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At least 73 records · Page 4

Algorithms for Spectral Decomposition with Applications to Optical Plume Anomaly Detection

The analysis of spectral signals for features that represent physical phenomenon is ubiquitous in the science and engineering communities. There are two main approaches that can be taken to extract relevant features from these high-dimensional data streams. The first set of approaches relies on extracting features using a physics-based paradigm where the underlying physical mechanism that generates the spectra is used to infer the most important features in the data stream. We focus on a complementary methodology that uses a data-driven technique that is informed by the underlying physics but also has the ability to adapt to unmodeled system attributes and dynamics. We discuss the following four algorithms: Spectral Decomposition Algorithm (SDA), Non-Negative Matrix Factorization (NMF), Independent Component Analysis (ICA) and Principal Components Analysis (PCA) and compare their performance on a spectral emulator which we use to generate artificial data with known statistical properties. This spectral emulator mimics the real-world phenomena arising from the plume of the space shuttle main engine and can be used to validate the results that arise from various spectral decomposition algorithms and is very useful for situations where real-world systems have very low probabilities of fault or failure. Our results indicate that methods like SDA and NMF provide a straightforward way of incorporating prior physical knowledge while NMF with a tuning mechanism can give superior performance on some tests. We demonstrate these algorithms to detect potential system-health issues on data from a spectral emulator with tunable health parameters.

Srivastava, Askok N.

High-Dimensional Similarity Search with Quantum-Assisted Variational Autoencoder

Recent progress in quantum algorithms and hardware indicates the potential importance of quantum computing in the near future. However, finding suitable application areas remains an active area of research. Quantum machine learning is touted as a potential approach to demonstrate quantum advantage within both the gate-model and the adiabatic schemes. For instance, the QVAE has been proposed as a quantum enhancement to the discrete VAE. We extend on previous work and study the real-world applicability of a QVAE by presenting a proof-of-concept for similarity search in large-scale high-dimensional datasets. While exact and fast similarity search algorithms are available for low dimensional datasets, scaling to high-dimensional data is non-trivial. We show how to construct a space-efficient search index based on the latent space representation of a QVAE. Our experiments show a correlation between the Hamming distance in the embedded space and the Euclidean distance in the original space on the MODIS dataset. Further, we find real-world speedups compared to linear search and demonstrate memory-efficient scaling to half a billion data points.

Data mining, similarity search, quantum machine le

Transcriptomics-based Machine Learning Analysis Predicts Space-Exposed Murine Livers

Limited sample sizes, high data dimensionality, and sensitivity to technical and biological variability of next generation sequencing (NGS), has typically limited machine learning (ML) in space studies and further study of 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 (RNAseq) data from 6 mouse liver GeneLab datasets (GLDS) with a total of 113 spaceflight and ground-control samples to determine top features relevant to spaceflight including the effect of radiation exposure. Data was normalized within each study, then merged and scaled across all datasets. Data dimensionality was reduced using a minimum redundancy maximum relevance (MRMR) methodology. The top MRMR features were used to predict spaceflight vs. ground-control samples using a Random Forest (RF) classifier with 5-fold cross validation (CV). The ML-based gene sets were further compared against differential gene expression results from individual GLDS. CV training using the top 100 MRMR genes show averages of 86% accuracy and 0.95 AUC value on the validation set over 5 folds (Figure 1A). Baseline set analysis on differentially expressed genes (DEGs) identified using padj ≤ 0.05 show 811 or 68 DEGs overlapping between at least 2 or 3 studies, respectively (Figure 1B). Over-representation analysis showed overlapping biological processes related to fatty acid and lipid metabolism. Set analysis between the MRMR features and the DEGs showed 60 or 8 genes overlapping with at least 1 or 2 studies, respectively. MRMR feature selection and ensemble ML methods (e.g. RF) improve performance relative to a Naïve Bayes classifier when NGS data sets are analyzed. A challenge of applying ML methods across heterogeneous NGS data is accounting for signal:noise ratio. Here, signal validation across studies was shown by intersecting sets between top MRMR genes and DEGs from RNASeq analysis. Non-intersecting sets introduce opportunity to explore spaceflight relevant genes and implementing ML methods across existing NGS datasets may overcome sample size limitations. ML coupled with existing analytical methods enhances understanding of disease by revealing common underlying pathways across datasets.

