MR-JEPA: A General Purpose Video Foundation Model for Cardiac MRI

arXiv:2608.30975v1 Announce Type: cross Abstract: Cardiac magnetic resonance imaging (CMR) produces rich sequential data such as temporal cine videos and spatial LGE/mapping stacks, yet most deep learning approaches process individual 2D slices, discarding this context. We present MR-JEPA, a self-supervised video foundation model for CMR that extends LeJEPA to 3D spatiotemporal inputs through tubelet tokenization, spatiotemporal masking augmentation, and initialization from a 2D CMR foundation model. Unlike prior CMR video models limited to cine data, MR-JEPA is pretrained on multi-sequence data (cine, LGE, mapping) from 10,505 patients across two centers without annotations. We evaluate the frozen encoder on six downstream tasks using a unified multi-view gated attention architecture: LV ejection fraction, RV ejection fraction, three myocardial strains (GLS, GCS, GRS), and four-class disease detection. MR-JEPA outperforms other compared methods on all five regression tasks, including both a domain-specific CMR model pretrained on more data with text supervision and a natural-video foundation model, achieving an LV EF MAE of 4.79% (r =0.764) and a GLS MAE of 1.87 (r=0.805), with 21-27% MAE reductions over baselines on strain tasks. For disease detection, MR-JEPA achieved a macro AUG of 0.868, remaining competitive with the domain-specific baseline despite using a fully self-supervised pretraining objective. These results demonstrate the potential of a unified video encoder for robust, multi-view utilization of diverse CMR sequences in clinical cardiac quantification and diagnosis.

Abstract:Cardiac magnetic resonance imaging (CMR) produces rich sequential data such as temporal cine videos and spatial LGE/mapping stacks, yet most deep learning approaches process individual 2D slices, discarding this context. We present MR-JEPA, a self-supervised video foundation model for CMR that extends LeJEPA to 3D spatiotemporal inputs through tubelet tokenization, spatiotemporal masking augmentation, and initialization from a 2D CMR foundation model. Unlike prior CMR video models limited to cine data, MR-JEPA is pretrained on multi-sequence data (cine, LGE, mapping) from 10,505 patients across two centers without annotations. We evaluate the frozen encoder on six downstream tasks using a unified multi-view gated attention architecture: LV ejection fraction, RV ejection fraction, three myocardial strains (GLS, GCS, GRS), and four-class disease detection. MR-JEPA outperforms other compared methods on all five regression tasks, including both a domain-specific CMR model pretrained on more data with text supervision and a natural-video foundation model, achieving an LV EF MAE of 4.79% (r =0.764) and a GLS MAE of 1.87 (r=0.805), with 21-27% MAE reductions over baselines on strain tasks. For disease detection, MR-JEPA achieved a macro AUG of 0.868, remaining competitive with the domain-specific baseline despite using a fully self-supervised pretraining objective. These results demonstrate the potential of a unified video encoder for robust, multi-view utilization of diverse CMR sequences in clinical cardiac quantification and diagnosis.

Computer Vision and Pattern Recognition (cs.CV); Artificial Intelligence (cs.AI)

arXiv:2608.30975 [cs.CV]

(or arXiv:2608.30975v1 [cs.CV] for this version)

https://doi.org/10.48550/arXiv.2608.30975 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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MR-JEPA: A General Purpose Video Foundation Model for Cardiac MRI

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