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Vasudevan, Rama

Publications and source records attributed to Vasudevan, Rama.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Toward Accelerating Discovery via Physics-Driven and Interactive Multifidelity Bayesian Optimization

Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and often nondifferentiable parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, processing spaces, and molecular embedding spaces. Often these systems are expensive or time consuming to evaluate a single instance, and hence classical approaches based on exhaustive grid or random search are too data intensive. This resulted in strong interest toward active learning methods such as Bayesian optimization (BO) where the adaptive exploration occurs based on human learning (discovery) objective. However, classical BO is based on a predefined optimization target, and policies balancing exploration and exploitation are purely data driven. In practical settings, the domain expert can pose prior knowledge of the system in the form of partially known physics laws and exploration policies often vary during the experiment. Here, we propose an interactive workflow building on multifidelity BO (MFBO), starting with classical (data-driven) MFBO, then expand to a proposed structured (physics-driven) structured MFBO (sMFBO), and finally extend it to allow human-in-the-loop interactive interactive MFBO (iMFBO) workflows for adaptive and domain expert aligned exploration. These approaches are demonstrated over highly nonsmooth multifidelity simulation data generated from an Ising model, considering spin–spin interaction as parameter space, lattice sizes as fidelity spaces, and the objective as maximizing heat capacity. Detailed analysis and comparison show the impact of physics knowledge injection and real-time human decisions for improved exploration with increased alignment to ground truth. Here, the associated notebooks allow to reproduce the reported analyses and apply them to other systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Selected Area Manipulation of MoS 2 via Focused Electron Beam-Induced Etching for Nanoscale Device Editing

Here we demonstrate direct-write patterning of single and multilayer MoS 2 via a focused electron beam-induced etching (FEBIE) process mediated with the XeF 2 precursor. MoS 2 etching is performed at various currents, areal doses, on different substrates, and characterized using scanning electron and atomic force microscopies as well as Raman and photoluminescence spectroscopies. Scanning transmission electron microscopy reveals a sub-40 nm etching resolution and the progression of point defects and lateral etching of the consequent unsaturated bonds. The results confirm that the electron beam-induced etching process is minimally invasive to the underlying material in comparison to ion beam techniques, which damage the subsurface material. Single-layer MoS 2 field-effect transistors are fabricated, and device characteristics are compared for channels that are edited via the selected area etching process. The source–drain current at constant gate and source–drain voltage scale linearly with the edited channel width. Moreover, the mobility of the narrowest channel width decreases, suggesting that backscattered and secondary electrons collaterally affect the periphery of the removed area. Focused electron beam doses on single-layer transistors below the etching threshold were also explored as a means to modify/thin the channel layer. The FEBIE exposures showed demonstrative effects via the transistor transfer characteristics, photoluminescence spectroscopy, and Raman spectroscopy. While strategies to minimize backscattered and secondary electron interactions outside of the scanned regions require further investigation, here, we show that FEBIE is a viable approach for selective nanoscale editing of MoS 2 devices.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Human-in-the-Loop: The Future of Machine Learning in Automated Electron Microscopy

Machine learning (ML) methods are progressively gaining acceptance in the electron microscopy community for de-noising, semantic segmentation, and dimensionality reduction of data post-acquisition. The introduction of the application programming interfaces (APIs) by major instrument manufacturers now allows the deployment of ML workflows in microscopes, not only for data analytics but also for real-time decision-making and feedback for microscope operation. However, the number of use cases for real-time ML remains remarkably small. Furthermore, we discuss some considerations in designing ML-based active experiments and pose that the likely strategy for the next several years will be human-in-the-loop automated experiments (hAE). In this paradigm, the ML learning agent directly controls beam position and image and spectroscopy acquisition functions, and a human operator monitors experiment progression in real and feature space of the system and tunes the policies of the ML agent to steer the experiment toward specific objectives.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Defects in MX2 (DMX) 2.0: STEM Digital Twins

DFT is used to optimize defects in monolayer MX2 phases. We calculate ~600 optimized defect structures, then use multislice simulations in abTEM to generate STEM digital twins, which can be used to train experimental ML. The reference paper for procedures and demonstration of their utility is https://arxiv.org/abs/2305.02917, and the images here correspond with the discussed Messy dataset. Version 2 includes an auxiliary dataset matched with experiment.

