Foundation models for molecular diagnostics - machine learning with biological ‘common sense’

Introduction

Molecular diagnostics is crucial in fulfilling the promise of personalized medicine. While we are amidst an AI revolution, current machine learning models (ML) struggle to effectively learn from molecular (‘omics’) patient profiles and fail to make robust predictions. Perhaps this is not a surprise. After all, molecular disease biology is immensely complex, and we ask ML models to predict such complicated things as patient prognosis, without them ‘knowing’ anything about molecular biology and based on limited training data.

Approach

To address this, I will create foundation models on top of the vast troves of available biomolecular data, such as:

• Multi-omics profiles in healthy and diseased tissues
• High-resolution single-cell data
• Biological knowledge graphs

This unique approach is driven by self-supervised learning (SSL), an important driver of AI, which offers the opportunity to learn a comprehensive representation of the multimodal biology of the cell – without the need for well-annotated patient data.

Model Development

Starting from this strong basis, the FoundationDX model can then reliably predict cancer subtype or prognosis as it no longer needs to start from scratch on too high-dimensional, too low sample-size datasets. Effectively, we give our systems biological ‘common sense’, foregoing the need for millions of labeled training samples. This uniquely enables us to address one of the most clinically relevant questions: which treatment is best for the patient?

Research Program

The FoundationDX research program is designed to deliver key insights into how the SSL revolution can be used to drive progress in the field of molecular diagnostics. It contains a ‘clinical-grade’ benchmarking module and solves three urgent diagnostic challenges, including:

1. Noninvasive subtyping of pediatric brain cancer
2. [Additional challenges can be listed here]
3. [Additional challenges can be listed here]

The time for powerful, robust and generalizable, knowledge-aware machine learning solutions to previously intractable molecular diagnostics problems has come. FoundationDX aims to deliver this.