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At least 1,405 records · Page 78
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Differences in substrate use linked to divergent carbon flow during litter decomposition

ABSTRACT Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Rotor blade imbalance fault detection for variable-speed marine current turbines via generator power signal analysis

Marine hydrokinetic (MHK) turbines extract renewable energy from oceanic environments. However, due to the harsh conditions that these turbines operate in, system performance naturally degrades over time. Thus, ensuring efficient condition-based maintenance is imperative towards guaranteeing reliable operation and reduced costs for marine hydrokinetic power. This work proposes a novel framework aimed at identifying and classifying the severity of rotor blade pitch imbalance faults experienced by marine current turbines (MCTs). In the framework, a Continuous Morlet Wavelet Transform (CMWT) is first utilized to acquire the wavelet coefficients encompassed within the 1P frequency range of the turbine's rotor shaft. From these coefficients, several statistical indices are tabulated into a six-dimensional feature space. Next, Principle Component Analysis (PCA) is employed on the resulting feature space for dimensionality reduction, and then the application of a K-Nearest Neighbor (KNN) machine learning algorithm is utilized for fault detection and severity classification. The effectiveness of the proposed framework is validated using a high-fidelity MCT numerical simulation platform, where results demonstrate that the presence of a pitch imbalance fault can be accurately detected 100% of the time and correctly classified based upon severity more than 97% of the time.

42 ENGINEERING↗
DOE OSTI2020

Microparticle cloud imaging and tracking for data-driven plasma science

Oceans of image and particle track data encountered in plasma interactions with microparticle clouds motivate development and applications of machine-learning (ML) algorithms. A local-constant-velocity tracker, a Kohonen neural network or self-organizing map, the feature tracking kit, and U-Net are described and compared with each other for microparticle cloud datasets generated from exploding wires, dusty plasmas, and atmospheric plasmas. Particle density and the signal-to-noise ratio have been identified as two important factors that affect the tracking accuracy. Fast Fourier transform is used to reveal how U-Net, a deep convolutional neural network developed for non-plasma applications, achieves the improvements for noisy scenes. Viscous effects are revealed in the ballistic motions of the particles from the exploding wires and atmospheric plasmas. Subdiffusion of microparticles satisfying Δr 2 ∝t k (k=0.84±0.02) is obtained from the dusty plasma datasets. Microparticle cloud imaging and tracking, when enhanced with data and ML models, present new possibilities for plasma physics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2

Motion-activated wildlife cameras (or “camera traps”) are frequently used to remotely and noninvasively observe animals. The vast number of images collected from camera trap projects has prompted some biologists to employ machine learning algorithms to automatically recognize species in these images, or at least filter-out images that do not contain animals. These approaches are often limited by model transferability, as a model trained to recognize species from one location might not work as well for the same species in different locations. Furthermore, these methods often require advanced computational skills, making them inaccessible to many biologists. We used 3 million camera trap images from 18 studies in 10 states across the United States of America to train two deep neural networks, one that recognizes 58 species, the “species model,” and one that determines if an image is empty or if it contains an animal, the “empty-animal model.” Our species model and empty-animal model had accuracies of 96.8% and 97.3%, respectively. Furthermore, the models performed well on some out-of-sample datasets, as the species model had 91% accuracy on species from Canada (accuracy range 36%–91% across all out-of-sample datasets) and the empty-animal model achieved an accuracy of 91%–94% on out-of-sample datasets from different continents. Our software addresses some of the limitations of using machine learning to classify images from camera traps. By including many species from several locations, our species model is potentially applicable to many camera trap studies in North America. We also found that our empty-animal model can facilitate removal of images without animals globally. We provide the trained models in an R package (MLWIC2: Machine Learning for Wildlife Image Classification in R), which contains Shiny Applications that allow scientists with minimal programming experience to use trained models and train new models in six neural network architectures with varying depths.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

A Science-Focused Artificial Intelligence (AI) Responding in Real-Time to New Information: Capability Demonstration for Ocean World Missions

