Krakencoder (Jamison, Gu, Wang, Tozlu, Sabuncu, Kuceyeski, Nature Methods 2025), ported to JAX / Equinox from the upstream PyTorch release (github.com/kjamison/krakencoder). A linked autoencoder that simultaneously bidirectionally translates between structural and functional brain connectivity across different atlases and processing variants ('flavors') via a common 128-dim L2-normalised latent representation. The Nature Methods 2025 publication's canonical model jointly encodes 15 flavors (3 atlases × {3 functional connectivity types + 2 structural tractography types}) and maps each to / from the shared latent. Architecture (per published recipe): per-flavor 256-dim PCA input transformation -> 256 -> 128 Linear encoder -> 128-dim L2-normalised latent -> 128 -> 256 Linear decoder -> inverse PCA to the destination flavor's full-dim connectivity space. v0 of this port ships the canonical bundle plus its 15-flavor PCA stack (separate krakencoder_pca_stack bundle that the KrakencoderPipeline co-loads).

The Nature Methods 2025 paper's published 15-flavor model. Encodes/decodes connectivity matrices in any of 3 atlases (FS86, Shen268, Coco439) x 5 modalities (3 functional connectivity types + 2 structural tractography variants) through a shared 128-dim L2-normalised latent. Trained on 710 HCP subjects. Consumed by KrakencoderPipeline together with the companion krakencoder_pca_stack.scfc-3atlas-pc256.1 bundle (the 15 PCA projections for these flavors).

Keith W. Jamison, Zijin Gu, Qinxin Wang, Ceren Tozlu, Mert R. Sabuncu, Amy Kuceyeski

Jamison K.W., Gu Z., Wang Q., Tozlu C., Sabuncu M.R., Kuceyeski A. (2025). Krakencoder: a unified brain connectome translation and fusion tool. Nature Methods. DOI: 10.1038/s41592-025-02706-2.

HF Hub license tag: mit

Effective terms: MIT (copyright (c) 2024 Keith W. Jamison) on both the network code (github.com/kjamison/krakencoder) and the pretrained weights + per-flavor PCA transforms hosted on OSF (osf.io/dfp92). The ilex JAX / Equinox port code is separately licensed under Apache-2.0 / GPL-3.0.

Upstream license reference: https://opensource.org/licenses/MIT

Network architecture, training code, and pretrained weights -- copyright (c) 2024 Keith W. Jamison; released under the MIT License. JAX / Equinox port code -- copyright (c) the ilex authors, released under the Apache-2.0 / GPL-3.0 dual license used by ilex itself.

Original weights / reference implementation: https://github.com/kjamison/krakencoder

This artefact was produced by ilex's save/load pipeline. The architecture is implemented in ilex.models.krakencoder.Krakencoder and the weights have been converted from their upstream format. See the upstream source above for the canonical reference.