Dane Morgan

Ni Li, Nuohao Liu, Ryan Jacobs et al.

Analyzing microstructural defects in transmission electron microscopy (TEM) images, particularly in irradiated metal alloys, is often limited by the availability of high-quality, labeled data. To address this, we introduce a generative data augmentation approach using a mask-conditioned latent diffusion model (LDM) for synthesizing realistic TEM images with controllable, automatically labeled multi-class defect masks. Without requiring manual annotations for generation, our method enables the creation of synthetic image-mask pairs by sampling distributions learned from experimental masks. These generated data were used to augment small experimental datasets of varying sizes (10, 50, and 100 labeled experimental images) to train a Mask Regional Convolutional Neural Network (R-CNN) model for defect detection and classification. Our results show that generative augmentation yields small overall model performance improvements, with up to a 0.02 gain in the harmonic mean of detection and classification F1 scores. However, we also find that the relative contributions to detection and classification improvement depend on the specific train/test data split. These findings highlight the potential of targeted generative models to enhance deep learning performance in data-scarce microscopy-based image quantification tasks.

Maciej P. Polak, Dane Morgan

There has been a growing effort to replace manual extraction of data from research papers with automated data extraction based on natural language processing, language models, and recently, large language models (LLMs). Although these methods enable efficient extraction of data from large sets of research papers, they require a significant amount of up-front effort, expertise, and coding. In this work we propose the ChatExtract method that can fully automate very accurate data extraction with minimal initial effort and background, using an advanced conversational LLM. ChatExtract consists of a set of engineered prompts applied to a conversational LLM that both identify sentences with data, extract that data, and assure the data's correctness through a series of follow-up questions. These follow-up questions largely overcome known issues with LLMs providing factually inaccurate responses. ChatExtract can be applied with any conversational LLMs and yields very high quality data extraction. In tests on materials data we find precision and recall both close to 90% from the best conversational LLMs, like ChatGPT-4. We demonstrate that the exceptional performance is enabled by the information retention in a conversational model combined with purposeful redundancy and introducing uncertainty through follow-up prompts. These results suggest that approaches similar to ChatExtract, due to their simplicity, transferability, and accuracy are likely to become powerful tools for data extraction in the near future. Finally, databases for critical cooling rates of metallic glasses and yield strengths of high entropy alloys are developed using ChatExtract.

Ryan Jacobs, Maciej P. Polak, Lane E. Schultz et al.

We demonstrate the ability of large language models (LLMs) to perform material and molecular property regression tasks, a significant deviation from the conventional LLM use case. We benchmark the Large Language Model Meta AI (LLaMA) 3 on several molecular properties in the QM9 dataset and 24 materials properties. Only composition-based input strings are used as the model input and we fine tune on only the generative loss. We broadly find that LLaMA 3, when fine-tuned using the SMILES representation of molecules, provides useful regression results which can rival standard materials property prediction models like random forest or fully connected neural networks on the QM9 dataset. Not surprisingly, LLaMA 3 errors are 5-10x higher than those of the state-of-the-art models that were trained using far more granular representation of molecules (e.g., atom types and their coordinates) for the same task. Interestingly, LLaMA 3 provides improved predictions compared to GPT-3.5 and GPT-4o. This work highlights the versatility of LLMs, suggesting that LLM-like generative models can potentially transcend their traditional applications to tackle complex physical phenomena, thus paving the way for future research and applications in chemistry, materials science and other scientific domains.

Mingren Shen, Dina Sheyfer, Troy David Loeffler et al.

Speckle patterns produced by coherent X-ray have a close relationship with the internal structure of materials but quantitative inversion of the relationship to determine structure from speckle patterns is challenging. Here, we investigate the link between coherent X-ray speckle patterns and sample structures using a model 2D disk system and explore the ability of machine learning to learn aspects of the relationship. Specifically, we train a deep neural network to classify the coherent X-ray speckle patterns according to the disk number density in the corresponding structure. It is demonstrated that the classification system is accurate for both non-disperse and disperse size distributions.

Maciej P. Polak, Shrey Modi, Anna Latosinska et al.

