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Results for “invariant variational autoencoder”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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18 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder

Carboxysomes are a class of bacterial microcompartments that form proteinaceous organelles within the cytoplasm of cyanobacteria and play a central role in photosynthetic metabolism by defining a cellular microenvironment permissive to CO2 fixation. Critical aspects of the assembly of the carboxysomes remain relatively unknown, especially with regard to the dynamics of this microcompartment. Progress in understanding carboxysome dynamics is impeded in part because analysis of the subtle changes in carboxysome morphology with microscopy remains a low-throughput and subjective process. Here we use deep learning techniques, specifically a Rotationally Invariant Variational Autoencoder (rVAE), to analyze fluorescence microscopy images of cyanobacteria bearing a carboxysome reporter and quantitatively evaluate how carboxysome shell remodelling impacts subtle trends in the morphology of the microcompartment over time. Toward this goal, we use a recently developed tool to control endogenous protein levels, including carboxysomal components, in the model cyanobacterium Synechococcous elongatus PCC 7942. By utilization of this system, proteins that compose the carboxysome can be tuned in real time as a method to examine carboxysome dynamics. We find that rVAEs are able to assist in the quantitative evaluation of changes in carboxysome numbers, shape, and size over time. Further, we propose that rVAEs may be a useful tool to accelerate the analysis of carboxysome assembly and dynamics in response to genetic or environmental perturbation and may be more generally useful to probe regulatory processes involving a broader array of bacterial microcompartments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Finding simplicity: unsupervised discovery of features, patterns, and order parameters via shift-invariant variational autoencoders *

Abstract Recent advances in scanning tunneling and transmission electron microscopies (STM and STEM) have allowed routine generation of large volumes of imaging data containing information on the structure and functionality of materials. The experimental data sets contain signatures of long-range phenomena such as physical order parameter fields, polarization, and strain gradients in STEM, or standing electronic waves and carrier-mediated exchange interactions in STM, all superimposed onto scanning system distortions and gradual changes of contrast due to drift and/or mis-tilt effects. Correspondingly, while the human eye can readily identify certain patterns in the images such as lattice periodicities, repeating structural elements, or microstructures, their automatic extraction and classification are highly non-trivial and universal pathways to accomplish such analyses are absent. We pose that the most distinctive elements of the patterns observed in STM and (S)TEM images are similarity and (almost-) periodicity, behaviors stemming directly from the parsimony of elementary atomic structures, superimposed on the gradual changes reflective of order parameter distributions. However, the discovery of these elements via global Fourier methods is non-trivial due to variability and lack of ideal discrete translation symmetry. To address this problem, we explore the shift-invariant variational autoencoders (shift-VAEs) that allow disentangling characteristic repeating features in the images, their variations, and shifts that inevitably occur when randomly sampling the image space. Shift-VAEs balance the uncertainty in the position of the object of interest with the uncertainty in shape reconstruction. This approach is illustrated for model 1D data, and further extended to synthetic and experimental STM and STEM 2D data. We further introduce an approach for training shift-VAEs that allows finding the latent variables that comport to known physical behavior. In this specific case, the condition is that the latent variable maps should be smooth on the length scale of the atomic lattice (as expected for physical order parameters), but other conditions can be imposed. The opportunities and limitations of the shift VAE analysis for pattern discovery are elucidated.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Physics and chemistry from parsimonious representations: image analysis via invariant variational autoencoders

