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Despite an ever-growing number of data sets that catalog and characterize interactions between microbes in different environments and conditions, many of these data are neither easily accessible nor intercompatible. These limitations present a major challenge to microbiome research by hindering the streamlined drawing of inferences across studies.
Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data, machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based neural network architectures have emerged in recent years as the most successful approach for predictions based on molecular structure and have consistently achieved the best performance on benchmark quantum chemical datasets. However, these models have typically required optimized 3D structural information for the molecule to achieve the highest accuracy. These 3D geometries are costly to compute for high levels of theory, limiting the applicability and practicality of machine learning methods in high-throughput screening applications. In this study, we present a new database of candidate molecules for organic photovoltaic applications, comprising approximately 91,000 unique chemical structures. Compared to existing datasets, this dataset contains substantially larger molecules (up to 200 atoms) as well as extrapolated properties for long polymer chains. We show that message-passing neural networks trained with and without 3D structural information for these molecules achieve similar accuracy, comparable to state-of-the-art methods on existing benchmark datasets. Furthermore, these results therefore emphasize that for larger molecules with practical applications, near-optimal prediction results can be obtained without using optimized 3D geometry as an input. We further show that learned molecular representations can be leveraged to reduce the training data required to transfer predictions to a new density functional theory functional.
Abstract In addition to being the core quantity in density-functional theory, the charge density can be used in many tertiary analyses in materials sciences from bonding to assigning charge to specific atoms. The charge density is data-rich since it contains information about all the electrons in the system. With the increasing prevalence of machine-learning tools in materials sciences, a data-rich object like the charge density can be utilized in a wide range of applications. The database presented here provides a modern and user-friendly interface for a large and continuously updated collection of charge densities as part of the Materials Project. In addition to the charge density data, we provide the theory and code for changing the representation of the charge density which should enable more advanced machine-learning studies for the broader community.
This paper addresses the identification (realization) of approximate linear models from response data for certain nonlinear dynamic systems. Response characteristics for several typical nonlinear joints are analyzed mathematically and represented by series expansions. The parameters of the series expansion are then compared with the modal parameters of a linear model identified by the Eigensystem Realization Algorithm. The agreement of the identified model and the analytically derived representation is excellent for the cases studied. Also laboratory data from a model which exhibited stiffening behavior was analyzed using the Eigensystem Realization algorithm and Fast Fourier Transform. The laboratory experiment demonstrated the ability of the technique to recover the model characteristics using real data.
Abstract Convolutional neural networks (CNNs) have been successfully used in many applications where important information about data is embedded in the order of features, such as speech and imaging. However, most tabular data do not assume a spatial relationship between features, and thus are unsuitable for modeling using CNNs. To meet this challenge, we develop a novel algorithm, image generator for tabular data (IGTD), to transform tabular data into images by assigning features to pixel positions so that similar features are close to each other in the image. The algorithm searches for an optimized assignment by minimizing the difference between the ranking of distances between features and the ranking of distances between their assigned pixels in the image. We apply IGTD to transform gene expression profiles of cancer cell lines (CCLs) and molecular descriptors of drugs into their respective image representations. Compared with existing transformation methods, IGTD generates compact image representations with better preservation of feature neighborhood structure. Evaluated on benchmark drug screening datasets, CNNs trained on IGTD image representations of CCLs and drugs exhibit a better performance of predicting anti-cancer drug response than both CNNs trained on alternative image representations and prediction models trained on the original tabular data.
Atomic vibrations govern many macroscopic properties of materials, but experiments to comprehensively probe them remain challenging. Inelastic neutron scattering (INS) is a powerful technique to map phonon dispersions in crystals, especially when leveraging modern time-of-flight (ToF) spectrometers with large detectors. However, efficiently and robustly extracting interatomic force constants (FCs) parameterizing phonon dynamics from experimental spectra remains a bottleneck due to the complexity and high dimensionality of ToF INS datasets. Here, we present a machine learning approach for the direct inversion of FCs from single-crystal INS measurements. The framework leverages synthetic training data generated using universal machine-learned force fields and an efficient physics-based forward model. We benchmark two neural architectures–one emphasizing structured latent representation learning and the other direct, supervised spectral regression–across simulated datasets for two materials under idealized and noisy conditions. The latent-representation model is subsequently applied to experimental single-crystal INS data on germanium. The model is shown to reproduce FCs derived from both first-principles simulations and from iterative optimization, and furthermore achieves reliable inference even from sparse, single-orientation measurements representing short data acquisitions. Analysis of the learned latent space reveals semantically continuous and physically interpretable encodings that support strong cross-domain generalization. By bridging theoretical and experimental domains, we establish a path toward rapid inversion of experimental spectra and data-driven interpretation of temperature-dependent lattice dynamics.
