Autoencoders

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Overview

Autoencoders learn a compact or structured latent representation by encoding data and training a decoder to reconstruct it, supporting dimensionality reduction, compression, and feature learning without labels. Common approaches include convolutional, recurrent, and transformer autoencoders; variational and sparse variants; and models with geometric, physical, or domain-specific constraints. They are used on images, audio and video, scientific simulations, medical data, and industrial time series, with evaluation ranging from reconstruction and compression to anomaly detection and downstream prediction. A central tension is that latents optimized for faithful reconstruction are not always useful for generation, interpretation, or stable long-horizon prediction, so current work increasingly evaluates and shapes representations for their intended downstream use.

Latest papers

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155 papers23 papers in the last four weeks, up 64% on the four weeks before. 0.1% of all new papers.

May 15, 2026

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.

Hazhir Aliahmadi, Irina Babayan, Greg van Anders

Department of Physics, Engineering Physics & Astronomy, Queen’s University, Kingston, ON, Canada

Variational AutoencodersPosterior CollapseAutoencodersEntropy Regularization
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May 13, 2026

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.

MD Shafikul Islam, Jordan Carden

Cyber-Physical SystemsAutoencodersIndustrial Anomaly DetectionProcess SupervisionAnomaly Detection
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May 13, 2026

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.

Zekai Zhang, Deqing Li, Kuan Cao +27

Qwen Team

Variational AutoencodersLearned Image CompressionAutoencodersImage ReconstructionDiffusion Autoencoder
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May 12, 2026

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.

Martin Hohmann

Institute of Photonic Technologies (LPT), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Konrad-Zuse-Straße 3/5, 91052 Erlangen, Germany

Spectral UnmixingAutoencodersTransformer AttentionPhysics-Informed MLSpectral Methods
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May 11, 2026

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 representation richness as a new, predictably scalable dimension for visual tokenizers analogous to vocabulary size in NLP.

Xuanyu Zhu, Yan Bai, Yang Shi +4

Peking University · Meituan Inc · Tsinghua University +1

AutoencodersVisual TokenizationImage GenerationFeature Fusion
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May 9, 2026

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.

Collin Francel

Department of Arts and Sciences, University of Alabama, Tuscaloosa, AL, United States.

AutoencodersLLM InterpretabilitySparse AutoencodersManifold Learning
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May 9, 2026

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.

Panteleimon Rodis

University of Macedonia, Greece

Irregular Time-Series ModelingAutoencodersTime-Series Anomaly Detection
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May 9, 2026

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.

Thomas Dooms, Ward Gauderis, Geraint Wiggins +1

University of Antwerp · Vrije Universiteit Brussel · University of Antwerp, sqIRL

Neural Representation GeometryAutoencodersLLM InterpretabilityManifold Learning
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May 8, 2026

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.

Zhengrong Yue, Taihang Hu, Mengting Chen +8

Shanghai Jiao Tong University · Alibaba Group · Beihang University +4

Latent Diffusion ModelsAutoencodersDiffusion-Based Image GenerationDiffusion Models
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May 6, 2026

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.

Philippe Hansen-Estruch, Jiahui Chen, Vivek Ramanujan +9

University of Texas, Austin · University of Washington · 3Stanford University +3

Image TokenizationAutoencodersPerceptual LossVisual TokenizationImage ReconstructionVisual Token Compression
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May 6, 2026

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.

Joao Batista Florindo, Amanda Pontes de Oliveira Ornelas

Institute of Mathematics, Statistics and Scientific Computing - University of Campinas, Rua S´ergio Buarque de Holanda, 651, Campinas, Brasil

Denoising AutoencodersSelf-Supervised Pre-TrainingAutoencodersMedical Image ClassificationMedical Image Representation Learning
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May 5, 2026

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).

Seifallah Fetni, Thinh Quy Duc Pham, Truong Vinh Hoang +4

University of Liège, UEE Research Unit, MSM division, allée de la Découverte, 9 B52/3, B 4000 Liège, Belgium · Chair of Mathematics for Uncertainty Quantification, RWTH-Aachen University, 52056 Aachen, Germany · Institute of Strategy Development, Thu Dau Mot University, 75100 Binh Duong Province, Viet Nam

Neural Surrogate ModelingAutoencodersDimensionality Reduction
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May 4, 2026

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.

