iPINN for Broadband CARS Phase Retrieval: A Framework for Function Approximation and Inverse Modeling Problems in Nonlinear Spectroscopy

Phase retrieval in broadband coherent anti-Stokes Raman spectroscopy (BCARS) is an ill-posed inverse problem. The Raman-like signal is encoded in the imaginary part of the resonant susceptibility, which mixes coherently with a non-resonant background (NRB) that varies across acquisitions. We introduce an inverse physics-informed neural network (iPINN) that predicts Lorentzian peak parameters from raw BCARS spectra and reconstructs the resonant susceptibility through a differentiable analytical forward model. A transformer encoder assigns spectral features to 24 learnable peak slots, and a multi-view consistency loss enforces invariance across NRB pattern, NRB strength, and noise. Unlike direct spectral regression approaches, the method retains accuracy under varying acquisition conditions. On a public benchmark, iPINN achieves the lowest error among the tested baselines (MAE 0.016 vs. next-best 0.046). On 28 zero-shot test spectra acquired across seven solvents and four focal positions, accuracy is depth-invariant in five of seven solvents. These results show that inverse parametric prediction with a differentiable physical decoder supports robust phase retrieval across measurement conditions.

S3C-LLM: Skill-Code Guided Agentic Language Models for Spectrum-to-Structure Elucidation

Spectroscopic structure elucidation is central to molecular analysis, but recent Large Language Model (LLM)-based methods mostly formulate it as direct spectrum-to-SMILES generation. Although this paradigm can leverage paired spectral data, it does not explicitly model the analytical workflow used by spectroscopists, such as diagnostic peak interpretation, fragment reasoning, formula constraints, and chemical consistency checking. In this paper, we introduce S3C-LLM, a skill-guided and code-grounded agentic LLM for spectrum-to-structure elucidation. Rather than directly predicting a molecule, S3C-LLM retrieves modality-specific spectroscopy skills, executes analysis code to instantiate these skills on the input spectra, and integrates the resulting peak-level evidence and formula constraints before generating SMILES. Specifically, we contribute a self-evolving spectroscopy skill library, a thinking-augmented skill-code trajectory construction pipeline, and a two-stage training strategy that teaches Qwen3-4B through supervised fine-tuning (SFT) followed by our proposed step-level reinforcement learning (RL). Experiments on diverse benchmarks show that S3C-LLM consistently outperforms current general LLMs and spectrum-specific models across spectra, while using less than 1/10th of SpectraLLM's training corpus.

Physics-informed learning for the inverse problem in resonant ultrasound spectroscopy

Inferring elastic constants from resonant ultrasound spectra is a nonlinear and typically overdetermined inverse problem based on finite spectral data. We formulate the Rayleigh-Ritz inverse problem as a constrained inverse-isospectral problem on the set of physically admissible elasticity tensors. This induces effective low-dimensional variables for the inverse map on the admissible elasticity manifold: length and elastic scales, aspect-ratio coordinates, scale-free spectral features, and stability-respecting elastic ratios. We use these variables to construct a physics-informed learning pipeline in which a regression model acts only on reduced spectral and geometric features, while scale recovery and final elastic-constant reconstruction are imposed analytically. For the full cubic benchmark, the reconstructed constants have MAE values of $20.37(35.15)$, $24.30(41.33)$, and $2.13(3.66)~\mathrm{GPa}$ for $C_{11}$, $C_{12}$, and $C_{44}$. In the fixed-geometry benchmark, the corresponding cubic MAPE values are $4.14(3.87)\%$, $8.31(8.50)\%$, and $2.44(2.86)\%$, while the isotropic values are $4.0(3.6)\%$ and $0.4(0.3)\%$ for the bulk and shear moduli. The inverse problem then becomes a constrained regression problem in variables adapted to the geometry, scaling, crystal symmetry, and thermodynamic stability of Hookean elasticity.

