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MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition

Motivation: Untargeted mass spectrometry experiments enable the profiling of metabolites in complex biological samples. The collected fragmentation spectra are the metabolite’s fingerprints that are used for molecule identification and discovery. Two main mass spectrometry strategies exist for the collection of fragmentation spectra: data-dependent acquisition (DDA) and data-independent acquisition (DIA). In the DIA strategy, all the metabolites ions in predefined mass-to-charge ratio ranges are co-isolated and co-fragmented, resulting in multiplexed fragmentation spectra that are challenging to annotate. In contrast, in the DDA strategy, fragmentation spectra are dynamically and specifically collected for the most abundant ions observed, causing redundancy and sub-optimal fragmentation spectra collection. Yet, DDA results in less multiplexed fragmentation spectra that can be readily annotated. Results: We introduce the MS2Planner workflow, an Iterative Optimized Data Acquisition strategy that optimizes the number of high-quality fragmentation spectra over multiple experimental acquisitions using topological sorting. Our results showed that MS2Planner increases the annotation rate by 38.6% and is 62.5% more sensitive and 9.4% more specific compared to DDA. Availability and implementation MS2Planner code is available at https://github.com/mohimanilab/MS2Planner. The generation of the inclusion list from MS2Planner was performed with python scripts available at https://github.com/lfnothias/IODA_MS.

47 OTHER INSTRUMENTATION↗

The entropy of galaxy spectra: how much information is encoded?

Abstract The inverse problem of extracting the stellar population content of galaxy spectra is analysed here from a basic standpoint based on information theory. By interpreting spectra as probability distribution functions, we find that galaxy spectra have high entropy, thus leading to a rather low effective information content. The highest variation in entropy is unsurprisingly found in regions that have been well studied for decades with the conventional approach. We target a set of six spectral regions that show the highest variation in entropy – the 4000 Å break being the most informative one. As a test case with real data, we measure the entropy of a set of high-quality spectra from the Sloan Digital Sky Survey, and contrast entropy-based results with the traditional method based on line strengths. The data are classified into star-forming (SF), quiescent (Q), and active galactic nucleus (AGN) galaxies, and show – independently of any physical model – that AGN spectra can be interpreted as a transition between SF and Q galaxies, with SF galaxies featuring a more diverse variation in entropy. The high level of entanglement complicates the determination of population parameters in a robust, unbiased way, and affects traditional methods that compare models with observations, as well as machine learning (especially deep learning) algorithms that rely on the statistical properties of the data to assess the variations among spectra. Entropy provides a new avenue to improve population synthesis models so that they give a more faithful representation of real galaxy spectra.

Ferreras, Ignacio (ORCID:0000000345843127)↗

Novel principal component analysis tool based on python for analysis of complex spectra of time-of-flight secondary ion mass spectrometry

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful surface analysis tool, which can simultaneously provide elemental, isotopic, and molecular information with part per million (ppm) sensitivity. However, each spectrum may be composed of hundreds of ion signals, which makes the spectra data complex. Principal component analysis (PCA) is a multivariate analysis technique that has been widely used to figure out the variances among samples in ToF-SIMS spectra data analysis and is showing great success in the explanation of complex ToF-SIMS spectra. So far, several software tools have been developed for PCA of ToF-SIMS spectra; however, none of them are freely available. Such a situation leads to some difficulties in extending applications of PCA to various research fields. More importantly, it has long been challenging for common researchers to understand PCA plots and extract chemical differences among samples. In this work, we developed a new and flexible software tool (named “advanced spectra pca toolbox”) based on python for PCA of complex ToF-SIMS spectra along with an easy-to-read manual. It can generate data analysis reports automatically to explain chemical differences among samples, allowing less experienced researchers to easily understand tricky PCA results. Moreover, it is expandable and compatible with artificial intelligence/machine learning functions. Pure goethite and different lignin adsorbed goethite samples were used as a model system to demonstrate our new software tool, proving that our software tool can be readily used in complex spectra data processing. Our new software tool is open-source, convenient, flexible, and expandable. We expect this open-source tool will benefit the ToF-SIMS community.

