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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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Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning
The macrodomain of severe acute respiratory syndrome coronavirus 2 nonstructural protein 3 is required for viral pathogenesis and is an emerging antiviral target. We previously performed an x-ray crystallography–based fragment screen and found submicromolar inhibitors by fragment linking. However, these compounds had poor membrane permeability and liabilities that complicated optimization. Here, we developed a shape-based virtual screening pipeline—FrankenROCS. We screened the Enamine high-throughput collection of 2.1 million compounds, selecting 39 compounds for testing, with the most potent binding with a 130 μM median inhibitory concentration (IC 50 ). We then paired FrankenROCS with an active learning algorithm (Thompson sampling) to efficiently search the Enamine REAL database of 22 billion molecules, testing 32 compounds with the most potent binding with a 220 μM IC 50 . Further optimization led to analogs with IC 50 values better than 10 μM. This lead series has improved membrane permeability and is poised for optimization. FrankenROCS is a scalable method for fragment linking to exploit synthesis-on-demand libraries.
Scalable multiplexed machine learning gas sensor chips for food classification
Multiplexed gas sensor arrays combined with machine learning have unlocked previously inaccessible applications for scent-based sensing. Current platforms are limited by overlapping sensing materials with similar compositions, leading to highly correlated responses, or multistep deposition processes that hinder scalability. In this work, we developed a 16-element monolithic chip with fully distinct sensing layers, enabling a truly heterogeneous array. The system consists of highly sensitive carbon nanotube field effect transistors that are functionalized through a single-step microdispensing method compatible with automated pipetting systems. The resulting chip produces characteristic signal patterns in response to object-specific scent profiles and, when combined with machine learning algorithms, can perform automated object identification. We demonstrate the classification of 16 different objects, including food spoilage and nut allergens, with a 92.6% overall prediction accuracy.
3D fault architecture controls the dynamism of earthquake swarms
The vibrant evolutionary patterns made by earthquake swarms are incompatible with standard, effectively two-dimensional (2D) models for general fault architecture. Here we leverage advances in earthquake monitoring with a deep-learning algorithm to image a fault zone hosting a 4-year-long swarm in southern California. We infer that fluids are naturally injected into the fault zone from below and diffuse through strike-parallel channels while triggering earthquakes. A permeability barrier initially limits up-dip swarm migration but ultimately is circumvented. This enables fluid migration within a shallower section of the fault with fundamentally different mechanical properties. Our observations provide high-resolution constraints on the processes by which swarms initiate, grow, and arrest. These findings illustrate how swarm evolution is strongly controlled by 3D variations in fault architecture.
Calorimetry with deep learning: particle simulation and reconstruction for collider physics
Using detailed simulations of calorimeter showers as training data, we investigate the use of deep learning algorithms for the simulation and reconstruction of single isolated particles produced in high-energy physics collisions. We train neural networks on single-particle shower data at the calorimeter-cell level, and show significant improvements for simulation and reconstruction when using these networks compared to methods which rely on currently-used state-of-the-art algorithms. We define two models: an end-to-end reconstruction network which performs simultaneous particle identification and energy regression of particles when given calorimeter shower data, and a generative network which can provide reasonable modeling of calorimeter showers for different particle types at specified angles and energies. We investigate the optimization of our models with hyperparameter scans. Furthermore, we demonstrate the applicability of the reconstruction model to shower inputs from other detector geometries, specifically ATLAS-like and CMS-like geometries. These networks can serve as fast and computationally light methods for particle shower simulation and reconstruction for current and future experiments at particle colliders.
Citizen science for IceCube: Name that Neutrino
Name that Neutrino is a citizen science project where volunteers aid in classification of events for the IceCube Neutrino Observatory, an immense particle detector at the geographic South Pole. From March 2023 to September 2023, volunteers did classifications of videos produced from simulated data of both neutrino signal and background interactions. Name that Neutrino obtained more than 128,000 classifications by over 1800 registered volunteers that were compared to results obtained by a deep neural network machine-learning algorithm. Possible improvements for both Name that Neutrino and the deep neural network are discussed.
