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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Data Science Shows that Entropy Correlates with Accelerated Zeolite Crystallization in Monte Carlo Simulations

We have performed a data science study of Monte Carlo simulation trajectories to understand factors that can accelerate formation of zeolite nanoporous crystals, a process that can take days or even weeks. In previous work, Monte Carlo simulations predicted and experiments confirmed that using a secondary organic structure-directing agent (OSDA) accelerates crystallization of all-silica LTA zeolite, with experiments finding a three-fold speedup [PCCP 24, 142-148 (2022)]. However, it remains unclear what physical factors cause the speed-up. Here, we apply data science to analyze the simulation trajectories to discover what drives accelerated zeolite crystallization in Monte Carlo going from a one-OSDA synthesis (1OSDA) to a two-OSDA version (2OSDA). We encoded simulation snapshots using the Smooth Overlap of Atomic Positions approach, which represents all 2- and 3-body correlations within a given cutoff distance. Principal component analyses failed to discriminate datasets of structures from 1OSDA and 2OSDA simulations, while the Support Vector Machine (SVM) approach succeeded at classifying such structures with an area-under-curve (AUC) score of 0.99 (where AUC = 1 is a perfect classification) with all 3-body correlations, and as high as 0.94 with only 2-body correlations. SVM decision functions reveal relatively broad / narrow histograms for 1OSDA / 2OSDA datasets, suggesting that the two simulations differ strongly in information heterogeneity. Informed by these results, we performed pair (2-body) entropy calculations during crystallization, resulting in entropy differences that semi-quantitatively account for the speedup observed in the previous Monte Carlo simulations. We conclude that altering synthesis conditions in ways that substantially changes the entropy of labile silica networks may accelerate zeolite crystallization, and we discuss possible approaches for achieving such acceleration.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Reinforcement Learning for Anomaly Detection in Nuclear Power Plant Operation and Maintenance

In nuclear power plants (NPPs), timely identification of sensor and human errors is critical to ensure safe and efficient plant operations. Anomaly detection models can be employed for this task. However, traditional anomaly detection approaches may have high dependency on labeled datasets and struggle with adaptability in complex, dynamic environments. Reinforcement learning (RL) has demonstrated significant potential in fault diagnosis and anomaly detection; however, its application to anomaly detection in NPPs remains a relatively underexplored research direction. Hence, to address this gap, in this study, we present a novel physics-informed reinforcement learning model, PIRL-AD: Physics-Informed Reinforcement Learning for Anomaly Detection, that integrates domain knowledge from calorimetric equations into the RL framework for enhanced sensor and human error anomaly detection. We evaluate the performance of PIRL-AD against a non-physics informed RL benchmark and a support vector machine (SVM) on data collected from a forced flow loop testbed. Experimental results suggest that PIRL-AD outperforms other baselines on a range of anomalous datasets that include both sensor and human-induced anomalies across key performance metrics, statistically outperforming the RL and SVM benchmarks with respect to geometric mean (respectively, 92.96% vs. 91.06% vs. 83.01%) and F1-score (respectively, 89.23% vs. 86.98% vs. 77.01%). Furthermore, the findings suggest the potential of physics-integrated reinforcement learning models for enhanced anomaly detection performance in NPPs.

Reinforcement learning↗
DOE OSTI2022

Wind turbine gearbox fault prognosis using high-frequency SCADA data

Condition-based maintenance using routinely collected Supervisory Control and Data Acquisition (SCADA) data is a promising strategy to reduce downtime and costs associated with wind farm operations and maintenance. New approaches are continuously being developed to improve the condition monitoring for wind turbines. Development of normal behaviour models is a popular approach in studies using SCADA data. This paper first presents a data-driven framework to apply normal behaviour models using an artificial neural network approach for wind turbine gearbox prognostics. A one-class support vector machine classifier, combining different error parameters, is used to analyse the normal behaviour model error to develop a robust threshold to distinguish anomalous wind turbine operation. A detailed sensitivity study is then conducted to evaluate the potential of using high-frequency SCADA data for wind turbine gearbox prognostics. The results based on operational data from one wind turbine show that, compared to the conventionally used 10-min averaged SCADA data, the use of high-frequency data is valuable as it leads to improved prognostic predictions. High-frequency data provides more insights into the dynamics of the condition of the wind turbine components and can aid in earlier detection of faults.

