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At least 1,243 records · Page 69

BrazilClim : The overcoming of limitations of pre‐existing bioclimate data

Abstract Species distribution modelling has become instrumental in assessing the influence of environmental conditions on the occurrence or abundance of taxa. The set of environmental layers used for this purpose is a crucial aspect, for which different climate‐based (bioclimatic) datasets have been recently developed. These bioclimatic variables result from combinations of precipitation and temperatures surfaces. Here, we explored both the performance and possibility of improving some of the currently available bioclimatic databases, through an evaluation of the precipitation and temperatures surfaces used to generate them. For this purpose, we used a combination of statistic and graphic approaches. We focused on Brazil, not only due to its natural megadiversity, but also due to its continental size and orographic heterogeneity: an excellent ground for refining methods replicable elsewhere. We found a better match between the climatic data measured on‐field and Tropical Rainfall Measuring Mission (TRMM 3B43 v7) in the case of precipitation, and the surfaces provided by the National Oceanic and Atmospheric Administration (NOAA) in the case of temperatures, sources uncommonly used for species niche modelling. We gauge‐calibrated the best performing surfaces using machine‐learning algorithms and generated corrected surfaces that allowed us to create BrazilClim: a database of bioclimatic variables, based on improved primary surfaces, which will result in more assertive predicted distributions and more actual pictures of the species' ecological requirements for megadiverse Brazil, an approach replicable elsewhere. All primary and bioclimatic surfaces generated for this study may be freely downloaded.

Ramoni‐Perazzi, Paolo↗

Methods for Explainable Artificial Intelligence

We explored ways of quantifying information in a neural network. This can be used to determine the right size of a network or to infer the way in which a network is processing information. The first year and a half was somewhat exploratory while the last half of the project focused on approaches that seemed to show the most promise. The introduce a new way of computing explainable artificial intelligence (XAI) saliency maps that is several orders of magnitude faster than methods with similar fidelity We call it FastCAM. The method works be combining a Class Activation Map (CAM) method such as GradCAM with a forward activation map computed with a statistic we call SMOE Scale. The addition of the forward activation maps to CAM methods seems to always improve their fidelity. At the same time, computational overhead is not increased by very much. While Gradients with SmoothGrad scores better on some fidelity measures, it is overall not as good and requires more than 1500 times to compute. We demonstrate two completed applications of FastCAM on tasks outside of the LDRD at LLNL. The source code for FastCAM is currently being implanted into Captum, the official XAI toolkit for the popular deep learning toolkit PyTorch. The LDRD currently has 13 publications released to the public. 10 of them are journal length.

97 MATHEMATICS AND COMPUTING↗

Development of Computer Models for the Assessment of Foreign Body Impact Events on Composite Structures

The objective of this project was to model the 5-3/4 inch pressure vessels used on the NASA RTOP program in an attempt to learn more about how impact damage forms and what are the residual effects of the resulting damage. A global-local finite element model was developed for the bottle and the states of stress in the bottles were determined down to the constituent level. The experimental data that was generated on the NASA RTOP program was not in a form that enabled the model developed under this grant to be correlated with the experimental data. As a result of this exercise it is recommended that an experimental program be designed using statistical design of experiment techniques to generate data that can be used to isolate the phenomenon that control the formation of impact damage. This data should include residual property determinations so that models for post impact structural integrity can be developed. It is also recommended that the global-local methodology be integrated directly into the finite element code. This will require considerable code development.

Bucinell, Ronald B.↗

Comparison of Multivariate Time Series Prediction Techniques for Emulating Noah-LSM Soil Moisture Outputs