Jeff Breeding-Allison, Emil Walleser

1Mars Petcare

AutoencodersElectrocardiography
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May 2, 2026

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.

Mohamed Sy

King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia

Denoising AutoencodersAutoencoders
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Apr 26, 2026

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.

Ines Abbes, Mahmood Alzubaidi, Mowafa Househ +3

College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar · Sidra Medicine, Doha, Qatar

AutoencodersImage ReconstructionConvolutional AutoencoderUltrasound ImagingMedical Image Representation Learning
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Apr 17, 2026

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.

Sean Hill, Felix X. -F. Ye

Department of Mathematics and Statistics, University at Albany, SUNY

Latent Dynamics ModelingAutoencodersManifold Learning
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Apr 15, 2026

Unsupervised Anomaly Detection in Process-Complex Industrial Time Series: A Real-World Case Study

Industrial time-series data from real production environments exhibits substantially higher complexity than commonly used benchmark datasets, primarily due to heterogeneous, multi-stage operational processes. As a result, anomaly detection methods validated under simplified conditions often fail to generalize to industrial settings. This work presents an empirical study on a unique dataset collected from fully operational industrial machinery, explicitly capturing pronounced process-induced variability. We evaluate which model classes are capable of capturing this complexity, starting with a classical Isolation Forest baseline and extending to multiple autoencoder architectures. Experimental results show that Isolation Forest is insufficient for modeling the non-periodic, multi-scale dynamics present in the data, whereas autoencoders consistently perform better. Among them, temporal convolutional autoencoders achieve the most robust performance, while recurrent and variational variants require more careful tuning.

Sergej Krasnikov, Lukas Meitz, Samineh Bagheri +3

Universität Augsburg Augsburg, Germany · Technische Hochschule Augsburg Augsburg, Germany · Independent Researcher Karlsruhe, Germany

Time-Series Anomaly DetectionIndustrial Anomaly DetectionUnsupervised Anomaly DetectionReconstruction-Based Anomaly DetectionAutoencoders
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Apr 14, 2026

Domain-Specific Latent Representations Improve the Fidelity of Diffusion-Based Medical Image Super-Resolution

Latent diffusion models for medical image super-resolution universally inherit variational autoencoders designed for natural photographs. We show that this default choice, not the diffusion architecture, is the dominant constraint on reconstruction quality. In a controlled experiment holding all other pipeline components fixed, replacing the generic Stable Diffusion VAE with MedVAE, a domain-specific autoencoder pretrained on more than 1.6 million medical images, yields +2.91 to +3.29 dB PSNR improvement across knee MRI, brain MRI, and chest X-ray (n = 1,820; Cohen's d = 1.37 to 1.86, all p < 10^{-20}, Wilcoxon signed-rank). Wavelet decomposition localises the advantage to the finest spatial frequency bands encoding anatomically relevant fine structure. Ablations across inference schedules, prediction targets, and generative architectures confirm the gap is stable within plus or minus 0.15 dB, while hallucination rates remain comparable between methods (Cohen's h < 0.02 across all datasets), establishing that reconstruction fidelity and generative hallucination are governed by independent pipeline components. These results provide a practical screening criterion: autoencoder reconstruction quality, measurable without diffusion training, predicts downstream SR performance (R^2 = 0.67), suggesting that domain-specific VAE selection should precede diffusion architecture search. Code and trained model weights are publicly available at https://github.com/sebasmos/latent-sr.

Sebastian Cajas, Ashaba Judith, Rahul Gorijavolu +8

MIT Critical Data, Massachusetts Institute of Technology, Cambridge, MA, USA. · Department of Biomedical Engineering, Mbarara University of Science and Technology, Uganda. · School of Medicine, Johns Hopkins University, Baltimore, MD, USA. +10

Medical Image Super-ResolutionDiffusion Models for Image RestorationLatent Diffusion ModelsAutoencodersVariational Autoencoders
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Apr 8, 2026

