Optimization of experimental materials synthesis and characterization through active learning methods has been growing over the last decade, with examples ranging from measurements of diffraction on combinatorial alloys at synchrotrons, to searches through chemical space with automated synthesis robots for perovskites. In virtually all cases, the target property of interest for optimization is defined apriori with limited human feedback during operation. In contrast, here we present the development of a new type of human in the loop experimental workflow, via a Bayesian optimized active recommender system (BOARS), to shape targets on the fly, employing human feedback. We showcase examples of this framework applied to pre-acquired piezoresponse force spectroscopy of a ferroelectric thin film, and then implement this in real time on an atomic force microscope, where the optimization proceeds to find symmetric piezoresponse amplitude hysteresis loops. It is found that such features appear more affected by subsurface defects than the local domain structure. This work shows the utility of human-augmented machine learning approaches for curiosity-driven exploration of systems across experimental domains. The analysis reported here is summarized in Colab Notebook for the purpose of tutorial and application to other data: https://github.com/arpanbiswas52/varTBO
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. 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.
Sergei V. Kalinin, Yongtao Liu, Arpan Biswas et al.
Machine learning 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 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. Here, 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 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 towards specific objectives.
Arpan Biswas, Rama Vasudevan, Maxim Ziatdinov et al.
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 regression of complex experimental data. Like other ML problems, VAEs require hyperparameter tuning, e.g., balancing the Kullback Leibler (KL) 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 explored a latent Bayesian optimization (zBO) approach for the hyperparameter trajectory optimization for the unsupervised and semi-supervised ML and demonstrate for joint-VAE with rotational invariances. We demonstrate an application of this method for finding joint discrete and continuous rotationally invariant representations for 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 tuning or trajectory optimization of other ML models.
Sergei V. Kalinin, Rama Vasudevan, Yongtao Liu et al.
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, DALLE 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 exogeneous 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 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 creating a novel set of development targets for the ML community by accelerating both real-world ML applications and scientific progress.
Jawad Chowdhury, Ganesh Narasimha, Jan-Chi Yang et al.
Autonomous experimental systems are increasingly used in materials research to accelerate scientific discovery, but their performance is often limited by low-quality, noisy data. This issue is especially problematic in data-intensive structure-property learning tasks such as Image-to-Spectrum (Im2Spec) and Spectrum-to-Image (Spec2Im) translations, where standard active learning strategies can mistakenly prioritize poor-quality measurements. We introduce a gated active learning framework that combines curiosity-driven sampling with a physics-informed quality control filter based on the Simple Harmonic Oscillator model fits, allowing the system to automatically exclude low-fidelity data during acquisition. Evaluations on a pre-acquired dataset of band-excitation piezoresponse spectroscopy (BEPS) data from PbTiO3 thin films with spatially localized noise show that the proposed method outperforms random sampling, standard active learning, and multitask learning strategies. The gated approach enhances both Im2Spec and Spec2Im by handling noise during training and acquisition, leading to more reliable forward and inverse predictions. In contrast, standard active learners often misinterpret noise as uncertainty and end up acquiring bad samples that hurt performance. Given its promising applicability, we further deployed the framework in real-time experiments on BiFeO3 thin films, demonstrating its effectiveness in real autonomous microscopy experiments. Overall, this work supports a shift toward hybrid autonomy in self-driving labs, where physics-informed quality assessment and active decision-making work hand-in-hand for more reliable discovery.
Boris N. Slautin, Yongtao Liu, Hiroshi Funakubo et al.