Land surface models are crucial tools for many earth science applications including numerical weather prediction, water resource and crop monitoring, and climatological analysis. Given a set of atmospheric forcings, seasonal data, and static parameters, models like Noah-LSM solve for land surface quantities including skin temperature, sensible heat flux, and soil moisture. While these calculations are theoretically robust, they are often computationally expensive. Since artificial neural networks (ANNs) are universal function approximators, they can learn to emulate the output of a deterministic numerical model given a time series of input forcings, with the learned ANN having substantially shorter execution time. The ANN could efficiently parameterize other models, generate ensembles, and provide first-guess inputs for retrievals. As such, with the goal of developing a model that efficiently mimics the output of Noah-LSM given NLDAS2 forcings on a region covering much of the central US, we examine and compare several neural network architectures for the multi-horizon multivariate time series forecasting problem. Recent literature includes a diverse set of approaches including autoregressive architectures like LSTM and GRU, parametric and non-parametric statistical predictors (ForecastNet and MQRNN), self-attention (LSTM-attention-LSTM), and temporal convovlution (DeepTCN). We implement several of these models for the Noah-LSM prediction task, highlighting the features and challenges for each and providing practical insight on the training process.

Mitchell Dodson↗

Formation and retrieval of cell assemblies in a biologically realistic spiking neural network model of area CA3 in the mouse hippocampus

The hippocampal formation is critical for episodic memory, with area Cornu Ammonis 3 (CA3) a necessary substrate for auto-associative pattern completion. Recent theoretical and experimental evidence suggests that the formation and retrieval of cell assemblies enable these functions. Yet, how cell assemblies are formed and retrieved in a full-scale spiking neural network (SNN) of CA3 that incorporates the observed diversity of neurons and connections within this circuit is not well understood. Here, we demonstrate that a data-driven SNN model quantitatively reflecting the neuron type-specific population sizes, intrinsic electrophysiology, connectivity statistics, synaptic signaling, and long-term plasticity of the mouse CA3 is capable of robust auto-association and pattern completion via cell assemblies. Our results show that a broad range of assembly sizes could successfully and systematically retrieve patterns from heavily incomplete or corrupted cues after a limited number of presentations. Furthermore, performance was robust with respect to partial overlap of assemblies through shared cells, substantially enhancing memory capacity. These novel findings provide computational evidence that the specific biological properties of the CA3 circuit produce an effective neural substrate for associative learning in the mammalian brain.

hetero-association↗

Efficient Trainability of Linear Optical Modules in Quantum Optical Neural Networks

The existence of “barren plateau landscapes” for generic discrete-variable quantum neural networks, which obstructs efficient gradient-based optimization of cost functions defined by global measurements, would be surprising in the case of generic linear optical modules in quantum optical neural networks due to the tunability of the intensity of continuous variable states and the relevant unitary group having exponentially smaller dimension. We demonstrate that coherent light in m modes can be generically compiled efficiently if the total intensity scales sublinearly with m, and extend this result to cost functions based on homodyne, heterodyne, or photon detection measurement statistics, and to noisy cost functions in the presence of attenuation. Here, we further demonstrate efficient trainability of m mode linear optical quantum circuits for variational mean field energy estimation of positive quadratic Hamiltonians for input states that do not have energy exponentially vanishing with m.

47 OTHER INSTRUMENTATION↗

Calibration of energy density functionals with deformed nuclei

Nuclear density functional theory is the prevalent theoretical framework for accurately describing nuclear properties at the scale of the entire chart of nuclides. Given an energy functional and a many-body scheme (e.g., single- or multireference level), the predictive power of the theory depends strongly on how the parameters of the energy functionals have been calibrated with experimental data. Expanded algorithms and computing power have enabled recent optimization protocols to include data in deformed nuclei in order to optimize the coupling constants of the energy functional. The primary motivation of this work is to test the robustness of such protocols with respect to some of the technical and numerical details of the underlying calculations, especially when the calibration explores a large parameter space. To this end, we quantify the effect of these uncertainties on both the optimization and statistical emulation of composite objective functions. We also emphasize that Bayesian calibration can provide better estimates of the theoretical errors used to define objective functions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Identifying Hydrometeorological Factors Influencing Reservoir Releases Using Machine Learning Methods

