Masked Autoencoders

The rapid advancement of high-throughput sequencing has led to large, high-dimensional omics datasets. Deep unsupervised learning architectures, particularly Autoencoders (AEs), are increasingly used for dimensionality reduction and representation learning in this domain. However, AEs are highly sensitive to architectural choices and hyperparameters, and unsupervised optimization typically relies on reconstruction loss, which may be a poor proxy for downstream utility. Exhaustive hyperparameter optimization (HPO) is computationally expensive, leading researchers to frequently rely on suboptimal default configurations. To democratize access to large-scale unsupervised HPO research, we introduce $\textbf{BBOmix}$, the first open-source tabular benchmark for unsupervised representation learning on real-world biological data. Our benchmark includes 105,000 evaluations across four AE architectures and seven multi-omics modalities from the TCGA and SCHC datasets. We quantify the correlation between reconstruction loss and downstream task performance and provide an extensive evaluation of state-of-the-art single-fidelity, multi-fidelity, and transfer learning HPO methods, establishing a rigorous baseline for future research in unsupervised biological representation learning.

Electro-Hydrostatic Actuators (EHAs) are widely used in aerospace and industrial systems, where timely detection of sensor anomalies is essential to ensure safe and reliable operation. However, the large volume and high sampling frequency of EHA sensor data pose challenges for accurate and efficient anomaly detection. Conventional statistical and classical machine-learning methods such as Z-score, Interquartile Range (IQR), Median Absolute Deviation (MAD), Isolation Forest, Gaussian Mixture, and k-means often fail to capture the temporal dependencies inherent in EHA signals, resulting in limited detection accuracy and elevated false-alarm rates. Furthermore, systematic evaluations of data-driven anomaly detection approaches for EHA systems remain scarce, particularly under varying operational conditions. This study presents an offline anomaly-detection framework for univariate EHA sensor signals, focusing on temperature and pressure data collected from a controlled test bench. The method employs a reconstruction-based Long Short-Term Memory (LSTM) autoencoder, calibrated and evaluated using validation-set reconstruction-error distributions. Performance is assessed across multiple fault-injection scenarios using accuracy, precision, recall, and F1-score, complemented by sensitivity analyses under varying operating conditions. The LSTM autoencoder achieved an average accuracy of 99.0%, precision up to 100%, recall between 90.2% and 99.6%, and F1-scores from 93.1% to 99.8%, demonstrating high detection sensitivity and a very low false-alarm rate across all evaluated sensors. These results highlight the feasibility of data-driven offline anomaly detection for EHAs. Future work will focus on adapting the developed framework for an online (real-time) environment.

We present in this paper a framework for the identification of control-affine reduced-order models (ROMs). The proposed method utilizes autoencoders (AEs) to transform the high-dimensional states, and potentially the high-dimensional inputs, into reduced latent ones suitable for control-affine state-space dynamics. This is achieved by simultaneous training of the AE and the state-space model. In addition, we extend the discrete ROM formulation to a sequence-based model, which processes state and input histories to improve prediction accuracy while preserving the control-affine structure. We motivate our framework by applying feedback linearization to the derived models, and we present guidelines for its efficient use. The proposed framework is assessed on two numerical examples and its performance is compared to a baseline model, where the AE identifies a latent space with linear state-space dynamics. The assessment involves evaluating the prediction accuracy of the ROM on test data and its effectiveness in controlling the system to a desired state or trajectory.

High-dimensional Hamiltonian systems play a central role in many scientific and engineering disciplines, with dynamics evolving on symplectic manifolds. Although deep learning provides powerful tools for constructing low-dimensional surrogates from data, the intrinsic symplectic structure is easily destroyed during model reduction. As a result, a standard autoencoder may produce latent coordinates that do not support a Hamiltonian flow, leading to unstable long-time prediction. In this paper, we first establish a universal approximation theorem for symplectic embeddings. Based on this theory, we propose symplecticity-preserving autoencoders (SpAE), in which the decoder is parameterized as a symplectic embedding and the encoder is constructed as the corresponding symplectic projection. This architecture is expressive enough to approximate nonlinear symplectic embeddings and the associated symplectic projections, preserves the symplectic structure exactly by construction, and can be trained by standard unconstrained optimization, thereby improving both reconstruction and prediction accuracy. Extensive experiments on high-dimensional lattice and particle systems demonstrate the effectiveness of the proposed method.

We present MeshFlow, a new method for generating artist-like 3D meshes. Current mesh generators often adopt Auto-Regressive (AR) next-token prediction, a natural choice given the discrete nature of mesh topology. However, AR methods scale poorly because the inference cost is quadratic in mesh size. They also require discretizing the vertex coordinates, which introduces quantization errors. To address these challenges, we introduce a Variational Autoencoder (VAE) that, supervised with a contrastive loss, represents both continuous vertex positions and discrete connectivity in a continuous latent space. This latent space is significantly more compact than prior token-based mesh representations. We then build a 3D generator based on a Rectified Flow transformer, generating all mesh vertices and edges in parallel. Our model generates meshes 18x faster than the fastest AR generator while also achieving excellent accuracy across standard mesh-generation metrics. Homepage: https://mesh-flow.github.io/, Code: https://github.com/facebookresearch/meshflow

Acquiring labeled medical image data is resource-intensive and a challenge further exacerbated in cross-domain scenarios where source and target datasets differ in imaging equipment, population, or clinical site. This study introduces XSSR (Cross-Domain Self-Supervised Representative Selection), a framework designed to minimize annotation effort in the target domain while maintaining robust segmentation performance. XSSR comprises three stages: first, a Masked Autoencoder (MAE) is trained on unlabeled source data to establish a shared embedding space without requiring target labels; second, a greedy selection algorithm scores unlabeled target samples based on a composite density, novelty, and diversity criterion; and third, a U-Net segmentation model is trained exclusively on the selected subset. The novelty-diversity trade-off parameter, alpha, is automatically calibrated by minimizing embedding-space coverage, eliminating manual tuning. We evaluate XSSR on three public benchmarks: Chest X-ray, RIGA+ retinal fundus imaging, and multi-site Prostate MRI, each under a fixed 5% annotation budget. XSSR achieves 99.3% of full-data performance on Chest X-ray using only 22 labeled samples, surpasses random selection by up to 2.5 Dice points on Prostate MRI, and consistently outperforms the CoreSet baseline by 0.4 to 1.2 Dice points across all datasets. Ablation studies indicate that diversity is the most influential scoring component, and per-site analysis shows that performance correlates with scanner similarity to the source domain.

Reconstruction-based methods are widely used for time series anomaly detection, where models are trained to reconstruct subsequences, and anomalies are identified through reconstruction errors. However, reported results are often hard to compare due to heterogeneous evaluation practices and underspecified inference procedures. In this paper, we revisit reconstruction-based anomaly detection in the univariate offline setting and study the role of the inference stride, which controls whether subsequences are processed as disjoint windows or with overlap. We propose a unified training, tuning, and multi-seed evaluation protocol on the curated TSB-AD benchmark, and study how overlapping inference affects anomaly detection performance for a range of reconstruction models, including PCA-based baselines, DLinear, an AutoEncoder, TimesNet, and Transformer variants. The results show that across all models, overlapping windows yield consistent improvements, with average relative gain up to +28%, and can alter method rankings. We further analyze variability across datasets, random seeds, and hyperparameter configurations. Finally, we complement the benchmark study with an evaluation on the full UCR archive using localization criteria aligned with sliding-window reconstruction. Overall, our results highlight that reconstruction-based anomaly detection performance depends not only on model architecture and training, but also on inference choices, motivating a clear and reproducible protocol. Our results show that reconstructionbased baselines achieve strong performance on both TSB-AD and UCR benchmarks, supporting them as competitive and practical approaches for univariate time series anomaly detection.