TC-AE: Unlocking Token Capacity for Deep Compression Autoencoders

We propose TC-AE, a ViT-based architecture for deep compression autoencoders. Existing methods commonly increase the channel number of latent representations to maintain reconstruction quality under high compression ratios. However, this strategy often leads to latent representation collapse, which degrades generative performance. Instead of relying on increasingly complex architectures or multi-stage training schemes, TC-AE addresses this challenge from the perspective of the token space, the key bridge between pixels and image latents, through two complementary innovations: Firstly, we study token number scaling by adjusting the patch size in ViT under a fixed latent budget, and identify aggressive token-to-latent compression as the key factor that limits effective scaling. To address this issue, we decompose token-to-latent compression into two stages, reducing structural information loss and enabling effective token number scaling for generation. Secondly, to further mitigate latent representation collapse, we enhance the semantic structure of image tokens via joint self-supervised training, leading to more generative-friendly latents. With these designs, TC-AE achieves substantially improved reconstruction and generative performance under deep compression. We hope our research will advance ViT-based tokenizer for visual generation.

Teng Li, Ziyuan Huang, Cong Chen +5

Inclusion AI, Ant Group · HKUST · ZJU +2

AutoencodersVisual Token CompressionVisual TokenizationVision Transformer
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Apr 8, 2026

Bi-Lipschitz Autoencoder With Injectivity Guarantee

Autoencoders are widely used for dimensionality reduction, based on the assumption that high-dimensional data lies on low-dimensional manifolds. Regularized autoencoders aim to preserve manifold geometry during dimensionality reduction, but existing approaches often suffer from non-injective mappings and overly rigid constraints that limit their effectiveness and robustness. In this work, we identify encoder non-injectivity as a core bottleneck that leads to poor convergence and distorted latent representations. To ensure robustness across data distributions, we formalize the concept of admissible regularization and provide sufficient conditions for its satisfaction. In this work, we propose the Bi-Lipschitz Autoencoder (BLAE), which introduces two key innovations: (1) an injective regularization scheme based on a separation criterion to eliminate pathological local minima, and (2) a bi-Lipschitz relaxation that preserves geometry and exhibits robustness to data distribution drift. Empirical results on diverse datasets show that BLAE consistently outperforms existing methods in preserving manifold structure while remaining resilient to sampling sparsity and distribution shifts. Code is available at https://github.com/qipengz/BLAE.

Qipeng Zhan, Zhuoping Zhou, Zexuan Wang +2

University of Pennsylvania

AutoencodersRepresentation LearningDimensionality ReductionManifold Learning
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Apr 8, 2026

Quantum-Inspired Tensor Network Autoencoders for Anomaly Detection: A MERA-Based Approach

We investigate whether a multiscale tensor-network architecture can provide a useful inductive bias for reconstruction-based anomaly detection in collider jets. Jets are produced by a branching cascade, so their internal structure is naturally organised across angular and momentum scales. This motivates an autoencoder that compresses information hierarchically and can reorganise short-range correlations before coarse-graining. Guided by this picture, we formulate a MERA-inspired autoencoder acting directly on ordered jet constituents. To the best of our knowledge, a MERA-inspired autoencoder has not previously been proposed, and this architecture has not been explored in collider anomaly detection. We compare this architecture to a dense autoencoder, the corresponding tree-tensor-network limit, and standard classical baselines within a common background-only reconstruction framework. The paper is organised around two main questions: whether locality-aware hierarchical compression is genuinely supported by the data, and whether the disentangling layers of MERA contribute beyond a simpler tree hierarchy. To address these questions, we combine benchmark comparisons with a training-free local-compressibility diagnostic and a direct identity-disentangler ablation. The resulting picture is that the locality-preserving multiscale structure is well matched to jet data, and that the MERA disentanglers become beneficial precisely when the compression bottleneck is strongest. Overall, the study supports locality-aware hierarchical compression as a useful inductive bias for jet anomaly detection.

