Masked Autoencoders

Modern action recognition models rely on video transformers pretrained on massive collections of web-crawled videos, such as Kinetics-700. However, the use of such data raises ethical concerns, as subjects' consent is typically not obtained. Recent high-quality synthetic video datasets generated from motion-capture data, such as BEDLAM2.0, offer a promising ethical alternative. In this work, we investigate self-supervised pretraining of video transformers on synthetic human-motion datasets. We first show that directly applying the standard VideoMAE masking strategy leads to substantially worse performance than pretraining on Kinetics. To address this limitation, we propose a human-centric masking scheme that leverages body keypoints and person bounding box regions. Our approach encourages the model to focus on the structure and dynamics of human motion during pretraining. Experiments on NTU RGB+D and Toyota-Smarthome demonstrate that our method significantly outperforms standard VideoMAE pretraining on synthetic data, closing 49% of the gap to Kinetics pretraining on NTU RGB+D cross-view-subject without using a single real frame during pretraining. To promote the use of ethical action recognition models, we will publicly release our pretrained models.

Geographic information systems increasingly rely on sophisticated spatial representation learning techniques to extract meaningful patterns from complex geospatial data. This paper introduces LEON, a novel self-supervised framework that adapts Graph Masked Autoencoders (GraphMAE) for geospatial region representation learning. Our method leverages the inherent spatial structure of geographic data by constructing hexagonal grid graphs using H3 indexing and applying masked autoencoding techniques to learn robust spatial embeddings from OpenStreetMap (OSM) amenity distribution patterns. We evaluate LEON on multiple real-world datasets including EuroSAT satellite imagery classification and various geographic prediction tasks (housing prices, crime prediction, and urban analytics). Experimental results demonstrate that LEON achieves significant improvements in spatial understanding, with up to 1.87% accuracy improvement on EuroSAT classification and consistent performance gains across geographic prediction benchmarks. The learned embeddings exhibit highly structured and distinct properties, making them particularly suitable for downstream spatial analysis tasks. Our findings suggest that self-supervised learning provides an effective paradigm for geospatial region representation learning using widely available crowdsourced data.

Why can masked prediction learn useful representations that unmasked reconstruction misses? We study this question in a high-dimensional model of a masked autoencoder (MAE) trained on data with shared latent structure and heterogeneous noise. We prove that masked linear reconstruction can recover the latent feature at linear sample complexity in regimes where unmasked linear reconstruction, equivalent to PCA, fails. The analysis also quantifies the statistical advantage of mask resampling, an established ingredient of masked pretraining. By introducing a fixed collection of $K$ masks per sample, we characterize its effect on feature recovery and downstream performance, identifying regimes where greater mask diversity lowers sample complexity. Guided by this prediction, we find that random cropping and flipping in standard image-training pipelines can obscure the advantage of mask resampling by renewing the prediction task even when the patch mask is fixed. Removing these transformations reveals a downstream advantage for dynamic over static masking in CNN autoencoders and vision transformers. A complementary BERT pilot finds benefits from greater mask diversity on downstream language tasks. Our results separate the benefit of the masked prediction objective from that of mask diversity, and show how a tractable theory can guide experiments that uncover advantages hidden by standard training practices.

Self-supervised learning draws inspiration from infant visual development, yet standard training pipelines bear little resemblance to it: images are independently sampled and globally shuffled across epochs. We study self-supervised learning from continuous video streams, where frames are consumed in temporal order using strict sliding-window batches, without global reshuffling or multi-epoch replay. To this end, we construct WT++, a 95-hour urban walking-tour video dataset for streaming pretraining. Combined with a comprehensive evaluation suite we find that contrastive and distillation-based methods struggle in this setting, while MAE is more robust but still falls short of standard i.i.d. pretraining. We find that high inter-batch similarity, caused by sliding-window consumption across consecutive batches, does not explain this gap. The main challenge is high intra-batch similarity, where frames within each batch are near-duplicates. To mitigate this, we propose StreamMAE, which preserves the core MAE reconstruction objective while adapting the input pipeline with stream-aware regularization and motion-biased crop selection. StreamMAE outperforms streaming baselines, matches i.i.d. MAE trained on the same video data, remains competitive with ImageNet-pretrained MAE, and scales positively as the pretraining stream grows from 12 to 95 hours.

Self-supervised learning (SSL) removes the need for annotations and makes models that are capable across more domains than supervised learning. The autoencoder SSL framework learns by reconstructing its own input after information loss through a bottleneck or noise injection. Masked autoencoders (MAE) are the most successful instantiation of this framework: they encode a random subset of patches, then decode the masked-out patches. In this work, we introduce key modifications to improve MAEs. Our method augments an image in two different ways, then masks and encodes each view separately. It then exchanges the global representations (CLS tokens) between views before decoding the masked patches. By design, our Masked Swingers encourages learning a view-agnostic summary of the image to facilitate efficient transfer. We perform extensive experiments, and find Masked Swingers outperforms MAE by +3-5% on ImageNet-1K kNN and provides large gains on fine-grained tasks, e.g., relative gains of +45% on instance retrieval, +22% on animal re-ID, and +76% on Omniglot character recognition. To boot, Swingers reduces error -64% relative to MAE on three new state-probing datasets, opening the door to world modeling. Welcome to our Swingers party.

EEG foundation models hold promise for scalable brain-signal decoding across clinical and cognitive neuroscience applications, yet their pre-training pipelines remain poorly understood. Among design choices, the masking strategy is particularly critical: it determines what the network must predict and from which context. Yet it has never been ablated in isolation, as each new model bundles a new masking strategy with a new backbone and objective. In this paper, we formalize the design choices for spatio-temporal masking strategies and train various models with a single pipeline under varying masking configurations across two SSL frameworks (MAE and JEPA). We then systematically evaluate the resulting 58 pre-trained models on the 12 datasets of OpenEEGBench under a linear probe. Both frameworks agree on an optimal masking configuration and on shared failure modes. Outside these, performance is robust: 11 MAE and 9 JEPA configurations are statistically indistinguishable from the best. We further identify a novel JEPA-specific failure mode, tagged bias-inflation collapse, invisible to standard detectors. With a well-chosen mask, our pipeline reaches REVE-level downstream performance at a fraction of REVE's pre-training compute.

Multi-center clinical studies and biomedical research collaborations increasingly seek to utilize data across centers to build models that generalize beyond any single center. This creates two distinct challenges: data protection regulations may restrict the sharing of raw patient data across institutions, while centers may collect only partially overlapping sets of features under different protocols. Federated learning enables collaborative model training without centralizing raw data. However, existing federated imputation methods rarely evaluate feature-level missingness, in which entire features are unobserved at some centers. To address this setting, we adapt the ReMasker masked autoencoder to federated learning (Fed-ReMasker), enabling centers to impute features never observed locally by leveraging knowledge learned across collaborating centers. We evaluate Fed-ReMasker in a benchmark spanning synthetic datasets with linear and nonlinear relationships and real-world tabular datasets, including clinical data. The benchmark varies the number of centers, the missingness ratios, and client heterogeneity. Fed-ReMasker achieves the lowest imputation error in 93.2% of value-level and 96.7% of feature-level scenarios in the homogeneous benchmark. It also remains robust to client heterogeneity using simple federated averaging, outperforming all baselines in all 36 value-level scenarios and each baseline in at least 35 of 36 feature-level scenarios, and comes within 3.0% on average of a centralized model trained on the pooled data.

Mitotic figure (MF) analysis supports tumor grading and prognostic assessment, but automated models remain sensitive to differences in tissue type and image acquisition. We present MiTHras, a task-specific pretraining framework that combines pseudo-label-guided image- and token-level contrastive learning with masked reconstruction. We construct TCGA-MF-Pseudo, a corpus of 1.8 million cell-centered images from 14 TCGA cohorts spanning 11 organ sites. Comprehensive evaluation on MF classification, detection, count-based survival prediction, and subtype classification demonstrates the efficacy of MiTHras. It achieves the highest mean F1 on all three MF classification benchmarks and both subtype benchmarks. MiTHras also outperforms general-purpose and pathology foundation encoders by a larger margin under frozen-encoder linear probing than under full fine-tuning. Although detection gains are modest due to a shared candidate-detection stage, ablations confirm that token-level supervision improves typical-versus-atypical classification and linear probing. These findings establish that MiTHras yields robust, transferable representations for automated mitotic activity assessment.