Simulation of reservoir releases plays a critical role in social-economic functioning and our nation's security. How-ever, it is challenging to predict the reservoir release accurately because of many influential factors from natural environments and engineering controls such as the reservoir inflow and storage. Moreover, climate change and hydrological intensification causing the extreme precipitation and temperature make the accurate prediction of reservoir releases even more challenging. Machine learning (ML) methods have shown some successful applications in simulating reservoir releases. However, previous studies mainly used inflow and storage data as inputs and only considered their short-term influences (e.g, previous one or two days). In this work, we use long short-term memory (LSTM) networks for reservoir release prediction based on four input variables including inflow, storage, precipitation, and temperature and consider their long-term influences. We apply the LSTM model to 30 reservoirs in Upper Colorado River Basin, United States. We analyze the prediction performance using six statistical metrics. More importantly, we investigate the influence of the input hydrometeorological factors, as well as their temporal effects on reservoir release decisions. Results indicate that inflow and storage are the most influential factors but the inclusion of precipitation and temperature can further improve the prediction of release especially in low flows. Additionally, the inflow and storage have a relatively long-term effect on the release. These findings can help optimize the water resources management in the reservoirs.

Fan, Ming↗

Integrating Survival Analysis with Bayesian Statistics to Forecast the Remaining Useful Life of a Centrifugal Pump Conditional to Multiple Fault Types

To improve the viability of nuclear power plants, there is a need to reduce their operational costs. Operational costs account for a significant portion of a plant’s yearly budget, due to their scheduled-based maintenance approach. In order to reduce these costs, proactive methods are required that estimate and forecast the state of a machine in real time to optimize maintenance schedules. In this research, we use Bayesian networks to develop a framework that can forecast the remaining useful life of a centrifugal pump. To do so, we integrate survival analysis with Bayesian statistics to forecast the health of the pump conditional to its current state. We complete our research by successfully using the Bayesian network on a case study. This solution provides an informed probabilistic viewpoint of the pumping system for the purpose of predictive maintenance.

42 ENGINEERING↗

Structure of merger remnants. 4: Isophotal shapes

This paper examines the shapes of isophotes of galaxy merger remnants. More specifically, we perform a series of numerical experiments to study galaxy mergers. The simulations explore a variety of encounter geometries, types of progenitor galaxies, and particle numbers. We 'observe' each of the remnants from 64 viewpoints to estimate how the isophotal shapes vary with the orientation of the remnant. Also, by comparing the results from the various simulations, we learn how encounter geometry and the structure of the progenitors can affect the shape of the remnants. The encounter geometry, the structure of the progenitors, and the orientation of the remnant play deciding roles in the shape of the 'observed' isophotes, so much so that these simulated merger remnants have both 'boxy' and 'disky' isophotes and ellipticities ranging from E0 to E7. Thus, the shapes seen in our merger simulation remnants span a similar range to observed isophotal shapes of real galaxies. Furthermore, to estimate the errors in this analysis, we introduce the statistical bootstrap. Bootstrapping is used rather widely in observational astronomy when dealing with small samples; however, its use is practically unheard of for tackling theoretical problems. We believe that bootstrapping can be extremely useful for dealing with the small samples found in numerical simulations; therefore, we present the rudiments and basis of the technique with emphasis on its use in N-body calculations. Also, by comparing the errors for the smaller simulations with those of the larger ones, we speculate on the number of particles required to accurately explore isophotal shapes in simulations.

