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Akers, Sarah

Publications and source records attributed to Akers, Sarah.

Identifying Sample Provenance From SEM/EDS Automated Particle Analysis via Few-Shot Learning Coupled With Similarity Graph Clustering

Automated particle analysis (APA) provides a vast amount of compositional data via energy-dispersive X-ray spectroscopy along with size and shape data via scanning electron microscopy for individual particles in a sample. In many instances, APA data are leveraged to support identification of the source of a sample based on the detection of particles of a specific composition. Often, the particles that provide context make up a minuscule portion of the sample. Additionally, the interpretation of complex samples can be difficult due to the diversity of compositions both in the mixture and within a particle. In this work, we demonstrate a method to compute and cluster similarity graphs that describe inter-particle relationships within a sample using a multi-modal few-shot learning neural network. Here, as a proof-of-concept, we show that samples known to have been exposed to gunshot residue can be distinguished from samples occasionally mistaken for gunshot residue. Our workflow builds upon standard APA techniques and data processing methods to unveil additional information in a readily interpretable and quantitatively comparable format.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

GraphEM

An unsupervised segmentation method for structural analysis of Scanning Transmission Electron Microscopy (STEM) images

Pope, Jenna↗

Fine-tuning TrailMap: The utility of transfer learning to improve the performance of deep learning in axon segmentation of light-sheet microscopy images

Light-sheet microscopy has made possible the 3D imaging of both fixed and live biological tissue, with samples as large as the entire mouse brain. However, segmentation and quantification of that data remains a time-consuming manual undertaking. Machine learning methods promise the possibility of automating this process. This study seeks to advance the performance of prior models through optimizing transfer learning. We fine-tuned the existing TrailMap model using expert-labeled data from noradrenergic axonal structures in the mouse brain. By changing the cross-entropy weights and using augmentation, we demonstrate a generally improved adjusted F1-score over using the originally trained TrailMap model within our test datasets.

97 MATHEMATICS AND COMPUTING↗

Classifying metal‐binding sites with neural networks

Abstract To advance our ability to predict impacts of the protein scaffold on catalysis, robust classification schemes to define features of proteins that will influence reactivity are needed. One of these features is a protein's metal‐binding ability, as metals are critical to catalytic conversion by metalloenzymes. As a step toward realizing this goal, we used convolutional neural networks (CNNs) to enable the classification of a metal cofactor binding pocket within a protein scaffold. CNNs enable images to be classified based on multiple levels of detail in the image, from edges and corners to entire objects, and can provide rapid classification. First, six CNN models were fine‐tuned to classify the 20 standard amino acids to choose a performant model for amino acid classification. This model was then trained in two parallel efforts: to classify a 2D image of the environment within a given radius of the central metal binding site, either an Fe ion or a [2Fe‐2S] cofactor, with the metal visible (effort 1) or the metal hidden (effort 2). We further used two sub‐classifications of the [2Fe‐2S] cofactor: (1) a standard [2Fe‐2S] cofactor and (2) a Rieske [2Fe‐2S] cofactor. The accuracy for the model correctly identifying all three defined features was >95%, despite our perception of the increased challenge of the metalloenzyme identification. This demonstrates that machine learning methodology to classify and distinguish similar metal‐binding sites, even in the absence of a visible cofactor, is indeed possible and offers an additional tool for metal‐binding site identification in proteins.

59 BASIC BIOLOGICAL SCIENCES↗

pnnl/Multimodal-Few-Shot

This project combines few-shot machine learning with a multimodal framework for electron microscope data quantification.

Doty, Christina↗

pnnl/EELSTM

EELSTM: Time Series Prediction on Electron Energy Loss Spectra - long short-term memory model approach to forecasting of electron energy loss spectroscopy, based on a Bayesian deep learning model

Doty, Christina↗