17 WIND ENERGY↗
DOE OSTI2024

A Novel Authentication Management for the Data Security of Smart Grid

Bidirectional wireless communication is employed in various smart grid components such as smart meters and control and monitoring applications where security is vital. The Trusted Third Party (TTP) and wireless connectivity between the smart meter and the third party in the key management-based encryption techniques for the smart grid are expected to be totally trustworthy and dependable. In a wired/wireless medium, however, a man-in-the-middle may seek to disrupt, monitor and manipulate the network, or simply execute a replay attack, revealing its vulnerability. Recognizing this, this study presents a novel authentication management (model) comprised of two layer security schema. The first layer implements an efficient novel encryption method for secure data exchange between meters and control center with the help of two partially trusted simple servers (constitutes the TTP). In this setting, one server handles the data encryption between the meter and control center/central database, and the other server administers the random sequence of data transmission. The second layer monitors and verifies exchanged data packets among smart meters. It detects abnormal packets from suspicious sources. To implement this node-to-node authentication, One class support vector machine algorithm is proposed which takes advantages of the location information as well as the data transmission history (node identification, packet size, and data transmission frequency). This schema secures data communication, and imposes a comprehensive privacy throughout the system without considerably extending the complexity of the conventional key management scheme.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Safe and Robust Binary Classification and Fault Detection Using Reinforcement Learning

In this paper, we propose a learning-based method utilizing the Soft Actor-Critic (SAC) algorithm to train a binary Support Vector Machine (SVM) classifier. This classifier is designed to identify valid input spaces in high-dimensional, highly constrained systems while minimizing the total runtime of offline simulations. The simulations adapt their runtime based on the likelihood that a given training input will be informative to the classifier. Furthermore, we introduce a method for using the trained SAC model to predict whether a desired system input is likely to violate constraints, along with a technique to adjust the input as necessary. Additionally, we explore the potential of this model to detect faults or adversarial attacks within the system. The effectiveness of our approach is demonstrated through various simulations of challenging classification problems and a constrained quadrotor model.

Netter, Josh [Georgia Institute of Technology, Atl↗
DOE OSTI2024

Scalable Risk Assessment of Rare Events in Power Systems With Uncertain Wind Generation and Loads

Risk assessment of rare events has become increasingly important in power system planning and operation with the increasing integration of renewable energy and the presence of system uncertainties. However, quantifying the risk posed by rare events via the traditional method, i.e., Monte Carlo sampling (MCS), incurs substantial computational expense stemming from the vast ensemble of power flow simulations. To accelerate the assessment, this paper proposes a Deep Neural Network (DNN)-kernelized vector-valued Gaussian Process (VVGP) approach with excellent computational efficiency while maintaining high accuracy. Consequently, serving as a surrogate model for the power flow solver, the DNN-kernelized VVGP enables significantly faster but accurate risk assessment compared to the power flow solver. The developed surrogate model evaluates low-order N - k events that contain more than 90% instances by adeptly capturing the topological features while the high-order N - k events are assessed via a power flow solver, thereby striking a balance between computational efficiency and uncertainty quantification accuracy. Moreover, the model incorporates a Support Vector Machine (SVM) classifier to resample concerning low-probability tail events to counteract the biases potentially introduced during the DNN-kernelized VVGP evaluations. Simulations conducted on the modified IEEE 24-bus, 118-bus, and European 1354-bus systems demonstrate that the proposed method maintains the accuracy benchmark set by MCS while significantly reducing computational demands in large-scale power systems as compared to other state-of-the-art methods.

