Masked Autoencoders

Numerical site-response predictions often deviate from observations, yet correcting these discrepancies is difficult because records are limited in both sensor coverage and number of events. This study proposes the Transfer-Enabled Forced Latent Autoencoder for Response Equations (FLARE-T) to improve these predictions by learning and calibrating low-dimensional latent dynamics that connect the base acceleration input to acceleration outputs at multiple depths. FLARE-T learns a low-dimensional response manifold and input-driven dynamics from dense finite-element simulations. It then trains a sparse encoder to map simulated sensor responses into the learned coordinates and uses limited records to calibrate the dynamics within them. A short response window initializes each prediction, while the complete base motion drives the response. The framework was evaluated using a layered-soil centrifuge test and the Lotung field vertical array. Test-set results show that FLARE-T improved multi-depth acceleration histories and 5%-damped pseudoacceleration response spectra relative to the original finite-element models, reducing errors at every evaluated sensor for motions of different intensities and, at Lotung, for both horizontal components. Two Lotung source models with different constitutive parameters achieved comparable test-set accuracy, indicating reduced dependence on precise prior calibration. FLARE-T therefore provides a data-efficient means of combining dense numerical response information with limited field records to improve future site-response predictions.

We study reconstruction in autoencoders that apply the same forward map before and after setting the observed coordinates to zero. For equal odd input and hidden dimensions $d\geq 3$, among orientation-preserving diffeomorphisms whose Jacobian singular values lie in $[m,M]$, we show that the least uniform reconstruction-derivative error is $\max\{1-M(M-m)/2,0\}$, with affine maps attaining this sharp bound at every prescribed depth. A translated radial rotation can nevertheless reconstruct any prescribed ball exactly with singular values arbitrarily close to one, motivating additional conditions for a finite-data bound. We test this prediction on a 798,452-point terrestrial LiDAR forest scan. At input scale $0.05$, the mean theoretical bound is $0.155$, about $84\%$ of the mean normalized training error $0.185$ across four spatial regions, two depths, and three seeds. At this scale, adding one hidden coordinate reduces the mean reconstruction error below $6\times10^{-6}$.

Prompt-conditioned piano MIDI-to-Music rendering aims to faithfully render target notes while reproducing the timbre of a reference recording. Existing approaches primarily follow two paradigms: autoregressive (AR) modeling and flow matching (or diffusion). Discrete-codec AR models provide causal temporal modeling, but quantization can discard acoustic detail. Flow matching better preserves acoustic structure in the cost of full-sequence attention costs and worse semantic structure. Continuous autoregressive models operate directly on continuous representations. It not only combines the condition-following ability of AR models and distribution-modeling capacity of flow matching but also bypasses the quantization bottleneck with lower computational costs. Building on this principle, we present Composer--Performer--Refiner (CPR) framework. Composer autoregressively predicts continuous hidden states, Performer generates 24kHz acoustic latents through local flow matching and Refiner then upsamples the waveform to 48 kHz. We further introduce Bottlenecked Representation Alignment (BREPA) and Modality--Time RoPE (MT-RoPE) to strengthen musical semantic structure in Composer hidden states and temporal alignments across modalities. Codes are available at https://github.com/FEAfeatherTHER/CPR_official

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 Language Models (LLMs) primarily perform inference at the token level, resulting in substantial memory overhead and compromised computational efficiency. In this paper, we propose a Dynamic Semantic Extraction and Inference (DSEI) framework, which achieves segment-level inference within the latent space through a two-stage training strategy. First, we construct a Dynamic Semantic Autoencoder (DSAE) via self-supervised learning. DSAE dynamically extracts segment-level semantics and compresses them into compact latent representations via adaptive semantic weighting and gated fusion. Subsequently, we integrate the DSAE into the LLM architecture and train the model to infer over dense latent space. DSEI substantially reduces both input and generation sequences and significantly enhances inference efficiency. Extensive experiments conducted on the Wanjuan dataset demonstrate that DSEI reduces perplexity by 48% compared to static sentence-level latent inference baseline. Furthermore, compared to standard LLMs using token-level inference, DSEI accelerates inference speed by 2.5$\times$ and reduces memory overhead by 90%.

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.

No Free Lunch theorem implies that any performance gains achieved by a classifier on a particular image distribution are necessarily offset by a loss of performance over the set of all possible problems; thus, no single model is universally optimal. Selecting the most suitable classifier for image datasets is a critical yet challenging task due to the intrinsic complexity and diversity of images. This paper proposes a meta-learning framework that leverages a comprehensive set of meta-features capturing dataset complexity to predict classifier performance without exhaustive training. By extracting and selecting features using methods such as autoencoders, pre-trained networks, and dimensionality reduction techniques, we train regression models to efficiently estimate classifier accuracies. Additionally, clustering techniques are employed to group classifiers with similar performance patterns, simplifying the recommendation process. The datasets used span a wide range of concepts, including nature, animals, numbers, motorcycles, medical images, and human bodies, to ensure broad generalization. Evaluated on 56 diverse image datasets, our approach achieves an average ranking prediction accuracy exceeding 86%, demonstrating its effectiveness in guiding model selection. This scalable and interpretable framework provides a practical solution to improve classification performance while reducing computational costs.

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.

Reconstruction-based anomaly detectors are accurate but opaque: a deep autoencoder flags a sample without telling a practitioner which feature ranges made it anomalous. We propose DIFFINT, an autoencoder whose latent bottleneck is structured as a set of soft, axis-aligned interval memberships learned end-to-end directly from raw numerical data, without any discretization or binarization. Each latent unit corresponds to a human-readable hyper-rectangle in feature space; an instance is encoded by how strongly it falls inside each interval relative to the other units, and its reconstruction error is the anomaly score. This keeps the power of differentiable representation learning while exposing an inspectable internal structure. We make the inductive bias precise: a certified reconstruction-error lower bound for points that fall outside every active coordinate of the learned support (with a Lipschitz-enforced decoder), and a graded, empirically verified suppression mechanism for the usual case in which only a few features are abnormal; and we provide a closed-form, label-free importance that ranks each (unit, feature) pair from quantities the model already maintains, turning trained intervals into auditable candidate constraints without ever seeing an anomaly label. On 48 ADBench benchmarks against 22 baselines under a common [-1, 1]-normalized protocol, DIFFINT attains the best mean rank overall on both metrics (4.10 on ROC-AUC, 4.16 on AUPR); among inlier-only detectors it leads its regime clearly, and it is competitive with the strongest contaminated-data detectors (see the stratified and complete-case analyses). It is the only interpretable detector in the statistically-tied leading cluster of seven methods.

