Harsy, Constantin Ulrich, Wald, Tassilo, Gotkowski, Karol, Kirchhoff, Yannick, Knopp, Marcel, Rokuss, Maximilian, Stegmeier, Elisa, Schader, Philipp, Trofimova, Dasha, Stock, Raphael, Kahl, Kim-Celine, Schaumann, Stephen, Erkan, Selen, Zimmerer, David, Denner, Stefan, Langenberg, Moritz, Ziegler, Sebastian, Eckstein, Katharina, Fischer, Maximilian, Suprijadi, Jonathan, Kovács, Bálint, Hamm, Benjamin, Deshpande, Anand, Bounias, Dimitrios, Disch, Nico, Xiao, Shuhan, Kächele, Jessica, Sellner, Jan, Baidya, Rajesh, Traub, Jeremias, Krämer, Lars, Zenk, Maximilian, Rädsch, Tim, Dvoretskii, Stefan, Peretzke, Robin, Deissler, Jonathan, Ertl, Alexandra, Ghosh, Partha, Dreher, Kris, Dinkelacker, Stefan, Reinke, Annika, Christodoulou, Evangelia, Saeed, Numan, Savriama, Yoland, Estrada, Santiago, Kügler, David, Barragan, Laura Alexandra Daza, Osorio, Cristina Isabel Gonzalez, Peeken, Jan, Baumgartner, Michael, Teichmann, Marvin, Chabin, Guillaume, Kirchler, Matthias, Koch, Valentin, study, for the ALFA, Hohenhaus, Markus, Koslov, Dimitri, Decker, Nina, Yaqub, Mohammad, Heuser, Arnd, Reuter, Martin, Schnabel, Julia A., Heimann, Tobias, Ghesu, Florin, Brachmann, Paul, Heußel, Claus P., Radbruch, Alexander, Brugnara, Gianluca, Rastogi, Aditya, Foltyn-Dumitru, Martha, Schlemmer, Heinz-Peter, Reicht, Ignaz, Holzschuh, Julius C., Bach, Michael, Stieltjes, Bram, Schlamp, Kai, Maier-Hein, Lena, Nolden, Marco, Floca, Ralf, Jäger, Paul F., Vollmuth, Philipp, Isensee, Fabian, Maier-Hein, Klaus H.
Abstract
Radiological artificial intelligence has advanced rapidly, yet most systems remain narrowly task-specific, data-intensive, and fragile under domain shift. Foundation models promise more transferable and data-efficient solutions, but existing approaches are limited in scale, evaluated narrowly, and often assume that a single pretrained model can support diverse downstream tasks. Here we present nnFoundation, complementary convolutional and transformer-based 3D radiological foundation models. Developed within the Human Radiome Project (THRP), nnFoundation is trained on 2.1 million CT, MRI, and PET image volumes from 125 institutional and public datasets. We evaluate them across 108 tasks spanning segmentation, detection, classification, report generation, and image retrieval, including evaluations under domain shift, by external partners and in low-data and low-compute regimes. Across all task types, our convolution- and transformer-based nnFoundation models consistently outperform both prior 3D foundation models and training from scratch, establishing state-of-the-art performance for radiological imaging. However, performance follows a consistent task-dependent structure: the convolutional nnFoundation model dominates spatially localized tasks, whereas the transformer-based nnFoundation model excels in tasks requiring global semantic reasoning and in frozen-feature settings. Dynamically aligning the foundation model topology with the dataset characteristics post-hoc further improves transfer across heterogeneous 3D settings. These results show that transferable 3D radiological performance is governed not by a single universal model, but by the interplay of scalable pretraining, complementary architectures, and dataset-aware adaptation. We release nnFoundation models integrated into nnU-Net and nnDetection, enabling immediate application across established radiology workflows.
Chinese Translation
放射学人工智能迅速发展,但大多数系统仍然局限于特定任务、数据密集,并且在领域转移下表现脆弱。基础模型承诺提供更具可转移性和数据高效的解决方案,但现有方法在规模上有限,评估范围狭窄,且通常假设单一的预训练模型可以支持多样的下游任务。在此,我们提出了nnFoundation,这是一种互补的基于卷积和变换器的3D放射学基础模型。nnFoundation在“人类放射组项目”(THRP)中开发,训练数据来自125个机构和公共数据集的210万CT、MRI和PET图像体积。我们在108个任务上进行评估,这些任务涵盖了分割、检测、分类、报告生成和图像检索,包括在领域转移下的评估,由外部合作伙伴进行,以及在低数据和低计算环境下的评估。在所有任务类型中,我们的基于卷积和变换器的nnFoundation模型始终优于之前的3D基础模型和从头训练,确立了放射学成像的最新性能。然而,性能遵循一致的任务依赖结构:卷积nnFoundation模型在空间局部化任务中占主导地位,而基于变换器的nnFoundation模型在需要全局语义推理和冻结特征设置的任务中表现优异。动态调整基础模型拓扑以与数据集特征后期对齐,进一步改善了在异构3D环境中的迁移。这些结果表明,可转移的3D放射学性能并非由单一的通用模型所决定,而是由可扩展的预训练、互补架构和数据集感知适应之间的相互作用所驱动。我们发布了集成到nnU-Net和nnDetection中的nnFoundation模型,使其能够立即应用于已建立的放射学工作流程。