Detection-free methods for image-to-point cloud registration are prone to erroneous correspondences caused by domain and modality discrepancies, limited sensitivity of feature extractors, and the presence of non-overlapping regions. The Masked Autoencoder (MAE) has shown strong performance in visual representation for images and point clouds. It may be helpful to apply this approach to image-to-point cloud registration, a task that requires unified feature extraction and accurate cross-modal correspondences. Standard MAE's random masking may overlook key regions due to limited camera views, reducing registration effectiveness. To address this, we propose the Intermodal Dual-MAE Framework (ID-MAE) with a Similarity-based RL Masking Strategy (SRLM), which adaptively masks informative positions by leveraging cross-modal similarity and reinforcement learning, thus narrowing the modality gap. Our method enhances cross-modal representation learning by enforcing representation consistency during feature extraction, thereby enabling more reliable 2D-3D correspondence estimation. Experiments on RGB-D Scenes v2 and 7-Scenes benchmarks show that our method achieves state-of-the-art performance in image-to-point cloud registration.

Large-scale pre-training has transformed representation learning in 2D vision, yet its transferability to 3D single object tracking (SOT) remains insufficiently understood. Directly fine-tuning self-supervised 3D encoders, such as masked autoencoders (MAE), often leads to sub-optimal adaptation because the reconstruction objective is not fully aligned with the spatial-temporal matching requirements of tracking. In this paper, we observe that this difficulty can be interpreted as a layer-wise transfer mismatch: shallow layers tend to preserve transferable geometric cues, while deeper layers become increasingly specialized to the reconstruction pretext task and are less suitable for downstream tracking. Based on this observation, we propose MAETrack, a lightweight adaptation framework for transferring pre-training MAE representations to 3D SOT. MAETrack includes Layer-Selective Initialization (LSI), which initializes only the shallow stages of the tracking backbone from pre-trained weights while re-initializing deeper stages, and Geometric Residual Gating (GRG), which reinforces structurally salient regions in the search BEV features before template-search fusion through residual spatial modulation. Extensive experiments on standard 3D SOT benchmarks show that MAETrack consistently improves upon vanilla fine-tuning baselines with limited computational overhead. More broadly, our results suggest that effective transfer from 3D reconstruction pre-training to 3D tracking is not merely a matter of partial fine-tuning, but depends on a tracking-oriented transfer principle that preserves shallow geometry while adapting deeper representations to the downstream objective.

Self-supervised learning (SSL) can reduce the need for labelled medical images, but the choice of pretext objective remains unclear for lung ultrasound (LUS). Contrastive learning, masked reconstruction, and joint-embedding predictive architectures (JEPA) differ in the space in which their targets are defined, yet existing ultrasound studies compare them under different corpora, backbones, and evaluation protocols. We compare these three objective families using the same encoder backbone, pretraining corpus, optimisation schedule, and frozen-evaluation protocol. Encoders are pretrained on COVID-BLUeS LUS videos and evaluated with linear, $k$NN, and attentive probes at 5%, 10%, 50%, and 100% label budgets. Evaluation is performed on POCUS using patient-level five-fold cross-validation and on the independently acquired Mendeley-Uganda dataset, which is excluded from both pretraining and probe fitting. At the full label budget under linear probing, VideoMAE and V-JEPA achieve $66.5 \pm 13.1$ and $65.4 \pm 11.7$ balanced accuracy on POCUS, while MoCo achieves $42.1 \pm 1.2$. On Mendeley-Uganda, the ranking reverses: MoCo performs best at $62.7 \pm 1.0$, followed by VideoMAE at $53.8 \pm 2.8$, while V-JEPA falls near chance at $35.1 \pm 4.9$. These results show that POCUS probe accuracy alone does not identify the objective that transfers best across datasets. We also outline planned representation-level analyses to examine this reversal. Code is publicly available at https://github.com/moeinheidari7829/LUSVideoSSL.

Procedural audio has emerged as a viable source for transferable audio representation learning, but its design principles remain unclear.We revisit two questions: how a procedural source should be scaled, and whether training choices developed on natural audio should transfer unchanged to procedural data.Using a controlled source, we separate scale into formula-class coverage C and within-class rendering diversity I.Experiments with FDSL and AudioMAE show that these two forms of scale provide different benefits and depend on the learning formulation and downstream task. A matched AudioMAE study further shows that procedural audio favors low mask ratios (10%--25%), whereas AudioSet-28K favors 50%--75%. Shared-codebook analysis reveals lower patch diversity and stronger temporal predictability in procedural audio. These results motivate source-aware procedural pre-training, where source scaling and learning configuration are considered jointly.Code is available at https://github.com/Cross-Innovation-Lab/Formula-Bank.

Masked reconstruction is widely used for EEG foundation models, but optimizing reconstruction on low-SNR waveforms does not necessarily produce the most useful latent representation. We introduce MANAS-2, a new EEG foundation model that combines a Raw-Band Hybrid (RBH) masked autoencoder with Constrained Reconstruction (ConRec), a physics-motivated regularizer. RBH jointly reconstructs temporal waveform patches and compact spectral-band targets, while ConRec acts only on the temporal decoder output, penalizing differences in RMS energy between adjacent short windows of the reconstructed waveform. ConRec is intended to shape the encoder by biasing it toward the organization of oscillatory-envelope information. Across seven held-out EEG datasets, adding ConRec to an otherwise identical RBH model increases frozen ridge recovery of six-band spectral power from mean R^2=0.860 to 0.906 and recovery of inter-patch band-energy dynamics from R^2=0.283 to 0.354, while temporal waveform information remains highly recoverable from the frozen latents. Applied to a temporal-only masked autoencoder, ConRec also improves frozen downstream transfer and frequency-dependent latent geometry despite receiving no spectral targets: i.e., the effects of ConRec are architecture-independent. MANAS-2 also outperforms leading EEG Foundation Models on most downstream knowledge-transfer tasks. From the effects of ConRec, we see that a physically motivated constraint imposed through the decoder can make for a more spectrally organized and transferable latent space. MANAS-2 therefore provides a new EEG foundation model built around constrained reconstruction as a mechanism for shaping representation--rather than reconstruction--quality.

Cardiovascular diagnosis and treatment rest on integrating complementary modalities, such as electrocardiogram, echocardiography, and chest X-rays, each capturing distinct but complementary aspects of cardiac pathophysiology. Yet most medical foundation models remain modality-specific, combining modalities only for finetuning or post-training. This discards the cross-modal evidence clinicians naturally integrate and ignores the structure within each modality. We introduce Latent-Attention Masked Autoencoder (LAMAE), a multimodal, structure-aware masked autoencoder that jointly learns patient-level representations during self-supervised pretraining. Instead of fusing modalities post hoc, LAMAE exchanges information directly in the latent space through a shared latent-attention module operating over a study-view-entity hierarchy, enabling aggregation of variable observations and handling of missing modalities. Pretrained on over 500'000 MIMIC-IV hospital stays, LAMAE outperforms modality-specific pretraining and strong contrastive and vision-language baselines across multimodal hospital-stay tasks, such as in-hospital mortality, ICD-10 and DRG coding, and length of stay, while remaining competitive on unimodal tasks. Modeling this structure also pays off within a single modality: even without cross-modal information, the latent-attention module improves representations over modality-specific pretraining.

Recent advances in Earth Observation representation learning accommodate heterogeneous sensors and missing observations, often through larger architectures. We present MEOX (Multimodal Earth Observation with eXperts), a multimodal masked autoencoder with a 2.939 million-parameter encoder and 3.115 million parameters in total. Sensor-specific adapters, explicit validity signals, and a shared sparse-expert block preserve modality-dependent processing before a learned patch-wise fusion. Four metadata tokens then accompany a single spatial sequence through fourteen further encoder blocks. Shared expert projections with private low-rank residuals constrain parameter growth, while rotary attention supports downstream spatial grids different from pretraining. The model is pretrained on 1.228 million MMEarth64 samples using modality-balanced masked reconstruction and structured sensor dropout. Frozen transfer is evaluated on six GEO-Bench tasks at both 64 and 224 pixels. The model reaches 64.42% mean intersection-over-union on cashew segmentation at 64 pixels and 90.56% average accuracy on EuroSAT at 224 pixels, exceeding the corresponding reported CSMoE results. BigEarthNet finetuning reaches 72.95% micro-average precision. Routing diagnostics distinguish expert participation, spatial dependence, modality association, and functional contribution. A held-out WorldCover probe measures a 0.64-percentage-point benefit from metadata, while retrieval separates same-sensor semantics from cross-sensor alignment. These results demonstrate sensor-flexible representation learning and strong task transfer using a compact parameter budget.