Electron, optical, and scanning probe microscopy methods are generating ever increasing volume of image data containing information on atomic and mesoscale structures and functionalities. This necessitates the development of the machine learning methods for discovery of physical and chemical phenomena from the data, such as manifestations of symmetry breaking phenomena in electron and scanning tunneling microscopy images, or variability of the nanoparticles. Variational autoencoders (VAEs) are emerging as a powerful paradigm for the unsupervised data analysis, allowing to disentangle the factors of variability and discover optimal parsimonious representation. Here, we summarize recent developments in VAEs, covering the basic principles and intuition behind the VAEs. The invariant VAEs are introduced as an approach to accommodate scale and translation invariances present in imaging data and separate known factors of variations from the ones to be discovered. We further describe the opportunities enabled by the control over VAE architecture, including conditional, semi-supervised, and joint VAEs. Several case studies of VAE applications for toy models and experimental datasets in Scanning Transmission Electron Microscopy are discussed, emphasizing the deep connection between VAE and basic physical principles. Python codes and datasets discussed in this article are available at https://github.com/saimani5/VAE-tutorials and can be used by researchers as an application guide when applying these to their own datasets.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Decoding the shift-invariant data: applications for band-excitation scanning probe microscopy *

A shift-invariant variational autoencoder (shift-VAE) is developed as an unsupervised method for the analysis of spectral data in the presence of shifts along the parameter axis, disentangling the physically-relevant shifts from other latent variables. Using synthetic data sets, we show that the shift-VAE latent variables closely match the ground truth parameters. The shift VAE is extended towards the analysis of band-excitation piezoresponse force microscopy data, disentangling the resonance frequency shifts from the peak shape parameters in a model-free unsupervised manner. The extensions of this approach towards denoising of data and model-free dimensionality reduction in imaging and spectroscopic data are further demonstrated. This approach is universal and can also be extended to analysis of x-ray diffraction, photoluminescence, Raman spectra, and other data sets.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Physical discovery in representation learning via conditioning on prior knowledge

Recent advances in electron, scanning probe, optical, and chemical imaging and spectroscopy yield bespoke data sets containing the information of structure and functionality of complex systems. In many cases, the resulting data sets are underpinned by low-dimensional simple representations encoding the factors of variability within the data. The representation learning methods seek to discover these factors of variability, ideally further connecting them with relevant physical mechanisms. However, generally, the task of identifying the latent variables corresponding to actual physical mechanisms is extremely complex. Here, we present an empirical study of an approach based on conditioning the data on the known (continuous) physical parameters and systematically compare it with the previously introduced approach based on the invariant variational autoencoders. The conditional variational autoencoder (cVAE) approach does not rely on the existence of the invariant transforms and hence allows for much greater flexibility and applicability. Interestingly, cVAE allows for limited extrapolation outside of the original domain of the conditional variable. However, this extrapolation is limited compared to the cases when true physical mechanisms are known, and the physical factor of variability can be disentangled in full. We further show that introducing the known conditioning results in the simplification of the latent distribution if the conditioning vector is correlated with the factor of variability in the data, thus allowing us to separate relevant physical factors. We initially demonstrate this approach using 1D and 2D examples on a synthetic data set and then extend it to the analysis of experimental data on ferroelectric domain dynamics visualized via piezoresponse force microscopy.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Latent Mechanisms of Polarization Switching from In Situ Electron Microscopy Observations

In situ scanning transmission electron microscopy enables observation of the domain dynamics in ferroelectric materials as a function of externally applied bias and temperature. The resultant data sets contain a wealth of information on polarization switching and phase transition mechanisms. However, identification of these mechanisms from observational data sets has remained a problem due to a large variety of possible configurations, many of which are degenerate. Here, an approach based on a combination of deep learning-based semantic segmentation, rotationally invariant variational autoencoder (VAE), and non-negative matrix factorization to enable learning of a latent space representation of the data with multiple real-space rotationally equivalent variants mapped to the same latent space descriptors is introduced. By varying the size of training sub-images in the VAE, the degree of complexity in the structural descriptors is tuned from simple domain wall detection to the identification of switching pathways. Importantly, this yields a powerful tool for the exploration of the dynamic data in mesoscopic electron, scanning probe, optical, and chemical imaging. Moreover, this work adds to the growing body of knowledge of incorporating physical constraints into the machine and deep-learning methods to improve learned descriptors of physical phenomena.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Probing atomic-scale symmetry breaking by rotationally invariant machine learning of multidimensional electron scattering

