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All sources NASA NTRS DOE OSTI

DOE OSTI2024

Pulse shape discrimination technique for diffuse supernova neutrino background search with JUNO

Pulse shape discrimination (PSD) is widely used in particle and nuclear physics. Specifically in liquid scintillator detectors, PSD facilitates the classification of different particle types based on their energy deposition patterns. This technique is particularly valuable for studies of the diffuse supernova neutrino background (DSNB), nucleon decay, and dark matter searches. This paper presents a detailed investigation of the PSD technique, applied in the DSNB search performed with the Jiangmen Underground Neutrino Observatory (JUNO). Instead of using conventional cut-and-count methods, we employ methods based on boosted decision trees and neural networks and compare their capability to distinguish the DSNB signals from the atmospheric neutrino neutral-current background events. The two methods demonstrate comparable performance, resulting in a 50–80% improvement in signal efficiency compared to a previous study performed for JUNO (An et al. [JUNO] in J Phys G 43(3):030401, 2016). Moreover, we study the dependence of the PSD performance on the visible energy and final state composition of the events and find a significant dependence on the presence/absence of 11 C. Finally, we evaluate the impact of the detector effects (photon propagation, PMT dark noise, and waveform reconstruction) on the PSD performance.

FOS: Physical sciences↗

DOE OSTI2025

Reconstruction and identification of pairs of collimated τ-leptons decaying hadronically using s=13 TeV pp collision data with the ATLAS detector

This paper describes an algorithm for reconstructing and identifying a highly collimated hadronically decaying τ$$\tau $$-lepton pair with low transverse momentum. When two τ$$\tau $$-leptons are highly collimated, their visible decay products might overlap, degrading the reconstruction performance for each of the τ$$\tau $$-leptons. A dedicated treatment attempting to tag the τ$$\tau $$-lepton pair as a single object is required. The reconstruction algorithm is based on a large radius jet and its associated two leading subjets, and the identification uses a boosted decision tree to discriminate between signatures from τ+τ-$$\tau ^+\tau ^-$$ systems and those arising from QCD jets. The efficiency of the identification algorithm is measured in Zγ$$Z\gamma $$ events using proton–proton collision data at s=13$$\sqrt{s}=13$$ TeV collected by the ATLAS experiment at the Large Hadron Collider between 2015 and 2018, corresponding to an integrated luminosity of 139fb-1$$139\,\text{ fb}^{-1}$$. The resulting data-to-simulation scale factors are close to unity with uncertainties ranging from 26 to 37%.

Aad, G↗

DOE OSTI2022

Measuring the electron Yukawa coupling via resonant s-channel Higgs production at FCC-ee

The Future Circular Collider (FCC-ee) offers the unique opportunity of studying the Higgs Yukawa coupling to the electron, $y_\mathrm {e}$ , via resonant s -channel production, $\mathrm {e^+e^-}\rightarrow \mathrm {H}$ , in a dedicated run at $\sqrt{s} = m_\mathrm {H}$ . The signature for direct Higgs production is a small rise in the cross sections for particular final states, consistent with Higgs decays, over the expectations for their occurrence due to Standard Model (SM) background processes involving $\mathrm {Z}^*$ , $\gamma ^*$ , or t -channel exchanges alone. Performing such a measurement is remarkably challenging for four main reasons. First, the low value of the e $^\pm $ mass leads to a tiny $y_\mathrm {e}$ coupling and correspondingly small cross section: $\sigma _\mathrm {ee\rightarrow H} \propto m_\mathrm {e}^2 = 0.57$ fb accounting for initial-state $\gamma $ radiation. Second, the $\mathrm {e^+e^-}$ beams must be monochromatized such that the spread of their centre-of-mass (c.m.) energy is commensurate with the narrow width of the SM Higgs boson, $\varGamma _\mathrm {H} = 4.1$ MeV, while keeping large beam luminosities. Third, the Higgs mass must also be known beforehand with a few-MeV accuracy in order to operate the collider at the resonance peak, $\sqrt{s} = m_\mathrm {H}$ . Last but not least, the cross sections of the background processes are many orders-of-magnitude larger than those of the Higgs decay signals. A preliminary generator-level study of 11 Higgs decay channels using a multivariate analysis, which exploits boosted decision trees to discriminate signal and background events, identifies two final states as the most promising ones in terms of statistical significance: $\mathrm {H}\rightarrow gg$ and $\mathrm {H}\rightarrow \mathrm {W}\mathrm {W}^*\!\rightarrow \ell \nu $ + 2 jets. For a benchmark monochromatization with 4.1-MeV c.m. energy spread (leading to $\sigma _\mathrm {ee\rightarrow H} = 0.28$ fb) and 10 ab $^{-1}$ of integrated luminosity, a $1.3\sigma $ signal significance can be reached, corresponding to an upper limit on the e $^\pm $ Yukawa coupling at 1.6 times the SM value: |y e | < 1.6|y e SM | at 95% confidence level, per FCC-ee interaction point per year. Directions for future improvements of the study are outlined.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Machine learning-based analysis of COVID-19 pandemic impact on US research networks