Field-based agricultural computer vision is important for precision agriculture, yet it largely depends on expensive annotations and costly adaptation of large pretrained models. We introduce AgriField-40K, a field-centric dataset curated from 17 public resources and covering diverse crops, weeds, and field conditions. Building on this, we present AgriMAE, a parameter-efficient continual pretraining baseline that adapts a masked autoencoder pretrained on natural images by training only lightweight adapters. We further explore semantic feature reconstruction as an alternative pretraining objective and evaluate transfer across multiple tasks. AgriMAE consistently improves downstream performance and can match or even outperform full fine-tuning while using up to $9\times$ fewer trainable parameters, showing that AgriField-40K is a practical resource for continual pretraining in agricultural vision. Project page: https://dtu-pas.github.io/agrifield40k/

Radiology foundation models learn transferable representations that can be adapted to new tasks by training only small layers on top of a frozen encoder. Dense prediction tasks such as 3D segmentation are, however, underrepresented in their evaluation, and, with the encoder kept frozen, pre-trained models still fall short of nnU-Net, the state-of-the-art reference trained from scratch. To close this gap we extend convolutional MAE pre-training with a robust reconstruction objective, a feature regularizer, and a local-global similarity objective. Using this method, we propose Curia-MAE, a multi-modal, multi-anatomy MAE model pre-trained on 300,000 CT and MRI images covering a large number of anatomical sites. On eight anatomy- and lesion-focused segmentation benchmarks, Curia-MAE improves frozen-encoder performance over a strong MAE baseline, while remaining competitive under full finetuning and superior on lesion tasks, where labeled data is scarce. These results indicate that a single frozen encoder can be reused across diverse segmentation tasks, reducing the cost of adapting and deploying such models in clinical workflows. Curia-MAE pre-trained model weights are made publicly available at https://huggingface.co/raidium/Curia-MAE.

Automated pain assessment in real clinics is limited by scarce clinically grounded facial video data with weak labels (often sequence-level self-report) and by the fact that pain cues can be subtle or near-neutral in RGB, while thermal and depth signals are informative yet impractical to deploy routinely. To address these challenges, we propose ReMiX-MAE (Reconstructing Missing Channel Cross-Modal Masked Autoencoder), a self-supervised multimodal masked pretraining framework that learns transferable facial representations from synchronized RGB, thermal, and depth videos and explicitly trains robustness to missing modalities, enabling RGB-only deployment. To fill the gap of clinically grounded facial pain data with video-level self-report and longitudinal treatment trajectories, we collect the Sympathetic Mediated Pain (SMP) dataset with paired pre- and post-recordings across multiple visits. Under RGB-only deployment, we evaluate ReMiX-MAE using both direct feature extraction and pseudo-multimodal features decoded from RGB. ReMiX-MAE consistently outperforms an RGB-only masked autoencoder baseline on SMP, with pseudo-multimodal features providing additional gains in the challenging five-class setting. Across external datasets, ReMiX-MAE further shows more robust and label-efficient transfer than RGB-only baselines, highlighting its advantage in data-limited clinical settings.

Increasing EEG pretraining data scale or model capacity does not consistently improve downstream performance. We identify a persistent low-frequency bias in representations learned by diverse EEG foundation models, which remains across dataset scales, model capacities, and pretraining objectives. Our analysis links this bias to the interaction between EEG's $1/f^α$-like spectral structure and neural networks' tendency to preferentially learn low-frequency components. In masked autoencoders, the $\ell_2$ reconstruction objective further amplifies this imbalance: under comparable relative reconstruction errors, high-power low-frequency components contribute disproportionately to the loss. To address this issue, we introduce FAME, a frequency-balanced masked autoencoding framework that reconstructs time--frequency activity in predefined EEG bands from masked EEG inputs. FAME independently standardizes the reconstruction targets within each band and assigns equal weight to all band-specific losses, thereby balancing supervision across the EEG spectrum. Evaluated on 41 downstream tasks in OmniEEG-Bench, FAME learns more spectrally balanced representations and achieves state-of-the-art performance on 24 of them. These results underscore the importance of balanced spectral supervision for learning transferable EEG representations.

This paper proposes a multitask wireless foundation model via adaptive low-rank masked autoencoders (WALoMA), a unified multi-task foundation model for sixth-generation (6G) wireless physical layer architectures, to address the limitations of specialized, task-specific deep learning models and the practical challenge of scarce labeled wireless datasets. By leveraging concepts inspired by foundation models, the proposed framework adopts a masked autoencoder (MAE) paradigm to learn from unlabeled channel data, to significantly reduce reliance on extensive annotations. The model treats wireless channel state information (CSI) as a universal modality and learns transferable representations through self-supervised channel reconstruction. Key architectural novelties include the use of 2D positional encoding (PE) to explicitly preserve the spatial-frequency relationships between antennas and subcarriers, and low-rank adaptation (LoRA) for parameter-efficient fine-tuning. The framework's efficacy is demonstrated across five downstream tasks, achieving individual scores of 96.47% for LoS/NLoS classification, 80.45% for beam prediction, 85.78% for channel interpolation, 99.12% for channel estimation, and 77.18% for channel charting. Consequently, numerical results show that the proposed model achieves a composite score of 87.80%, significantly outperforming the 59.90% achieved by the large wireless model (LWM) baseline while training an average of only 14.68% of total parameters, and maintaining strong performance even under extremely limited labeled data conditions.

In this paper, we propose the MAEConformer, a novel self-supervised learning framework that combines the Conformer architecture with the Masked Autoencoder (MAE) paradigm for large-scale representation learning from unlabelled electroencephalography (EEG) and heart rate variability (HRV) signals. By integrating convolutional operations with Transformer-based self-attention, MAEConformer effectively captures both local temporal patterns and long-range contextual dependencies in physiological time series. To enhance reconstruction fidelity and representation quality, a multi-resolution short-time Fourier transform (MR-STFT) loss is incorporated alongside the reconstruction objective, enabling the model to jointly learn temporal and spectral characteristics across multiple scales. Modality-specific EEG and HRV MAEConformer models were pretrained on 6,030h and 4,868h of unlabelled recordings, respectively, and subsequently transferred to expert-annotated downstream tasks. Experimental results demonstrate that the learned representations provide strong transferability and data efficiency. In EEG-based hypoxic ischemic encephalopathy (HIE) severity classification, the pretrained MAE-EEG model achieved test AUCs of 97.19% and 96.56% for binary and four-class classification tasks, respectively, outperforming a range of state-of-the-art supervised and self-supervised baselines. On the HRV-based HIE severity classification task, MAE-HRV achieved a test AUC of 82.42%, surpassing both self-supervised Transformer-based and supervised convolutional baselines. These findings demonstrate the effectiveness of MAEConformer for learning robust and transferable representations across multiple physiological modalities.

Robust and accurate neural decoders are integral to neurotechnologies such as brain-computer interfaces and closed-loop experiments. Recent work has shown that tokenizing neural data at the spike level facilitates multi-session pretraining and delivers state-of-the-art decoding performance. However, current spike-based models are restricted to supervised learning (SL), limiting training to datasets with paired behavioural labels. To address this limitation, we introduce MOJO (Masked autOencoder-based JOint training), a training framework for spike-tokenizing models that jointly leverages self-supervised learning (SSL) via masked autoencoding and SL objectives. We evaluate MOJO on three spiking datasets spanning monkey motor cortex during reaching tasks and multi-regional mouse recordings during vision and decision making tasks, demonstrating superior performance over purely SL-trained models. This improvement is especially pronounced when training with limited labelled data, particularly in few-shot finetuning, where only a small amount of labelled data from a new session is available. Incorporating SSL also yields more interpretable neuronal representations, improving performance on brain region classification and spike-statistics prediction without explicit optimization for these tasks. We further show that MOJO generalizes beyond spiking data to human electrocorticography during speech, where it continues to outperform purely SL-trained models and achieves performance comparable to neuro-foundation models (NFMs) designed specifically for continuous signals. Overall, augmenting spike-tokenizing models with SSL improves performance in label-impoverished settings and enables the use of unlabelled data across various tasks and species, while generalizing to other neural modalities. These results suggest a path towards more flexible and scalable data usage when training NFMs.

Automated visual inspection of steel surface defects is a recurring quality control task in which labeled defect data is scarce and costly to obtain, while unlabeled surface images are abundant, which motivates self supervised methods that learn useful representations without class labels. A Transformer based Masked Autoencoder is used here to learn representations of steel surface defects for unsupervised grouping. During pretraining, 75% of the input image patches are randomly masked, and a lightweight decoder reconstructs the masked regions from the visible 25%. The encoder is trained jointly with an auxiliary defect localization objective, used only as a training signal and not evaluated as a detector. The decoder reaches a structural similarity score of 0.92 and a mean squared error of 0.47. Features from the pretrained encoder are then clustered using UMAP for dimensionality reduction and Agglomerative clustering, reaching a Hungarian matched accuracy of 91.3% against the six known defect categories.