Foundations of automatic feature extraction at LHC–point clouds and graphs
Abstract Deep learning algorithms will play a key role in the upcoming runs of the Large Hadron Collider (LHC), helping bolster various fronts ranging from fast and accurate detector simulations to physics analysis probing possible deviations from the Standard Model. The game-changing feature of these new algorithms is the ability to extract relevant information from high-dimensional input spaces, often regarded as “replacing the expert” in designing physics-intuitive variables. While this may seem true at first glance, it is far from reality. Existing research shows that physics-inspired feature extractors have many advantages beyond improving the qualitative understanding of the extracted features. In this review, we systematically explore automatic feature extraction from a phenomenological viewpoint and the motivation for physics-inspired architectures. We also discuss how prior knowledge from physics results in the naturalness of the point cloud representation and discuss graph-based applications to LHC phenomenology.
Characterizing the Spread of COVID-19 from Human Mobility Patterns and SocioDemographic Indicators
Mobility is an indicator of human movement through space and time. With the increasing availability of geolocated data (from GPS, accelerometers, etc.), it is now possible to examine individual as well as group human mobility patterns. Human mobility is influenced by both intrinsic (i.e. personal motivations) and extrinsic (i.e., events like natural hazards or a pandemic like the COVID-19) factors. However, the intricate relationships between human mobility patterns and sociodemographic characteristics in the context of a pandemic are yet to be fully explored. Our goal is to overcome this gap by using human mobility data at the census block group level from mobile phones and combining those with social vulnerability indicators to examine the overall spread of COVID-19 at local spatial scales. We used 585,878 weekly visits to 37,871 points of interests (POIs) from Safegraph to quantify mobility indices and social distancing metrics in 2,820 census block groups in the city of Los Angeles (LA) - before and during lockdown as well as during the phase1 and phase 2 reopening. Finally, using supervised machine learning algorithms, we classified the census block groups in LA into High, Medium and Low categories that represented the vulnerability of these block groups based on the cumulative number of occurrences of COVID-19 cases till July 24, 2020. Our results indicate that the tree-based classifiers performed well in comparison to the Support Vector Machines and Multinomial Logit models. Gradient Boosting had the highest classification accuracy of 97.4% COVID-19 with an AUC score of 0.987. The block groups with high COVID-19 cases also had a high concentration of socially vulnerable populations, high human mobility index and a low social distancing index.
Direction-optimizing Label Propagation Framework for Structure Detection in Graphs: Design, Implementation, and Experimental Analysis
Label Propagation is not only a well-known machine learning algorithm for classification but also an effective method for discovering communities and connected components in networks. We propose a new Direction-optimizing Label Propagation Algorithm (DOLPA) framework that enhances the performance of the standard Label Propagation Algorithm (LPA), increases its scalability, and extends its versatility and application scope. As a central feature, the DOLPA framework relies on the use of frontiers and alternates between label push and label pull operations to attain high performance. It is formulated in such a way that the same basic algorithm can be used for finding communities or connected components in graphs by only changing the objective function used. Additionally, DOLPA has parameters for tuning the processing order of vertices in a graph to reduce the number of edges visited and improve the quality of solution obtained. We present the design and implementation of the enhanced algorithm as well as our shared-memory parallelization of it using OpenMP. We also present an extensive experimental evaluation of our implementations using the LFR benchmark and real-world networks drawn from various domains. Compared with an implementation of LPA for community detection available in a widely used network analysis software, we achieve at most five times the F-Score while maintaining similar runtime for graphs with overlapping communities. We also compare DOLPA against an implementation of the Louvain method for community detection using the same LFR-graphs and show that DOLPA achieves about three times the F-Score at just 10% of the runtime. For connected component decomposition, our algorithm achieves orders of magnitude speedups over the basic LP-based algorithm on large-diameter graphs, up to 13.2× speedup over the Shiloach-Vishkin algorithm, and up to 1.6× speedup over Afforest on an Intel Xeon processor using 40 threads.