47 OTHER INSTRUMENTATION↗

Automated Stellar Spectra Classification with Ensemble Convolutional Neural Network

Large sky survey telescopes have produced a tremendous amount of astronomical data, including spectra. Machine learning methods must be employed to automatically process the spectral data obtained by these telescopes. Classification of stellar spectra by applying deep learning is an important research direction for the automatic classification of high-dimensional celestial spectra. In this paper, a robust ensemble convolutional neural network (ECNN) was designed and applied to improve the classification accuracy of massive stellar spectra from the Sloan digital sky survey. We designed six classifiers which consist six different convolutional neural networks (CNN), respectively, to recognize the spectra in DR16. Then, according the cross-entropy testing error of the spectra at different signal-to-noise ratios, we integrate the results of different classifiers in an ensemble learning way to improve the effect of classification. The experimental result proved that our one-dimensional ECNN strategy could achieve 95.0% accuracy in the classification task of the stellar spectra, a level of accuracy that exceeds that of the classical principal component analysis and support vector machine model.

79 ASTRONOMY AND ASTROPHYSICS↗

Zero-Field NMR and Millitesla-SLIC Spectra for >200 Molecules from Density Functional Theory and Spin Dynamics

NMR is usually performed at magnetic fields of 1 T and above to obtain sufficient sensitivity and spectral dispersion to identify chemicals based on chemical shifts and J couplings. At lower fields, the advent of hyperpolarization technologies and sensitive detectors can address sensitivity concerns. However, it remains disputed whether spectral signatures at zero and ultra-low fields are sufficient for chemical identification. Here, we report an all–electron DFT-based batch calculation of J-coupling constants, which are used to generate J coupling NMR spectra at zero field and 6.5 mT for over 200 small molecules. In the developed computational tool chain, we first used the all-electron FHI-aims code to calculate the molecular J couplings and chemical shifts. We then fed the calculated NMR parameters into the NMR simulation package SPINACH to simulate both heteronuclear J coupling spectra at zero-field, and homonuclear J coupling spectra as spin-lock induced crossing (SLIC) spectra at ultra-low field (6.5 mT). The resulting spectra demonstrate that zero and ultra-low field NMR spectra can represent unique identifiers of chemical structure for small molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A database of synthetic inelastic neutron scattering spectra from molecules and crystals

Abstract Inelastic neutron scattering (INS) is a powerful tool to study the vibrational dynamics in a material. The analysis and interpretation of the INS spectra, however, are often nontrivial. Unlike diffraction, for which one can quickly calculate the scattering pattern from the structure, the calculation of INS spectra from the structure involves multiple steps requiring significant experience and computational resources. To overcome this barrier, a database of INS spectra consisting of commonly seen materials will be a valuable reference, and it will also lay the foundation of advanced data-driven analysis and interpretation of INS spectra. Here we report such a database compiled for over 20,000 organic molecules and over 10,000 inorganic crystals. The INS spectra are obtained from a streamlined workflow, and the synthetic INS spectra are also verified by available experimental data. The database is expected to greatly facilitate INS data analysis, and it can also enable the utilization of advanced analytics such as data mining and machine learning. Notice: This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan ( http://energy.gov/downloads/doe-public-access-plan ).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DIGS: deep inference of galaxy spectra with neural posterior estimation