In robotics systems, vast amounts of visual data are easily captured at high resolution using low-cost, low-power hardware. Yet, limited bandwidth and on-device compute resources prevent full utilization when transmitted via conventional codecs like JPEG/MPEG. Newer codecs, like AV1/AVIF, improve the rate-distortion trade-off, but demand far more resources for encoding, impractical without custom ASICs. Recent asymmetric autoencoders deliver high quality under extreme power and bandwidth constraints, but add prohibitive decoding cost and use bespoke formats that ignore decades of infrastructure built around standards like JPEG. To address these limitations, we introduce a compression framework for cloud robotics based on a Sensor Embedded Autoencoder paired with a One-Time Transcode for Efficient Reconstruction (SEAOTTER). Because the sensor, cloud, and consumer stages face very different power and bandwidth budgets, SEAOTTER combines the compactness of a learned latent with the broad usability of a standard JPEG file. Since naive transcoding degrades performance, we propose a learnable JPEG color and quantization transform that enables increased accuracy for global, dense, and vision-language-based perception. Using SEAOTTER, we train both general-purpose and task-aware transcoding pipelines for a pre-trained, frozen encoder. At a compression ratio of 200:1 and compared to AVIF, we observe 7 times faster encoding, 3.5 times faster decoding, and +8% ImageNet top-1 accuracy, while retaining compatibility with JPEG infrastructure. Our code is available at https://github.com/UT-SysML/seaotter .

Our work presents a method for ECG segmentation and arrhythmia detection using Tiny Machine Learning (TinyML) models for real-time, on-device inference on resource-constrained embedded systems. We develop INT8 quantized autoencoder-based TinyML models with minimal layers and parameters for embedded deployment. These models are evaluated using a custom dataset derived from the MIT-BIH Arrhythmia Database and validated in both PC-based simulations and on-device environments. For the evaluations, over 95,000 ECG segments are processed on an ESP32-S3 microcontroller running the TensorFlow Lite Micro runtime. Post-evaluation, detailed analysis, including annotation-wise and record-wise failure analysis, is conducted to characterize model behavior across diverse ECG morphologies and rhythm patterns and to explain missed detections. In several cases, apparent misclassifications may correspond to early or subtle anomaly patterns labeled as normal in the reference annotations, highlighting the model's sensitivity. A refined evaluation by filtering out ambiguous cases in the dataset shows that the best-performing DNN-based autoencoder achieves a recall of 84%, an F1-score of 79%, a model size of approximately 180 KB, and an inference latency of 9 ms on-device. These results demonstrate the feasibility of low-power, privacy-preserving embedded wearable systems capable of performing accurate arrhythmia detection entirely on-device.

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.

Accurately modeling the macroscopic dynamics of high-dimensional microscopic systems is of broad interest across the sciences. Many data-driven approaches learn a low-dimensional latent state through an autoencoder trained for pointwise input reconstruction. These methods typically assume a fixed ordering of microscopic degrees of freedom in the input. However, in many settings, such as particle systems, the microscopic state is inherently unordered. This motivates an autoencoder framework that learns permutation-invariant latent representations. To this end, we adopt a permutation-invariant encoder and design the decoder to reconstruct the mass distribution centered at the observed points rather than per-sample reconstruction. We then jointly learn the macroscopic dynamics of the observables together with the latent states. We demonstrate the effectiveness and robustness of the proposed method across a range of microscopic settings, including learning the energy dynamics in interacting particle systems, predicting mixing dynamics in Lennard-Jones fluids, and modeling the stretching dynamics from video data of polymers moving in an elongational force field.

Cross-Reynolds generalisation in neural PDE solvers remains poorly characterised. On the canonical forced 2D Navier-Stokes benchmark, a trained Fourier Neural Operator reaches 46.68% relative L2 error under a 10x Reynolds-number shift, yet zero-forward-model retrieval baselines already improve to 41-42%. This suggests representation geometry as a major organising variable among the tested methods. We test this hypothesis through ConvAE-Relay, which matches states in a source-trained convolutional autoencoder latent space and borrows dynamics from a source-regime database, achieving 38.34+/-0.07% using only a source-regime database and no target-regime fitting, labels, or database entries. A 2x2 ablation isolates matching quality as dominant over the update rule. Oracle experiments confirm that source-regime dynamics directions remain transferable (cosine similarity ~0.84) when matching stays on-manifold; autoregressive drift is the primary bottleneck (~12 percentage points). From the learned-prediction side, a U-Net with multi-scale skip connections achieves 34.72+/-0.60%, consistent with the retrieval-side finding that local, multi-scale representations organise cross-Reynolds transfer among tested methods. All claims are scoped to this benchmark.

Patient-voiced clinical-triage benchmarks report high under-triage rates for consumer LLMs for constrained multiple-choice output, yet the same cases score differently with free-text. We ask whether output format changes the model's \emph{clinical representation} or only the mapping from a preserved representation to an answer. Using sparse-autoencoder (SAE) features in Gemma 3 4B/12B IT and Qwen3-8B, we find the same medical features fire on the shared clinical narrative under both formats but go {silent} at the multiple-choice decision token in all the cases at every model. Three independent methods (natural-language autoencoder verbalization, decision-token logit attribution, and top-feature characterization) agree that scaffold and format features, but not medical features, drive the decision logits. Behaviorally, the multiple-choice penalty inverts under both structured and natural-language input, option-order shuffle rules out positional bias, and the gap is dominated by off-by-one decision (the model picks an adjacent acuity letter to the gold answer) rather than knowledge failure. Thus, the failure originates in the output format and not in the clinical representation.

Data stream processing has become a landmark in modern machine learning applications, with concept drifts and novel class appearances posing the primary challenges faced by sophisticated recognition methods. This work proposes an unsupervised concept drift detection method that identifies shifts in known class distributions based on the reconstruction errors of an autoencoder, while also enabling the recognition of novel class samples through density estimation of a proxy representation of samples. Using mirrored autoencoders allows for independent incremental adaptation to changing problem distributions for the two considered tasks, resulting in continuous adjustment to evolving concepts and reliable recognition of unknown samples. Conducted experiments used a diverse set of synthetic tabular data streams, where both concept drifts and the emergence of novelties were observed. The results show that the proposed approach is competitive with current state-of-the-art unsupervised drift detectors and novelty classifiers.

Methods to represent literary texts as graphs or sequences of graphs mainly focus on representing character interactions, and often overlook another crucial aspect: the textual context in which characters interact. We introduce Dynamic Heterogeneous Character Networks (DHCNs), which organize long novels into temporally localized heterogeneous graphs that align characters with their textual contexts. We extract around 20,000 DHCNs from Project Gutenberg, and propose GraphLit, a self-supervised learning framework that learns rich literary representations through a masked graph autoencoder objective. Across a wide range of 12 character-related tasks, GraphLit improves over text-only, graph-only and prior hybrid baselines. Ablations over different kinds of dynamic graph structures and architectural elements show that grounding characters in their context is the main performance driver, while explicitly encoding narrative order and character relationships provide task-dependent improvements. Finally, we demonstrate the applicability of DHCNs and GraphLit for literary analysis by studying the link between narrative non-linearity and dynamic social features.

