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At least 523 records · Page 29

Analyzing machine learning models to accelerate generation of fundamental materials insights

Abstract Machine learning for materials science envisions the acceleration of basic science research through automated identification of key data relationships to augment human interpretation and gain scientific understanding. A primary role of scientists is extraction of fundamental knowledge from data, and we demonstrate that this extraction can be accelerated using neural networks via analysis of the trained data model itself rather than its application as a prediction tool. Convolutional neural networks excel at modeling complex data relationships in multi-dimensional parameter spaces, such as that mapped by a combinatorial materials science experiment. Measuring a performance metric in a given materials space provides direct information about (locally) optimal materials but not the underlying materials science that gives rise to the variation in performance. By building a model that predicts performance (in this case photoelectrochemical power generation of a solar fuels photoanode) from materials parameters (in this case composition and Raman signal), subsequent analysis of gradients in the trained model reveals key data relationships that are not readily identified by human inspection or traditional statistical analyses. Human interpretation of these key relationships produces the desired fundamental understanding, demonstrating a framework in which machine learning accelerates data interpretation by leveraging the expertize of the human scientist. We also demonstrate the use of neural network gradient analysis to automate prediction of the directions in parameter space, such as the addition of specific alloying elements, that may increase performance by moving beyond the confines of existing data.

36 MATERIALS SCIENCE↗

Using machine learning techniques to automate sky survey catalog generation

We describe the application of machine classification techniques to the development of an automated tool for the reduction of a large scientific data set. The 2nd Palomar Observatory Sky Survey provides comprehensive photographic coverage of the northern celestial hemisphere. The photographic plates are being digitized into images containing on the order of 10(exp 7) galaxies and 10(exp 8) stars. Since the size of this data set precludes manual analysis and classification of objects, our approach is to develop a software system which integrates independently developed techniques for image processing and data classification. Image processing routines are applied to identify and measure features of sky objects. Selected features are used to determine the classification of each object. GID3* and O-BTree, two inductive learning techniques, are used to automatically learn classification decision trees from examples. We describe the techniques used, the details of our specific application, and the initial encouraging results which indicate that our approach is well-suited to the problem. The benefits of the approach are increased data reduction throughput, consistency of classification, and the automated derivation of classification rules that will form an objective, examinable basis for classifying sky objects. Furthermore, astronomers will be freed from the tedium of an intensely visual task to pursue more challenging analysis and interpretation problems given automatically cataloged data.

Fayyad, Usama M.↗

ScienceSearch: Enabling Search through Automatic Metadata Generation

© 2018 IEEE. Scientific facilities are increasingly generating and handling large amounts of data from experiments and simulations. Next-generation scientific discoveries rely on insights derived from data, especially across domain boundaries. Search capabilities are critical to enable scientists to discover datasets of interest. However, scientific datasets often lack the signals or metadata required for effective searches. Thus, we need formalized methods and systems to automatically annotate scientific datasets from the data and its surrounding context. Additionally, a search infrastructure needs to account for the scale and rate of application data volumes. In this paper, we present ScienceSearch, a system infrastructure that uses machine learning techniques to capture and learn the knowledge, context, and surrounding artifacts from data to generate metadata and enable search. Our current implementation is focused on a dataset from the National Center for Electron Microscopy (NCEM), an electron microscopy facility at Lawrence Berkeley National Laboratory sponsored by the Department of Energy which supports hundreds of users and stores millions of micrographs. In this paper, we describe a) our search infrastructure and model, b) methods for generating metadata using machine learning techniques, and c) optimizations to improve search latency, and deployment on an HPC system. We demonstrate that ScienceSearch is capable of producing valid metadata for NCEM's dataset and providing low-latency good quality search results over a scientific dataset.