Heyl, Jeremy S.↗

Mineralogy of the Solar System

The coming decade will witnesses the first sample return missions from solar system bodies in 30 years. These samples will all be very small, some missions return only a few milligrams of total mass. Fortunately, the capability of modem methods to characterize ultra-small samples is well established from analysis of interplanetary dust particles (IDPs), interstellar grains recovered from meteorites, and other materials requiring ultra-sensitive analytical capabilities. Powerful analytical techniques are available that require, under favorable circumstances, single particles of only a few nanograms for entire suites of fairly comprehensive characterizations. A returned sample of greater than 1,000 particles with total mass of just one microgram permits comprehensive quantitative geochemical measurements that are impractical to can-y out in situ by flight instruments. With the Galileo flybys of Gaspra and Ida, it is now recognized that even very small airless bodies have indeed developed a particulate regolith. Acquiring a sample of the bulk regolith, a simple sampling strategy, provides two critical pieces of information about the body. Regolith samples are excellent bulk samples since they normally contain all the key components of the local environment, albeit in particulate form. Furthermore, since this fine fraction dominates remote measurements, regolith samples also provide information about surface alteration processes and are a key link to remote sensing of other bodies. Studies indicate that a statistically significant number of nanogram-sized particles should be able to characterize the regolith of a primitive asteroid, although the presence of larger components within even primitive meteorites (e.g.. Murchison), e.g. chondrules, CAI, large crystal fragments, etc., points out the limitations of using data obtained from nanogram-sized samples to characterize entire primitive asteroids. However, most important asteroidal geological processes have left their mark on the matrix, since this is the finest-grained portion and therefore most sensitive to chemical and physical changes. Thus, the following information can be learned from this fine grain size fraction alone: (1) mineral paragenesis; (2) regolith processes, (3) bulk composition; (4) conditions of thermal and aqueous alteration (if any); (5) relationships to planets, comets, meteorites (via isotopic analyses, including oxygen; (6) abundance of water and hydrated material; (7) abundance of organics; (8) history of volatile mobility, (9) presence and origin of presolar and/or interstellar material.

Zolensky, Michael E.↗

Data Summarization and Inference at Scale

This is the final report for the DOE ASCR grant SC-0022260, Data Summarization and Inference at Scale, PI: Alex Pothen, Purdue University. The goal of the project was to solve data-intensive and compute-intensive problems in the physical sciences, engineering, information science, data science, etc. by designing and implementing new algorithms that could work with a subset of the data. The four subgoals were: (a) The solution of problems where the data is too large to be stored in the memory of a computer. In this streaming model of computation, the data arrives as a stream of elements to the computer, each element is processed as it arrives, and a decision is made to discard the data or to store it; only a small subset of the data proportional to the size of the output solution is stored, and when all the data has been streamed, a solution to the problem is computed from the stored subset. (b) The use of machine learning methods to compute solutions to data-intensive problems. The use of GPUs is critical to obtain high performance on machine learning tasks, but their memory sizes are smaller relative to that of CPUs. For large-scale problems, the data is sampled many times, and small samples are used with repetition, for robustness, to compute solutions to inference tasks. This sampling reduces the memory required to solve the problem, but attention is needed to avoid slow convergence to the solutions, and reduced accuracy of inference. We propose submodular optimization, Large Language Models, and physics-informed neural networks to enable GPU computations here. (c) Modeling and visualization of high-dimensional data using interpretable features. Clinical proteomic data sets from immunology for the detection of cancer and other diseases are temporal and high-dimensional, and algorithms for visualizing these data sets using clinically interpretable features are lacking. We propose methods that compute distances based on the optimal transportation problem and graph edit distances to address this problem. We also propose the use of optimal transport-based distances, spatial statistics, and network structure to classify image data sets, We apply these algorithms to electron micrographs of the peripheral nervous system in the digestive tract. (d) The design of data-intensive algorithms on emerging architectures, specifically, noisy, intermediate-scale quantum (NISQ) devices. Quantum computers offer the possibility of exploring large solution spaces due to the principle of superposition, but current quantum computers are limited by few qubits, short coherence times due to noise, poor interconections among the qubits, etc. We propose the use of the divide and conquer paradigm to solve large-scale problems, wherein collections of small subproblems are solved on the quantum devices, and the solutions to the subproblems are integrated into a solution for the original problem on a classical computer.

97 MATHEMATICS AND COMPUTING↗

A Hybrid Deep Learning Approach to Cosmological Constraints from Galaxy Redshift Surveys

We present a deep machine learning (ML)–based technique for accurately determining σ g and Ω m from mock 3D galaxy surveys. The mock surveys are built from the AbacusCosmos suite of N -body simulations, which comprises 40 cosmological volume simulations spanning a range of cosmological parameter values, and we account for uncertainties in galaxy formation scenarios through the use of generalized halo occupation distributions (HODs). We explore a trio of ML models: a 3D convolutional neural network (CNN), a power spectrum–based fully connected network, and a hybrid approach that merges the two to combine physically motivated summary statistics with flexible CNNs. We describe best practices for training a deep model on a suite of matched-phase simulations, and we test our model on a completely independent sample that uses previously unseen initial conditions, cosmological parameters, and HOD parameters. Despite the fact that the mock observations are quite small (~0.07 h -3 Gpc 3 ) and the training data span a large parameter space (six cosmological and six HOD parameters), the CNN and hybrid CNN can constrain estimates of σ g and Ω m to ~3% and ~4%, respectively.

