A Practical Noise2Noise Denoising Pipeline for High-Throughput Raman Spectroscopy

Raman spectra obtained in real world applications are often a noisy combination of several spectra of various substances in a tested sample. Unmixing such spectra into individual components corresponding to each of the substances is of great value and has been a longstanding challenge in Raman spectroscopy. Existing unmixing methods are predominantly designed to invert an overdetermined mixed model and therefore require multiple mixed spectra as input. However, open domain and/or non-cooperative detection applications in Raman spectroscopy such as controlled substance detection, call for single-channel solutions which can identify individual components from thousands of candidates by analyzing only a single noisy mixed spectrum. To our knowledge, sparse regression is the only existing solution which can cope with this scenario, yet it has very low tolerance to noises and can hardly be applicable in practice. To address these limitations, we introduce a novel neural approach for single-channel Raman spectrum unmixing inspired by speech separation. It aims at solving underdetermined systems and can decompose a noisy mixed spectrum from a library of thousands of components (substances). The core of our method is a deep separation neural network (RSSNet) which takes a mixed spectrum as input and outputs spectra of pure components. We created two synthetic datasets of single-channel Raman spectra unmixing and demonstrated feasibility and superiority of RSSNet on these datasets (outperform competing methods by >4dB). Furthermore, we verified that RSSNet, trained solely on synthetic data, can successfully unmix real-world mixed spectra of mixtures of mineral powders, exhibiting strong generalization. Our approach represents a new paradigm for Raman unmixing and enables new possibilities for fast detection of Raman mixtures.

Raman spectroscopy enables non-destructive, label-free molecular characterization across materials science, biomedicine and process monitoring. Predictive Raman datasets often contain few labelled spectra and thousands of ordered wavenumbers, with informative variation within bands and across distant spectral regions. Latent-variable chemometrics accommodates collinear small-sample data but can obscure fine peak morphology, whereas deep spectral networks resolve this structure only after task-specific training. TabPFN avoids task-specific parameter fitting through pretrained in-context inference, but processes very wide inputs as feature-subsampled views that do not preserve joint visibility of related bands. We present RamanPFN, a spectral representation framework that encodes these dependencies before TabPFN inference. Global Compositional Unmixing constructs non-negative coordinates over the complete spectrum so that distant bands with shared latent variation occupy a common predictive axis. Local Vibrational Subspace Encoding represents contiguous wavenumber regions with multiple orthogonal modes that retain independent changes in peak shape, intensity and position. The representations are evaluated separately and combined at the prediction level. Evaluation covered 150 tasks from 74 public Raman datasets. RamanPFN reduced root-mean-square error by 19.6% on average across 129 regression targets relative to direct TabPFN inference and further reduced the remaining classification error by 9.0% across 21 classification tasks. These results establish explicit spectral representation as an effective interface between high-dimensional Raman measurements and reusable tabular inference.

Antimicrobial resistance is expected to claim 10 million lives per year by 2050, and resource-limited regions are most affected. Raman spectroscopy is a novel pathogen diagnostic approach promising rapid and portable antibiotic resistance testing within a few hours, compared to days when using gold standard methods. However, current algorithms for Raman spectra analysis 1) are unable to generalize well on limited datasets across diverse patient populations and 2) require increased complexity due to the necessity of non-trivial pre-processing steps, such as feature extraction, which are essential to mitigate the low-quality nature of Raman spectral data. In this work, we address these limitations using Sharpness-Aware Minimization (SAM) to enhance model generalization across a diverse array of hyperparameters in clinical bacterial isolate classification tasks. We demonstrate that SAM achieves accuracy improvements of up to 10.5% on a single split, and an increase in average accuracy of 2.7% across all splits in spectral classification tasks over the traditional optimizer, Adam. These results display the capability of SAM to advance the clinical application of AI-powered Raman spectroscopy tools.