Rodrigo, Gonzalo P.↗

Electric Field’s Dueling Effects through Dehydration and Ion Separation in Driving NaCl Nucleation at Charged Nanoconfined Interfaces

Investigating nucleation in charged nanoconfined environments under electric fields is crucial for many scientific and engineering applications. Here we study the nucleation of NaCl from aqueous solution near charged surfaces using machine-learning-augmented enhanced sampling molecular dynamics simulations. Our simulations successfully drive phase transitions between the liquid and solid phases of NaCl. The solid phase is stabilized under electric fields, particularly at an intermediate surface charge density. We examine which physical characteristics drive the nucleation of NaCl from aqueous solutions and find that the removal of solvent water from Cl– at the solid precursor surface plays a more critical role than the accumulation of ions. Our simulations reveal the competing effects of electric fields on nucleation processes: they facilitate the removal of water, promoting nucleation, but also promote the separation of ion pairs, thereby hindering nucleation. Here, this work provides a framework for studying nucleation processes in nanoconfined environments under electric fields and provides physical insights for the design of electrochemistry materials.

Electric fields↗

Identifying Outliers in AI-based Image Compression

Image compression using artificial intelligence (AI) is becoming increasingly prevalent across various fields, including scientific research. Scientific instruments can generate hundreds of images per second, and effectively compressing these images with high compression ratios is crucial for facilitating scientific discoveries. However, automatically detecting outlier cases, where compression may not have succeeded or where interesting scientific phenomena are present, poses a significant challenge. To address this, we have developed a methodology based on unsupervised machine learning techniques for detecting outlier compressed images. This methodology utilizes metrics such as peak signal-to-noise ratio (PSNR), structural similarity index measure (SSIM), structural texture similarity index measure (STSIM), and deep image and structural texture similarity index (DISTS). We have evaluated our methodology on several unlabeled datasets, including microscopy and x-ray images, and have successfully identified multiple outlier images using our proposed approach. Furthermore, our approach has enabled us to identify image semantics that are valuable for post-experiment analysis by scientists.

Data Analysis↗

Educational and Scientific Applications of Climate Model Diagnostic Analyzer

Climate Model Diagnostic Analyzer (CMDA) is a web-based information system designed for the climate modeling and model analysis community to analyze climate data from models and observations. CMDA provides tools to diagnostically analyze climate data for model validation and improvement, and to systematically manage analysis provenance for sharing results with other investigators. CMDA utilizes cloud computing resources, multi-threading computing, machine-learning algorithms, web service technologies, and provenance-supporting technologies to address technical challenges that the Earth science modeling and model analysis community faces in evaluating and diagnosing climate models. As CMDA technology and infrastructure have matured, we have developed the educational and scientific applications of CMDA. Educationally, CMDA supported the summer school of the JPL Center for Climate Sciences in 2014, 2015, and 2016. In the summer school, the students work on group research projects where CMDA provide datasets, analysis tools, and provenance support utility tools. Each student is assigned to a virtual machine with CMDA installed in Amazon Web Services. Scientifically, we have developed several science use cases of CMDA covering various topics, datasets, and analysis types. Each of the science use cases is described in terms of a scientific goal, datasets used, the analysis tools used, scientific results discovered, an analysis result such as output plots and data files, and a link to the corresponding analysis service call with all the input arguments filled.

Bao, Qihao↗

Multivariate statistical analysis software technologies for astrophysical research involving large data bases

We developed a package to process and analyze the data from the digital version of the Second Palomar Sky Survey. This system, called SKICAT, incorporates the latest in machine learning and expert systems software technology, in order to classify the detected objects objectively and uniformly, and facilitate handling of the enormous data sets from digital sky surveys and other sources. The system provides a powerful, integrated environment for the manipulation and scientific investigation of catalogs from virtually any source. It serves three principal functions: image catalog construction, catalog management, and catalog analysis. Through use of the GID3* Decision Tree artificial induction software, SKICAT automates the process of classifying objects within CCD and digitized plate images. To exploit these catalogs, the system also provides tools to merge them into a large, complete database which may be easily queried and modified when new data or better methods of calibrating or classifying become available. The most innovative feature of SKICAT is the facility it provides to experiment with and apply the latest in machine learning technology to the tasks of catalog construction and analysis. SKICAT provides a unique environment for implementing these tools for any number of future scientific purposes. Initial scientific verification and performance tests have been made using galaxy counts and measurements of galaxy clustering from small subsets of the survey data, and a search for very high redshift quasars. All of the tests were successful, and produced new and interesting scientific results. Attachments to this report give detailed accounts of the technical aspects for multivariate statistical analysis of small and moderate-size data sets, called STATPROG. The package was tested extensively on a number of real scientific applications, and has produced real, published results.