Scientific advancement is universally based on the dynamic interplay between theoretical insights, modelling, and experimental discoveries. However, this feedback loop is often slow, including delayed community interactions and the gradual integration of experimental data into theoretical frameworks. This challenge is particularly exacerbated in domains dealing with high-dimensional object spaces, such as molecules and complex microstructures. Hence, the integration of theory within automated and autonomous experimental setups, or theory in the loop automated experiment, is emerging as a crucial objective for accelerating scientific research. The critical aspect is not only to use theory but also on-the-fly theory updates during the experiment. Here, we introduce a method for integrating theory into the loop through Bayesian co-navigation of theoretical model space and experimentation. Our approach leverages the concurrent development of surrogate models for both simulation and experimental domains at the rates determined by latencies and costs of experiments and computation, alongside the adjustment of control parameters within theoretical models to minimize epistemic uncertainty over the experimental object spaces. This methodology facilitates the creation of digital twins of material structures, encompassing both the surrogate model of behavior that includes the correlative part and the theoretical model itself. While demonstrated here within the context of functional responses in ferroelectric materials, our approach holds promise for broader applications, the exploration of optical properties in nanoclusters, microstructure-dependent properties in complex materials, and properties of molecular systems. The analysis code that supports the funding is publicly available at https://github.com/Slautin/2024_Co-navigation/tree/main
Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and multimodal parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, material structure image spaces, and molecular embedding spaces. Often these systems are black-box and time-consuming to evaluate, which resulted in strong interest towards active learning methods such as Bayesian optimization (BO). However, these systems are often noisy which make the black box function severely multi-modal and non-differentiable, where a vanilla BO can get overly focused near a single or faux optimum, deviating from the broader goal of scientific discovery. To address these limitations, here we developed Strategic Autonomous Non-Smooth Exploration (SANE) to facilitate an intelligent Bayesian optimized navigation with a proposed cost-driven probabilistic acquisition function to find multiple global and local optimal regions, avoiding the tendency to becoming trapped in a single optimum. To distinguish between a true and false optimal region due to noisy experimental measurements, a human (domain) knowledge driven dynamic surrogate gate is integrated with SANE. We implemented the gate-SANE into a pre-acquired Piezoresponse spectroscopy data of a ferroelectric combinatorial library with high noise levels in specific regions, and a piezoresponse force microscopy (PFM) hyperspectral data. SANE demonstrated better performance than classical BO to facilitate the exploration of multiple optimal regions and thereby prioritized learning with higher coverage of scientific values in autonomous experiments. Our work showcases the potential application of this method to real-world experiment, where such combined strategic and human intervening approaches can be critical to unlocking new discoveries in autonomous research.
Asraful Haque, Daniel T. Yimam, Jawad Chowdhury et al.
Autonomous laboratories typically rely on data-driven decision-making, occasionally with human-in-the-loop oversight to inject domain expertise. Fully leveraging AI agents, however, requires tightly coupled, collaborative workflows spanning hypothesis generation, experimental planning, execution, and interpretation. To address this, we develop and deploy a human-AI collaborative (HAIC) workflow that integrates large language models for hypothesis generation and analysis, with collaborative policy updates driving autonomous pulsed laser deposition (PLD) experiments for remote epitaxy of BaTiO$_3$/graphene. HAIC accelerated the hypothesis formation and experimental design and efficiently mapped the growth space to graphene-damage. In situ Raman spectroscopy reveals that chemistry drives degradation while the highest energy plume components seed defects, identifying a low-O$_2$ pressure low-temperature synthesis window that preserves graphene but is incompatible with optimal BaTiO$_3$ growth. Thus, we show a two-step Ar/O$_2$ deposition is required to exfoliate ferroelectric BaTiO$_3$ while maintaining a monolayer graphene interlayer. HAIC stages human insight with AI reasoning between autonomous batches to drive rapid scientific progress, providing an evolution to many existing human-in-the-loop autonomous workflows.
Utkarsh Pratiush, Austin Houston, Kamyar Barakati et al.
