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At least 523 records · Page 29

D–MOPH–25: diverse MOF–molecule pairs for Henry’s constants prediction

Computational methods like grand-canonical Monte Carlo simulations and machine learning (ML) have accelerated metal–organic frameworks (MOF) exploration but are typically limited to a narrow range of adsorbates due to data availability and force field constraints. In this study, we introduce a dataset of diverse MOF–molecule pairs for Henry’s constant prediction, D–MOPH–25, which systematically explores a diverse chemical space by combining 113 molecular adsorbates with over 5000 MOF structures through an active learning process. D–MOPH–25 constitutes the most diverse adsorbate dataset used in any ML study of molecular adsorption in MOFs to date. Our workflow builds a benchmark for predicting Henry’s constants at 300 K, leveraging conformal prediction for uncertainty quantification. Assessment through Shannon entropy and uniform manifold approximation and projection confirms the comprehensiveness of D–MOPH–25 while highlighting the importance of robust classification to filter out unphysical data points in regression tasks. Although future enhancements in model architecture and sampling criteria could improve predictive performance, our dataset already spans the target space using only 2.31% of total possibilities. This comprehensive dataset facilitates assessment of model generalizability across adsorbate species and can establish a foundation for high-throughput MOF screening and ML-driven separation processes.

active learning↗

Enhancing transfer learning in angle-resolved photoemission spectroscopy (ARPES) with spatially-aware representations via graph convolution

A recent application of machine learning has been to spatially-resolved angle-resolved photoemission spectroscopy (ARPES). Here we advance the state-of-the-art by applying representational learning to transform ARPES data into an embedding space of a pre-trained self-supervised learning model, thus enhancing the pipeline that improves the bandstructure classification and domain assignment/segmentation performance compared to a k-means clustering method. In the current iteration, the real-space information is entered into the domain assignment through the graph convolution method, which improves the transfer learning performance of the original self-supervised model. Lastly, an unsupervised automated tool is developed that incorporates these techniques to enable automatic domain assignment.

ARPES↗

Wasserstein normalized autoencoder for anomaly detection

A novel anomaly detection algorithm is presented. The Wasserstein normalized autoencoder (WNAE) is a normalized probabilistic model that minimizes the Wasserstein distance between the learned probability distribution—a Boltzmann distribution where the energy is the reconstruction error of the autoencoder (AE)—and the distribution of the training data. This algorithm has been developed and applied to the identification of semivisible jets—conical sprays of visible standard model (SM) particles and invisible dark matter states—with the CMS experiment at the CERN LHC. Trained on jets of particles from simulated SM processes, the WNAE is shown to learn the probability distribution of the input data in a fully unsupervised fashion, such that it effectively identifies new physics jets as anomalies. The model exhibits stable, convergent training and recovers strong classification performance for a wide range of signals against the selected background process, for which a standard AE fails because of outlier reconstruction. In addition, the model improves upon standard normalized autoencoders while remaining fully agnostic to the signal. The WNAE directly tackles the problem of outlier reconstruction, a common failure mode of autoencoders in anomaly detection tasks.

Hayrapetyan, Aram [Yerevan Phys. Inst.]↗

Sub-millisecond keyhole pore detection in laser powder bed fusion using sound and light sensors and machine learning

Laser powder bed fusion is a mainstream additive manufacturing technology widely used to manufacture complex parts in prominent sectors, including aerospace, biomedical, and automotive industries. However, during the printing process, the presence of an unstable vapor depression can lead to a type of defect called keyhole porosity, which is detrimental to the part quality. In this study, we developed an effective approach to locally detect the generation of keyhole pores during the printing process by leveraging machine learning and a suite of optical and acoustic sensors. Simultaneous synchrotron x-ray imaging allows the direct visualization of pore generation events inside the sample, offering high-fidelity ground truth. A neural network model adopting SqueezeNet architecture using single-sensor data was developed to evaluate the fidelity of each sensor for capturing keyhole pore generation events. Our comparative study shows that the near infrared images gave the highest prediction accuracy, followed by 100 kHz and 20 kHz microphones, and the photodiode sensitive to processing laser wavelength had the lowest accuracy. Using a single sensor, over 90% prediction accuracy can be achieved with a temporal resolution as short as 0.1 ms. A data fusion scheme was also developed with features extracted using SqueezeNet neural network architecture and classification using different machine learning algorithms. Our work demonstrates the correlation between the characteristic optical and acoustic emissions and the keyhole oscillation behavior, and thereby provides strong physics support for the machine learning approach.