This paper examines the relationship between the parameters of autoencoder models and the statistical properties of the data on which they are trained. Autoencoders are defined as models with an encoder-decoder architecture, trained to reconstruct input data through a compressed latent representation. It is proposed that the model parameters can be viewed as a dense vector representation of the corresponding sample. To test this hypothesis, a theoretical and experimental study is conducted in which a vector representation is formed based on the spectral characteristics of the autoencoder parameter matrices. Theoretical analysis shows that the singular values of the model parameter matrices are related to the eigenvalues of the covariance matrix of the training data, ensuring the transfer of information between the data space and the parameter space. Experimental results on the CIFAR-10 and FashionMNIST datasets confirm that the resulting vector representations allow for a high degree of accuracy in distinguishing between models trained on different data subsets, without resorting to complex vector generation algorithms or using the original samples. These results suggest that the parameters of trained autoencoders can be viewed as sample representations.

In many settings, studying causal questions based on text data requires adjusting for confounding information within texts. Yet there is a tradeoff in constructing text representations for adjustment: they must be sufficiently large and/or dense to preserve the confounding variables necessary for unbiased effect estimation, but sufficiently small and/or sparse to satisfy finite-sample overlap and yield low-variance estimates. To address this tradeoff, we turn to sparse autoencoders (SAEs), and propose a novel causal adjustment pipeline that iteratively selects a minimal set of SAE features via conditional independence tests. We find that SAE representations achieve better adjustments (lower bias and and higher coverage) than alternative representations in standard semi-synthetic evaluations with binary confounders, and their interpretability offers opportunities for falsification. We also introduce a more realistic semi-synthetic evaluation that uses multi-label data as the unobserved confounders and find off-the-shelf adjustment methods require increased investigation for these more complex settings. Code: https://github.com/mianzg/sae-text-confounder

Autoencoders typically meet tight latent-memory budgets by making each latent representation smaller, sacrificing representational capacity. We ask a different question: can multiple wider latents be stored together instead? We introduce the Superposed Latent Autoencoder (SLAE), which preserves high-capacity latent representations while sharing storage through learned superposition. SLAE transforms latents into storage-friendly codes, binds them with randomized keys, superposes multiple codes into a single memory tensor, and learns to recover each latent before decoding. Under the same storage budget, SLAE replaces irreversible dimensional bottlenecks with structured interference that can be suppressed. Across CIFAR-10/100, SVHN, STL-10, Tiny ImageNet, and a wide range of memory budgets, SLAE substantially improves the reconstruction--memory tradeoff, reducing reconstruction error by up to 56% over conventional autoencoders at matched storage. Further analysis shows that SLAE's advantage comes from making wider representations usable under the same storage budget. These gains also extend beyond reconstruction: the information preserved by SLAE improves downstream classification by up to 16.79 percentage points under the same memory budget. Our results suggest a new principle for representation compression: instead of making every latent smaller, keep representations wide and let them share memory.

Denoising diffusion models are the dominant architecture for image generation, whereas most natural language generation and modeling are primarily handled by well-known transformer architectures employing attention mechanism. Here, we show that diffusion models also inherently use an attention mechanism very similar to that of transformers. Therefore, attention emerges as a universal machine learning principle, based on a general training objective. We also show similarities in basic functional principle of auto-encoders and attention-based models. These equivalences allows us to interchange these designs based on practical requirements. As an example, we can reformulate the diffusion framework to reduce the lengthy training process and computation-intensive image generation. Using this approach, a simplified algorithm is proposed for image generation which is based on attention mechanism. Results show that the attention-based implementation achieves comparable performance with significantly less effort and computational resources.

Scientific discovery often requires reasoning over competing hypotheses that are consistent with experimental observations. For mixed-variable and combinatorial hypothesis spaces, however, constructing probabilistic representations remains challenging because both the active model components and their associated parameters are unknown. In this work, we present a framework for learning continuous latent representations of admissible partial differential equations (PDEs) by embedding a scientific inductive bias directly into the training distribution. Progressively richer structural principles (e.g., sparsity, logical dependencies, common PDE families, and physical admissibility) are used to generate a structured distribution of hypotheses from which a gated variational autoencoder learns a continuous latent manifold. Experimental results show that the resulting 11-dimensional representation accurately reconstructs a broad collection of representative PDEs, while exhibiting smooth geometric transitions both within and across equation families. Through an ablation study we further demonstrate that introducing scientific principles reduces both structural misclassifications of equation forms and parameter estimation errors when reconstructing a representative benchmark set of admissible partial differential equations. These results show that embedding a scientific inductive bias in the training distribution enables the learning of compact and geometrically meaningful hypothesis manifolds, providing a principled foundation for future inference over competing governing equations.

Autoencoders are widely used for nonlinear dimensionality reduction and manifold learning. While most common implementations rely on both nonlinear encoders and decoders, we investigate the specific role of the encoder and the extent to which it can be constrained to be linear without reducing accuracy. We conduct a comparative study on four autoencoder architectures: standard fully nonlinear autoencoders (AE), linear-encoder autoencoders (Lenc-AE), linear-decoder autoencoders (Ldec-AE), and fully linear autoencoders (LAE), evaluated on synthetic manifolds, computational mechanics data sets, and real-world image data sets including MNIST. We demonstrate that imposing a linear encoder preserves most of the representational capacity of the autoencoder, provided the decoder remains nonlinear. In particular, Lenc-AE consistently outperforms both Ldec-AE and LAE, and achieves reconstruction quality comparable to fully nonlinear AE, while offering advantages in terms of parsimony and interpretability of the latent representation. These results suggest that the nonlinear decoder is the critical component for manifold learning, rather than the encoder. A geometric interpretation of this finding is developed, which identifies the precise conditions under which a linear encoder is sufficient, and the specific manifold configurations that expose its limitations.