79 ASTRONOMY AND ASTROPHYSICS↗

ForSE: A GAN-based Algorithm for Extending CMB Foreground Models to Subdegree Angular Scales

We present ForSE (Foreground Scale Extender), a novel Python package that aims to overcome the current limitations in the simulation of diffuse Galactic radiation, in the context of cosmic microwave background (CMB) experiments. ForSE exploits the ability of generative adversarial neural networks (GANs) to learn and reproduce complex features present in a set of images, with the goal of simulating realistic and non-Gaussian foreground radiation at subdegree angular scales. This is of great importance in order to estimate the foreground contamination to lensing reconstruction, delensing, and primordial B-modes for future CMB experiments. We applied this algorithm to Galactic thermal dust emission in both total intensity and polarization. Our results show how ForSE is able to generate small-scale features (at 12') having as input the large-scale ones (80'). The injected structures have statistical properties, evaluated by means of the Minkowski functionals, in good agreement with those of the real sky and which show the correct amplitude scaling as a function of the angular dimension. Furthermore, the obtained thermal dust Stokes Q and U full-sky maps as well as the ForSE package are publicly available for download.

79 ASTRONOMY AND ASTROPHYSICS↗

A Prognostic Launch Vehicle Probability of Failure Assessment Methodology for Conceptual Systems Predicated on Human Causal Factors

Lessons learned from past failures of launch vehicle developments and operations were used to create a new method to predict the probability of failure of conceptual systems. Existing methods such as Probabilistic Risk Assessments and Human Risk Assessments were considered but found to be too cumbersome for this type of system-wide application for yet-to-be-flown vehicles. The basis for this methodology were historic databases of past failures, where it was determined that various faulty human-interactions were the predominant root causes of failure rather than deficient component reliabilities evaluated through statistical analysis. This methodology contains an expert scoring part which can be used in either a qualitative or a quantitative mode. The method produces two products: a numerical score of the probability of failure and guidance to program management on critical areas in need of increased focus to improve the probability of success. In order to evaluate the effectiveness of this new method, data from a concluded vehicle program (USAF's Titan IV with the Centaur G-Prime upper stage) was used as a test case. The theoretical vs. actual probability of failure was found to be 4.46% vs. 6.67% respectively. Recommendations are made for future applications of this method to ongoing launch vehicle development programs.

Launch Vehicle↗

Prognostic Launch Vehicle Probability of Failure Assessment Methodology for Conceptual Systems Predicated on Human Causal Factors

Lessons learned from past failures of launch vehicle developments and operations were used to create a new method to predict the probability of failure of conceptual systems. Existing methods such as Probabilistic Risk Assessments and Human Risk Assessments were considered but found to be too cumbersome for this type of system-wide application for yet-to-be-flown vehicles. The basis for this methodology were historic databases of past failures, where it was determined that various faulty human-interactions were the predominant root causes of failure rather than deficient component reliabilities evaluated through statistical analysis. This methodology contains an expert scoring part which can be used in either a qualitative or a quantitative mode. The method produces two products: a numerical score of the probability of failure or guidance to program management on critical areas in need of increased focus to improve the probability of success. In order to evaluate the effectiveness of this new method, data from a concluded vehicle program (USAF's Titan IV with the Centaur G-Prime upper stage) was used as a test case. Although the theoretical vs. actual probability of failure was found to be in reasonable agreement (4.46% vs. 6.67% respectively) the underlying sub-root cause scoring had significant disparities attributable to significant organizational changes and acquisitions. Recommendations are made for future applications of this method to ongoing launch vehicle development programs.

