Diffusion MRI requires repeated k-space acquisitions over multiple diffusion-encoding directions, making acquisition time dependent on both spatial and angular sampling. Existing joint k-q methods either associate directional parameters with fixed voxels or separate spatial reconstruction from angular completion. However, diffusion-weighted images acquired under different directions share the same anatomical organization, while their local signal intensities vary with diffusion encoding. Existing formulations do not fully exploit the complementarity between shared anatomy and direction-dependent signal variation. Consequently, residual spatial errors may be misinterpreted as genuine angular variation and propagated to unobserved directions. We propose a subject-specific spatial-angular Gaussian field for self-supervised joint k-q dMRI reconstruction. Shared 3D Gaussian primitives provide local spatial support, with each primitive carrying a continuous q-conditioned tensor-residual response. The signal at each location is synthesized from multiple overlapping primitive responses, coupling neighboring spatial regions and diffusion directions. The field is progressively optimized from undersampled k-space measurements of observed directions, without fully sampled targets or held-out-direction supervision. Experiments on three HCP diffusion shells under multiple acceleration settings demonstrated consistent improvements in missing-direction DWI reconstruction, tensor-derived metrics, and principal diffusion orientation estimation.
In computational pathology (CPath), developing omni-modal self-supervised learning (SSL) models that integrate histology, genomics, and clinical reports enables transferable representation learning for whole slide images (WSIs). Existing approaches implicitly force heterogeneous modalities into a uniform latent space by contrastive alignment, causing modality collapse where unique, synergistic diagnostic signals (termed as $\mathrmΦ$) are discarded in favor of trivial redundancy. We hypothesize that the strongest task-agnostic SSL training signal stems from distilling the synergistic interactions over merely aligning shared redundancy. To this end, we introduce \textsc{$\mathrmΦ$-Omni}, a synergistic information disentanglement framework grounded in Partial Information Decomposition (PID) theory for slide representation learning. Unlike standard contrastive approaches, \textsc{$\mathrmΦ$-Omni} employs a Synergistic Information Bottleneck (SIB) regulated by the proposed $\mathrmΦ\text{ID}$ objective, which explicitly suppresses marginal redundancy while maximizing irreducible synergy, thereby distilling high-order cross-modal interactions. Following pretraining on breast ($n$=1031) and lung ($n$=919) cohorts, \textsc{$\mathrmΦ$-Omni} demonstrates superior few-shot performance across five independent external datasets spanning eight tasks compared to supervised and SSL baselines. Source code is available here.
Dense self-supervised learning (SSL) is a powerful paradigm for learning without annotations the local descriptors required to solve dense medical imaging tasks. We present Pix2Rep-v2, a framework for SSL of pixel- and voxel-level representations suitable for few-shot downstream applications. Pix2Rep-v2 addresses the main challenges of dense SSL by leveraging a redundancy reduction objective at the pixel-level with a principle of equivariance of dense representations, that scales efficiently to 3D or wide field-of-view applications. We evaluate our method on four datasets, across multiple tasks, multiple modalities and anatomical structures using multiple backbones in 2D and 3D, and under various data regimes. As an alternative to linear probing or full fine-tuning on the downstream task, we also propose an in-context variant, without downstream training, based on a dense prototype approach. Pix2Rep-v2 shows substantially higher data-efficiency in few-shot scenarios compared to fully supervised baselines, and is competitive with the state-of-the-art e.g., +9.3 Dice points in one-shot segmentation on the M&Ms-2 dataset. Our code and pre-trained models are publicly available at https://github.com/BioMedTP/pix2rep-v2.
Athira J. Jacob, Puneet Sharma, Daniel Rueckertcs.CV
Cardiac magnetic resonance (CMR) imaging provides complementary information on cardiac anatomy, function, and tissue characterization across multiple sequences and views. In this work, we investigate foundation model pretraining for 2D CMR and introduce CMRVision, a CMR-specific foundation model trained using DINOv3-style self-supervised learning on a multi-center, multi-sequence cohort of 36 million CMR images. We systematically evaluate architectural and training design choices for domain-specific pretraining. CMRVision is evaluated on two downstream tasks: multi-task segmentation across cine, late gadolinium enhancement (LGE), and mapping sequences, and cine view classification. Our experiments show that CMR-specific pretraining, smaller patch sizes, and patch-level objectives consistently improve downstream performance. Across a multi-task segmentation benchmark, CMRVision achieved the strongest overall performance, outperforming prior natural-image (NI), medical-image, supervised, and CMR foundation model baselines. Improvements were modest but consistent across structures and sequences, with Dice scores ranging from 0.940-0.967 for LV and 0.855-0.905 for myocardium, and reaching 0.929 for RV, 0.920 for LA, and 0.931 for RA. The largest gains were observed for myocardium segmentation in LGE and mapping images. In a zero-shot segmentation task on unseen LGE long-axis views, the model achieved an average Dice score of 0.692, demonstrating cross-view generalization. For cine view classification, CMRVision achieved the highest average accuracy (0.906), compared to prior methods reported in the literature. These results highlight the potential of CMRVision to support robust and generalizable cardiac MRI analysis across multiple sequences and views.