Emre Gurkanli, Michael Spannowsky

Department of Physics, Sinop University, Turkiye · Institute for Theoretical Physics, Campus Süd, Karlsruhe Institute of Technology (KIT), D-76128 Karlsruhe, Germany · Institute for Quantum Materials and Technologies, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany

Anomaly DetectionAutoencodersReconstruction-Based Anomaly DetectionHierarchical Representation LearningHigh-Energy Physics
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Apr 6, 2026

A Robust SINDy Autoencoder for Noisy Dynamical System Identification

Sparse identification of nonlinear dynamics (SINDy) has been widely used to discover the governing equations of a dynamical system from data. It uses sparse regression techniques to identify parsimonious models of unknown systems from a library of candidate functions. Therefore, it relies on the assumption that the dynamics are sparsely represented in the coordinate system used. To address this limitation, one seeks a coordinate transformation that provides reduced coordinates capable of reconstructing the original system. Recently, SINDy autoencoders have extended this idea by combining sparse model discovery with autoencoder architectures to learn simplified latent coordinates together with parsimonious governing equations. A central challenge in this framework is robustness to measurement error. Inspired by noise-separating neural network structures, we incorporate a noise-separation module into the SINDy autoencoder architecture, thereby improving robustness and enabling more reliable identification of noisy dynamical systems. Numerical experiments on the Lorenz system show that the proposed method recovers interpretable latent dynamics and accurately estimates the measurement noise from noisy observations.

Kairui Ding

Department of Mathematics, Columbia University

Nonlinear System IdentificationSystem IdentificationSparse Identification of Nonlinear DynamicsLatent Dynamics ModelingAutoencoders
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Apr 5, 2026

A Logical-Rule Autoencoder for Interpretable Recommendations

Most deep learning recommendation models operate as black boxes, relying on latent representations that obscure their decision process. This lack of intrinsic interpretability raises concerns in applications that require transparency and accountability. In this work, we propose a Logical-rule Interpretable Autoencoder (LIA) for collaborative filtering that is interpretable by design. LIA introduces a learnable logical rule layer in which each rule neuron is equipped with a gate parameter that automatically selects between AND and OR operators during training, enabling the model to discover diverse logical patterns directly from data. To support functional completeness without doubling the input dimensionality, LIA encodes negation through the sign of connection weights, providing a parameter-efficient mechanism for expressing both positive and negated item conditions within each rule. By learning explicit, human-readable reconstruction rules, LIA allows users to directly trace the decision process behind each recommendation. Extensive experiments show that our method achieves improved recommendation performance over traditional baselines while remaining fully interpretable. Code and data are available at https://github.com/weibowen555/LIA.

Jinhao Pan, Bowen Wei, Ziwei Zhu

Department of Computer Science, George Mason University, Fairfax, Virginia, USA

Explainable RecommendationCollaborative FilteringAutoencodersNeurosymbolic Learning
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Apr 5, 2026

Autoencoder-Based Parameter Estimation for Superposed Multi-Component Damped Sinusoidal Signals

Damped sinusoidal oscillations are widely observed in many physical systems, and their analysis provides access to underlying physical properties. However, parameter estimation becomes difficult when the signal decays rapidly, multiple components are superposed, and observational noise is present. In this study, we develop an autoencoder-based method that uses the latent space to estimate the frequency, phase, decay time, and amplitude of each component in noisy multi-component damped sinusoidal signals. We investigate multi-component cases under Gaussian-distribution training and further examine the effect of the training-data distribution through comparisons between Gaussian and uniform training. The performance is evaluated through waveform reconstruction and parameter-estimation accuracy. We find that the proposed method can estimate the parameters with high accuracy even in challenging setups, such as those involving a subdominant component or nearly opposite-phase components, while remaining reasonably robust when the training distribution is less informative. This demonstrates its potential as a tool for analyzing short-duration, noisy signals.

Momoka Iida, Hayato Motohashi, Hirotaka Takahashi

Graduate School of Integrative Science and Engineering, Tokyo City University, 1-28-1 Tamazutsumi, Setagaya-ku, Tokyo 158-8557, Japan · Research Center for Space Science, Advanced Research Laboratories, Tokyo City University, 1-28-1 Tamazutsumi, Setagaya-ku, Tokyo 158-8557, Japan · Department of Physics, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan +2

Parameter EstimationAutoencoders
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Apr 3, 2026

Improving Feasibility via Fast Autoencoder-Based Projections

Enforcing complex (e.g., nonconvex) operational constraints is a critical challenge in real-world learning and control systems. However, existing methods struggle to efficiently enforce general classes of constraints. To address this, we propose a novel data-driven amortized approach that uses a trained autoencoder as an approximate projector to provide fast corrections to infeasible predictions. Specifically, we train an autoencoder using an adversarial objective to learn a structured, convex latent representation of the feasible set. This enables rapid correction of neural network outputs by projecting their associated latent representations onto a simple convex shape before decoding into the original feasible set. We test our approach on a diverse suite of constrained optimization and reinforcement learning problems with challenging nonconvex constraints. Results show that our method effectively enforces constraints at a low computational cost, offering a practical alternative to expensive feasibility correction techniques based on traditional solvers.

