# Representation learning of human cortical folding to reveal long lasting neurodevelopmental signatures

arXiv: https://arxiv.org/abs/2609.05438 · HTML: https://mlsanity.com/paper/2609.05438/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 23 of its 94 references that are in the map.
- First posted on arXiv 22 Jul 2026.

## Builds on (most cited first, 23 of 23)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [Barlow Twins: Self-Supervised Learning via Redundancy Reduction](https://mlsanity.com/paper/2103.03230/) (2021)
- [Similarity of Neural Network Representations Revisited](https://mlsanity.com/paper/1905.00414/) (2019)
- [Improved Regularization of Convolutional Neural Networks with Cutout](https://mlsanity.com/paper/1708.04552/) (2017)
- [DINOv3](https://mlsanity.com/paper/2508.10104/) (2025)
- [Self-Supervised Learning from Images with a Joint-Embedding Predictive Architecture](https://mlsanity.com/paper/2301.08243/) (2023)
- [Point-M2AE: Multi-scale Masked Autoencoders for Hierarchical Point Cloud Pre-training](https://mlsanity.com/paper/2205.14401/) (2022)
- [A Cookbook of Self-Supervised Learning](https://mlsanity.com/paper/2304.12210/) (2023)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging](https://mlsanity.com/paper/2406.05285/) (2024)
- [Understanding Collapse in Non-Contrastive Siamese Representation Learning](https://mlsanity.com/paper/2209.15007/) (2022)
- [BrainSegFounder: Towards 3D Foundation Models for Neuroimage Segmentation](https://mlsanity.com/paper/2406.10395/) (2024)
- [Joint Embedding vs Reconstruction: Provable Benefits of Latent Space Prediction for Self Supervised Learning](https://mlsanity.com/paper/2505.12477/) (2025)
- [A generalizable 3D framework and model for self-supervised learning in medical imaging](https://mlsanity.com/paper/2501.11755/) (2025)
- [Anatomical Foundation Models for Brain MRIs](https://mlsanity.com/paper/2408.07079/) (2024)
- [Identification of Rare Cortical Folding Patterns using Unsupervised Deep Learning](https://mlsanity.com/paper/2211.16213/) (2022)

## Abstract (arXiv)

The human brain folds in utero, primarily during late gestation. Shortly after birth, cortical folding patterns are established and remain stable thereafter, making them promising early neurodevelopmental markers. Yet it is unclear whether the representations given by current neuroimaging foundation models capture cortical folding variability. Here, we introduce Champollion, a self-supervised learning framework that learns interpretable local representations of cortical folding from structural MRI. Optimized on representative folding-related tasks, Champollion accurately captures known folding patterns across cortical regions and external datasets. In a comprehensive benchmark, it consistently outperforms neuroimaging and general-purpose foundation models. Furthermore, Champollion reveals richer genetic associations than conventional morphometric descriptors and identifies localized folding signatures associated with incomplete hippocampal inversion, prematurity, and maternal smoking. These results establish cortical folding as a rich and largely untapped source of neurodevelopmental information, and Champollion provides a unified framework for discovering, localizing and interpreting long lasting cortical folding signatures.