Introduction: Artificial intelligence (AI) has long been considered a potential mechanism to explore increasingly challenging environments, including those with extreme temperatures and pressures, limited communication capabilities, or those with demanding terrain. We posit that missions in extreme environments could deploy an onboard AI focused on science observations and goals in order to augment a traditional concept(s) of operations (ConOps). An onboard AI capability could perform functions such as data analysis in order to make high-level decisions, including prioritized data transmission for analysis by ground-based teams or autonomously-guided follow-on analyses that maximize science return. Such a capability would empower missions to respond to scientific data of interest in real-time; a mission could make observations and perform a preliminary analysis to alert ground-based scientists to an observation of interest, enabling an informed, rapid response from Earth-based teams. Enceladus Case Study for Onboard AI: We are developing an onboard AI capability for real-time telemetry response that formulates and carries-out informed decisions in service to established mission goals, enabling increased science return of a mission. We focus our AI development for use on a constellation of SmallSats orbiting Enceladus. Our Enceladus case study tests autonomous decision-making capabilities in scenarios with complex orbital dynamics, plume ejecta, extreme cold environments, power restrictions, and a requirement to maximize science return for a potential positive detection of life, while critically evaluating the potential for false positives. Telemetry includes simulated scientific data, spacecraft onboard operational data (e.g., position, velocity, and rotation), and engineering hardware performance data. Enceladus SmallSat Constellation. Our constellation includes eight SmallSat spacecraft in an 8:35 resonant orbit-based formation, leveraging Saturn’s gravitational forces to maintain stable orbits with global coverage around Enceladus. To our knowledge, we simulate the first stable configuration of multiple spacecraft in closed orbits around Enceladus, using a full ephemeris force model (Russell and Lara, 2009). Each spacecraft’s orbit will precess, causing an eastward ground track shift (from an orbiter’s perspective) of each spacecraft for each orbit. However, all spacecraft return to their original positions relative to Enceladus after eight Enceladus revolutions around Saturn. We model communication pathways between SmallSats to understand how information would need to be transmitted across the constellation to enable AI-driven decision-making and resource allocation across the fleet. Capability Demonstration. Our simulated capability demonstration inputs position, velocity, and rotation telemetry from our Enceladus-focused constellation simulations, and mass spectrometry data collected from abiotic and biotic laboratory-analog ocean world experiments (Theiling et al., 2018; Theiling, 2021; Da Poian et al., 2023). Data from these experiments are used to simulate MS measurements and different scenarios of science observations for onboard analysis performed on each of the eight spacecraft. For these demonstrations, we integrate 24 machine learning (ML) algorithms into an onboard intelligence as a ‘knowledge base’, including algorithms evaluating data quality and those predicting (with % confidence) gas composition, ocean aqueous chemistry, and whether the sample was influenced by microbial life. The onboard AI capability is designed to use the knowledge base to come to a consensus-based decision in the interpretation of the observed data in order to request additional action outside of a pre-defined ConOps. Requested actions could include e.g., prioritized downlink to Earth (for analysis by ground-based teams) or follow-on analyses performed across the constellation. The spacecraft’s intelligent onboard planner must then determine whether sufficient resources (e.g., time, power, etc.) are available and weigh the request with mission priorities. In our simulation, the constellation is able to identify potential biosignatures using onboard ML algorithms, evaluate the confidence of that prediction, and perform follow-on analyses across the fleet to confirm the detection, in order to best prepare a transmission of these data to Earth-based teams.

astrobiology↗
DOE OSTI2021

Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions

Abstract New drug production, from target identification to marketing approval, takes over 12 years and can cost around $2.6 billion. Furthermore, the COVID-19 pandemic has unveiled the urgent need for more powerful computational methods for drug discovery. Here, we review the computational approaches to predicting protein–ligand interactions in the context of drug discovery, focusing on methods using artificial intelligence (AI). We begin with a brief introduction to proteins (targets), ligands (e.g. drugs) and their interactions for nonexperts. Next, we review databases that are commonly used in the domain of protein–ligand interactions. Finally, we survey and analyze the machine learning (ML) approaches implemented to predict protein–ligand binding sites, ligand-binding affinity and binding pose (conformation) including both classical ML algorithms and recent deep learning methods. After exploring the correlation between these three aspects of protein–ligand interaction, it has been proposed that they should be studied in unison. We anticipate that our review will aid exploration and development of more accurate ML-based prediction strategies for studying protein–ligand interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Measuring Young Stars in Space and Time. II. The Pre-main-sequence Stellar Content of N44

The Hubble Space Telescope survey Measuring Young Stars in Space and Time (MYSST) entails some of the deepest photometric observations of extragalactic star formation, capturing even the lowest-mass stars of the active star-forming complex N44 in the Large Magellanic Cloud. We employ the new MYSST stellar catalog to identify and characterize the content of young pre-main-sequence (PMS) stars across N44 and analyze the PMS clustering structure. To distinguish PMS stars from more evolved line of sight contaminants, a non-trivial task due to several effects that alter photometry, we utilize a machine-learning classification approach. This consists of training a support vector machine (SVM) and a random forest (RF) on a carefully selected subset of the MYSST data and categorize all observed stars as PMS or non-PMS. Combining SVM and RF predictions to retrieve the most robust set of PMS sources, we find ∼26,700 candidates with a PMS probability above 95% across N44. Employing a clustering approach based on a nearest neighbor surface density estimate, we identify 16 prominent PMS structures at 1σ significance above the mean density with sub-clusters persisting up to and beyond 3σ significance. The most active star-forming center, located at the western edge of N44's bubble, is a subcluster with an effective radius of ∼5.6 pc entailing more than 1100 PMS candidates. Furthermore, we confirm that almost all identified clusters coincide with known H ii regions and are close to or harbor massive young O stars or YSOs previously discovered by MUSE and Spitzer observations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Enabling real-time adaptation of machine learning models at x-ray Free Electron Laser facilities with high-speed training optimized computational hardware

The emergence of novel computational hardware is enabling a new paradigm for rapid machine learning model training. For the Department of Energy’s major research facilities, this developing technology will enable a highly adaptive approach to experimental sciences. In this manuscript we present the per-epoch and end-to-end training times for an example of a streaming diagnostic that is planned for the upcoming high-repetition rate x-ray Free Electron Laser, the Linac Coherent Light Source-II. We explore the parameter space of batch size and data parallel training across multiple Graphics Processing Units and Reconfigurable Dataflow Units. We show the landscape of training times with a goal of full model retraining in under 15 min. Although a full from scratch retraining of a model may not be required in all cases, we nevertheless present an example of the application of emerging computational hardware for adapting machine learning models to changing environments in real-time, during streaming data acquisition, at the rates expected for the data fire hoses of accelerator-based user facilities.

97 MATHEMATICS AND COMPUTING↗