Michael Pekala

Edward W. Staley, Tom Arbaugh, Michael Pekala et al.

Modern generative machine learning (ML) models can propose novel inorganic crystalline materials with targeted properties; however, synthesis planning of these materials remains difficult due to the complexity of the associated physical processes and limited availability of computational tools. We introduce a novel hybrid framework to evaluate Large Language Models (LLMs) in inorganic synthesis planning by combining thermodynamic databases with simplified kinetics models to approximate realistic synthesis conditions. As a case study, we focus on the niobium-oxygen system, which features multiple industrially relevant oxide phases with well-characterized data. In computational simulations, we compare LLM-generated synthesis routes with classical path-planning algorithms, showing that the implicit priors in LLMs can yield more viable strategies. In our evaluation setting, classical search methods serve primarily as a foil rather than a direct competitor. This illustrates the relative complexity of the problem and highlights where the LLM's implicit priors add value.

Alexander New, Michael Pekala, Elizabeth A. Pogue et al.

Generative machine learning models can use data generated by scientific modeling to create large quantities of novel material structures. Here, we assess how one state-of-the-art generative model, the physics-guided crystal generation model (PGCGM), can be used as part of the inverse design process. We show that the default PGCGM's input space is not smooth with respect to parameter variation, making material optimization difficult and limited. We also demonstrate that most generated structures are predicted to be thermodynamically unstable by a separate property-prediction model, partially due to out-of-domain data challenges. Our findings suggest how generative models might be improved to enable better inverse design.

Brittany V. Lancellotti, Jordan M. Malof, Aaron Davitt et al.

Global greenhouse gas emissions estimates are essential for monitoring and mitigation planning. Yet most datasets lack one or more characteristics that enhance their actionability, such as accuracy, global coverage, high spatial and temporal resolution, and frequent updates. To address these gaps, we present Climate TRACE (climatetrace.org), an open-access platform delivering global emissions estimates with enhanced detail, coverage, and timeliness. Climate TRACE synthesizes existing emissions data, prioritizing accuracy, coverage, and resolution, and fills gaps using sector-specific estimation approaches. The dataset is the first to provide globally comprehensive emissions estimates for individual sources (e.g., individual power plants) for all anthropogenic emitting sectors. The dataset spans January 1, 2021, to the present, with a two-month reporting lag and monthly updates. The open-access platform enables non-technical audiences to engage with detailed emissions datasets for most subnational governments worldwide. Climate TRACE supports data-driven climate action at scales where decisions are made, representing a major breakthrough for emissions accounting and mitigation.

Michael Pekala, Gregory Canal, Samuel Barham et al.

A key factor for lunar mission planning is the ability to assess the local availability of raw materials. However, many potentially relevant measurements are scattered across a variety of scientific publications. In this paper we consider the viability of obtaining lunar composition data by leveraging LLMs to rapidly process a corpus of scientific publications. While leveraging LLMs to obtain knowledge from scientific documents is not new, this particular application presents interesting challenges due to the heterogeneity of lunar samples and the nuances involved in their characterization. Accuracy and uncertainty quantification are particularly crucial since many materials properties can be sensitive to small variations in composition. Our findings indicate that off-the-shelf LLMs are generally effective at extracting data from tables commonly found in these documents. However, there remains opportunity to further refine the data we extract in this initial approach; in particular, to capture fine-grained mineralogy information and to improve performance on more subtle/complex pieces of information.

Wojciech Czaja, Neil Fendley, Michael Pekala et al.

This paper considers attacks against machine learning algorithms used in remote sensing applications, a domain that presents a suite of challenges that are not fully addressed by current research focused on natural image data such as ImageNet. In particular, we present a new study of adversarial examples in the context of satellite image classification problems. Using a recently curated data set and associated classifier, we provide a preliminary analysis of adversarial examples in settings where the targeted classifier is permitted multiple observations of the same location over time. While our experiments to date are purely digital, our problem setup explicitly incorporates a number of practical considerations that a real-world attacker would need to take into account when mounting a physical attack. We hope this work provides a useful starting point for future studies of potential vulnerabilities in this setting.

William Gray Roncal, Dean M. Kleissas, Joshua T. Vogelstein et al.

Reconstructing a map of neuronal connectivity is a critical challenge in contemporary neuroscience. Recent advances in high-throughput serial section electron microscopy (EM) have produced massive 3D image volumes of nanoscale brain tissue for the first time. The resolution of EM allows for individual neurons and their synaptic connections to be directly observed. Recovering neuronal networks by manually tracing each neuronal process at this scale is unmanageable, and therefore researchers are developing automated image processing modules. Thus far, state-of-the-art algorithms focus only on the solution to a particular task (e.g., neuron segmentation or synapse identification). In this manuscript we present the first fully automated images-to-graphs pipeline (i.e., a pipeline that begins with an imaged volume of neural tissue and produces a brain graph without any human interaction). To evaluate overall performance and select the best parameters and methods, we also develop a metric to assess the quality of the output graphs. We evaluate a set of algorithms and parameters, searching possible operating points to identify the best available brain graph for our assessment metric. Finally, we deploy a reference end-to-end version of the pipeline on a large, publicly available data set. This provides a baseline result and framework for community analysis and future algorithm development and testing. All code and data derivatives have been made publicly available toward eventually unlocking new biofidelic computational primitives and understanding of neuropathologies.

William Gray Roncal, Michael Pekala, Verena Kaynig-Fittkau et al.

An open challenge problem at the forefront of modern neuroscience is to obtain a comprehensive mapping of the neural pathways that underlie human brain function; an enhanced understanding of the wiring diagram of the brain promises to lead to new breakthroughs in diagnosing and treating neurological disorders. Inferring brain structure from image data, such as that obtained via electron microscopy (EM), entails solving the problem of identifying biological structures in large data volumes. Synapses, which are a key communication structure in the brain, are particularly difficult to detect due to their small size and limited contrast. Prior work in automated synapse detection has relied upon time-intensive biological preparations (post-staining, isotropic slice thicknesses) in order to simplify the problem. This paper presents VESICLE, the first known approach designed for mammalian synapse detection in anisotropic, non-post-stained data. Our methods explicitly leverage biological context, and the results exceed existing synapse detection methods in terms of accuracy and scalability. We provide two different approaches - one a deep learning classifier (VESICLE-CNN) and one a lightweight Random Forest approach (VESICLE-RF) to offer alternatives in the performance-scalability space. Addressing this synapse detection challenge enables the analysis of high-throughput imaging data soon expected to reach petabytes of data, and provide tools for more rapid estimation of brain-graphs. Finally, to facilitate community efforts, we developed tools for large-scale object detection, and demonstrated this framework to find $\approx$ 50,000 synapses in 60,000 $μm ^3$ (220 GB on disk) of electron microscopy data.