Krakencoder: a unified brain connectome translation and fusion tool.

Publication Type	Academic Article
Authors	Jamison K, Gu Z, Wang Q, Tozlu C, Sabuncu M, Kuceyeski A
Journal	Nat Methods
Date Published	06/05/2025
ISSN	1548-7105
Abstract	Brain connectivity can be estimated in many ways, depending on modality and processing strategy. Here, we present the Krakencoder, a joint connectome mapping tool that simultaneously bidirectionally translates between structural and functional connectivity, and between different atlases and processing choices via a common latent representation. These mappings demonstrate exceptional accuracy and individual-level identifiability; the mapping between structural and functional connectivity has identifiability 42-54% higher than existing models. The Krakencoder combines all connectome flavors via a shared low-dimensional latent space. This fusion representation better reflects familial relatedness, preserves age- and sex-relevant information, and enhances cognition-relevant information. The Krakencoder can be applied, without retraining, to new out-of-distribution data while still preserving inter-individual differences in the connectome predictions and familial relationships in the latent representations. The Krakencoder is a notable leap forward in capturing the relationship between multimodal brain connectomes in an individualized, behaviorally and demographically relevant way.
DOI	10.1038/s41592-025-02706-2
PubMed ID	40473984