# DCA: Graph-Guided Deep Embedding Clustering for Brain Atlases

arXiv: https://arxiv.org/abs/2509.01426 · HTML: https://mlsanity.com/paper/2509.01426/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 12 of its 57 references that are in the map.
- First posted on arXiv 1 Sep 2025.

## Builds on (most cited first, 12 of 12)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [Unsupervised Deep Embedding for Clustering Analysis](https://mlsanity.com/paper/1511.06335/) (2015)
- [UNETR++: Delving into Efficient and Accurate 3D Medical Image Segmentation](https://mlsanity.com/paper/2212.04497/) (2022)
- [Community detection in networks: A user guide](https://mlsanity.com/paper/1608.00163/) (2016)
- [SwiFT: Swin 4D fMRI Transformer](https://mlsanity.com/paper/2307.05916/) (2023)
- [NeuroGraph: Benchmarks for Graph Machine Learning in Brain Connectomics](https://mlsanity.com/paper/2306.06202/) (2023)
- [Multi-Class Cell Detection Using Spatial Context Representation](https://mlsanity.com/paper/2110.04886/) (2021)
- [Brain Networks and Intelligence: A Graph Neural Network Based Approach to Resting State fMRI Data](https://mlsanity.com/paper/2311.03520/) (2023)
- [Deep Learning and Bayesian Deep Learning Based Gender Prediction in Multi-Scale Brain Functional Connectivity](https://mlsanity.com/paper/2005.08431/) (2020)

## Built on by (most cited first, 4 of 4)

- [SLIM-Brain: A Data- and Training-Efficient Foundation Model for fMRI Data Analysis](https://mlsanity.com/paper/2512.21881/) (2025)
- [FlexiBrain: Resolution-Agnostic Voxel-Level Encoding for Native fMRI](https://mlsanity.com/paper/2606.11500/) (2026)
- [Beyond the Academic Monoculture: A Unified Framework and Industrial Perspective for Attributed Graph Clustering](https://mlsanity.com/paper/2603.20829/) (2026)
- [FlatClip: Reusing Image Foundation Models for fMRI Representation Learning via Cortical Flatmaps](https://mlsanity.com/paper/2609.31204/) (2026)

## Abstract (arXiv)

Brain atlases are essential for reducing the dimensionality of neuroimaging data and enabling interpretable analysis. However, most existing atlases are predefined, group-level templates with limited flexibility and resolution. We present Deep Cluster Atlas (DCA), a graph-guided deep embedding clustering framework for generating individualized, voxel-wise brain parcellations. DCA combines a pretrained autoencoder with spatially regularized deep clustering to produce functionally coherent and spatially contiguous regions. Our method supports flexible control over resolution and anatomical scope, and generalizes to arbitrary brain structures. We further introduce a standardized benchmarking platform for atlas evaluation, using multiple large-scale fMRI datasets. Across multiple datasets and scales, DCA outperforms state-of-the-art atlases, improving functional homogeneity by 98.8% and silhouette coefficient by 29%, and achieves superior performance in downstream tasks such as autism diagnosis and cognitive decoding. We also observe that a fine-tuned pretrained model achieves superior results on the corresponding task. Codes and models are available at https://github.com/ncclab-sustech/DCA .