36 MATERIALS SCIENCE↗

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗

Chemical reaction enhanced graph learning for molecule representation

Abstract Motivation Molecular representation learning (MRL) models molecules with low-dimensional vectors to support biological and chemical applications. Current methods primarily rely on intrinsic molecular information to learn molecular representations, but they often overlook effectively integrating domain knowledge into MRL. Results In this article, we develop a reaction-enhanced graph learning (RXGL) framework for MRL, utilizing chemical reactions as domain knowledge. RXGL introduces dual graph learning modules to model molecule representation. One module employs graph convolutions on molecular graphs to capture molecule structures. The other module constructs a reaction-aware graph from chemical reactions and designs a novel graph attention network on this graph to integrate reaction-level relations into molecular modeling. To refine molecule representations, we design a reaction-based relation learning task, which considers the relations between the reactant and product sides in reactions. In addition, we introduce a cross-view contrastive task to strengthen the cooperative associations between molecular and reaction-aware graph learning. Experiment results show that our RXGL achieves strong performance in various downstream tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation The code is publicly available at https://github.com/coder-ACAC/RLM.

Biochemistry & Molecular Biology↗

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings

SUMMARY: We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 28 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Zhou, Zhihan↗

CSGL: chemical synthesis graph learning for molecule representation

Abstract Motivation Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. Results Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation https://github.com/li-2023/CSGL.

Biochemistry & Molecular Biology↗

Meta2DB: Curated Shotgun Metagenomic Feature Sets and Metadata for Health State Prediction

Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13 897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on 4 January 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.

Kok, C [Lawrence Livermore National Laboratory (LL↗

OrthoPhyl—streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales

Abstract There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Application of Weak-Beam Dark-Field STEM for Dislocation Loop Analysis

Nanoscale dislocation loops formed by irradiation can significantly contribute to both irradiation hardening and embrittlement of materials when subjected to extreme nuclear reactor environments. Here, this study explores the application of weak-beam dark-field (WBDF) scanning transmission electron microscopy (STEM) methods for quantitative irradiation-induced defect analysis in crystalline materials, with a specific focus on dislocation loop imaging and analysis. A high-purity Fe-5 wt% Cr model alloy was irradiated with 8 MeV Fe 2+ ions at 450°C to a fluence of 8.8 × 10 19 m -2 , inducing dislocation loops for analysis. While transmission electron microscopy (TEM) has traditionally been the primary tool for dislocation imaging, recent advancements in STEM technology have reignited interest in using STEM for defect imaging. This study introduces and compares three WBDF STEM methods, demonstrating their effectiveness in suppressing background contrasts, isolating defect information for dislocation loop type classification, providing finer dislocation line images for small loop analysis, and presenting inside–outside contrast for identifying loop nature. Experimental findings indicate that WBDF STEM methods surpass traditional TEM approaches, yielding clearer and more detailed images of dislocation loops. The study concludes by discussing the potential applications of WBDF STEM techniques in defect analysis, emphasizing their adaptability across various material systems beyond nuclear materials.