Accurate and comprehensive material databases extracted from research papers are crucial for materials science and engineering, but their development requires significant human effort. With large language models (LLMs) transforming the way humans interact with text, LLMs provide an opportunity to revolutionize data extraction. In this study, we demonstrate a simple and efficient method for extracting materials data from full-text research papers leveraging the capabilities of LLMs combined with human supervision. This approach is particularly suitable for mid-sized databases and requires minimal to no coding or prior knowledge about the extracted property. It offers high recall and nearly perfect precision in the resulting database. The method is easily adaptable to new and superior language models, ensuring continued utility. We show this by evaluating and comparing its performance on GPT-3 and GPT-3.5/4 (which underlie ChatGPT), as well as free alternatives such as BART and DeBERTaV3. We provide a detailed analysis of the method's performance in extracting sentences containing bulk modulus data, achieving up to 90% precision at 96% recall, depending on the amount of human effort involved. We further demonstrate the method's broader effectiveness by developing a database of critical cooling rates for metallic glasses over twice the size of previous human curated databases.

Matthew J. Lynch, Ryan Jacobs, Gabriella Bruno et al.

The integration of machine learning (ML) models enhances the efficiency, affordability, and reliability of feature detection in microscopy, yet their development and applicability are hindered by the dependency on scarce and often flawed manually labeled datasets and a lack of domain awareness. We addressed these challenges by creating a physics-based synthetic image and data generator, resulting in a machine learning model that achieves comparable precision (0.86), recall (0.63), F1 scores (0.71), and engineering property predictions (R2=0.82) to a model trained on human-labeled data. We enhanced both models by using feature prediction confidence scores to derive an image-wide confidence metric, enabling simple thresholding to eliminate ambiguous and out-of-domain images resulting in performance boosts of 5-30% with a filtering-out rate of 25%. Our study demonstrates that synthetic data can eliminate human reliance in ML and provides a means for domain awareness in cases where many feature detections per image are needed.

Quanliang Liu, Maciej P. Polak, So Yeon Kim et al.

Materials design often relies on human-generated hypotheses, a process inherently limited by cognitive constraints such as knowledge gaps and limited ability to integrate and extract knowledge implications, particularly when multidisciplinary expertise is required. This work demonstrates that large language models (LLMs), coupled with prompt engineering, can effectively generate non-trivial materials hypotheses by integrating scientific principles from diverse sources without explicit design guidance by human experts. These include design ideas for high-entropy alloys with superior cryogenic properties and halide solid electrolytes with enhanced ionic conductivity and formability. These design ideas have been experimentally validated in high-impact publications in 2023 not available in the LLM training data, demonstrating the LLM's ability to generate highly valuable and realizable innovative ideas not established in the literature. Our approach primarily leverages materials system charts encoding processing-structure-property relationships, enabling more effective data integration by condensing key information from numerous papers, and evaluation and categorization of numerous hypotheses for human cognition, both through the LLM. This LLM-driven approach opens the door to new avenues of artificial intelligence-driven materials discovery by accelerating design, democratizing innovation, and expanding capabilities beyond the designer's direct knowledge.

Ryan Jacobs, Mingren Shen, Yuhan Liu et al.

In this work, we perform semantic segmentation of multiple defect types in electron microscopy images of irradiated FeCrAl alloys using a deep learning Mask Regional Convolutional Neural Network (Mask R-CNN) model. We conduct an in-depth analysis of key model performance statistics, with a focus on quantities such as predicted distributions of defect shapes, defect sizes, and defect areal densities relevant to informing modeling and understanding of irradiated Fe-based materials properties. To better understand the performance and present limitations of the model, we provide examples of useful evaluation tests which include a suite of random splits, and dataset size-dependent and domain-targeted cross validation tests. Overall, we find that the current model is a fast, effective tool for automatically characterizing and quantifying multiple defect types in microscopy images, with a level of accuracy on par with human domain expert labelers. More specifically, the model can achieve average defect identification F1 scores as high as 0.8, and, based on random cross validation, have low overall average (+/- standard deviation) defect size and density percentage errors of 7.3 (+/- 3.8)% and 12.7 (+/- 5.3)%, respectively. Further, our model predicts the expected material hardening to within 10-20 MPa (about 10% of total hardening), which is about the same error level as experiments. Our targeted evaluation tests also suggest the best path toward improving future models is not expanding existing databases with more labeled images but instead data additions that target weak points of the model domain, such as images from different microscopes, imaging conditions, irradiation environments, and alloy types. Finally, we discuss the first phase of an effort to provide an easy-to-use, open-source object detection tool to the broader community for identifying defects in new images.