36 MATERIALS SCIENCE↗
DOE OSTI2023

High-speed mapping of surface charge dynamics using sparse scanning Kelvin probe force microscopy

Unraveling local dynamic charge processes is vital for progress in diverse fields, from microelectronics to energy storage. This relies on the ability to map charge carrier motion across multiple length- and timescales and understanding how these processes interact with the inherent material heterogeneities. Towards addressing this challenge, we introduce high-speed sparse scanning Kelvin probe force microscopy, which combines sparse scanning and image reconstruction. This approach is shown to enable sub-second imaging (>3 frames per second) of nanoscale charge dynamics, representing several orders of magnitude improvement over traditional Kelvin probe force microscopy imaging rates. Bridging this improved spatiotemporal resolution with macroscale device measurements, we successfully visualize electrochemically mediated diffusion of mobile surface ions on a LaAlO 3 /SrTiO 3 planar device. Such processes are known to impact band-alignment and charge-transfer dynamics at these heterointerfaces. Furthermore, we monitor the diffusion of oxygen vacancies at the single grain level in polycrystalline TiO 2 . Through temperature-dependent measurements, we identify a charge diffusion activation energy of 0.18 eV, in good agreement with previously reported values and confirmed by DFT calculations. Together, these findings highlight the effectiveness and versatility of our method in understanding ionic charge carrier motion in microelectronics or nanoscale material systems.

25 ENERGY STORAGE↗
DOE OSTI2023

Probe microscopy is all you need *

We pose that microscopy offers an ideal real-world experimental environment for the development and deployment of active Bayesian and reinforcement learning methods. Indeed, the tremendous progress achieved by machine learning (ML) and artificial intelligence over the last decade has been largely achieved via the utilization of static data sets, from the paradigmatic MNIST to the bespoke corpora of text and image data used to train large models such as GPT3, DALL·E and others. However, it is now recognized that continuous, minute improvements to state-of-the-art do not necessarily translate to advances in real-world applications. We argue that a promising pathway for the development of ML methods is via the route of domain-specific deployable algorithms in areas such as electron and scanning probe microscopy and chemical imaging. This will benefit both fundamental physical studies and serve as a test bed for more complex autonomous systems such as robotics and manufacturing. Favorable environment characteristics of scanning and electron microscopy include low risk, extensive availability of domain-specific priors and rewards, relatively small effects of exogenous variables, and often the presence of both upstream first principles as well as downstream learnable physical models for both statics and dynamics. Recent developments in programmable interfaces, edge computing, and access to application programming interfaces (APIs) facilitating microscope control, all render the deployment of ML codes on operational microscopes straightforward. We discuss these considerations and hope that these arguments will lead to create novel set of development targets for the ML community by accelerating both real world ML applications and scientific progress.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Optimizing Patient-Specific Medication Regimen Policies Using Wearable Sensors in Parkinson’s Disease

Effective treatment of Parkinson’s disease (PD) is a continual challenge for healthcare providers, and providers can benefit from leveraging emerging technologies to supplement traditional clinic care. We develop a data-driven reinforcement learning (RL) framework to optimize PD medication regimens through wearable sensors. We leverage a data set of n = 26 PD patients who wore wrist-mounted movement trackers for two separate six-day periods. Using these data, we first build and validate a simulation model of how individual patients’ movement symptoms respond to medication administration. We then pair this simulation model with an on-policy RL algorithm that recommends optimal medication types, timing, and dosages during the day while incorporating human-in-the-loop considerations on medication administration. The results show that the RL-prescribed medication regimens outperform physicians’ medication regimens, despite physicians having access to the same data as the RL agent. To validate our results, we assess our wearable-based RL medication regimens using n = 399 PD patients from the Parkinson’s Progression Markers Initiative data set. We show that the wearable-based RL medication regimens would lead to significant symptom improvement for these patients, even more so than training RL policies directly from this data set. In doing so, we show that RL models from even small data sets of wearable data can offer novel, generalizable clinical insights and medication strategies, which may outperform those derived from larger data sets without wearable data.

