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At least 109 records · Page 6

Structure-aware annotation of leucine-rich repeat domains

Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plant Arabidopsis thaliana and validated against a benchmark dataset of 172 manually-annotated LRR domains.

Xu, Boyan

Regime Characterization of Offshore Wind Resource Using Unsupervised Learning

Predictability of wind resource conditions is critical for offshore wind design and operations. While many studies of extreme wind conditions focus on specific events such as low-level jets or ramps, these rely on threshold definitions that limit generality. Here we present a data-driven framework that combines principal component analysis (PCA), self-organizing maps (SOM), and k-means clustering to classify wind resource conditions as typical and anomalous from climatological data. Anomalies are defined not by fixed thresholds but by flagging samples located far from SOM node centers inside the baseline SOM structure. This reframes extremes as rare ebents and hence, likely difficult to anticipate by numerical weather prediction models. We applied this approach to 23 years (2000–2022) of hourly profiles from the NOW-23 hindcast model at the Humboldt Wind Energy Area. Classification is conducted on a feature space consisting of 10 m wind speed and direction, bulk shear and veer across 30–270 m, and a low-level jet index. Dimensionality reduction is achieved through PC. A 2 × 3 OM lattice trained on the PCA vectors identified six baseline regimes spanning weak to strong flow states. High quantization-error profiles are identified and re-clustered into four anomalous regimes. The baseline regimes exhibited clear seasonal and diurnal cycles. Meanwhile, the anomalous regimes represented <10 % of all hours but showed distinct combinations of speed, shear, and veer, when compared to the baseline regimes. Anomalous regimes are typically short-lived (~few hours), yet their transitions can lead to hub-height wind changes of −18 to +9 m s -1 . For a representative 15 MW turbine, these shifts imply rapid swings in capacity factor from near-full output to negligible generation. Validation with lidar buoy data showed 51% agreement in SOM labels across ~6,000 overlapping hours, with most mismatches confined to adjacent speed classes. HRRR comparisons further revealed that anomalous regimes were disproportionately associated with forecast biases exceeding 5 m s -1 . Together, these results reframe extremes in offshore wind from absolute maxima or minima to weather states that are difficult to anticipate from models.

17 WIND ENERGY

Toward Drilling the Perfect Geothermal Well: An International Research Coordination Network for Geothermal Drilling Optimization Supported by Deep Machine Learning and Cloud Based Data Aggregation

The EDGE project, supported by the U.S. Department of Energy Geothermal Technologies Office under award DE-EE0008793, established a data-driven framework for improving the efficiency, cost-effectiveness, and reliability of geothermal well drilling. The project focused on developing scalable data infrastructure, advanced machine learning and probabilistic models, and integrated analytics tools to support continuous drilling optimization. A central objective was to reduce geothermal drilling costs by up to seventy percent while minimizing the risk of well failure through predictive diagnostics and adaptive planning. Over the project period, a comprehensive data repository was designed and deployed, incorporating records from over one hundred geothermal wells across varied geological settings. This repository supported both structured and unstructured data and adhered to FAIR data principles, enabling provenance tracking, quality control, and standardized metadata. The project introduced automated ingestion pipelines and a cloud-hosted platform that facilitated access to raw, processed, and derived datasets. This infrastructure served as the foundation for model development and analysis. Machine learning workflows were developed to predict key drilling metrics including rate of penetration, non-productive time, and total drilling costs. Self-organizing maps and dimensionality reduction methods were used to uncover operational patterns and outliers, while supervised learning algorithms such as random forests and deep neural networks were applied to forecast performance outcomes. The models were validated on heterogeneous datasets from both U.S. and Icelandic fields, demonstrating variable but significant predictive accuracy. The results indicated that finer temporal resolution, inclusion of lithological data, and consistency in operational annotations could substantially improve model performance. The project also implemented process mining techniques to reconstruct state-transition models from drilling event logs. These models enabled the identification of deviations from optimal workflows and provided insights into recurring failure modes. Analysis of non-productive time highlighted the impact of equipment failures, geological challenges, and human factors, offering opportunities for targeted mitigation strategies. The EDGE Dashboard was developed as a web-based expert system integrating data visualization, model outputs, and user-driven queries. It provided an accessible interface for operators to explore historical data, evaluate predicted outcomes, and compare drilling scenarios. Initial feedback from project partners suggested that the dashboard could serve as a foundation for more advanced advisory and optimization tools. Overall, the EDGE project demonstrated the feasibility and value of applying modern data science techniques to geothermal drilling. It delivered a set of interoperable tools and models that can support more efficient, lower-risk well development. The findings point toward a viable path for transitioning from advisory analytics to semi-autonomous drilling systems, contingent on continued collaboration, expanded datasets, and field validation. The project results have immediate relevance for drilling operations, data management practices, and future geothermal R&D efforts aimed at achieving reliable, cost-competitive geothermal energy at scale.