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.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Deep Bayesian local crystallography

Abstract The advent of high-resolution electron and scanning probe microscopy imaging has opened the floodgates for acquiring atomically resolved images of bulk materials, 2D materials, and surfaces. This plethora of data contains an immense volume of information on materials structures, structural distortions, and physical functionalities. Harnessing this knowledge regarding local physical phenomena necessitates the development of the mathematical frameworks for extraction of relevant information. However, the analysis of atomically resolved images is often based on the adaptation of concepts from macroscopic physics, notably translational and point group symmetries and symmetry lowering phenomena. Here, we explore the bottom-up definition of structural units and symmetry in atomically resolved data using a Bayesian framework. We demonstrate the need for a Bayesian definition of symmetry using a simple toy model and demonstrate how this definition can be extended to the experimental data using deep learning networks in a Bayesian setting, namely rotationally invariant variational autoencoders.

36 MATERIALS SCIENCE↗
DOE OSTI2022

AtomAI framework for deep learning analysis of image and spectroscopy data in electron and scanning probe microscopy

Over the past several decades, electron and scanning probe microscopes have become critical components of condensed matter physics, materials science and chemistry research. At the same time, the infrastructure for establishing a connection between microscopy observations and materials behaviour over a broader parameter space is lacking. In this work, we introduce AtomAI, an open-source software package bridging instrument-specific Python libraries, deep learning and simulation tools into a single ecosystem. AtomAI allows direct applications of deep neural networks for atomic and mesoscopic image segmentation converting image and spectroscopy data into class-based local descriptors for downstream tasks such as statistical and graph analysis. For atomically resolved imaging data, the output is types and positions of atomic species, with an option for subsequent refinement. AtomAI further allows the implementation of a broad range of image and spectrum analysis functions, including invariant variational autoencoders for disentangling structural factors of variation and im2spec type of encoder–decoder models for mapping structure–property relationships. Finally, our framework allows seamless connection to the first principles modelling with a Python interface on the inferred atomic positions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Unsupervised learning of ferroic variants from atomically resolved STEM images

An approach for the analysis of atomically resolved scanning transmission electron microscopy data with multiple ferroic variants in the presence of imaging non-idealities and chemical variabilities based on a rotationally invariant variational autoencoder (rVAE) is presented. We show that an optimal local descriptor for the analysis is a sub-image centered at specific atomic units, since materials and microscope distortions preclude the use of an ideal lattice as a reference point. The applicability of unsupervised clustering and dimensionality reduction methods is explored and is shown to produce clusters dominated by chemical and microscope effects, with a large number of classes required to establish the presence of rotational variants. Comparatively, the rVAE allows extraction of the angle corresponding to the orientation of ferroic variants explicitly, enabling straightforward identification of the ferroic variants as regions with constant or smoothly changing latent variables and sharp orientational changes. This approach allows further exploration of the chemical variability by separating the rotational degrees of freedom via rVAE and searching for remaining variability in the system. The code used in this article is available at https://github.com/saimani5/ferroelectric_domains_rVAE.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2023

Unsupervised machine learning discovery of structural units and transformation pathways from imaging data

We show that unsupervised machine learning can be used to learn chemical transformation pathways from observational Scanning Transmission Electron Microscopy (STEM) data. To enable this analysis, we assumed the existence of atoms, a discreteness of atomic classes, and the presence of an explicit relationship between the observed STEM contrast and the presence of atomic units. With only these postulates, we developed a machine learning method leveraging a rotationally invariant variational autoencoder (VAE) that can identify the existing molecular fragments observed within a material. The approach encodes the information contained in STEM image sequences using a small number of latent variables, allowing the exploration of chemical transformation pathways by tracing the evolution of atoms in the latent space of the system. The results suggest that atomically resolved STEM data can be used to derive fundamental physical and chemical mechanisms involved, by providing encodings of the observed structures that act as bottom-up equivalents of structural order parameters. The approach also demonstrates the potential of variational (i.e., Bayesian) methods in the physical sciences and will stimulate the development of more sophisticated ways to encode physical constraints in the encoder–decoder architectures and generative physical laws and causal relationships in the latent space of VAEs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Discovering invariant spatial features in electron energy loss spectroscopy images on the mesoscopic and atomic levels

