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DOE OSTI2024

Novel symmetry-preserving neural network model for phylogenetic inference

Abstract Motivation Scientists world-wide are putting together massive efforts to understand how the biodiversity that we see on Earth evolved from single-cell organisms at the origin of life and this diversification process is represented through the Tree of Life. Low sampling rates and high heterogeneity in the rate of evolution across sites and lineages produce a phenomenon denoted “long branch attraction” (LBA) in which long nonsister lineages are estimated to be sisters regardless of their true evolutionary relationship. LBA has been a pervasive problem in phylogenetic inference affecting different types of methodologies from distance-based to likelihood-based. Results Here, we present a novel neural network model that outperforms standard phylogenetic methods and other neural network implementations under LBA settings. Furthermore, unlike existing neural network models in phylogenetics, our model naturally accounts for the tree isomorphisms via permutation invariant functions which ultimately result in lower memory and allows the seamless extension to larger trees. Availability and implementation We implement our novel theory on an open-source publicly available GitHub repository: https://github.com/crsl4/nn-phylogenetics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Towards the extraction of the crystal cell parameters from pair distribution function profiles

The approach based on atomic pair distribution function (PDF) has revolutionized structural investigations by X-ray/electron diffraction of nano or quasi-amorphous materials, opening up the possibility of exploring short-range order. However, the ab initio crystal structural solution by the PDF is far from being achieved due to the difficulty in determining the crystallographic properties of the unit cell. A method for estimating the crystal cell parameters directly from a PDF profile is presented, which is composed of two steps: first, the type of crystal cell is inferred using machine-learning approaches applied to the PDF profile; second, the crystal cell parameters are extracted by means of multivariate analysis combined with vector superposition techniques. The procedure has been validated on a large number of PDF profiles calculated from known crystal structures and on a small number of measured PDF profiles. The lattice determination step has been benchmarked by a comprehensive exploration of different classifiers and different input data. The highest performance is obtained using the k -nearest neighbours classifier applied to whole PDF profiles. Descriptors calculated from the PDF profiles by recurrence quantitative analysis produce results that can be interpreted in terms of PDF properties, and the significance of each descriptor in determining the prediction is evaluated. The cell parameter extraction step depends on the cell metric rather than its type. Monometric, dimetric and trimetric cells have top-1 estimates that are correct 40, 20 and 5% of the time, respectively. Promising results were obtained when analysing real nanocrystals, where unit cells close to the true ones are found within the top-1 ranked solution in the case of monometric cells and within the top-6 ranked solutions in the case of dimetric cells, even in the presence of a crystalline impurity with a weight fraction up to 40%.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Privacy-Preserving Robust Consensus for Distributed Microgrid Control Applications

Consensus-based distributed control has been proposed for coordinating distributed energy resources (DERs) in microgrids (MGs). As one key component, distributed average observers are used to estimate the average of a group of reference signals (e.g., voltage, current, or power). State-of-the-art distributed average observers could lead to loss of privacy due to information exchange on the communication channels. The DERs' reference signals, which contain private information, could be inferred by an eavesdropper. In this article, a privacy-preserving distributed average observer is proposed that is based on robust consensus and uses the state decomposition method to preserve privacy. Compared to the existing methods, the proposed observer does not require the knowledge of the reference signal's derivative and gives accurate and smooth estimation, and is thus applicable for MG distributed control applications. A detailed analysis regarding the convergence and privacy properties of the proposed observer is presented. Here, the proposed observer is implemented on hardware controllers and validated in the context of distributed MG control applications through hardware-in-the-loop (HIL) tests.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2019

Towards Improved Real-Time Observability of Behind-Meter PhotoVoltaic Systems: A Data-Driven Approach

The stochasticity in energy supply introduced by increased PV penetration in grid distribution systems can lead to frequent and sudden supply-demand imbalances, thereby causing voltage and frequency fluctuations. Enhanced observability, in real-time, of grid attributes such as real and reactive power flows, power injections/consumption and voltages is becoming increasingly essential to ensure smooth grid operation under these new large-scale PV integration scenarios. Two significant challenges prevent grid operators from achieving this objective: 1) Computational complexity of quasi-static timeseries simulations, and 2) Partial observability of behind-meter grid assets. In this work, we take a step towards this objective by enhancing the observability of smart inverter equipped PV systems located behind AMI meters. Smart inverters convert the DC output of PV systems into real and reactive power, the ratio of which is governed by a power factor setting. This in turn is governed by the real-time voltage at its terminal, as per a pre-set volt/var curve. While it is possible to infer the power factor setting - thereby, real and reactive power injection of the PV system - at each time interval by quasi-static time series simulations, such methods are not scalable to large grid sizes. We propose to reduce the reliance on simulations by developing a deep neural network based data-driven model which predicts the time dependent power factors of the PV systems in the grid. The model uses a small amount of simulated data to learn the dependence of power factor on 1) load and apparent PV power injection (root mean square of real and reactive power) data, and 2) AMI net-load data (for BTM PV assets). Our results show that our model can predict power factors with mean absolute error of less than 6.2% under full observability scenario and under 8.6% under the partial observability scenario. Thus, our data-driven model can reduce the amount of simulations required to compute real and reactive injections from PV systems in the distribution system with or without complete information.