15 GEOTHERMAL ENERGY

Data and Code for Understanding Generative AI Content with Embedding Models

This repository contains code for the experiments in the paper "Understanding Generative AI Content with Embedding Models". Constructing high-quality features is critical to any quantitative data analysis. While feature engineering was historically addressed by carefully hand-crafting data representations based on domain expertise, deep neural networks (DNNs) now offer a radically different approach. DNNs implicitly engineer features by transforming their input data into hidden feature vectors called embeddings. For embedding vectors produced by foundation models -- which are trained to be useful across many contexts -- we demonstrate that simple and well-studied dimensionality-reduction techniques such as Principal Component Analysis uncover inherent heterogeneity in input data concordant with human-understandable explanations. Of the many applications for this framework, we find empirical evidence that there is intrinsic separability between real samples and those generated by artificial intelligence (AI).

Vargas, Max [Pacific Northwest National Laboratory

Uncovering Structure–Conductivity Relationships in Anion Exchange Membranes (AEMs) Using Interpretable Machine Learning

Anion exchange membranes (AEMs) play a vital role in the performance of water electrolyzers and fuel cells, yet their discovery and optimization remain challenging due to the complexity of structure–property relationships. In this study, we introduce a machine learning framework that leverages conditional graph neural networks (cGNNs) and descriptor-based models and a hybrid graph neural network (HGARE) to predict and interpret ionic conductivity. The descriptor-based pipeline employs principal component analysis (PCA), ablation, and SHAP analysis to identify factors governing anion conductivity, revealing electronic, topological, and compositional descriptors as key contributors. Beyond prediction, dimensionality reduction and clustering are performed by employing t-SNE and KMeans as well as SOM, which reveal distinct membranes clusters, some of which were enriched with high anion conductivity. Among graph-based approaches, the graph convolutional (GCN) achieved strong predictive performance, while the Hybrid Graph Autoencoder-Regressor Ensemble (HGARE) achieved the highest accuracy. Additionally, atom-level saliency maps from GCN provide spatial explanations for conductive behavior, revealing the importance of polarizable and flexible regions. This work contributes to the accelerated and data-driven design of high-performance AEMs.

Naghshnejad, Pegah [Department of Chemical Enginee

A Structure-Preserving Decorated Particle Method for the Vlasov-Poisson System

We revisit the Scovel-Weinstein framework (Scovel & Weinstein, CPAM 1994) for reducing the Vlasov-Poisson system while preserving its Hamiltonian structure. Standard particle-in-cell (PIC) algorithms approximate the distribution function by macro-particles with position and velocity. In contrast, Scovel-Weinstein decorated particles involve additional shape degrees of freedom, while maintaining a finite-dimensional reduction with Hamiltonian structure inherited from the continuum model. Although the original work established this structure three decades ago, its computational potential has remained largely unexplored. We present a practical implementation of the Scovel-Weinstein model and compare it with a standard PIC algorithm. Numerical experiments demonstrate that macro-particles in standard PIC can be replaced by far fewer decorated particles while retaining comparable accuracy. This decorated particle approach offers a new structure-preserving paradigm for kinetic plasma simulation.

