METABIOMICS 2020

Metabiomics: Pioneering Early Detection of Colorectal Cancer through Advanced Data Science
📅 (Updated July 2020)

Company Overview:
Metabiomics is an early stage, private equity backed start-up focused on developing a non-invasive stool test for early detection of colon polyps and colorectal cancer using multi-omic biomarkers derived from the human gut microbiome.

🧑‍🔬 My Role: Leading Metagenomics Data Science
In my role as the lead Metagenomics Data Scientist, I orchestrate the development and refinement of sophisticated algorithms essential for our innovative diagnostic tools. While the specifics of our algorithms are proprietary, I can share insights into the overarching strategies and methodologies we employ:

 🔍 Innovative Feature Engineering:
My team and I employ advanced techniques to interpret both unassembled and assembled metagenomics datasets. Our analytical approach integrates diverse omic data sources—including 16S rRNA gene surveys, comprehensive shotgun sequencing data, proteomics, RNA sequencing, metabolomics, and extensive literature insights—to uncover novel biomarkers for early disease detection.

🧠 Databasing and Knowledge Graphs for Robust ML/AI Applications:
Once features are available, we organise them in a structure that is amenable for machine learning and/or artificial intelligence prediction workflows.

🤖 Advanced ML/AI Predictive Models:
We used custom and off-the-shelf solutions to accurately predict very early stage colon cancer. The type of data going into the training sets, how we validated the the data, and how the predictions were executed is somewhat of the secret sauce, so let's just leave this as a blockbox for now. But at a high level, it implements many of the very buzzy AI/ML algorithms one hears about in related and adjacent fields.

🔄 Continuous Model Validation and Optimization:
As we integrate new data, we continuously refine our models through automated systems and custom dashboards, enabling straightforward interpretation of results for our stakeholders.

⚙️ Scaling with Precision:
Handling the vast scale of omics data, we implement tailored data processing and storage solutions, adhering to AWS best practices to maintain efficiency and reliability in our operations.