Abstract With the advent of billion-galaxy surveys with complex data, the need of the hour is to efficiently model galaxy spectral energy distributions (SEDs) with robust uncertainty quantification. The combination of simulation-based inference (SBI) and amortized neural posterior estimation (NPE) has been successfully used to analyse simulated and real galaxy photometry both precisely and efficiently. In this work, we utilise this combination and build on existing literature to analyse simulated noisy galaxy spectra. Here, we demonstrate a proof-of-concept study of spectra that is (a) an efficient analysis of galaxy SEDs and inference of galaxy parameters with physically interpretable uncertainties; and (b) amortized calculations of posterior distributions of said galaxy parameters at the modest cost of a few galaxy fits with Markov chain Monte Carlo (MCMC) methods. We utilise the SED generator and inference framework Prospector to generate simulated spectra, and train a dataset of 2 × 10 6 spectra (corresponding to a five-parameter SED model) with NPE. We show that SBI—with its combination of fast and amortized posterior estimations—is capable of inferring accurate galaxy stellar masses and metallicities. Our uncertainty constraints are comparable to or moderately weaker than traditional inverse-modelling with Bayesian MCMC methods (e.g. 0.17 and 0.26 dex in stellar mass and metallicity for a given galaxy, respectively). We also find that our inference framework conducts rapid SED inference (0.9–1.2 × 10 5 galaxy spectra via SBI/NPE at the cost of 1 MCMC-based fit). With this work, we set the stage for further work that focuses of SED fitting of galaxy spectra with SBI, in the era of JWST galaxy survey programs and the wide-field Roman Space Telescope spectroscopic surveys.

spectroscopy↗

Efficient analysis routines for single and double peaked Type 2 AGN spectra

Driven by the imminent need to rapidly process and classify millions of AGN spectra drawn from next generation astronomical facilities, we present a spectral fitting routine for Type 2 AGN spectra optimized for high volume processing, using the quasar spectral fitting library (qsfit). We analyse an optically selected sample of 813 luminous Type 2 AGN spectra at z < 0.83 from the Sloan Digital Sky Survey (SDSS) to qualify its performance. We report a median narrow line H α/H β Balmer decrement of 4.5 ± 0.8, alluding to the presence of dust in the narrow line region (NLR). We publish a specialized QSFIT fitting routine for high signal-to-noise ratio spectra and general fitting routine for double peaked Type 2 AGN spectra applied on a subsample of 45 spectra from our parent sample. We report a median red and blue peak velocity separation of 390 ± 60 kms −1 . No trend is found for red or blue peaks to exhibit systematically different luminosity or ionization properties. Emission line diagnostics show that the double peaks in all sources are illuminated by an AGN-powered ionizing continuum. Finally, we examine the morphology of host galaxies of our double peaked sample. We find double peaked Type 2 AGN reside in merging systems at a comparable frequency to single peaked AGN. This suggests that the double peaked AGN phenomenon is likely to have a bi-conical outflow origin in the majority of cases. We publicly release the code used for spectral analysis and produced catalogues used in this work.

79 ASTRONOMY AND ASTROPHYSICS↗

Identifying Anomalous DESI Galaxy Spectra with a Variational Autoencoder

The tens of millions of spectra being captured by the Dark Energy Spectroscopic Instrument (DESI) provide tremendous discovery potential. In this work we show how Machine Learning, in particular Variational Autoencoders (VAE), can detect anomalies in a sample of approximately 200,000 DESI spectra comprising galaxies, quasars and stars. We demonstrate that the VAE can compress the dimensionality of a spectrum by a factor of 100, while still retaining enough information to accurately reconstruct spectral features. We then detect anomalous spectra as those with high reconstruction error and those which are isolated in the VAE latent representation. The anomalies identified fall into two categories: spectra with artefacts and spectra with unique physical features. Awareness of the former can help to improve the DESI spectroscopic pipeline; whilst the latter can lead to the identification of new and unusual objects. To further curate the list of outliers, we use the Astronomaly package which employs Active Learning to provide personalised outlier recommendations for visual inspection. In this work we also explore the VAE latent space, finding that different object classes and subclasses are separated despite being unlabelled. We demonstrate the interpretability of this latent space by identifying tracks within it that correspond to various spectral characteristics. For example, we find tracks that correspond to increasing star formation and increase in broad emission lines along the Balmer series. In upcoming work we hope to apply the methods presented here to search for both systematics and astrophysically interesting objects in much larger datasets of DESI spectra.