Nick Lawrence, Mingren Shen, Ruiqi Yin et al.

The use of accurate scanning transmission electron microscopy (STEM) image simulation methods require large computation times that can make their use infeasible for the simulation of many images. Other simulation methods based on linear imaging models, such as the convolution method, are much faster but are too inaccurate to be used in application. In this paper, we explore deep learning models that attempt to translate a STEM image produced by the convolution method to a prediction of the high accuracy multislice image. We then compare our results to those of regression methods. We find that using the deep learning model Generative Adversarial Network (GAN) provides us with the best results and performs at a similar accuracy level to previous regression models on the same dataset. Codes and data for this project can be found in this GitHub repository, https://github.com/uw-cmg/GAN-STEM-Conv2MultiSlice.

Ryan Jacobs, Dane Morgan, Siamak Attarian et al.

The rapid development and large body of literature on machine learning interatomic potentials (MLIPs) can make it difficult to know how to proceed for researchers who are not experts but wish to use these tools. The spirit of this review is to help such researchers by serving as a practical, accessible guide to the state-of-the-art in MLIPs. This review paper covers a broad range of topics related to MLIPs, including (i) central aspects of how and why MLIPs are enablers of many exciting advancements in molecular modeling, (ii) the main underpinnings of different types of MLIPs, including their basic structure and formalism, (iii) the potentially transformative impact of universal MLIPs for both organic and inorganic systems, including an overview of the most recent advances, capabilities, downsides, and potential applications of this nascent class of MLIPs, (iv) a practical guide for estimating and understanding the execution speed of MLIPs, including guidance for users based on hardware availability, type of MLIP used, and prospective simulation size and time, (v) a manual for what MLIP a user should choose for a given application by considering hardware resources, speed requirements, energy and force accuracy requirements, as well as guidance for choosing pre-trained potentials or fitting a new potential from scratch, (vi) discussion around MLIP infrastructure, including sources of training data, pre-trained potentials, and hardware resources for training, (vii) summary of some key limitations of present MLIPs and current approaches to mitigate such limitations, including methods of including long-range interactions, handling magnetic systems, and treatment of excited states, and finally (viii) we finish with some more speculative thoughts on what the future holds for the development and application of MLIPs over the next 3-10+ years.

Maciej P. Polak, Dane Morgan

Automated data extraction from research texts has been steadily improving, with the emergence of large language models (LLMs) accelerating progress even further. Extracting data from plots in research papers, however, has been such a complex task that it has predominantly been confined to manual data extraction. We show that current multimodal large language models, with proper instructions and engineered workflows, are capable of accurately extracting data from plots. This capability is inherent to the pretrained models and can be achieved with a chain-of-thought sequence of zero-shot engineered prompts we call PlotExtract, without the need to fine-tune. We demonstrate PlotExtract here and assess its performance on synthetic and published plots. We consider only plots with two axes in this analysis. For plots identified as extractable, PlotExtract finds points with over 90% precision (and around 90% recall) and errors in x and y position of around 5% or lower. These results prove that multimodal LLMs are a viable path for high-throughput data extraction for plots and in many circumstances can replace the current manual methods of data extraction.

Vidit Agrawal, Shixin Zhang, Lane E. Schultz et al.

Ensemble models can be used to estimate prediction uncertainties in machine learning models. However, an ensemble of N models is approximately N times more computationally demanding compared to a single model when it is used for inference. In this work, we explore fitting a single model to predicted ensemble error bar data, which allows us to estimate uncertainties without the need for a full ensemble. Our approach is based on three models: Model A for predictive accuracy, Model $A_{E}$ for traditional ensemble-based error bar prediction, and Model B, fit to data from Model $A_{E}$, to be used for predicting the values of $A_{E}$ but with only one model evaluation. Model B leverages synthetic data augmentation to estimate error bars efficiently. This approach offers a highly flexible method of uncertainty quantification that can approximate that of ensemble methods but only requires a single extra model evaluation over Model A during inference. We assess this approach on a set of problems in materials science.

Ni Li, Ryan Jacobs, Matthew Lynch et al.

