3D Masked Autoencoders

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.

Cardiovascular diagnosis rests on integrating complementary modalities, like ECG, echocardiography, chest radiographs, and clinical variables, each capturing distinct but correlated aspects of cardiac physiology. 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 Autoencoders (LAMAE), a multimodal, structure-aware masked autoencoder that jointly learns patient-level representations during self-supervised pretraining. Rather than 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 graceful handling of missing modalities. Pretrained on over 1.2 million 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. These gains persist even when only a single modality is available at test time, showing that modeling both intra- and inter-modal structure yields more robust, transferable representations.

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.

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.

Cyberattack detection in electric vehicle charging infrastructure is complicated by legitimate post-activation revisions to requested energy and departure time. Charging manipulation attacks can exploit the same interface and variables; therefore, detecting a request change alone does not establish malicious intent. This paper develops a leakage-controlled session-level benchmark that preserves the ordered inputs of real Adaptive Charging Network (ACN) sessions and models legitimate revisions as normal behavior. A fixed pool keeps each generated attack in its source session's split and contains six physically motivated attacks and their coordinated variants. We compare 22 profile-only, transition-aware, and context-stratified model families under common source-grouped folds, attack data, and operating constraints. The proposed Dual-Branch Masked-Autoencoder (Masked-AE) Transition Boost model evaluates whether the current request is normal and whether its producing transition resembles an observed benign update. Its state branch combines masked reconstruction with a radial-basis-function one-class support boundary, while its transition branch combines masked reconstruction with shrinkage covariance distance. Source-grouped five-fold cross-validation selects complete configurations under explicit overall-normal and benign-update acceptance constraints; disjoint normal data then calibrate the final threshold before one test evaluation. The developed dual-branch model provides the strongest robust validation performance while detecting malicious request manipulations without learning to reject legitimate user choices.

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.

Weakly supervised hierarchical models exhibit a persistent asymmetry: coarse lesion-type features are preserved under reconstruction while fine-grained malignancy cues degrade---a pattern with direct consequences for the clinical reliability of breast cancer screening pipelines. We introduce gradient-based orthogonal latent decomposition for hierarchical Variational Autoencoders~(H-VAEs) to mechanistically explain this asymmetry. The latent space is partitioned into a task-aligned component~($z_1$), shaped by coarse supervisory gradients, and an orthogonal residual~($z_{\text{res}}$) capturing remaining representational capacity. On3,550 mammographic Regions of Interest(ROIs) from CBIS-DDSM, only~$\sim$4.4% of latent magnitude aligns with supervisory gradients, leaving~$\sim$95.6% in the orthogonal residual upon which fine-grained pathology prediction primarily depends. The model achieves Stage-1AUC0.866 and Stage 2AUC0.552, with a reconstruction stability gap of $Δ_{\text{diag}}=5\%$ ($p=0.005$) and a classification gap of $Δ_{\text{AUC}}=0.314$ ($p{<}0.001$). Latent ablation confirms that features for both tasks reside heavily in~$z_{\text{res}}$, structurally explaining why reconstruction degrades pathology stability disproportionately. Comparisons with Multi-Instance Learning~(MIL) and Multi-Task Learning~(MTL) confirm generalization across architectures and modalities. These findings reveal that in high-dimensional spaces, a single coarse supervisory signal isolates only a sparse 1D latent direction, forcing critical fine-grained features into the vulnerable residual subspace.

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.

Recently, Vision-Language-Action (VLA) models have demonstrated strong generalization across diverse tasks. However, effective robotic manipulation in physical environments fundamentally requires geometric understanding and spatial reasoning. While some VLA approaches attempt to incorporate 3D information, they are constrained by limited data availability and geometric information loss in current 3D encoding pipelines, and fail to jointly capture 3D geometry and temporally structured actions in dynamic environments. To address these limitations, we introduce Lift3D-VLA, a unified VLA framework that equips models with explicit 3D point cloud reasoning and enables temporally coherent action generation. First, building upon our previous work Lift3D, an enhanced 2D model-lifting strategy is proposed to geometrically align 3D points with pretrained 2D positional embeddings. This design enables direct point-cloud encoding within the VLA vision encoder while minimizing spatial information loss. Based on explicit 3D inputs, we propose Geometry-Centric Masked Autoencoding (GC-MAE), a dual-objective self-supervised framework that reconstructs the current point cloud while predicting its future geometric evolution. This formulation allows the 2D vision encoder to internalize both 3D structure and physical dynamics. To fully exploit 3D representations, we further design layer-wise temporal action modeling, which leverages multiple layers of the LLM to collaboratively predict action chunks, enabling temporally consistent predictions. Across 22 simulated tasks and 8 real-world manipulation tasks, Lift3D-VLA achieves 10.8% and 11.1% higher mean success rates on MetaWorld and RLBench than the best-performing prior VLA methods, and outperforms the strongest real-world baseline by 4 percentage points, while exhibiting stronger generalization to out-of-distribution perturbations.

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 .

