Alert button
Picture for Maxim A. Ziatdinov

Maxim A. Ziatdinov

Alert button

A dynamic Bayesian optimized active recommender system for curiosity-driven Human-in-the-loop automated experiments

Apr 05, 2023
Arpan Biswas, Yongtao Liu, Nicole Creange, Yu-Chen Liu, Stephen Jesse, Jan-Chi Yang, Sergei V. Kalinin, Maxim A. Ziatdinov, Rama K. Vasudevan

Figure 1 for A dynamic Bayesian optimized active recommender system for curiosity-driven Human-in-the-loop automated experiments
Figure 2 for A dynamic Bayesian optimized active recommender system for curiosity-driven Human-in-the-loop automated experiments
Figure 3 for A dynamic Bayesian optimized active recommender system for curiosity-driven Human-in-the-loop automated experiments
Figure 4 for A dynamic Bayesian optimized active recommender system for curiosity-driven Human-in-the-loop automated experiments

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

* 7 figures in main text, 3 figures in Supp Material 
Viaarxiv icon

Deep Learning for Automated Experimentation in Scanning Transmission Electron Microscopy

Apr 04, 2023
Sergei V. Kalinin, Debangshu Mukherjee, Kevin M. Roccapriore, Ben Blaiszik, Ayana Ghosh, Maxim A. Ziatdinov, A. Al-Najjar, Christina Doty, Sarah Akers, Nageswara S. Rao, Joshua C. Agar, Steven R. Spurgeon

Figure 1 for Deep Learning for Automated Experimentation in Scanning Transmission Electron Microscopy
Figure 2 for Deep Learning for Automated Experimentation in Scanning Transmission Electron Microscopy
Figure 3 for Deep Learning for Automated Experimentation in Scanning Transmission Electron Microscopy
Figure 4 for Deep Learning for Automated Experimentation in Scanning Transmission Electron Microscopy

Machine learning (ML) has become critical for post-acquisition data analysis in (scanning) transmission electron microscopy, (S)TEM, imaging and spectroscopy. An emerging trend is the transition to real-time analysis and closed-loop microscope operation. The effective use of ML in electron microscopy now requires the development of strategies for microscopy-centered experiment workflow design and optimization. Here, we discuss the associated challenges with the transition to active ML, including sequential data analysis and out-of-distribution drift effects, the requirements for the edge operation, local and cloud data storage, and theory in the loop operations. Specifically, we discuss the relative contributions of human scientists and ML agents in the ideation, orchestration, and execution of experimental workflows and the need to develop universal hyper languages that can apply across multiple platforms. These considerations will collectively inform the operationalization of ML in next-generation experimentation.

* Review Article 
Viaarxiv icon

Deep Kernel Methods Learn Better: From Cards to Process Optimization

Mar 25, 2023
Mani Valleti, Rama k. Vasudevan, Maxim A. Ziatdinov, Sergei V. Kalinin

Figure 1 for Deep Kernel Methods Learn Better: From Cards to Process Optimization
Figure 2 for Deep Kernel Methods Learn Better: From Cards to Process Optimization
Figure 3 for Deep Kernel Methods Learn Better: From Cards to Process Optimization
Figure 4 for Deep Kernel Methods Learn Better: From Cards to Process Optimization

The ability of deep learning methods to perform classification and regression tasks relies heavily on their capacity to uncover manifolds in high-dimensional data spaces and project them into low-dimensional representation spaces. In this study, we investigate the structure and character of the manifolds generated by classical variational autoencoder (VAE) approaches and deep kernel learning (DKL). In the former case, the structure of the latent space is determined by the properties of the input data alone, while in the latter, the latent manifold forms as a result of an active learning process that balances the data distribution and target functionalities. We show that DKL with active learning can produce a more compact and smooth latent space which is more conducive to optimization compared to previously reported methods, such as the VAE. We demonstrate this behavior using a simple cards data set and extend it to the optimization of domain-generated trajectories in physical systems. Our findings suggest that latent manifolds constructed through active learning have a more beneficial structure for optimization problems, especially in feature-rich target-poor scenarios that are common in domain sciences, such as materials synthesis, energy storage, and molecular discovery. The jupyter notebooks that encapsulate the complete analysis accompany the article.