60 APPLIED LIFE SCIENCES↗
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↗
DOE OSTI2022

Bayesian Active Learning for Scanning Probe Microscopy: From Gaussian Processes to Hypothesis Learning

Recent progress in machine learning methods and the emerging availability of programmable interfaces for scanning probe microscopes (SPMs) have propelled automated and autonomous microscopies to the forefront of attention of the scientific community. However, enabling automated microscopy requires the development of task-specific machine learning methods, understanding the interplay between physics discovery and machine learning, and fully defined discovery workflows. This, in turn, requires balancing the physical intuition and prior knowledge of the domain scientist with rewards that define experimental goals and machine learning algorithms that can translate these to specific experimental protocols. Here, we discuss the basic principles of Bayesian active learning and illustrate its applications for SPM. We progress from the Gaussian process as a simple data-driven method and Bayesian inference for physical models as an extension of physics-based functional fits to more complex deep kernel learning methods, structured Gaussian processes, and hypothesis learning. These frameworks allow for the use of prior data, the discovery of specific functionalities as encoded in spectral data, and exploration of physical laws manifesting during the experiment. Here, the discussed framework can be universally applied to all techniques combining imaging and spectroscopy, SPM methods, nanoindentation, electron microscopy and spectroscopy, and chemical imaging methods and can be particularly impactful for destructive or irreversible measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Building Atomic and Plasmonic Devices via Electron Beams: from Desired Structures to Desired Properties

The evolution of the aberration correction in Scanning Transmission Electron Microscopy (STEM) has enabled multiple advances including high-resolution structural imaging, pm-level position detection of atomic columns, and ~3-5 mV resolution electron energy loss spectroscopy of the chemical and physical functionalities. These developments have further enabled the precise manipulation of the atomic structure of materials, including removal and formation of atomic planes in 3D materials, controlled atomic motion, and even direct atomic assembly of homo- and heteroatomic artificial molecules. Here, we will discuss several recent advances in STEM-EELS automated experiments as applied to quantum and nanoplasmonic systems.

42 ENGINEERING↗
DOE OSTI2022

Adapting Reinforcement Learning Treatment Policies Using Limited Data to Personalize Critical Care

We report reinforcement learning (RL) demonstrates promise for developing effective treatment policies in critical care settings. However, existing RL methods often require large and comprehensive patient data sets and do not readily lend themselves to settings in which certain patient subpopulations are severely underrepresented. In this study, we develop a new method, noisy Bayesian policy updates (NBPU), for selecting high-performing reinforcement learning–based treatment policies for underrepresented patient subpopulations using limited observations. Our method uses variational inference to learn a probability distribution over treatment policies based on a reference patient subpopulation for which sufficient data are available. It then exploits limited data from an underrepresented patient subpopulation to update this probability distribution and adapts its recommendations to this subpopulation. We demonstrate our method’s utility on a data set of ICU patients receiving intravenous blood anticoagulant medication. Our results show that NBPU outperforms state-of-the-art methods in terms of both selecting effective treatment policies for patients with nontypical clinical characteristics and predicting the corresponding policies’ performance for these patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Bayesian Learning of Adatom Interactions from Atomically Resolved Imaging Data