An important challenge in texture recognition is the limited amount of data for training frequently found in real-world applications. In computer vision in general, a successful strategy to mitigate this issue is the use of a pretraining stage where the neural network learns to identify relations between parts of the data in a self-supervised manner. A well-established framework in this direction is masked autoencoder. Nevertheless, these models usually rely on computationally intensive architectures, such as vision transformers. In the particular case of texture images, most of the relevant information is compacted within a delimited area around each pixel, which suggests that capturing long-range dependence via the attention mechanism may be unnecessary. Based on that assumption, here we propose a framework where the pretraining model is a convolutional autoencoder. To leverage the rich information conveyed by texture patterns, we employ deep filters coupled with Fisher vector pooling. In this way, we improve the performance of texture recognition without adding significant computational burden. Our approach is compared with several state-of-the-art methods in different texture databases, confirming its potential both in terms of classification accuracy and computational complexity.

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.

While multimodal data integrating diverse imaging and clinical tabular records is crucial for accurate medical diagnosis, the arbitrary absence of specific modalities is prevalent in clinical practice, severely degrading the performance of multimodal models. Existing methods either discard missing modalities, leading to information loss, or struggle to synthesize them without capturing complex inter-modal dependencies. To address these limitations, we propose a novel Context-driven Missing-Modality Learning (CMML) framework, which sequentially performs modality synthesis and semantic alignment to achieve robust diagnosis under arbitrary missing conditions. Specifically, we design a Cascade Residual Transformer-based Autoencoder (CRTA) that leverages learnable context tokens acting as dataset-level semantic prior to capture inter-modal dependencies and synthesize key missing representations. These representations are further enriched by modality-specific memory banks. To resolve the discrepancy between original available and synthesized representations, we transform the learned context tokens into instance-adaptive semantic references by infusing multimodal representations from the CRTA's outputs. This reference guides the alignment of heterogeneous modality representations into a unified space, where class-aware contrastive refinement is finally applied to explore discriminative diagnostic cues. Extensive evaluations on skin lesion (Derm7pt), ocular disease (ODIR), and meningioma (MEN) datasets demonstrate that CMML significantly outperforms state-of-the-art (SOTA) methods, yielding AVG AUC improvements of 1.26%, 0.97%, and 1.32%, respectively.

Time series anomaly detection (TSAD) has long been a hot research topic in data mining due to its various applications. Recent studies challenge the effectiveness of popular deep learning methods for TSAD, suggesting their failure in detecting subtle and prolonged anomalies. Outlier Exposure (OE) and Masked Autoencoder (MAE) emerge as two promising paradigms (classification and reconstruction) for solving the above problems. However, OE-based methods are constrained by poor generalization, while MAE-based methods are limited by masking misalignment issues. To address these limitations, this paper proposes a novel framework, CoAD, which unifies the two paradigms to leverage their complementary strengths while mitigating their respective weaknesses. In this framework, the classification module generates probability-informed soft masks for the reconstruction module, which in turn alleviates the generalization problem of the classification module. This cooperative design enables CoAD to effectively detect subtle and complex anomalies that are often overlooked by existing methods. Additionally, the classification module is carefully designed to resolve issues related to improper classification granularity and the neglect of frequency information. Extensive experiments on high-quality benchmark datasets, conducted under rigorous evaluation protocols, demonstrate that CoAD significantly outperforms both state-of-the-art deep learning and traditional data mining methods, highlighting the potential of deep learning in TSAD. Moreover, CoAD is lightweight and substantially faster than existing SOTA methods, demonstrating its practical value for large-scale, real-time applications.

The rapid proliferation of Internet of Things (IoT) devices has created an urgent demand for adaptive, resource-efficient Intrusion Detection Systems (IDS) capable of handling dynamic and evolving cyber threats. This paper investigates AOC-IDS, a state-of-the-art autonomous online IDS published at IEEE INFOCOM 2024, which employs an Autoencoder (AE) with Cluster Repelling Contrastive (CRC) loss and an autonomous Gaussian-based decision module. We first successfully replicate AOC-IDS on the UNSW-NB15 benchmark, achieving 89.39% accuracy in close agreement with the published 89.19%. We then identify four key limitations: class imbalance, unreliable pseudo-label generation, limited generalization, and computational overhead for IoT deployment, and propose targeted improvements for each. Our XGBoost-BalSamp method achieves 95.45% accuracy on UNSW-NB15, a gain of 6.26% over the baseline. Our combined deep learning approach (PseudoFilter, MixupAug, and LiteAE) achieves a best-run accuracy of 90.88% (F1: 91.45%), surpassing the base paper while reducing model parameters by 55%.These results demonstrate that targeted improvements to AOC-IDS yield consistent accuracy gains while improving practical deployability on IoT edge devices.

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.

Low-dimensional embeddings are widely used as visual summaries of high-dimensional data and to enable downstream scientific discoveries. Yet, popular nonlinear dimension reduction methods, such as t-SNE and UMAP, are often selected based on visual appeal alone and without rigorous quantitative validation. A major reason is that manifold embeddings typically do not provide an out-of-sample map nor an inverse back to the original feature space; this makes held-out validation, the gold standard in supervised learning, all but impossible. To address these challenges, we develop a novel framework, MEDAL (Manifold Embedding Distillation via Autoencoder Learning), which distills a fitted manifold embedding into a reusable encoder--decoder model. MEDAL trains a constrained autoencoder whose bottleneck exactly matches any teacher embedding while the decoder reconstructs the original input; this yields an explicit map for new samples, an approximate inverse, and a pointwise reconstruction-based measure of distortion in the manifold space. This converts static manifold embeddings into models that can be evaluated on held-out data, enabling quantitative validation including comparing different dimension reduction methods as well as hyperparameter tuning. Across multiple benchmark and scientific case studies, we show that MEDAL enables held-out validation to determine optimal manifold embeddings and hyperparameters, reveals biologically coherent regions that are difficult to preserve in two dimensional embeddings, and detects distribution shift when new samples are mapped into a fixed reference manifold. MEDAL provides a general validation wrapper to any existing dimension reduction technique that will improve the rigor and reliability of dimension reduction in scientific workflows.

Real-world image super-resolution aims to recover high-quality images from complex and unknown real-world degradations. However, existing generative Real-ISR methods largely inherit the dense latent representations and quadratic-cost global modeling paradigm developed for high-resolution image synthesis, causing computation, memory usage, and inference latency to scale unfavorably with resolution and thus limiting practical deployment. We argue that the key bottleneck lies not in insufficient restoration priors, but in excessive token redundancy and costly token interactions during high-resolution restoration. Motivated by this observation, we revisit Real-ISR from the perspectives of compact latent representation and linear-complexity modeling, and propose SANA-SR, an efficient one-step restoration framework. Specifically, SANA-SR employs a deep compression autoencoder with a 32x compression ratio to drastically reduce latent tokens while preserving restoration-relevant structures and textures. On top of this compact latent space, we introduce a linear-attention DiT with LoRA fine-tuning, enabling efficient high-resolution restoration with linear-complexity token mixing. Extensive experiments on all benchmark datasets demonstrate that SANA-SR achieves highly competitive and often superior quantitative performance against existing methods, while restoring clearer and more realistic textures. Moreover, after pruning, the deployed model runs in 0.019s with 407.95G MACs and 344M parameters, highlighting its strong potential for practical mobile deployment.