Djorgovski, S. George↗

Multivariate Statistical Analysis Software Technologies for Astrophysical Research Involving Large Data Bases

We developed a package to process and analyze the data from the digital version of the Second Palomar Sky Survey. This system, called SKICAT, incorporates the latest in machine learning and expert systems software technology, in order to classify the detected objects objectively and uniformly, and facilitate handling of the enormous data sets from digital sky surveys and other sources. The system provides a powerful, integrated environment for the manipulation and scientific investigation of catalogs from virtually any source. It serves three principal functions: image catalog construction, catalog management, and catalog analysis. Through use of the GID3* Decision Tree artificial induction software, SKICAT automates the process of classifying objects within CCD and digitized plate images. To exploit these catalogs, the system also provides tools to merge them into a large, complex database which may be easily queried and modified when new data or better methods of calibrating or classifying become available. The most innovative feature of SKICAT is the facility it provides to experiment with and apply the latest in machine learning technology to the tasks of catalog construction and analysis. SKICAT provides a unique environment for implementing these tools for any number of future scientific purposes. Initial scientific verification and performance tests have been made using galaxy counts and measurements of galaxy clustering from small subsets of the survey data, and a search for very high redshift quasars. All of the tests were successful and produced new and interesting scientific results. Attachments to this report give detailed accounts of the technical aspects of the SKICAT system, and of some of the scientific results achieved to date. We also developed a user-friendly package for multivariate statistical analysis of small and moderate-size data sets, called STATPROG. The package was tested extensively on a number of real scientific applications and has produced real, published results.

Djorgovski, S. G.↗

Applications and Techniques for Fast Machine Learning in Science

In this community review report, we discuss applications and techniques for fast machine learning (ML) in science—the concept of integrating powerful ML methods into the real-time experimental data processing loop to accelerate scientific discovery. The material for the report builds on two workshops held by the Fast ML for Science community and covers three main areas: applications for fast ML across a number of scientific domains; techniques for training and implementing performant and resource-efficient ML algorithms; and computing architectures, platforms, and technologies for deploying these algorithms. We also present overlapping challenges across the multiple scientific domains where common solutions can be found. This community report is intended to give plenty of examples and inspiration for scientific discovery through integrated and accelerated ML solutions. This is followed by a high-level overview and organization of technical advances, including an abundance of pointers to source material, which can enable these breakthroughs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Advanced Method Optimization for Sampling and Analysis Instrumentation

This work presents a generalized approach for analytical method optimization that branches the gap between techniques historically employed and accurate modern optimization techniques suitable for various applications. The novelty of the described strategy is the utilization of multivariate, multiobjective optimization with Karush-Kuhn-Tucker conditions to bound the optimization space to solutions within the physical limitations of instrumentation. Briefly, the basic steps outlined in this paper are to (1) determine the objective(s) that should be maximized or minimized based on the goals of the analytical application, (2) conduct a screening experiment, (3) perform ANOVA to determine the parameters which have a statistically significant effect on the objective, (4) conduct an experiment (e.g., Box-Behnken design) to collect data for fitting the objective equation, and (5) determine the physical constraints of the parameters and solve the Lagrangian to determine the optimal method parameters. A broad approach to optimization target selection allows for robust method tuning to develop improved data sets amenable for chemometrics and machine learning algorithm development. Gas chromatography-mass spectrometry was selected as a use case due to its broad use across scientific fields and time-consuming method development involving numerous parameters. In conclusion, this strategy can reduce the cost of research, improve data quality, and enable the rapid development of new analytical technique.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

IRNet: A General Purpose Deep Risidual Regression Framework for Materials Discovery