Over the last two decades, Electron Energy Loss Spectroscopy (EELS) imaging with a scanning transmission electron microscope has emerged as a technique of choice for visualizing complex chemical, electronic, plasmonic, and phononic phenomena in complex materials and structures. The availability of the EELS data necessitates the development of methods to analyze multidimensional data sets with complex spatial and energy structures. Traditionally, the analysis of these data sets has been based on analysis of individual spectra, one at a time, whereas the spatial structure and correlations between individual spatial pixels containing the relevant information of the physics of underpinning processes have generally been ignored and analyzed only via the visualization as 2D maps. Here, we develop a machine learning-based approach and workflows for the analysis of spatial structures in 3D EELS data sets using a combination of dimensionality reduction and multichannel rotationally invariant variational autoencoders. This approach is illustrated for the analysis of both the plasmonic phenomena in a system of nanowires and in the core excitations in functional oxides using low loss and core-loss EELS, respectively. The code developed in this manuscript is open sourced and freely available and provided as a Jupyter notebook for the interested reader.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Disentangling Rotational Dynamics and Ordering Transitions in a System of Self-Organizing Protein Nanorods via Rotationally Invariant Latent Representations

The dynamics of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally invariant variational autoencoder-based analysis of orientation and shape evolution. The latter allows for disentanglement of the particle orientation from other degrees of freedom and compensates for lateral shifts. The disentangled representations in the latent space encode the rich spectrum of local transitions that can now be visualized and explored via continuous variables. The time dependence of ensemble averages allows insight into the time dynamics of the system and, in particular, illustrates the presence of the potential ordering transition. Finally, analysis of the latent variables along the single-particle trajectory allows tracing these parameters on a single-particle level. The proposed approach is expected to be universally applicable for the description of the imaging data in optical, scanning probe, and electron microscopy seeking to understand the dynamics of complex systems where rotations are a significant part of the process.

representation learning↗
DOE OSTI2023

Efficient 3D Molecular Design with an E(3) Invariant Transformer VAE

This work introduces a three-dimensional (3D) invariant graph-to-string transformer variational autoencoders (VAE) (Vagrant) for generating molecules with accurate density functional theory (DFT)-level properties. Vagrant learns to model the joint probability distribution of a 3D molecular structure and its properties by encoding molecular structures into a 3D-aware latent space. Directed navigation through this latent space implicitly optimizes the 3D structure of a molecule, and the latent embedding can be used to condition a generative transformer to predict the candidate structure as a one-dimensional (1D) sequence. Additionally, we introduce two novel sampling methods that exploit the latent characteristics of a VAE to improve performance. Here, we show that our method outperforms comparable 3D autoregressive and diffusion methods for predicting quantum chemical property values of novel molecules in terms of both sample quality and computational efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Disentangling ferroelectric domain wall geometries and pathways in dynamic piezoresponse force microscopy via unsupervised machine learning

In this work, domain switching pathways in ferroelectric materials visualized by dynamic piezoresponse force microscopy (PFM) are explored via variational autoencoder, which simplifies the elements of the observed domain structure, crucially allowing for rotational invariance, thereby reducing the variability of local polarization distributions to a small number of latent variables. For small sampling window sizes the latent space is degenerate, and variability is observed only in the direction of a single latent variable that can be identified with the presence of domain wall. For larger window sizes, the latent space is 2D, and the disentangled latent variables can be generally interpreted as the degree of switching and complexity of domain structure. Applied to multiple consecutive PFM images acquired while monitoring domain switching, the polarization switching mechanism can thus be visualized in the latent space, providing insight into domain evolution mechanisms and their correlation with the microstructure.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Masked Particle Modeling on Sets: Towards Self-Supervised High Energy Physics Foundation Models