Video representation learning has seen tremendous progress in recent years. This has been driven by many factors, including the scale of training and the success of visual models trained contrastively with language. While these factors have pushed the boundaries of what video models can do, they also introduce their own set of limitations: first, scaling video models can reach prohibitive costs and second, learning from language restricts the range of concepts that can be learned to those in captions. As a result, video models still struggle with temporal understanding. In this paper we propose a novel approach that uses motion as the central modality for video representation. In particular, given the motion in a video in the form of point-tracks, we use a masked-autoencoder to mask some of the tracks and train the autoencoder to reconstruct the missing tracks. This allows us to learn a representation in a self-supervised manner. We show that using motion to represent videos actually addresses both of the core limitations of video technology. First, it allows us to massively reduce the scale of training data, as motion is inherently appearance-independent and hence needs fewer examples to generalize well. Second, motion allows us to bypass the language-dependent training paradigm, learning better fine-grained concepts. The result is an embedding that we call TIME (Temporally Informed Motion Embedding), a representation trained exclusively on synthetic motion data. We test this embedding on a wide set of tasks in a zero-shot manner. We observe that without bells and whistles, performance is on par with state-of-the-art models using up to 4 orders of magnitude less training data. This is a stepping stone towards a new paradigm of video models that are both more temporally aware as well as more scalable.

Representation Autoencoders (RAEs) leverage frozen vision foundation models (VFMs) as tokenizer encoders, providing robust high-level representations that facilitate fast convergence and high-quality generation in latent diffusion models. However, freezing the VFM inherently constrains its spatial reconstruction capacity, limiting fine-grained generation and image editing; in contrast, incorporating reconstruction-oriented signals via fine-tuning disrupts the pretrained semantic space and degrades generative fidelity. To address this trade-off, we propose DecQ, a simple yet effective framework for RAEs. Specifically, DecQ introduces lightweight detail-condensing queries that extract fine-grained information from intermediate VFM features through condenser modules. These queries are incorporated into the decoder to support reconstruction and are jointly generated with patch tokens during generative modeling. By aggregating information from both shallow and deep layers, DecQ effectively mitigates the reconstruction--generation trade-off, improving both reconstruction quality and generative performance. Our experiments demonstrate that: (1) with only 8 additional queries and 3.9% extra computation, DecQ improves reconstruction over the frozen DINOv2-based RAE, increasing PSNR from 19.13 dB to 22.76 dB; and (2) for generative modeling, DecQ achieves 3.3$\times$ faster convergence than RAE, attaining an FID of 1.41 without guidance and 1.05 with guidance.

Learning to generalise from limited data is a fundamental challenge for both artificial and biological systems. A common strategy is to extract reusable structure from abundant unlabelled data, enabling efficient adaptation to new tasks from limited labelled data. This two-stage paradigm is now standard in modern training pipelines, where pretraining is followed by fine-tuning or linear probing. We provide an analytical model of this process: structure extraction is formalized as principal component analysis on unlabelled data, and downstream learning as linear regression on a separate labelled dataset. In the high-dimensional regime, we derive exact expressions for training and generalisation error showcasing their dependence on representation dimensionality, unlabelled and labelled sample sizes, and task alignment. Our results show that pretrained representations strongly influence downstream generalisation, and we characterize the optimal representation size as a function of task parameters: with abundant pretraining data but scarce downstream data, maximally compressed representations are optimal, whereas with limited pretraining data, higher-dimensional representations generalise better. Furthermore, we establish an exact trade-off between pretraining and supervision, quantifying how much unlabelled data is required to replace a single labelled sample. Beyond our idealised model, we observe similar phenomenology in autoencoders and pretrained LLMs. Altogether, we highlight that optimising representation size is critical, giving conditions for when compression during pretraining improves generalisation.

Inferring unknown initial states in shock-dominated compressible flows from sparse and noisy measurements is a challenging ill-posed inverse problem due to nonlinear wave interactions and limited sensing. In this work, we develop a non-intrusive reduced-order modeling framework for efficient Bayesian initial-state inversion with uncertainty quantification. The framework combines a convolutional autoencoder with a learned latent-space forward operator. The autoencoder compresses high-dimensional flow fields into a compact nonlinear latent representation, while the forward operator predicts final-time latent states from encoded initial conditions. This AE-ROM surrogate enables rapid forward evaluations and is embedded within a No-U-Turn Sampler (NUTS) for posterior exploration. The framework is demonstrated using 500 high-fidelity Sod shock tube simulations generated through Latin hypercube sampling and solved using a fifth-order WENO scheme. The inverse problem seeks to recover unknown left and right density and pressure states from sparse noisy observations of final-time density and pressure fields. Results show that the AE-ROM accurately reconstructs key shock-tube structures, including the rarefaction wave, contact discontinuity, and shock front. A latent dimension of 32 provides an effective balance between reconstruction accuracy and reduced-space compactness, while 250 training simulations are sufficient for accurate reconstruction. Increasing observation density significantly contracts posterior uncertainty, reducing the mean posterior standard deviation by approximately 78% for density and 76% for pressure. Overall, the proposed framework provides a computationally efficient and uncertainty-aware approach for inverse analysis of shock-dominated flows, with potential extensions to multidimensional compressible-flow and digital-twin applications.

Latent representations are at the heart of the majority of modern generative models. In the audio domain they are typically produced by a neural-audio-codec autoencoder. In this work we introduce SAME (Semantically-Aligned Music autoEncoder), an autoencoder for stereo music and general audio that reaches a 4096$\times$ temporal compression ratio while maintaining reconstruction quality and downstream generative performance. We achieve this by combining a tranformer-based backbone with set of semantic regularisation approaches, phase-aware reconstruction losses and improved discriminator designs. The architecture delivers substantial computational cost benefits, through both its high compression ratio and its reliance on well-optimised transformer primitives. Two variants (a large SAME-L and a CPU-deployable SAME-S) are released in open-weights form.

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

A lightweight and reproducible denoising pipeline for high-throughput Raman spectroscopy is presented. The approach relies on a one-dimensional convolutional autoencoder trained using a Noise2Noise strategy, requiring neither external spectral libraries nor high signal-to-noise reference spectra for training. From a reduced training subset composed of repeated short-exposure acquisitions, the model learns to reconstruct Raman spectra while efficiently suppressing stochastic noise. The method is evaluated on a heterogeneous mineral sample, using both quantitative spectral fidelity metrics (RMSE, SNR, SSIM) and task-oriented criteria based on unsupervised K-means classification. Results demonstrate that integration times as short as 5 ms per spectrum, which are typically insufficient for reliable interpretation, yield denoised spectra with high fidelity to the reference data while preserving chemically coherent maps. This work provides a practical trade-off between spectral quality and acquisition speed, enabling fast, adaptable Raman workflows compatible with routine laboratory use. It also offers a transferable framework for other one-dimensional spectroscopic modalities.