Low-dose computed tomography (LDCT) measurements contain mixed Poisson-Gaussian noise. However, most self-supervised methods rely on generic image statistics and do not explicitly model this noise, which may limit their ability to effectively suppress realistic LDCT noise. To address this issue, we propose a physics-driven framework with cross-domain iteration for self-supervised LDCT denoising. The proposed framework proceeds in three main steps. First, a learned sinogram prior and the LDCT noise model guide posterior inference of photon counts, enabling separation of the Poisson and Gaussian components. Second, the separated Poisson and Gaussian components are respectively processed by binomial thinning and Gaussian data thinning to construct two branches, and residual scaling matches each branch's noise level to that of the observation, yielding a training pair with approximately independent noise realizations from one low-dose measurement. Finally, the pair is used to train an image-domain network whose forward-projected outputs update the prior. Through cross-domain iteration, the prior and the training pair are progressively refined while maintaining consistency with CT acquisition physics. Experiments on simulated data from AAPM, LIDC-IDRI, and LoDoPaB-CT and on real LDCT data show consistent gains over the evaluated self-supervised baselines across dose levels, with performance comparable to the evaluated supervised baseline.
Athira J. Jacob, Puneet Sharma, Dorin Comaniciu +1cs.CV cs.AI
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.
David Sulu, Lorenzo Di Fruscia, Jana M. Webercs.LG q-bio.BM
Molecular self-supervised learning uses chemical structures to guide which molecular embeddings should be similar. We study whether explicitly encoding a molecule's Bemis-Murcko scaffold and using it to supervise the molecular embedding changes what the model learns. We further test whether this effect depends on the embedding geometry by comparing Euclidean and Lorentz contrastive objectives. Across two augmentation strengths, scaffold-supervised models consistently organize molecules according to both identical and structurally related scaffolds. The resulting embeddings also improve molecular property prediction on several tasks, while the exact gains depend on the predicted property. The effect of scaffold supervision on molecular organization is stronger under Lorentz objectives, but neither geometry provides a consistent overall advantage. These results show that explicitly teaching the relation between a molecule and its structural core can reliably shape the organization of molecular embedding space, while the extent of usefulness of this organization remains task dependent.
Much of human health and function unfolds beyond the clinic, through the movements of everyday life. Wrist-worn accelerometers capture these movements continuously, yet their rich signals are often reduced to a small set of predefined behavioural summary measures. Here, we present Sensori, a self-supervised foundation model that learns general-purpose health representations directly from 24 hours of raw tri-axial wrist movement. We developed and evaluated the model across four population-based cohorts from the United Kingdom, China and the United States, comprising 122,640 participants contributing 683,617 person-days of free-living recordings. Sensori condensed each day of movement into a representation that captured diverse movement behaviours, demographic characteristics, health axes and physical function. Evaluation in independent cohorts showed that these representations generalised across populations and measurement settings without retraining. When added to common clinical covariates, Sensori significantly improved prevalent disease classification for 52 of 102 eligible conditions (median delta AUROC, 0.060; range, 0.012-0.242) and incident disease risk prediction for 26 of 87 eligible conditions (median delta Uno's C-index, 0.064; range, 0.025-0.172), with the largest gains for neurological and psychiatric disorders. These findings establish 24-hour wrist movement as a rich and scalable source of health information, with the potential to support passive health monitoring and disease prediction at population scale.