Latent video generation relies on autoencoders to define a compact space in which generative models operate. Although video autoencoder architectures have evolved substantially, their latent spaces are still optimized primarily for pixel-level reconstruction and provide limited high-level semantic organization. A reconstruction-optimal latent space, however, need not be well suited to generative modeling. We propose V-RAE, a video representation autoencoder that builds compact generative latents on top of frozen vision foundation model representations. A lightweight temporal pooling module removes temporal redundancy while preserving semantic structure, and a video decoder reconstructs continuous motion from the compressed features. We evaluate V-RAE with four representative frozen encoders on video reconstruction, semantic probing, and class-conditional generation. V-RAE achieves 2.13 rFVD on K600, outperforming all evaluated large-scale pretrained video VAEs. Its latents retain substantially more semantic information than conventional video tokenizer latents. Under matched generation settings, our best variant achieves gFVD scores of 117.86 and 19.16 on UCF101 and K600, respectively, while converging up to 6x faster}. We further show that reconstruction quality alone is insufficient to characterize generative utility and introduce tFVD, a temporal-coherence diagnostic that correlates more reliably with downstream generation quality. Beyond video generation, V-RAE also improves future video prediction on Cityscapes over the Wan 2.2 VAE latent space under matched prediction settings. Taken together, the experiments show that frozen semantic representations can support video reconstruction, generation, and predictive modeling. The project page: https://v-rae.github.io/.

Adaptive latent tokenization maps a fine-grained input to a shorter sequence of continuous representations associated with input-dependent spans. We introduce ReconSpan, which divides text into chunks that a backward decoder can reconstruct from a single contextual prefix code and retains one such code as the latent token for each chunk. The reconstruction criterion is applied when chunks are formed, allowing one trained autoencoder to produce average chunk lengths from 6.5 to 12.2. At matched average length, reconstruction-guided boundaries preserve more text than random boundaries. Readers of the resulting latent sequence recover topic information reliably but struggle to extract exact details.

We consider the setting of Normalizing flows with approximate inverses, an established paradigm spanning both full-dimensional ($d=D$) and bottleneck ($d<D$) settings, and group these models under the term flow autoencoders. We present a theoretical investigation into their training dynamics and prove that the proposed loss used by existing approaches is suboptimal; specifically, both encoder and decoder surrogates must be optimized in alignment with reconstruction loss. Guided by these insights, we propose Normalizing Autoencoder (NAE), which employs a novel conditional loss that aligns the surrogate loss gradient with that of reconstruction loss, directly improving upon the current standard. Extensive experiments across molecule generation, tabular data, and image benchmarks demonstrate that NAE achieves state of the art performance. Our work highlights the importance of loss alignment in flow autoencoders and establishes NAE as a powerful generative framework.

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.

Outlier detection in decentralized data environments is a challenging task for many machine learning implementations, particularly in settings where data cannot be shared. Recently, there have been advances in federated outlier detection, some of which are based on the use of autoencoder networks. The introduction of attention mechanisms to autoencoders boosts their efficiency. However, the application of attention-based models in federated learning remains underdeveloped due to the absence of proper aggregation functions for these types of networks. In our work, we propose two novel aggregation functions tailored for attention-based autoencoders, which better preserve the learned information stored within the memory modules of these networks. We evaluated our approach on the KDDCUP10 dataset, and we showed that the proposed methods achieve up to 2.9% and 5.1% better results for F1 score and AUC ROC respectively when compared to traditional autoencoders.

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/

Learning disentangled representations is a key requirement for developing versatile, general-purpose, and sustainable models in multi-modal wearable computing. However, existing approaches do not operate as full-stack wearable processors, i.e., they do not simultaneously address task-specific classification performance, disentangled and interpretable representation learning, fusion, and generative modeling of highly heterogeneous multi-modal time series. To address this gap, we introduce Omni-modal Variational Decomposition Autoencoders (OmniDecVAEs), a framework that efficiently learns multi-purpose representations in a unified and scalable manner from arbitrarily many modalities. OmniDecVAEs extend DecVAEs by learning modality-conditioned time-frequency latent subspaces through a multi-view self-supervised decomposition loss and a shared asymmetric autoencoder (AE) architecture. Results on a challenging omni-modal human activity recognition (HAR) setting with up to thirty modalities, demonstrate the ability of OmniDecVAEs to learn full-stack wearable representations. When compared to transformer-based and VAE-based methods, OmniDecVAEs full-stack disentangled representation properties lead to accuracy improvements of 1.01% and 6.75% in activity and identity recognition, respectively. Furthermore, OmniDecVAEs synthesize realistic omni-modal time-frequency data that manifest with enhanced reconstructions (mean absolute error improves by 76.84%) and distributional similarity between real and synthetic data (maximum mean discrepancy improves by 13.85%). Our results highlight OmniDecVAEs potential as a lightweight model suitable for intelligent edge wearables and clinical healthcare, unifying processing requirements and abilities in a single model, through its enhanced representational capacity, modality-invariant spatial complexity (4.1M parameters), and real-time latency.

Attention layers are the backbone of today's most powerful and impactful models. Models with multi-million and billion parameters rely on contextual knowledge provided by attention layers. However, their use goes well beyond just being the core component of large language models. One particularly interesting application is in Memory Augmented Autoencoders (MemAE), specifically for unsupervised representation learning in outlier detection tasks. It was shown that attention helps these models be more effective in centralized learning scenarios. Our work aims to address the lack of specialized aggregation techniques in Federated Learning (FL) when it comes to MemAE models. In this paper we analyze the intricacies of the architecture behind Memory Augmented Autoencoders, and propose novel, guided approaches to effectively aggregate these models in federated scenarios. We demonstrate our approach on non-IID datasets and show that these novel aggregation schemes are more robust when dealing with numerous edge nodes in environments with unbalanced datasets, specifically for unsupervised anomaly detection scenarios. This approach improves the performance of even very shallow autoencoders, allowing them to be used in resource constrained environments.

High-fidelity 3D MRI synthesis requires both globally coherent anatomy and fine-grained voxel-level detail. Although latent diffusion makes volumetric generation tractable, its image autoencoder introduces a reconstruction bottleneck that can limit the fine detail recoverable in the final volume. We present VoxStruct3D, a voxel-space flow-matching framework that directly models full-resolution MRI volumes using a clean-data prediction objective. Its Volumetric Voxel Generator (VVG) combines factorized 3D patch embedding with overlapping upsampling, time-modulated residual refinement, and skip fusion, enabling neighboring tokens to jointly reconstruct shared voxel regions and suppress patch-boundary artifacts. To complement direct voxel-space modeling with an explicit anatomical prior, we further introduce a Structure-First, Image-Follows (SFIF) strategy. A frozen pretrained 3D medical encoder and a StructVAE extract compact structure tokens that preserve dominant anatomy, while a structure-leading schedule keeps their trajectory ahead of the image trajectory. Patch-Aligned RoPE spatially aligns the unequal token grids, and asymmetric attention enforces one-way guidance from structure to image. Experiments on pathological and healthy T1-weighted brain MRI datasets show that VoxStruct3D achieves the strongest overall performance across feature-distribution alignment, sample diversity, and perceptual quality, producing anatomically coherent and visually realistic volumes.