17 WIND ENERGY↗
DOE OSTI2024

Cy-Phy ADS: Cyber Physical Anomaly Detection Framework for EV Charging Systems

Today’s large-scale Electric Vehicle (EV) infrastructures are heavily dependent on information communication technologies to maintain their operation and to support communication within sub-system components as well as the outside world. These technologies are vulnerable to various cyber and physical threats. Timely identification and mitigation of these threats are critical for improving human safety, avoiding economic losses, and preventing catastrophic system failures. By addressing this, our work presents a ResNet Autoencoder (AE) based Cyber-Physical Anomaly Detection System (Cy-Phy ADS) for detecting anomalies in EV Controller Area Network (CAN) protocol communication. It consists of four main components: Cyber-Physical Feature Extractor, ResNet AE-based Anomaly Detection Framework, Cyber-Physical Health Metric (CPHM), and Visualization Dashboard. The presented framework was trained and tested using CAN data collected from the EV charging system testbed at the Idaho National Laboratory. The presented Cy-Phy ADS compared against six widely used unsupervised anomaly detection algorithms: One Class Support Vector Machine (OCSVM), Variational Autoencoder (VAE), LSTM Autoencoder (LSTM AE), Isolation Forest (IForest), Principle Component Analysis (PCA) and Local Outlier Factor (LOF). Here the presented approach showed the highest accuracy among the compared methods. Further, the proposed approach showed comparable performance in terms of precision, F1, and False positive rate. It also showed the lowest training and inference time compared to the neural network-based baseline algorithms compared against with. Additionally, the Cy-Phy ADS has advantages such as unsupervised training, the ability to provide a holistic metric for system health characterization, and non-linear feature extraction.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2022

Segmenting water and shadow regions within WorldView imagery using local binary patterns

Many shadow detection algorithms pertaining to remotely sensed imagery exist. Several of these algorithms exploit the spectral characteristics of shadows within imagery to identify shaded regions. However, these algorithms can have problems when water is also present within the imagery because water shares similar spectral characteristics with shadows. Many of these algorithms are applied to small image subsets instead of the image as a whole and frequently are applied to urban environments that require additional use of the normalized difference water index or other features to affect the removal of water from the shadow mask. This diversity of the image scene content coupled with the complexity and wide variety of environmental conditions that satellite imagery can acquire makes reliably separating shadow and water within larger images a complex problem. Thresholding various spectral indices to produce segmentation maps can be challenging when large, complex, and often imbalanced scenes are captured, which may require manual adjustment of algorithmic parameters for different image areas. Here, we present a methodology that makes use of the near-infrared channel using a watershed segmentation algorithm, local binary pattern measurements, and a support vector machine to classify shadow and water within a full WorldView scene. Results are promising with initial accuracies above 97% for both shadow and water.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

A Data-Driven Approach for High-Impedance Fault Localization in Distribution Systems [SWR-24-13]

This software provides a data-driven approach for efficiently identifying high impedance faults (HIFs) in distribution systems. To tackle the nonlinearity of the voltage current trajectory of HIFs, we first formulate linear least squares problems to approximate the trajectory with piecewise functions. Then we collect the function features of all segments as inputs and use the support vector machine approach to efficiently identify HIFs at different locations.

Zhou, Yuqi↗
DOE OSTI2025

Multiphysics Meshfree Degradation Modeling of Energy Storage Materials with Kernel Enrichment

Energy storage materials exhibit strong electro-chemo-mechanical coupling and highly anisotropic material properties, contributing to the formation and propagation of micro-cracking during charge/discharge cycling and ultimately diminishing performance and service life. With microstructural images supplied by the National Renewable Energy Laboratory (NREL), pixel-based meshfree model construction by the reproducing kernel particle method (RKPM) is used to represent the complex material microstructures that dictate the coupled physics of these systems. Traditional electro-chemo-mechanical models rely on mesh-based finite element methods, which can lead to difficulties in meshing such complex geometries and capturing crack propagation due to mesh dependency. The first kernel enrichment discussed will be the interface modified reproducing kernel (IM-RK) [1, 2], constructed by scaling a smooth kernel function with an interface-distance function to achieve strategic discontinuity types (i.e. weak discontinuities for strain discontinuities and strong discontinuities for cracks) and alleviate Gibbs oscillations near these transition zones. The IM-RK is especially useful for areas in which a known discontinuity-type is expected a priori. The second kernel enrichment to be discussed is a neural network-enhanced reproducing kernel (NN-RK) [3, 4], which is introduced to effectively model non-obvious damage and crack propagation in the material microstructures; the location, orientation, and solution transition near a localization are automatically captured by superimposed block-level NN optimizations. This NN enrichment approach allows for effective modeling of localizations via a fixed background discretization, relieving tedious efforts for adaptive refinement in traditional mesh-based methods. Applications to the heterogeneous microstructures of Li-ion battery cathodes will be presented to demonstrate the effectiveness of the proposed methods. NN-RK is additionally used to inform how crack opening and closure in turn affect the electro-chemo-mechanical responses in the material microstructure. Reference: [1] Wang, Y., Baek, J., Tang, Y. et al. "Support vector machine guided reproducing kernel particle method for image-based modeling of microstructures," Comput Mech 73, 907-942 (2024). https://doi.org/10.1007/s00466-023-02394-9. [2] Susuki, K., Allen, J. & Chen, J. S.. "Image-based modeling of coupled electro-chemo-mechanical behavior of Li-ion battery cathode using an interface-modified reproducing kernel particle method," Engineering with Computers (2024). https://doi.org/10.1007/s00366-024-02016-9. [3] Baek, J., Chen, J. S., Susuki, K., "Neural Network enhanced Reproducing Kernel Particle Method for Modeling Localizations," International Journal for Numerical Methods in Engineering, Vol. 123, 4422-4454 (2022). https://doi.org/10.1002/nme.7040.

