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DOE OSTI2023

Method for simultaneous characterization and expansion of reference libraries for small molecule identification

A variational autoencoder (VAE) has been developed to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. The VAE has been extended to include a chemical property decoder, trained as a multitask network, to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, focused on properties that are obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involves a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training. Finally, the network is further refined by being trained with the experimental data. The trained network is used to predict chemical properties directly from structure and generate candidate structures with desired chemical properties. The network is extensible to other training data and molecular representations, and for use with other analytical platforms, for both chemical property and feature prediction as well as molecular structure generation.

Colby, Sean M.↗

DOE OSTI2020

Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples

Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g. mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e. without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller datasets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.

Colby, Sean M.↗

DOE OSTI2019

Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples

Colby, Sean M↗

NASA NTRSDate not supplied

3D Scanning System to Assess Gravity-Dependent Body Shape Changes

The human body shows unique morphological changes when exposed to different gravity conditions, including muscle atrophy, fluid shift, and spinal elongation. Such changes need to be incorporated for human-system integration in the vehicle habitat, garment, and spacesuit designs, as inaccurate body measurements can result in suboptimal crew protection that can potentially decrease injury tolerance. However, measurement tools have not been available for accurate assessments of body shape changes. This work aimed to develop a prototype 3-D body scanning system with the configuration and performance optimized for in-flight crewmember body scanning. A scan hardware system was developed using Intel RealSense commercial off-the-shelf 3D sensors. The sensor parameters were iteratively optimized and tested to obtain the performance level needed for body scanning. A scan booth structure was fabricated, with the overall size 4 x 4 x 8 feet. The specific number of sensors and mounting positions were determined by iterative simulations, which indicated that 16 cameras can capture 94% and 96% of body surface area from the 1st percentile female and 99th percentile male crew population subject. The mounted sensors were linked through a mix of USB-C and USB-3 cables and operated for data acquisition from a Linux laptop computer. A software prototype was developed using Python and Tkinter graphical user interface toolkit. A calibration procedure was also built using a panel of QR codes. A computer vision tool detected and decoded the unique ID and pattern locations of the QR codes. The calibration information determined the position and orientation of the 3D sensors with respect to each other. The scanner performance was assessed using a set of 3D printed custom manikins. The manikin size and shape were derived from the previous ISS study, which measured the crewmembers’ anthropometry changes across the different flight phases. The average anthropometric measurements at the pre-flight and flight day 15 were sampled and projected onto the 1st percentile female and 99th percentile male body shapes. Another pair of manikins were also 3D printed to simulate the neutral body posture, estimated from ISS microgravity environments. A preliminary analysis assessed the performance of the newly developed scanner against the reference scanner, which has been used at the NASA JSC for crew and test subject anthropometry. Although the new scanner data showed several artifacts and missing geometries in the occluded body areas such as armpits and crotch, overall shape matched with the reference scan. When the manikin surface coordinates were compared, a root mean square error of 1.3 cm was observed from the manikin torso segment. Linear measurements including the stature, knee height and circumference measurements at the chest and calf showed differences from the reference scan measurements, ranging between 0.3 and 0.9 cm. Overall, this work demonstrated a development framework for an in-flight scanner with design and operation optimized for crewmember body scanning. Further improvement can potentially provide previously unavailable anthropometric data from different gravitational environments, including 0-g, 1/6-g, and 1-g. Such data can improve suit fit, habitat design, exercise efficacy quantification and sizing of orthostatic intolerance garments.