Recent brain decoding studies have made substantial progress in reconstructing externally perceived visual content from neural signals. However, using electroencephalography (EEG) recordings to guide facial expression editing remains largely unexplored and poses a distinct challenge: rather than recovering what a subject sees, it requires identifying facial-action related patterns from noisy EEG signals and grounding them in localized, identity-preserving expression edits. In this paper, we investigate EEG-conditioned facial image editing for fine-grained facial action unit (AU) control and propose MindAU, a unified framework for controlling facial AU edits from EEG signals. MindAU first learns noise-robust and AU-discriminative EEG representations through temporal masked reconstruction and AU classification supervision. It then bridges the modality gap via Dual-Stream Manifold Alignment, aligning EEG features with AU-level text semantics and identity-reduced visual displacement trajectories in the multimodal space of Qwen2.5-VL. Finally, MindAU incorporates EEG-aware Multimodal Rotary Positional Embeddings, landmark-guided reference masking, and AU-aware region supervision into a multimodal diffusion-based editor for high-fidelity identity-preserving editing. We also introduce E-CAFE, a curated benchmark for EEG-Conditioned Action-Unit Facial Editing with paired EEG-face editing samples and standardized evaluation protocols. Extensive experiments demonstrate the effectiveness of MindAU and suggest its potential as a step towards future assistive expression technologies for individuals with facial neuromuscular disorders.

Synthetic aperture radar automatic target recognition (SAR ATR) is critical for Earth observation and defense, but its practical deployment is constrained by scarce annotated training data. Self-supervised pre-training alleviates this label bottleneck, yet prevailing Transformer architectures incur prohibitive quadratic computational complexity, and conventional universal masking neglects the unique electromagnetic scattering properties intrinsic to SAR imagery. To address these limitations, we propose SAMBA (Scattering-Guided Bidirectional Mamba), an efficient self-supervised pre-training foundation model for SAR target interpretation. Our framework features three core innovations: (i) a linear-complexity Mamba encoder with a mid-sequence class token to mitigate computational bottlenecks; (ii) a three-level hierarchical Scattering-Guided Masked Autoencoder (SG-MAE) masking strategy guided by SAR physical priors, aligning the pretext task with SAR's intrinsic imaging mechanism; (iii) a lightweight SpatialMix feature interaction module to enhance cross-region feature fusion. We also design a two-stage cross-domain pre-training pipeline to optimize the overall pre-training process. Extensive evaluations demonstrate that SAMBA consistently delivers superior performance across all pre-training configurations, with substantially fewer parameters than both CNN and Transformer baselines. Compared with the default masking strategy in standard MAE, the proposed SG-MAE strategy further boosts the model's few-shot transfer capability. Benchmarking on seven downstream datasets covering classification and detection tasks shows SAMBA achieves state-of-the-art (SOTA) performance on most metrics, fully validating its robust generalizability across diverse SAR interpretation tasks. Source code and pre-trained weights are publicly available at https://github.com/mynswkk/SAMBA.

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.

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.

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.

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.

In this work we introduce a novel approach to domain incremental learning, adapting models over time to evolving, non-stationary data. In contrast to other works, we do not attempt to avoid catastrophic forgetting, but rather allow it and exploit it. Our model combines a main task head with a self-supervised masked autoencoder (MAE) head. We then learn domain-specific LoRA adapters during incremental training. Each adapter specializes to its domain, naturally inducing forgetting on other domains in both heads. At inference, we perform online test-time training on the self-supervised MAE head to identify which LoRAs best matches the current input, so the model can `remember' the domain again. Our scheme is especially well-suited to real-world streaming data, such as video, where consecutive samples are highly correlated and domain shifts are gradual. We demonstrate our method on domain-incremental action recognition and semantic segmentation tasks.

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.

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.

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.

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.

Cone Beam Computed Tomography (CBCT) is pivotal for 3D diagnostic imaging in dentistry. However, the development of robust AI models for volumetric analysis is often constrained by the scarcity of large, annotated datasets. Self-supervised learning (SSL), particularly Masked Image Modeling (MIM), offers a promising pathway to leverage unlabeled data. A limitation of standard MIM is its reliance on random masking, which fails to prioritize diagnostically critical regions in dental CBCT volumes, such as subtle pathological changes and intricate anatomical boundaries. To address this, we propose ATMask, a novel adaptive masking strategy. Instead of applying random masks or employing computationally intensive attention modules, ATMask computes an inter-slice texture variation map to identify regions with high structural or textural complexity. These high-variation areas are then selectively masked during pre-training, compelling the model to learn richer contextual representations essential for inferring complex 3D morphological transitions. Furthermore, we contribute the first large-scale CBCT dataset, curated from both public and private sources, comprising 6,314 scans, for the dental AI model pretraining. Extensive experiments on three downstream dental CBCT tasks demonstrate that our ATMask enables more data-efficient and powerful representation learning than standard random masking and other advanced SSL baselines. The dataset and code will be released.