Representation Autoencoders (RAE) replace traditional VAE with pretrained vision encoders. In this paper, we systematically investigate several design choices and find three insights which simplify and improve RAE. First, we study a generalized formulation where the representation is defined as sum of the last k encoder layers rather than solely the final layer. This simple change greatly improves reconstruction without encoder finetuning or specialized data (e.g., text, faces). Second, we study the prevalent assumption that RAE (using pretrained representation as encoder) replaces representation alignment (REPA), which distills the same representation to intermediate layers instead. Through large-scale empirical analysis, we uncover a surprising finding: RAE and REPA exhibit complementary working mechanisms, allowing the same representation to be used as both encoder and target for intermediate diffusion layers. Finally, the original RAE struggles with classifier-free guidance (CFG) and requires training a second, weaker diffusion model for AutoGuidance (AG). We show that REPA itself can be viewed as x-prediction in RAE latent space. By simply re-parameterizing the output of the DiT model, it can provide guidance for "free". Overall, RAEv2 leads to more than 10x faster convergence over the original RAE, achieving a state-of-the-art gFID of 1.06 in just 80 epochs on ImageNet-256. On FDr6, RAEv2 achieves a state-of-the-art 2.17 at just 80 epochs compared to the previous best 3.26 (800 epochs) without any post-training. This motivates EPFID@k (epochs to reach unguided gFID < k) as a measure of training efficiency. RAEv2 attains an EPFID@2 of 35 epochs, versus 177 for the original RAE. We also validate our approach across diverse settings for text-to-image generation and navigation world models, showing consistent improvements. The code is available at https://raev2.github.io.

Sparse autoencoders (SAEs) are a core interpretability tool for large language models, and progress on SAE architectures depends on benchmarks that reliably distinguish better SAEs from worse ones. We audit the SAE quality metrics in SAEBench, the de-facto standard SAE evaluation suite, through three complementary lenses: reseed noise on a fixed SAE, ground-truth correlation on synthetic SAEs, and discriminability across training trajectories. We find that two of these metrics, Targeted Probe Perturbation (TPP) and Spurious Correlation Removal (SCR), fail multiple lenses at their canonical settings and should not be used to evaluate SAEs. The other metrics show higher reseed noise and lower discriminability than the field assumes. The sae-probes variant of $k$-sparse probing is the most reliable metric we tested, but even sae-probes struggles to separate variants of the same SAE architecture. Our results show the field needs better SAE benchmarks.

Anomaly detection in batch processes is hindered by transient dynamics, scarce fault labels, and reliance on single-modality sensor data. This work introduces UTOPYA (Unified Temporal Observation for Physics-Informed Anomaly Detection and Time-Series Prediction), a 15.2M-parameter multimodal framework that jointly addresses anomaly detection, time-series prediction, and phase classification in batch distillation by fusing eight data modalities through Feature-wise Linear Modulation (FiLM) conditioned cross-modal attention and gated fusion. A physics-informed regularisation scheme introduced in this work enforces temporal smoothness and thermodynamic monotonicity, while curriculum learning introduces training samples in order of physical difficulty. On the 119-experiment multimodal batch distillation dataset of Arweiler et al. (2026), UTOPYA achieves a window-level test AUROC of 0.832 and 0.874 under multi-signal experiment-level scoring, substantially outperforming four external baselines (PCA, autoencoder, Isolation Forest, and LSTM autoencoder) evaluated under identical conditions (+0.147 window-level AUROC over the best baseline). A multimodal ablation over 15~architectural configurations shows that static context via FiLM conditioning is the key enabler, lifting experiment-level multi-signal AUROC by +0.145 over the unimodal baseline (0.729 to 0.874). Separately, a training ablation across 14 design choices reveals that several widely-adopted techniques, including instance normalisation, Mixup, ensembling, test-time augmentation, and stochastic weight averaging, fail to improve or actively degrade generalisation in this data-scarce setting. These negative results expose a fundamental tension between smoothing-based regularisation and anomaly detection, providing practical guidance for multimodal process monitoring deployment.

Generative data augmentation with latent diffusion models is a promising strategy for addressing class imbalance in medical imaging, yet current approaches focus on perceptual fidelity and domain-specific autoencoder fine-tuning while neglecting a more fundamental bottleneck. We identify and formalize the learnability gap: large-scale pretrained autoencoders faithfully encode discriminative features for medical classification, as evidenced by near-lossless performance in reconstruction space, yet their latent representations are structured in ways that are difficult for classifiers to learn from. Across five autoencoder families and four medical benchmarks spanning chest radiography, dermatoscopy, computed tomography, and echocardiography, we show that this gap persists regardless of architecture, initialization strategy, or hyperparameter tuning, and that medical-domain fine-tuning of the autoencoder does not close it. To probe and partially narrow the gap, we develop noise-conditioned latent classifiers with FiLM layers and image-space distillation that offer 64x throughput and 120x memory gains over image-space models while serving as diagnostic tools for latent space quality. Our analysis provides a new framework for evaluating autoencoder latent spaces and identifies their structure, rather than their fidelity or domain specificity, as the primary obstacle to closing the performance gap between real and synthetic medical training data.

Latent diffusion models have emerged as the dominant paradigm for many generation tasks including audio generation such as text-to-audio, text-to-music and text-to-speech. A key component of latent diffusion is an autoencoder (VAE) that compresses high-dimensional signals into a low frame rate continuous representation that is conducive for downstream prediction. Regularizing these VAEs is challenging, as there is a trade-off between over-regularized (poor output quality) and under-regularized (difficult to predict) latent representations. We propose a framework for studying this trade-off through compression and train Audio VAEs at specific bitrates via target-KL regularization. This allows direct comparison to well-studied discrete neural audio codec models, and the construction of rate-distortion curves for audio VAEs. We evaluate the impact of target-KL regularization on text-to-sound generation and find that sweeping compression rates is helpful in identifying the optimal generation setting.

Despite their ubiquity, variational autoencoders (VAEs) inherently suffer from posterior collapse, a failure mode in which latent variables are effectively ignored. This failure arises because explicit prior imposition drives optimization toward loss landscape regions corresponding to uninformative latent representations. Here, we introduce Entropic Autoencoders (EAEs), a framework in which reconstruction loss is the only explicit objective, and entropy generates the latent variables' prior implicitly through a free energy-minimizing ensemble of encoders. This ensemble biases learning toward high-volume regions of near-optimal solutions, while decoder updates direct the search trajectories toward informative latent representations. We demonstrate that EAEs mitigate posterior collapse by learning non-Gaussian, multimodal latent distributions that yield diverse, data-consistent generations and preserve different forms of underlying structure in the data. As a proof-of-concept, we show that an EAE captures a superposition of the known low-dimensional dynamics of a reaction-diffusion process. Then, we show that an EAE identifies implicit categorical distinctions in MNIST latent representations, and displays a hierarchical understanding of facial structure on the CelebA dataset, from an "all-human" face to individual-dependent features.

What does it mean to create a new concept, rather than retrieve a familiar one? Repeatedly sampling a generative model at the same prompt produces variations with similar styles and typical content. We propose that creativity is the production of stimuli that are unfamiliar to an adaptive observer at first sight, but quickly learnable from a few exposures. We formalize this as a Creator-Appraiser pair: a Creator generates a candidate, an Appraiser adapts to it for a few inner-loop learning steps, and the Appraiser's improvement becomes the reward the Creator optimizes through. We instantiate the framework with diffusion as the Creator, an autoencoder Appraiser on MNIST, and a CLIP Appraiser with a low-rank adapter for natural images. The diffusion model remains frozen with no additional language conditioning; the meta-learning gradient is enough to produce both stylistic variations and concept compositions that the base model does not generate on its own.