K H Kim↗

DOE OSTI2023

Deployment of Dynamic Neural Network Optimization to Minimize Heat Rate During Ramping for Coal Power Plants (Final Technical Report)

Much success was achieved throughout the course of this project. A successful implementation of Dynamic Neural Network Optimization (D-NNO) was coupled with Adaptive Predictive Controls (APC) and a novel hardware installation comprised of an advanced sensor network (ASN) measuring mass-weighted averages of flue gas constituents above the horizontal superheater of a coal-fired utility boiler. From 2019 through 2023 (including an extension due to COVID delays), the team was able to prototype, evaluate, deploy, iterate, and ultimately finalize an advanced closed-loop control D-NNO system which demonstrated the ability to: •improve unit efficiency ~2.0% relative to unoptimized operation (represented as total fuel fired per MWh generated) •improve unit NOx emission rates 10%+ beyond static optimization baselines •improve unit temperature stability as much as 58% and on average 12% •improve operating load stability as much as 35% The culmination of this project has generated an advanced methodology of deploying specially designed recurrent neural networks (long short-term memory, gated recurrent unit, encoder-decoder networks, transformers, etc.), customized trajectory planning and closed-loop optimization modules capable of adapting to live electric grid responses and demands, self-tuning and adaptive expert controls constantly adjusting prediction parameters to real-time unit behavior, and a hardware/software package able to reliably calculate net unit heat rate (NUHR) in real-time using flue gas constituents, machine learning, and known combustion relationships. Through this real-time NUHR value, immediate feedback on system adjustments relative to operating efficiency was available, allowing for rapid improvements to system performance. In addition to development and deployment of the advanced D-NNO system, the approach methodology has been readily commercialized through the project platform Griffin Open Systems, LLC, the D-NNO software platform host. Similar methodologies to those developed by this project have already been deployed at 5 other units across the United States, with another 6 implementations scheduled, and more expected. Over the course of the project, multiple academic papers were submitted and accepted for publication within esteemed academic journals, and PhD students were trained and graduated, as well as undergraduate students becoming involved and participating to project objectives.

01 COAL, LIGNITE, AND PEAT↗

NASA NTRS1996

Coset Codes Viewed as Terminated Convolutional Codes

In this paper, coset codes are considered as terminated convolutional codes. Based on this approach, three new general results are presented. First, it is shown that the iterative squaring construction can equivalently be defined from a convolutional code whose trellis terminates. This convolutional code determines a simple encoder for the coset code considered, and the state and branch labelings of the associated trellis diagram become straightforward. Also, from the generator matrix of the code in its convolutional code form, much information about the trade-off between the state connectivity and complexity at each section, and the parallel structure of the trellis, is directly available. Based on this generator matrix, it is shown that the parallel branches in the trellis diagram of the convolutional code represent the same coset code C(sub 1), of smaller dimension and shorter length. Utilizing this fact, a two-stage optimum trellis decoding method is devised. The first stage decodes C(sub 1), while the second stage decodes the associated convolutional code, using the branch metrics delivered by stage 1. Finally, a bidirectional decoding of each received block starting at both ends is presented. If about the same number of computations is required, this approach remains very attractive from a practical point of view as it roughly doubles the decoding speed. This fact is particularly interesting whenever the second half of the trellis is the mirror image of the first half, since the same decoder can be implemented for both parts.