MM-Spectrum: Multimodal Multi-spectral Molecular Structural Elucidation with a Stable MoE Framework

Inferring molecular structures from multimodal spectroscopic measurements requires integrating complementary yet highly heterogeneous signals. However, the common paradigm of directly concatenating multispectral sequences can exhibit anomalous performance degradation, primarily due to pronounced heterogeneity and the resulting multimodal imbalance across modalities. As a remedy, we propose MM-Spectrum, a sparse Mixture-of-Experts framework tailored for multimodal multispectral spectra-to-structure elucidation. To better match the information characteristics under multispectral imbalance, MM-Spectrum introduces an explicit modality-aware routing mechanism that exposes spectral identity to the router in addition to token content representations. Moreover, it incorporates shared and interaction experts, together with heterogeneous expert capacities, to extract multispectral modality-unique and cross-modal synergistic information while suppressing noise-induced interference. Across full-modality, bimodal, and missing-modality settings on molecular structural elucidation, MM-Spectrum achieves consistent and substantial improvements, supported by ablation studies and interpretability analyses.

Traceable Spectral Inference via Influence Functions: Efficient Data Attribution and Error Proxies for the Ariel Mission

Interpretability is critical for machine learning models deployed in scientific space missions such as ESA's Ariel, where ground truth is unavailable during operations and physical plausibility must be assessed. While most explainable AI methods focus on feature attribution, this work investigates training data attribution through influence functions and introduces three key contributions for operational spectroscopy pipelines. First, influence is reformulated in terms of prediction rather than loss, enabling label-free deployment. Second, by leveraging the closed-form ridge solution of an Extreme Learning Machine, infinitesimal prediction influence is efficiently computed. Third, an influence-based conservative error proxy is derived by propagating training residuals through the influence sensitivities. Evaluated against simulated spectra, the proposed proxy correlates strongly with scale and shape-based spectral errors. Furthermore, influence functions enable the identification of the most influential samples and the approximation of the most harmful ones. Together, these results suggest that this approach can serve as an operational framework for scientific machine learning.

Meta-clustering of milk mid-infrared spectra identifies dairy cow groups associated with negative energy balance in early lactation

Clustering methods have been used to identify distinct groups of milk samples, cows, or herds. Fourier-transform infrared (FTIR) spectroscopy, particularly mid-infrared (MIR) spectroscopy, has been applied to individual cow milk samples to predict various milk traits. Applying clustering directly to MIR spectral data may reveal latent groups of cows associated with milk traits or health disorders and can help prevent these conditions or monitor at-risk animals. This study aimed to identify groups of individual dairy cows in early lactation directly from milk MIR spectra and to analyze their associations with milk traits. Using a dataset of 407,632 individual milk MIR records from 3,408 commercial farms, we combined (i) spectral filtering that selects informative wavenumbers, (ii) two dimensionality-reduction methods: principal component analysis (PCA) and an autoencoder, and (iii) two clustering algorithms: k-means and spectral clustering to yield eight different clustering approaches. We regrouped the assigned clusters into meta-clusters that encompassed the most similar ones identified by the eight approaches. Our results revealed five distinct meta-clusters of early-lactation individual dairy cows significantly associated with milk traits. Despite substantial differences, the eight approaches converged on the same five meta-clusters, and the classic, computationally efficient PCA-based k-means approach using the full spectrum recaptured clusters identified by more sophisticated, computationally intensive approaches. The five meta-clusters were strongly associated with DIM and appeared to reflect a gradient of negative energy balance (NEB) severity: severe, moderate, and possibly mild, while the remaining two likely represented cows recovering from NEB, one with rapid restoration of energy balance and one in early recovery.

