Autoencoders

Latest papers 93

May 23, 2026cond-mat.dis-nn

High-Dimensional Latents Should Be Diagnosed Through Phase Structure

We study autoencoder and variational-autoencoder latent spaces through the lens of spin-glass theory. The paper has two components. First, we formalize a latent-space spin-glass dictionary: for a fixed decoder, the reconstruction term together with a hyperspherical coordinates prior induces a Hamiltonian on the latent sphere, where latent coordinates play the role of continuous spins and the prior acts as an external magnetic field. This allows us to import operational spin-glass diagnostics -- overlap distributions, susceptibility, and block-spin coarse-graining -- to detect ordered, disordered, and edge-of-stability phases in trained latent representations. Second, we show that deliberately driving the latent system toward the edge-of-stability of the topological trivialization regime has concrete downstream consequences. In generation, hyperspherical compression improves the reconstruction-generation trade-off on CIFAR-10 and CelebA64, yielding lower self-FID while preserving or improving reconstruction. In anomaly detection, the same semi-ordered latent geometry improves both fully unsupervised and conditional OOD detection, including real-world Mars Rover and Galaxy Zoo datasets, as well as CIFAR-10/100 and Imagenette-based OOD benchmarks. We therefore advocate a phase-aware evaluation paradigm for AEs/VAEs, in which spin-glass observables complement standard ML metrics and expose the latent regimes that underlie downstream success or failure in many cases.
May 22, 2026stat.ML

MEDAL: Manifold Embedding Distillation via Autoencoder Learning

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.
May 21, 2026cs.CV

DecQ: Detail-Condensing Queries for Enhanced Reconstruction and Generation in Representation Autoencoders

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.
May 18, 2026cs.SD

SAME: A Semantically-Aligned Music Autoencoder

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.
May 18, 2026cs.CV

Improved Baselines with Representation Autoencoders

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.
May 15, 2026cs.LG

Entropic Auto-Encoding via Implicit Free-Energy Minimization

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.
May 13, 2026cs.AI

Product-Aware Deep Autoencoders for Robust Process Monitoring in Multi-Product Cyber-Physical Systems

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.
May 13, 2026cs.CV

Qwen-Image-VAE-2.0 Technical Report

We present Qwen-Image-VAE-2.0, a suite of high-compression Variational Autoencoders (VAEs) that achieve significant advances in both reconstruction fidelity and diffusability. To address the reconstruction bottlenecks of high compression, we adopt an improved architecture featuring Global Skip Connections (GSC) and expanded latent channels. Moreover, we scale training to billions of images and incorporate a synthetic rendering engine to improve performance in text-rich scenarios. To tackle the convergence challenges of high-dimensional latent space, we implement an enhanced semantic alignment strategy to make the latent space highly amenable to diffusion modeling. To optimize computational efficiency, we leverage an asymmetric and attention-free encoder-decoder backbone to minimize encoding overhead. We present a comprehensive evaluation of Qwen-Image-VAE-2.0 on public reconstruction benchmarks. To evaluate performance in text-rich scenarios, we propose OmniDoc-TokenBench, a new benchmark comprising a diverse collection of real-world documents coupled with specialized OCR-based evaluation metrics. Qwen-Image-VAE-2.0 achieves state-of-the-art reconstruction performance, demonstrating exceptional capabilities in both general domains and text-rich scenarios at high compression ratio. Furthermore, downstream DiT experiments reveal our models possess superior diffusability, significantly accelerating convergence compared to existing high-compression baselines. These establish Qwen-Image-VAE-2.0 as a leading model with high compression, superior reconstruction, and exceptional diffusability.
May 12, 2026physics.optics

Bin Latent Transformer (BiLT): A shift-invariant autoencoder for calibration-free spectral unmixing of turbid media

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 R2=0.979R^2 = 0.979 and 0.9750.975 for μa(λ)μ_a(λ) and μs′(λ)μ_s'(λ), respectively, on held-out test spectra, maintaining R2>0.90R^2 > 0.90 for μaμ_a and R2≈0.99R^2 \approx 0.99 for μs′μ_s' across the full tested shift range of ±10\pm 10 spectral bands. The model generalises to a simulated spectrometer with a broader instrument line shape (≈24{\approx}24nm FWHM) without retraining, retaining R2≈0.96R^2 \approx 0.96 and 0.9740.974 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.
May 11, 2026cs.CV