Fossorier, Marc P. C.↗

NASA NTRS2018

Simulation and Analysis of Opportunistic MSPA for Multiple Cubesat Deployments

We describe a software approach for simultaneous demodulation and decoding of multiple frequency- multiplexed spacecraft across multiple ground stations. The approach involves the use of a single ground antenna with wide enough aperture to receive multiple angularly adjacent spacecraft simultaneously. This technique uses a wide-band RF signal digitizer coupled with easily and cheaply duplicated software-receiver modules to independently process the frequency-channelized downlink signals from the spacecraft. This approach relaxes the need for realizable modems at each antenna, for example in the Deep-SpaceNetwork (DSN), and can also function as a delayed data retrieval method for cubesat missions with routine science data return. Thus, we hope that this solution can enable more efficient utilization of DSN assets. We concentrate on a simulation similar to the proposed Exploration Mission 1 (EM-1) mission from a geometric perspective. To that end, the simulated scenario involves ten secondary cubesats deployed and tracked for a span of four days (the modeled motion over the first four days of the mission does not include any Trajectory Correction Maneuvers (TCMs) that may be necessary as the cubesats approach the moon). Transmissions from the cubesats may be received through a combination of DSN ground sites based on visibility. The cubesats are assumed to utilize typical cubesat transmit powers and a waveform similar to that of the Iris radio. One cubesat is chosen as the “target” and is considered tracked by all ground-stations throughout the simulation (i.e., it is consistently at the center of the main lobe of each ground station antenna when the ground station is in view of the cubesat in terms of elevation angle). The simulation effort involves synthesizing a wideband signal that includes the ten cubesats across a large bandwidth due to each cubesat having its own center-frequency in X-band, near 8.4 GHz. Each signal is characterized by its own Doppler-frequency shift and free-space path-loss computed through the underlying geometry of the simulation as well as the cubesat transmit power. Finally, each cubesat signal experiences a unique antenna gain at each ground station due to the underlying antenna pattern and spacecraft-ground station geometry. We establish two interesting findings: First, the link-budget for the EM-1-like scenario is almost completely limited by the angle between the center of the antenna main beam and the cubesat, which means that the signal-to-noise ratio is wholly adequate for demodulation and decoding at the simulated bitrates unless the cubesat exits the main beam. Secondly, and fortunately due to the use of a software radio architecture, we show that it is possible to successfully receive signals from most cubesats for the entire 4-day simulation. Due to the signal-to-noise ratio being sufficient for demodulation even after the side-lobe’s 17dB reduction in SNR, the software radio can still demodulate such cubesats as long as the radio is capable of re-establishing carrier lock as the cubesats leave the main beam and enter the side-lobe. Considering that the target application utilizes offline processing, a loss of lock can be detected and lock can be re-established by iterating over the data. Extensive simulations demonstrate these results.

Abraham, Douglas S.↗

DOE OSTI2021

Multiscale Data-Driven Seismic Full-Waveform Inversion With Field Data Study

Seismic full-waveform inversion (FWI), which uses iterative methods to estimate high-resolution subsurface models from seismograms, is a powerful imaging technique in exploration geophysics. In recent years, the computational cost of FWI has grown exponentially due to the increasing size and resolution of seismic data. Moreover, it is a nonconvex problem and can encounter local minima due to the limited accuracy of the initial velocity models or the absence of low frequencies in the measurements. To overcome these computational issues, we develop a multiscale data-driven FWI method based on fully convolutional networks (FCNs). In preparing the training data, we first develop a real-time style transform method to create a large set of synthetic subsurface velocity models from natural images. We then develop two convolutional neural networks with encoder-decoder structures to reconstruct the low- and high-frequency components of the subsurface velocity models, separately. To validate the performance of our data-driven inversion method and the effectiveness of the synthesized training set, we compare it with conventional physics-based waveform inversion approaches using both synthetic and field data. Finally, these numerical results demonstrate that, once our model is fully trained, it can significantly reduce the computation time and yield more accurate subsurface velocity models in comparison with conventional FWI.

58 GEOSCIENCES↗

NASA NTRS2012

Combining Ratio Estimation for Low Density Parity Check (LDPC) Coding

The Low Density Parity Check (LDPC) Code decoding algorithm make use of a scaled receive signal derived from maximizing the log-likelihood ratio of the received signal. The scaling factor (often called the combining ratio) in an AWGN channel is a ratio between signal amplitude and noise variance. Accurately estimating this ratio has shown as much as 0.6 dB decoding performance gain. This presentation briefly describes three methods for estimating the combining ratio: a Pilot-Guided estimation method, a Blind estimation method, and a Simulation-Based Look-Up table. The Pilot Guided Estimation method has shown that the maximum likelihood estimates of signal amplitude is the mean inner product of the received sequence and the known sequence, the attached synchronization marker (ASM) , and signal variance is the difference of the mean of the squared received sequence and the square of the signal amplitude. This method has the advantage of simplicity at the expense of latency since several frames worth of ASMs. The Blind estimation method s maximum likelihood estimator is the average of the product of the received signal with the hyperbolic tangent of the product combining ratio and the received signal. The root of this equation can be determined by an iterative binary search between 0 and 1 after normalizing the received sequence. This method has the benefit of requiring one frame of data to estimate the combining ratio which is good for faster changing channels compared to the previous method, however it is computationally expensive. The final method uses a look-up table based on prior simulated results to determine signal amplitude and noise variance. In this method the received mean signal strength is controlled to a constant soft decision value. The magnitude of the deviation is averaged over a predetermined number of samples. This value is referenced in a look up table to determine the combining ratio that prior simulation associated with the average magnitude of the deviation. This method is more complicated than the Pilot-Guided Method due to the gain control circuitry, but does not have the real-time computation complexity of the Blind Estimation method. Each of these methods can be used to provide an accurate estimation of the combining ratio, and the final selection of the estimation method depends on other design constraints.

