Multi-encoder nnU-Net outperforms transformer models with self-supervised pretraining

Seyedeh Sahar Taheri Otaghsara; Reza Rahmanzadeh

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arXiv · 2504.03474

Multi-encoder nnU-Net outperforms transformer models with self-supervised pretraining

Seyedeh Sahar Taheri Otaghsara·Reza Rahmanzadeh

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Abstract

This study addresses the essential task of medical image segmentation, which involves the automatic identification and delineation of anatomical structures and pathological regions in medical images. Accurate segmentation is crucial in radiology, as it aids in the precise localization of abnormalities such as tumors, thereby enabling effective diagnosis, treatment planning, and monitoring of disease progression. Specifically, the size, shape, and location of tumors can significantly influence clinical decision-making and therapeutic strategies, making accurate segmentation a key component of radiological workflows. However, challenges posed by variations in MRI modalities, image artifacts, and the scarcity of labeled data complicate the segmentation task and impact the performance of traditional models. To overcome these limitations, we propose a novel self-supervised learning Multi-encoder nnU-Net architecture designed to process multiple MRI modalities independently through separate encoders. This approach allows the model to capture modality-specific features before fusing them for the final segmentation, thus improving accuracy. Our Multi-encoder nnU-Net demonstrates exceptional performance, achieving a Dice Similarity Coefficient (DSC) of 93.72%, which surpasses that of other models such as vanilla nnU-Net, SegResNet, and Swin UNETR. By leveraging the unique information provided by each modality, the model enhances segmentation tasks, particularly in scenarios with limited annotated data. Evaluations highlight the effectiveness of this architecture in improving tumor segmentation outcomes.

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BibTeX RIS

Seyedeh Sahar Taheri Otaghsara, Reza Rahmanzadeh. 2025-06-29. Multi-encoder nnU-Net outperforms transformer models with self-supervised pretraining. https://arxiv.org/abs/2504.03474

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