14 SOLAR ENERGY↗

DOE OSTI2019

O3BNN: An Out-Of-Order Architecture for High-Performance Binarized Neural Network Inference with Fine-Grained Pruning

In this work, we demonstrate that the highly-condensed BNN model can be shrunk significantly further by dynamically pruning irregular redundant edges. Based on two new observations on BNN-specific properties, our out-of-order (OoO) architecture – O3BNN, can curtail remaining edge evaluation in cases where the binary output of a neuron can be determined early. Similar to Instruction-Level-Parallelism (ILP), these fine-grained, irregular, runtime pruning opportunities are traditionally presumed to be di cult to exploit. We evaluate our design on an FPGA platform using three well-known networks, including VggNet-16, AlexNet for ImageNet, and a VGG-like network for Cifar-10. Results show that our out-of-order approach can prune 27%, 16%, and 42% of the operations for the three networks respectively, without any accuracy loss, leading to at least 1.7×, 1.5×, and 2.1× speedups over state-of-the-art implementations on FPGA/GPU/CPU BNN implementations. Our approach is inference runtime pruning, so no retrain or fine-tuning is needed. We demonstrate our design on an FPGA platform. However, this is only for showcasing the method; the approach does not rely on any FPGA-specific features and can thus be adopted by other devices as well.

Geng, Tong↗

DOE OSTI2024

High throughput, accurate gene annotation through AI and HPC-enabled structural analysis

With the advances in next generation sequencing technologies, the number of sequenced genomes is growing exponentially, resulting in a technology bottleneck for the translation of sequence information into usable hypotheses about the function of each gene. We have proposed leveraging our leadership high-performance computing (HPC) resources to help break this annotation bottleneck. Here we design an HPC-based framework to infer gene function from gene sequence by incorporating information about protein structure and interactions predicted by deep learning approaches. Accurate functional prediction and gene annotation using computational methods will facilitate breakthroughs in the genomic sciences essential to understanding and harnessing life processes in bacteria, fungi and plants. The development and applications of the state-of-the-art deep neural networks to protein structural modeling, interaction prediction, sequence comparison, and quality assessment of protein structural models will be made possible by leadership computational resources. These HPC-enabled bioinformatics and molecular modeling tools will provide powerful insights into molecular functions of genes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

$\overline{TKE}$ Parameterization and $\bar{v}$ Uncertainty Analysis for CGMF

Previous work was performed on tuning CGMF parameters for 235 U, 238 U, and Plutonium isotopes. Now work is being done to tune minor uranium isotopes. However, uranium isotopes like 232 U and 236 U have almost no experimental data. We are applying cross-isotope models to extrapolate and tune CGMF on isotopes that lack experimental data. There exist several internal CGMF physics quantities that affect the output of CGMF—multi-chance fission probability, excitation energy sharing, spin-cutoff factor, spin scaling, and fragment total kinetic energy to name a few. The mean fragment total kinetic energy, $\overline{TKE}$, is particularly interesting because of its strong anti-correlation with $\bar{v}$. We are most interested in the mean fragment total kinetic energy before neutron emissions. $\overline{TKE}$ is assumed to be pre-neutron emission unless otherwise stated. Currently in CGMF, the $\overline{TKE}$ model for 233,234,235,238 U are tuned independently to reproduce ν for the associated isotopes. In this report, we will tune a cross-isotope $\overline{TKE}$ model to experimental $\overline{TKE}$ data for 232,233,234,235,236,238 U. Because of the unreliable and sparse nature of $\overline{TKE}$ experimental data, future work will use more reliable experimental $\bar{v}$ data to infer the $\overline{TKE}$ model (and likely other internal CGMF parameters) for uranium isotopes. Such work has been performed previously using a sensitivity analysis and Kalman filter methods.

