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Less is more: AMBER-AFNO - a new benchmark for lightweight 3D medical image segmentation

Year: 2026
Type: article
Abstract: • First AFNO-based spectral mixing for 3D medical segmentation • Eliminates quadratic token-to-token attention entirely • Linear memory scaling for high-resolution 3D volumes • 78% fewer parameters than UNETR++ • SOTA or near-SOTA on ACDC, Synapse, and BraTS We adapt the remote sensing-inspired AMBER model (Dosi et al., 2025) from multi-band image segmentation to 3D medical datacube segmentation. To address the computational bottleneck of the volumetric transformer, we propose the AMBER-AFNO architecture. This approach uses Adaptive Fourier Neural Operators (AFNO) instead of the multi-head self-attention mechanism. Unlike spatial pairwise interactions between tokens, global token mixing in the frequency domain avoids O ( N 2 ) attention-weight calculations. As a result, AMBER-AFNO achieves quasi-linear computational complexity and linear memory scaling. This new way to model global context reduces reliance on dense transformers while preserving global contextual modeling capability. By using attention-free spectral operations, our design offers a compact parameterization and maintains a competitive computational complexity. We evaluate AMBER-AFNO on three public datasets: ACDC, Synapse, and BraTS. On these datasets, the model achieves state-of-the-art or near-state-of-the-art results for DSC and HD95. Compared with recent compact CNN and Transformer architectures, our approach yields higher Dice scores while maintaining a compact model size. Overall, our results show that frequency-domain token mixing with AFNO provides a fast and efficient alternative to self-attention mechanisms for 3D medical image segmentation.
DOI: 10.1016/j.eswa.2026.132518
Language: English
Open Access status: hybrid
Estimated APC paid: $3,500
OpenAlex ID: W4417101593
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