Finding MIDDLE Ground: Scalable and Secure Distributed Learning
Edge computing methods allow devices to efficiently train a high-performing, robust, and personalized model for predictive tasks. However, these methods succumb to privacy and scalability concerns such as adversarial data recovery and expensive model communication. Furthermore, edge computing methods unrealistically assume that all devices train an identical model. In practice, edge devices have varying computational and memory constraints which may not allow certain devices to have the space or speed to train a specific model. To overcome these issues, we propose MIDDLE: a model independent distributed learning algorithm which allows heterogeneous edge devices to assist each other’s training while communicating only non-sensitive information. MIDDLE unlocks the ability for edge devices, regardless of computational or memory constraints, to assist each other even with completely different model architectures. Furthermore, MIDDLE does not require model or gradient communication which greatly reduces communication size and time. We prove that MIDDLE attains the optimal convergence rate O(1/sqrt(TM)) of stochastic gradient descent for convex and non-convex smooth optimization (for total iterations T and batch size M). Finally, our experimental results demonstrate that MIDDLE (even in non-IID data settings) attains robust and high-performing models without model or gradient communication.
FlexDRL v1.0
FlexDRL is a framework that can be used as a benchmarking tool to evaluate different Deep Reinforcement Learning algorithms in a building energy management setting. OpenAI Gym was used as wrapper to the co-simulation environment (EnergyPlus for envelope and HVAC and Modelica for battery and PV) to interface with DRL algorithms, which are developed in PyTorch. In order to facilitate the usage of FlexDRL, all the required dependencies have been packaged into a Docker container.
Aerial 3D Building Reconstruction from Drone Imagery (A3DBR) v1
This toolkit is composed of several modules for extracting buildings geometrical and thermal characteristics from RGB and thermal imagery captured using a drone. - Building 3D reconstruction module: leverage a photogrammetry software to construct a 3D point cloud from RGB drone imagery, which is then used in conjunction with image processing and geometric methods to extract building footprint and building height (i.e., 3D model of the building). - Windows to wall ratio estimation module: leverage deep learning semantic segmentation modeling to detect windows on 2D drone RGB images. The detected windows are then projected onto the extracted building 3D model (using building 3D reconstruction module) and their area is computed to obtain window to wall ratio estimation. - Thermal anomalies detection module: leverage image processing and machine learning algorithm to detect on 2D drone thermal images potential thermal anomalies within building's facades and roofs.
AI-Batt (Autonomous Identification of Battery Life Models) [SWR 21-36]
Autonomous Identification of Battery Life Models (AI-Batt) AI-Batt is a MATLAB code base for developing lifetime models for batteries from accelerated aging data. The code base provides many functions for processing, visualizing, and modeling battery aging data, making the data processing, exploration, and modeling workflow substantially faster. These tools are tailored for working with battery aging data sets, which usually consist of many separate time-series for each cell, with many test conditions and possible replicates at each condition, which makes it difficult to simply process or visualize the data set. Complex modeling tasks, such as cross-validation, sensitivity analysis, and uncertainty quantification have been implemented to enable thorough statistical investigation of model predictions. Additionally, several machine-learning algorithms are implemented to autonomously identify suitable models via symbolic regression. Data processing functions automatically cast data from the struct data type, which is commonly used to store experimental data, but is not an acceptable input for most algorithms, to the table data type, which can be easily used as input to any optimization algorithm. Also, the data can be separated into time-invariant and time-variant data tables, which is helpful for exploring the data set as well as developing separate models for time-variant and time-invariant aging mechanisms. For example, in aging tests with constant temperature, temperature is a time-invariant experimental condition. Visualization tools enable plotting of data, model fits, and model simulations possible with single-line function calls, empowering data exploration of complex data sets with both time-varying and time-invariant trends. Plots can be automatically generated for the whole data set, or separated by data group (groups of test replicates) or individual data series. Data points or data series can be automatically colored by the value of a variable with a variety of color maps, and model predictions can also be colored by the value of a fit statistic. Comparisons between data sets and the predictions/simulations of different models on the same data set can be easily plotted as well. Distributions of parameter values from bootstrap resampling can be plotted to visualize the reliability of parameter estimation, or determine any correlations between parameters. Modeling tools handle the complex task of creating and parsing symbolic equations for modeling battery lifetime. Equations are parsed to grab relevant data variables, parameter values, or specified sub-models for input into optimization, evaluation, or simulation functions. Models can be optimized locally (one set of parameters for each data series), bi-level (some parameters shared across the data set), or globally (single set of parameters for all data). Functions implementing symbolic regression algorithms help users to discover effective model equations, even in poorly sampled, high-dimensional data.