Microscopy is a primary source of information on materials structure and functionality at nanometer and atomic scales. The data generated is often well-structured, enriched with metadata and sample histories, though not always consistent in detail or format. The adoption of Data Management Plans (DMPs) by major funding agencies promotes preservation and access. However, deriving insights remains difficult due to the lack of standardized code ecosystems, benchmarks, and integration strategies. As a result, data usage is inefficient and analysis time is extensive. In addition to post-acquisition analysis, new APIs from major microscope manufacturers enable real-time, ML-based analytics for automated decision-making and ML-agent-controlled microscope operation. Yet, a gap remains between the ML and microscopy communities, limiting the impact of these methods on physics, materials discovery, and optimization. Hackathons help bridge this divide by fostering collaboration between ML researchers and microscopy experts. They encourage the development of novel solutions that apply ML to microscopy, while preparing a future workforce for instrumentation, materials science, and applied ML. This hackathon produced benchmark datasets and digital twins of microscopes to support community growth and standardized workflows. All related code is available at GitHub: https://github.com/KalininGroup/Mic-hackathon-2024-codes-publication/tree/1.0.0.1
Arpan Biswas, Sai Mani Prudhvi Valleti, Rama Vasudevan et al.
Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and often non-differentiable 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 towards 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 on the system in form of partially known physics laws and often varies exploration policies during the experiment. Here, we explore interactive workflows building on multi-fidelity BO (MFBO), starting with classical (data-driven) MFBO, then structured (physics-driven) sMFBO, and extending it to allow human in the loop interactive iMFBO workflows for adaptive and domain expert aligned exploration. These approaches are demonstrated over highly non-smooth multi-fidelity 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 on-the-fly human decisions for improved exploration, current challenges, and potential opportunities for algorithm development with combining data, physics and real time human decisions.
Ralph Bulanadi, Jawad Chowdhury, Funakubo Hiroshi et al.
Autonomous experiments (AEs) are transforming how scientific research is conducted by integrating artificial intelligence with automated experimental platforms. Current AEs primarily focus on the optimization of a predefined target; while accelerating this goal, such an approach limits the discovery of unexpected or unknown physical phenomena. Here, we introduce a novel framework, INS2ANE (Integrated Novelty Score-Strategic Autonomous Non-Smooth Exploration), to enhance the discovery of novel phenomena in autonomous experimentation. Our method integrates two key components: (1) a novelty scoring system that evaluates the uniqueness of experimental results, and (2) a strategic sampling mechanism that promotes exploration of under-sampled regions even if they appear less promising by conventional criteria. We validate this approach on a pre-acquired dataset with a known ground truth comprising of image-spectral pairs. We further implement the process on autonomous scanning probe microscopy experiments. INS2ANE significantly increases the diversity of explored phenomena in comparison to conventional optimization routines, enhancing the likelihood of discovering previously unobserved phenomena. These results demonstrate the potential for AE to enhance the depth of scientific discovery; in combination with the efficiency provided by AEs, this approach promises to accelerate scientific research by simultaneously navigating complex experimental spaces to uncover new phenomena.
Aditya Vatsavai, Ganesh Narasimha, Yongtao Liu et al.
Rapidly determining structure-property correlations in materials is an important challenge in better understanding fundamental mechanisms and greatly assists in materials design. In microscopy, imaging data provides a direct measurement of the local structure, while spectroscopic measurements provide relevant functional property information. Deep kernel active learning approaches have been utilized to rapidly map local structure to functional properties in microscopy experiments, but are computationally expensive for multi-dimensional and correlated output spaces. Here, we present an alternative lightweight curiosity algorithm which actively samples regions with unexplored structure-property relations, utilizing a deep-learning based surrogate model for error prediction. We show that the algorithm outperforms random sampling for predicting properties from structures, and provides a convenient tool for efficient mapping of structure-property relationships in materials science.
Ganesh Narasimha, Mykola Telychko, Wooin Yang et al.