Large-scale pre-trained vision-language models like CLIP demonstrate remarkable zero-shot performance across diverse tasks. However, fine-tuning these models to improve downstream performance often degrades robustness against distribution shifts. Recent approaches have attempted to mitigate this trade-off, but often rely on computationally expensive text-guidance. We propose a novel method for robust fine-tuning, SAE-FT, which operates only on the model's visual representations. SAE-FT regularizes changes to these representations by penalizing the addition and removal of semantically meaningful features identified by a Sparse Autoencoder trained on the pre-trained model. This constraint prevents catastrophic forgetting and makes the fine-tuning process interpretable, enabling direct analysis of semantic changes. SAE-FT is both mechanistically transparent and computationally efficient, matching or exceeding state-of-the-art performance on ImageNet and its associated distribution shift benchmarks. Code is publicly available at: https://github.com/Fabian-Mor/sae-ft.

We introduce Tadpole, a novel foundation model for three-dimensional partial differential equations (PDEs) that addresses key challenges in transferability, scalability to high dimensionality, and multi-functionality. Tadpole is pre-trained as an autoencoder on synthetic 3D PDE data generated by an efficient online data-generation framework. This enables large-scale, diverse training without storage or I/O overhead, demonstrated by scaling to an equivalent of hundreds of terabytes of training data. By autoencoding single-channel spatial crops, Tadpole learns rich and transferable representations across heterogeneous physical systems with varying numbers of state variables and spatial resolutions. Although pre-trained solely as an autoencoder, Tadpole can be efficiently applied for multiple downstream tasks beyond reconstruction, including dynamics learning and generative modeling. For dynamics learning, we propose a novel parameter-efficient fine-tuning strategy that integrates low-rank adaptation, latent-space transformations, and reintroduced skip connections, achieving accurate temporal modeling with a minimal number of trainable parameters. Tadpole demonstrates strong fine-tuning performance across various downstream tasks, highlighting its versatility and effectiveness as a foundation model for 3D PDE learning. Source code and pre-trained weights of Tadpole are available at https://github.com/tum-pbs/tadpole

As Industry 4.0 accelerates the integration of Cyber-Physical Systems (CPS) in manufacturing, robust anomaly detection has become critical for ensuring process safety and security. Current data-driven approaches typically employ "product-agnostic" or global models trained on the aggregate of all normal operating data. However, modern industrial facilities frequently operate under diverse product grades. While computationally simple, these global models inherently expand their decision boundaries to accommodate the variance of multiple modes, creating a "blind spot" where subtle anomalies or targeted cyber-physical attacks may be masked by the wide acceptance region of the model. In this work, we first demonstrate that the vulnerability described above is present in global-agnostic models operating across multiple product grades. We then present a Product-Aware Autoencoder as a principled mitigation that restricts the learning domain to grade-specific distributions. While this approach reduces the identified blind-spot risk, we do not claim it as the optimal mitigation among all possible alternatives. We rigorously validate this approach against a Global Agnostic baseline using the Extended Tennessee Eastman Process (TEP) benchmark. Our empirical results indicate that the Product-Aware framework performs comparably to the global baseline on standard detection metrics, while offering improved robustness to product-grade-specific operating modes. Most critically, stress tests simulating our hypothetical attack scenarios reveal that while the global model fails to detect operational deviations in 77.8% of the scenarios, the product-aware system achieves 100% detection accuracy. These findings suggest that, in flexible manufacturing environments, generalized anomaly detectors can pose non-trivial security risks, motivating a shift toward mode-aware diagnostic architectures.

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

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

Recent 3D generative models can synthesize high-quality assets, but their outputs are typically static: they lack the skeletal rigs, joint hierarchies, and skinning weights required for animation. This limits their use in games, film, simulation, virtual agents, and embodied AI, where assets must not only look plausible but also move plausibly. We introduce Rigel3D, a generative method for animation-ready 3D assets represented as rigged meshes. Unlike post-hoc auto-rigging methods that attach rigs to completed shapes, our method jointly models geometry and rig structure through coupled surface and skeleton structured latent representations. A rig-aware autoencoder decodes these representations into mesh geometry, skeleton topology, joint coordinates, and skinning weights, while a two-stage latent generative model synthesizes both surface and skeleton representations for image-conditioned generation. To support downstream animation workflows, we further introduce an open-vocabulary joint labeling module that embeds generated joints into a shared vision-language space, enabling correspondence to arbitrary retargeting templates. Experiments on large-scale rigged asset datasets demonstrate that our method generates diverse, high-quality animation-ready assets and outperforms existing rigging baselines across multiple metrics.

The general-purpose nature of Large Language Models (LLMs) presents a significant challenge for domain-specific applications, often leading to out-of-domain (OOD) interactions that undermine the provider's intent. Existing methods for detecting such scenarios treat the LLM as an uninterpretable black box and overlook the internal processing of inputs. In this work we show that layer transitions provide a promising avenue for extracting domain-specific signature. Specifically, we present several lightweight ways of learning on internal dynamics encoded using a sparse autoencoder (SAE) that exhibit great capability in distinguishing OOD texts. Building on top of SAEs representation transitions enables us to better interpret the LLM internal evolution of input processing and shed light on its decisions. We provide a comprehensive analysis of the method and benchmark it with the gemma-2 2B and 9B models. Our results emphasize the efficacy of the internal process in capturing fine-grained input-related details.

The accurate recovery of constituent-level optical properties from integrating sphere measurements is a central analytical challenge in pharmaceutical analysis, food science, and biomedical diagnostics. Neural network autoencoders can extract spectrally resolved absorption and scattering coefficients for each constituent without prior knowledge, but their fully connected encoders bind learned features to absolute wavelength indices, causing accuracy loss under spectrometer calibration drift or hardware exchange. This work introduces the Bin Latent Transformer (BiLT)-Autoencoder, in which the dense encoder is replaced by a cross-attention scanner: 16 learnable probe vectors query a convolutional feature map, aggregating morphological spectral information independently of absolute wavelength position. A physics-constrained linear decoder with enforced absorption/scattering separation and a three-phase curriculum augmentation strategy complete the architecture. On a liquid phantom benchmark (intralipid and two ink absorbers; 496 samples), the model achieves $R^2 = 0.979$ and $0.975$ for $μ_a(λ)$ and $μ_s'(λ)$, respectively, on held-out test spectra, maintaining $R^2 > 0.90$ for $μ_a$ and $R^2 \approx 0.99$ for $μ_s'$ across the full tested shift range of $\pm 10$ spectral bands. The model generalises to a simulated spectrometer with a broader instrument line shape (${\approx}24$nm FWHM) without retraining, retaining $R^2 \approx 0.96$ and $0.974$ for the two channels. Attention map analysis reveals a physically interpretable two-component probe strategy: sparse anchor probes at absorption-edge wavelengths combined with a diffuse, SNR-driven ensemble at the high-transmittance long-wavelength region, which recruits additional probes dynamically under noise to provide implicit spectral averaging.

Recent published evidence from frontier laboratories shows that contemporary AI models can recognise evaluation contexts, latently represent them, and behave differently under those contexts than under deployment-continuous conditions. Anthropic's BrowseComp incident, the Natural Language Autoencoder findings on SWE-bench Verified and destructive-coding evaluations, and the OpenAI / Apollo anti-scheming work all document instances of this phenomenon. We argue that these findings create a claim-validity problem for safety conclusions drawn from frontier evaluations. We introduce the Evaluation Differential (ED), a conditional divergence in a target behavioural property between recognised-evaluation and deployment-continuous contexts, define a normalised effect-size form (nED) for cross-property comparison, and prove that marginal evaluation scores cannot identify ED. We develop a typology of safety claims (ED-stable, ED-degraded, ED-inverted, ED-undetermined) by their warrant-status under documented divergence, and specify TRACE (Test-Recognition Audit for Claim Evaluation), an audit protocol that wraps existing evaluation infrastructure and produces restricted claims rather than capability scores. We apply the framework retrospectively to three publicly documented evaluation incidents and discuss governance implications for system cards, conformity assessment, and the international network of AI safety and security institutes. TRACE does not eliminate adversarial adaptation; it disciplines the claims drawn from evaluation evidence by making explicit the conditions under which that evidence was produced.