Joint-embedding predictive architectures (JEPAs) have primarily been developed for self-supervised representation learning. Denoising JEPA (D-JEPA) recently demonstrated strong generative capabilities on natural images, yet the applicability to 3D medical imaging remains unexplored. Building on the D-JEPA framework, we present Med-D-JEPA, a systematic adaptation and evaluation of joint-embedding predictive generation for 3D brain MRI. Med-D-JEPA operates on continuous latent tokens produced by a 3D KL-regularized adversarial variational autoencoder, and combines masked context prediction, representation-level alignment, per-token diffusion, and iterative next-set-of-token sampling. We evaluate unconditional and class-conditional generation quality on BraTS2019 and OASIS-1 datasets; downstream classification utility; and preliminary whole-tumor segmentation on BraTS2020. Across different generation settings, Med-D-JEPA achieves superior or competitive performance compared to several strong baselines on fidelity and diversity metrics. Compared to training with real samples, Med-D-JEPA-based synthetic pretraining improves classification AUC from 0.63 to 0.85 on BraTS2019 and from 0.78 to 0.87 on OASIS-1. In the segmentation study, pretraining on Med-D-JEPA samples improves Dice from 0.74 to 0.80 and reduces HD95 from 13.40 to 9.56 mm. These findings establish joint-embedding predictive generation as a promising direction for 3D medical image synthesis and encourage further research in this direction.
12-lead electrocardiogram (ECG) is a standard, non-invasive examination widely used for diagnosing coronary artery disease, where clinical interpretation relies on comparing waveform patterns across multiple leads. However, most existing ECG analysis methods focus on single-lead signals or treat each lead independently, and typically process ECG signals as one-dimensional time-series data using CNNs or RNNs. While effective in modeling local waveform changes, such approaches have difficulty capturing inter-lead dependency and global waveform patterns essential for clinical diagnosis. To address this limitation, we propose a graph-based pseudo-multimodal contrastive learning framework called Graph-CMMC. ECG waveforms are transformed into Gramian Angular Difference Field (GADF) images to construct complementary representations of the same cardiac activity, enabling a pseudo-multimodal learning setting. Using all 12 leads, Graph-CMMC aligns waveform and GADF representations in a self-supervised manner, while a graph-based relational module is employed to model inter-lead dependency and enforce structural consistency across leads during contrastive learning. Experimental results on a multi-label coronary artery occlusion classification task demonstrate that the proposed framework achieves competitive performance compared to supervised learning methods. These results further suggest the effectiveness of using GADF as a complementary representation and incorporating explicit graph-based modeling of inter-lead dependency for learning robust 12-lead ECG representations.
Despite the growing number of public datasets, annotated medical images remain scarce. Supervised learning methods achieve strong performance on many benchmarks, however require large amounts of labeled data, which are costly and time-consuming to obtain in the medical domain. To address this limitation, contrastive self-supervised learning (SSL) has emerged as a promising alternative for learning useful representations from unlabeled data. In this work, we investigate two SSL frameworks, SimSiam and SimCLR, for retinal disease classification from fundus images. We focus on understanding how augmentation strategies and training parameters influence representation learning under resource-constrained settings. Given limited data and computational capacity, we explore the feasibility of training SSL models with small batch sizes incorporated with retinal-specific augmentation techniques. Through a series of experiments, we assess the quality of learned representations via linear evaluation and fine-tuning across downstream tasks, including multi-disease classification and diabetic retinopathy grading. Our results show that tailoring augmentation strategies to the characteristics of retinal images plays a critical role in improving performance. Even under constrained settings, lightweight SSL frameworks can learn transferable representations that reduce dependence on large annotated datasets and achieve competitive results.
