Spatial Omics
High-resolution modeling of spatial transcriptomics and tissue architecture.
Spatial omics · multimodal learning · biomedical AI
Multimodal AI for spatial omics.
I build models that integrate spatial transcriptomics, histology, and molecular imaging to study tissue organization and disease biology.
About Me
Hello! I am Zhaoqi Song, currently an M.Eng. student in Bioengineering at Xiamen University. I am advised by Prof. Chaoyong Yang and expect to graduate in June 2027. Before joining Xiamen University, I received my bachelor's degree in Bioinformatics from Fujian Medical University in June 2024.
My work sits at the intersection of computational biology, bioinformatics, deep learning, and spatial transcriptomics. I am especially interested in multimodal and AI-driven frameworks for spatial omics analysis, disease modeling, and biomedical discovery.
Research Interests
Multimodal Learning
Fusion of histology, molecular imaging, and omics profiles for biomedical inference.
Biomedical AI
Deep learning systems for disease modeling, prognosis, and translational discovery.
Bioinformatics
Computational pipelines for biological data integration and reproducible analysis.
Selected Work
View all research →
Featured Paper · Searchable
ProCLIP: contrastive multimodal prediction of spatial proteomics
Search the full manuscript and jump directly from each result to its source page.
Spatial Proteomics AI-driven virtual spatial proteomicsPredicting missing protein channels from spatial transcriptomics and multimodal tissue imaging.
Spatial Omics SMART-Spatial super-resolution enhancementMultimodal fusion for higher-resolution gene expression and tissue structure mapping.
Education
Xiamen University
M.Eng. in Bioengineering
2024 - 2027 · expected
Fujian Medical University
Bachelor's degree in Bioinformatics
GPA: 3.51 / 4.0
2020 - 2024
Publications
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MMiKG: a knowledge graph-based platform for path mining of microbiota-mental diseases interactionsBriefings in Bioinformatics, 24(6): bbad340.
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Depression-associated gut microbes, metabolites and clinical trialsFrontiers in Microbiology, 15:1292004.
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DeepALM: A Context-Aware Deep Learning Framework for Antimicrobial Peptide PredictionCurrent Bioinformatics, in press.
Patent
Song Z, Sun H, Chen Q, Wang M, Yang F. (2023). A knowledge graph construction method targeting the gut-brain axis. China Patent No. 202310235160.3.
Manuscripts in Preparation
- Song Z. spmCLIP: Protein-Prior Guided Multimodal Contrastive Learning for Zero-Shot Spatial Proteomics Prediction.
- Zou Y*, Song Z*. SMART-Spatial: Super-resolution Multimodal Atlas Reconstruction-driven Transcriptomics for spatial RNA sequencing.
- Xie J*, Song Z*. Transformer-based Cancer of Unknown Primary Classification and Prognosis.
- Shi W*, Cao J*, Song Z*. Tetrahedral DNA Nanoframe Arrays Enhance mRNA Capture Kinetics in Spatial RNA Sequencing.
* indicates co-first author
Awards & Honors
Wang Deyao Outstanding Student Scholarship, Xiamen University
Outstanding Graduate, Fujian Medical University
Outstanding Student Scholarship, Fujian Medical University, second class (2023) and third class (2024)
Merit Student, Fujian Medical University
MCM/ICM Honorable Mention, top 20%, 2023
CUMCM, provincial first prize (2023) and provincial second prize (2022)
FLTRP Cup National English Public Speaking Contest, provincial first prize (2022) and provincial third prize (2021)
NECCS, third prize, 2022
Workshops & Visits
Chinese Institute for Brain Research Winter School
Peking University, Beijing, China
2025
Visiting Research Intern
Department of Bioinformatics, Prof. Yong Zhang Laboratory, Tongji University
2023
Outstanding Undergraduate Summer Camp
Shanghai Institute of Precision Medicine, Shanghai Jiao Tong University
2023
Outstanding Undergraduate Summer Camp
Liangzhu Laboratory, Zhejiang University
2023
Outstanding Undergraduate Summer Camp
School of Basic Medical Sciences, Southern Medical University
2023