07 ISOTOPE AND RADIATION SOURCES↗

NASA NTRS1979

Lidar temperature profiling: Performance simulations of Masons method

Several methods of using lasers to measure atmospheric temperature profiles were described. Mason's suggestion was analyzed here to assess its capabilities for various lidar configurations. Temperatures were inferred from a measure of the Boltzmann distribution of rotational states in one of the vibrational bands of O2. Differential absorption was measured using three tunable, narrowband pulsed lasers. The outputs of two were tuned to wavelengths at the centers of absorption lines at either end of a particular branch in the band. The third wave-length was in a region of no absorption; its lidar return measured only the atmospheric backscatter, and therefore allowed calculations of the absorption coefficients at the other two wavelengths as a function of altitude. From the ratio of the two line absorption coefficients plus a priori knowledge of the line parameters, the temperature-altitude profile were calculated.

Schwemmer, G. K.↗

NASA NTRS1983

The dust around the carbon star IRC +10216

Mass loss from late-type stars is important both in the evolution of these objects and for replenishment of the interstellar medium with processed material. Because the outflows are cool and dense, grains form. The present investigation is concerned with the nature of the extinction of the grains in the carbon star IRC+10216. The basic method employed involves the study of the extinction as a function of wavelength around IRC+10216. By a comparison with different models, it is then possible to infer which grain model is more likely to be correct. It is concluded that the dust around IRC+10216 is composed of relatively small grains. The grains are either amorphous carbon or graphite similar to that described by Mezger et al. (1982), but not like the graphite described by Mitchell and Robinson (1980). In particular, the grains around IRC + 10216 are relatively efficient emitters in the infrared. If this result is true of carbon stars in general, it means that the carbon grains present in the interstellar medium are much cooler than often believed.

Jura, M.↗

NASA NTRS1991

The least-squares mixing models to generate fraction images derived from remote sensing multispectral data

Constrained-least-squares and weighted-least-squares mixing models for generating fraction images derived from remote sensing multispectral data are presented. An experiment considering three components within the pixels-eucalyptus, soil (understory), and shade-was performed. The generated fraction images for shade (shade image) derived from these two methods were compared by considering the performance and computer time. The derived shade images are related to the observed variation in forest structure, i.e., the fraction of inferred shade in the pixel is related to different eucalyptus ages.

Shimabukuro, Yosio Edemir↗

NASA NTRS1991

Gravity anomalies, compensation mechanisms, and the geodynamics of western Ishtar Terra, Venus

Pioneer Venus line-of-sight orbital accelerations were utilized to calculate the geoid and vertical gravity anomalies for western Ishtar Terra on various planes of altitude z sub 0. The apparent depth of isostatic compensation at z sub 0 = 1400 km is 180 + or - 20 km based on the usual method of minimum variance in the isostatic anomaly. An attempt is made here to explain this observation, as well as the regional elevation, peripheral mountain belts, and inferred age of western Ishtar Terra, in terms of one or three broad geodynamic models.