The development of foundation models (FMs) is crucial for advancing endoscopic image analysis. However, existing endoscopy FMs mainly rely on self-supervised learning from uni-modal images or videos, overlooking the rich semantic knowledge contained in clinical reports. Furthermore, effectively leveraging these records is hindered by a fundamental modality gap: structured anatomical descriptions are not naturally mapped to specific frames within the high-redundancy, uncurated visual streams. In this paper, we present EndoVLM, a novel vision-language FM pre-trained on over 348K endoscopic examinations, each pairing a clinical report with its corresponding image collection. An Anatomy-Guided Sparse Pooling mechanism utilizes textual descriptions as queries to drive sparse attention, efficiently aggregating semantically salient frames into anatomy-specific visual representations across redundant image-sets. Next, a Progressive Semantic-Aware Alignment strategy models clinical taxonomy (anatomy and pathological status) via structured soft targets, bridging the gap from global patient-level matching to fine-grained localized alignment. Finally, a Semantic-Concentrated Masked Autoencoder is applied exclusively to these semantic-rich frames, integrating low-level visual precision with robust high-level semantic representation. Extensive experiments across various downstream tasks demonstrate that EndoVLM outperforms existing foundation models and remains competitive with task-specific methods. Remarkably, EndoVLM also exhibits robust zero-shot generalization capabilities, highlighting its potential for broader clinical application.

Collaborative music agents need internal representations rich enough to support both understanding and generation, yet flexible enough for a workflow where the human retains agency. We present a hierarchical self-supervised ``world model'' for symbolic music: a 2.55M-parameter Swin V2 encoder trained on MIDI piano-roll images with JEPA-style objectives (pitch- and time-shift equivariance, masked embedding prediction, and a distributional regularizer), using no labels and no music-theory vocabulary. Probing the frozen embeddings shows that the level at which a musical property becomes decodable tracks its musical time scale: phrase boundaries are read off the coarsest levels, note density and harmonic detail off the finest. Temporal and phrase structure emerge from the self-supervised objectives alone, while harmonic content must be asked for; a small chord-supervision head raises joint chord recovery from .18 to .54, and key detection, which is never supervised, from .16 to .70. Following the Representation AutoEncoder paradigm, a conditional flow-matching model stands in for a trained decoder, flowing in pixel space from PCA-reduced conditioning: it reproduces a target window at pixel F1 $0.996$, and the same per-level conditioning dropout that controls how far variations stray also enables graphical prompting for masked inpainting with no inpainting-specific sampler. The pipeline runs on CPU producing a suggestion in $2.8$ s, or $0.6$ s on Apple MPS, which we demonstrate in a live interactive demo. In concert with an LLM-based brain, these capabilities supply the core of a collaborative music creation agent in service of, rather than in place of, human agency.

Virtual contrast enhancement (VCE) synthesizes enhanced breast MR images from pre-contrast acquisitions. Modern latent generators offer strong image priors, but their bounded natural-image autoencoders conflict with the non-canonical intensity scale of MRI. We show that the upper bound can alter radiomic fidelity before generation, while scaling source and target independently creates a coordinate inconsistency. We propose Predictive Enhancement Calibration (PEC), which represents each pair in a shared, case-adaptive coordinate during training and predicts its unavailable upper endpoint from the pre-contrast image at inference. We integrate PEC with a pretrained FLUX latent flow transformer via parameter-efficient reference conditioning. Target round trips first isolate representation loss before generation; near-matched conditional models then compare PEC with fixed-wide and separate coordinates under comparable training budgets and backbone settings. On the fixed internal MAMA100 development cohort, PEC improves all eight point estimates in this source-only VCE setting, with paired evidence strongest for MSE and LPIPS.\noindent\textbf{Code:} https://github.com/tanlei0/pec-breast-mri-vce

How can we better represent the impact of sociocultural structures on decision making in computational cognitive models? Modeling this impact requires traversing multiple levels of semantic representation, however it is not immediately clear to a modeler which levels of representation are most salient to a given situation. Though large language models and cognitively grounded corpus models can represent broad semantic associations through co-occurences, the role of self representations in memory should be accounted for to determine how cultural associations shape decision making. We propose a declarative memory system to be used in the ACT-R cognitive architecture that represents semantic associations at multiple levels via a vector-symbolic autoencoder. We use a simple HRR operation to encode episodic memories differently from semantic memory vectors extracted from text to produce a final chunk activation for a memory request. We use ACT-R cognitive models of a racially contextualized implicit association test (IAT) to test this new declarative memory system.

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.

Music restoration seeks to recover a clean signal from an observed recording degraded by an unknown effect, distortion, or corruption. Existing systems often rely on paired training data and distortion-specific supervision, which limits their use when the forward process is not known in advance. We propose LOUDAR (Latent-space Optimization of Unknown Distortion for Audio Restoration) a general-purpose restoration method that operates in the latent space of a pretrained audio autoencoder and models the unknown distortion as a learnable latent operator. At inference time, LOUDAR alternates between estimating the clean latent variable and updating the latent operator parameters. An unconditional latent diffusion model provides a prior over clean audio and regularizes this inference by steering the latent estimate toward the manifold of clean recordings. Because the degradation model is adapted per input, the approach is broadly applicable across diverse restoration problems. We evaluate LOUDAR on singing voice effect removal and restoration, as well as guitar distortion removal, and show that it consistently improves over degraded inputs and is competitive with supervised and unsupervised baselines in waveform and latent domains.

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.

Latents from vision foundation models (VFMs) are semantically rich and well suited for visual understanding. Recent representation autoencoder methods such as RAE have shown that they can provide promising latent spaces for image generation. However, VFM latents remain difficult to model directly: DiT-generated latents exhibit spectral mismatch with encoder latents, especially in high-frequency components. Our channel-wise spectral analysis further reveals that these high-frequency components are diffusely distributed across latent channels and entangled with semantic information, making the latent space difficult for DiT to model. To address these challenges, we propose SPAE, latent adaptation framework for generation. Specifically, SPAE employs a compact bottleneck to distill stable semantic information while suppressing high-frequency components, thereby improving the alignment between DiT-generated latents and encoder latents. In addition, we apply a channel-wise masking strategy to promote the decoupling of semantic information and high-frequency details across bottleneck channels. Experiments show that SPAE achieves a favorable balance among visual understanding, generation quality, and reconstruction fidelity.