25 ENERGY STORAGE↗
DOE OSTI2026

Kernel Enriched Meshfree Multiphysics Degradation Modeling of Energy Storage Materials

Energy storage materials exhibit strong electro-chemo-mechanical coupling and highly anisotropic material properties, contributing to the formation and propagation of micro-cracking during charge/discharge cycling and ultimately diminishing performance and service life. With microstructural images supplied by the National Laboratory of the Rockies (NLR), pixel-based meshfree model construction by the reproducing kernel particle method (RKPM) is used to represent the complex material microstructures that dictate the coupled physics of these systems. Traditional electro-chemo-mechanical models rely on mesh-based finite element methods, which can lead to difficulties in meshing such complex geometries and capturing crack propagation due to mesh dependency. The first kernel enrichment discussed will be the interface modified reproducing kernel (IM-RK) [1, 2], constructed by scaling a smooth kernel function with an interface-distance function to achieve strategic discontinuity types (i.e. weak discontinuities for strain discontinuities and strong discontinuities for cracks) and alleviate Gibbs oscillations near these transition zones. The IM-RK is especially useful for areas in which a known discontinuity-type is expected a priori. The second kernel enrichment to be discussed is a neural network-enhanced reproducing kernel (NN-RK) [3, 4], which is introduced to effectively model non-obvious damage and crack propagation in the material microstructures; the location, orientation, and solution transition near a localization are automatically captured by superimposed block-level NN optimizations. This NN enrichment approach allows for effective modeling of localizations via a fixed background discretization, relieving tedious efforts for adaptive refinement in traditional mesh-based methods. Applications to the heterogeneous microstructures of Li-ion battery cathodes will be presented to demonstrate the effectiveness of the proposed methods. NN-RK is additionally used to inform how crack opening and closure in turn affect the electro-chemo-mechanical responses in the material microstructure. References: [1] Wang, Y., Baek, J., Tang, Y. et al. "Support vector machine guided reproducing kernel particle method for image-based modeling of microstructures," Comput Mech 73, 907-942 (2024). https://doi.org/10.1007/s00466-023-02394-9. [2] Susuki, K., Allen, J. & Chen, J. S.. "Image-based modeling of coupled electro-chemo-mechanical behavior of Li-ion battery cathode using an interface-modified reproducing kernel particle method," Engineering with Computers (2024). https://doi.org/10.1007/s00366-024-02016-9. [3] Baek, J., Chen, J. S., Susuki, K., "Neural Network enhanced Reproducing Kernel Particle Method for Modeling Localizations," International Journal for Numerical Methods in Engineering, Vol. 123, 4422-4454 (2022). https://doi.org/10.1002/nme.7040.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Comparing Calibration Algorithms for the Rapid Characterization of Pretreated Corn Stover Using Near-Infrared Spectroscopy