Grimm, Robert E.↗

NASA NTRS1999

Strategies and Technologies for In Situ Mineralogical Investigations on Mars

Surface landers on Mars (Viking and Pathfinder) have not revealed satisfying answers to the mineralogy and lithology of the planet's surface. In part, this results from their prime directives: Viking focused on exobiology, Pathfinder focused on technology demonstration. The analytical instruments on board the landers made admirable attempts to extract the mineralogy and geology of Mars, as did countless modeling efforts after the missions. Here we suggest a framework for elucidating martian, or any other planetary geology, through an approach that defines (a) type of information required, (b) explorational strategy harmonious with acquisition of these data, (c) interpretation approach to the data, (d) compatible mission architecture, (e) instrumentation for interrogating rocks and soil. (a) Data required: The composition of a planet is ordered at scales ranging from molecules to minerals to rocks, and from geological units to provinces to planetary-scale systems. The largest ordering that in situ compositional instruments can attempt to interrogate is rock type "aggregate" information. This is what the geologist attempts to identify first. From this, mineralogy can be either directly seen or inferred. From mineralogy can be determined elemental abundances and perhaps the state of the compounds as being crystalline or amorphous. Knowledge of rock type and mineralogy is critical for elucidating geologic process. Mars landers acquired extremely valuable elemental data, but attempted to move from elements to aggregates, but this can only be done by making many assumptions and sometimes giant leaps of faith. Data we believe essential are elements, minerals, degree of ordering of compounds, and the aggregate or rock type that these materials compose. (b) Explorational strategy: A lander should function as a surrogate geologist. Of the total landscape, a geologist sees much, but gives detailed attention to an infinitesimally small amount of what is seen. To acquire samples worth detailed scrutiny, as many samples as possible need examining at a cursory or reconnaissance level. A representative, statistically-meaningful sample number cannot be overemphasized. This maxim still applies to geological exploration of our own planet of which we have abundant knowledge. Analysis of many samples mandates low-power consumption per sample. (c) Data interpretation: No single instrument can analyze the full spectrum of the x-axis. An instrument is optimized for detecting certain material characteristics and must therefore affix itself to some point on the x-axis. Any conclusions drawn about data to the left or right of the instrument's position on this axis must necessarily be derived by inference. Hence, it seems logical to include on a mission, instruments that are not closely spaced in their x-axis-position, and if only two analytical methods are used, as shown, they should start at opposite ends of the axis and work towards the center. As examples, we depict a high-resolution camera to evaluate rock type ("aggregate" state) and mineralogy, and an x-ray diffractometer-fluorescence spectrometer (XRD-XRF) to determine elements, minerals, and the degree of order of materials. (d) Mission architecture: No instrument or suite of instruments can be relied upon to always give truly unequivocal analyses. The suite of instruments should therefore permit conclusions of one instrument to be checked against those of another through closed analytical loops. These "loops" can be structured by a combination of orbital imagery, descent imagery, broad-band site viewing/analysis, and data that cover both x and y axes. For example, the detection of a basaltic-looking rock with a microscope should be checked against the elements detected, the appearance of the rock as a lava flow from descent imagery, and so forth. (e) Instrumentation: To satisfy the above criteria, it is necessary to: (i) See the rock or soil with high resolution + magnification, (ii) Examine many samples, (iii) Consume little power per analysis, (iv) Determine elemental species, (v) Determine mineralogy directly (not inferentially) and the degree of ordering of compounds, (vi) Start analyzing from both ends of the x-axis. Every geologist wants to see the hand sample first, and apply a hand lens to its surface. This has not been the starting point for missions to Mars. Thus, our technology satisfies all these criteria . This XRD-XRF-Optical instrument currently being developed, analyses rock or soil surfaces without the need for sample acquisition or preparation; this satisfies the power criterion, and enables many analyses. The device acquires direct mineralogy and determines elemental species. The embedded endoscopic camera satisfies the critical criterion of close inspection of samples; the fiber optic cable can also be used for IR, LTV, or laser sample analysis. Additional information is contained in the original (Figures).

Marshall, J. R.↗

NASA NTRS2000

Freja Studies of the Current-Voltage Relation in Substorm-Related Events

Field-aligned currents and electrostatic potentials play important roles in the coupling between the magnetosphere and the ionosphere. If one assumes that the ionosphere-magnetosphere potential difference is mainly due to the mirror force, one can use the single particle adiabatic kinetic theory to describe the system. From this theory, a linear relationship j(sub II) = KV between field-aligned current density j(sub II) and potential drop V along the same field line can be derived, provided that the potential drop is not too large and not too small. With rare exceptions, observational tests of this relation have mainly concentrated on quiet magnetospheric situations, with acceleration voltages V approx. less than 5 kV. Here we use observations from the Freja satellite of precipitating auroral electrons at 1.700 km altitude to study substorm related events, with acceleration voltages up to 20 keV. The observations are found to be consistent with a linear current-voltage relation even i n these conditions, although with values of the field aligned K lower than previously reported (1-5 x 10(exp 11 S/sq m). This can be explained by lower densities and higher characteristic electron energies in the magnetospheric source region of the precipitating electrons. We analyze the data by three different methods, which are all found to be in general agreement. The results are in agreement with a previous study, where the spectra of precipitating electrons --were indirectly inferred by inversion of data from the EISCAT incoherent scatter radar, thereby validating the use of radar data for studies of auroral electrons. Comparisons with previous studies are made, emphasizing the dependence of the results on the type of auroral structure and magnetospheric conditions.