Beyond the Last Layer: Multi-Layer Representation Fusion for Visual Tokenization

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 (R2=0.86R^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.
May 9, 2026cs.LG

SMIXAE: Towards Unsupervised Manifold Discovery in Language Models

Sparse autoencoders (SAEs) have been used widely to decompose and interpret neural network activations, especially those of transformer language models. One key issue with SAEs is their inability to directly model multidimensional features. Instead, SAEs may tile such features by a set of independent directions that must be grouped together after the SAE training phase, impeding discoverability and interpretation of learned feature representations. We begin to address this issue by introducing the Sparse MIXture of Autoencoders (SMIXAE) architecture. Empirically, we provide evidence that SMIXAE models have success both in directly learning previously identified manifold structures, as well as finding novel structures, within the open source Gemma 2 2B and 9B models. Finally, we discuss several limitations and point towards areas for future work.
May 9, 2026cs.LG

Transformer autoencoder with local attention for sparse and irregular time series with application on risk estimation

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.
May 9, 2026cs.LG

Bilinear autoencoders find interpretable manifolds

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.
May 8, 2026cs.CV

What Matters for Diffusion-Friendly Latent Manifold? Prior-Aligned Autoencoders for Latent Diffusion

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.
May 6, 2026cs.CV

ViTok-v2: Scaling Native Resolution Auto-Encoders to 5 Billion Parameters

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.
May 6, 2026cs.CV

Attention-Based Chaotic Self-Supervision for Medical Image Classification

Deep learning models for medical image classification usually achieve promising results but typically rely on large, annotated datasets or standard transfer learning from ImageNet. Self-Supervised Learning (SSL) has emerged as a powerful alternative, yet common methods like masked autoencoders (MAEs) may inadvertently destroy fine-grained diagnostic features by using random masking. In this paper, we propose a novel SSL pre-training strategy, the Chaotic Denoising Autoencoder (CDAE). Instead of masking, we apply a chaotic transformation to the input image, tasking an autoencoder to reconstruct the original. We hypothesize this forces the encoder to learn robust, domain-specific features by "inverting the chaos". Furthermore, we propose an attentive fusion mechanism that combines features from our CDAE-trained encoder with a standard encoder, leveraging the strengths of both general and domain-specific representations. Our method is evaluated on two public medical datasets: ISIC 2018 (skin lesions) and APTOS 2019 (diabetic retinopathy). The proposed model achieves high performance, with an accuracy of 0.9221 and an F1-macro of 0.8530 on ISIC 2018, and an accuracy of 0.8644 and F1-macro of 0.7433 on APTOS 2019, demonstrating the efficacy of our approach.
May 5, 2026cs.LG

Capabilities of Auto-encoders and Principal Component Analysis of the Reduction of Microstructural Images; Application on the Acceleration of Phase-Field Simulations

In this work, a data-driven framework based on Phase-Field simulations data is proposed to highlight the capabilities of neural networks to ensure accurate low dimensionality reduction of simulated microstructural images and to provide time-series analysis. The dataset was indeed constructed from high-fidelity Phase-Field simulations. Analyses demonstrated that the association of auto-encoder neural networks and principal component analyses leads to ensure efficient and significant dimensionality reduction: 1/196 of reduction ratio with more than 80% of accuracy. These findings give insight to apply analyses on data from the latent dimension. Application of Long Short Term Memory (LSTM) neural networks showed the possibility of making next frame predictions; that makes possible the acceleration of Phase-Field simulation without the need of high computing resources. We discussed the application of such a framework on various areas of research. Different methods are proposed from the conducted analyses, in order to ensure dimensionality reduction, including auto-encoders, principal component analysis and Artificial Neural Networks, and time-series analysis, including LSTM and Gated Recurrent Unit (GRU).
May 4, 2026cs.LG