Posterior Inference of Hamiltonian Parameters from RIXS Spectroscopy

We present the first application of simulation-based inference to resonant inelastic X-ray scattering spectroscopy. Using truncated marginal neural ratio estimation to efficiently restrict the prior and conditional flow matching as the joint density estimator, we infer full posteriors with a modest simulation budget for two Ni$^{2+}$ compounds---NiPS$_3$ as a representative covalent case and K$_2$NiF$_4$ as a more atomic one. We demonstrate that a vision transformer encoder whose tokenization matches the physical layout of the RIXS map yields better-covered and sharper posteriors than generic image encoders. Applying the validated method to experimental NiPS$_3$ and K$_2$NiF$_4$ data, we recover a joint posterior that reveals parameter correlations invisible to point estimators, and a posterior predictive distribution that closely matches the observed spectrum. The amortized posterior unlocks a class of analyses not previously available to the field such as nuisance-marginalized uncertainty quantification, multi-measurement posterior fusion and active experimental design.

Multi-Agent Closed-Loop Reasoning for Organic Structure Elucidation from Multimodal Spectra

Following the molecular discovery and synthesis revolutions, scalable automated structure elucidation from routine spectroscopic data remains an outstanding challenge. Despite decades of computational efforts, no existing system achieved reliable reasoning over unseen spectra. Here, we propose MACROS, a multi-agent system automating structure elucidation by emulating expert iterative hypothesis-testing. Trained on 100M simulated and 1.6M experimental spectra-molecule pairs, it natively supports arbitrary combinations of routine spectroscopic techniques. It achieves unprecedented zero-shot generalization to diverse real-world samples, correctly identifying synthetic compounds, natural products and metabolites above 500 Da with 1D NMR. Remarkably, MACROS spontaneously recovers textbook spectroscopic correlations from unassigned data and exhibits emergent chemical intuition such as a ring-first parsing preference, learning fundamental chemical principles rather than memorizing database patterns. MACROS augments chemists via collaboration to deliver sixfold faster, 40% more accurate elucidation. MACROS establishes a scalable foundation for fully automated structure elucidation, and catalyzes accelerated molecular discovery toward autonomous laboratories.

NMR Elucidation as an Agentic Search Problem, Not a Modeling Problem

Structural elucidation from Nuclear Magnetic Resonance (NMR) data remains a fundamental bottleneck across chemistry, materials science, and biology. We demonstrate that an agentic AI system can perform this task at a level comparable to graduate-level chemistry students. Instead of training a model to directly map spectra to structures, we build a single autonomous agent, backed by a frozen LLM, that interacts with a curated environment with access to domain-specific processing tools, validation checks, tabulated chemical shifts, and instructions that outline the stepwise nature of a chemist's thinking process. On the Alberts dataset, our agent elucidates structures with a top-1 accuracy of 71%, comparable to the performance of graduate students at 66% top-1 accuracy. On the van Bramer and AstraZeneca datasets, our agent achieved 80% and 20% top-1 accuracy respectively, outperforming zero-shot end-to-end deep learning models which were trained on large datasets of simulated spectra. These results show that reframing NMR elucidation as an LLM-guided constrained search, rather than a modeling task, yields substantial gains and suggests a path toward multi-step orchestration frameworks that integrate a variety of tools, models, and domain knowledge to assist in automating spectroscopic analysis.

Batch-Invariant Spectral Intelligence for Robust and Explainable Insect Authentication

Edible insects offer an efficient source of alternative protein, requiring less land, water and emitting less greenhouse gas than conventional livestock. However, their successful integration into the food supply chain demands reliable species authentication to control allergen exposure, prevent adulteration, and meet regulatory standards. Near-infrared spectroscopy provides a rapid analytical tool, but its performance drops when applied to production batches unseen during training due to batch-to-batch variation in spectral measurements. We introduce the Batch-Invariant Spectral Network (BISN), an end-to-end framework that combines a learnable preprocessing module, initialised with Savitzky-Golay filtering, with an entropy-regularised adversarial objective to suppress batch-specific spectral variation. In contrast to Domain-Adversarial Neural Networks, which enforce domain adaptation only after feature extraction, BISN suppress batch-effects before species-specific features are learned. Using 2,700 spectra from three species (Acheta domesticus, Hermetia illucens, and Tenebrio molitor) collected across three independent production batches, BISN achieves a mean leave-one-batch-out accuracy of 0.93 (standard deviation 0.04), outperforming the strongest baseline by four percent. Further insights gained by using explainable AI confirm that model decisions consistently rely on the lipid and protein absorption regions across all folds, connecting predictive performance to known insect biochemistry. BISN addresses both cross-batch robustness and biochemical interpretability for automated insect species authentication under realistic industrial conditions. The source code and dataset are publicly available at https://github.com/majharB/bisn.

