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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Bridging cognitive gaps between user and model in interactive dimension reduction

Interactive machine learning (ML) systems are difficult to design because of the "Two Black Boxes" problem that exists at the interface between human and machine. Many algorithms that are used in interactive ML systems are black boxes that are presented to users, while the human cognition represents a second black box that can be difficult for the algorithm to interpret. These two black boxes create cognitive gaps between the user and the interactive ML model when a user interacts with the system. In this paper, we identify several cognitive gaps that exist in a previously-developed interactive visual analytics (VA) system, Andromeda. These cognitive gaps that we are addressing in Andromeda are representative of common problems in other VA systems. Our goal with this work is to open both black boxes and bridge these cognitive gaps by making improvements to the original Andromeda system, including designing new visual features to help people better understand how Andromeda processes and interacts with data and improving the underlying algorithm so that the Andromeda system can better understand the intent of the user during the data exploration process. We evaluate our designs through both qualitative and quantitative analysis (i.e., user study and simulation analysis), and the results confirm that the improved Andromeda system outperforms the original version significantly in a series of high-dimensional data understanding tasks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Use of Physics to Improve Solar Forecast: Part II, Machine Learning and Model Interpretability

Machine learning (ML) models have been applied to forecast solar energy; however, they often lack clarity of interpretability and underlying physics. This work addresses such challenges by developing a hierarchy of ML models that gradually introduce predictors to improve the forecast accuracy based on a physics-based framework. Three ML models (ARIMA, LSTM, and XGBoost) are examined and compared with four physics-informed persistence models reported in Part I and the simple persistence model to assess the improvement of different models. The 7-year measurements at the U.S. Department of Energy's Atmospheric Radiation Measurement's Southern Great Plains Central Facility site are used for forecasts and evaluations. The results reveal that the step-by-step introduction of predictors leads to different improvements for models at different hierarchical levels. Comparison of the ML models with persistence models shows that LSTM and XGBoost outperform all the persistence models, with LSTM having the overall best performance; however, ARIMA underperforms the four physics-informed persistence models. This study demonstrates the importance and utility of incorporating physics into ML models in improving forecast accuracy by introducing a hierarchy of physics-based predictors, distinguishing predictor contributions, and enhancing the ML interpretability. The combined use of Global Horizontal Irradiance (GHI) and Direct Normal Irradiance (DNI) significantly improves the forecast accuracy compared to using individual irradiances alone because the pair contains more information on cloud-radiation interactions.

interpretability↗
DOE OSTI2022

High-Accuracy Semiempirical Quantum Models Based on a Minimal Training Set

A great need exists for computationally efficient quantum simulation approaches that can achieve an accuracy similar to high-level theories at a fraction of the computational cost. In this regard, we have leveraged a machine-learned interaction potential based on Chebyshev polynomials to improve density functional tight binding (DFTB) models for organic materials. The benefit of our approach is two-fold: (1) many-body interactions can be corrected for in a systematic and rapidly tunable process, and (2) high-level quantum accuracy for a broad range of compounds can be achieved with ~0.3% of data required for one advanced deep learning potential. Our model exhibits both transferability and extensibility through comparison to quantum chemical results for organic clusters, solid carbon phases, and molecular crystal phase stability rankings. Overall, our efforts thus allow for high-throughput physical and chemical predictions with up to coupled-cluster accuracy for systems that are computationally intractable with standard approaches.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Interactive Corpus Analysis Tool

The Interactive Corpus Analysis Tool (ICAT) is an interactive machine learning dashboard for unlabeled text/natural language processing datasets that allows a user to iteratively and visually define features, explore and label instances of their dataset, and simultaneously train a logistic regression model. ICAT was created to allow subject matter experts in a specific domain to directly train their own models for unlabeled datasets visually, without needing to be a machine learning expert or needing to know how to code the models themselves. This approach allows users to directly leverage the power of machine learning, but critically, also involves the user in the development of the machine learning model.

Martindale, Nathan [Oak Ridge National Lab. (ORNL)↗
DOE OSTI2018

Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks

Different organisms in a microbial community may drastically affect each other’s growth phenotypes, significantly affecting the community dynamics, with important implications for human and environmental health. Novel culturing methods and the decreasing costs of sequencing will gradually enable high-throughput measurements of pairwise interactions in systematic coculturing studies. However, a thorough characterization of all interactions that occur within a microbial community is greatly limited both by the combinatorial complexity of possible assortments and by the limited biological insight that interaction measurements typically provide without laborious specific follow-ups. Here, we show how a simple and flexible formal representation of microbial pairs can be used for the classification of interactions via machine learning. The approach we propose predicts with high accuracy the outcome of yet-to-be performed experiments and generates testable hypotheses about the mechanisms of specific interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A machine learning-based interaction force model for non-spherical and irregular particles in low Reynolds number incompressible flows

In this study, interaction force of non-spherical particles in low Reynolds number gas-solid flow is investigated by neural network approaches. An artificial neural network (ANN) model is developed to correlate the non-spherical particle shape and the flow conditions with the interaction force. To define the particle shape, spherical harmonic expansion is applied. Furthermore, variational autoencoder model is then used to extract latent geometric features. The latent vector is utilized as an input with the Reynolds number for the ANN. The interaction force data, which is used as output data of the ANN, is obtained by particle resolved direct numerical simulation for 5200 non-spherical particles. The proposed model enables unsupervised extraction for non-spherical particle shapes and accurate predictions on the interaction force without heavy computation. This study provides the model that can explain complicated shapes of particles and be applied to a large scale, computational fluid dynamics simulation.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