Mahmoud, Saad↗

DOE OSTI2025

DS-TIDE: Harnessing Dynamical Systems for Efficient Time-Independent Differential Equation Solving

Time-Independent Differential Equations (TIDEs) are central to modeling equilibrium behavior across a wide range of scientific and engineering domains, from electrostatics to porous media flow. Conventional numerical solvers offer reliable solutions but incur significant computational costs due to fine-grained discretization and iterative procedures. Machine learning-based approaches address this by replacing iterative solving processes with one-time inference; however, their sophisticated models require extensive training resources that often exceed those of traditional solvers. Consequently, designing a TIDE solver that achieves high accuracy, broad applicability, and exceptional computational efficiency remains a fundamental challenge. In this paper, we propose DS-TIDE, a novel hardware solver that is inspired by, and subsequently leverages, the intrinsic connection between Dynamical Systems (DS) and Differential Equations (DEs) to efficiently and accurately solve TIDEs. DS-TIDE employs a CMOS-compatible DS-based processor, whose physical states evolve under carefully designed DE-driven dynamics and naturally converge to equilibrium -- the solution of the target TIDE -- within ~1µs on a ~1-watt DS-TIDE processor. To enhance expressivity, DS-TIDE incorporates Heterogeneous Dynamics with Temporal Layering (HDTL), which solves TIDEs through a three-stage DS evolution -- conditioning, solving, and decoding -- each governed by specialized dynamics. The entire evolution process is analogous to an infinitely deep neural network temporally unrolled, offering the system the capability of representing complex equations. Furthermore, DS-TIDE is equipped with an on-device DS-DE Auto-Alignment mechanism that dynamically adapts intrinsic hardware dynamics within milliseconds, effectively aligning the system’s dynamics to diverse target DEs. Experimental results across TIDEs from a wide range of scientific and engineering domains demonstrate that DS-TIDE achieves ~10^3× speedup, ~10^5× energy savings, and competitive or superior accuracy compared to state-of-the-art numerical and ML-based solvers.

Liu, Chuan↗

DOE OSTI2021

Encoder–decoder neural network for solving the nonlinear Fokker–Planck–Landau collision operator in XGC

An encoder–decoder neural network has been used to examine the possibility for acceleration of a partial integro-differential equation, the Fokker–Planck–Landau collision operator. This is part of the governing equation in the massively parallel particle-in-cell code XGC, which is used to study turbulence in fusion energy devices. The neural network emphasizes physics-inspired learning, where it is taught to respect physical conservation constraints of the collision operator by including them in the training loss, along with the ℓ 2 loss. In particular, network architectures used for the computer vision task of semantic segmentation have been used for training. A penalization method is used to enforce the ‘soft’ constraints of the system and integrate error in the conservation properties into the loss function. During training, quantities representing the particle density, momentum and energy for all species of the system are calculated at each configuration vertex, mirroring the procedure in XGC. This simple training has produced a median relative loss, across configuration space, of the order of 10 –4 , which is low enough if the error is of random nature, but not if it is of drift nature in time steps. The run time for the current Picard iterative solver of the operator is O(n 2 ), where n is the number of plasma species. As the XGC1 code begins to attack problems including a larger number of species, the collision operator will become expensive computationally, making the neural network solver even more important, especially since its training only scales as O(n). Here, a wide enough range of collisionality has been considered in the training data to ensure the full domain of collision physics is captured. An advanced technique to decrease the losses further will be subject of a subsequent report. Eventual work will include expansion of the network to include multiple plasma species.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