, 132, 107948 (2024) - Gene expression prediction from histology images via hypergraph neural networks
Bo Li, Yong Zhang, Qing Wang, Chengyang Zhang, Mengran Li, Guangyu Wang, et al.
Briefings in Bioinformatics, 25, bbae500 (2024) - Lite-UNet: A lightweight and efficient network for cell localization
Bo Li, Yong Zhang, Yunhan Ren, Chengyang Zhang, Baocai Yin
Engineering Applications of Artificial Intelligence, 129, 107634 (2024) - Multi-scale hypergraph-based feature alignment network for cell localization
Bo Li, Yong Zhang, Chengyang Zhang, Xinglin Piao, Yongli Hu, Baocai Yin
Pattern Recognition, 149, 110260 (2024)
2023
- CCST: crowd counting with swin transformer
Bo Li, Yong Zhang, Haihui Xu, Baocai Yin
The Visual Computer, 39, 2671-2682 (2023) - Hypergraph Association Weakly Supervised Crowd Counting
Bo Li, Yong Zhang, Chengyang Zhang, Xinglin Piao, Baocai Yin
ACM Transactions on Multimedia Computing, Communications, and Applications, 19, 1-20 (2023)
2022
- Suitability Evaluation of Crop Variety via Graph Neural Network
Qiusi Zhang, Bo Li, Yong Zhang, Shufeng Wang
Computational Intelligence and Neuroscience, 2022, 1-10 (2022)
2021
- Approaches on crowd counting and density estimation: a review
Bo Li, Hongbo Huang, Ang Zhang, Peiwen Liu, Cheng Liu
Pattern Analysis and Applications, 24, 853-874 (2021)
🛠 Open Source
Research code and community resources, 700+ GitHub stars in total.
| Project | What it is | Stars |
|---|---|---|
| Nature-Paper-Skills | Agent skills for drafting, revising, auditing, and resubmitting Nature-style manuscripts |  |
| Awesome-Virtual-Cell | Papers, datasets, benchmarks, and community resources for AI virtual cells |  |
| Awesome-Phenotypic-Drug-Discovery | Curated resources for phenotypic drug discovery |  |
| PhenoProfiler | End-to-end phenotypic profiling for image-based drug discovery |  |
| SpaIM | Style-transfer imputation for spatial transcriptomics |  |
| MHFAN | Multi-scale hypergraph feature alignment for cell localization |  |
| UM_CS_QE | Study resources for the University of Macau CIS Ph.D. qualifying exam |  |
📖 Education
-
2026.06 – 2027.06: National University of Singapore
- Visiting Student, School of Computing. Host: Prof. Yang Zhang
-
2024.08 – Present: University of Macau
- Ph.D. in Computer Science, Department of Artificial Intelligence, Full Scholarship. Advisors: Prof. Bob Zhang, Prof. Qianqian Song
-
2021.09 – 2024.07: Beijing University of Technology
- M.Eng. in Electronic Information. Advisors: Prof. Yong Zhang, Prof. Baocai Yin
-
2017.09 – 2021.07: Beijing Information Science & Technology University
- B.Eng. in Robotics Engineering. Advisor: Prof. Hongbo Huang
🎖 Honors and Awards
- 2024: Ph.D. Scholarship, University of Macau
- 2024.07: Top 100 Graduates of BJUT (Top 100 / 6331)
- 2024.07 & 2021.07: Beijing Outstanding Graduate
- 2023.10: Xiaomi Scholarship
- 2023.10 & 2022.10: First-Class Academic Scholarship, BJUT
- 2022.10: National Scholarship
- 2021: First Prize, Science & Technology Innovation Scholarship, BISTU
- 2020.12: Second Prize, National Mathematics Competition
📜 Patents
Co-inventor of three Chinese invention patents on cell image density map generation and cell localization: CN115457546A, CN115810046A, CN115457547A.
💼 Academic Service
Journal reviewer: Science Advances, IEEE TIP, IEEE TNNLS, IEEE TCE, IEEE TSMCS, Medical Image Analysis, Bioinformatics, Briefings in Bioinformatics, BMC Biology, Engineering Applications of Artificial Intelligence, Expert Systems with Applications, Knowledge-Based Systems, CAAI Transactions on Intelligence Technology, and Artificial Intelligence Review.
Collaborations: Purdue University, Cornell University, University of Florida, National University of Singapore, Sun Yat-sen University, Sichuan University, Beijing University of Technology, and Macao Polytechnic University.
🧰 Skills
- Research: multimodal representation learning, medical image analysis, spatial omics modeling, phenotypic drug discovery, virtual cell modeling and benchmarking.
- Agent systems: multi-agent design, skill-based architectures, memory-augmented systems, reusable workflow design for scientific applications.
- Engineering: Python, PyTorch, CUDA, Linux.