A Standard Processing Pipeline for High-accuracy Measurement of Few-shot Regression on Laser Induced Breakdown Spectroscopy

Laser-induced breakdown spectroscopy (LIBS) faces challenges in high-accuracy quantitative measurement under few-shot scenarios due to spectral noise and data scarcity. Traditional preprocessing methods often fail to preserve subtle spectral features or capture nonlinear correlations. This work proposes a standardized processing pipeline integrating diffusion-based denoising, attention-based autoencoder for dimensionality reduction, group shuffling data augmentation, and ordinary least squares regression. The diffusion module employs a 3D UNet architecture to remove spectral noise while preserving essential emission features. The attention-autoencoder captures nonlinear spectral correlations, effectively reducing high-dimensional spectral data to compact latent representations. Group shuffling data augmentation enhances model robustness by creating synthetic samples through feature group permutation. Experimental results on multiple elemental concentrations demonstrate that our Diffusion-DA-AE pipeline achieves superior performance with a mean RMAE of 0.2847, representing 37.7\% and 37.6\% improvements over baseline autoencoder and traditional PCA-PLS regression, respectively. The framework's effectiveness validates its generalizability and establishes a new benchmark for few-shot LIBS regression.

Multi-Adapter PPO: A Cross-Attention Enhanced Wavelength Selection Framework for LIBS Quantitative Analysis

Laser-induced breakdown spectroscopy (LIBS) quantitative analysis faces critical challenges in wavelength selection due to high-dimensional spectral data and the fundamental trade-off between prediction accuracy and feature efficiency. This paper presents a novel Multi-Adapter PPO framework that transforms wavelength selection into a reinforcement learning problem, leveraging cross-attention mechanisms and multiple specialized adapters to capture complex spectral relationships. Our approach outperforms traditional Particle Swarm Optimization (PSO) by an average of 28.4\% in comprehensive score and 45.2\% in prediction accuracy across steel and coal datasets. The proposed method demonstrates superior performance in balancing prediction accuracy with feature efficiency, achieving state-of-the-art results in LIBS quantitative analysis while maintaining interpretability and computational efficiency. We released our code and dataset here: https://github.com/Hflying/MAPPO

Multi-Variable Stellar Parameter Estimation Using Residual Multitask Neural Networks

We present an end-to-end pipeline for estimating stellar parameters from Sloan Digital Sky Survey Data Release 12 spectra using a fully connected multitask neural network with residual blocks, whose hyperparameters are tuned via Bayesian optimization. The preprocessing pipeline includes per-spectrum standardization, RobustScaler normalization of the target variables -- effective temperature $T_{\mathrm{eff}}$, metallicity $[\mathrm{Fe/H}]$, and surface gravity $\log g$ -- and data augmentation via Gaussian noise injection. On a held-out test set, the model achieved Mean Absolute Errors (MAE) of $59.76~\mathrm{K}$ for $T_{\mathrm{eff}}$, $0.103~\mathrm{dex}$ for $[\mathrm{Fe/H}]$, and $0.130~\mathrm{dex}$ for $\log g$. Normalized against the full-scale range of each parameter, these results represent range-normalized errors between $1\%$ and $3\%$, achieved with a highly efficient model complexity of approximately 540,000 trainable parameters. These results demonstrate that a compact residual multitask architecture, combined with principled signal preprocessing, provides a parameter-efficient solution for nonlinear parameter estimation in large-scale spectral datasets. In particular, the proposed model achieves competitive performance with substantially lower complexity than deeper neural network baselines.