The Jacchia models are represented in terms of spherical harmonic functions. This representation has the advantages of ease of comparison with theoretical and other observational models and data, mathematical analyticity and relative simplicity. The symmetry properties of the models are emphasized by this representation and some physical characteristics like the increase of the amplitude of the diurnal density variation with decreasing solar activity become more apparent.
Reanalyses in the Arctic are widely used for model evaluation and for understanding contemporary climate change. Nevertheless, differences among reanalyses in fundamental meteorological variables including surface air temperature are large. For example, the 1980-2009 mean surface air temperature for the north polar cap (70ÂdegN-90ÂdegN) among global reanalyses span a range of 2.4 K, which approximates the average warming trend from these reanalyses over the 30-year period of 2.1 K. Understanding these differences requires evaluation over the three principal surface domains of the Arctic: glaciated land, the unglaciated terrestrial surface, and sea ice/ocean. An examination is conducted of contemporary global reanalyses of the ECMWF Interim project, NASA MERRA, MERRA-2, JRA-55, and NOAA CFSR using available in situ data and assessments of the surface energy budget. Overly-simplistic representations of the Greenland Ice Sheet surface are found to be associated with local warm air temperature biases in winter. A review of progress made in the development of the MERRA-2 land-ice representation is presented. Large uncertainty is also found in temperatures over the Arctic tundra and boreal forest zone. But a key focus of temperature differences for northern high latitudes is the Arctic Ocean. Near-surface air temperature differences over the Arctic Ocean are found to be related to discrepancies in sea ice and sea surface temperature boundary data, which are severely compromised in current reanalyses. Issues with the modeled representation of sea ice cover are an additional factor in reanalysis temperature trends. Differences in the representation of the surface energy budget among the various reanalyses are also reviewed.
We develop an algebraic framework for sequential data assimilation of partially observed dynamical systems. In this framework, Bayesian data assimilation is embedded in a nonabelian operator algebra, which provides a representation of observables by multiplication operators and probability densities by density operators (quantum states). In the algebraic approach, the forecast step of data assimilation is represented by a quantum operation induced by the Koopman operator of the dynamical system. Moreover, the analysis step is described by a quantum effect, which generalizes the Bayesian observational update rule. Projecting this formulation to finite-dimensional matrix algebras leads to computational schemes that are i) automatically positivity-preserving and ii) amenable to consistent data-driven approximation using kernel methods for machine learning. Moreover, these methods are natural candidates for implementation on quantum computers. Applications to the Lorenz 96 multiscale system and the El Niño Southern Oscillation in a climate model show promising results in terms of forecast skill and uncertainty quantification.