Graph-Env
The Graph-Env library provides a framework for adapting graph search problems into OpenAI Gym environments for reinforcement learning. In other words, Graph-Env enables reinforcement learning algorithms to be applied to graph search problems. Graph search problems include molecule and crystal structure design problems; route planning problems, including traveling salesperson problem; puzzles and games, such as chess and go; shortest path problems; minimum spanning tree; vehicle path generation; and others.
CEGANN: CRYSTAL EDGE GRAPH ATTENTION NEURAL NETWORK
SF-22-156 Machine learning (ML) models and applications in materials design and discovery typically involve the use of feature representations or descriptors followed by a learning algorithm that maps them to user desired properties of interest. Most popular mathematical formulation-based descriptors are not unique across atomic environments and suffer from transferability issues across different application domains and/or material classes. The CEGANN code provides a unified interface to facilitate material characterization across materials across multiple scales (from atomic to mesoscale) and diverse classes of materials ranging from metals oxides, non-metals, and even hierarchical materials such as zeolites and semi ordered materials such as mesophases. CEGANN implements a Graph Attention Network (GAT) type convolution architecture. The details of network architecture can be found in the paper https://doi.org/10.48550/arXiv.2207.10168. The software comes with pretrained examples and dataset for the classification of the following representative systems: (1) Structure-level representation such as space group (2) Structural dimensionality (e.g., bulk, 2D, clusters etc.) (3) Grain boundary identification (4) Nucleation and growth of a zeolite polymorph (5) Characterization of binary mesophases and their phase transitions (6) Growth of ice. The code is written in python programming language.
Master State Threat Identifier (masti)
The MSE cyber sensor offers a novel approach for scalable network monitoring using heterogeneous computing. Packet data is collected, analyzed, and stored by a stand alone cyber sensor. Machine learning algorithms are run to discover patterns in the communication without the need for deep packet inspection. Tuning of the detection algorithms happens automatically, without need for an engineer to manually create detection rules.
ExaDigiT/RAPS
ExaDigiT is a framework for developing comprehensive digital twins of liquid-cooled supercomputers, which has three main modules: (1) a python-based Resource Allocator and Power Simulator (RAPS), (2) a Modelica-based Thermo-Fluidic cooling model, and (3) a C++-based augmented reality model built on Unreal Engine 5. RAPS either simulates workloads or replays historical workloads from system telemetry, and is able to predict dynamic energy consumption, as well as interact with the cooling model to predict cooling system behavior. Such a tool can be used together with reinforcement learning algorithms to provide an end-to-end optimization tool for data centers.
Environmental Molecular Network (ENVnet) v1
Here, we present an approach that integrates mass difference based deconvolution with molecular networking to build a static reference network from all publicly available organic matter metabolomics datasets. This is accomplished using MS/MS deconvolution coupled with both recently reported (BUDDY) and novel machine learning algorithms to determine chemical formulas and perform MS/MS alignments (REM-BLINK).