Whole slide images (WSIs) provide rich diagnostic information for computational pathology, but their gigapixel scale, stain variation, scanner differences, tissue artifacts, and limited expert annotation make robust model training challenging. This paper presents a multi-source Masked Autoencoder (MAE) framework, named ProsMAE, for histopathology representation learning. Tiles from Prostate cANcer graDe Assessment (PANDA), CAncer MEtastases in LYmph nOdes challeNge 2017 (CAMELYON17), and BReAst Carcinoma Subtyping (BRACS) are used for ProsMAE pretraining to expose the encoder to diverse tissue morphology and acquisition conditions. The learned encoder is transferred for International Society of Urological Pathology (ISUP) grade classification through ProsCLS, using a frozen encoder and a linear classification head. ProsMAE achieved a higher mean validation quadratic weighted kappa (QWK) than the vanilla MAE frozen linear-probe baseline under the evaluated disjoint PANDA split. Repeated-split evaluation remains necessary to further establish robustness across split compositions.

Decades of orbital missions have produced multi-modal remote sensing data for the Moon, spanning optical imagery, spectroscopy, thermal emission, radar, gravity, and elemental composition. Yet these datasets remain fragmented across archives, and no benchmark exists for evaluating machine learning on lunar data. We introduce Moonstone, the first multi-modal foundation model benchmark for lunar remote sensing. Our contributions are: (1) a 28-channel, 128 pixels-per-degree (~237 m) global lunar pretraining dataset from seven instrument families across five missions, (2) MG-MAE, a modality-grouped masked autoencoder with per-group convolutional tokenizers, a shared Vision Transformer encoder, attention masking for missing modalities, coverage-adaptive masking for heterogeneous spatial coverage, and spectral continuity regularization for physically plausible reconstructions, and (3) a benchmark of six downstream tasks covering classification, regression, and segmentation. MG-MAE pretrained features outperform scratch baselines on all tasks and surpass both ImageNet-pretrained and vanilla MAE baselines by large margins. Data and code are available at https://huggingface.co/datasets/ayushprd/Moonstone and https://github.com/ayushprd/Moonstone .

We propose MABLE (Masked Autoencoding with Bi-Lipschitz Decoding for Embeddings and Graph Metric Learning), a self-supervised framework for learning node and graph embeddings from large, heterogeneous graphs, demonstrated here on geospatial mineral-exploration data. MABLE combines masked reconstruction with fixed cosine-similarity losses that align matched augmented views while keeping unpaired embeddings well spread. A bi-Lipschitz feature decoder ties a low-dimensional reconstruction component of each node embedding to feature similarity, while matched-node consistency shapes the remaining context used by graph pooling. Lipschitz-controlled pooling helps stabilize graph-level representations under perturbations of retained node embeddings, while augmentation alignment trains robustness to masking, node dropping, and sampling variation. Across local copper and regional Arabian Shield studies, MABLE embeddings provide complementary downstream signal and produce coherent embedding-derived layers for hypothesis generation without learned discriminators or hard-negative selection.

Masked autoencoding has emerged as a prominent paradigm for self-supervised learning on 3D point clouds, achieving competitive performance across downstream tasks. Unlike its 2D counterpart, 3D masked autoencoding directly reconstructs spatial coordinates, making it inherently susceptible to positional leakage. In this work, we identify that the decoder in existing 3D MAE frameworks tends to over-rely on positional information, which weakens semantic representation learning and leads to suboptimal feature quality. To address this issue, we propose MPL-MAE, a masked point learning framework that mitigates positional over-reliance while enhancing the utilization of encoder features. Specifically, we introduce a recalibrated positional embedding module that suppresses metric-dominant coordinate signals while preserving geometric topology, together with a gated positional interface module that dynamically regulates positional injection during reconstruction. These designs promote a more balanced interaction between spatial priors and semantic features, yielding robust and informative representations. Extensive experiments across downstream tasks demonstrate that MPL-MAE consistently achieves competitive performance, validating its effectiveness. Code is available at https://github.com/yanx57/MPL-MAE.

We present OctoSense, an open-source sensor platform with stereo RGB and event cameras, LiDAR, a thermal camera, an inertial measurement unit, RTK-corrected global positioning system, and proprioception (CAN bus data from a car, and joint angles for a quadruped robot). The eponymous OctoSense dataset contains 59 hours of time-synchronized driving data across different types of environments at different times of the day, including situations with highly degraded sensors. We demonstrate multi-modal self-supervised learning using such real-world robotics data, where sensors have different representations, frequencies, latencies and noise. Our approach, a "late-fusion" masked autoencoder, (i) uses modality-specific tokenizers to account for different spatiotemporal characteristics of these sensors, and (ii) caches modality-specific tokens at inference time to process new measurements as they come. This architecture (i) is fast (6.68 ms and 112 ms on NVIDIA 5090 and Orin NX respectively, to compute the representation), (ii) performs better than existing image-only foundation models on tasks such as estimation of optical flow, depth, semantic segmentation, and ego-motion (translation, rotation, and steering angle), and (iii) predicts robustly at nighttime or in situations where sensory data is degraded. See our project page for links to the dataset, code, and supplementary videos: https://abisulco.com/octosense/.

Self-supervised learning in fluorescence microscopy often relies on 2D projections, despite the inherently three-dimensional nature of cells. We present a systematic comparison of 2D and 3D masked autoencoders (MAE-2D vs. MAE-3D) on volumetric microscopy data. Under matched architectures and training protocols, MAE-3D consistently outperforms 2D max-projection and slice-based variants on downstream single-cell tasks. We further align visual representations with a pretrained protein language model (ESM2) and show that cross-modal supervision yields larger gains for volumetric models. Channel cross-attention and frequency-domain regularization are critical for leveraging 3D spatial context. On protein--protein interaction prediction, our best model achieves a ROC--AUC of 0.86, while on protein localization it reaches an AUC$_{\text{micro}}$ of 0.95 and an F1$_{\text{micro}}$ of 0.74, demonstrating competitive performance on both tasks. Overall, our findings highlight the potential of volumetric modeling and multimodal alignment for representation learning in single-cell microscopy.

Nondestructive detection methods, based on vibrational spectroscopy, are vitally important in a wide range of applications including industrial chemistry, pharmacy and national defense. Recently, deep learning has been introduced into vibrational spectroscopy showing great potential. Different from images, text, etc. that offer large labeled data sets, vibrational spectroscopic data is very limited, which requires novel concepts beyond transfer and meta learning. To tackle this, we propose a task-enhanced augmentation network (TeaNet). The key component of TeaNet is a reconstruction module that inputs randomly masked spectra and outputs reconstructed samples that are similar to the original ones, but include additional variations learned from the domain. These augmented samples are used to train the classification model. The reconstruction and prediction parts are trained simultaneously, end-to-end with back-propagation. Results on both synthetic and real-world datasets verified the superiority of the proposed method. In the most difficult synthetic scenarios TeaNet outperformed CNN by 17%. We visualized and analysed the neuron responses of TeaNet and CNN, and found that TeaNet's ability to identify discriminant wavenumbers was excellent compared to CNN. Our approach is general and can be easily adapted to other domains, offering a solution to more accurate and interpretable few-shot learning.

The high cost of spatial transcriptomics (ST) has driven extensive studies into predicting gene expression directly from H&E histology images. However, this prediction task faces an inherent limitation, as tissue morphology alone provides insufficient information to fully resolve underlying gene expression. To address this limitation, a recent study leverages partial gene expression to guide the prediction process alongside histology images. Building on this paradigm, we approach the prediction task as a spatial imputation problem, employing a Masked Autoencoder (MAE) to utilize a small fraction of gene expression as genetic anchors for inferring whole-slide gene expression profiles. Specifically, we propose a bio-saliency score and a learning-to-rank strategy to adaptively identify the most informative spots within the tissue. Based on these identified spots, our framework selects contiguous regions as genetic anchors to ensure suitability for real-world ST profiling hardware. To effectively leverage these anchors, we design a cross-modal joint encoder that integrates visual and genetic modalities. By aligning the selected anchors with their corresponding visual features via contrastive learning, the encoder generates robust joint representations to accurately predict gene expression across the whole slide. Notably, our framework consistently surpasses existing methods in both histology-only prediction and spatial imputation, achieving superior accuracy even without genetic anchors and further excelling with as little as 10% transcriptomic coverage. Our code is available at https://github.com/Kyyle2114/CAMMST.

Three-dimensional (3D) brain MRI is central to clinical neurology and neuro-oncology, where generative models could augment under-represented cohorts, simulate disease trajectories, and support privacy-preserving data sharing. Latent diffusion has been the go-to solution for modeling imaging data, but it places two competing demands on the tokenizer: encoder embeddings must retain the clinical information that downstream tasks act on, and the decoder must reconstruct anatomically faithful volumes. Existing reconstruction-driven tokenizers achieve the second at the expense of the first. To address this, we introduce a fully volumetric masked-autoencoder (MAE) based tokenizer for 3D brain MRI latent diffusion, decoupling encoder and decoder: a frozen 3D MAE encoder produces clinically informative embeddings, while a dedicated CNN decoder reconstructs voxels from a linear projection of those embeddings. We pretrain the encoder on 35,309 volumes from 18 public cohorts spanning four modalities, ten disease categories, and 200+ acquisition sites, and demonstrate its dual utility in two settings. First, on a 23-task linear-probing benchmark, the encoder outperforms or matches SOTA models (i.e., BrainIAC, BrainSegFounder, and MedicalNet) on 21 of 23 tasks. Second, a conditional diffusion transformer (DiT) trained on these clinically informative embeddings supports both conditional generation across six variables and patient-specific longitudinal forecasting. Together these results establish a single 3D brain-MRI embedding space capable of both downstream clinical tasks and controllable generation.