Machine Learning

Transcriptomics-based Machine Learning 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% was shown 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

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

Transcriptomics-based Machine Learning 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% was shown 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

Interactive Visualization of High-Dimensional Petascale Ocean Data

We describe an application for interactive visualization of 5 petabytes of time-varying multivariate data from a high-resolution global ocean circulation model. The input data are 10311 hourly (ocean time) time steps of various 2D and 3D fields from a 22-billion point 1/48- degree “lat-lon cap” configuration of the MIT General Circulation Model (MITgcm). We map the global horizontal model domain onto our 128-screen (8x16) tiled display wall to produce a canonical tiling with approximately one MITgcm grid point per display pixel, and using this tiling we encode the entire time series for multiple native and computed scalar quantities at a collection of ocean depths. We reduce disk bandwidth requirements by converting the model’s floating point data to 16-bit fixed point values, and compressing those values with a lossless video encoder, which together allow synchronized playback at 24 time steps per second across all 128 displays. The application allows dynamic assignment of any two encoded tiles to any display, and has multiple interfaces for quickly specifying various orderly arrangements of tiles. All subsequent rendering is done on the fly, with run time control of colormaps, transfer functions, histogram equalization, and labeling. The two data streams on each screen can be rendered independently and combined in various ways, including blending, differencing, horizontal/ vertical wipes, and checkerboarding. The two data streams on any screen can optionally be displayed as a scatterplot in their joint attribute space. All scatterplots and map-view plots from the same x/y location and depth are linked so they all show the current brushable selection. Ocean scientists have used the system, and have found previously unidentified features in the data.

Interactive

Parametric Testing of Launch Vehicle FDDR Models

For the safe operation of a complex system like a (manned) launch vehicle, real-time information about the state of the system and potential faults is extremely important. The on-board FDDR (Failure Detection, Diagnostics, and Response) system is a software system to detect and identify failures, provide real-time diagnostics, and to initiate fault recovery and mitigation. The ERIS (Evaluation of Rocket Integrated Subsystems) failure simulation is a unified Matlab/Simulink model of the Ares I Launch Vehicle with modular, hierarchical subsystems and components. With this model, the nominal flight performance characteristics can be studied. Additionally, failures can be injected to see their effects on vehicle state and on vehicle behavior. A comprehensive test and analysis of such a complicated model is virtually impossible. In this paper, we will describe, how parametric testing (PT) can be used to support testing and analysis of the ERIS failure simulation. PT uses a combination of Monte Carlo techniques with n-factor combinatorial exploration to generate a small, yet comprehensive set of parameters for the test runs. For the analysis of the high-dimensional simulation data, we are using multivariate clustering to automatically find structure in this high-dimensional data space. Our tools can generate detailed HTML reports that facilitate the analysis.

Schumann, Johann

powersqueeze

powersqueeze (psqz) is a truncated power iteration library intended for high-performance computing platforms. psqz efficiently produces low-dimensional, linear measurements of graph matrix spectra by combining classical power iteration with sparse Johnson-Lindenstrauss transforms. psqz is intended to produce high-quality, fast, data-oblivious low-dimensional representations of high-dimensional sparse data such as graphs and term-document matrices. psqz is intended to replace similar workflows that depend on directly approximating a truncated eigendecomposition (e.g., the first step of spectral clustering), which is a much more expensive operation.

Priest, BenjaminW [Lawrence Livermore National Lab

Physical Interpretation of Early Battery Life Prediction Models

Early battery life prediction models are most useful for R&D if they help us understand the early changes in battery electrochemical response that correspond with long-term degradation and failure. Linear regression models such as Fused lasso and Partial Least Squares can fit coefficients directly to high-dimensional electrochemical data like capacity-voltage and ΔV–state-of-charge, i.e., Q(V) and ΔV(SOC) curves, learning coefficients that can be physically interpreted. We leverage the ISU-ILCC battery aging data set to learn high-dimensional coefficients for early battery life prediction from traditional slow-rate capacity check data, demonstrating learning on Q(V), d Q· d V −1 , and ΔV(SOC) curves. A thorough study on the dependence of coefficient values on train/test size and data preprocessing methods is made, demonstrating the reliability of high-dimensional regression approaches unless very small amounts of data are used for model training. For this data set, coefficients from Q(V) and d Q· d V −1 models highlight changes in electrode stoichiometry due to lithium loss, while ΔV(SOC) coefficients highlight changes in positive electrode diffusivity due to particle cracking as well as electrode stoichiometry shifts. By directly interpreting the coefficients of a regression model, we make physical insights into battery degradation mechanisms without requiring the assumptions of traditional battery data analysis methods.