Rapid characterization of biomass composition is a key enabling technology for biorefineries—the ability to measure the chemical composition of biomass materials entering the biorefinery as well as the composition of key process intermediate streams would allow real-time process control and the development of robust models to predict process performance. The utility of near-infrared (NIR) spectroscopy for rapid characterization requires multivariate algorithms for building calibration models. The most prevalent algorithm used for building calibration models using NIR spectra is the linear modeling algorithm Partial Least Squares Regression (PLS). Nonlinear regression algorithms (which are typically more computationally intensive than linear modeling approaches) have gained popularity in recent years due to their ability to solve a wide variety of classification and regression problems and the dramatic increase in available computational resources. In this work, we demonstrate that a calibration model can predict the composition of corn stover process intermediate samples pretreated with three different treatments—hot water (HW), dilute acid (DA), and deacetylation followed by dilute acid (DDA). We quantitatively compare three different algorithms for building prediction models based on near-infrared spectroscopy—partial least squares (PLS), support vector machines (SVM), and random forests (RF). We demonstrate the utility of improving model performance by accounting for instrument performance variability using repeated measurements of standard materials (e.g., the “repeatability file” strategy) and investigate its performance with nonlinear regression techniques, and we discuss methods for quantifying the uncertainties of specific predictions among the three methods.

09 BIOMASS FUELS↗
DOE OSTI2026

Unsupervised Detection of SOC Spoofing in OCPP 2.0.1 EV Charging Communication Protocol Using One-Class SVM

The electric vehicles (EVs) market keeps growing globally; thus, it is critical to secure the EV charging communication protocols in order to guarantee reliable and fair charging operations among the customers. The Open Charge Point Protocol (OCPP) 2.0.1 supports the communication between the Electric Vehicle Supply Equipment (EVSE) and Charging Station Management Systems (CSMSs); therefore, it becomes vulnerable to several types of attacks, which aim to jeopardize smart charging, billing, and energy management. Specifically, OCPP 2.0.1 allows the self-reporting of the State of Charge (SOC) values, which makes it vulnerable to spoofing-based cyberattacks, which target manipulating the scheduling priorities, distorting the load forecasts, and extending the charging sessions in an unfair manner. In this paper, we try to address this type of attack by providing a comprehensive analysis of the SOC spoofing attacks and introducing a novel unsupervised detection framework based on the One-Class Support Vector Machine (OCSVM) algorithm. Specifically, two types of attack scenarios are analyzed (i.e., priority manipulation and session extension) by deriving engineered features that capture the nonlinear relationships under normal charging behavior. Detailed simulation-based results are derived by utilizing the DESL-EPFL Level 3 EV charging dataset. Our results demonstrate high F1-score and recall in identifying spoofed SOC values and that the proposed OCSVM model demonstrates superior performance compared to alternative clustering and deep-learning based detectors.

EV charging↗
DOE OSTI2023

Using Downwelling Far- and Thermal-Infrared Hyperspectral Radiance for Cloud Phase Classification in the Antarctic

The cloud phase is one of the most important parameters of clouds. In this paper, we propose a method for cloud phase classification that synergistically utilizes the far- and thermal-infrared bands based on the Atmospheric Emitted Radiance Interferometer (AERI) at the Atmospheric Radiation Measurement West Antarctic Radiation Experiment (AWARE) observatory in 2016. The possible features in the far- and thermal-infrared bands are analyzed based on the differences in the simulated cloud brightness temperature (BT) spectra with different cloud phases. Using the support vector machine (SVM) algorithm, four features are determined to identify the cloud phase, which include the BT at 900 cm -1 , the slope of the fitted function of BT in the 900–1000 cm -1 interval, the BT difference (BTD) between 512 cm -1 and 726 cm -1 , and the BTD between 550 cm -1 and 726 cm -1 . Here, the performance of the proposed method is evaluated with Shupe’s and Turner’s method. The monthly average accuracy of the proposed method, the method without the two far-infrared features, and Turner’s method are about 76%, 36%, and 49%, respectively, which infer the good performance of the proposed method and also indicate that the far-infrared band features can effectively enhance cloud phase classification. It is notable that, compared to Shupe’s method, the accuracy for the proposed method is only 61% during the Antarctic summer, which results from the definitions of cloud phase and radiative effect. In addition, the accuracy is only 44% for Turner’s method in seasons with a low frequency of mixed clouds due to the significant effect of water vapor.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Machine Learning in the Context of Laser-Induced Breakdown Spectroscopy