65M75, 70H05, 70G65

An efficient hybrid downscaling framework to estimate high-resolution river hydrodynamics

Flow depth and velocity are the most important hydrodynamic variables that govern various river functions, including water resources, navigation, sediment transport, and biogeochemical cycling. Existing high-resolution flow depth simulations rely on either computationally expensive river hydrodynamic models (RHMs) or data-driven models with formidable training costs, whereas data-driven modeling of flow velocity has rarely been explored. Here, using the hybrid Low-fidelity, Spatial analysis, and Gaussian process learning (LSG) model, we developed a downscaling approach to construct high-resolution flow depth and velocity from a two-dimensional (2-D) RHM simulation at coarse resolution. The LSG models were trained and tested in an urban watershed in Houston using two different hurricane-driven flood events. The high-resolution (as fine as 30 m resolution) and low-resolution (mostly 1000 m resolution) meshes include 664 724 and 14 536 grid cells, respectively. The results showed that through downscaling, the simulation errors were reduced to less than one-fourth and one-third of the errors of the low-resolution 2-D RHM for flow depth and velocity, respectively. Our analysis further revealed that the dominant uncertainty sources of the downscaled hydrodynamics are different, with flow velocity dominated by the dimensionality reduction error, which we reduced by using a regionalized training procedure. The downscaling approach achieves an 84-fold acceleration in computational time compared to the high-resolution 2-D RHM, making high-fidelity ensemble flood modeling feasible. More importantly, the developed method provides an opportunity to couple large-scale hydrodynamical processes with local physical, chemical, and biological processes in river models.

Tan, Zeli [Pacific Northwest National Laboratory (

A dimensionality reducing model for distributed filtering.

An approach is made to filtering of two-dimensional steady-state problems based on the notion of nearest neighbor interaction, i.e., at a given point in the spatial grid, the value at the variable of interest can be assumed to depend only on the values at adjacent grid points. It is shown that for linear steady-state problems significant dimensionality reductions can be accomplished. It was possible to achieve the desired results using a small amount of computer time and without getting into stability difficulties.

Angel, E.

A nearest neighbors approach to multidimensional filtering.

The concept of nearest neighbor interaction is applied as a basis for data filtering in two-dimensional steady state problems. A steady state process represented by a potential equation with additive white noise is used to illustrate the application of this concept. It is demonstrated that significant dimensionality reductions can be achieved by applying this concept to various linear steady state problems.

Angel, E.

High gas velocity burner tests on silicon carbide and silicon nitride at 1200 C

Specimens of silicon carbide and silicon nitride were exposed to a Mach one gas velocity burner simulating a turbine engine environment. Cyclic tests up to 100 hour duration were conducted at specimen temperatures of 1200 C. A specimen geometry was used that develops thermal stresses during thermal cycling in a manner similar to blades and vanes of a gas turbine engine. Materials were compared on a basis of weight change, dimensional reductions, metallography, fluorescent penetrant inspection, X-ray diffraction analyses, failure mode, and general appearance. One hot pressed SiC, one reaction sintered SiC, and three hot pressed Si3N4 specimens survived the program goal of 100 one-hour cycle exposures. Of the materials that failed to meet the program goal, thermal fatigue was identified as the exclusive failure mode.

Sanders, W. A.

Multispectral combination and display of ERTS-1 data

Standard NASA color composites combine the most relevant 3 bands from the 4 MSS bands available. An alternate approach is to extract the principal components of the data by a linear transformation of the 4 bands. This approach leads to a low dimensionality representation of ERTS-1 data with the least degradation, in the mean square sense, of the radiometric accuracy. The technique has been applied with success to ERTS-1 MSS data for several geographic areas in California. For all examples considered the mean square representation error is less than one percent. By combining this dimensionality reduction which our previous results on image enhancement for visual display, color composites are obtained which contain and display most of the information provided by the ERTS-1 sensors.

Algazi, V. R.