Geodesy is the science of measuring the gravitational field of and positions on the Earth. Estimation of the gravitational field via gravitation gradiometry, the measurement of variations in the direction and magnitude of gravitation with respect to position, is this dissertation's focus. Gravity Probe B (GP-B) is a Stanford satellite experiment in gravitational physics. GP-B will measure the precession the rotating Earth causes on the space time around it by observing the precessions of four gyroscopes in a circular, polar, drag-free orbit at 650 km altitude. The gyroscopes are nearly perfect niobium-coated spheres of quartz, operating at 1.8 K to permit observations with extremely low thermal noise. The permissible gyroscope drift rate is miniscule, so the torques on the gyros must be tiny. A drag-free control system, by canceling accelerations caused by nongravitational forces, minimizes the support forces and hence torques. The GP-B system offers two main possibilities for geodesy. One is as a drag-free satellite to be used in trajectory-based estimates of the Earth's gravity field. We described calculations involving that approach in our previous reports, including comparison of laser only, GPS only, and combined tracking and a preliminary estimate of the possibility of estimating relativistic effects on the orbit. The second possibility is gradiometry. This technique has received a more cursory examination in previous reports, so we concentrate on it here. We explore the feasibility of using the residual suspension forces centering the GP-B gyros as gradiometer signals for geodesy. The objective of this work is a statistical prediction of the formal uncertainty in an estimate of the Earth's gravitation field using data from GP-B. We perform an instrument analysis and apply two mathematical techniques to predict uncertainty. One is an analytical approach using a flat-Earth approximation to predict geopotential information quality as a function of spatial wavelength. The second estimates the covariance matrix arising in a least-squares estimate of a spherical harmonic representation of the geopotential using GP-B gradiometer data. The results show that the GP-B data set can be used to create a consistent estimate of the geopotential up to spherical harmonic degree and order 60. The formal uncertainty of all coefficients between degrees 5 and 50 is reduced by factors of up to 30 over current satellite-only estimates and up to 7 over estimates which include surface data. The primary conclusion resulting from this study is that the gravitation gradiometer geodesy coexperiment to GP-B is both feasible and attractive.
Proper application of the FAIR data principles is what separates a vibrant data ecosystem, in which research data are frequently shared and reused, from a lifeless data graveyard. Automated metadata extraction systems have been proposed as a means of bolstering the findability, interoperability, and reusabil- ity of data repositories with little or no human intervention. These extraction systems mine metadata by crawling a repository and applying lightweight extractors that, for various types of file (e.g., image, CSV file), extract or synthesize relevant attributes. In practice, however, the automated creation of generally useful metadata is fraught with challenges. Data consumers may have different perspectives as to what metadata representations are useful, the standards for recording metadata tend to change over time, and the software model for processing updates can introduce unnecessary human and computational effort. Thus, generalizing extraction for a broad audience of data consumers is a difficult and relatively unsolved problem.In this work, we explore these challenges faced by extraction systems in the context of constructing our own extraction system for science data. We first define the metadata extraction problem and provide context to the issues faced in generalizing metadata. Additionally, we identify potential research directions to help alleviate many of these challenges for all automated extraction systems. Ultimately, this work represents a first step in designing ubiquitous metadata extraction systems that can maximize the value of research data while minimizing the human efforts required in doing so.
Bayesian Blocks are optimal piecewise linear representations (step function fits) of light-curves. The simple algorithm implementing this idea, using dynamic programming, has been extended to include more data modes and fitness metrics, multivariate analysis, and data on the circle (Studies in Astronomical Time Series Analysis. VI. Bayesian Block Representations, Scargle, Norris, Jackson and Chiang 2013, ApJ, 764, 167), as well as new results on background subtraction and refinement of the procedure for precise timing of transient events in sparse data. Example demonstrations will include exploratory analysis of the Kepler light curve archive in a search for "star-tickling" signals from extraterrestrial civilizations. (The Cepheid Galactic Internet, Learned, Kudritzki, Pakvasa1, and Zee, 2008, arXiv: 0809.0339; Walkowicz et al., in progress).
Real-time monitoring of a research nuclear reactor, a system in which all generated power is dissipated to the environment, can be performed via analysis of the heat rejection from the cooling system. Given an inlet water temperature and flow rate, the reactor power can be well-approximated from the outlet water temperature; however, the instrumentation to measure outlet conditions may not be robust or accurate. If we know how a cooling tower performs from historical data, but cannot measure the outlet temperature, a mathematical representation of the system can be inverted to obtain the outlet water temperature that describes the cooling capacity. Unfortunately, model inversion processes are computationally expensive. To address this, an artificial neural network (ANN) is implemented to assess the performance of a multi-cell cooling tower for a nuclear reactor. This approach leverages the Merkel model to obtain an extensive data set describing performance of the cooling tower cells throughout a wide array of potential operating conditions. The Merkel model is expressed as a function of four parameters: the inlet and outlet water temperatures, inlet air wet bulb temperature, and ratio of liquid-to-gas mass flow rates (L/G), which together provide a non-dimensional number indicative of cooling tower performance, called the Merkel integral. Computing a 4-dimensional data structure that describes finite combinations of the Merkel integral, an inverse model is then generated using an ANN to determine the cell outlet water temperature from the other three model parameters along with the computed Merkel integral. Compared to traditional model inversion methods, the ANN reduces the computational time by approximately 4 orders of magnitude, with effectively no sacrifice to solution accuracy, and could be applied for different cooling towers in the event the performance curve is known. Finally, three use cases of the ANN are then reviewed: (1) determining the cell outlet water temperatures when gas flow at rated conditions (GFRC) is known, (2) performing the prior case without knowledge of the GRFC, and (3) assessing performance differences between the individual tower cells.