25 ENERGY STORAGE

Streaming Compression of Scientific Data via Weak-SINDy

Here, in this paper, a streaming weak-SINDy algorithm is developed specifically for compressing streaming scientific data. The production of scientific data, either via simulation or experiments, is undergoing a stage of exponential growth, which makes data compression important and often necessary for storing and utilizing large scientific data sets. As opposed to classical “offline” compression algorithms that perform compression on a readily available data set, streaming compression algorithms compress data “online” while the data generated from simulation or experiments is still flowing through the system. This feature makes streaming compression algorithms well suited for scientific data compression, where storing the full data set offline is often infeasible. This work proposes a new streaming compression algorithm, streaming weak-SINDy, which takes advantage of the underlying data characteristics during compression. The streaming weak-SINDy algorithm constructs feature matrices and target vectors in the online stage via a streaming integration method in a memory efficient manner. The feature matrices and target vectors are then used in the offline stage to build a model through a regression process that aims to recover equations that govern the evolution of the data. For compressing high-dimensional streaming data, we adopt a streaming proper orthogonal decomposition (POD) process to reduce the data dimension and then use the streaming weak-SINDy algorithm to compress the temporal data of the POD expansion. We propose modifications to the streaming weak-SINDy algorithm to accommodate the dynamically updated POD basis. By combining the built model from the streaming weak-SINDy algorithm and a small amount of data samples, the full data flow could be reconstructed accurately at a low memory cost, as shown in the numerical tests.

97 MATHEMATICS AND COMPUTING

Wire Detection Algorithms for Navigation

In this research we addressed the problem of obstacle detection for low altitude rotorcraft flight. In particular, the problem of detecting thin wires in the presence of image clutter and noise was studied. Wires present a serious hazard to rotorcrafts. Since they are very thin, their detection early enough so that the pilot has enough time to take evasive action is difficult, as their images can be less than one or two pixels wide. Two approaches were explored for this purpose. The first approach involved a technique for sub-pixel edge detection and subsequent post processing, in order to reduce the false alarms. After reviewing the line detection literature, an algorithm for sub-pixel edge detection proposed by Steger was identified as having good potential to solve the considered task. The algorithm was tested using a set of images synthetically generated by combining real outdoor images with computer generated wire images. The performance of the algorithm was evaluated both, at the pixel and the wire levels. It was observed that the algorithm performs well, provided that the wires are not too thin (or distant) and that some post processing is performed to remove false alarms due to clutter. The second approach involved the use of an example-based learning scheme namely, Support Vector Machines. The purpose of this approach was to explore the feasibility of an example-based learning based approach for the task of detecting wires from their images. Support Vector Machines (SVMs) have emerged as a promising pattern classification tool and have been used in various applications. It was found that this approach is not suitable for very thin wires and of course, not suitable at all for sub-pixel thick wires. High dimensionality of the data as such does not present a major problem for SVMs. However it is desirable to have a large number of training examples especially for high dimensional data. The main difficulty in using SVMs (or any other example-based learning method) is the need for a very good set of positive and negative examples since the performance depends on the quality of the training set.

Kasturi, Rangachar

Implicit neural representations for experimental steering of advanced experiments

Scattering measurements using electrons, neutrons, or photons are essential for obtaining microscopic insights into materials. However, limited facility availability and high-dimensional scattering data necessitate more efficient experimental steering techniques. Here, we report a machine learning method that guides scattering data collection and facilitates real-time estimation of model parameters, given a reliable forward model to simulate experimental signals. We employ implicit neural representations as efficient surrogates that link model parameters with simulated spectroscopies. This enables a Bayesian optimal experimental design framework to estimate the probability distributions of parameters from high-dimensional scattering data. We demonstrate the proposed method using inelastic neutron scattering with simulated and real experimental data, highlighting the method’s ability to provide real-time parameter estimation with quantified uncertainties and to deliver informed experimental guidance that reduces experimental time while maximizing scientific output. This approach paves the way for accelerated discoveries in condensed matter through scattering measurements.