Enhancing AI-Based ECG Delineation with Deep Learning Denoising Techniques

Evaluating canine electrocardiograms (ECGs) is challenging due to noise that can obscure clinically relevant cardiac electrical activity. Common sources of interference include respiration, muscle activity, poor lead contact, and external electrical artifacts. Classical signal denoising techniques, such as filtering and wavelet-based methods, struggle to suppress diverse noise patterns while preserving morphological features critical for accurate ECG delineation. We propose an autoencoder-based neural network model and training strategy for ECG denoising as a preprocessing step for canine ECG analysis. The model is trained to reconstruct clean cardiac signals from noisy inputs, enabling effective noise reduction without degrading diagnostically important waveforms. Our approach demonstrates strong performance across both noisy and clean ECG recordings, indicating robustness to varying signal conditions and suitability for downstream delineation tasks.
May 2, 2026physics.optics

Machine Learning Enhanced Laser Spectroscopy for Multi-Species Gas Detection in Complex and Harsh Environments

Laser absorption spectroscopy (LAS) is a well-established technique for non-intrusive measurement of gas species in combustion and atmospheric environments, but conventional methods struggle with multi-species mixtures under dynamic or interference-laden conditions. Overlapping spectral features, noise, and incomplete reference data limit reliability when unknown or weakly absorbing species are present. This dissertation develops diagnostics combining LAS with machine learning (ML) to address these limitations. Deep denoising autoencoders (DDAEs) are applied to shock-tube measurements during high-speed hydrocarbon pyrolysis, improving signal fidelity and detection limits for trace species. A structured unsupervised framework, HT-SIMNet, then mitigates interference from unknown species without full calibration data, using spectral augmentation and a Noise2Noise-inspired scheme to isolate species in reactive systems. Where reference spectra are unavailable, UnblindMix, an autoencoder-based blind source separation method, reconstructs concentrations and spectral signatures directly from mixture data, validated on mixtures of up to eight components. To recover weakly absorbing species masked by broader absorbers, a feature-engineering method based on first derivatives and convolutions selectively highlights minor species. Finally, VOC-certifire combines randomized smoothing with Voigt-based spectral perturbation to provide certifiable classification of volatile organic compounds under varying conditions. All techniques are experimentally validated and benchmarked. The integration of spectroscopic hardware with ML offers a path toward real-time, interference-resilient, reference-free gas detection for combustion science, environmental monitoring, and industrial safety.
Apr 26, 2026cs.CV

Focus on What Matters: Two-Stage ROI-Aware Refinement for Anatomy-Preserving Fetal Ultrasound Reconstruction

Measurement-critical ultrasound tasks often depend on a small anatomical region, making global reconstruction metrics an unreliable proxy for clinical fidelity. We propose an ROI-aware representation learning framework and instantiate it for first-trimester nuchal translucency (NT) screening under multi-hospital domain shift. A two-phase convolutional autoencoder (CAE) first learns a globally faithful 128-D latent code via MS-SSIM, then refines the NT ROI using intensity (L1) and normalized Sobel-edge constraints. To combine these heterogeneous objectives without manual tuning, we initialize loss weights via gradient-based calibration from per-term gradient magnitudes. Under strict hospital-wise evaluation with one hospital held out, ROI refinement improves both global and measurement-relevant quality: on the standard dev split it increases PSNR by +0.27 dB (val) and +0.29 dB (held-out test), reduces ROI MAE by 8.87% (val) and 6.43% (held-out test), and reduces ROI Edge-MAE by 11.10% on source hospitals and 4.90% on the unseen hospital. Beyond reconstruction, frozen-latent probes provide additional evidence of generalization: hospital provenance becomes less confidently predictable on the unseen site (0.556 to 0.541 max-softmax; 0.684 to 0.688 entropy) while OOD detection remains strong across site-held-out protocols (Mahalanobis AUROC up to 0.9956, with modest KNN gains in challenging splits). The same ROI-aware refinement principle is anatomy-agnostic and can be adopted for other fetal biometry targets (e.g., crown-rump length (CRL), nasal bone (NB)) and broader medical imaging settings where small ROIs dominate clinical decisions.
Apr 17, 2026cs.LG

