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Circular van Krevelen diagram for visualizing metabolic pathways

Li, S.

2025-06-03 bioinformatics
10.1101/2025.05.31.657198 bioRxiv
Show abstract

Emerging biochemical data require effective pathway visualization. However, traditional metabolic maps were based on manual layouts, falling behind new scientific discoveries. Automated visualization of metabolic pathways has been investigated heavily, but resulted in few consensuses. We report here a new approach based on circularized van Krevelen diagram. This method is based on chemical principles, providing the consistency critical for community exchanges and collaborations. Example applications include metabolomics data interpretation and a new set of metabolic maps.

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The top 2 journals account for 50% of the predicted probability mass.

1
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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.