Simplicity within biological complexity

TL;DR

This paper advocates for a comprehensive, scalable framework for embedding multi-scale molecular network data to enhance precision medicine through explainable, efficient models that overcome current methodological limitations.

Contribution

It proposes developing a general embedding framework for multi-omic data, enabling better exploitation of network topology for biomedical applications.

Findings

Survey of existing network embedding methods

Identification of limitations in current approaches

Proposal for a new comprehensive embedding framework

Abstract

Heterogeneous, interconnected, systems-level, molecular data have become increasingly available and key in precision medicine. We need to utilize them to better stratify patients into risk groups, discover new biomarkers and targets, repurpose known and discover new drugs to personalize medical treatment. Existing methodologies are limited and a paradigm shift is needed to achieve quantitative and qualitative breakthroughs. In this perspective paper, we survey the literature and argue for the development of a comprehensive, general framework for embedding of multi-scale molecular network data that would enable their explainable exploitation in precision medicine in linear time. Network embedding methods map nodes to points in low-dimensional space, so that proximity in the learned space reflects the network's topology-function relationships. They have recently achieved unprecedented performance on hard problems of utilizing few omic data in various biomedical applications. However, research thus far has been limited to special variants of the problems and data, with the performance depending on the underlying topology-function network biology hypotheses, the biomedical applications and evaluation metrics. The availability of multi-omic data, modern graph embedding paradigms and compute power call for a creation and training of efficient, explainable and controllable models, having no potentially dangerous, unexpected behaviour, that make a qualitative breakthrough. We propose to develop a general, comprehensive embedding framework for multi-omic network data, from models to efficient and scalable software implementation, and to apply it to biomedical informatics. It will lead to a paradigm shift in computational and biomedical understanding of data and diseases that will open up ways to solving some of the major bottlenecks in precision medicine and other domains.