Geometric regularization of autoencoders via observed stochastic dynamics

Stochastic dynamical systems with slow or metastable behavior evolve, on long time scales, on an unknown low-dimensional manifold in high-dimensional ambient space. Building a reduced simulator from short-burst ambient ensembles is a long-standing problem: local-chart methods like ATLAS suffer from exponential landmark scaling and per-step reprojection, while autoencoder alternatives leave tangent-bundle geometry poorly constrained, and the errors propagate into the learned drift and diffusion. We observe that the ambient covariance~ΛΛ already encodes coordinate-invariant tangent-space information, its range spanning the tangent bundle. Using this, we construct a tangent-bundle penalty and an inverse-consistency penalty for a three-stage pipeline (chart learning, latent drift, latent diffusion) that learns a single nonlinear chart and the latent SDE. The penalties induce a function-space metric, the ρρ-metric, strictly weaker than the Sobolev H1H^1 norm yet achieving the same chart-quality generalization rate up to logarithmic factors. For the drift, we derive an encoder-pullback target via Itô's formula on the learned encoder and prove a bias decomposition showing the standard decoder-side formula carries systematic error for any imperfect chart. Under a W2,∞W^{2,\infty} chart-convergence assumption, chart-level error propagates controllably to weak convergence of the ambient dynamics and to convergence of radial mean first-passage times. Experiments on four surfaces embedded in up to 201201 ambient dimensions reduce radial MFPT error by 5050--70%70\% under rotation dynamics and achieve the lowest inter-well MFPT error on most surface--transition pairs under metastable Müller--Brown Langevin dynamics, while reducing end-to-end ambient coefficient errors by up to an order of magnitude relative to an unregularized autoencoder.
Mar 16, 2026physics.flu-dyn

A convolutional autoencoder and neural ODE surrogate modeling framework applied to transient counterflow flames

A novel convolutional autoencoder and neural ODE (CAE-NODE) framework is proposed for a reduced-order model (ROM) applied to transient 2D counterflow flames, as an extension of AE-NODE methods in homogeneous reactive systems to spatially resolved flows. The multidimensional thermochemical fields (256 x 256 grid, 21 variables) obtained from direct numerical simulations (DNS) are used in training the CAE, where convolutional layers learned the underlying spatial correlations, allowing the CAE to construct an unsupervised 3D latent manifold that is physically meaningful, smooth, and continuous in time. This results in a compression ratio of over 400,000 times. The NODE then subsequently learns the continuous-time dynamics on the latent manifold, enabling the prediction of the full temporal evolution of the flames by integrating forward in time from an initial condition. The results demonstrate that the CAE-NODE can accurately capture the entire transient process, including ignition, flame propagation, and the gradual transition to a non-premixed condition, with excellent agreement with the DNS, while adhering to conservation principles at virtually no computational cost compared to the reference DNS. Predictions remain accurate at strain rates outside the training range. Moreover, despite being unsupervised, the learned latent manifold is highly correlated with the flame-state descriptors such as the progress variable, mixture fraction, and the scalar dissipation rate. This study, for the first time, highlights the potential of CAE-NODE for surrogate modeling of unsteady dynamics of multi-dimensional reacting flows.
Mar 13, 2026cs.LG

Deep Invertible Autoencoders for Dimensionality Reduction of Dynamical Systems

Constructing reduced-order models (ROMs) capable of efficiently predicting the evolution of parameter-dependent high-dimensional dynamical systems is crucial in many applications in engineering and applied sciences. A popular class of projection-based ROMs projects the high-dimensional full-order model (FOM) dynamics onto a low-dimensional manifold. These projection-based ROMs approaches often rely on classical model reduction techniques such as proper orthogonal decomposition (POD) or, more recently, on neural network architectures such as autoencoders (AEs). In the case that the ROM is constructed by the POD, one has approximation guaranteed based based on the singular values of the problem at hand. However, POD-based techniques can suffer from slow decay of the singular values in transport- and advection-dominated problems. In contrast to that, AEs allow for better reduction capabilities than the POD, often with the first few modes, but at the price of theoretical considerations. In addition, it is often observed, that AEs exhibits a plateau of the projection error with the increment of the dimension of the trial manifold. In this work, we propose an invertible AE architecture, named inv-AE, that computationally improves upon the stagnation of the reconstruction error typical of traditional AE architectures. Inv-AE is composed of several invertible neural network layers that allows for gradually recovering more information about the FOM solutions the more we increase the dimension of the reduced manifold. Through the application of inv-AE to a 1-dimensional Burgers' equation, a 2-dimensional fluid flow around an obstacle with variable geometry, and a 3-dimensional Korteweg-de Vries, we show that (i) inv-AE mitigates the issue of the characteristic plateau of AEs and (ii) inv-AE can be combined with popular autoencoder-based ROM approaches, e.g., DL-ROM, to improve their accuracy.
Mar 6, 2026cs.LG