Uncertainty visualization is a key component in translating important insights from ensemble simulation data into actionable decision-making by visually conveying various aspects of uncertainty within a system. With the recent advent of fast surrogate models trained on ensemble data, we can substitute computationally expensive simulations, which allows users to interact with more aspects of data spaces than ever before. However, the use of ensemble data with surrogate models in a decision-making tool brings up new challenges for uncertainty visualization, namely how to reconcile and communicate the new and different types of uncertainties brought in by surrogates and how to utilize these new data estimates in actionable ways. In this work, we examine these issues as they relate to high-dimensional data visualization, the integration of discrete datasets and the continuous representations of those datasets, and the unique difficulties associated with systems that allow users to iterate between input and output spaces. We assess the role of uncertainty visualization in facilitating intuitive and actionable interaction with ensemble data and surrogate models, and highlight key challenges in this new frontier of computational simulation.
Uncertainty visualization is a key component in translating important insights from ensemble data into actionable decision-making by visually conveying various aspects of uncertainty within a system. With the recent advent of fast surrogate models for computationally expensive simulations, users can interact with more aspects of data spaces than ever before. However, the integration of ensemble data with surrogate models in a decision-making tool brings up new challenges for uncertainty visualization, namely how to reconcile and communicate the new and different types of uncertainties brought in by surrogates and how to utilize these new data estimates in actionable ways. In this work, we examine these issues as they relate to high-dimensional data visualization, the integration of discrete datasets and the continuous representations of those datasets, and the unique difficulties associated with systems that allow users to iterate between input and output spaces. We assess the role of uncertainty visualization in facilitating intuitive and actionable interaction with ensemble data and surrogate models, and highlight key challenges in this new frontier of computational simulation.
The successful landing of the Mars Pathfinder spacecraft on Mars allows the review of the process of selecting the landing site and assessing predictions made for the site based on Viking and Earth-based data. Selection of the landing site for Mars Pathfinder was a two-phase process. The first phase took place from October 1993 to June 1994 and involved: initial identification of engineering constraints, definition of environmental conditions at the site for spacecraft design, and evaluation of the scientific potential of different landing sites. This phase culminated with the first "Mars Pathfinder Landing Site Workshop", held at the Lunar and Planetary Institute in Houston, Texas on April 18-19, 1994, in which suggested approaches and landing sites were solicited from the entire scientific community. A preliminary site was selected by the project for design purposes in June 1994. The second phase took place from July 1994 to March 1996 and involved: developing criteria for evaluating site safety using images and remote sensing data, testing of the spacecraft and landing subsystems (with design improvements) to establish quantitative engineering constraints on landing site characteristics, evaluating all potential landing sites on Mars, and certification of the site by the project. This phase included a second open workshop, "Mars Pathfinder Landing Site Workshop II: Characteristics of the Ares Vallis Region and Field Trips in the Channeled Scabland, Washington" held in Spokane and Moses Lake September 24-30, 1995 and formal acceptance of the site by NASA Headquarters. Engineering constraints on Pathfinder landing sites were developed from the initial design of the spacecraft and the entry, descent and landing scenario. The site must be within 5 degrees of the subsolar latitude at the time of landing (15N for maximum solar power and flexible communications with Earth. It also must be below 0 km elevation to enable enough time for the parachute to bring the lander to the proper terminal velocity for landing. The entire landing ellipse, which is 70 km by 200 km due to navigational, ephemeris and atmospheric uncertainties, must be free of steep slopes, scarps and obvious hazards in Viking orbiter images, have acceptable radar reflectivity, moderate rock abundances and have little or no dust. Scientific considerations of the Mars Pathfinder payload and mission indicate that analyses of "grab bag" samples at the mouths of outflow channels can offer a first order assessment of a variety of rock types on Mars. Highland sites offer the advantage of in situ analysis of ancient rocks on