Self-supervised pretraining is promising for large-scale neuroimaging, yet the impact of region-aware masking and hybrid sequence modeling remains underexplored. In this work, we introduce Rhamba, a region-aware pretraining framework that integrates anatomically guided masking with hybrid Attention-Mamba architectures for resting state functional magnetic resonance imaging (fMRI) analysis. Models were pretrained on the ABIDE dataset using region-aligned patch embeddings and three masking strategies (Any, Majority, and Pure) with increasing spatial specificity. We evaluated four architectural variants: a Mamba only model, an Alternate architecture with interleaved Mamba and Attention blocks, and two hybrid encoder-decoder configurations (Attention-Mamba (AM) and Mamba-Attention (MA)). The pretrained models were fine-tuned on downstream classification tasks using the COBRE and ADHD-200 datasets for schizophrenia and attention-deficit/hyperactivity disorder discrimination. We employed Integrated Gradients, an explainable AI method, to identify the brain regions contributing to model predictions. Masking strategy strongly influenced reconstruction behavior, with reconstruction loss following a consistent ordering (Any > Majority > Pure). However, this trend did not directly translate into downstream performance, where differences were modest and dataset-dependent. The hybrid architecture with the MA configuration achieved the highest average AUROC across both datasets, and Rhamba outperformed state-of-the-art methods in comparative evaluation. Region-wise analysis showed that peak performance depends on the interaction between masking strategy and architecture rather than a single dominant configuration. Overall, Rhamba offers a flexible framework for balancing interpretability, scalability, and performance in large-scale fMRI representation learning.

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.

Self-supervised pretraining has transformed computer vision by enabling data-efficient fine-tuning, yet high-resolution pretraining typically requires server-scale infrastructure, limiting custom in-domain training for many research laboratories. Masked Autoencoders (MAE) reduce computation by encoding only visible tokens, but combining MAE with hierarchical downsampling architectures has remained structurally challenging due to dense grid priors and mask-aware design compromises. We introduce AFFMAE, a masking-friendly hierarchical pretraining framework built on adaptive, off-grid token merging. AFFMAE removes dense-grid assumptions while preserving hierarchical scalability during pre-training and fine-tuning. To support this architecture, we developed numerically stable mixed-precision Triton kernels and a lightweight, point-based decoder that can be directly repurposed as a segmentation head. On high-resolution microscopy segmentation, AFFMAE matches MAE finetuning performance on foot process width estimation with ViT backbone at equal parameter counts while being 2x faster during pre-training and halving peak memory usage. Furthermore, AFFMAE achieves up to 5x throughput speedups fine-tuning at the 1024px resolution, providing high-resolution model training on desktop hardware. Code available at https://github.com/najafian-lab/affmae.

Cardiac Magnetic Resonance (CMR) imaging provides a comprehensive assessment of cardiac structure and function but remains constrained by high acquisition costs and reliance on expert annotations, limiting the availability of large-scale labeled datasets. In contrast, electrocardiograms (ECGs) are inexpensive, widely accessible, and offer a promising modality for conditioning the generative synthesis of cine CMR. To this end, we propose ECGFlowCMR, a novel ECG-to-CMR generative framework that integrates a Phase-Aware Masked Autoencoder (PA-MAE) and an Anatomy-Motion Disentangled Flow (AMDF) to address two fundamental challenges: (1) the cross-modal temporal mismatch between multi-beat ECG recordings and single-cycle CMR sequences, and (2) the anatomical observability gap due to the limited structural information inherent in ECGs. Extensive experiments on the UK Biobank and a proprietary clinical dataset demonstrate that ECGFlowCMR can generate realistic cine CMR sequences from ECG inputs, enabling scalable pretraining and improving performance on downstream cardiac disease classification and phenotype prediction tasks.

Medical imaging plays a vital role in clinical diagnosis, yet AI-driven imaging methods remain challenged by patient variability, image artifacts, and limited robustness across acquisition conditions. Although deep learning has advanced medical image analysis, 3D image translation remains hindered by limited training data and variability arising from scanner differences, imaging protocols, and patient motion. Conventional data augmentation typically relies on a single transformation pipeline, overlooking augmentation-specific characteristics and limiting representation learning. To address these challenges, we propose Multi-Encoder Augmentation-Aware Learning (MEAL), which processes multiple augmentation variants through dedicated encoder pathways. Three feature integration strategies are investigated: encoder concatenation (MEAL-CC), fusion layer (MEAL-FL), and an adaptive controller block (MEAL-BD). By dynamically weighting augmentation-specific features before decoding, MEAL-BD preserves complementary representations and improves robustness to clinically relevant variability. We evaluate MEAL using CT-to-T1-weighted MRI translation, a clinically relevant task when MRI is unavailable, contraindicated, or delayed. Across predefined and unseen test datasets, MEAL-BD consistently outperformed competing approaches under both geometric perturbations and standard imaging conditions, achieving higher peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM). By prioritizing structural fidelity over perceptual realism, MEAL supports clinical interpretation and downstream image analysis rather than replacing diagnostic MRI, demonstrating that augmentation-aware representation learning improves the robustness and clinical applicability of medical image translation.