EEG foundation models pretrained via self-supervised learning promise transferable representations, but their generalization remains limited, especially across diverse clinical datasets. Full fine-tuning is impractical for resource-constrained clinical settings due to high computational requirements. In this work, we investigate whether parameter-efficient self-supervised adaptation, updating only 9% of parameters suffices to align representations to target tasks. We evaluate our method on two state-of-the-art models with different pretraining objectives: BIOT (contrastive) and CBraMod (masked reconstruction), and evaluate on three clinical EEG datasets for abnormality detection (TUAB), event classification (TUEV), and seizure detection (CHB-MIT) under both in-distribution and out-of-distribution conditions. SSL adaptation yields consistent gains over linear probing, up to 20x AUCPR. Under a fixed compute budget, peak performance requires only 20--50% of available unlabeled data. Critically, when total window count is fixed, performance remains invariant to patient count, suggesting that performance is dependent on overall temporal window diversity only. Our findings demonstrate that parameter-efficient adaptation enables effective deployment of EEG Foundation models (EEG-FM) with minimal computational overhead and data collection burden. Code available at: https://github.com/c3n-group/efficient-eeg-adapt
Sebastián González, Karen Sanchez, José M. Saavedra +2cs.CV
Self-supervised pretraining enables transferable representations for medical imaging, yet most CT encoders remain biased toward coarse semantic understanding, limiting their sensitivity to fine-grained anatomical structures such as vessels or small tumors. In this paper, we introduce Biased Masked Image Modeling (B-MIM), a modification of the iBOT objective that stochastically reduces global semantic alignment to prioritize local patch reconstruction. This bias encourages the encoder to capture high-frequency morphological details and structural continuity. We curate a multi-institutional CT abdominal dataset of 9,955 filtered studies from 17 public sources and pretrain a 3D Swin Transformer backbone using B-MIM. Across inter-dataset experiments on liver vessel segmentation, the proposed encoder improves topological fidelity (clDice) and achieves competitive Dice scores in tumor segmentation, compared to fully fine-tuned baselines, despite updating only a fraction of the parameters. Our results suggest that reducing global semantic pressure during pretraining enhances generalization to intricate anatomical structures.
Ioannis N. Ziogas, Leontios J. Hadjileontiadis, Ahsan H. Khandoker +1cs.LG cs.AI eess.SP
Wearable and smartphone-based emotion recognition (WER) remains a challenging setting in affective computing, due to the notorious difficulty and bias associated with in-the-wild label collection. The high inter-and intra-subject emotional variability motivates us to explore WER modeling through graph node classification in a limited resources learning scheme powered by Self-Supervised Learning (SSL) graph masking augmentation tasks. We employ a subgraph sampling approach during training, utilizing labeled and unlabeled data, along with supervised, semi-supervised, and SSL mechanisms in a multi-task inductive graph neural network architecture. Our evaluations on K-EmoPhone through leave-one-group-out cross-validation in the binary arousal and valence tasks yield average accuracy gains of 4.3% and 7.8%, compared to the full resource setting, utilizing only 20% and 25% of the labels, respectively. Our model analysis sheds light on the relation of SSL graph augmentations to emotional arousal and valence and justifies the approach of SSL-driven subgraph training for in-the-wild WER.
Blaise Delaney, Dominic Dootson, Juan Jose Juan Castella +5cs.LG
The cyclic structure of physiological processes offers a natural prior for self-supervised representation learning, and the cardiac cycle provides a particularly well-defined setting in which to exploit it. We derive a phase-equivariant self-supervised objective and introduce Winder, a joint-embedding architecture that organises representations into phase-invariant coordinates and phase-rotating harmonic subspaces. Its transport operator is fixed and closed-form, derived from the cycle's geometry rather than learned, and adds no parameters. Evaluated on PTB-XL under a frozen linear-probe protocol, Winder attains diagnostic accuracy within the range reported by state-of-the-art self-supervised methods at a ~1 M parameter footprint, while exhibiting phase-equivariant latent geometry. These findings demonstrate that explicitly encoding cardiac-phase symmetry can preserve diagnostically useful information while yielding a latent geometry that is legible, parameter-efficient, and directly tied to a measurable physiological quantity.
Deep learning-based whole-body PET-CT lesion segmentation can support cancer staging, treatment planning, and response assessment, but generalization is limited by scarce annotations and domain shifts. Self-supervised learning (SSL) can address these challenges but remains underexplored in pan-cancer, multi-tracer PET-CT. In this work, we propose MUST-PET (MUltimodal Self-Supervised learning across Tracers), a multimodal, multi-tracer SSL framework for generalizable whole-body PET-CT lesion segmentation. MUST-PET is trained and validated on a diverse, multi-institutional collection of pan-cancer PET-CT scans acquired with FDG and prostate-specific membrane antigen (PSMA)-targeted radiotracers. MUST-PET uses context-aware masked reconstruction, where one modality is partially masked and reconstructed using complementary information from both PET and CT. The pretrained model is subsequently fine-tuned with labeled samples and evaluated for reconstruction quality, lesion segmentation, label efficiency, and generalizability across independent held-out datasets. MUST-PET reduces reconstruction error, improves lesion segmentation over training from scratch, and performs well with limited labeled data and on unseen external datasets, demonstrating the potential of multi-tracer SSL for label-efficient, generalizable whole-body PET-CT. segmentation.