Representation autoencoders that reuse frozen pretrained vision encoders as visual tokenizers have achieved strong reconstruction and generation quality. However, existing methods universally extract features from only the last encoder layer, discarding the rich hierarchical information distributed across intermediate layers. We show that low-level visual details survive in the last layer merely as attenuated residuals after multiple layers of semantic abstraction, and that explicitly fusing multi-layer features can substantially recover this lost information. We propose DRoRAE (Depth-Routed Representation AutoEncoder), a lightweight fusion module that adaptively aggregates all encoder layers via energy-constrained routing and incremental correction, producing an enriched latent compatible with a frozen pretrained decoder. A three-phase decoupled training strategy first learns the fusion under the implicit distributional constraint of the frozen decoder, then fine-tunes the decoder to fully exploit the enriched representation. On ImageNet-256, DRoRAE reduces rFID from 0.57 to 0.29 and improves generation FID from 1.74 to 1.65 (with AutoGuidance), with gains also transferring to text-to-image synthesis. Furthermore, we uncover a log-linear scaling law ($R^2{=}0.86$) between fusion capacity and reconstruction quality, identifying \textit{representation richness} as a new, predictably scalable dimension for visual tokenizers analogous to vocabulary size in NLP.

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.

Direct diffusion modeling of high-resolution spatiotemporal fields is computationally challenging. Parameter-efficient primitives address this by representing high-dimensional data with a compact set of parameters. In this paper, we construct data-dependent tensor primitives without pretrained compression autoencoders. Our construction starts from Tucker decomposition, which captures low-rank multilinear structure through a core tensor and mode-wise factors. However, Tucker factors are non-unique: the same tensor can be represented by different rotated factors, which complicates generative modeling. We address this issue with orthogonal Procrustes (OP) alignment. Specifically, we select medoid anchor matrices from the data and align the factor matrices to resolve the gauge ambiguity. This yields matrix Grassmannian primitives and tensor Grassmannian primitives that are compact, data-adaptive, and directly decodable by explicit multilinear reconstruction. Theoretically, we prove that the proposed primitive maps are homeomorphisms between low-rank tensors and their corresponding primitive spaces, certifying that the representations are non-degenerate and topologically faithful. Building on these primitives, we propose Diffusion in Aligned Tensor Space (DiffATS), a generative framework that trains diffusion models directly on aligned tensor primitives. Across images, videos, and PDE solutions, DiffATS achieves strong unconditional and conditional generation performance while compressing original data by $3.9\times$ to $210\times$, without relying on any pretrained deep compression autoencoders.

This paper introduces a framework specifically designed for sparse and irregular time series {risk estimation}. It is based on a Transformer Autoencoder with local attention, which leverages the powerful pattern identification capabilities of transformers complemented by traditional data cleaning and normalization methods. It efficiently captures relevant patterns within irregular sequences suffering from sparse data collection, benefiting from the discriminative ability of the local attention mechanism. The proposed framework is applied to a real-world case study, on the risk estimation of non-technical losses in electrical power systems in a wide area in Greece. Non-technical losses in electrical power systems, primarily stemming from electricity theft, pose significant economic and operational challenges. Detecting these anomalies is particularly challenging due to the inherent sparse and irregular nature of real-world data collection practices. Traditional risk estimation methods struggle with effectively capturing long-range dependencies and robustly handling such data characteristics. We demonstrate that our approach effectively yields highly discriminative latent features, which results in more consistent risk estimation compared with existing state-of-the-art and widely used methods. It achieves high recall and precision, meeting the critical objectives of the problem. As such, our solution offers a robust and effective tool for risk detection in irregular time series datasets.

Sparse autoencoders have become a standard tool for uncovering interpretable latent representations in neural networks. Yet salient concepts often span manifolds that current linear methods cannot capture without post hoc analysis. This paper uses quadratic latents to close this gap: we implement these with bilinear autoencoders, which decompose activations into low-rank quadratic forms, compose linearly in weight space, and admit input-independent geometric analysis. This qualitative difference in what concepts quadratic latents can detect challenges the standard linear representation hypothesis. Our experiments and visualisations show that multi-dimensional geometries are highly prevalent and that composite latents capture them well, systematically improving reconstruction error in language models. Furthermore, we show that autoencoders with varying geometric priors recover the same input subspace despite their dictionary entries being distinct. Practically, these models serve as an unsupervised tool for manifold discovery, which we demonstrate through an interactive online visualizer for Qwen 3.5. This is a step toward nonlinear but mathematically tractable latent representations whose composition is expressive and interpretable by design.

Learning hierarchical features in Sparse Autoencoders (SAEs) is essential for capturing the structured nature of real-world data and mitigating issues like feature absorption or splitting. Existing works attempt to identify hierarchical relationships within independent feature sets by relying on activation coverage, the assumption that child feature should only activate when its parent feature activates. However, we demonstrate that this condition alone is insufficient; that is, it often produces false positives where parent and child concepts are semantically unrelated. To address this, we introduce a novel reconstruction condition that enforces a deeper functional link between hierarchical levels. By combining both activation and reconstruction constraints, we propose the Tree SAE, a model designed to learn hierarchical structures directly from within the feature set. Our results demonstrate that Tree SAEs significantly surpass the existing SAEs at learning hierarchical pairs while maintaining competitive performance to the state-of-the-art on several key benchmarks. Finally, we demonstrate the practical utility of our Tree SAE in mapping the geometry of child feature subspaces and uncovering the complex hierarchical concept structures encoded within large language models.

Tokenizers are a crucial component of latent diffusion models, as they define the latent space in which diffusion models operate. However, existing tokenizers are primarily designed to improve reconstruction fidelity or inherit pretrained representations, leaving unclear what kind of latent space is truly friendly for generative modeling. In this paper, we study this question from the perspective of latent manifold organization. By constructing controlled tokenizer variants, we identify three key properties of a diffusion-friendly latent manifold: coherent spatial structure, local manifold continuity, and global manifold semantics. We find that these properties are more consistent with downstream generation quality than reconstruction fidelity. Motivated by this finding, we propose the Prior-Aligned AutoEncoder (PAE), which explicitly shapes the latent manifold instead of leaving diffusion-friendly manifold to emerge indirectly from reconstruction or inheritance. Specifically, PAE leverages refined priors derived from VFMs and perturbation-based regularization to turn spatial structure, local continuity, and global semantics into explicit training objectives. On ImageNet 256x256, PAE improves both training efficiency and generation quality over existing tokenizers, reaching performance comparable to RAE with up to 13x faster convergence under the same training setup and achieving a new state-of-the-art gFID of 1.03. These results highlight the importance of organizing the latent manifold for latent diffusion models.