The target representation defines the distribution an image generator must learn, yet it is often treated as an interchangeable interface. This assumption is particularly questionable for continuous masked generators, which combine contextual inference from visible tokens with conditional modeling of each missing token. We study raw pixels, SD-VAE latents and DINOv2 as well as MAE representation-autoencoder features within a unified masked autoregressive rectified-flow model. Under a shared ImageNet training budget, these spaces exhibit distinct optimization and inference regimes. DINOv2 converges fastest in both iterations and computation but benefits strongly from a wider local denoiser and direct context fusion. Pixels optimize substantially more slowly and require a different prediction, masking, and guidance configuration. MAE reconstructs images more faithfully and exhibits clear semantic clustering, yet produces generations substantially worse than DINOv2. The representations also respond differently to classifier-free guidance and occupy distinct precision-recall trade-offs. Together, our results show that compression, reconstruction fidelity, token dimensionality, and visible semantic clustering do not individually predict generative behavior. Instead, target representations redistribute difficulty across contextual modeling, per-token denoising, and inference-time distributional control.

Despite the widespread adoption of foundation models as feature extractors for medical imaging, relatively little is understood about how different pretraining strategies influence the transferability of learned representations to weakly supervised ophthalmic imaging tasks. We investigate this question in ultra-widefield (UWF) retinal imaging by evaluating foundation model representations within a patch-based multiple instance learning (MIL) framework for disease classification on UWF images. We compare Vision Transformer encoders pretrained with supervised, Masked Autoencoder (MAE), and self-distillation objectives, while keeping the downstream aggregation architecture unchanged. Within a controlled comparison of ViT-B encoders pretrained on ImageNet-1k, the choice of pretraining objective substantially influenced frozen representation transfer, with supervised and self-distillation-based models outperforming MAE. A contemporary DINOv3 model pretrained at a larger scale achieved the strongest overall performance, with a quadratic weighted kappa of 0.863 for five-class diabetic retinopathy grading, comparable with DINOv1. Attention analysis further revealed distinct patch-aggregation behaviours associated with the different pretrained representations, while partial fine-tuning substantially reduced the performance gap for MAE. These findings suggest that pretraining strategy influences both representation transferability and the subsequent aggregation of patch-level evidence within MIL, resulting in differences in downstream classification performance.

Latent Flow Models have revolutionized compressed-space image synthesis, yet their application to high-fidelity inverse problems remains bottlenecked. In this paper, we trace this dilemma to a fundamental geometric limitation of pre-trained autoencoders, which we term \emph{First-Order Manifold Blindness}. Severe decoder compression (e.g., retaining only $\sim\!2\%$ of the original degrees of freedom) produces a rank-deficient Jacobian, rendering high-frequency measurement residuals in its orthogonal complement invisible to latent gradients even when the decoder can represent the target image. To overcome this bottleneck, we propose Hybrid-Domain Posterior Sampling (HDPS), a decoupled inference framework that disentangles physical measurement consistency from semantic prior modeling. HDPS diverges into the pixel space, leveraging Langevin dynamics to absorb precise orthogonal measurement gradients, and subsequently projects these structural corrections back onto the generative manifold. An optimization-based latent alignment is introduced to filter pixel-space artifacts while avoiding the semantic drift of direct encoding. Extensive experiments on diverse inverse problems demonstrate that HDPS establishes a new state-of-the-art, successfully recovering the high-frequency structural precision that latent-only solvers inherently discard. The code is available at \href{https://github.com/74587887/HDPS}{https://github.com/74587887/HDPS}.

Text-to-motion generation must produce motions that are semantically correct, temporally coherent, and physically plausible. A natural approach is to first project motion data into a structured semantic space and then train a generative model within that space. Such a paradigm has been highly successful in image generation through Representation Autoencoders (RAEs), where a frozen self-supervised encoder provides semantic features for diffusion or flow models to learn from. However, direct transfer of such a paradigm to motion space using Motion-JEPA as the frozen encoder fails dramatically. We diagnose this failure geometrically and identify two motion-specific bottlenecks: (1) the JEPA feature space is spectrally ill-conditioned, making the Gaussian-to-data transport unstable; and (2) even with a well-conditioned spectrum, flow residuals tend to align with decoder-sensitive directions, where small latent errors are amplified into large motion artifacts after decoding. Based on these insights, we propose MoRAE. MoRAE addresses the two bottlenecks separately. A compact bottleneck distills the structured JEPA representation while removing weak and redundant directions, bringing the latent spectrum into a transport-stable regime. Motion-coupled training then aligns the retained latent geometry with the decoder, making characteristic flow errors less costly after decoding. With this flow-friendly latent, a standard non-autoregressive Flow-Matching DiT achieves state-of-the-art performance.

Existing watermark attacks typically rely on predefined signal-processing operations or locally constrained restoration networks, making it difficult to capture the long-range dependencies of globally distributed watermark signals and resulting in an unfavorable trade-off between removal effectiveness and visual fidelity. In this paper, we propose SPFM-Net, a semantic-prior-guided and frequency-constrained Mamba framework for invisible watermark attack. SPFM-Net first employs high-ratio masking to disrupt the spatial coherence of invisible watermark signals, and then utilizes a partially fine-tuned pretrained Masked Autoencoder to reconstruct semantically consistent image from sparse observations while suppressing watermark-related information. A Multi-scale Residual Frequency Feature Interaction module subsequently aggregates watermark-related residual features across multiple receptive fields, while adaptively suppressing responses from watermark-irrelevant regions. To further capture the long-range dependencies of globally distributed watermark signals, a lightweight Mamba-based Global State-space Feature Modeling (GSFM) unit is introduced to separate watermark-related features from natural image content and suppress the remaining watermark traces. In addition, SPFM-Net is optimized using a multi-level objective that jointly imposes spatial-, frequency-, and edge-domain constraints, enabling effective watermark suppression while preserving perceptual quality. Extensive experiments on representative spatial-domain, transform-domain, orthogonal moment-based, and deep learning-based watermarking schemes demonstrate that SPFM-Net achieves a favorable trade-off between watermark attack effectiveness and perceptual fidelity.