36 MATERIALS SCIENCE↗

Evaluation of Saccadic Component Measure on Smooth Pursuit Tests

ABSTRACT Introduction Despite the advancement of eye-tracking technology for smooth pursuit (SP) eye movement evaluation, qualitative observation offers much information that is not captured by computers; hence, both objective and qualitative information should be utilized to evaluate SP. This study examined the consistency among our clinicians when evaluating SP using normal (N), grossly normal (GN), mildly abnormal (MA), and abnormal (AB) as classifications. We then evaluated the effect of combining GN and MA into a single subclinical (SUBC) category. We also evaluated the computerized percent saccade (PS) metric by determining its sensitivity and specificity in classifying SP. Materials and Methods Retrospective horizontal and vertical SP test videos and numerical data for 70 participants were obtained from the Neuro Kinetics Neuro-Otologic Test Center and de-identified. From this, eye-tracking videos, time plots of eye-tracking positional data, and tables of SP eye-tracking performance data were generated for 0.1, 0.3, and 0.5 Hz in both horizontal and vertical planes, totaling 6 tests per subject. Three clinicians rated each subject’s SP performance as N, GN, MA, or AB for a total of 6 ratings (3 frequencies, horizontal and vertical). This process was repeated using N, SUBC, and AB as rating categories. Clinicians also provided an overall SP rating for each plane as follows: AB if the results were abnormal for 2 or more frequencies tested. Alternatively, if fewer than 2 frequencies presented with a rating of AB, then an overall rating of MA, GN, or N was determined at the respective clinician’s discretion. Results When the 3 clinicians were tasked with classifying SP videos using 4 clinical categories, fair overall agreement was demonstrated. However, when MA and GN categories were combined into an SUBC category, the overall agreement for the 3 clinicians improved slightly for both horizontal SP (HSP) and vertical SP (VSP). This pattern of agreement did not differ considerably when comparing HSP versus VSP, and good consistency and reliability was observed across clinicians. Again, inter-rater consistency was smaller for VSP versus HSP despite the reduction in clinical categories. Cut-off values were generated for the PS metric and demonstrated good specificity and sensitivity when they were exceeded for 2 or more frequencies in a particular plane when evaluating a subject’s SP test. Conclusions

General & Internal Medicine↗

Statistical properties of filaments in the cosmic web

ABSTRACT In the context of the cosmological and constrained Exploring the Local Universe with the reConstructed Initial Density field (ELUCID) simulation, this study explores the statistical characteristics of filaments within the cosmic web, focussing on aspects such as the distribution of filament lengths and their radial density profiles. Using the classification of the cosmic web environment through the Hessian matrix of the density field, our primary focus is on how cosmic structures react to the two variables $R_{\rm s}$ and $\lambda _{\rm th}$. The findings show that the volume fractions of knots, filaments, sheets, and voids are highly influenced by the threshold parameter $\lambda _{\rm th}$, with only a slight influence from the smoothing length $R_{\rm s}$. The central axis of the cylindrical filament is pinpointed using the medial-axis thinning algorithm of the COsmic Web Skeleton (COWS) method. It is observed that median filament lengths tend to increase as the smoothing lengths increase. Analysis of filament length functions at different values of $R_{\rm s}$ indicates a reduction in shorter filaments and an increase in longer filaments as $R_{\rm s}$ increases, peaking around $2.5R_{\rm s}$. The study also shows that the radial density profiles of filaments are markedly affected by the parameters $R_{\rm s}$ and $\lambda _{\rm th}$, showing a valley at approximately $2R_{\rm s}$, with increases in the threshold leading to higher amplitudes of the density profile. Moreover, shorter filaments tend to have denser profiles than their longer counterparts.

Zhang, Youcai (ORCID:0000000319674091)↗

The DESI Early Data Release white dwarf catalogue

The Early Data Release (EDR) of the Dark Energy Spectroscopic Instrument (DESI) comprises spectroscopy obtained from 2020 December 14 to 2021 June 10. White dwarfs were targeted by DESI both as calibration sources and as science targets and were selected based on Gaia photometry and astrometry. Here, we present the DESI EDR white dwarf catalogue, which includes 2706 spectroscopically confirmed white dwarfs of which approximately 60 per cent have been spectroscopically observed for the first time, as well as 66 white dwarf binary systems. We provide spectral classifications for all white dwarfs, and discuss their distribution within the Gaia Hertzsprung–Russell diagram. We provide atmospheric parameters derived from spectroscopic and photometric fits for white dwarfs with pure hydrogen or helium photospheres, a mixture of those two, and white dwarfs displaying carbon features in their spectra. We also discuss the less abundant systems in the sample, such as those with magnetic fields, and cataclysmic variables. The DESI EDR white dwarf sample is significantly less biased than the sample observed by the Sloan Digital Sky Survey, which is skewed to bluer and therefore hotter white dwarfs, making DESI more complete and suitable for performing statistical studies of white dwarfs.

