Mondrian Abstraction and Language Model Embeddings for Differential Pathway Analysis

In this study, we introduce the Mondrian Map, an innovative visualization tool inspired by Piet Mondrian’s abstract art, to address the complexities inherent in visualizing biological networks. The Mondrian Map enables clear and meaningful representations of biological pathways by converting intricate biological data into a structured and intuitive format, facilitating a deeper understanding of molecular dynamics. Each pathway is represented by a square whose size corresponds to fold change, with color indicating the direction of regulation (up or down) and statistical significance. The spatial arrangement of pathways is derived from language model embeddings, preserving neighborhood relationships and enabling the identification of clusters of related pathways. Additionally, colored lines highlight potential crosstalk between pathways, with distinctions between short- and long-range functional interactions. In a glioblastoma multiforme (GBM) case study, the Mondrian Map effectively revealed distinct pathway patterns across patient profiles at different stages of disease progression. By surpassing traditional enriched pathway tables and presenting pathways in a relative context without causing visual information overload, this work highlights the tool’s potential to enhance downstream bioinformatics analyses by providing a more comprehensive and visually accessible overview of pathway interactions, offering new avenues for therapeutic exploration and personalized medicine.