36 MATERIALS SCIENCE

In Situ Data Analysis Through Physics-informed Tensor Decompositions (LDRD Final Report)

We introduce a new low-dimensional model of high-dimensional numerical simulation data based on low-rank tensor decompositions. Our new model aims to minimize differences between the model data and simulation data as well as functions of the model data and functions of the simulation data. This novel approach to dimensionality reduction of simulation data provides a means of directly incorporating quantities of interests and invariants associated with conservation principles associated with the simulation data into the low-dimensional model, thus enabling more accurate analysis of the simulation without requiring access to the full set of high-dimensional data. Computational results of applying this approach to two standard low-rank tensor decompositions of data arising from simulation of combustion and plasma physics are presented.

97 MATHEMATICS AND COMPUTING

Generalization error guaranteed auto-encoder-based nonlinear model reduction for operator learning

Many physical processes in science and engineering are naturally represented by operators between infinite-dimensional function spaces. The problem of operator learning, in this context, seeks to extract these physical processes from empirical data, which is challenging due to the infinite or high dimensionality of data. An integral component in addressing this challenge is model reduction, which reduces both the data dimensionality and problem size. In this paper, we utilize low-dimensional nonlinear structures in model reduction by investigating Auto-Encoder-based Neural Network (AENet). AENet first learns the latent variables of the input data and then learns the transformation from these latent variables to corresponding output data. Our numerical experiments validate the ability of AENet to accurately learn the solution operator of nonlinear partial differential equations. Furthermore, we establish a mathematical and statistical estimation theory that analyzes the generalization error of AENet. Finally, our theoretical framework shows that the sample complexity of training AENet is intricately tied to the intrinsic dimension of the modeled process, while also demonstrating the robustness of AENet to noise.

Auto-encoder

Get Non-Real: Randomized Sketching for High-Dimensional Non-Real Valued Data (Final Report)

In our final report for DE-C0022186, we describe the work we did on this grant towards the goals we proposed. Our first goal was characterizing fundamental limits for sketching of discrete high-dimensional matrices with low-dimensional structures. Our second main goal was designing algorithms for data reconstruction from sketches. We focus on approaches that are either specifically designed for non-real-valued data (binary, finite field) or that will translate more readily to that setting.

97 MATHEMATICS AND COMPUTING

Supervised Classification Techniques for Hyperspectral Data

The recent development of more sophisticated remote sensing systems enables the measurement of radiation in many mm-e spectral intervals than previous possible. An example of this technology is the AVIRIS system, which collects image data in 220 bands. The increased dimensionality of such hyperspectral data provides a challenge to the current techniques for analyzing such data. Human experience in three dimensional space tends to mislead one's intuition of geometrical and statistical properties in high dimensional space, properties which must guide our choices in the data analysis process. In this paper high dimensional space properties are mentioned with their implication for high dimensional data analysis in order to illuminate the next steps that need to be taken for the next generation of hyperspectral data classifiers.

Jimenez, Luis O.

Score-based deterministic density sampling

We propose a deterministic sampling framework using Score-Based Transport Modeling for sampling an unnormalized target density π given only its score ∇ log π. Our method approximates the Wasserstein gradient flow on KL($f_t$∥π) by learning the time-varying score ∇ log $f_t$ on the fly using score matching. While having the same marginal distribution as Langevin dynamics, our method produces smooth deterministic trajectories, resulting in monotone noise-free convergence. We prove that our method dissipates relative entropy at the same rate as the exact gradient flow, provided sufficient training. Numerical experiments validate our theoretical findings: our method converges at the optimal rate, has smooth trajectories, and is often more sample efficient than its stochastic counterpart. Experiments on high-dimensional image data show that our method produces high-quality generations in as few as 15 steps and exhibits natural exploratory behavior. The memory and runtime scale linearly in the sample size.

97 MATHEMATICS AND COMPUTING