Olsson, A.↗

NASA NTRS2017

Network Analysis of Rodent Transcriptomes in Spaceflight

Network analysis methods leverage prior knowledge of cellular systems and the statistical and conceptual relationships between analyte measurements to determine gene connectivity. Correlation and conditional metrics are used to infer a network topology and provide a systems-level context for cellular responses. Integration across multiple experimental conditions and omics domains can reveal the regulatory mechanisms that underlie gene expression. GeneLab has assembled rich multi-omic (transcriptomics, proteomics, epigenomics, and epitranscriptomics) datasets for multiple murine tissues from the Rodent Research 1 (RR-1) experiment. RR-1 assesses the impact of 37 days of spaceflight on gene expression across a variety of tissue types, such as adrenal glands, quadriceps, gastrocnemius, tibalius anterior, extensor digitorum longus, soleus, eye, and kidney. Network analysis is particularly useful for RR-1 -omics datasets because it reinforces subtle relationships that may be overlooked in isolated analyses and subdues confounding factors. Our objective is to use network analysis to determine potential target nodes for therapeutic intervention and identify similarities with existing disease models. Multiple network algorithms are used for a higher confidence consensus.

genomics↗

DOE OSTI2023

Count Every Trip: Finding the Uncertainty in Energy Estimates Made from Inferred Travel Modes

To properly inform transport policy and infrastructure changes, transportation related metrics need both measured values and uncertainties of those values. Travel monitoring smartphone apps can record people's travel behavior, but trip data quality is limited by sensor errors, user labeling rates and the accuracy of inference algorithms used for travel diary creation. We discuss the use of phone app recorded travel diary data to estimate energy consumption, and propose the use of propagation of variance to find error bars for such estimates. We define energy consumption for one trip as trip length times the energy intensity per distance unit of the travel mode used. We characterize trip length errors with relative error and inferred trip mode errors with confusion matrix columns. The resulting variances of each measurement are then propagated to the final calculated energy consumption. We tested our uncertainty methods on a dataset that used phone app data combined with prompted recall, consisting of 92,234 labeled trips for over 500,000 miles. Accounting for uncertainty using expected energy intensities and variance propagation gives a dataset-wide aggregate energy consumption percent error of about 9%, within one standard deviation from the truth. Future work could involve applying similar methods to other travel diary based metrics.

ADVANCED PROPULSION SYSTEMS,MATHEMATICS AND COMPUT↗

DOE OSTI2023

Count Every Trip: Finding the Uncertainty in Energy Estimates Made from Inferred Travel Modes

ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2023

Estimating Travel Energy Consumption Uncertainty Based on Inferred Travel Mode and Sensed Travel Length

To properly inform transport policy and infrastructure changes, transportation related metrics need both measured values and uncertainties of those values. Travel monitoring smartphone apps can record people's travel behavior, but trip data quality is limited by sensor errors, user labeling rates and the accuracy of inference algorithms used for travel diary creation. We discuss the use of phone app recorded travel diary data to estimate energy consumption, and propose the use of propagation of variance to find error bars for such estimates. We define energy consumption for one trip as trip length times the energy intensity per distance unit of the travel mode used. We characterize trip length errors with relative error and inferred trip mode errors with confusion matrix columns. The resulting variances of each measurement are then propagated to the final calculated energy consumption. We tested our uncertainty methods on a dataset that used phone app data combined with prompted recall, consisting of 92,234 labeled trips for over 500,000 miles. Accounting for uncertainty using expected energy intensities and variance propagation gives a dataset-wide aggregate energy consumption percent error of about 8%, within one standard deviation from the truth. Future work could involve applying similar methods to other travel diary based metrics.

ADVANCED PROPULSION SYSTEMS,ENERGY PLANNING, POLIC↗

DOE OSTI2013

In situ dating on Mars: A new approach to the K–Ar method utilizing cosmogenic argon

In this paper, cosmogenic argon isotopes are produced in feldspars via nuclear reactions between cosmic rays and Ca and K atoms within the lattice. These cosmogenic isotopes can be used as proxies for K and Ca, much like nuclear reactor-derived 39 Ar and 37 Ar are used as proxies for K and Ca, respectively, in 40 Ar/ 39 Ar geochronology. If Ca and K are uniformly distributed, then the ratio of radiogenic 40 Ar ( 40 Ar*) to cosmogenic 38 Ar or 36 Ar ( 38 Ar cos or 36 Ar cos ) is proportional to the difference between the radioisotopic and exposure ages, as well as the K/Ca ratio of the degassing phase. Thus cosmogenic, radiogenic, and trapped Ar isotopes, all of which can be measured remotely and are stable over geologic time, are sufficient to generate an isochron-like diagram from which the isotopic composition of the trapped component may be inferred. Finally, such data also provide a means to assess the extent to which the system has remained closed with respect to 40 Ar*, thereby mitigating otherwise unquantifiable uncertainties that complicate the conventional K–Ar dating method.

58 GEOSCIENCES↗