Materials discovery is crucial for making scientific advances in many domains. Collections of data from experiments and first-principle computations have spurred interest in applying machine learning methods to create predictive models capable of mapping from composition and crystal structures to materials properties. Generally, these are regression problems with the input being a 1D vector composed of numerical attributes representing the material composition and/or crystal structure. While neural networks consisting of fully connected layers have been applied to such problems, their performance often suffers from the vanishing gradient problem when network depth is increased. Hence, predictive modeling for such tasks has been mainly limited to traditional machine learning techniques such as Random Forest. In this paper, we study and propose design principles for building deep regression networks composed of fully connected layers with numerical vectors as input. We introduce a novel deep regression network with individual residual learning, IRNet, that places shortcut connections after each layer so that each layer learns the residual mapping between its output and input. We use the problem of learning properties of inorganic materials from numerical attributes derived from material composition and/or crystal structure to compare IRNet’s performance against that of other machine learning techniques. Using multiple datasets from the Open Quantum Materials Database (OQMD) and Materials Project for training and evaluation, we show that IRNet provides significantly better prediction performance than the state-of-the-art machine learning approaches currently used by domain scientists. We also show that IRNet’s use of individual residual learning leads to better convergence during the training phase than when shortcut connections are between multi-layer stacks while maintaining the same number of parameters.

deep learning↗

Towards reverse mode automatic differentiation of Kokkos-based codes

Derivative computation is a key component of optimization, sensitivity analysis, uncertainty quantification, and the solving of nonlinear problems. Automatic differentiation (AD) is a powerful technique for evaluating such derivatives, and in recent years, has been integrated into programming environments such as Jax, PyTorch, and TensorFlow to support derivative computations needed for training of machine learning models, facilitating wide-spread use of these technologies. The C++ language has become the de facto standard for scientific computing due to numerous factors, yet language complexity has made the wide-spread adoption of AD technologies for C++ difficult, hampering the incorporation of powerful differentiable programming approaches into C++ scientific simulations. This is exacerbated by the increasing emergence of architectures, such as GPUs, with limited memory capabilities and requiring massive thread-level concurrency. C++ AD tools must effectively use these environments to bring novel scientific simulations to next-generation DOE experimental and observational facilities. In this project, we investigated source transformation-based automatic differentiation using LLVM compiler infrastructure to automatically generate portable and efficient gradient computations of Kokkos-based code. We have demonstrated that our proposed strategy is feasible by investigating the usage of a prototype LLVM-based source transformation tool to generate gradients of simple functions made of sequences of simple Kokkos parallel regions. Speedups of up to 500x compared to Sacado were observed on NVIDIA V100 GPU.

97 MATHEMATICS AND COMPUTING↗

Scientific Discovery with Physics-Informed System Identification (Abbreviated Report)

My fellowship research focused on making physics-based simulations faster and more useful through machine learning. Many problems in science and engineering are governed by partial differential equations, but high-fidelity simulations are often too expensive to run repeatedly. I worked on improving Latent Space Dynamics Identification (LaSDI), a reduced-order modeling framework that compresses large simulation data sets into a smaller representation and then learns how that representation evolves over time. The motivation was to develop reduced models that remain accurate for more challenging systems, especially when predictions must remain reliable over long time intervals or when the underlying dynamics are more complicated than standard methods can easily handle. I also contributed to related work on Quandary, a high-performance software effort for simulation and control of open quantum systems, before focusing primarily on Latent Space Dynamics Identification methods. The main outcomes of the fellowship were two new algorithms (both of which were published), Rollout-LaSDI and Higher-Order LaSDI, together with supporting work on multi-stage Latent Space Dynamics Identification. Rollout-LaSDI improved long-term prediction by training the model to stay accurate over extended time horizons, and Higher-Order LaSDI broadened the method so it could model systems with higher-order time dynamics. My contributions to multistage Latent Space Dynamics Identification also helped show that its later training stages could be simplified without losing effectiveness, and that this behavior held across different model architectures and training strategies. Taken together, these advances improved the accuracy, flexibility, and practical value of reduced-order modeling tools for computational science.