Here in this study we explore how fallout from the changing public health policy around COVID-19 has changed how researchers access and process their science experiments. Using a combination of techniques from statistical analysis and machine learning, we conduct a retrospective analysis of historical network data for a period around the stay-at-home orders that took place in March 2020. Our analysis takes data from the entire ESnet infrastructure to explore DOE high-performance computing (HPC) resources at OLCF, ALCF, and NERSC, as well as User sites such as PNNL and JLAB. We look at detecting and quantifying changes in site activity using a combination of t-Distributed Stochastic Neighbor Embedding (t-SNE) and decision tree analysis. Our findings bring insights into the working patterns and impact on data volume movements, particularly during late-night hours and weekends.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Accelerating FEM-Based Corrosion Predictions Using Machine Learning

Atmospheric corrosion of metallic parts is a widespread materials degradation phenomena that is challenging to predict given its dependence on many factors (e.g. environmental, physiochemical, and part geometry). For materials with long expected service lives, accurately predicting the degree to which corrosion will degrade part performance is especially difficult due to the stochastic nature of corrosion damage spread across years or decades of service. The Finite Element Method (FEM) is a computational technique capable of providing accurate estimates of corrosion rate by numerically solving complex differential Eqs. characterizing this phenomena. Nevertheless, given the iterative nature of FEM and the computational expense required to solve these complex equations, FEM is ill-equipped for an efficient exploration of the design space to identify factors that accelerate or deter corrosion, despite its accuracy. In this work, a machine learning based surrogate model capable of providing accurate predictions of corrosion with significant computational savings is introduced. Specifically, this work leverages AdaBoosted Decision trees to provide an accurate estimate of corrosion current per width given different values of temperature, water layer thickness, molarity of the solution, and the length of the cathode for a galvanic couple of aluminum and stainless steel.

36 MATERIALS SCIENCE↗

DOE OSTI2022

IViz-OT (Intrusion Detection Visualizer for Operational Technology Network) [SWR-22-63]

The Visualizer dashboard provides grid operator highly-trusted alarming environment for an ongoing or potential cyber-attack based on system anomalies and network-based verification. Once anomalies are detected by the IDS tool (HIDES, NREL SWR-19-65), this platform stores the signatures or alert logs that are generated by the intrusion detector, lays out the detailed summary of the possible alerts, and maps these attacks with high-level scenarios. These scenarios are later combined to define a final event using a decision tree approach and a final report is generated out of this tool for further forensic analysis. It also supports authentication and authorization to support roles-based access control (RBAC) for users and a group of people.

Singh, Vivek Kumar↗

DOE OSTI2025

Decayheatml

This code is designed to predict and analyze the decay heat generated in molten salt reactors (MSRs) using a hybrid approach that combines machine learning and segmented polynomial fitting. The accurate prediction of decay heat is essential for reactor safety and the optimization of spent fuel storage. The code operates through several key components: 1) Data Architecture: It incorporates a modular data architecture that handles various MSR-specific operational parameters such as power density, humidity content, and air ingress. These parameters are sampled using Sobol sequences to ensure comprehensive coverage of operational uncertainties. 2) Machine Learning Framework: The code employs a diverse set of machine learning models, including polynomial regression, decision trees, random forests, gradient boosting, support vector regression, k-nearest neighbors, multi-layer perceptrons, and symbolic regression. These models are trained to predict decay heat over a wide temporal range, from immediate shutdown up to 10,000 years. 3) Region-Optimized Training: The temporal domain is divided into multiple regions, each modeled separately to capture distinct decay heat characteristics across different time scales. This approach significantly improves the accuracy and interpretability of predictions. 4) Segmented Polynomial Interpretation (SPI): The SPI method translates machine learning predictions into piecewise polynomial equations. These equations are physically interpretable and can be directly integrated into existing engineering workflows and safety analyses. 5) Front-End Interfaces: The code includes both a Jupyter notebook interface for research development and a Streamlit web application for operational deployment. These interfaces allow users to interactively explore decay heat predictions, adjust operational parameters, and visualize results in real-time. 6) Applications: The framework supports various applications, including safety system validation and spent fuel container optimization. It enables real-time evaluation of worst-case decay heat scenarios, informing the design of passive safety systems and optimizing container designs for long-term storage. Overall, this code provides a robust, accurate, and user-friendly tool for predicting decay heat in MSRs, enhancing reactor safety, and optimizing spent fuel management.