Implementation of Quantum Implicit Neural Representation in Deterministic and Probabilistic Autoencoders for Image Reconstruction/Generation Tasks

We propose a quantum implicit neural representation (QINR)-based autoencoder (AE) and variational autoencoder (VAE) for image reconstruction and generation tasks. Our purpose is to demonstrate that the QINR in VAEs and AEs can transform information from the latent space into highly rich, periodic, and high-frequency features. Additionally, we aim to show that the QINR-VAE can be more stable than various quantum generative adversarial network (QGAN) models in image generation because it can address the low diversity problem. Our quantum-classical hybrid models consist of a classical convolutional neural network (CNN) encoder and a quantum-based QINR decoder. We train the QINR-AE/VAE with binary cross-entropy with logits (BCEWithLogits) as the reconstruction loss. For the QINR-VAE, we additionally employ Kullback-Leibler divergence for latent regularization with beta/capacity scheduling to prevent posterior collapse. We introduce learnable angle-scaling in data reuploading to address optimization challenges. We test our models on the MNIST, E-MNIST, and Fashion MNIST datasets to reconstruct and generate images. Our results demonstrate that the QINR structure in VAE can produce a wider variety of images with a small amount of data than various generative models that have been studied. We observe that the generated/reconstructed images from the QINR-VAE/AE are clear with sharp boundaries and details. Overall, we find that the addition of QINR-based quantum layers into the AE/VAE frameworks shows improved performance of reconstruction/generation under the constrained experimental setting relative to the specific baselines.
Feb 10, 2026astro-ph.EP

Efficient reduction of stellar contamination and noise in planetary transmission spectra using neural networks

The characterization of exoplanetary atmospheres has been transformed by the James Webb Space Telescope (JWST), whose infrared sensitivity enables transmission spectroscopy at unprecedented precision. However, stellar heterogeneities (e.g., spots and faculae) remain a dominant source of contamination that can bias atmospheric retrievals if not properly corrected. We present a methodology for reducing stellar contamination and instrument-specific noise from exoplanet transmission spectra using neural networks, in particular the so-called Denoising AutoEncoders (DAEs). Our goals are to enable fast, accurate corrections that improve the reliability of atmospheric parameter retrievals and to promote the use of unsupervised algorithms for efficient data processing. We designed and trained DAE architectures using large synthetic datasets of terrestrial (TRAPPIST-1e analogues) and sub-Neptune (K2-18b analogues) planets. Atmospheric retrieval experiments were then performed on contaminated spectra in order to compare our deep-learning approach against standard correction methods in terms of accuracy and computational cost. Our autoencoders successfully reconstruct uncontaminated spectra, preserving essential molecular features even in low-S/N regimes. In retrieval tests, the denoising autoencoder pre-processing yields atmospheric parameter estimates broadly comparable to those obtained with simultaneous stellar-contamination fitting. Notably, our method maintains a much lower computational cost, approximately one order of magnitude smaller. These results demonstrate that DAEs outperform conventional correction methods in computational efficiency while maintaining high accuracy, paving the way for their integration into future atmospheric characterization pipelines for both rocky and sub-Neptune exoplanets.
Feb 3, 2026cs.LG

Variational Sparse Paired Autoencoders (vsPAIR) for Inverse Problems and Uncertainty Quantification

Inverse problems are fundamental to many scientific and engineering disciplines; they arise when one seeks to reconstruct hidden, underlying quantities from noisy measurements. Many applications demand not just point estimates but interpretable uncertainty. Providing fast inference alongside uncertainty estimates remains challenging yet desirable in numerous applications. We propose the Variational Sparse Paired Autoencoder (vsPAIR) to address this challenge. The architecture pairs a standard VAE encoding observations with a sparse VAE encoding quantities of interest (QoI), connected through a learned latent mapping. The variational structure enables uncertainty estimation, the paired architecture encourages interpretability by anchoring QoI representations to clean data, and sparse encodings provide structure by concentrating information into identifiable factors rather than diffusing across all dimensions. To validate the effectiveness of our proposed architecture, we conduct experiments on blind inpainting, computed tomography (CT), and initial-condition inference for the heat equation, demonstrating that vsPAIR is a capable inverse problem solver that can provide interpretable and structured uncertainty estimates.
Dec 10, 2025cs.CV