Modern deep learning architectures have demonstrated strong performance in dental CBCT segmentation. One remaining crucial challenge is accurate tooth labeling in cases with missing or malpositioned teeth, which are highly relevant for dental practice. Transformer-based architectures should in theory be able to resolve such ambiguities using global anatomical context. However, due to the high resolution of CBCT volumes and the wide spatial distribution of teeth within volumes, dense patch-based volumetric processing faces an inherent trade-off. Computational costs limit the number of patches that can be used in self-attention and thus, one can either increase the extent of the context captured in self-attention or capture fine-grained structural details by using small patches, but not both. In this work, we present Teeth2Point, an efficient point-based transformer framework for dental CBCT semantic segmentation that can avoid this trade-off. Teeth2Point first localizes volumetric regions of interest (ROIs) surrounding teeth using a convolutional model, then converts ROIs into point tokens using adaptive sampling. A transformer model predicts accurate segmentations using the point tokens, which allow capturing global context while retaining high resolution. The transformer is first pretrained using self-supervised learning (SSL), in the style of DINO but using domain-specific augmentation strategies, followed by supervised finetuning. The SSL pretraining, which includes random token masking, provides robustness to complex anatomical variations. Compared with the strongest two-stage baseline, Teeth2Point improves abnormal-case performance by 1.44 DSC points on average across four datasets; relative to the first-stage nnU-Net, the gain is 1.9 points.
Samuel Kostousov, Abhinn Kaushik, Brokoslaw Laschowskics.LG cs.AI
Recent work has shown that representational alignment between biological and artificial neural networks is asymmetric: model representations predict neural responses much better than neural responses predict model representations. This asymmetry raises the question of whether representational geometry contributes to bidirectional representational alignment. We hypothesized that steering representational geometry during training can systematically influence bidirectional alignment. To test this hypothesis, we developed a computational framework that integrates spectral regularization with bidirectional predictivity analyses. As an initial demonstration, we evaluated our framework using self-supervised contrastive vision models. Steering the spectral geometry of the learned representations substantially increased reverse predictivity with modest reductions in forward predictivity, yielding a 55% relative improvement in bidirectional predictivity. These improvements were accompanied by reduced effective dimensionality and a reorganization of the shared representational subspace, within which forward and reverse predictivity became approximately symmetric at intermediate spectral exponents. Overall, these findings demonstrate that representational geometry can be systematically steered to modulate bidirectional representational alignment between biological and artificial neural networks.
Low-cost, scalable screening for dementia remains an open problem. Imaging-based diagnosis is costly and hard to deploy widely. Electroencephalography (EEG) is portable and inexpensive, but its recordings are noisy, vary widely across subjects, and carry few clinical labels. We tackle this with Delta2Gamma, a self-supervised framework that learns EEG representations from unlabeled data by contrasting augmented views of each signal. Rather than treat EEG as a single stream, Delta2Gamma decomposes every recording into the five canonical neural rhythms (delta, theta, alpha, beta, gamma). Each band gets its own encoder and projection head. Each also gets a temperature that is predicted adaptively during contrastive training, so bands with different signal statistics are balanced automatically. On the ADFTD cohort under a strict leave-one-subject-out protocol, Delta2Gamma separates Alzheimer's disease from cognitively normal controls with 92.4\% accuracy. This exceeds both supervised backbones and recent dedicated EEG methods.
Fine-grained wrist activity recognition can support applications such as procedural step guidance and context-aware assistance, yet acquiring labeled data for every new task, user, and activity granularity remains a bottleneck. We present TransfHAR, a self-supervised wrist IMU framework for on-demand, fine-grained activity recognition by learning transferable motion priors from global, unlabeled activities. We show that self-supervised pretraining on coarse wrist IMU activities (e.g., sitting, walking, exercise) learns motion structure rich enough to transfer to fine-grained manipulative, gestural, and procedural activities (e.g., snapping, stirring, waving) that are absent from pretraining. We implement TransfHAR as a real-time smartwatch application that lets users define and expand their own activity set for personalized recognition from only a few demonstrations. Across three offline cross-dataset evaluations, TransfHAR matches or exceeds fully supervised baselines that use complete label sets with equal or additional sensor channels, by 6.2 balanced-accuracy points on average. In an in-lab study with 10 participants each performing seven novel wrist activities, TransfHAR reaches 86.7% balanced accuracy across participants with five examples per class and 90.4% when updated from a single one-minute recording per class. These results indicate that broad self-supervised wrist pretraining provides an effective foundation for on-demand fine-grained activity recognition.
