Denoising Autoencoders

Noise2Noise (N2N) trains denoisers on pairs of independently corrupted observations, eliminating clean references. We stress-test two natural conjectures about why the L1 loss outperforms L2 here. First, the hypothesis that the L1 loss confers robustness via parameter sparsity confuses the loss with Lasso regularization: an explicit Lasso penalty produces the predicted sparsity yet fails to reproduce L1's cross-noise behavior, while L1- and L2-trained weight distributions are indistinguishable. Second, the population optima of the two losses coincide exactly for symmetric signal posteriors and nearly so for concentrated ones. Measured differences are therefore dominated by optimization dynamics (bounded-influence gradients), which we probe with gradient statistics and contaminated-target training. On Kodak24 with five synthetic noise families, the L1 loss holds a statistically significant edge over L2, below 1 dB PSNR, holding across three seeds on 13 of the 14 noise columns. On real camera noise the loss is not the decisive variable in distribution: on official SIDD validation blocks, synthetic-Gaussian-trained N2N models gain only 0.8 to 3.7 dB over the noisy input regardless of loss, while retraining on SIDD's own noisy pairs, never reading ground truth, gains 9.4 to 11.0 dB, far ahead of BM3D. All metrics are on raw network outputs, and the study makes no leaderboard claim. The training pair distribution, not the loss, carries the inductive bias. That design rule applies wherever clean references are unobtainable, from microscopy to industrial inspection sensors.

Pre-trained language models have significantly improved sentence representation learning, yet their embedding remain sensitive to semantic preserving textual perturbations such as synonym substitution, masking and word dropout. This work proposes a lightweight Contrastive Denoising Autoencoder (CDAE) that refines pre-trained BERT embedding by jointly optimizing contrastive and reconstruction objective to learn perturbation-invariant representation. We evaluate the proposed framework using multiple perturbation strategies with varying strengths and compare it against the original BERT embeddings and SimCSE. Experimental results show that CDAE consistently preserves higher embedding similarity under perturbations, with the improvements becoming more pronounced as framework effectively enhances representation stability while preserving semantic information, highlighting perturbation-invariant learning as a promising direction for improving sentence embeddings. The source code is publicly available at: https://github.com/ComputationIASBS/CDAE

Medical visual question answering (Med-VQA) has strong potential for clinical decision support by enabling AI models to interpret medical images and answer clinically relevant queries. Recent approaches typically connect off-the-shelf vision encoders with large language models (LLMs) through lightweight mapping networks to reduce computational cost. However, these methods often overlook the importance of handling noise and small irrelevant changes in visual representations. To address these challenges, we propose a noise-aware Med-VQA framework that incorporates a denoising autoencoder before visual embeddings are mapped into the input space of an LLM. The denoising autoencoder is pretrained to reconstruct clean visual embeddings from corrupted inputs, encouraging the model to learn robust visual representations that are less sensitive to noise. The resulting embeddings are then projected into the language model embedding space using a multi-layer perceptron (MLP), forming visual prefix tokens that provide image information to the LLM. To enable efficient adaptation without full retraining, we employ parameter-efficient fine-tuning using low-rank adaptation (LoRA). The proposed method is evaluated on the SLAKE and PathVQA benchmarks. Experimental results show improved robustness to noisy input embeddings while maintaining competitive clean performance across multiple evaluation criteria. These findings suggest that learning more robust visual representations can enhance Med-VQA performance and robustness.

We present a fully convolutional denoising autoencoder (FC-DAE) for denoising two-time intensity-intensity correlation functions ($C_2$) in X-ray photon correlation spectroscopy (XPCS). Unlike conventional denoising autoencoders that are typically restricted to fixed input sizes, the FC-DAE accepts inputs of arbitrary dimensions while preserving correlation structures across diverse dynamical regimes. The model is trained using experimentally derived $C_2$ data collected at NSLS-II beamlines, with data augmentation applied to expand the diversity of the dataset and reduce overfitting. The FC-DAE successfully recovers intricate dynamical features in low signal-to-noise conditions while maintaining structural fidelity. To assess reconstruction reliability, we employ quantitative metrics to evaluate structural fidelity and identify potential model-induced bias. Our results demonstrate that the FC-DAE provides robust denoising performance with high computational efficiency, enabling recovery of XPCS dynamics under photon-limited and low-dose measurement conditions.

Accurately predicting crystal properties is critical for accelerating materials discovery, but it is often limited by scarce labeled data and costly theoretical calculations. To alleviate this, we propose UNATE (Unsupervised Atomic Embedding), a framework that leverages structural information extracted from unlabeled crystal structures. UNATE integrates an unsupervised denoising autoencoder with self-supervised contrastive learning to learn robust atomic representations, which are then used as input features for downstream property prediction. Experimental results show that replacing raw atomic numbers with UNATE-pretrained node embeddings yields a 2.7% improvement over the full-data baseline. Notably, the benefits become more pronounced in scenarios with limited labeled data, reaching improvements of up to 10% when only 25% of the labeled data is used.

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

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.

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.

Urban bike-sharing systems require strategic station expansion to meet growing demand. Traditional allocation approaches rely on explicit demand modelling that may not capture the urban characteristics distinguishing successful stations. This study addresses the need to exploit patterns from existing stations to inform expansion decisions, particularly in data-constrained environments. We present a data-driven framework leveraging existing stations deemed desirable by operational metrics. A hybrid denoising autoencoder (HDAE) learns compressed latent representations from multi-source grid-level features (socio-demographic, built environment, and transport network), with a supervised classification head regularising the embedding space structure. Expansion candidates are selected via greedy allocation with spatial constraints based on latent-space similarity to existing stations. Evaluation on Trondheim's bike-sharing network demonstrates that HDAE embeddings yield more spatially coherent clusters and allocation patterns than raw features. Sensitivity analyses across similarity methods and distance metrics confirm robustness. A consensus-based procedure across multiple parametrisations distils 32 high-confidence extension zones where all parametrisations agree. The results demonstrate how representation learning captures complex patterns that raw features miss, enabling evidence-based expansion planning without explicit demand modelling. The consensus procedure strengthens recommendations by requiring agreement across parametrisations, while framework configurability allows planners to incorporate operational knowledge. The methodology generalises to any location-allocation problem where existing desirable instances inform the selection of new candidates.

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.

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.