Maria Chzhen, Priya L. Donti

University of Toronto Toronto, ON, Canada · Massachusetts Institute of Technology Cambridge, MA, USA

Constrained OptimizationConstrained RLAutoencoders
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Apr 2, 2026

Rare-Aware Autoencoding: Reconstructing Spatially Imbalanced Data

Autoencoders can be challenged by spatially non-uniform sampling of image content. This is common in medical imaging, biology, and physics, where informative patterns occur rarely at specific image coordinates, as background dominates these locations in most samples, biasing reconstructions toward the majority appearance. In practice, autoencoders are biased toward dominant patterns resulting in the loss of fine-grained detail and causing blurred reconstructions for rare spatial inputs especially under spatial data imbalance. We address spatial imbalance by two complementary components: (i) self-entropy-based loss that upweights statistically uncommon spatial locations and (ii) Sample Propagation, a replay mechanism that selectively re-exposes the model to hard to reconstruct samples across batches during training. We benchmark existing data balancing strategies, originally developed for supervised classification, in the unsupervised reconstruction setting. Drawing on the limitations of these approaches, our method specifically targets spatial imbalance by encouraging models to focus on statistically rare locations, improving reconstruction consistency compared to existing baselines. We validate in a simulated dataset with controlled spatial imbalance conditions, and in three, uncontrolled, diverse real-world datasets spanning physical, biological, and astronomical domains. Our approach outperforms baselines on various reconstruction metrics, particularly under spatial imbalance distributions. These results highlight the importance of data representation in a batch and emphasize rare samples in unsupervised image reconstruction. We will make all code and related data available.

Alejandro Castañeda Garcia, Jan van Gemert, Daan Brinks +1

Delft University of Technology (TU Delft), Delft, The Netherlands

AutoencodersImage Reconstruction
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Apr 2, 2026

RAE-AR: Taming Autoregressive Models with Representation Autoencoders

The latent space of generative modeling is long dominated by the VAE encoder. The latents from the pretrained representation encoders (e.g., DINO, SigLIP, MAE) are previously considered inappropriate for generative modeling. Recently, RAE method lights the hope and reveals that the representation autoencoder can also achieve competitive performance as the VAE encoder. However, the integration of representation autoencoder into continuous autoregressive (AR) models, remains largely unexplored. In this work, we investigate the challenges of employing high-dimensional representation autoencoders within the AR paradigm, denoted as RAE-AR. We focus on the unique properties of AR models and identify two primary hurdles: complex token-wise distribution modeling and the high-dimensionality amplified training-inference gap (exposure bias). To address these, we introduce token simplification via distribution normalization to ease modeling difficulty and improve convergence. Furthermore, we enhance prediction robustness by incorporating Gaussian noise injection during training to mitigate exposure bias. Our empirical results demonstrate that these modifications substantially bridge the performance gap, enabling representation autoencoder to achieve results comparable to traditional VAEs on AR models. This work paves the way for a more unified architecture across visual understanding and generative modeling.

Hu Yu, Hang Xu, Jie Huang +4

University of Science and Technology of China · JD Explore Academy · The University of Hong Kong

Exposure BiasAutoregressive Image GenerationVisual Autoregressive ModelsAutoencoders
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Mar 25, 2026