The integration of machine learning (ML) with Laser-Induced Breakdown Spectroscopy (LIBS) has revolutionized the analytical capabilities of LIBS. The combi-nation of both methods enables more accurate and efficient data analysis. While LIBS itself is a powerful technique for elemental analysis, the vast amount of spectral data it generates can be hard to interpret. Machine learning addresses these challenges by leveraging algorithms that can learn from data, identify patterns, and make predictions without explicit programming for the interpretation of each specific task. In LIBS application, ML techniques are used to enhance various analytical processes. For example, ML algorithms can classify materials based on their spectral fingerprints, predict the concentration of elements in a sample, and identify underlying patterns within complex datasets. Here, this application improves the precision of LIBS analyses while significantly reducing the time required for data processing and interpretation. In this chapter, the fundamental concepts of ML will be discussed first. Following this, the process of data splitting and the importance of feature selection will be examined. Several machine learning methods will then be closely examined, exploring how each can benefit LIBS analysis and highlighting their respective advantages and shortcomings. This structured approach will provide a comprehensive understanding of the integration of ML in the context of LIBS analysis.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

A Practical Comparison of Data-Driven Prognostics Methods for Energy Systems

This study explores data-driven prognostics for nuclear power plant (NPP) condensers, focusing on tube fouling. We utilized the Asherah nuclear power plant simulator (ANS) to compare four methods: Random Forest (RF), Support Vector Regressor (SVR), Fully Connected Neural Network (FCNN), and Long Short-Term Memory Neural Network (LSTM). By simulating various fouling scenarios in the ANS, we generated data with different degradation rates under transient operations. The models were trained and tested on these data, with performance evaluated visually and numerically including uncertainty assessment. The LSTM model excelled, exhibiting minimal prediction noise and the most accurate remaining useful life estimates across all degradation levels. Its ability to capture long-term dependencies and produce cleaner outputs makes it a strong candidate, although accurate training data across the entire component lifespan are crucial. The RF model emerged as a robust alternative, providing reliable predictions with high confidence. The FCNN and SVR models, while less effective overall, showed potential under specific conditions. FCNN offers a less complex alternative to LSTM and might benefit from larger datasets. SVR excels in precision when the quality of the training data is high. Furthermore, this study highlights the operational benefits of advanced prognostics in the energy sector and emphasizes the need for further research in NPP condenser health management through real-life experiments.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

Inferring Neutron Star Merger Ejecta Morphology with Kilonovae

In this study we incorporate a new grid of kilonova simulations produced by the Monte Carlo radiative transfer code SuperNu in an inference pipeline for astrophysical transients and evaluate their performance. These simulations contain four different two-component ejecta morphology classes. We analyze follow-up observational strategies by Vera Rubin Observatory in optical and James Webb Space Telescope (JWST) in mid-infrared (MIR). Our analysis suggests that, within these strategies, it is possible to discriminate between the four different morphologies only when late-time JWST observations in MIR are available. We conclude that follow-ups by the new Vera Rubin Observatory alone are not sufficient to determine ejecta morphology. Additionally, we make comparisons between surrogate models based on radiative transfer simulation grids by SuperNu and POSSIS, by analyzing the historic kilonova AT2017gfo that accompanied the gravitational wave event GW170817. We show that both SuperNu and POSSIS models provide similar fits to photometric observations but their qualitative interpretations differ.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes

Microbial natural products represent a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class that include antibiotics, immunosuppressants, anticancer agents, toxins, siderophores, pigments, and cytostatics. The discovery of novel NRPs remains a laborious process because many NRPs consist of nonstandard amino acids that are assembled by nonribosomal peptide synthetases (NRPSs). Adenylation domains (A-domains) in NRPSs are responsible for selection and activation of monomers appearing in NRPs. During the past decade, several support vector machine-based algorithms have been developed for predicting the specificity of the monomers present in NRPs. These algorithms utilize physiochemical features of the amino acids present in the A-domains of NRPSs. In this article, we benchmarked the performance of various machine learning algorithms and features for predicting specificities of NRPSs and we showed that the extra trees model paired with one-hot encoding features outperforms the existing approaches. Moreover, we show that unsupervised clustering of 453560 A-domains reveals many clusters that correspond to potentially novel amino acids. While it is challenging to predict the chemical structure of these amino acids, we developed novel techniques to predict their various properties, including polarity, hydrophobicity, charge, and presence of aromatic rings, carboxyl, and hydroxyl groups.

59 BASIC BIOLOGICAL SCIENCES↗