VBayesMM: Variational Bayesian Microbiome Multiomics 

🏥 BREAKTHROUGH: Our New AI Can Predict How Gut Bacteria Control Your Body Chemistry and Disease Risk 💊

🩺 The medical problems we solved: 

- Why do certain foods affect us all so uniquely? 

- Why do some people develop certain diseases while others don't? 

- Why do identical drug doses work differently in different patients? 

The answer lies in your gut microbiome.

🔬 Precision Body Metabolism Prediction: Instead of drowning in data from thousands of bacterial species, our AI acts like an intelligent filter, pinpointing the exact bacteria that truly matter for chemical production in your body.

🧠 Confidence Levels: Unlike other systems that just say "Bacteria A affects Chemical B," our AI tells you HOW confident it is in each prediction - crucial for making informed health decisions.

⚡ Lightning Fast: What used to take enormous computing power and time can now be done rapidly, making personalized gut health insights more accessible than ever.

Software: https://tungtokyo1108.github.io/VBayesMM/

Funding: JST CREST (1-years project: ¥4,600,000)  

Paper: Briefings in Bioinformatics (2025 Impact Factor: 8.7)
Language: Python

I-SVVS: Integrative Stochastic Variational Variable Selection 

🔬 Breakthrough Multi-Omics Integration

The breakthrough I-SVVS method transforms how scientists analyze complex microbiome and metabolome data. Using advanced hierarchical Dirichlet mixture models, I-SVVS seamlessly integrates multiple datasets to reveal hidden biological patterns with unprecedented precision.

🏆 Superior Performance: Achieves unprecedented clustering precision for multi-dimensional biological data.

🎯 Smart Discovery: Automatically identifies core representative features that reveal hidden relationships between metabolites and microbiome community structure.

🚀 Lightning-Fast Analysis: Stochastic variational inference dramatically accelerates processing of massive, high-dimensional datasets - making the impossible routine.

Software: https://tungtokyo1108.github.io/I-SVVS/

Funding: Research Fellowships for Young Scientists and Grants-in-Aid for Scientific Research-KAKEN (3-years project: ¥9,400,000)  

Paper: Briefings in Bioinformatics (2025 Impact Factor: 8.7)
Language: Python

SVVS: Stochastic Variational Variable Selection

Introduction  
Introducing the groundbreaking Stochastic Variational Variable Selection (SVVS) method—a transformative advance in the field of microbial community analysis. This innovative approach reshapes our ability to manage and interpret the vast, complex data typical of microbiome research, setting a new standard for accuracy and efficiency.

SVVS introduces three significant improvements that directly address the challenges faced by traditional Dirichlet multinomial mixture (DMM) models:

1. Enhanced Precision in Feature Selection: SVVS integrates a novel indicator variable that identifies key operational taxonomic units essential for cluster differentiation. This innovation allows for a refined focus on the most impactful microbial species, significantly enhancing the model's accuracy and the relevance of its findings.

2. Advanced Computational Efficiency: the computation of SVVS is the application of stochastic variational inference, a sophisticated technique that utilizes a controllable variational distribution. This approach, combined with stochastic optimization algorithms, facilitates incredibly fast computations. By drastically reducing the time required to process complex datasets, SVVS enables the analysis of larger datasets than ever before, achieving results in a fraction of the time taken by traditional methods.

3. Dynamic Cluster Estimation: SVVS incorporates Dirichlet process mixtures to transition into an infinite model framework. This adaptation allows for automatic estimation of the number of clusters based on the data itself, introducing a level of adaptability and scale previously unattainable. 

Software: https://github.com/tungtokyo1108/SVVS
Funding: Research Fellowships for Young Scientists and Grants-in-Aid for Scientific Research-KAKEN (2-years project: ¥6,200,000) 

Paper: Microbiome (2022 Impact Factor: 16.837) 

Language: Python

SVBPhylo: Stochastic Variational Inference for Bayesian Phylogenetics

Introduction  
A significant advancement in phylogenetic analysis with our new variational Bayesian procedure, was specifically designed to enhance the PhyloBayes MPI program. This innovative approach is set to revolutionize genomic studies by significantly reducing the computational demand of Bayesian analysis, particularly in the context of large and complex genomic datasets.

Traditional methods, while robust, rely on computationally intensive Markov chain Monte Carlo (MCMC) sampling techniques, which become increasingly impractical as data sets grow in size and complexity. Our new method cleverly circumvents this issue by introducing a variational Bayesian approach that approximates the (unknown) posterior distribution with a controllable variational distribution. What sets this method apart is its optimization strategy: rather than sampling, it estimates the parameters of the variational distribution by minimizing Kullback-Leibler divergence. This innovative technique not only speeds up the computation dramatically but also maintains the accuracy and integrity of the Bayesian inference.

Funding: Grant-in-Aid for Scientific Research (B) (3-years project: ¥1,000,000) 

Paper: Molecular Biology and Evolution (2019 Impact Factor: 14.797) 

Open-source code: https://github.com/tungtokyo1108/My-Project--Machine-Learning-Algorithm-in-Parallel-Environment-for-Biological-Computation 

Language: C++