TopoMesh: High-Fidelity Mesh Autoencoding via Topological Unification

The dominant paradigm for high-fidelity 3D generation relies on a VAE-Diffusion pipeline, where the VAE's reconstruction capability sets a firm upper bound on generation quality. A fundamental challenge limiting existing VAEs is the representation mismatch between ground-truth meshes and network predictions: GT meshes have arbitrary, variable topology, while VAEs typically predict fixed-structure implicit fields (\eg, SDF on regular grids). This inherent misalignment prevents establishing explicit mesh-level correspondences, forcing prior work to rely on indirect supervision signals such as SDF or rendering losses. Consequently, fine geometric details, particularly sharp features, are poorly preserved during reconstruction. To address this, we introduce TopoMesh, a sparse voxel-based VAE that unifies both GT and predicted meshes under a shared Dual Marching Cubes (DMC) topological framework. Specifically, we convert arbitrary input meshes into DMC-compliant representations via a remeshing algorithm that preserves sharp edges using an L∞\infty distance metric. Our decoder outputs meshes in the same DMC format, ensuring that both predicted and target meshes share identical topological structures. This establishes explicit correspondences at the vertex and face level, allowing us to derive explicit mesh-level supervision signals for topology, vertex positions, and face orientations with clear gradients. Our sparse VAE architecture employs this unified framework and is trained with Teacher Forcing and progressive resolution training for stable and efficient convergence. Extensive experiments demonstrate that TopoMesh significantly outperforms existing VAEs in reconstruction fidelity, achieving superior preservation of sharp features and geometric details.

Guan Luo, Xiu Li, Rui Chen +6

Tsinghua University · ByteDance Seed · HKUST

AutoencodersVariational Autoencoders3D Mesh Generation3D Mesh Reconstruction
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Mar 23, 2026

End-to-End Training for Unified Tokenization and Latent Denoising

Latent diffusion models (LDMs) enable high-fidelity synthesis by operating in learned latent spaces. However, training state-of-the-art LDMs requires complex staging: a tokenizer must be trained first, before the diffusion model can be trained in the frozen latent space. We propose UNITE - an autoencoder architecture for unified tokenization and latent diffusion. UNITE consists of a Generative Encoder that serves as both image tokenizer and latent generator via weight sharing. Our key insight is that tokenization and generation can be viewed as the same latent inference problem under different conditioning regimes: tokenization infers latents from fully observed images, whereas generation infers them from noise together with text or class conditioning. Motivated by this, we introduce a single-stage training procedure that jointly optimizes both tasks via two forward passes through the same Generative Encoder. The shared parameters enable gradients to jointly shape the latent space, encouraging a "common latent language". Across image and molecule modalities, UNITE achieves near state of the art performance without adversarial losses or pretrained encoders (e.g., DINO), reaching FID 2.12 and 1.73 for Base and Large models on ImageNet 256 x 256. We further analyze the Generative Encoder through the lenses of representation alignment and compression. These results show that single stage joint training of tokenization & generation from scratch is feasible.

Shivam Duggal, Xingjian Bai, Zongze Wu +5

Massachusetts Institute of Technology · Adobe

Latent Diffusion ModelsImage GenerationAutoencoders
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Mar 20, 2026

Data-driven discovery of roughness descriptors for surface characterization and intimate contact modeling of unidirectional composite tapes

Unidirectional tapes surface roughness determines the evolution of the degree of intimate contact required for ensuring the thermoplastic molecular diffusion and the associated inter-tapes consolidation during manufacturing of composite structures. However, usual characterization of rough surfaces relies on statistical descriptors that even if they are able to represent the surface topology, they are not necessarily connected with the physics occurring at the interface during inter-tape consolidation. Thus, a key research question could be formulated as follows: Which roughness descriptors simultaneously enable tape classification-crucial for process control-and consolidation modeling via the inference of the evolution of the degree of intimate contact, itself governed by the process parameters?. For providing a valuable response, we propose a novel strategy based on the use of Rank Reduction Autoencoders (RRAEs), autoencoders with a linear latent vector space enforced by applying a truncated Singular Value Decomposition (SVD) to the latent matrix during the encoder-decoder training. In this work, we extract useful roughness descriptors by enforcing the latent SVD modes to (i) accurately represent the roughness after decoding, and (ii) allow the extraction of existing a priori knowledge such as classification or modelling properties.

Sebastian Rodriguez, Mikhael Tannous, Jad Mounayer +3

Univ Toulouse, IMT Mines Albi, INSA Toulouse, ISAE-SUPAERO, CNRS, ICA, Albi, France

ManufacturingAutoencoders
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