Quantifying prediction uncertainty when applying object detection models to new, unlabeled datasets is critical in applied machine learning. This study introduces an approach to estimate the performance of deep learning-based object detection models for quantifying defects in transmission electron microscopy (TEM) images, focusing on detecting irradiation-induced cavities in TEM images of metal alloys. We developed a random forest regression model that predicts the object detection F1 score, a statistical metric used to evaluate the ability to accurately locate and classify objects of interest. The random forest model uses features extracted from the predictions of the object detection model whose uncertainty is being quantified, enabling fast prediction on new, unlabeled images. The mean absolute error (MAE) for predicting F1 of the trained model on test data is 0.09, and the $R^2$ score is 0.77, indicating there is a significant correlation between the random forest regression model predicted and true defect detection F1 scores. The approach is shown to be robust across three distinct TEM image datasets with varying imaging and material domains. Our approach enables users to estimate the reliability of a defect detection and segmentation model predictions and assess the applicability of the model to their specific datasets, providing valuable information about possible domain shifts and whether the model needs to be fine-tuned or trained on additional data to be maximally effective for the desired use case.

Mingren Shen, Guanzhao Li, Dongxia Wu et al.

Electron microscopy is widely used to explore defects in crystal structures, but human detecting of defects is often time-consuming, error-prone, and unreliable, and is not scalable to large numbers of images or real-time analysis. In this work, we discuss the application of machine learning approaches to find the location and geometry of different defect clusters in irradiated steels. We show that a deep learning based Faster R-CNN analysis system has a performance comparable to human analysis with relatively small training data sets. This study proves the promising ability to apply deep learning to assist the development of automated microscopy data analysis even when multiple features are present and paves the way for fast, scalable, and reliable analysis systems for massive amounts of modern electron microscopy data.

Mingren Shen, Guanzhao Li, Dongxia Wu et al.

Videos captured using Transmission Electron Microscopy (TEM) can encode details regarding the morphological and temporal evolution of a material by taking snapshots of the microstructure sequentially. However, manual analysis of such video is tedious, error-prone, unreliable, and prohibitively time-consuming if one wishes to analyze a significant fraction of frames for even videos of modest length. In this work, we developed an automated TEM video analysis system for microstructural features based on the advanced object detection model called YOLO and tested the system on an in-situ ion irradiation TEM video of dislocation loops formed in a FeCrAl alloy. The system provides analysis of features observed in TEM including both static and dynamic properties using the YOLO-based defect detection module coupled to a geometry analysis module and a dynamic tracking module. Results show that the system can achieve human comparable performance with an F1 score of 0.89 for fast, consistent, and scalable frame-level defect analysis. This result is obtained on a real but exceptionally clean and stable data set and more challenging data sets may not achieve this performance. The dynamic tracking also enabled evaluation of individual defect evolution like per defect growth rate at a fidelity never before achieved using common human analysis methods. Our work shows that automatically detecting and tracking interesting microstructures and properties contained in TEM videos is viable and opens new doors for evaluating materials dynamics.

Xiaoyu Sun, Nathaniel J. Krakauer, Alexander Politowicz et al.

Flash points of organic molecules play an important role in preventing flammability hazards and large databases of measured values exist, although millions of compounds remain unmeasured. To rapidly extend existing data to new compounds many researchers have used quantitative structure-property relationship (QSPR) analysis to effectively predict flash points. In recent years graph-based deep learning (GBDL) has emerged as a powerful alternative method to traditional QSPR. In this paper, GBDL models were implemented in predicting flash point for the first time. We assessed the performance of two GBDL models, message-passing neural network (MPNN) and graph convolutional neural network (GCNN), by comparing methods. Our result shows that MPNN both outperforms GCNN and yields slightly worse but comparable performance with previous QSPR studies. The average R2 and Mean Absolute Error (MAE) scores of MPNN are, respectively, 2.3% lower and 2.0 K higher than previous comparable studies. To further explore GBDL models, we collected the largest flash point dataset to date, which contains 10575 unique molecules. The optimized MPNN gives a test data R2 of 0.803 and MAE of 17.8 K on the complete dataset. We also extracted 5 datasets from our integrated dataset based on molecular types (acids, organometallics, organogermaniums, organosilicons, and organotins) and explore the quality of the model in these classes.against 12 previous QSPR studies using more traditional