* 8 Figures, 26 pages 
Viaarxiv icon

Roadmap on Deep Learning for Microscopy

Mar 07, 2023
Giovanni Volpe, Carolina Wählby, Lei Tian, Michael Hecht, Artur Yakimovich, Kristina Monakhova, Laura Waller, Ivo F. Sbalzarini, Christopher A. Metzler, Mingyang Xie, Kevin Zhang, Isaac C. D. Lenton, Halina Rubinsztein-Dunlop, Daniel Brunner, Bijie Bai, Aydogan Ozcan, Daniel Midtvedt, Hao Wang, Nataša Sladoje, Joakim Lindblad, Jason T. Smith, Marien Ochoa, Margarida Barroso, Xavier Intes, Tong Qiu, Li-Yu Yu, Sixian You, Yongtao Liu, Maxim A. Ziatdinov, Sergei V. Kalinin, Arlo Sheridan, Uri Manor, Elias Nehme, Ofri Goldenberg, Yoav Shechtman, Henrik K. Moberg, Christoph Langhammer, Barbora Špačková, Saga Helgadottir, Benjamin Midtvedt, Aykut Argun, Tobias Thalheim, Frank Cichos, Stefano Bo, Lars Hubatsch, Jesus Pineda, Carlo Manzo, Harshith Bachimanchi, Erik Selander, Antoni Homs-Corbera, Martin Fränzl, Kevin de Haan, Yair Rivenson, Zofia Korczak, Caroline Beck Adiels, Mite Mijalkov, Dániel Veréb, Yu-Wei Chang, Joana B. Pereira, Damian Matuszewski, Gustaf Kylberg, Ida-Maria Sintorn, Juan C. Caicedo, Beth A Cimini, Muyinatu A. Lediju Bell, Bruno M. Saraiva, Guillaume Jacquemet, Ricardo Henriques, Wei Ouyang, Trang Le, Estibaliz Gómez-de-Mariscal, Daniel Sage, Arrate Muñoz-Barrutia, Ebba Josefson Lindqvist, Johanna Bergman

Figure 1 for Roadmap on Deep Learning for Microscopy
Figure 2 for Roadmap on Deep Learning for Microscopy
Figure 3 for Roadmap on Deep Learning for Microscopy
Figure 4 for Roadmap on Deep Learning for Microscopy

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.

Viaarxiv icon

Discovery of structure-property relations for molecules via hypothesis-driven active learning over the chemical space

Jan 06, 2023
Ayana Ghosh, Sergei V. Kalinin, Maxim A. Ziatdinov

Figure 1 for Discovery of structure-property relations for molecules via hypothesis-driven active learning over the chemical space
Figure 2 for Discovery of structure-property relations for molecules via hypothesis-driven active learning over the chemical space
Figure 3 for Discovery of structure-property relations for molecules via hypothesis-driven active learning over the chemical space
Figure 4 for Discovery of structure-property relations for molecules via hypothesis-driven active learning over the chemical space

Discovery of the molecular candidates for applications in drug targets, biomolecular systems, catalysts, photovoltaics, organic electronics, and batteries, necessitates development of machine learning algorithms capable of rapid exploration of the chemical spaces targeting the desired functionalities. Here we introduce a novel approach for the active learning over the chemical spaces based on hypothesis learning. We construct the hypotheses on the possible relationships between structures and functionalities of interest based on a small subset of data and introduce them as (probabilistic) mean functions for the Gaussian process. This approach combines the elements from the symbolic regression methods such as SISSO and active learning into a single framework. Here, we demonstrate it for the QM9 dataset, but it can be applied more broadly to datasets from both domains of molecular and solid-state materials sciences.

Viaarxiv icon

Automated and Autonomous Experiment in Electron and Scanning Probe Microscopy

Mar 22, 2021
Sergei V. Kalinin, Maxim A. Ziatdinov, Jacob Hinkle, Stephen Jesse, Ayana Ghosh, Kyle P. Kelley, Andrew R. Lupini, Bobby G. Sumpter, Rama K. Vasudevan

Figure 1 for Automated and Autonomous Experiment in Electron and Scanning Probe Microscopy
Figure 2 for Automated and Autonomous Experiment in Electron and Scanning Probe Microscopy
Figure 3 for Automated and Autonomous Experiment in Electron and Scanning Probe Microscopy
Figure 4 for Automated and Autonomous Experiment in Electron and Scanning Probe Microscopy

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.

Viaarxiv icon