Integral Field Unit Spectroscopy with One Fiber

Integral field unit (IFU) spectroscopy provides spatially resolved spectra across galaxies, offering crucial insights into their evolution. However, its high observational cost limits current IFU datasets to $\sim 10^4$ objects. We present a multi-modal, probabilistic foundation model that predicts high-resolution spectra with calibrated uncertainties at arbitrary spatial locations within a galaxy directly from broadband images. Built on a masked autoencoder framework, our architecture injects fiber positional encodings and redshift aware wavelength encodings, enabling spatially conditioned predictions. Trained on 4.7 million images and single fiber spectroscopic observations from the Dark Energy Spectroscopic Instrument (DESI) survey, our model exploits the natural variance of fiber placements and the morphological self-similarity of galaxies to achieve IFU-like capabilities without any IFU training data. Predicted emission line flux maps match independent IFU observations from the Mapping Nearby Galaxies at APO (MaNGA) survey, with performance comparable to a supervised baseline trained directly on IFU data.

Spectral Model eXplainer: a chemically-grounded explainability framework for spectral-based machine learning models

Spectral-based machine learning models have been increasingly deployed in chemometrics and spectroscopy, where predictive accuracy is as important as explainability. Current employed eXplainable Artificial Intelligence (XAI) methods are largely adapted from tabular or generic multivariate domains, assigning relevance to isolated spectral variables rather than to the chemically meaningful spectral zones. Widely adopted tools such as SHapley Additive exPlanations (SHAP), Permutation Feature Importance (PFI), and Variable Importance in Projection scores (VIP) were not designed for the physical continuity and high collinearity of spectral data, and their variable-level outputs require post-hoc aggregation to recover zone-level information. This study introduces the Spectral Model eXplainer (SMX), a post-hoc, global, model-agnostic XAI framework that explains spectral classifiers through expert-informed spectral zones. SMX summarizes each zone via PCA, defines quantile-based logical predicates, estimates predicate relevance with perturbation in stochastic subsamples, and aggregates bag-wise rankings in a directed weighted graph summarized by Local Reaching Centrality. A key component is threshold spectrum reconstruction, which back-projects predicate boundaries to the original spectral domain in natural measurement units, enabling direct visual comparison with measured spectra. The method was evaluated on eight real spectral datasets (six based on X-ray Fluorescence--XRF and two based on Gamma-ray Spectrometry) and one synthetic benchmark with known gr

CNNs for Vis-NIR Chemometrics: From Contradiction to Conditional Design

Near-infrared (NIR; a.k.a.\ NIRS) deep-learning studies in chemometrics increasingly report mutually inconsistent conclusions regarding convolutional neural network (CNN) design, including small versus large kernels, shallow versus deep architectures, raw spectra versus preprocessing, and single-domain training versus transfer learning. As a result, the same architecture can appear superior in one study and inferior in another, creating a practical impasse for chemometric practitioners. In this review, we argue that these contradictions are not evidence of irreconcilable methods but a structurally expected consequence of uncontrolled moderating variables. Specifically, we trace recurring disagreements to (i) the indirect nature of Vis--NIR measurement in water-dominated matrices, (ii) mismatch between effective receptive field (ERF) and the width of informative spectral structure, and (iii) validation design (including split strategy, hyperparameter tuning budget, and exposure to deployment-like shifts) acting as a hidden hyperparameter that can dominate model ranking. Building on evidence from published chemometrics and spectroscopy studies, we propose a conditional design framework that links architecture and preprocessing choices to spectral physics, dataset regime, and intended deployment scenario. Overall, the proposed perspective moves DL Chemometrics from template-driven architecture selection toward reproducible, physics-aware, and deployment-aligned model comparison.