ECGFlowCMR: Pretraining with ECG-Generated Cine CMR Helps Cardiac Disease Classification and Phenotype Prediction
Authors: Xiaocheng Fang, Zhengyao Ding, Guangkun Nie, Jieyi Cai, Yujie Xiao, Bo Liu, Jiarui Jin, Haoyu Wang, +4 more
Abstract
Cardiac Magnetic Resonance (CMR) imaging provides a comprehensive assessment of cardiac structure and function but remains constrained by high acquisition costs and reliance on expert annotations, limiting the availability of large-scale labeled datasets. In contrast, electrocardiograms (ECGs) are inexpensive, widely accessible, and offer a promising modality for conditioning the generative synthesis of cine CMR. To this end, we propose ECGFlowCMR, a novel ECG-to-CMR generative framework that integrates a Phase-Aware Masked Autoencoder (PA-MAE) and an Anatomy-Motion Disentangled Flow (AMDF) to address two fundamental challenges: (1) the cross-modal temporal mismatch between multi-beat ECG recordings and single-cycle CMR sequences, and (2) the anatomical observability gap due to the limited structural information inherent in ECGs. Extensive experiments on the UK Biobank and a proprietary clinical dataset demonstrate that ECGFlowCMR can generate realistic cine CMR sequences from ECG inputs, enabling scalable pretraining and improving performance on downstream cardiac disease classification and phenotype prediction tasks.
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.
Athira J. Jacob, Puneet Sharma, Dorin Comaniciu +1
Chagas disease is a major cause of cardiomyopathy in Latin America. Cardiac magnetic resonance (CMR) imaging can characterize its structural abnormalities, but scanners and expert readers remain scarce in endemic regions. Electrocardiography (ECG) is inexpensive and widely available, yet structural disease must be inferred indirectly from electrical signals. We propose to transfer CMR-derived structural knowledge to ECG through contrastive pre-training. Using 63,193 paired ECG-CMR examinations from the UK Biobank, we align an ECG encoder with a clinically grounded CMR embedding space using an asymmetric InfoNCE objective. Despite seeing no Chagas cases during pre-training, the resulting representation improves ECG-based Chagas detection. Across CODE-15% and SaMi-Trop, a frozen linear probe achieves an AUROC of 0.851 and sensitivity at the top 5% of predicted risk (Top5%-TPR) of 0.427 in five-fold cross-validation, compared with 0.827 and 0.377 for an unaligned ECG-FM baseline. On the PhysioNet/CinC 2025 Challenge test set, our model obtains the highest AUROC on SaMi-Trop-3 and the best ELSA-Brasil challenge score among the three top-performing methods, indicating that imaging-supervised ECG representations can generalize to populations and settings beyond the pre-training distribution.
Laura Alvarez-Florez, Daniel Uyterlinde, Samuel Ruipérez-Campillo +3
Cine cardiac magnetic resonance is the gold standard for assessing cardiac function, but the scarcity of public datasets limits the development of advanced data-driven models. To address this limitation, we propose a generative method for synthesizing temporally coherent and anatomically consistent cardiac sequences. Our text-to-video framework decouples cardiac spatial structure from temporal motion. First, a fine-tuned diffusion model synthesizes an initial frame from a clinical text prompt, controlling anatomical features. Then, a latent flow model conditioned on a cardiac phase embedding generates the complete cardiac motion, ensuring spatial consistency and temporal control. Our model generates anatomically and pathologically diverse sequences with high temporal coherence and strong fidelity to input prompts, achieving a FID of 31.68 for image realism and a CLIP score of 31.04 for text-image alignment. These experimental results highlight its potential to produce high-fidelity, on-demand medical data, offering a scalable solution to data scarcity.