Motor unit parameters such as the innervation zone centre or the conduction velocity of the electrical potential harbour the potential to improve the fidelity of neuromechanical models used for movement and force prediction. Determining these parameters in a non-invasive way is challenging, as they are subject-specific and may vary with muscle contraction. Existing work on the estimation of motor unit parameters mainly relies on white-box modelling and therefore requires substantial manual modelling effort. This work targets the simultaneous estimation of multiple subject-specific motor unit parameters from electromyography (EMG) recordings measured non-invasively at the skin surface. This results in an inverse problem with a nonlinear loss function. To address this problem, an informed autoencoder is developed. This autoencoder reconstructs the surface EMG recordings while learning the parameters in its latent space and adhering to physical laws that relate the parameters to the EMG signals. In experiments on synthetic data, innervation zone centres are estimated with a mean absolute error of 2.5989 $\mathrm{mm}$, and conduction velocities of the electric potential are estimated with a mean absolute error of 0.1697 $\mathrm{m}\mathrm{s}^{-1}$. These results demonstrate the plausibility of this novel approach, which enables the simultaneous estimation of several motor unit parameters while reducing manual modelling effort through the integration of data-driven machine learning.

Embedding models in natural language processing (NLP) increasingly rely on deep architectures such as BERT, while simpler models such as Word2Vec provide efficient representations but limited interpretability. The Tsetlin Machine (TM) offers an alternative logic-based learning paradigm. Omni TM Autoencoder (Omni TM-AE) applies this paradigm to static embedding by exploiting automaton state distributions within a single clause layer, but its training process remains slow. In this work, we propose FastOmniTMAE, a reformulation of Omni TM-AE that replaces sequential training dependencies with a two-stage parallel process: evaluation and update. Using a Single-Run Multi-Environment Benchmark covering classification, similarity, and clustering, FastOmniTMAE achieves up to 5$\times$ faster training in classification while maintaining comparable embedding quality under both Spearman and Kendall similarity measures. To address the limited efficiency of TM training on conventional GPUs, we further implement FastOmniTMAE as a reusable accelerator on SoC-FPGA platforms. The Multi-Hardware Benchmark shows that FastOmniTMAE achieves similarity scores of 0.669 on a resource-constrained FPGA and 0.696 on an UltraScale+ SoC, demonstrating efficient logic-based embedding training with a small hardware footprint.

Order-Agnostic autoregressive models have demonstrated strong performance in deep generative modeling, yet their use in settings with incomplete data remains largely unexplored. In this work, we reinterpret them through the lens of missing data. First, we show that their standard training procedure on fully observed data implicitly performs imputation under a missing completely at random mechanism, resulting in robust out-of-sample imputation performance in settings with high missingness. Second, we introduce the first principled framework for training them directly on incomplete datasets under general missingness mechanisms. Third, we leverage their amortized conditional density estimation to perform active information acquisition, i.e., sequentially selecting the most informative missing variables for downstream prediction or inference. Across a suite of real-world benchmarks, our Missingness-Aware Order-Agnostic Autoregressive Model (MO-ARM) consistently outperforms established imputation baselines.

We introduce a hybrid quantum-classical pipeline, based on neutral-atom reservoir computing, for medical image classification, focusing on the binary classification task of polyp detection. To deal effectively with the high dimensionality, we integrate a guided auto-encoder. This pipeline learns compact and discriminative representations of image data that are also well-suited for quantum reservoir computing. A key challenge in such systems is the non-differentiable nature of quantum measurements, which creates a 'gradient barrier' for standard training. We overcome this barrier by incorporating a differentiable surrogate model that emulates the quantum layer, enabling end-to-end backpropagation through the entire system. This guided training process is jointly optimized for classification accuracy and for faithful image recovery from the auto-encoder. The learned latent representations are encoded as pulse detuning parameters within a Rydberg Hamiltonian, and quantum embeddings are subsequently obtained through expectation values. These embeddings are then passed to a linear classifier. Our simulations show that this method outperforms some traditional approaches that use PCA or unguided autoencoders. We also conduct ablation studies to assess the impact of various quantum and training parameters, demonstrating the robustness and flexibility of our proposed pipeline for real-world medical imaging applications, even in the current NISQ era.

Semantic communication (SemCom) with learned encoder-decoder architectures enables end-to-end learning of compact task-oriented representations optimized for the wireless channel, reducing channel resources needed to convey task-relevant information and improving spectrum efficiency. This paper studies semantic image transmission over block Rayleigh fading with AWGN using a multi-task semantic autoencoder that jointly reconstructs images and predicts labels from the received waveform. The latent dimension (complex channel uses per source sample) serves as a cross-layer control variable governing semantic fidelity and channel resource usage. We characterize the resulting latency-task fidelity tradeoff: larger latent representations improve inference accuracy but increase service time, channel uses, and queueing delay. Building on this insight, we develop online semantic-rate controllers that adapt the latent dimension per update under a long-term semantic error constraint. A queue-aware drift-plus-penalty policy minimizes delay subject to an average semantic error cap, while a complementary age-aware policy minimizes time-average Age of Information (AoI). By adapting the semantic rate to congestion and fidelity requirements, the proposed framework improves spectrum utilization and enables timely semantic updates with significantly lower delay and AoI than fixed-rate baselines.

Sparse autoencoders (SAEs) are used to disentangle the dense, polysemantic internal representations of large language models (LLMs) into interpretable, monosemantic concepts. However, standard $\ell_1$-regularized SAEs suffer from feature starvation (dead neurons) and shrinkage bias, often requiring computationally expensive heuristic resampling and nondifferentiable hard-masking methods to bypass these challenges. We argue that feature starvation is not merely an empirical artifact of poor data diversity, but a fundamental optimization-geometric pathology of overcomplete dictionaries: the $\ell_1$-induced sparse coding map is unstable and fundamentally misaligned with shallow, amortized encoders. To address this structural instability, we introduce adaptive elastic net SAEs (AEN-SAEs), a fully differentiable architecture grounded in classical sparse regression. AEN-SAEs combine an $\ell_2$ structural term that enforces strong convexity and Lipschitz stability with adaptive $\ell_1$ reweighting that eliminates shrinkage bias and suppresses spurious features, thereby jointly controlling the curvature and interaction structure of the induced polyhedral geometry. Theoretically, we show that AEN-SAEs yield a Lipschitz-continuous sparse coding map and recover the global feature support under mild assumptions. Empirically, across synthetic settings and LLMs (Pythia 70M, Llama 3.1 8B), AEN-SAEs mitigate feature starvation without auxiliary heuristics while maintaining competitive reconstruction abilities.

Vision Transformer (ViT) autoencoders have emerged as compelling tokenizers for images, offering improved reconstruction over convolutional tokenizers. However, existing ViT tokenizers cannot explore this landscape as performance degrades outside training resolutions, and reliance on adversarial losses prevents stable scaling. ViTok (Hansen-Estruch et al., 2025) found that the compression ratio r mediates a reconstruction-generation trade-off where lower r means better reconstructions but harder generations, so improving tokenizer reconstruction is key to more Pareto-optimal tokenizers. We introduce ViTok-v2, which addresses these limitations with native resolution support via NaFlex for generalization across resolutions and aspect ratios, and a novel DINOv3 perceptual loss that replaces both LPIPS and GAN objectives for stable training at any scale. ViTok-v2 is trained on about 2B images and scaled to 5B parameters, the largest image autoencoder to date. ViTok-v2 matches or exceeds state-of-the-art reconstruction at 256p and outperforms all baselines at 512p and above. In joint scaling experiments with flow matching generators, we show that scaling both the autoencoder and the generator advances the Pareto frontier of this trade-off.