Grounding human motion in language, and language in motion, is a central step toward physical AI systems that can understand, generate, and communicate human behavior. Unified motion--language systems first coupled the two directions through a shared discrete motion codebook, but quantization limits generation quality. The strongest generators buy quality back at growing cost: stacked residual codebooks enlarge the representation; masked decoding stages, long autoregressive rollouts, and denoising chains of tens to hundreds of steps stretch inference; even the continuous-latent designs among them reach their latent only through an iterative diffusion head; and none of this decoding machinery serves understanding. We therefore propose MUGEN, a unified motion--language framework that pays neither cost: no codebook, one draw. A single adaptive-length autoencoder compresses any-length motion into a few continuous latent slots, the system's only motion representation: the language model generates them for text-to-motion and reads them back for motion understanding. Depth-routed hidden states let each slot read from the transformer depth it needs, and a calibrated head predicts a joint distribution over the full latent set, so a single draw carries the text-conditional, cross-slot variation a description permits. At a decoding cost of K language-model steps, one draw, and one decoder pass, MUGEN leads language-model baselines on FID on HumanML3D while raising retrieval precision above the real-motion reference under the standard evaluator, achieves the best CIDEr and BLEU@4 scores, and surpasses the discrete-token state of the art on every retrieval and alignment metric on SnapMoGen.

We present a lightweight approach to foundation modeling (\textbf{NEXUS}) that leverages pre-trained learning from collider physics data towards out-of-domain tasks in other scientific datasets, using a fully connected autoencoder model with approximately 3 million parameters. The model pre-trains with no supervision over a large-scale collision dataset from the Large Hadron Collider modeled by charged particle track features. Downstream tasks for collider analyses, such as kinematic regression and event classification, are developed on pre-trained model weights and achieve improved accuracy with only small labeled datasets when compared to equivalent architectures trained from scratch. The benefits of pre-training are additionally investigated through latent space interpretation and application to other domains, including gravitational waves, flood forecasting, and neural activity. Furthermore, the relative computational simplicity of NEXUS is demonstrated compared to transformer approaches at comparable scale, opening the door to power-efficient inference and real-time or edge applications of foundation models in scientific experiments.

Existing benchmarks for electrocardiogram foundation models primarily evaluate downstream predictive performance, providing limited insight into whether their internal representations can be faithfully decomposed, clinically interpreted, or reproduced across independent analyses. We introduce ECG-InterpBench, a benchmark designed to systematically evaluate the interpretability of ECG foundation-model representations. ECG-InterpBench uses sparse autoencoders as standardized measurement instruments and matches their capacity across models to enable controlled comparisons. We evaluate six frozen ECG foundation models across five standardized encoder depths, five matched dictionary widths, and three random seeds, producing a 450-cell interpretability atlas comprising 75 exactly matched six-model comparison blocks. The benchmark evaluates complementary dimensions of representation interpretability, including sparse reconstruction fidelity, single-feature accessibility and coverage of 49 clinically meaningful ECG measurements, and cross-seed feature reproducibility. The evaluation further quantifies patient-sampling uncertainty, depth- and seed-dependent variation, and sensitivity to the sparsity parameterization. The benchmark reveals that ECG foundation models exhibit distinct interpretability profiles. A matched replication on MIMIC-IV-ECG confirms that reconstruction fidelity and clinical accessibility identify different leading models. The benchmark is accompanied by executable evaluation code, standardized manifests, cell-level metrics, and reproducibility audits. ECG-InterpBench complements performance-centered ECG benchmarks by providing a capacity-controlled and reproducible framework for comparing ECG foundation models across distinct dimensions of representation interpretability.

We introduce ZUNA1.1, a 380M-parameter diffusion autoencoder for flexible EEG signal reconstruction. ZUNA1.1 is capable of reconstructing variable length sequences of up to 30s, with an arbitrary number of EEG channels at arbitrary scalp locations, and can reconstruct arbitrary temporal intervals within channels in addition to reconstructing entire channels. We demonstrate that ZUNA1.1 performs at least on par with our earlier ZUNA1 model, while being far more flexible and capable of handling a wide range of reconstruction tasks. ZUNA1.1 continues to substantially outperform standard EEG denoising and reconstruction methods such as spherical spline interpolation, which is ubiquitously deployed in the MNE package. The ZUNA1.1 model is released open source under the permissive Apache 2.0 license.

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.

In this work, we aim to discretize the high-dimensional visual representations to bridge the gap with language models - a non-trivial challenge, as existing quantization methods suffer from codebook collapse, failing to scale while preserving semantic coherence. We identify the root cause as metric mismatch: standard Euclidean codebook objectives are fundamentally misaligned with the anisotropic geometry of representation space, leading to codebook embeddings with high-variance magnitude scales and uneven angular distributions that hinder scalability. To address this, we propose Hyper-Spherical Quantization (HSQ), which decouples semantic content from feature magnitude via angular routing, preventing code assignment from being dominated by scale rather than meaning. The resulting discrete Representation Autoencoder (dRAE) achieves high-fidelity reconstruction while preserving semantic integrity and supporting scalable codebook budget. Extensive experiments demonstrate consistent performance gains as the vocabulary size scales to 131{,}072, along with 100% codebook utilization, simplified training pipeline, and strong performance across understanding and generation tasks.

Large language models may infer demographic attributes from subtle linguistic cues even when those attributes are not explicitly stated. This pilot study examines whether Qwen2.5-7B-Instruct internally represents Colombian identity, socioeconomic status, or stereotype-related information when processing Colombian-Spanish and English prompts. We use Natural Language Autoencoders (NLA) to verbalize residual-stream activations from layer 20 across four positional quartiles per prompt. Our dataset contains 30 prompts arranged as 15 matched Spanish-English pairs, spanning explicit Colombian cues, implicit Colombian cues, and neutral controls. We report descriptive rates and qualitative evidence rather than statistically powered effects, focusing on whether latent nationality or stereotype representations appear before they are verbalized in the model output. This work connects activation-level interpretability with bias evaluation for underrepresented Spanish varieties.

Scientific machine learning methods such as neural operators and physics-informed neural networks have advanced engineering applications and inverse problems, but their training typically requires large volumes of simulated data. This makes data preparation and model training expensive. We propose Graph Wavelet Compressed Sensing (GWCS), a learning-based framework for offline compression of graph signals by representing them as sparse, interpretable wavelet-domain representations using the spectral graph wavelet transform. The framework combines a nonparametric multilevel importance sampler, which retains high-energy wavelet coefficients within each scale for a given compression ratio, with a scale-aware graph neural network that reconstructs the signal from the sparse coefficients. We evaluate the proposed framework on synthetic approximately band-limited graph signals over random graphs and four PDE simulation datasets over meshes, which include Turbulent Radiative Layer, Viscoelastic Instability, Kolmogorov Flow, and Dynamic Stall. We compare against graph signal sampling methods and graph autoencoder baselines. Results demonstrate that the framework achieves high reconstruction fidelity and substantial data compression compared to existing benchmarks.