Syed Abdul Haseeb Qadri, Bjarne C. Hiller, Felix Blanke +7cs.LG
Cytometry measures the complex characteristics of single cells (e.g., counts and protein expression of immune cells) and is widely used across immunological research and clinical settings. However, cytometry data is highly heterogeneous and unstandardized due to experimental protocols and the choice of measured features. While machine learning methods hold the potential to gain deeper insights into cell biology, these challenges make them difficult to apply and transfer across studies. Recent advances in foundation models can alleviate these issues, but corresponding approaches are still scarce in this field. To address this, we provide CytoBERT, a publicly available, open-source, open-weight foundation model for single-cell cytometry data with variable marker panels. CytoBERT is pretrained in a self-supervised manner on a large-scale cytometry corpus (15 human datasets with heterogeneous marker panels and more than 50 million cells) curated through marker standardization, enabling it to learn transferable inter-marker relationships within cells. Fine-tuning CytoBERT for sample-level classification demonstrates that transfer learning across heterogeneous cytometry datasets is feasible, providing a starting point for scalable, generalizable cytometry analysis. Code is available at GitHub.
Serli Kopar, Sam Gijsen, Abner Hernandez +2cs.CL eess.AS eess.SP
Self-supervised learning (SSL) speech representations achieve strong performance for Parkinson's disease (PD) detection within individual corpora. However, it remains unclear whether these models capture disease-related characteristics or exploit dataset-specific confounds, particularly since most SSL backbones are pretrained exclusively on healthy speech. To investigate this question, we perform a layer-wise analysis of nine SSL speech backbones using a low-capacity logistic regression probe across three languages. We structure the evaluation as multiple scenarios that progressively introduce distribution shifts in participant identity, recording conditions, language, and pathology. Our results reveal two key findings. First, layer selection is highly corpus-dependent: the optimal representation layer is determined primarily by the source dataset rather than by the SSL architecture itself. Second, the transferred discriminative signal lacks pathological specificity: classifiers trained to detect PD assign similarly high probabilities to both PD and dementia speech in the target corpus. These results highlight critical limitations that must be addressed before speech-based pathology recognition models can be reliably deployed in clinical settings.
Hamza Shafiq, Hung Manh Pham, Bin Zhu +3cs.LG eess.IV stat.ML
Electrocardiography (ECG), photoplethysmography (PPG), and phonocardiography (PCG) provide complementary views of the same cardiac cycle, yet existing cardiac foundation models are trained for a single sensing modality, leaving the shared physiology across sensors unexploited. We introduce CardioState-JEPA, a cardiac foundation model to learn a single shared representation jointly across ECG, PPG, and PCG, built on a physiology-aware joint-embedding predictive architecture. The model maps heterogeneous waveforms into a common token space, processes them with a single shared Transformer encoder, and learns by predicting masked latent cardiac states, placing the pretraining target on shared physiology rather than sensor-specific waveform appearance. To handle the temporal offsets between electrical, mechanical, and hemodynamic events, cross-modal prediction uses a learned delay aligner that matches signals at the corresponding cardiac time. Because synchronized multi-sensor recordings are scarce, CardioState-JEPA first learns within-modality structure from abundant unimodal data and then uses paired data to align modalities in latent cardiac time. Evaluated as a frozen encoder across 25 downstream tasks spanning ECG, PPG, and PCG, our encoder improves average PPG classification by 8.2 AUROC points, PCG murmur detection by 18.8 AUROC points, and ECG classification by 15.5 AUROC points over the best self-supervised signal baseline and matches or exceeds cardiac models trained with privileged clinical text or supervised labels on several ECG benchmarks. These results establish that heterogeneous cardiac signals can mutually supervise a single foundation model of cardiac physiology.