97 MATHEMATICS AND COMPUTING↗

Artificial Intelligence Enhancements to Imagery for Space Operations

Philosophy classes still ponder the question asked by Dr. George Berkely, an Anglican Bishop and philosopher in the 1600’s-- “If a tree falls in a forest and no one is around to hear it, does it make a sound?” With that in mind, I ask the following—If a still image or motion imagery from a space mission cannot be found during a search, does it exist? Since the beginning of spaceflight, imagery has been a key form of data collected. Whether for mere curiosity (what does Earth look like from Space?), or for operational reasons (did the solar panel deploy?), or for engineering purposes (what was that object that floated away from the spacecraft?), imagery has been included in space missions. To be useful, though, the image or motion imagery must be accessible and accessed when needed. During the analog era, that typically meant captions and numbers associated with the physical media. With “born digital” imagery, it is possible to add metadata to the image data file. This metadata might include the date and time of capture, mission, camera, exposure data, and similar data fields. Many modern cameras embed some basic metadata into the image file at the moment of capture. The reality, though, is even with today’s born-digital enhancements with embedded metadata at the time of capture, reviewing and cataloging still and motion imagery is very labor intensive. Humans review the imagery for sensitive content (privacy concerns, imagery containing proprietary data/subject matter), and to identify imagery containing crew members or imagery that should be reviewed for engineering or scientific reasons. All this review and manual data entry is very time-consuming. Many improvements in Artificial Intelligence (AI), Machine Learning, and processing power now make it possible to identify persons, objects, motion, color, audio with sensitive content, and other details after or while the imagery is captured.

Rodney Grubbs↗

Modeling the 4D discharge of lithium-ion batteries with a multiscale time-dependent deep learning framework

The lithium-ion battery (LIB) field is moving towards the direction of investigating spatially resolved physical phenomena in the 3D porous microstructure of electrodes. These pore-scale simulations give new insights into the local dynamics of lithiation/de-lithiation and charge transport, Nevertheless, the computational time of these simulations limits the integration of these models in optimization workflows of cycling conditions or electrode manufacturing processes. Machine learning models present a way of assessing in real-time the performance of materials. While several successful techniques for replicating simulations with machine learning have been proposed, this case study presents a more demanding problem, due to the necessity of understanding the behavior of heterogeneous 3D local data, as it evolves in time: this poses both a scientific and a technical challenge. To this end, we propose an autoregressive multiscale convolutional neural network model to predict relevant quantities at the pore-scale in the solid phase: the lithium concentration (in the active material) and potential (in the active material and carbon binder). Here, these are ultimately used to reconstruct the battery discharge curve. 3D images of the electrode microstructures are the input to the network, trained with a dataset of finite element method simulations to predict the discharge behavior of the cathode side in lithium ion batteries. We propose this machine learning model as a proof-of-concept of the applicability of multiscale networks for time-dependent physics problems. The trained model exhibits very high accuracy (with errors lower than 2 %) in forecasting the discharge behavior of new unseen cathodes.

25 ENERGY STORAGE↗

Turbulence theories and statistical closure approaches

When discussing research in physics and in science more generally, it is common to ascribe equal importance to the three components of the scientific trinity: theoretical, experimental, and computational studies. This review will explore the future of modern turbulence theory by tracing its history, which began in earnest with Kolmogorov’s 1941 analysis of turbulence cascade and inertial range [A.N. Kolmogorov, Dokl. Akad. Nauk SSSR, 30, 299, (1941); 32, 19, (1941)]. The 80th Anniversary of Kolmogorov’s landmark study is a welcome opportunity to survey the achievements and evaluate the future of the theoretical approach of turbulence research. Over the years, turbulence theories have been critically important in laying the foundation of our understanding of the nature of turbulent flows. In particular, the Direct Interaction Approximation (DIA) [R.H. Kraichnan, J. Fluid Mech., 5, 497 (1959)] and its subsequent development, known as the statistical closure approach, can be identified as perhaps the most profound single advancement. The remarkable success of the statistical closure has furnished a platform to study such essential concepts as the energy transfer process and interacting scales, and the roles of the straining and sweeping motions. More recently, the quasi-Lagrangian formulation of V. L’vov & I. Procaccia and Kraichnan’s solvable passive scalar model provided powerful ways to explore another fundamental aspect of turbulent flows, the phenomena of intermittency, and the associated anomalous scaling exponents. In the meantime, the theory of fluid equilibria has been developed to describe the large-scale structures that can emerge from turbulent cascades of two-dimensional and geophysical flows at a later time. And yet, despite all these successes, analytical treatments suffer from mathematical complexities. As a result, the utility of theoretical approaches has been limited to relatively idealized flows. On the other hand, in recent decades, computational abilities and experimental facilities have reached an unprecedented scale. Looking beyond the horizon, the imminent deployment of exascale supercomputers will generate complete datasets of the entire flow field of key benchmark flows, allowing researchers to extract additional measurements concerning fully developed, complex turbulent flow fields far beyond those available from the statistical closure theories. Some other developments that could potentially influence the future course of turbulence theories include the advancement of machine learning, artificial intelligence, and data science; likely disruptions arising from the advent of quantum computation; and the increasingly prominent role of turbulence research in providing more accurate climate scientific data. Finally, turbulence theorists can leverage these developments by asking the right questions and developing advanced, sophisticated frameworks that will be able to predict and correlate vast amounts of data from the other two components of the trinity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Developing Open-Source Training Materials for AI/ML and Space Biological Sciences Using NASA Cloud-Based Data