Weakly supervised pipelines for medical imaging have become increasingly popular over the years. These systems often include multiple stages and components, such as reconstruction, generation, and localization, yet standard evaluation metrics provide limited insight into whether clinically relevant information is preserved across each stage. We present the diagnostic gap framework, a practical evaluation tool that measures decision preservation and explanation preservation as a function of measured reconstruction fidelity. To isolate the effect of reconstruction from localization, we evaluate on curated lesion ROI crops using a fidelity ladder of three class-conditional reconstructors---VQ-VAE-GAN, VAE-GAN, and diffusion (SDEdit)---spanning a twenty-fold range in perceptual distance (LPIPS 0.029--0.584). At autoencoder fidelity, both decision and explanation are preserved: AUC changes remain within $\pm$0.005 and attribution similarity (HiResCAM, Grad-CAM++) stays high. At diffusion fidelity, both collapse: pooled AUC drops by 0.253 and mass-pathology AUC falls below chance. The diagnostic gap is thus a measurable function of reconstruction fidelity rather than an intrinsic cost of reconstruction, and the framework provides an architecture-agnostic instrument for identifying when and where multi-stage pipelines lose diagnostic signal.

Autoregressive context models are foundational for learned image compression,but they suffer from slow serial inference. Existing acceleration methods such as checkerboard context require architectural changes and retraining, thus are inapplicable to pre-trained models. We propose a completely training-free inference-time acceleration algorithm inspired by wavefront parallelism in video coding standards. Our method reorganizes inference into an optimal ``staggered'' wavefront order, minimizing sequential steps while maintaining exact autoregressive dependencies. Experimental results show our approach accelerates pre-trained autoregressive models (e.g., Cheng et al.) by more than $13\times$ while preserving the original rate-distortion performance. We also demonstrate that faster decoding is possible by trading off precise context dependencies. Source code will be available at https://github.com/tokkiwa/compressai-wavefront.

Large-scale scientific simulations generate volumetric data at rates that far outpace advances in storage and network bandwidth, making effective lossy compression increasingly critical. However, conventional compressors often struggle to preserve fine structural details at high compression ratios (CRs), and implicit neural representations (INRs) require costly per-volume optimization and produce models with fixed CRs. To respond, we present EVOLVE, an autoencoder (AE)-based volume-compression framework that targets high CRs for offline compression, with three key contributions. First, we construct a large-scale cross-domain database of 6,376 volumes from 21 scientific simulations, curated via perceptual hashing to ensure diversity, enabling the optimized model to extract features that generalize across volumes within the covered scientific simulation domains. Second, we reexamine the design space of AE-based compressors and incorporate several macro- and micro-designs into a vanilla AE to develop EVOLVE, which substantially improves the expressive power and compression capability. Third, we develop a learnable gain mechanism with a three-stage training strategy to enable variable-rate encoding, allowing a single model to support continuous CR adjustment at inference time. Experiments on multiple unseen scientific simulation datasets demonstrate that EVOLVE achieves substantially higher CRs than conventional compressors at comparable reconstruction quality, while delivering compression speeds that are orders of magnitude faster than INR-based methods, highlighting its promise as a strong alternative for compressing scientific data. The code, model weights, and results are available on our project page at https://evolve-vis.github.io.

Distributed Fine-Tuning (DFT) of large-scale Foundation Models (FMs) on resource-constrained edge devices is limited by local compute constraints and communication overhead. Parallel Split Learning (PSL) reduces client-side computation by keeping few model layers on each client and offloading the remaining computation to the server; however, clients must exchange intermediate activations and gradients with the server at every training step. Existing SL communication-compression methods mainly rely on task-agnostic heuristics, such as sparsification and quantization. While learnable SL compressors can better adapt to intermediate representations, they require co-training with the target model. Therefore, directly inserting them into off-the-shelf FMs introduces feature-distribution misalignment and degrades DFT performance. To address this, we propose AE-PSL, a communication-efficient PSL framework that compresses intermediate activations and gradients using a lightweight AutoEncoder (AE) placed at the split layer. To ensure compatibility of AE compression with pre-trained FMs, AE-PSL introduces a novel two-stage alignment mechanism, which adapts the AE to the pre-trained model's feature manifold and client-specific feature distributions before DFT.

Foundation models pretrained using self-supervised learning have transformed computer vision by learning transferable representations from large-scale unlabeled data. However, existing foundation models for neuroimaging remain limited by task-specific training, slice-based learning strategies, or relatively small pretraining datasets, restricting their generalizability across diverse brain MRI applications. In this work, we present BrainNext, a general-purpose self-supervised foundation model for volumetric brain MRI analysis. BrainNext combines masked autoencoder (MAE) pretraining with a native three-dimensional Bi-Directional xLSTM-UNet architecture to learn rich anatomical representations from 60,551 unlabeled brain MRI examinations spanning multiple MRI modalities. The pretrained model is subsequently adapted to downstream tasks through lightweight task-specific fine-tuning. We evaluate BrainNext on the Foundation Models for Medical Imaging (FOMO) 2025 Method Track, encompassing classification, segmentation, and brain-age estimation, where it achieved second place overall and ranked first in the meningioma segmentation task on the official FOMO 2025 challenge leaderboard, demonstrating strong transferability across heterogeneous neuroimaging tasks. These results highlight the potential of large-scale self-supervised pretraining to learn robust and transferable volumetric representations, establishing BrainNext as a scalable foundation model for diverse brain MRI applications.