FunPhase: A Periodic Functional Autoencoder for Motion Generation via Phase Manifolds

Learning natural body motion remains challenging due to the strong coupling between spatial geometry and temporal dynamics. Embedding motion in phase manifolds, latent spaces that capture local periodicity, has proven effective for motion prediction; however, existing approaches are tied to fixed skeletons and narrow motion distributions, limiting their applicability across diverse settings. We introduce FunPhase, a functional periodic autoencoder that learns a phase manifold for motion and replaces discrete temporal decoding with a function-space formulation, enabling smooth trajectories that can be sampled at arbitrary temporal resolutions. FunPhase unifies motion prediction and generation within a single interpretable phase manifold, enabling motion generation via latent diffusion, generalizes across skeletons and datasets, and supports downstream tasks such as motion super-resolution and partial-body completion. Our model achieves substantially lower reconstruction error than prior periodic autoencoder baselines, achieving uniform improvements of at least 45%45\% across all metrics, while enabling a broader range of applications and performing on par with state-of-the-art motion generation methods.
Nov 20, 2025cs.CV

A Machine Learning-Driven Solution for Denoising Inertial Confinement Fusion Images

Neutron imaging is essential for diagnosing and optimizing inertial confinement fusion implosions at the National Ignition Facility. Due to the required 10-micrometer resolution, however, neutron image require image reconstruction using iterative algorithms. For low-yield sources, the images may be degraded by various types of noise. Gaussian and Poisson noise often coexist within one image, obscuring fine details and blurring the edges where the source information is encoded. Traditional denoising techniques, such as filtering and thresholding, can inadvertently alter critical features or reshape the noise statistics, potentially impacting the ultimate fidelity of the iterative image reconstruction pipeline. However, recent advances in synthetic data production and machine learning have opened new opportunities to address these challenges. In this study, we present an unsupervised autoencoder with a Cohen-Daubechies- Feauveau (CDF 97) wavelet transform in the latent space, designed to suppress for mixed Gaussian-Poisson noise while preserving essential image features. The network successfully denoises neutron imaging data. Benchmarking against both simulated and experimental NIF datasets demonstrates that our approach achieves lower reconstruction error and superior edge preservation compared to conventional filtering methods such as Block-matching and 3D filtering (BM3D). By validating the effectiveness of unsupervised learning for denoising neutron images, this study establishes a critical first step towards fully AI-driven, end-to-end reconstruction frameworks for ICF diagnostics.
Nov 7, 2025cs.SD

Perceptually Aligning Representations of Music via Noise-Augmented Autoencoders

We argue that training autoencoders to reconstruct inputs from noised versions of their encodings, when combined with perceptually motivated losses, yields encodings that are structured according to a perceptual hierarchy. We demonstrate the emergence of this hierarchy by showing that, after training an audio autoencoder in this manner, perceptually salient information is captured in coarser representation structures than with conventional training. Furthermore, we show that such perceptual hierarchies improve latent diffusion decoding in the context of estimating pitch surprisal in music and predicting EEG-brain responses to music listening. In both cases, our results surpass those of previous methods. Pretrained weights are available on github.com/CPJKU/pa-audioic.
Jun 13, 2025math.NA

Deep Symmetric Autoencoders from the Eckart-Young-Schmidt Perspective

Deep autoencoders have become a fundamental tool in various machine learning applications, ranging from dimensionality reduction and reduced order modeling of partial differential equations to anomaly detection and neural machine translation. Despite their empirical success, a solid theoretical foundation for their expressiveness remains elusive, particularly when compared to classical projection-based techniques. In this work, we aim to take a step forward in this direction by presenting a comprehensive analysis of what we refer to as symmetric autoencoders, a broad class of deep learning architectures that have surfaced frequently in the recent literature. Specifically, we introduce a formal distinction between different classes of symmetric architectures, analyzing their strengths and limitations from a mathematical perspective. For instance, we show that the reconstruction error of symmetric autoencoders with orthonormality constraints can be understood by leveraging the well-renowned Eckart-Young-Schmidt (EYS) theorem. As a byproduct of our analysis, we end up developing the EYS initialization strategy for symmetric autoencoders, which is based on an iterated application of the Singular Value Decomposition (SVD). To validate our findings, we conduct a series of numerical experiments where we benchmark our proposal against conventional deep autoencoders, discussing the importance of model design and initialization.
May 28, 2025eess.SP

