Lipidome visualisation, comparison, and analysis in a vector space

TL;DR

This paper introduces a new method to visualize and compare lipid structures using a neural network and web-based software called Lipidome Projector.

Contribution

A shallow neural network is used to embed lipid structures in a vector space, enabling automatic clustering and structural analysis.

Findings

The neural network successfully embeds lipid structures in a way that structurally similar species cluster together.

The Lipidome Projector software allows for exploratory analysis and quantitative comparison of lipidomes in 2D or 3D scatterplots.

Abstract

A shallow neural network was used to embed lipid structures in a 2- or 3-dimensional space with the goal that structurally similar species have similar vectors. Tests on complete lipid databanks show that the method automatically produces distributions which follow conventional lipid classifications. The embedding is accompanied by the web-based software, Lipidome Projector. This displays user lipidomes as 2D or 3D scatterplots for quick exploratory analysis, quantitative comparison and interpretation at a structural level. Examples of published data sets were used for a qualitative comparison with literature interpretation.

Lipids are not just the basis of membranes. They carry signals and metabolic energy. This means that the presence, absence, and quantity of lipids reflects a cell’s biochemical state - starving, nourished, sick or healthy. Lipidomics (measuring all lipids in a biological specimen) provides lists of the chemical species and their quantities.

We have used a shallow neural network from natural language modelling to embed lipids in a continuous vector space. Firstly, this means that similar molecules have similar positions in this space. Conventional lipid categories cluster automatically. Secondly, the accompanying web-based software, Lipidome Projector imports a lipidome and displays it as a set of points. Reading several lipidomes at once allows quantitative and structural comparisons. Combined with the ability to show structure and abundance diagrams, the software allows exploratory analysis and interpretation of lipidomics datasets.

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