Self-supervised foundation models have shown strong promise in medical imaging. However, existing MRI foundation-model studies have primarily emphasized segmentation and dense prediction tasks, while systematic investigation of self-supervised foundation models for MRI-based disease detection remains limited. In this work, we investigate two major self-supervised pretraining paradigms for MRI-based disease detection: reconstruction-based learning via Masked Autoencoders (MAE) and predictive representation learning via Joint Embedding Predictive Architectures (JEPA). We study the role of auxiliary objectives by introducing a novel spectral-domain reconstruction loss for MAE to enhance sensitivity to fine-grained anatomical structure, and by integrating variance--covariance regularization (VCR) within our JEPA framework to encourage decorrelated latent representations. Our models are pretrained on heterogeneous single-contrast MRI volumes in a contrast-agnostic setting, without modality concatenation. Across five downstream disease detection tasks, our results highlight the importance of self-supervised objective design for medical foundation model pretraining, demonstrating that the downstream benefit of each objective is determined by its relevance to the task's structure. Specifically, spectral regularization yields the largest improvements when the downstream discriminative signal is characterized by strong high-frequency anatomical structures, while covariance regularization is most beneficial when discriminative information spans multiple decorrelated feature dimensions. MAE with spectral-domain supervision consistently achieves superior downstream performance for MRI-based disease detection. These findings suggest that self-supervised objectives in medical imaging encode specific biases, and their downstream benefit is fundamentally conditioned on the task's structure.

In this paper, we introduce Representation Prediction via Autoencoding using Iterative Refinement (RePAIR) - a novel self-supervised representation learning architecture that synthesizes Masked Autoencoders (MAE), Joint Embedding Predictive Architectures (JEPA), and Bidirectional Encoder Representations from Transformers (BERT). We demonstrate how it can be used to encode objects in sequential data like consecutive chess positions into compact yet meaningful representations. The basic principle of the architecture is to mask large portions of a sequence of latent states, similar to BERT and MAE. Then, we apply a lightweight Predictor to the latent representations that repairs gaps in the sequence in a lower-dimensional embedding space akin to JEPA. Our experiments in the domain of chess show that the Encoder refines the board representations such that meaningful chess concepts emerge clustered in the latent space. Furthermore, reconstructions of the masked board states show that the model is able to reason about the piece movements without relying on costly reinforcement learning methods. Lastly, we find that the resulting representation space allows for quick and intuitive dissections of chess games by observing the game path trajectories in this semantically rich space.

Recently, masked skeleton reconstruction models have emerged as strong action representation learners, driving significant progress in self-supervised skeleton-based action recognition. However, existing state-of-the-art methods must predict an exceedingly large number of spatiotemporal patches, significantly prolonging training time. Besides, by treating all spatiotemporal regions equally during reconstruction, these models are distracted from learning the critical motion patterns that underlie action semantics. To address these challenges, we propose Adaptive Masked Reconstruction (AMR), a faster and stronger pre-training framework. We first decouple the decoder from the encoder, enabling flexible prediction of larger spatiotemporal patches and dramatically reducing reconstruction complexity. Given that larger patches contain more complex information, which is challenging to predict and consequently degrades performance, we accordingly introduce an adaptive guidance module. This module identifies regions of high motion informativeness, guiding the model to focus on the most discriminative parts of each patch and alleviating reconstruction difficulty. Experiments on NTU RGB+D 60, NTU RGB+D 120, and PKU-MMD datasets demonstrate that AMR not only accelerates pre-training substantially but also improves downstream recognition accuracy, surpassing current state-of-the-art approaches.

Clinical diagnosis often requires combining imaging with physiological measurements, yet deployed models typically operate on unimodal data. We present PaCX-MAE, a cross-modal distillation framework that injects physiological priors into chest X-ray (CXR) encoders while remaining strictly unimodal at inference. PaCX-MAE augments in-domain masked autoencoding with a dual contrastive-predictive objective, aligning CXR representations with paired ECG and laboratory embeddings. Extensive evaluation across nine benchmarks demonstrates consistent improvements over domain-specific MAE, particularly on physiology-dependent tasks (e.g., +2.7 AUROC on MedMod; +6.5 F1 on VinDr). The method proves highly label-efficient in the 1% regime and preserves anatomical fidelity, achieving parity with MAE on segmentation tasks. Zero-shot and attention analyses confirm that PaCX-MAE successfully learns to attend to physiological indicators, such as the cardiac silhouette, absent in standard visual pretraining.

RNA sequencing produces rich and diverse datasets of gene expression, offering compelling insights into cellular state and function that have many applications in drug discovery. Modeling such data is challenging due to inherent technical noise and experimental batch effects, as evidenced by many existing transcriptomic foundation models (FMs) underperforming relative to linear baselines. Such results raise the question of whether deep representation learning provides a distinct advantage over the direct use of raw transcript counts. Our work explores this by developing a new self-supervised model, TxFM, with a focus on inductive representation learning evaluations. TxFM employs a masked autoencoding approach tailored to diverse RNA-seq count data, and our ablation study empirically identifies crucial architecture configurations required for strong transfer performance. Additionally, we curate a public training corpus, DiverseRNA-1.4M, and find that TxFM trained on this curated dataset yields high-fidelity gene representations that outperform FMs trained on atlas-scale corpora over 100x larger. Overall, our results indicate that inductive self-supervised learning is a viable modeling approach for transcriptomics representation, provided a careful synthesis of model architecture and training data curation.

Approximately 10% of newborns require assistance to initiate breathing at birth, and around 5% need ventilation support. Fetal heart rate (FHR) monitoring plays a crucial role in assessing fetal well-being during prenatal care, enabling the detection of abnormal patterns and supporting timely obstetric interventions to mitigate fetal risks during labor. Applying artificial intelligence (AI) methods to analyze large datasets of continuous FHR monitoring episodes with diverse outcomes may offer novel insights into predicting the risk of needing breathing assistance or interventions. Recent advances in wearable FHR monitors have enabled continuous fetal monitoring without compromising maternal mobility. However, sensor displacement during maternal movement, as well as changes in fetal or maternal position, often lead to signal dropout, resulting in gaps in recorded FHR data. Such missing data limits the extraction of meaningful insights and complicates automated (AI-based) analysis. Traditional approaches to handling missing data, such as simple interpolation techniques, often fail to preserve the spectral characteristics of the signals. In this paper, we propose a masked transformer-based autoencoder approach to reconstruct missing FHR signals by capturing both local temporal and frequency components of the data. The proposed method demonstrates robustness across varying durations of missing data and can be used for signal inpainting and forecasting. The proposed approach can be applied retrospectively to research datasets to support the development of AI-based risk algorithms. In the future, the proposed method could be integrated into wearable FHR monitoring devices to achieve earlier and more robust risk detection.

Masked autoencoders (MAE) have shown great promise in medical image classification. However, the random masking strategy employed by traditional MAEs may overlook critical areas in medical images, where even subtle changes can indicate disease. To address this limitation, we propose a novel approach that utilizes a multifractal measure (Renyi entropy) to optimize the masking strategy. Our method, termed Multifractal-Optimized Masked Autoencoder (MO-MAE), employs a multifractal analysis to identify regions of high complexity and information content. By focusing the masking process on these areas, MO-MAE ensures that the model learns to reconstruct the most diagnostically relevant features. This approach is particularly beneficial for medical imaging, where fine-grained inspection of tissue structures is crucial for accurate diagnosis. We evaluate MO-MAE on several medical datasets covering various diseases, including MedMNIST and COVID-CT. Our results demonstrate that MO-MAE achieves promising performance, surpassing other basiline and state-of-the-art models. The proposed method also adds minimum computational overhead as the computation of the proposed measure is straightforward. Our findings suggest that the multifractal-optimized masking strategy enhances the model's ability to capture and reconstruct complex tissue structures, leading to more accurate and efficient medical image representation. The proposed MO-MAE framework offers a promising direction for improving the accuracy and efficiency of deep learning models in medical image analysis, potentially advancing the field of computer-aided diagnosis.