Mars that record crustal differentiation and the nature of the early environment. Dark gray sites offer the potential of analyzing unweathered and unoxidized materials. Following a general assessment of the safety of different sites, a preliminary selection of a "grab bag" site was made. This site, Ares Vallis, is near the mouth of an outflow channel that may contain ancient Noachian terrain, Hesperian ridged plains, and reworked channel materials. All potential landing sites on Mars that met basic safety criteria were analyzed in detail. Sites (100 by 200 km target ellipses) were considered safe if they were below 0 km elevation, were free of obvious hazards (high relief surface features) in high-resolution (< 50 m/pixel) Viking orbiter images and had acceptable reflectivity and roughness at radar wavelengths, high thermal inertia, moderate rock abundance, low red to violet ratio, and low albedo. Only 4 sites on Mars met all the above criteria, which included 1995 opposition 3.5 cm delay-Doppler radar data. Complete data were evaluated for 7 sites and the Viking landing sites for comparison for all the above criteria as well as crater abundance, hill and mesa abundance, slopes over meter to kilometer scales, low altitude winds (from global circulation models and slopes), the size-frequency distribution of large rocks, as well as rover trafficability and science potential. Discussion of potential hazards at Ares Vallis using a variety of data sets (including radar) at a second open workshop, indicated this site cannot be shown to be any more hazardous than the Viking landing sites. Field trips to the Channeled Scabland and the Ephrata Fan, analogs for Ares Vallis and the landing site, respectively, provided valuable insight into possible geologic processes and potential surface characteristics. Three sites met all the data requirements and safety criteria for landing Pathfinder. Ares Vallis was selected by the project because it appeared acceptably safe (although it appeared to have greater rock abundances than other sites, its elevation was likely the best known) and offered the prospect of analyzing a variety of rock types expected to be deposited by catastrophic floods, which would enable addressing first-order scientific questions such as differentiation of the crust, the development of weathering products, and the nature of the early martian environment and its subsequent evolution. The selection was reviewed by an external board at a number of meetings and accepted, and the site was approved by NASA Headquarters. Data gathered by the Pathfinder lander' and rover provides the opportunity to test the predictions made for the site in the selection process based on remote observations from Earth, orbit, and the surface. The discussion below is taken from Golombek et al. to which the reader is referred for a more complete discussion and a complete list of references, which are omitted here for brevity. Many characteristics of the landing site are consistent with its being shaped and deposited by the Ares and Tiu catastrophic floods. The rocky surface is consistent a depositional plain comprising semi-rounded pebbles, cobbles and tabular boulders (some of which appear imbricated and/or inclined in the direction of flow) that appear similar to depositional plains in terrestrial catastrophic floods. The Twin Peaks appear to be streamlined hills in lander images, which is consistent with interpretations of larger hills in Viking orbiter images of the region that suggest the lander is on the flank of a broad, gentle ridge trending northeast from Twin Peaks. This ridge, which is the rise to the north of the lander, is aligned in the downstream direction from the Ares and Tiu Valles floods, and may be a debris tail deposited in the wake of the Twin Peaks. Channels visible throughout the scene may be a result of late stage drainage. As predicted by delay-Doppler radar measurements and tracking results, the average elevation of the center of the site was about the same as Viking Lander I relative to the 6.1 mbar geoid. The Doppler tracking and two-way ranging estimate for the elevation of the spacecraft is only 45 in lower than the Viking I Lander and within 100 in of that expected, which is within the uncertainties of the measurements. After landing, surface pressures and winds (5-10 m/s) were found to be similar to expectations based on Viking data, although temperatures were about 10 K warmer. The temperature profile below 50 km was also roughly 20 K warmer. As a result, predicted densities were 5% higher near the surface and up to 40% lower at 50 km but within the entry, descent and landing design margins. The populations of craters and small hills and the slopes of the hills measured in high-resolution (38 m/pixel) Viking orbiter images and the radar derived slopes of the landing site are all consistent with observations of these properties in the lander images. A rocky surface was expected from Viking Infra-Red Thermal Mapper (IRTM) observations and comparisons with the Viking landing