Craig H Williams↗

DefectTrack: a deep learning-based multi-object tracking algorithm for quantitative defect analysis of in-situ TEM videos in real-time

Abstract In-situ irradiation transmission electron microscopy (TEM) offers unique insights into the millisecond-timescale post-cascade process, such as the lifetime and thermal stability of defect clusters, vital to the mechanistic understanding of irradiation damage in nuclear materials. Converting in-situ irradiation TEM video data into meaningful information on defect cluster dynamic properties (e.g., lifetime) has become the major technical bottleneck. Here, we present a solution called the DefectTrack , the first dedicated deep learning-based one-shot multi-object tracking (MOT) model capable of tracking cascade-induced defect clusters in in-situ TEM videos in real-time. DefectTrack has achieved a Multi-Object Tracking Accuracy (MOTA) of 66.43% and a Mostly Tracked (MT) of 67.81% on the test set, which are comparable to state-of-the-art MOT algorithms. We discuss the MOT framework, model selection, training, and evaluation strategies for in-situ TEM applications. Further, we compare the DefectTrack with four human experts in quantifying defect cluster lifetime distributions using statistical tests and discuss the relationship between the material science domain metrics and MOT metrics. Our statistical evaluations on the defect lifetime distribution suggest that the DefectTrack outperforms human experts in accuracy and speed.

42 ENGINEERING↗

Transcriptomics-based Machine Learning (ML) Analysis Predicts Space-Exposed Murine Livers

Limited sample sizes, high data dimensionality, and sensitivity to technical and biological variability of next generation sequencing (NGS), typically limits machine learning (ML) approaches in spaceflight studies that include radiation effects. However, pooling smaller studies while addressing intra- and inter-study variabilities allows for ML predictive modeling. Here, integration methods were applied to whole transcriptome shotgun sequencing (RNA-seq) data from six mouse liver GeneLab datasets (GLDS) (n ranging from 6 to 39 samples) from with a total of 81 spaceflight and ground-control samples to determine top features (i.e. genes) relevant to spaceflight including the effect of radiation exposure. RNASeq counts were normalized for each study, then merged and scaled across all datasets. Data dimensionality was reduced using a minimum redundancy maximum relevance (MRMR) methodology. Redundancy and relevance were computed using the Pearson correlation and F-statistic, respectively. The top 100 MRMR features were used to predict spaceflight vs. ground-control samples using Random Forest (RF), Support Vector Machine (SVM), and Linear Discriminant Analysis (LDA) classifiers with 5-fold cross validation (CV). Principal component analysis (PCA) on the complete feature set versus the MRMR features shows separation between spaceflight samples and ground controls (Figure 1A). The ML-based gene sets were compared against differential gene expression results obtained with DESeq2 from individual GLDS. Using all features or randomly sampled subsets at matching set sizes with MRMR, a maximum classifier accuracy of 69% on the test set over 5 folds. For all classifiers, CV training using at least the top 30 MRMR genes show minimum 89% accuracy and 0.95 AUC value on the test set over 5 folds (Figure 1B). Baseline set analysis on differentially expressed genes (DEGs) identified using padj ≤ 0.05 show 295 DEGs that overlap at least two studies and 13 DEGs that overlap three studies (Figure 1C). Set analysis between the top 100 MRMR features and the DEGs showed 47 genes that overlap at least one study and 24 genes that overlap two studies. Over-representation analysis showed overlapping biological processes related to fatty acid and lipid metabolism which may indicate these processes in the response to spaceflight stressors. MRMR feature selection for the selected ML methods improve performance relative to a classifier built on all features or randomly sampled subsets. Permutation feature importance within the decorrelated MRMR features showed concordance in feature ranking between ML methods. A challenge of applying ML methods across heterogeneous NGS data is accounting for signal:noise. Here, signal validation across studies was shown by intersecting sets between top MRMR genes and DEGs from DESeq2 analysis. Non-intersecting sets introduce opportunity to explore genes relevant to differentiating space flight exposed groups and implementing ML methods across existing NGS datasets may overcome sample size limitations.

Machine Learning↗