Accurate 3D bird's-eye view (BEV) object detection is essential for autonomous driving, and depends strongly on effective multimodal representations from complementary sensors such as cameras and LiDAR. Multimodal masked autoencoders have shown strong potential for learning such representations for downstream 3D BEV object detection. However, existing methods typically apply uniform random masking to camera and LiDAR inputs, treating all regions equally, and learn representations only through masked reconstruction. We propose a semantics-guided multimodal masked autoencoder framework that introduces semantic information during pretraining through two separate components: (i) semantics-guided LiDAR voxel masking, which preserves semantically important LiDAR regions more strongly, and (ii) an auxiliary point-wise LiDAR semantic decoder branch that injects semantic guidance in addition to reconstruction. On BEVFusion 3D object detection, our semantics-guided pretraining strategy improves performance on the nuScenes mini validation set compared to the standard UniM2AE baseline: semantics-guided LiDAR voxel masking yields +1.49% mean Average Precision (mAP) and +1.66% nuScenes Detection Score (NDS), while decoder-side point semantic supervision yields +1.39% mAP and +3.22% NDS over the baseline.

A central challenge in electroencephalography (EEG) foundation modeling is learning transferable representations across recordings with diverse tasks, montages, references, and spectral characteristics. Existing masked modeling approaches often rely on broadband continuous patches or a single discrete representation, which may underrepresent frequency-specific activity. This paper proposes BandVQ, a band-wise vector-quantized EEG foundation model that decomposes EEG into delta, theta, alpha, beta, and gamma bands, trains an independent VQ-VAE tokenizer for each band, and pretrains a shared Transformer encoder on the resulting discrete VQ code indices. The encoder uses masked code tokens, quantized absolute log-power tokens, channel and temporal embeddings, and metadata prefix tokens representing reference, band, task family, and phase. Region-based masking is also introduced to reduce the trivial reconstruction of spatially adjacent electrodes. The model is pretrained on 71 public EEG corpora comprising over 9,200 subjects and 357,000 single-channel hours and evaluated on six subject-independent classification datasets. Under the current evaluation setting, the proposed model achieves strong transfer performance, with the highest reported results on three cognitive tasks and competitive performance on three motor imagery tasks.

Channel foundation models assume access to fully observed channels, an assumption that fails in deployment. We introduce PilotWiMAE, a self-supervised framework whose encoder ingests noisy pilot observations directly and whose attention factorizes along the axis separating temporal from joint space-frequency processing, an inductive bias inspired by the physics of the problem. Pilot input shrinks the observation space by up to two orders of magnitude and also removes the unrealistic assumption of full-CSI availability while incurring lower latency. The factorized design generates robust representations by exploiting the separable channel structure and allows a pretraining mask ratio of $99\%$. We pair patch-normalized reconstruction, which captures small-scale fading structure, with an auxiliary scale loss that recovers the large-scale fading features, and use an AWGN curriculum to match pilot noise at pretraining and deployment. Pretrained solely on $3.5$,GHz and evaluated at $28$,GHz across in-distribution and out-of-distribution settings, PilotWiMAE's cross-frequency beam selection and channel characterization beat supervised baselines despite operating on a smaller observation space. To weaken the coupling between decoder capacity and representation quality, we further propose a decoder-centric pretraining stage following the encoder-decoder joint pretraining, which allows PilotWiMAE to demonstrate competitive channel estimation without sacrificing representation quality. To foster further work in this direction, we release the PilotWiMAE pretrained weights and training pipeline, together with CSIGen, our Sionna-based ray-tracing channel-generation tool, and the channel datasets used in this work.

Classifying protein topology is essential for deciphering biological function, but progress is held back by the lack of large-scale benchmarks that avoid duplicates and by models that do not scale well. We introduce TEDBench, a large-scale, non-redundant benchmark for protein fold classification constructed from the Encyclopedia of Domains (TED) and Foldseek-clustered AlphaFold structures. We show that on TEDBench, current protein representation learning methods either require very large models or fail to deliver strong performance. To address this challenge, we propose Masked Invariant Autoencoders (MiAE), a self-supervised framework for protein structure representation learning. MiAE uses an extremely high masking ratio of up to 90% with an $\mathrm{SE(3)}$-invariant encoder and a lightweight decoder that reconstructs backbone coordinates from the latent representation and mask tokens. MiAE scales well and outperforms supervised counterparts and state-of-the-art baselines on TEDBench, establishing a strong recipe for protein fold classification. To test transfer beyond AlphaFold structures, we further benchmark on a curated dataset from experimental structures of CATH v4.4. TEDBench is available at https://github.com/BorgwardtLab/TEDBench.

Modeling hyperspectral imagery (HSI) across different sensors presents a fundamental challenge due to variations in wavelength coverage, band sampling, and channel dimensionality. As a result, models trained under a fixed spectral configuration often fail to generalize to other sensors. Existing Vision Transformer (ViT) approaches either rely on implicit spectral modeling with fixed channel assumptions or adopt explicit spatial-spectral attention with prohibitive computational cost, leading to a fundamental trade-off between efficiency and expressiveness. In this work, we introduce Low-rank Efficient Spatial-Spectral ViT (LESSViT), a sensor-flexible architecture for cross-spectral generalization. LESSViT is built on LESS Attention, a structured low-rank factorization that models joint spatial-spectral interactions through separable spatial and spectral components, reducing the complexity of full spatial-spectral attention from $O(N^2 C^2)$ to $O(rNC)$, where $N$ is the number of spatial tokens, $C$ is the number of spectral channels, and $r$ is the rank of the low-rank approximation. We further incorporate channel-agnostic patch embedding and wavelength-aware positional encoding to support flexible spectral inputs. To enable efficient and robust pretraining, we introduce a hyperspectral masked autoencoder (HyperMAE) with decoupled spatial-spectral masking and hierarchical channel sampling. We evaluate LESSViT under a cross-spectral generalization setting that simulates cross-sensor variability. Experiments on the SpectralEarth benchmark demonstrate that LESSViT improves robustness under spectral shifts while remaining competitive in-distribution, and explicit and efficient spatial-spectral modeling is essential for scalable and generalizable hyperspectral representation learning.

Foundation models pre-trained through masked reconstruction on large-scale EEG data have emerged as a promising paradigm for learning generalizable neural representations across diverse brain-computer interface applications. However, a critical yet overlooked challenge is that EEG encoders must learn representations invariant to incomplete observations-when different masked views of the same signal have minimal overlap, existing methods fail to constrain them to a consistent latent subspace, leading to degraded transferability. To address this, we propose DARE-EEG, a self-supervised foundation model that explicitly enforces the mask-invariance property through dual-aligned representation learning during pre-training. Specifically, we introduce mask alignment that constrains representations from multiple masked views of the same EEG sample via contrastive learning, complementing anchor alignment that aligns masked representations to momentum-updated complete features for semantic stability. Additionally, we propose conv-linear-probing, a parameter-efficient strategy that adapts pre-trained representations to heterogeneous electrode configurations and sampling rates through decoupled spectro-spatial projections. Extensive experiments across diverse EEG benchmarks demonstrate that DARE-EEG consistently achieves state-of-the-art in accuracy performance while maintaining relatively low parameter complexity and superior cross-dataset portability compared to existing methods. Furthermore, DARE-EEG contributes to effectively discovering and utilizing the rich potential representations in EEG.

Extreme low-data fine-grained classification is common in expert domains where labeling is expensive, yet practitioners still need principled guidance for selecting pretrained encoders. We study emerald inclusion grading with a custom dataset of labeled images across three classes and ask: under matched backbone capacity, how does pretraining objective affect downstream representation quality? We compare four frozen ViT-B/16 encoders trained with supervised classification, contrastive learning (SigLIP2), masked reconstruction (MAE), and self-distillation (DINOv3), and evaluate them with leave-one-out cross-validation using linear and nonlinear probes. To control statistical noise in the low-N regime, we use permutation testing (N=1000) on macro one-vs-rest AUC. Supervised and contrastive encoders provide the strongest linear separability (logistic AUC: 0.768 and 0.735; SVM AUC: 0.739 and 0.697), while MAE improves under nonlinear probes (XGBoost AUC: 0.713). We find that DINOv3 underperforms across probe families in this domain. These results support a practical recommendation for extreme low-data FGVC: prioritize margin-enforcing pretraining objectives when data scarcity restricts probing to linear decision rules, and consider reconstruction-style encoders when nonlinear classifiers are feasible given dataset constraints.