Atomic structures and adatom geometries of surfaces encode information about the thermodynamics and kinetics of the processes that lead to their formation, and which can be captured by a generative physical model. In this work, we develop a workflow based on a machine-learning-based analysis of scanning tunneling microscopy images to reconstruct the atomic and adatom positions, and a Bayesian optimization procedure to minimize statistical distance between the chosen physical models and experimental observations. We optimize the parameters of a 2- and 3-parameter Ising model describing surface ordering and use the derived generative model to make predictions across the parameter space. For concentration dependence, we compare the predicted morphologies at different adatom concentrations with the dissimilar regions on the sample surfaces that serendipitously had different adatom concentrations. The proposed workflow can be used to reconstruct the thermodynamic models and associated uncertainties from the experimental observations of materials microstructures. The code used in the manuscript is available at https://github.com/saimani5/Adatom_interactions.

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

Improving Medication Regimen Recommendation for Parkinson’s Disease Using Sensor Technology

Parkinson’s disease medication treatment planning is generally based on subjective data obtained through clinical, physician-patient interactions. The Personal KinetiGraph™ (PKG) and similar wearable sensors have shown promise in enabling objective, continuous remote health monitoring for Parkinson’s patients. In this proof-of-concept study, we propose to use objective sensor data from the PKG and apply machine learning to cluster patients based on levodopa regimens and response. The resulting clusters are then used to enhance treatment planning by providing improved initial treatment estimates to supplement a physician’s initial assessment. We apply k-means clustering to a dataset of within-subject Parkinson’s medication changes—clinically assessed by the MDS-Unified Parkinson’s Disease Rating Scale-III (MDS-UPDRS-III) and the PKG sensor for movement staging. A random forest classification model was then used to predict patients’ cluster allocation based on their respective demographic information, MDS-UPDRS-III scores, and PKG time-series data. Clinically relevant clusters were partitioned by levodopa dose, medication administration frequency, and total levodopa equivalent daily dose—with the PKG providing similar symptomatic assessments to physician MDS-UPDRS-III scores. A random forest classifier trained on demographic information, MDS-UPDRS-III scores, and PKG time-series data was able to accurately classify subjects of the two most demographically similar clusters with an accuracy of 86.9%, an F1 score of 90.7%, and an AUC of 0.871. A model that relied solely on demographic information and PKG time-series data provided the next best performance with an accuracy of 83.8%, an F1 score of 88.5%, and an AUC of 0.831, hence further enabling fully remote assessments. These computational methods demonstrate the feasibility of using sensor-based data to cluster patients based on their medication responses with further potential to assist with medication recommendations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

MoWSSe HAADF Image Dataset

High angle annular dark field scanning transmission electron microscopy images of MoWSSe (2D quaternary alloy system), by Jordan Hachtel (Center for Nanophase Materials Sciences, Oak Ridge National Laboratory). Comes with an ipython notebook for analysis purposes.

2D materials↗
DOE OSTI2021

Separating Physically Distinct Mechanisms in Complex Infrared Plasmonic Nanostructures via Machine Learning Enhanced Electron Energy Loss Spectroscopy

Electron energy loss spectroscopy (EELS) enables direct exploration of plasmonic phenomena at the nanometer level. To isolate individual plasmon modes, linear unmixing methods can be used to separate different physical mechanisms, but in larger and more complex systems the interpretability of the components becomes uncertain. Here, infrared plasmonic resonances in self-assembled heterogeneous monolayer films of doped-semiconductor nanoparticles are examined beyond linear unmixing techniques, and both supervised and unsupervised machine-learning-based analyses of hyperspectral EELS datasets are demonstrated. Additionally, in the supervised approach, a human operator labels a small number of pixels in the hyperspectral dataset corresponding to features of interest which are then propagated across the entire dataset. In the unsupervised approach, non-linear autoencoders are used to create a highly-reduced latent-space representation of the dataset, within which insight into the relevant physics can be gleaned from straightforward distance metrics that do not depend on operator input and bias. The advantage of these approaches is that the labeling separates physical mechanisms without altering the data, enabling robust analyses of the influence of heterogeneities in mesoscale complex systems.

36 MATERIALS SCIENCE↗