Microbiome
foundation models
Learning transferable representations from large-scale microbial data to support diverse biological questions.
Bioinformatics · AI for biology
Haohong Zhang.
Learning the language
of microbial life.
I build foundation models to understand microbial communities and connect biological complexity with interpretable AI.
Latest research · 2026
MGM2
A unified foundation model for microbiome world exploration.
bioRxiv · PreprintRead paper
Microbiome / Foundation models / Computational biologyDiscover more
About meBiology is complex.
Biology is complex.
Understanding it
should be possible.
I am a direct-track Ph.D. student in bioinformatics and computational biology at HUST, working in Prof. Kang Ning’s group.
My research brings deep learning and large-scale pretraining to microbiome analysis. I am interested in representations that transfer across communities, cohorts and biological contexts—and in making what these models learn interpretable.
My work spans microbiome foundation models, microbial community dynamics, biosynthetic gene clusters and antimicrobial peptide discovery.
ORCID 0000-0001-6267-4244Education
2023 — Present
Ph.D. in Bioinformatics
Direct-track · Huazhong University of Science and Technology
2019 — 2023
Bachelor of Science
Huazhong University of Science and Technology
Research directionsFrom microbial communities
From microbial communities
to biological understanding.
Generalizable models.
Interpretable representations.
Biologically meaningful insights.
Microbiome
Community
dynamics
Modeling how microbial communities change over time, with context-aware prediction and digital-twin frameworks.
Microbial
functional discovery
Exploring biosynthetic gene clusters and antimicrobial peptides with context-aware protein language models.
Learning
across cohorts
Transferring knowledge across regions and datasets for robust microbiome-based classification and prediction.
Publications
All citations on Scholar Selected work.
2026Preprint
MGM2 as a Unified Foundation Model for Microbiome World Exploration
- Foundation models
- Microbiome
- Representation learning
2026Preprint
MetaClaw: an auditable AI agent for end-to-end, multi-directional metagenomic and multi-omics analysis
- AI agents
- Metagenomics
- Reproducible workflows
2026Journal article
MGM as a Large-Scale Pretrained Foundation Model for Microbiome Analyses in Diverse Contexts
- Large-scale pretraining
- Microbiome
- Transfer learning
2024Journal article
Deep learning enabled integration of tumor microenvironment microbial profiles and host gene expressions for interpretable survival subtyping in diverse types of cancers
- Multi-omics integration
- Cancer survival
- Interpretable deep learning
More publications 18 entries · 2023–2025
2025
2025Preprint
Towards a generative paradigm for large-scale microbiome analysis by generative language model
- Generative language models
- Microbiome
2025Journal article
Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model
- Biosynthetic gene clusters
- Microbial genomes
- Neural networks
2025Journal article
Techniques for learning and transferring knowledge for microbiome-based classification and prediction: review and assessment
- Transfer learning
- Microbiome classification
- Benchmarking
2025Journal article
A temporal-aware machine learning framework enables microbial community dynamics prediction with personalized precision
- Temporal modeling
- Community dynamics
- Personalized prediction
2025Preprint
Microprophet: A digital twin framework for predicting microbial community dynamics with personalized precision
- Digital twins
- Community dynamics
- Personalized prediction
2025Journal article
Intra-tumor microbiome-based tumor survival indices predict immune interaction and drug sensitivity on pan-cancer scale
- Tumor microbiome
- Survival indices
- Drug sensitivity
2025Preprint
Deciphering Biosynthetic Gene Clusters with a Context-Aware Protein Language Model
- Protein language models
- Genomic context
- Biosynthetic gene clusters
2025Preprint
AI-driven discovery and optimization of antimicrobial peptides from extreme environments on global scale
- Antimicrobial peptides
- AI-guided discovery
- Extreme environments
2025Conference abstract
Discovery and optimization of antimicrobial peptides from extreme environments on global scale
- Antimicrobial peptides
- Peptide optimization
- Extreme environments
2025Journal article
Potential biases and limitations in inferring the historic range of Yangtze finless porpoises from classic poems
- Historical ecology
- Evidence bias
- Yangtze finless porpoise
2025Journal article
Microbial resources and interactions across three-dimensional space for a freshwater ecosystem
- Freshwater microbiome
- Spatial ecology
- Microbial interactions
2025Journal article
Transfer learning identifies bacterial signatures for cross-regional diagnosis of type 2 diabetes and enable stage-sensitive dietary fiber intervention
- Transfer learning
- Type 2 diabetes
- Dietary intervention
2024
2024Journal article
Highly accurate diagnosis of pancreatic cancer by integrative modeling using gut microbiome and exposome data
- Pancreatic cancer
- Gut microbiome
- Exposome integration
2023
2023Journal article
Tracing human life trajectory using gut microbial communities by context-aware deep learning
- Life trajectories
- Gut microbiome
- Context-aware learning
2023Journal article
Artificial intelligence-enabled microbiome-based diagnosis models for a broad spectrum of cancer types
- Cancer diagnosis
- Microbiome
- Artificial intelligence
2023Journal article
Tumor microenvironment interplay amid microbial community, host gene expression and pathological features elucidates cancer heterogeneity and prognosis risk
- Tumor microenvironment
- Multi-omics integration
- Cancer prognosis
2023Conference abstract
Integration of gut microbiome and exposome data through artificial intelligence enables accurate diagnosis of pancreatic cancer with high fidelity (IDDF2023-ABS-0078)
- Pancreatic cancer
- Gut microbiome
- Exposome integration
2023Conference abstract
Utilizing tumor microenvironment microbial profiles and host gene expressions for reliable survival subtyping in liver hepatocellular carcinoma (IDDF2023-ABS-0080)
- Liver cancer
- Microbial profiles
- Survival subtyping
Open source
Explore GitHub Research, in code.
Foundation modelMGM2
A unified foundation model for microbiome representations, prediction and interpretation.
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Foundation modelMGM
Large-scale pretraining for transferable microbiome analysis across diverse contexts.
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Genome foundation modelMicroVQVAE
A genome foundation model that learns discrete, context-aware genome tokens from ordered prokaryotic protein sequences.
View repository
Microbial source trackingEXPERT-lightning
Context-aware microbial source tracking with transfer learning and biome ontology.
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Microbiome & cancerDeepMicroCancer
Microbiome-based models for the diagnosis of a broad spectrum of cancer types.
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Multi-omics integrationASD-cancer
Interpretable survival subtyping from microbial profiles and host gene expression.
View repository