Masked autoencoders (MAEs) have recently shown promise for self-supervised representation learning of resting-state brain functional connectivity (FC). However, a fundamental question remains unresolved: how should FC matrices be tokenized to align with the intrinsic modular organization of large-scale brain networks? Existing approaches typically adopt region-centric or graph-based schemes that treat FC as structurally homogeneous elements and overlook the large-scale network brain organization. We introduce NERVE (Network-Aware Representations of Brain Functional Connectivity via Bilinear Tokenization), a self-supervised learning framework that redefines FC tokenization by partitioning FC matrices into patches of intra- and inter-network connectivity blocks. Unlike image-based MAE, where fixed-size patches share a common tokenizer, FC patches defined by network pairs are heterogeneous in size and correspond to distinct functional roles. To resolve this problem, NERVE embeds FC patches through a novel structured bilinear factorization. This formulation preserves network identity and reduces parameter complexity from quadratic to linear scaling in the number of networks. We evaluate NERVE across three large-scale developmental cohorts (ABCD, PNC, and CCNP) for behavior and psychopathology prediction. Compared to structurally agnostic MAE variants and graph-based self-supervised baselines, the proposed network-aware formulation yields more stable and transferable representations, particularly in cross-cohort evaluation. Ablation studies confirm that the proposed bilinear network embedding and anatomically grounded parcellation are critical for performance. These findings highlight the importance of incorporating domain-specific structural priors into self-supervised learning for functional connectomics. Code is available at: https://github.com/leomlck/NERVE.

Bioacoustic recognition requires fine-grained acoustic understanding to distinguish similar-sounding species. However, many large-scale data repositories such as iNaturalist are weakly annotated, often with only a single positive species label per recording, making supervised learning particularly challenging. Inspired by advances in computer vision, recent approaches have shifted toward self-supervised learning to capture the underlying structure of audio without relying on exhaustive annotations. In particular, masked autoencoders (MAE) have shown strong transferability on massive audio corpora, yet their effectiveness in more modest bioacoustic settings remains underexplored. In this work, we conduct a systematic study of MAE pretraining for species classification on iNatSounds, analyzing the impacts of pretraining data scale, domain specificity, data curation, and transfer strategies. Consistent with prior work, we find that models pretrained on diverse general audio data achieve the best transfer performance on iNatSounds. Contrary to observations from large-scale audio benchmarks, we find that (1) additional masked reconstruction pretraining on domain-specific data provides limited benefits and may even degrade performance relative to off-the-shelf models, and (2) selective data filtering offers a negligible advantage when the overall data scale is limited. Our results indicate that, in moderate-sized fine-grained bioacoustic settings, pretraining scale dominates objective design. These findings further clarify when MAE-based pretraining is effective and provide practical guidance for model selection under limited supervision.

Clinical diagnostic workups typically follow a modality escalation pathway: after initial clinical evaluation, clinicians begin with routine structural imaging (e.g., MRI), selectively add sequences such as FLAIR or T2 to refine the differential, and reserve molecular imaging (e.g., amyloid-PET) for cases that remain uncertain after standard evaluation. Consequently, patients are observed with heterogeneous and often incomplete modality subsets. However, most current AI models assume fixed data modalities as the model inputs. In this paper, we present BrainAnytime, a unified pretraining framework pretrained on 34,899 3D brain scans from five datasets that support brain image analysis under arbitrary modality availability spanning multi-sequence MRI and amyloid-PET. A single model accepts whatever imaging is available, from a lone T1 scan to a full multimodal workup. Pretraining learns structural-molecular correspondences between MRI and PET via cross-modal distillation (RCMD) and prioritizes disease-vulnerable anatomy via atlas-guided curriculum masking (PACM), all within a shared 3D masked autoencoder (Multi-MAE3D). Across four downstream tasks and five clinically motivated modality settings, BrainAnytime largely outperforms modality-specific models, missing-modality baselines, and large-scale brain MRI pretrained foundation models on most modality settings. Notably, it surpasses the strongest missing-modality baselines with relative improvements of 6.2% and 7.0% in average accuracy on CN vs. AD and CN vs. MCI classification, respectively. Code is available at https://github.com/SDH-Lab/BrainAnytime.

Cardiovascular disease remains the leading cause of global mortality, yet scalable cardiac monitoring is hindered by the gap between diagnostic-rich ECG and ubiquitous wearable PPG. Bridging this gap requires representations that are compact, transferable across modalities and devices, and deployable without task-specific retraining. Here we introduce biosignal fingerprints: compact latent representations of cardiovascular state derived from a cross-modal foundation model, the Multi-modal Masked Autoencoder (M2AE), trained on over 3.4 million paired ECG and PPG signals. M2AE integrates modality-specific encoders with a shared bottleneck and dual decoders, jointly optimized using reconstruction and cross-modal contrastive objectives, yielding generalizable fingerprints that retain intra- and inter-modality features. Like a biometric fingerprint, these representations uniquely encode an individual's cardiovascular state in a modality-agnostic, privacy-preserving form reusable across clinical tasks without exposing raw waveform data or requiring model retraining. Across 7 downstream tasks, spanning cross-modal reconstruction, cardiovascular disease classification, hypertension detection, mortality prediction, and demographic inference, biosignal fingerprints achieve competitive or superior performance compared to leading domain-specialist foundation models in frozen settings, including an AUROC of 0.974 for five-class CVD classification and 0.877 for hypertension detection, with a maximum improvement of 27.7% in AUROC across 5 classification tasks. Critically, strong performance is maintained with only a single modality, enabling deployment in resource-constrained, single-sensor environments typical of real-world wearable monitoring, with direct implications for continuous cardiovascular monitoring across clinical and consumer health settings.

The advent of foundation models has heralded a new era in medical artificial intelligence (AI), enabling the extraction of generalizable representations from large-scale unlabeled datasets. However, current ophthalmic AI paradigms are predominantly constrained to single-modality inference, thereby creating a dissonance with clinical practice where diagnosis relies on the synthesis of complementary imaging modalities. Furthermore, the deployment of high-performance AI in resource-limited settings is frequently impeded by the unavailability of advanced three-dimensional imaging hardware. Here, we present the Ophthalmic multimodal Masked Autoencoder (OphMAE), a multi-imaging foundation model engineered to synergize the volumetric depth of 3D Optical Coherence Tomography (OCT) with the planar context of 2D en face OCT. By implementing a novel cross-modal fusion architecture and a unique adaptive inference mechanism, OphMAE was pre-trained on a massive dataset with of 183,875 paired OCT images derived from 32,765 patients. In a rigorous benchmark encompassing 17 diverse diagnostic tasks with 48,340 paired OCT images from 8,191 patients, the model demonstrated state-of-the-art performance, achieving an Area Under the Curve (AUC) of 96.9% for Age-related Macular Degeneration (AMD) and 97.2% for Diabetic Macular Edema (DME), consistently surpassing existing single-modal and multimodal foundation models. Crucially, OphMAE exhibits robust engineering adaptability: it maintains high diagnostic accuracy, such as 93.7% AUC for AMD, even when restricted to single-modality 2D inputs, and demonstrates exceptional data efficiency by retaining 95.7% AUC with as few as 500 labeled samples. This work establishes a scalable and adaptable framework for ophthalmic AI, ensuring robust performance across different tasks.

Biosignals acquired from different locations on the body often provide temporally ordered views of the same underlying physiological process. However, most existing self supervised learning methods treat these signals as interchangeable views, overlooking the directional temporal dynamics that link them. A canonical example is the relationship between electrocardiography (ECG), which captures the electrical activation initiating each heartbeat, and photoplethysmography (PPG), which records the resulting peripheral pulse delayed by vascular dynamics. To capture this structured relationship, we introduce xMAE, a biosignal pretraining framework that leverages masked cross modal reconstruction across temporally ordered biosignals as a training time constraint to encourage physiologically meaningful timing structure in the learned representations. We show that pretraining with xMAE yields representations that outperform both unimodal and multimodal baselines on 15 of 19 downstream tasks, including cardiovascular outcome prediction, abnormal laboratory test detection, sleep staging, and demographic inference, while generalizing across devices, body locations, and acquisition settings. Further analysis suggests that the ECG PPG timing structure is reflected in the learned PPG representations. More broadly, xMAE demonstrates the effectiveness of incorporating temporal structure into multimodal pretraining when signals observe different stages of a shared underlying process. Code is available at https://github.com/hzhou3/xMAE.

Millimetre-wave (mmWave) radar offers a more privacy-preserving alternative to RGB-based human pose estimation. However, existing methods typically rely on pre-extracted intermediate representations such as sparse point clouds or spectrogram images, where the rich spatiotemporal information naturally present in radar video streams is discarded for model learning, while such signal processing adds system complexity. In addition, existing solutions are mainly conducted in an end-to-end supervised manner without leveraging unlabelled raw video streams to learn generalized representations. In this study, we present MAEPose, a masked autoencoding-based human pose estimation approach that operates directly on mmWave spectrogram videos. MAEPose learns spatiotemporal motion-aware generalized representations from unlabelled radar video, and leverages its heatmap decoder for multi-frame pose estimation predictions. We evaluate it across three datasets based on leave-one-person-out cross-validation with rigorous statistical testing. MAEPose consistently outperforms state-of-the-art baselines by up to 22.1% in MPJPE p<0.05, and maintains robust accuracy under zero-shot bystander interference with only a 6.5% error increase. Ablation studies confirm that both the pre-training and the heatmap decoder contribute substantially, while modality analysis indicates that leveraging Range-Doppler video as input achieves better pose estimation performance than Range-Azimuth or their fusion, with lower computational cost.