79 ASTRONOMY AND ASTROPHYSICS↗

The ones that got away: chemical tagging of globular cluster-origin stars with Gaia BP/RP spectra

ABSTRACT Globular clusters (GCs) are sites of extremely efficient star formation, and recent studies suggest they significantly contributed to the early Milky Way’s stellar mass build-up. Although their role has since diminished, GCs’ impact on the Galaxy’s initial evolution can be traced today by identifying their most chemically unique stars – those with anomalous nitrogen and aluminum overabundances and oxygen depletion. While they are a perfect tracer of clusters, be it intact or fully dissolved, these high-[N/O], high-[Al/Fe] GC-origin stars are extremely rare within the current Galaxy. To address the scarcity of these unusual, precious former GC members, we train a neural network (NN) to identify high-[N/O], high-[Al/Fe] stars using low-resolution Gaia Blue Photometer/Red Photometer spectra. Our NN achieves a classification accuracy of approximately $\approx 99~{{\ \rm per\ cent}}$ and a false positive rate of around $\approx 7~{{\ \rm per\ cent}}$, identifying 878 new candidates in the Galactic field. We validate our results with several physically motivated sanity checks, showing, for example, that the incidence of selected stars in Galactic GCs is significantly higher than in the field. Moreover, we find that most of our GC-origin candidates reside in the inner Galaxy, having likely formed in the proto-Milky Way, consistent with previous research. The fraction of GC candidates in the field drops at a metallicity of [Fe/H]$\approx -1$, approximately coinciding with the completion of spin-up, i.e. the formation of the Galactic stellar disc.

Kane, Sarah G. (ORCID:0000000184111012)↗

The ambiguous AT2022rze: changing-look AGN mimicking a supernova in a merging galaxy system

AT2022rze is a luminous, ambiguous transient located south-east of the geometric centre of its host galaxy at redshift $z = 0.08$. The host appears to be formed by a merging galaxy system. The observed characteristics of AT2022rze are reminiscent of active galactic nuclei (AGNs), tidal disruption events, and superluminous supernovae. The transient reached a peak absolute magnitude of $-$20.2 $\pm$ 0.2 mag, showing a sharp rise (t$_{\mathrm{rise,1/e}} = 27.5 \pm 0.6$ d) followed by a slow decline (t$_{\mathrm{dec,1/e}} = 382.9 \pm 0.6$). Its bumpy light curve and narrow Balmer lines indicate the presence of gas (and dust). Its light curve shows rather red colours, indicating that the transient could be affected by significant host extinction. The spectra reveal coronal lines, indicative of high-energy (X-ray/UV) emission. Archival data reveal no prior activity at this location, disfavouring a steady-state AGN, although an optical spectrum obtained prior to the transient is consistent with an AGN classification of the host. Based on this, we conclude that the transient most likely represents a changing-look AGN at the centre of the smallest component of the merging system.

galaxies: active↗

Joint cosmic density reconstruction from photometric and spectroscopic samples

ABSTRACT We reconstruct the dark matter density field from spatially overlapping spectroscopic and photometric redshift catalogues through a field-level forward modelling approach. Instead of directly inferring the underlying density field, we find the best-fitting initial Gaussian fluctuations that will evolve into the observed cosmic volume. To account for the substantial uncertainty of photometric redshifts we employ a differentiable continuous Poisson process. As an initial test, we construct a mock based on the upcoming Prime Focus Spectrograph combined with photometric sample modelled on the Subaru Hyper Suprime-Cam. Depending on the statistic of interest, we find improvements in cosmic structure classification equivalent to 50–100 per cent more spectroscopic targets by combining relatively sparse spectroscopic with dense photometric samples.

Horowitz, B.↗

Year six photometric measurements of known Trans-Neptunian Objects and Centaurs by the Dark Energy Survey

ABSTRACT We identified known Trans-Neptunian Objects (TNOs) and Centaurs in the complete Dark Energy Survey (DES) year six catalogue (DES Y6) through the Sky Body Tracker (SkyBoT) tool. We classified our data set of 144 objects into a widely used 4-class taxonomic system of TNOs. No such previous classification was available in the literature for most of these objects. From absolute magnitudes and average albedos, an estimation of the diameters of all these objects is obtained. Correlations involving colours, orbital parameters, dynamical classes, and sizes are also discussed. In particular, our largest reddest object has a diameter of $390^{+68}_{-53}$ km and our largest cold classical, $255^{+19}_{-17}$ km. Also, a weak correlation between colour and inclination is found within the population of resonant TNOs in addition to weak correlations between colour and phase slope in different bands.

79 ASTRONOMY AND ASTROPHYSICS↗