Abstract We propose masked particle modeling (MPM) as a self-supervised method for learning generic, transferable, and reusable representations on unordered sets of inputs for use in high energy physics (HEP) scientific data. This work provides a novel scheme to perform masked modeling based pre-training to learn permutation invariant functions on sets. More generally, this work provides a step towards building large foundation models for HEP that can be generically pre-trained with self-supervised learning and later fine-tuned for a variety of down-stream tasks. In MPM, particles in a set are masked and the training objective is to recover their identity, as defined by a discretized token representation of a pre-trained vector quantized variational autoencoder. We study the efficacy of the method in samples of high energy jets at collider physics experiments, including studies on the impact of discretization, permutation invariance, and ordering. We also study the fine-tuning capability of the model, showing that it can be adapted to tasks such as supervised and weakly supervised jet classification, and that the model can transfer efficiently with small fine-tuning data sets to new classes and new data domains.

Heinrich, Lukas (ORCID:0000000240487584)↗
DOE OSTI2025

Invariant discovery of features across multiple length scales: Applications in microscopy and autonomous materials characterization

Physical imaging is a foundational characterization method in areas from condensed matter physics and chemistry to astronomy and spans length scales from atomic to universe. Images encapsulate crucial data regarding atomic bonding, materials microstructures, and dynamic phenomena such as microstructural evolution and turbulence, among other phenomena. The challenge lies in effectively extracting and interpreting this information. Variational Autoencoders (VAEs) have emerged as powerful tools for identifying the underlying factors of variation in image data, providing a systematic approach to distilling meaningful patterns from complex data sets. However, a significant hurdle in their application is the definition and selection of appropriate descriptors reflecting local structures. Here, we introduce the scale-invariant VAE approach (SI-VAE) based on the progressive training of the VAE with the descriptors sampled at different length scales. The SI-VAE allows the discovery of the length scale-dependent factors of variation in the system. Here, we illustrate this approach using the ferroelectric domain images and generalize it to the movies of the electron-beam induced phenomena in graphene and topography evolution across combinatorial libraries. This approach can further be used to initialize the decision making in automated experiments including structure–property discovery and can be applied across a broad range of imaging methods. This approach is universal and can be applied to any spatially resolved data including both experimental imaging studies and simulations, and can be particularly useful for exploration of phenomena such as turbulence and scale-invariant transformation fronts.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Optimizing training trajectories in variational autoencoders via latent Bayesian optimization approach *

Unsupervised and semi-supervised ML methods such as variational autoencoders (VAE) have become widely adopted across multiple areas of physics, chemistry, and materials sciences due to their capability in disentangling representations and ability to find latent manifolds for classification and/or regression of complex experimental data. Like other ML problems, VAEs require hyperparameter tuning, e.g. balancing the Kullback–Leibler and reconstruction terms. However, the training process and resulting manifold topology and connectivity depend not only on hyperparameters, but also their evolution during training. Because of the inefficiency of exhaustive search in a high-dimensional hyperparameter space for the expensive-to-train models, here we have explored a latent Bayesian optimization (zBO) approach for the hyperparameter trajectory optimization for the unsupervised and semi-supervised ML and demonstrated for joint-VAE with rotational invariances. We have demonstrated an application of this method for finding joint discrete and continuous rotationally invariant representations for modified national institute of standards and technology database (MNIST) and experimental data of a plasmonic nanoparticles material system. The performance of the proposed approach has been discussed extensively, where it allows for any high dimensional hyperparameter trajectory optimization of other ML models.

42 ENGINEERING↗