Downhole drilling telemetry presents a fundamental labeling asymmetry: surface sensor data are generated continuously at 1Hz, while labeled downhole measurements are costly, intermittent, and scarce. Current machine learning approaches for downhole metric prediction universally adopt fully supervised training from scratch, which is poorly suited to this data regime. We present the first empirical evaluation of masked autoencoder (MAE) pretraining for downhole drilling metric prediction. Using two publicly available Utah FORGE geothermal wells comprising approximately 3.5 million timesteps of multivariate drilling telemetry, we conduct a systematic full-factorial design space search across 72 MAE configurations and compare them against supervised LSTM and GRU baselines on the task of predicting Total Mud Volume. Results show that the best MAE configuration reduces test mean absolute error by 19.8% relative to the supervised GRU baseline, while trailing the supervised LSTM baseline by 6.4%. Analysis of design dimensions reveals that latent space width is the dominant architectural choice (Pearson $r = -0.59$ with test MAE), while masking ratio has negligible effect, an unexpected finding attributed to high temporal redundancy in 1Hz drilling data. These results establish MAE pretraining as a viable paradigm for drilling analytics and identify the conditions under which it is most beneficial.

Learning robust representations across extremely heterogeneous modalities remains a fundamental challenge in multi-modal vision. As a critical and profound instantiation of this challenge, high-resolution (HR) joint optical and synthetic aperture radar (SAR) pretraining seeks modality synergy to mutually enhance single-source representations; its potential is severely hindered by the Heterogeneity-Resolution Paradox: finer spatial scales drastically amplify the physical divergence between complex radar geometries and non-homologous optical textures. Consequently, migrating medium-resolution-oriented rigid alignment paradigms to HR scenarios triggers either severe feature suppression to force equivalence, or feature contamination driven by extreme epistemic uncertainty. Both extremes inevitably culminate in profound representation degradation and negative transfer. To overcome this bottleneck, we propose CoDe-MAE, pioneering a \textit{better synergy with less alignment} philosophy. First, Optical-anchored Knowledge Distillation (OKD) implicitly regularizes SAR's speckle noise by mapping it into a pure semantic manifold. Building on this, Conditioned Contrastive Learning (CCL) utilizes a gradient buffering mechanism to align shared consensus while safely preserving divergent physical signatures. Concurrently, Cross-Modal Degraded Reconstruction (CDR) deliberately strips non-homologous spectral pseudo-features, truncating the inherently ill-posed mapping to capture true structural invariants. Extensive analyses validate our theoretical claims. Pretrained on 1M samples, CoDe-MAE demonstrates remarkable data efficiency, successfully preventing representation degradation and establishing new state-of-the-art performance across diverse single- and bi-modal downstream tasks, substantially outperforming foundation models scaled on vastly larger datasets.

Intelligent fetal ultrasound (US) interpretation is crucial for prenatal diagnosis, but high annotation costs and operator-induced variance make unsupervised pre-training a highly promising paradigm. However, existing pre-training methods largely ignore US-specific characteristics -- severe data redundancy, fan-shaped locality, and polar coordinate beamforming -- limiting their effectiveness in downstream tasks. To address this, we propose PolarMAE, a novel and efficient pre-training framework tailored for US images. Specifically, to mitigate continuous scanning redundancy, we introduce a Progressive Visual-Semantic Screening (PVSS) that adaptively extracts high-value samples, significantly boosting pre-training efficiency. Furthermore, we design an Acoustic-Bounded Region Constraint (ABRC) to accommodate US locality, forcing the model to focus strictly on valid acoustic regions rather than invalid dark backgrounds. Finally, leveraging the beamforming prior and local details, we propose a Polar-Texture Collaborative Masking (PTCM), enabling the model to capture underlying radial imaging patterns and critical tissue structures. Extensive experiments across diverse datasets and downstream interpretation tasks demonstrate that our method achieves state-of-the-art performance with strong pre-training scalability and efficiency.

Oil and gas drilling operations generate extensive time-series data from surface sensors, yet accurate real-time prediction of critical downhole metrics remains challenging due to the scarcity of labelled downhole measurements. This systematic mapping study reviews thirteen papers published between 2015 and 2025 to assess the potential of Masked Autoencoder Foundation Models (MAEFMs) for predicting downhole metrics from surface drilling data. The review identifies eight commonly collected surface metrics and seven target downhole metrics. Current approaches predominantly employ neural network architectures such as artificial neural networks (ANNs) and long short-term memory (LSTM) networks, yet no studies have explored MAEFMs despite their demonstrated effectiveness in time-series modeling. MAEFMs offer distinct advantages through self-supervised pre-training on abundant unlabeled data, enabling multi-task prediction and improved generalization across wells. This research establishes that MAEFMs represent a technically feasible but unexplored opportunity for drilling analytics, recommending future empirical validation of their performance against existing models and exploration of their broader applicability in oil and gas operations.

Echocardiography is a widely used modality for cardiac assessment due to its non-invasive and cost-effective nature, but the sparse and heterogeneous spatiotemporal views of the heart pose distinct challenges. Existing masked autoencoder (MAE) approaches typically process images or short clips independently, failing to capture the inherent multi-view structure required for coherent cardiac representation. We introduce Latent Attention Masked Autoencoder (LAMAE), a foundation model architecture tailored to the multi-view nature of medical imaging. LAMAE augments the standard MAE with a latent attention module that enables information exchange across frames and views directly in latent space. This allows the model to aggregate variable-length sequences and distinct views, reconstructing a holistic representation of cardiac function from partial observations. We pretrain LAMAE on MIMIC-IV-ECHO, a large-scale, uncurated dataset reflecting real-world clinical variability. To the best of our knowledge, we present the first results for predicting ICD-10 codes from MIMIC-IV-ECHO videos. Furthermore, we empirically demonstrate that representations learned from adult data transfer effectively to pediatric cohorts despite substantial anatomical differences. These results provide evidence that incorporating structural priors, such as multi-view attention, yields significantly more robust and transferable representations.

Masked image modeling (MIM) is a highly effective self-supervised learning (SSL) approach to extract useful feature representations from unannotated data. Predominantly used random masking methods make SSL less effective for medical images due to the contextual similarity of neighboring patches, leading to information leakage and SSL simplification. Hierarchical shifted window (Swin) transformer, a highly effective approach for medical images cannot use advanced masking methods as it lacks a global [CLS] token. Hence, we introduced an attention guided masking mechanism for Swin within a co-distillation learning framework to selectively mask semantically co-occurring and discriminative patches, to reduce information leakage and increase the difficulty of SSL pretraining. However, attention guided masking inevitably reduces the diversity of attention heads, which negatively impacts downstream task performance. To address this, we for the first time, integrate a noisy teacher into the co-distillation framework (termed DAGMaN) that performs attentive masking while preserving high attention head diversity. We demonstrate the capability of DAGMaN on multiple tasks including full- and few-shot lung nodule classification, immunotherapy outcome prediction, tumor segmentation, and unsupervised organs clustering.

Time series anomaly detection (TSAD) is essential for maintaining the reliability and security of IoT-enabled service systems. Existing methods require training one specific model for each dataset, which exhibits limited generalization capability across different target datasets, hindering anomaly detection performance in various scenarios with scarce training data. To address this limitation, foundation models have emerged as a promising direction. However, existing approaches either repurpose large language models (LLMs) or construct largescale time series datasets to develop general anomaly detection foundation models, and still face challenges caused by severe cross-modal gaps or in-domain heterogeneity. In this paper, we investigate the applicability of large-scale vision models to TSAD. Specifically, we adapt a visual Masked Autoencoder (MAE) pretrained on ImageNet to the TSAD task. However, directly transferring MAE to TSAD introduces two key challenges: overgeneralization and limited local perception. To address these challenges, we propose VAN-AD, a novel MAE-based framework for TSAD. To alleviate the over-generalization issue, we design an Adaptive Distribution Mapping Module (ADMM), which maps the reconstruction results before and after MAE into a unified statistical space to amplify discrepancies caused by abnormal patterns. To overcome the limitation of local perception, we further develop a Normalizing Flow Module (NFM), which combines MAE with normalizing flow to estimate the probability density of the current window under the global distribution. Extensive experiments on nine real-world datasets demonstrate that VAN-AD consistently outperforms existing state-of-the-art methods across multiple evaluation metrics.We make our code and datasets available at https://github.com/PenyChen/VAN-AD.