Nicolaou, C. [University Coll. London] (ORCID:0000↗

Constraining calculations of Pu 239 ( n , γ ) cross sections with multistep cascade γ -ray spectra measured at the DANCE facility

Measurements of multistep cascade gamma-ray spectra from several low-lying 1 + resonances in the Pu 239 ( n , γ ) reaction were made using the DANCE detector. The measured spectra are compared to spectra simulated using several models for the photon strength function and the nuclear level density, representing the first analysis of this nature on a fissile nucleus. In general, models of the photon strength function that included a strong M 1 “scissors mode” contribution coupled with a Gilbert-Cameron nuclear level density provided a reasonable description of the spectra. Simulations using photon strength functions and nuclear level densities specifically for Pu 240 , extracted by the Oslo method, resulted in a very good representation of the measured spectra. Neutron-capture cross section calculations that included the scissors mode provided a good estimate of the previously measured values, without additional normalization. However, the scissors-mode energy that produced the best description of the multistep cascade spectra was different from the value that best reproduced the capture cross section. In addition, the 〈 Γ γ 〉 inferred from the multistep cascade calculations was somewhat less than the tabulated value, which was determined from resonance analysis. Published by the American Physical Society 2025

Ullmann, J. L. (ORCID:0000000207784405)↗

Using synthetic infrared spectra derived from n/k optical constants for standoff detection of chemical deposits

We report results from a recent field experiment to test the validity of using physics-based synthetic infrared spectra to serve as endmembers in a spectral database targeted at chemical deposits. Specifically, the optical constants n and k, (the real and imaginary part of the refractive index) were used to first model infrared reflectance spectra for different thicknesses of chemical layers (e.g. acetaminophen, methylphosphonic acid – MPA, etc.) on various conducting and insulating substrates such as aluminum, wood, and glass. In the experimental portion of the research, thin films of the solid and liquid analytes were deposited onto such substrates to form micron-thick layers of the analytes at different thicknesses: Standoff data from an imaging instrument were then recorded and analyzed to not only identify the different analytes, but also quantify the layer/deposit thickness. To gauge success, the detection results using the synthetic data were compared to the results from hemispherical reflectance (HRF) spectra that were collected for the same sample planchets measured in the field via standoff methods. Preliminary results indicate good agreement between the synthetic reference data as compared to the lab-measured HRF data in terms of their ability to quantitatively reduce longwave infrared data. Specifically, modeled IR spectra for acetaminophen on an aluminum planchet at various thicknesses (1, 2, 5, 10, 15, and 20 µm) were synthesized and compared with standoff field reflectance data as well as HRF laboratory reflectance spectra for two samples: a 5.2 µm- and 12.8 µm-thick layer of acetaminophen on aluminum. Using a first-order approximation, analysis of the field data estimates the thicknesses of the samples to be 2 and 10 µm for the two samples, respectively, while the HRF laboratory data yields thickness estimates of between 5-10 µm and 10 µm, respectively. Both yield reasonable estimates, with the uncertainty most likely due to factors yet to be accounted for in the synthetic spectra such as light scattering.

complex index of refraction, optical constants, hy↗

Modeling aerosol transmission spectra from n(λ) and k(λ) infrared optical constants measurements of organic liquids and solids

The effects of light scattering and refraction play significantly different roles for aerosols than for bulk materials, making it challenging to identify aerosolized chemicals using traditional spectral methods or spectral reference libraries. Due to a potentially infinite number of particle morphologies, sizes, and compositions, constructing a database of laboratory-measured aerosol spectra is not a practical solution. Here, as an alternative approach, the measured n / k optical vectors of two example organic materials (diethyl phthalate and D-mannitol) are used in combination with particle absorption / scattering theory (Mie theory and FDTD) and the Beer-Lambert law to generate a series of synthetic infrared transmission / scattered light spectra. The synthetic spectra show significant differences versus simple slab transmission spectra, even for small changes in particle size (e.g., 5 vs. 10 µm) for both single particles and ensembles, potentially serving as useful reference data for aerosol sensing. For spherical single particles with diameters of 1 to 10 µm, FDTD simulations predict changes in the magnitudes of spectral shifts and the shapes of the peaks vs. particle size with only small deviations from Mie theory predictions, yet reliably capture the direction of the shifts. Typical spectral peak shifts in the longwave infrared correspond to Δλ ∼0.20 µm (∼34 cm -1 ) when compared to corresponding slab transmission spectra. Additionally, synthetic spectra generated from the n / k values derived using two different methods (KBr pellet transmission and single-angle reflectance) are compared using the Mie theory model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Utilization of Synthetic Near-Infrared Spectra via Generative Adversarial Network to Improve Wood Stiffness Prediction