Manipulating matter with a scanning tunneling microscope (STM) enables creation of atomically defined artificial structures that host designer quantum states. However, the time-consuming nature of the manipulation process, coupled with the sensitivity of the STM tip, constrains the exploration of diverse configurations and limits the size of designed features. In this study, we present a reinforcement learning (RL)-based framework for creating artificial structures by spatially manipulating carbon monoxide (CO) molecules on a copper substrate using the STM tip. The automated workflow combines molecule detection and manipulation, employing deep learning-based object detection to locate CO molecules and linear assignment algorithms to allocate these molecules to designated target sites. We initially perform molecule maneuvering based on randomized parameter sampling for sample bias, tunneling current setpoint and manipulation speed. This dataset is then structured into an action trajectory used to train an RL agent. The model is subsequently deployed on the STM for real-time fine-tuning of manipulation parameters during structure construction. Our approach incorporates path planning protocols coupled with active drift compensation to enable atomically precise fabrication of structures with significantly reduced human input while realizing larger-scale artificial lattices with desired electronic properties. To underpin of efficiency of our approach we demonstrate the automated construction of an extended artificial graphene lattice and confirm the existence of characteristic Dirac point in its electronic structure. Further challenges to RL-based structural assembly scalability are discussed.
Yongtao Liu, Rama K. Vasudevan, Kyle Kelley et al.
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 (BE-PFM) 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.
Sergei V. Kalinin, Maxim A. Ziatdinov, Jacob Hinkle et al.
Machine learning and artificial intelligence (ML/AI) are rapidly becoming an indispensable part of physics research, with domain applications ranging from theory and materials prediction to high-throughput data analysis. In parallel, the recent successes in applying ML/AI methods for autonomous systems from robotics through self-driving cars to organic and inorganic synthesis are generating enthusiasm for the potential of these techniques to enable automated and autonomous experiment (AE) in imaging. Here, we aim to analyze the major pathways towards AE in imaging methods with sequential image formation mechanisms, focusing on scanning probe microscopy (SPM) and (scanning) transmission electron microscopy ((S)TEM). We argue that automated experiments should necessarily be discussed in a broader context of the general domain knowledge that both informs the experiment and is increased as the result of the experiment. As such, this analysis should explore the human and ML/AI roles prior to and during the experiment, and consider the latencies, biases, and knowledge priors of the decision-making process. Similarly, such discussion should include the limitations of the existing imaging systems, including intrinsic latencies, non-idealities and drifts comprising both correctable and stochastic components. We further pose that the role of the AE in microscopy is not the exclusion of human operators (as is the case for autonomous driving), but rather automation of routine operations such as microscope tuning, etc., prior to the experiment, and conversion of low latency decision making processes on the time scale spanning from image acquisition to human-level high-order experiment planning.
Rama K. Vasudevan, Maxim Ziatdinov, Lukas Vlcek et al.
Deep neural networks ("deep learning") have emerged as a technology of choice to tackle problems in natural language processing, computer vision, speech recognition and gameplay, and in just a few years has led to superhuman level performance and ushered in a new wave of "AI." Buoyed by these successes, researchers in the physical sciences have made steady progress in incorporating deep learning into their respective domains. However, such adoption brings substantial challenges that need to be recognized and confronted. Here, we discuss both opportunities and roadblocks to implementation of deep learning within materials science, focusing on the relationship between correlative nature of machine learning and causal hypothesis driven nature of physical sciences. We argue that deep learning and AI are now well positioned to revolutionize fields where causal links are known, as is the case for applications in theory. When confounding factors are frozen or change only weakly, this leaves open the pathway for effective deep learning solutions in experimental domains. Similarly, these methods offer a pathway towards understanding the physics of real-world systems, either via deriving reduced representations, deducing algorithmic complexity, or recovering generative physical models. However, extending deep learning and "AI" for models with unclear causal relationship can produce misleading and potentially incorrect results. Here, we argue the broad adoption of Bayesian methods incorporating prior knowledge, development of DL solutions with incorporated physical constraints, and ultimately adoption of causal models, offers a path forward for fundamental and applied research. Most notably, while these advances can change the way science is carried out in ways we cannot imagine, machine learning is not going to substitute science any time soon.