Artificial Intelligence (AI) and Machine Learning (ML) has gained significant traction in the biological and biomedical research fields, in part due to a culture of open data sharing and reuse. AI/ML methodology is well-suited to recognize and predict biological patterns from high-dimensional next-generation sequencing data (e.g. whole genome sequencing, transcriptomic sequencing), as well as from biological or medical imaging data (e.g. microscopy, computed tomography, ultrasound, magnetic resonance imaging, radiography). These methodologies hold particular promise for space biosciences research and automated space health monitoring systems. However, there are key considerations for properly training, validating, and testing a machine learning model in biological research or clinical application. Inexperienced researchers can produce models that perform poorly outside of the training dataset. Open Science principles such as data sharing and open-source code must go hand-in-hand with publicly available, high-quality training curricula in best practices, with modules centered on real-life scientific use cases and data so future AI/ML practitioners gain experience on real problems. Here we present the development of open-source training materials for AI/ML and space biosciences, as part of the NASA Transform to Open Science Training (TOPST) initiative. We develop 4 independent training programs, focused on the following topics: 1) Fundamentals of Machine Learning and Space Biosciences Domain, 2) Open Science, Artificial Intelligence, and Ethical Best Practices for Data Sharing and Analysis, 3) Using AI/ML Classification to Identify Gene Networks Affected By Space Exposure in Mouse Liver, and 4) Using Neural Networks to Find DNA Damage Patterns in Immune Cells after Radiation. All programs leverage cloud-based NASA biological datasets. The curriculum we present will enable worldwide access to training in AI/ML and scientific analysis.

James Casaletto↗

Modeling Atmospheric Science Knowledge from Research Publications

NASA Earth Science Data Centers contain enormous amounts of remote sensing digital data. It is often a significant challenge for users to find data suitable for their research topic in these vast archives. One of the approaches is the usage-driven dataset discovery, where users seek publications on projects similar to their intended study. For this approach to be effective, users need a clear connection between the underlying data in the publications and the study objectives; this is not often apparent to non-expert users. Tools and methodologies that can help facilitate and organize these connections are therefore valuable for creating improved knowledge mappings, which can be further used by search engines to suggest data or publications best tailored to a user’s specific research goal. As an illustration of these challenges, in this work we focus on the atmospheric chemistry processes related to Earth environmental impacts such as ozone depletion, aerosols, smog formation, acid rain, and radiative forcing. We further limit our study to publications that use data from the Microwave Limb Sounder (MLS) instrument flown on the Aura Earth Observing System. To create knowledge representations of science carried out in these publications, we use existing ontologies such as the Global Change Master Directory (GCMD) and Semantic Web for Earth and Environmental Terminology (SWEET). These ontologies together encompass term dictionaries that include measured variables, names of molecules or radicals, mission and instrument names, locations, action words, among many others. Based on these terms acknowledge graph database was populated with the terms retrieved from scientific publications that study atmospheric chemistry. These databases can be used to further enhance the automation of knowledge discovery and facilitate machine learning and artificial intelligence algorithms or applications. These tools and methods can also be extended to apply to content from other related Earth science domains.

Irina Gerasimov↗