Driver monitoring systems (DMS) increasingly rely on facial cues to infer drowsiness, distraction, and cognitive load in real time. Facial Action Units (AUs), grounded in the Facial Action Coding System (FACS), provide an objective and interpretable representation of such states, but their automatic detection in the driving context is complicated by low and variable illumination, partial occlusion, head-pose variation, and the subtlety and short duration of relevant AU activations. Existing AU detectors largely treat spatial appearance and temporal dynamics separately, limiting their ability to exploit self-supervisory signal from abundant unlabeled driving video. We propose the Twin Cycle Autoencoder (TCA), a spatiotemporal architecture composed of two coupled cycle-consistent autoencoder branches: a Spatial Cycle Autoencoder that disentangles AU-relevant appearance from identity through image-level cycle consistency, and a Temporal Cycle Autoencoder that enforces forward-backward consistency over latent AU trajectories to capture onset-apex-offset dynamics. The two branches are coupled through a cross-branch latent alignment loss and fused via an attention module before multi-label AU classification. We evaluate TCA on the DISFA and BP4D benchmarks and on an in-cabin naturalistic driving dataset, and observe consistent improvements over CNN-RNN, 3D-CNN, and graph-based AU baselines, particularly for low-intensity and rapidly transitioning AUs relevant to fatigue (AU45, AU43) and yawning (AU26). We further show the model sustains real-time throughput on an embedded Jetson Xavier NX platform, supporting its use in production-grade advanced driver assistance systems (ADAS).

Backdoor attacks pose a critical threat to neural network models, allowing attackers to implant a backdoor during the training phase by manipulating a small portion of the training data. In security-sensitive applications such as voice interaction for autonomous driving, the presence of backdoor attacks introduces substantial security risks. This study focuses on implementing backdoor defense measures for speech recognition models in run-time, taking into account the characteristics of audio signals. We propose SpeechGuard, the first online backdoor defense pipeline designed to identify and purify poisoned audio samples. Specifically, we improve STRIP method to perform adaptive perturbation injection to detect and filter poisoned samples, named as S-STRIP. More importantly, we further consider the purification of poisoned samples. We utilize time-frequency (T-F) masking to suppress the expression of trigger signals and autonomously generate masks based on an autoencoder. The two-stage processing prevents the backdoor in the model from being triggered, and even input speech carrying triggers can be accurately predicted. Extensive experimental demonstrate that SpeechGuard can accurately filter out poisoned samples. Through purification, it can significantly mitigate the backdoor threat while maintaining a certain prediction accuracy.

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.

We introduce TCAM-Diff, a novel 3D medical image generation model that reduces the memory requirements to encode and generate high-resolution 3D data. This model utilizes a decoder-only autoencoder method to learn triplane representation from dense volume and leverages generalization operations to prevent overfitting. Subsequently, it uses a triplane-aware cross-attention diffusion model to learn and integrate these features effectively. Furthermore, the features generated by the diffusion model can be rapidly transformed into 3D volumes using a pre-trained decoder module. Our experiments on three different scales of medical datasets, BrainTumour 128 x 128 x 128, Pancreas 256 x 256 x 256, and Colon 512 x 512 x 512, demonstrate outstanding results. We utilized MSE and SSIM to assess reconstruction quality and leveraged the Wasserstein Generative Adversarial Network (W-GAN) critic to assess generative quality. Comparisons with existing approaches show that our method gives better reconstruction and generation results than other encoder-decoder methods with similar-sized latent spaces.

Humans recognize movements effortlessly, even from noisy and complex visual input. But what information in the stimulus allows humans to rapidly classify movements? No framework has systematically compared different strategies of movement analysis to address this question. Here, we used videos of 16 daily activities from the MoVi dataset and compared three strategies: Temporal Movement Primitives (TMPs), which decompose movements into weighted sums of temporally smooth basis functions; Legendre polynomial coefficients, which project joint-coordinate trajectories onto an orthogonal polynomial basis; and Autoencoder latent embeddings. Legendre coefficients and TMPs achieved the highest classifier accuracy, followed by autoencoders. We found two discriminative features for movement classification. The most informative is the general posture of the body, the average spatial configuration that distinguishes one activity from another. Additionally, we identified 9 critical joints that are most predictive for movement classification. Interestingly, good classification accuracy did not automatically lead to good movement generation: when we reconstructed movements for each activity, TMPs preserved the temporal dynamics and produced perceptually natural motion, whereas reconstructions from Legendre coefficients retained only the average posture and appeared frozen. These results reveal a dissociation in how movement information is organized: the static configuration of the body suffices to classify what activity is performed, but the temporal dynamics of movement are required to reconstruct how it unfolds. This distinction clarifies which features the visual system may rely upon for rapid action recognition, and suggests that postural features could enable efficient movement screening in clinical applications, while dynamic information remain essential wherever movement generation is the goal.

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.

Time-series anomaly detection is increasingly important in IoT systems, sensor networks, and edge monitoring applications, where models must operate under strict constraints on memory, latency, and power consumption. While recent deep-learning approaches have improved detection accuracy, many remain computationally expensive and often fail to capture subtle anomalies due to limited multi-scale sensitivity. Autoencoders are widely used for anomaly detection because they reconstruct normal patterns well, leading to elevated reconstruction errors for anomalous inputs. Their simplicity and efficiency also make them suitable lightweight backbones for handling multi-scale inputs. To address these challenges, we propose a Lightweight MultiScale AutoEncoder (LMSAE) network for univariate time-series anomaly detection, designed to be compact and computationally efficient. LMSAE leverages the Discrete Wavelet Transform (DWT) to extract multi-scale features and employs a multi-scale loss function to improve sensitivity to subtle or hidden anomalies. Experiments on benchmark datasets demonstrate competitive or superior detection performance despite using significantly fewer parameters and a model size of less than 500 KB. LMSAE also achieves low-latency, low-power inference on the NVIDIA Jetson Nano, with 9x reduction in inference latency and 2x reduction in power consumption, making it ideal for edge deployment.

Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its own graph, equivariant, or frame-based architecture. Cross-domain training would mitigate per-domain data scarcity, but direct generation in 3D coordinate space cannot easily handle the heterogeneous structural priors of all three domains, and no prior latent autoencoder is simultaneously lossless and architecturally general across all three. We introduce SinAE, a single-architecture flow-matching autoencoder for molecules, crystals, and proteins, with vanilla Transformer encoder and decoder and no equivariant, graph, or domain-specific operators. Rather than requiring the encoder to capture fine-grained geometry, SinAE shifts the reconstruction burden into an iterative flow-matching decoder, achieving near-lossless reconstruction across domains and reducing reconstruction errors by orders of magnitude relative to prior latent baselines. The same per-token latent supports a standard Diffusion Transformer prior that reaches strong performance on molecular, crystal, and protein generation benchmarks. Joint molecule--crystal training strictly improves both domains, providing direct evidence of cross-domain transfer through a shared atomic latent. Code is available at https://github.com/BlueWhaleLab/SinAE .