sites. The observed cumulative fraction of area covered by rocks with diameters greater than 3 cm and heights greater than 0.5 in (potentially hazardous to landing) at Ares is similar to that predicted by IRTM observations and models of Viking lander and Earth analog rock size-frequency distributions. The IRTM prediction postulated an effective thermal inertia of 30 (10(exp -3) cgs units - cal/cubic cm/s(exp 0.5)/K) for the rock population, but we obtain a slightly different effective thermal inertia for the actual rock population. The validity of interpretations of radar echoes prior to landing are supported by a simple radar echo model, an estimate of the reflectivity of the soil from its bulk density, and the fraction of area covered by rocks. In the calculations, the soil produces the quasi-specular echo and the rocks produce the diffuse echo. The derived quasispecular cross section is comparable to the cross-sections and reflectivities reported for 3.5-cm wavelength observations. The model yields a diffuse echo that is modestly larger than the polarized diffuse echo reported for 3.5-cm wavelength observations. At 12.5-cm wavelength, similar rock populations at Ares and the Viking I site were expected because the diffuse echoes are comparable, but the large normal reflectivities suggests that bulk densities of the soils at depth are greater than those at the surface. We also obtain a fine-component inertia near 8.4 which agrees with the fine-component inertia of 8.7 (in 10(exp -3) cgs units) estimated from thermal observations from orbit by the IRTM; for this estimate, we used a bulk thermal inertia of 10.4 for the landing site, an effective thermal inertia near 40 (10(exp -3) cgs units) for the rock population, and a graphical representation of Kieffer's model. Color and albedo data for Ares suggested surfaces of materials at Ares Vallis would be relatively dust free or unweathered prior to landing compared with the materials at the Viking landing sites. This suggestion is supported by the abundance of relatively dark-gray rocks at Ares and their relative rarity at the Viking landing sites, where rocks are commonly coated with bright red dust. Finally, the 40 km long Ephrata Fan of the Channeled Scabland in Washington state, which was deposited where c
Abstract The 4D scanning transmission electron microscopy (STEM) method maps the structure and functionality of solids on the atomic scale, yielding information-rich data sets describing the interatomic electric and magnetic fields, structural and electronic order parameters, and other symmetry breaking distortions. A critical bottleneck is the dearth of analytical tools that can reduce complex 4D-STEM data to physically relevant descriptors. We propose an approach for the systematic exploration of 4D-STEM data using rotationally invariant variational autoencoders (rrVAE), which disentangle the general rotation of the object from other latent representations. The implementation of purely rotational rrVAE is discussed as are applications to simulated data for graphene and zincblende structures. The rrVAE analysis of experimental 4D-STEM data of defects in graphene is illustrated and compared to the classical center-of-mass analysis. This approach is universal for probing symmetry-breaking phenomena in complex systems and can be implemented for a broad range of diffraction methods.
Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML training. In this study, we report a data-efficient, deep-learning framework for molecular discovery that integrates a coarse-grained functional-group representation with a self-attention mechanism to capture intricate chemical interactions. Our approach exploits group-contribution concepts to create a graph-based intermediate representation of molecules, serving as a low-dimensional embedding that substantially reduces the data demands typically required for training. Using a self-attention mechanism to learn the subtle but highly relevant chemical context of functional groups, the method proposed here consistently outperforms existing approaches for predictions of multiple thermophysical properties. In a case study focused on adhesive polymer monomers, we train on a limited dataset comprising only 6,000 unlabeled and 600 labeled monomers. The resulting chemistry prediction model achieves over 92% accuracy in forecasting properties directly from SMILES strings, exceeding the performance of current state-of-the-art techniques. Furthermore, the latent molecular embedding is invertible, enabling the design pipeline to automatically generate new monomers from the learned chemical subspace. We illustrate this functionality by targeting several properties, including high and low glass transition temperatures (Tg), and demonstrate that our model can identify new candidates with values that surpass those in the training set. The ease with which the proposed framework navigates both chemical diversity and data scarcity offers a promising route to accelerate and broaden the search for functional materials.