Application of machine learning for modeling brønsted-guggenheim-scatchard specific ion interaction theory (SIT) coefficients

Machine learning methodologies can provide insight into Brønsted-Guggenheim-Scatchard specific ion interaction theory (SIT) parameter values where experimental data availability may be limited. This study develops and executes machine learning frameworks to model the SIT interaction coefficient, ε. Key findings include successful estimations of ε via artificial neural networks using clustering and value prediction approaches. Additionally, applicability to other chemical parameters is also assessed briefly. Models developed here provide support for a use-case of machine learning in geologic nuclear waste disposal research applications, namely in predictions of chemical behaviors of high ionic strength solutions (i.e., subsurface brines).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD–ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Uncertainty Propagation within Chained Models for Machine Learning Reconstruction of Neutrino-LAr Interactions

Sequential or chained models are increasingly prevalent in machine learning for scientific applications, due to their flexibility and ease of development. Chained models are particularly useful when a task is separable into distinct steps with a hierarchy of meaningful intermediate representations. In reliability-critical tasks, it is important to quantify the confidence of model inferences. However, chained models pose an additional challenge for uncertainty quantification, especially when input uncertainties need to be propagated. In such cases, a fully uncertainty-aware chain of models is required, where each step accepts a probability distribution over the input space, and produces a probability distribution over the output space. In this work, we present a case study for adapting a single model within an existing chain, designed for reconstruction within neutrino-Argon interactions, developed for neutrino oscillation experiments such as MicroBooNE, ICARUS, and the future DUNE experiment. We test the performance of an input uncertainty-enabled model against an uncertainty-blinded model using a method for generating synthetic noise. By comparing these two, we assess the increase in inference quality achieved by exposing models to upstream uncertainty estimates.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery

Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) structural interaction fingerprints offer enhanced structural features specific to target proteins. Machine learning models trained on interaction fingerprints enable precise binding prediction. Recent focus has shifted to structure-based predictive modeling, with machine-learning scoring functions excelling due to feature engineering guided by key interactions. Notably, 3D interaction fingerprints are gaining ground due to their robustness. Various structural interaction fingerprints have been developed and used in drug discovery, each with unique capabilities. This review recapitulates the developed structural interaction fingerprints and provides two case studies to illustrate the power of interaction fingerprint-driven machine learning. The first elucidates structure–activity relationships in β2 adrenoceptor ligands, demonstrating the ability to differentiate agonists and antagonists. The second employs a retrosynthesis-based pre-trained molecular representation to predict protein–ligand dissociation rates, offering insights into binding kinetics. Despite remarkable progress, challenges persist in interpreting complex machine learning models built on 3D fingerprints, emphasizing the need for strategies to make predictions interpretable. Binding site plasticity and induced fit effects pose additional complexities. Interaction fingerprints are promising but require continued research to harness their full potential.

3D structural interaction fingerprints↗
DOE OSTI2025

professor

Professor is a tool to help you study complicated physical phenomena by providing tools to 1) fit machine learning models to 2D image arrays from simulations and 2) interactively explore these machine learning models in real time. Professor is most useful when studying ensembles of simulations. A typically workflow would look like: 1. A user is interested in how parameters A, B, C, & D influence some complicated physics 2. User setups up parameterized simulations to study ABCD and the results of these simulations to be image arrays (a 2d matrix of float32 values) 3. User runs an ensemble of simulations studying ABCD creating a dataset of image arrays 4. User runs `prof-trainer` to fit a machine learning model to learn the mapping from [A,B,C,D] to the image arrays 5. User then uses `prov-vis` to interactively explore the machine learning model in real time, gaining their insight into how those parameters influence the physics 6. Go profess your idea about ABCD!

Collis, HenryH [Lawrence Livermore National Labora↗
DOE OSTI2023

Inferring colloidal interaction from scattering by machine learning

A machine learning solution for the potential inversion problem in elastic scattering is outlined. The inversion scheme consists of two major components, a generative network featuring a variational autoencoder which extracts the targeted static two-point correlation functions from experimentally measured scattering cross sections, and a Gaussian process framework which probabilistically infers the relevant structural parameters from the inverted correlation functions. Via a case study of charged colloidal suspensions, the feasibility of this approach for quantitative study of molecular interaction is critically benchmarked and its merit over existing deterministic approaches, in terms of numerical accuracy and computationally efficiency, is demonstrated.

36 MATERIALS SCIENCE↗
DOE OSTI2022

ppdx : Automated modeling of protein–protein interaction descriptors for use with machine learning

This paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein–protein interactions. The descriptors can be used to predict various properties of interest, such as protein–protein binding affinities, or inhibitory concentrations (IC 50 ), using approaches that range from simple regression to more complex machine learning models. The software is highly modular. It supports different protocols for generating structures, and 95 descriptors can be currently computed. More protocols and descriptors can be easily added. The implementation is highly parallel and can fully exploit the available cores in a single workstation, or multiple nodes on a supercomputer, allowing many systems to be analyzed simultaneously. As an illustrative application, ppdx is used to parametrize a model that predicts the IC 50 of a set of antigens and a class of antibodies directed to the influenza hemagglutinin stalk.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