Temporal Convolutional Autoencoder for Interference Mitigation in FMCW Radar Altimeters

Reliable altitude estimation with frequency-modulated continuous wave (FMCW) radar altimeters is increasingly a challenge due to in-band interference from modern communication systems. In this paper, we present a temporal convolutional autoencoder (TCAE) that directly processes in-phase and quadrature (IQ) samples to suppress structured interference while preserving signal phase and frequency content for range estimation. The model is trained and initially evaluated within a full radar altimeter simulation chain, then further validated via over-the-air (OTA) experiments using a universal software radio peripheral (USRP)-based testbed. Results show that the TCAE reduces altitude estimation error by more than 85% compared to least mean squares (LMS) adaptive filtering under severe interference conditions, including low signal-to-interference-plus-noise ratio (SINR) and full temporal overlap between interfering and radar signals. Unlike conventional methods, the TCAE maintains phase fidelity and beat structure, enabling accurate range estimation even when interferers occupy more than one-quarter of the radar bandwidth. The implemented TCAE performs mitigation directly on fixed-length IQ windows using a single feed-forward pass and was integrated into the MATLAB/ONNX-based evaluation chain used for both simulation and OTA testing. These findings demonstrate that learned IQ-domain interference mitigation can enhance radar-altimeter resilience under a range of tested interference conditions.
Aug 2, 2024stat.ML

Autoencoders in Function Space

Autoencoders have found widespread application in both their original deterministic form and in their variational formulation (VAEs). In scientific applications and in image processing it is often of interest to consider data that are viewed as functions; while discretisation (of differential equations arising in the sciences) or pixellation (of images) renders problems finite dimensional in practice, conceiving first of algorithms that operate on functions, and only then discretising or pixellating, leads to better algorithms that smoothly operate between resolutions. In this paper function-space versions of the autoencoder (FAE) and variational autoencoder (FVAE) are introduced, analysed, and deployed. Well-definedness of the objective governing VAEs is a subtle issue, particularly in function space, limiting applicability. For the FVAE objective to be well defined requires compatibility of the data distribution with the chosen generative model; this can be achieved, for example, when the data arise from a stochastic differential equation, but is generally restrictive. The FAE objective, on the other hand, is well defined in many situations where FVAE fails to be. Pairing the FVAE and FAE objectives with neural operator architectures that can be evaluated on any mesh enables new applications of autoencoders to inpainting, superresolution, and generative modelling of scientific data.
Date pendingcs.LG

Surrogate Modeling of 3D Rayleigh-Benard Convection with Equivariant Autoencoders

The use of machine learning for modeling, understanding, and controlling large-scale physics systems is quickly gaining in popularity, with examples ranging from electromagnetism over nuclear fusion reactors and magneto-hydrodynamics to fluid mechanics and climate modeling. These systems - governed by partial differential equations - present unique challenges regarding the large number of degrees of freedom and the complex dynamics over many scales both in space and time, and additional measures to improve accuracy and sample efficiency are highly desirable. We present an end-to-end equivariant surrogate model consisting of an equivariant convolutional autoencoder and an equivariant convolutional LSTM using GG-steerable kernels. As a case study, we consider the three-dimensional Rayleigh-B'enard convection, which describes the buoyancy-driven fluid flow between a heated bottom and a cooled top plate. While the system is E(2)-equivariant in the horizontal plane, the boundary conditions break the translational equivariance in the vertical direction. Our architecture leverages vertically stacked layers of D4D_4-steerable kernels, with additional partial kernel sharing in the vertical direction for further efficiency improvement. We demonstrate significant gains in sample and parameter efficiency, as well as a better scaling to more complex dynamics. The accompanying code is available under https://github.com/FynnFromme/equivariant-rb-forecasting.