Near-infrared (NIR) spectroscopy is widely used as a nondestructive evaluation (NDE) tool for predicting wood properties. When deploying NIR models, one faces challenges in ensuring representative training data, which large datasets can mitigate but often at a significant cost. Machine learning and deep learning NIR models are at an even greater disadvantage because they typically require higher sample sizes for training. In this study, NIR spectra were collected to predict the modulus of elasticity (MOE) of southern pine lumber (training set = 573 samples, testing set = 145 samples). To account for the limited size of the training data, this study employed a generative adversarial network (GAN) to generate synthetic NIR spectra. The training dataset was fed into a GAN to generate 313, 573, and 1000 synthetic spectra. The original and enhanced datasets were used to train artificial neural networks (ANNs), convolutional neural networks (CNNs), and light gradient boosting machines (LGBMs) for MOE prediction. Overall, results showed that data augmentation using GAN improved the coefficient of determination (R 2 ) by up to 7.02% and reduced the error of predictions by up to 4.29%. ANNs and CNNs benefited more from synthetic spectra than LGBMs, which only yielded slight improvement. All models showed optimal performance when 313 synthetic spectra were added to the original training data; further additions did not improve model performance because the quality of the datapoints generated by GAN beyond a certain threshold is poor, and one of the main reasons for this can be the size of the initial training data fed into the GAN. LGBMs showed superior performances than ANNs and CNNs on both the original and enhanced training datasets, which highlights the significance of selecting an appropriate machine learning or deep learning model for NIR spectral-data analysis. The results highlighted the positive impact of GAN on the predictive performance of models utilizing NIR spectroscopy as an NDE technique and monitoring tool for wood mechanical-property evaluation. Further studies should investigate the impact of the initial size of training data, the optimal number of generated synthetic spectra, and machine learning or deep learning models that could benefit more from data augmentation using GANs.

59 BASIC BIOLOGICAL SCIENCES↗

The Stars of the HETDEX Survey. I. Radial Velocities and Metal-poor Stars from Low-resolution Stellar Spectra

The Hobby–Eberly Telescope Dark Energy Experiment (HETDEX) is an unbiased, massively multiplexed spectroscopic survey, designed to measure the expansion history of the universe through low-resolution ( R ~ 750) spectra of Ly α emitters. In its search for these galaxies, HETDEX will also observe a few times 10 5 stars. In this paper, we present the first stellar value-added catalog within the internal second data release of the HETDEX Survey (HDR2). The new catalog contains 120,571 low-resolution spectra for 98,736 unique stars between 10 < G < 22 spread across the HETDEX footprint at relatively high ( b ~ 60°) Galactic latitudes. With these spectra, we measure radial velocities (RVs) for ~42,000 unique FGK-type stars in the catalog and show that the HETDEX spectra are sufficient to constrain these RVs with a 1 σ precision of 28.0 km s -1 and bias of 3.5 km s -1 with respect to the Large Sky Area Multi-Object Fibre Spectroscopic Telescope surveys and 1 σ precision of 27.5 km s -1 and bias of 14.0 km s -1 compared to the Sloan Extension for Galactic Understanding and Exploration survey. Since these RVs are for faint ( G ≥ 16) stars, they will be complementary to Gaia. Using t-Distributed Stochastic Neighbor Embedding (tSNE), we also demonstrate that the HETDEX spectra can be used to determine a star’s T eff , and log g and its [Fe/H]. With the tSNE projection of the FGK-type stars with HETDEX spectra we also identify 416 new candidate metal-poor ([Fe/H] < -1 dex) stars for future study. These encouraging results illustrate the utility of future low-resolution stellar spectroscopic surveys.