Ahmed Sameh, Ramzi Al-Sharawi, Yogatheesan Varatharajahcs.LG eess.SP
Self-supervised electrocardiogram (ECG) models are often trained on a few seconds of ECG signal and, increasingly, on discretized token sequences. It remains unclear whether these choices sacrifice information needed for rhythm inference and longitudinal consistency in real-world ambulatory recordings. We present a controlled study on the Icentia11k single-lead dataset that varies (i) the input horizon (16 seconds, 1 minute, 5 minutes, and 10 minutes) and (ii) the front-end representation (continuous convolutional patch embeddings vs. fixed vector-quantized tokens), while holding the Transformer backbone and training protocol constant. Representations are assessed by downstream abnormal rhythm detection and by patient-level retrieval that probes cross-session stability. Our results show that increasing temporal context beyond 16-second snapshots yields stronger transfer and higher retrieval accuracy, with the strongest performance achieved by the 5- and 10-minute models, indicating improved capture of slow-varying rhythm dynamics and individual-specific structure. Across all evaluated horizons, continuous patch embeddings outperform discretized tokens, suggesting that quantization can discard clinically relevant waveform detail. These findings motivate ECG foundation models that emphasize extended context and continuous encoders for clinical prediction and similarity-based applications. Our code and pretrained models are publicly available at https://github.com/muha-0/ecg-ssl-representation-learning.
Kolmogorov--Arnold Networks (KANs) introduce explicit functional representations by parameterizing each network edge as a learnable univariate function. However, existing KAN-based segmentation models optimize edge functions only through objectives defined after edge aggregation, leaving individual functions without an explicit pre-aggregation learning target. To address this limitation, we propose Function-Space Joint-Embedding Predictive Learning (FS-JEPA) for medical image segmentation. Our FS-JEPA framework moves predictive learning into the pre-aggregation function space of KANs. A masked online branch predicts structured signatures of sampled KAN edge functions generated by a full-context exponential moving average target branch, while shared edge indices preserve correspondence between predictions and targets. Rather than predicting an isolated edge response, we represent each sampled edge function using a multi-radius signature composed of function evaluations around its input anchor. This structured representation captures local functional variations that cannot be characterized by a single response and provides a more informative predictive target. The function-space objective is jointly optimized with the segmentation loss during training, while the predictive branch is removed at inference. Experiments on five medical image segmentation benchmarks show that our FS-JEPA achieves the best average Dice and outperforms the strongest competing KAN-based method by +2.25 percentage points.
Patient motion remains a source of image degradation in brain MRI, leading to signal loss, blurring, and geometric distortion that compromise quantitative analysis. Existing deep learning methods for motion correction typically rely on paired clean-corrupted data or k-space acquisitions, which are rarely available in clinical settings. We propose SSRL-MAR, a motion artifact-aware unpaired representation learning framework for motion artifact reduction that requires neither paired training data nor explicit motion labels. SSRL-MAR employed a three-stage training strategy: (1) contrastive learning on 3D patches to extract motion representations by contrasting clean and synthetically corrupted images, (2) a motion artifact-aware synthesis network to generate motion artifacts from clean scans, and (3) a motion artifact-aware generator to restore clean volumes using the learned degrader for self-supervised supervision. On in-silico dataset, SSRL-MAR achieved PSNR 23.81dB, SSIM 91.55%, and NMSE 0.79%. On in-vivo MR-ART dataset, the pretrained model reduced motion distortion, and unsupervised domain adaptation further improved anatomical fidelity. Against a source-only supervised model trained on the same simulated pairs, SSRL-MAR improved PSNR by up to 2.0 dB on MR-ART after unsupervised domain adaptation, and remained within 0.25-0.47 dB of an oracle supervised model that requires real paired data unavailable in practice. At the milder motion level, volumetric error in structures such as the corpus callosum and ventricular system decreased by more than 50%, confirming improved neuroanatomical consistency. These results indicate that SSRL-MAR provides a robust and scalable image-domain solution for 3D brain MRI motion correction, enabling reliable structural quantification in large-scale neuroimaging studies without requiring prospectively acquired pairs or acquisition-specific calibration.
Julia Anna Mielcarz, Daniel Klaaby, Mostafa Mehdipour Ghazics.CV cs.AI
Self-supervised 3D medical foundation models are increasingly used as general-purpose feature extractors, yet their sensitivity to MRI artifacts remains poorly understood. We present a controlled evaluation of representation robustness across five pretrained 3D encoders spanning different architectures, objectives, pretraining domains, and dataset scales. Using BraTS-Africa cases with four MRI sequences, we generate seven frequency- and image-domain artifacts at five predefined corruption settings. Robustness is assessed using linear centered kernel alignment (CKA), RankMe, and UMAP, complemented by an independent segmentation-consistency analysis. We find that robustness is strongly model- and artifact-dependent. 3DINO exhibits the most consistently stable representations, while BrainIAC is highly sensitive to several corruptions; NeuroVFM, BrainFM, and Neuro-SimCLR show intermediate but distinct artifact-specific profiles. Across many conditions, CKA decreases substantially while RankMe remains comparatively stable, indicating that artifacts often distort representation geometry without causing dimensional collapse. Segmentation consistency also degrades under corruption, particularly for ghosting and Rician noise, but aligns only partially with representation-level robustness. These findings show that larger-scale or domain-specific pretraining alone does not guarantee artifact invariance and motivate explicit robustness evaluation before deploying 3D foundation models in heterogeneous MRI settings.
Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes. Here we present BioM-JEPA, a joint-embedding predictive architecture that instead predicts aggregate representations of graph-connected gene blocks defined by protein-association and corpus-derived coexpression evidence. A student network infers each target-block representation from the remaining genes in a cell, while a slowly updated teacher supplies the corresponding target from the full observed gene set. Under the reported extraction procedure, block-level prediction produced embeddings with higher effective rank and weaker association with detected-gene depth in the tested diagnostics than token-prediction, random-block and reconstruction controls. Across CellBench tasks, frozen BioM-JEPA embeddings retained expression, pathway and neighbourhood information and achieved the lowest aggregate perturbation-response error among the evaluated models. Representation diagnostics were also consistent with canonical pancreatic programmes and compositional relationships between genetic perturbations. Linear attention avoids constructing a quadratic gene-by-gene attention matrix; in a matched one-epoch hPancreas experiment at batch size 8, BioM-JEPA provided 5.75-fold higher fine-tuning throughput and 3.76-fold higher held-out embedding throughput than scFoundation. Together, these results support graph-connected gene blocks as useful prediction units for JEPA-style representation learning in single-cell biology.
Mahmut S. Gokmen, Evan W. Damron, Mitchell A. Klusty +3cs.CV
Self-supervised pretraining objectives are spatially uniform: the teacher temperature and the per-patch loss weight are identical everywhere in the image, so a lesion a few patches wide contributes no more to the training signal than the surrounding parenchyma. Prior work biases the views toward annotated regions, which changes what the model sees but adds no pressure on the objective. We instead condition the targets of self-distillation, a method we call SALT (Spatially Adaptive Label-guided Temperature). Weak, box-derived labels, available only during pretraining, define a compact region on the encoder's patch grid, inside which the teacher's softmax temperature is sharpened and the masked-patch loss is up-weighted. The objectives, the masking policy and the centering statistics are otherwise unchanged, and at every downstream use the encoder is a plain feature extractor with no labels and no conditioning. We evaluate by freezing the encoder and training only a lightweight multi-depth CenterNet-style head, detecting lesions in 3D on four CT cohorts, and we isolate the mechanism against a backbone identical in architecture, pretraining data, schedule and label-guided cropping but with no target conditioning. We report patch-level separability, 3D detection stratified by cohort and by lesion size, box quality, and a detector-free probe in which a single frozen patch embedding re-identifies a lesion in a follow-up scan without registration, masks or fine-tuning. Because the conditioning is expressed through a spatial indicator rather than through label semantics, the formulation admits any weak spatial annotation; we instantiate and validate it for lesions.
Basit Alawode, Moshira Ali Abdalla, Dwarikanath Mahapatra +2cs.CV
Vision Transformers (ViTs) and their hierarchical variants have achieved strong performance in Computational Pathology (CPath). However, most are pre-trained on single-resolution Whole Slide Images (WSIs), limiting their generalization across arbitrary resolutions. Gigapixel WSIs inherently contain diagnostic patterns at multiple scales, including cellular morphologies, tissue architectures, and global context, mirroring how expert pathologists examine WSIs. We introduce Multi-Resolution Pyramid Transformer (MRPT), a model that hierarchically aggregates multi-resolution information from cellular to tissue and WSI levels. MRPT employs a biologically meaningful Consecutive Cross-Resolution Attention (CCRA) mechanism to capture scale-independent interactions and enforces multi-resolution semantic consistency by aligning embeddings across resolutions, yielding robust and generalizable WSI representations. Pre-trained in a multi-resolution self-supervised manner on 624M patches, 2.4M regions, and 36K WSIs, MRPT learns rich coarse-to-fine histopathology features. Extensive experiments on 34 diverse datasets show that MRPT surpasses recent foundation models and Multimodal Large Language Models (MLLMs) in cancer subtype classification, tissue phenotyping, and Visual Question Answering (VQA) for WSI understanding.