Behavior of ceramics at 1200 C in a simulated gas turbine environment

This report summarizes programs at the NASA Lewis Research Center evaluating several classes of commercial ceramics, in a high gas velocity burner rig simulating a gas turbine engine environment. Testing of 23 ceramics in rod geometry identified SiC and Si3N4 as outstanding in resistance to oxidation and thermal stress and identified the failure modes of other ceramics. Further testing of a group of 15 types of SiC and Si3N4 in simulated vane shape geometry has identified a hot pressed SiC, a reaction sintered SiC, and hot pressed Si3N4 as the best of that group. SiC and Si3N4 test specimens were compared on the basis of weight change, dimensional reductions, metallography, fluorescent penetrant inspection, X-ray diffraction analyses, and failure mode.

Sanders, W. A.

High gas velocity burner tests on silicon carbide and silicon nitride at 1200 C

Ten SiC materials and five Si3N4 materials were exposed in a Mach 1-gas-velocity burner simulating a gas-turbine engine environment. All materials studied are commercially available. Cyclic tests up to 100 hours' duration were conducted at specimen temperatures of 1200 C. A specimen geometry was used that develops thermal stresses during thermal cycling in a manner similar to blades and vanes of a gas turbine engine. Materials were compared on a basis of weight change, dimensional reductions, metallography, fluorescent-penetrant inspection, X-ray diffraction analyses, failure mode, and general appearance. One hot-pressed SiC, one reaction-sintered SiC, and three hot-pressed Si3N4 materials survived the program goal of 100 one-hour cycles of exposures. Of the materials that failed to meet the program goal, thermal fatigue was identified as the exclusive failure mode.

Sanders, W. A.

AHIMSA - Ad hoc histogram information measure sensing algorithm for feature selection in the context of histogram inspired clustering techniques

An algorithm is proposed for dimensionality reduction in the context of clustering techniques based on histogram analysis. The approach is based on an evaluation of the hills and valleys in the unidimensional histograms along the different features and provides an economical means of assessing the significance of the features in a nonparametric unsupervised data environment. The method has relevance to remote sensing applications.

Dasarathy, B. V.

Stability of constant gain systems with vector feedback

The state space, the controllability, and the observability concepts are discussed in connection with the proposed stability analysis which permits drastic dimensional reductions for a vector feedback problem. Any constant gain system's stability can thus be analyzed in the frequency domain with a single Nyquist plot. The analysis considers the total system with all loops closed, a disturbance vector as input, and the feedback vector as output. All constant gain systems are shown to be decomposable into stable subsystems where the degree of the decomposition determines the dimensions. The maximum decomposition results in the state-space approach which is the limit case. The method is demonstrated with the stability analysis of the pogo phenomenon, an oscillatory interaction between the propulsion and the structure of a space vehicle. This problem, with eigenvalues over a hundred, was drastically but rigorously reduced to a stability analysis of a 4x4 matrix.

Vonpragenau, G. L.

Linear feature selection with applications

Several ways in which feature selection techniques were used in LACIE are discussed. In all cases, the methods require some a priori information and assumptions; in most, the classification procedure (Bayes optimal) was chosen in advance. The transformations used for dimensionality reduction are linear, that is, the variables in feature space are always linear combinations of the original measurements. Several numerically tractable criteria developed for LACIE, which provide information about the probability of misclassification, are discussed. Recent results on linear feature selection techniques are included. Their use in LACIE is discussed. Related open questions are mentioned.

Decell, H. P., Jr.

Visual enhancement of images of natural resources: Applications in geology

The principal components technique for use in multispectral scanner LANDSAT data processing results in optimum dimensionality reduction. A powerful tool for MSS IMAGE enhancement, the method provides a maximum impression of terrain ruggedness; this fact makes the technique well suited for geological analysis.

Dejesusparada, N.

A new method for mapping multidimensional data to lower dimensions

A multispectral mapping method is proposed which is based on the new concept of BEND (Bidimensional Effective Normalised Difference). The method, which involves taking one sample point at a time and finding the interrelationships between its features, is found very economical from the point of view of storage and processing time. It has good dimensionality reduction and clustering properties, and is highly suitable for computer analysis of large amounts of data. The transformed values obtained by this procedure are suitable for either a planar 2-space mapping of geological sample points or for making grayscale and color images of geo-terrains. A few examples are given to justify the efficacy of the proposed procedure.

Gowda, K. C.