Astronomy & Astrophysics↗

Fantastic Fits with fantasy of Active Galactic Nuclei Spectra: Exploring the Fe II Emission near the Hα Line

In this study, a refined approach for multicomponent fitting of active galactic nuclei (AGNs) spectra is presented utilizing the newly developed Python code Fully Automated pythoN Tool for AGN Spectra analYsis (fantasy). AGN spectra are modeled by simultaneously considering the underlying broken power-law continuum, predefined emission line lists, and an Fe II model, which is here extended to cover the wavelength range 3700–11000 Å. The Fe II model, founded solely on atomic data, effectively describes the extensive emission of the complex iron ion in the vicinity of the Hγ and Hβ lines, as well as near the Hα line, which was previously rarely studied. The proposed spectral fitting approach is tested on a sample of high-quality AGN spectra from the Sloan Digital Sky Survey Data Release 17. The results indicate that when Fe II emission is present near Hβ, it is also detected redward from Hα, potentially contaminating the broad Hα line wings and thus affecting the measurements of its flux and width. The production of Fe II emission is found to be strongly correlated with Eddington luminosity and appears to be controlled by a similar mechanism as the hydrogen Balmer lines. The study highlights the benefits of fitting type 1 AGN spectra with the fantasy code, pointing that it may be used as a robust tool for analyzing a large number of AGN spectra in the coming spectral surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Computational optimal transport for molecular spectra: The fully discrete case

In this study, the use of computational optimal transport is investigated as a tool for comparing two molecular spectra. Unlike other techniques for comparing molecular spectra in a pattern-recognition framework, transport distances simultaneously encode information about line positions and intensities. In addition, it is shown that transport distances are a useful alternative to Euclidean distances as Euclidean distances are based on line-by-line comparisons, while transport distances reflect broader features of molecular spectra and adequately compare spectra with different resolutions. This paper includes a tutorial on the use of optimal transport and investigates several well-chosen examples to illustrate the utility of computational optimal transport for comparing molecular spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Advancing the Prediction of MS/MS Spectra Using Machine Learning

Tandem mass spectrometry (MS/MS) is an important tool for the identification of small molecules and metabolites where resultant spectra are most commonly identified by matching them with spectra in MS/MS reference libraries. While popular, this strategy is limited by the contents of existing reference libraries. In response to this limitation, various methods are being developed for the in silico generation of spectra to augment existing libraries. Recently, machine learning and deep learning techniques have been applied to predict spectra with greater speed and accuracy. Here, in this work, we investigate the challenges these algorithms face in achieving fast and accurate predictions on a wide range of small molecules. The challenges are often amplified by the use of generic machine learning benchmarking tactics, which lead to misleading accuracy scores. Curating data sets, only predicting spectra for sufficiently high collision energies, and working more closely with experimental mass spectrometrists are recommended strategies to improve overall prediction accuracy in this nuanced field.

47 OTHER INSTRUMENTATION↗

MSR Transient Simulation and MSRE Transient Benchmark with SAM and SPECTRA

In recent years, there has been renewed interest in molten salt reactors (MSRs) for their potential advantages compared to reactors that rely on solid fuel. In response to such interest, many methods and codes have been developed to capture the unique features of MSRs. Among them, SPECTRA and SAM are two system analysis codes that have been enhanced to include MSR-specific modeling capabilities, including delayed neutron precursor drift and modified point kinetics equations.This paper discusses the efforts taken to verify and validate these features. A standard MSR system test problem was developed to verify and demonstrate the capability of SPECTRA and SAM on the MSR transient simulation. Sixteen transients were simulated. Further, the results obtained from SPECTRA and SAM show good agreement. The Molten Salt Reactor Experiment transient experiments were reviewed and selected to validate the SPECTRA and SAM codes. The experiments included pump startup and coastdown tests at zero power, reactivity insertion tests at different power levels, frequency tests, and a natural convection test. The simulation results from SPECTRA and SAM show good agreement with the experimental data.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