Retamales, Mauricio Eduardo Tano [Idaho National L↗

DOE OSTI2021

Learning curves for drug response prediction in cancer cell lines

Motivated by the size and availability of cell line drug sensitivity data, researchers have been developing machine learning (ML) models for predicting drug response to advance cancer treatment. As drug sensitivity studies continue generating drug response data, a common question is whether the generalization performance of existing prediction models can be further improved with more training data. We utilize empirical learning curves for evaluating and comparing the data scaling properties of two neural networks (NNs) and two gradient boosting decision tree (GBDT) models trained on four cell line drug screening datasets. The learning curves are accurately fitted to a power law model, providing a framework for assessing the data scaling behavior of these models. The curves demonstrate that no single model dominates in terms of prediction performance across all datasets and training sizes, thus suggesting that the actual shape of these curves depends on the unique pair of an ML model and a dataset. The multi-input NN (mNN), in which gene expressions of cancer cells and molecular drug descriptors are input into separate subnetworks, outperforms a single-input NN (sNN), where the cell and drug features are concatenated for the input layer. In contrast, a GBDT with hyperparameter tuning exhibits superior performance as compared with both NNs at the lower range of training set sizes for two of the tested datasets, whereas the mNN consistently performs better at the higher range of training sizes. Moreover, the trajectory of the curves suggests that increasing the sample size is expected to further improve prediction scores of both NNs. These observations demonstrate the benefit of using learning curves to evaluate prediction models, providing a broader perspective on the overall data scaling characteristics. A fitted power law learning curve provides a forward-looking metric for analyzing prediction performance and can serve as a co-design tool to guide experimental biologists and computational scientists in the design of future experiments in prospective research studies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Human limits in machine learning: prediction of potato yield and disease using soil microbiome data

Abstract Background The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide one of the first comprehensive investigations into the predictive potential of machine learning models for understanding the connections between soil and biological phenotypes. We investigate an integrative framework performing accurate machine learning-based prediction of plant performance from biological, chemical, and physical properties of the soil via two models: random forest and Bayesian neural network. Results Prediction improves when we add environmental features, such as soil properties and microbial density, along with microbiome data. Different preprocessing strategies show that human decisions significantly impact predictive performance. We show that the naive total sum scaling normalization that is commonly used in microbiome research is one of the optimal strategies to maximize predictive power. Also, we find that accurately defined labels are more important than normalization, taxonomic level, or model characteristics. ML performance is limited when humans can’t classify samples accurately. Lastly, we provide domain scientists via a full model selection decision tree to identify the human choices that optimize model prediction power. Conclusions Our study highlights the importance of incorporating diverse environmental features and careful data preprocessing in enhancing the predictive power of machine learning models for soil and biological phenotype connections. This approach can significantly contribute to advancing agricultural practices and soil health management.

Aghdam, Rosa↗

DOE OSTI2024

NANO.PTML model for read-across prediction of nanosystems in neurosciences. computational model and experimental case of study

Abstract Neurodegenerative diseases involve progressive neuronal death. Traditional treatments often struggle due to solubility, bioavailability, and crossing the Blood-Brain Barrier (BBB). Nanoparticles (NPs) in biomedical field are garnering growing attention as neurodegenerative disease drugs (NDDs) carrier to the central nervous system. Here, we introduced computational and experimental analysis. In the computational study, a specific IFPTML technique was used, which combined Information Fusion (IF) + Perturbation Theory (PT) + Machine Learning (ML) to select the most promising Nanoparticle Neuronal Disease Drug Delivery (N2D3) systems. For the application of IFPTML model in the nanoscience, NANO.PTML is used. IF-process was carried out between 4403 NDDs assays and 260 cytotoxicity NP assays conducting a dataset of 500,000 cases. The optimal IFPTML was the Decision Tree (DT) algorithm which shown satisfactory performance with specificity values of 96.4% and 96.2%, and sensitivity values of 79.3% and 75.7% in the training (375k/75%) and validation (125k/25%) set. Moreover, the DT model obtained Area Under Receiver Operating Characteristic (AUROC) scores of 0.97 and 0.96 in the training and validation series, highlighting its effectiveness in classification tasks. In the experimental part, two samples of NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) were synthesized by thermal decomposition of an iron(III) oleate (FeOl) precursor and structurally characterized by different methods. Additionally, in order to make the as-synthesized hydrophobic NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) soluble in water the amphiphilic CTAB (Cetyl Trimethyl Ammonium Bromide) molecule was employed. Therefore, to conduct a study with a wider range of NP system variants, an experimental illustrative simulation experiment was performed using the IFPTML-DT model. For this, a set of 500,000 prediction dataset was created. The outcome of this experiment highlighted certain NANO.PTML systems as promising candidates for further investigation. The NANO.PTML approach holds potential to accelerate experimental investigations and offer initial insights into various NP and NDDs compounds, serving as an efficient alternative to time-consuming trial-and-error procedures.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Mitigating Algorithmic Bias in Cancer Site Classification Models

Purpose Integrating artificial intelligence in cancer diagnostics has improved tumor classification beyond rule-based systems. Despite these advancements, these models may still encode demographic biases. We conducted a large-scale, applied bias-probing study of a deep learning–based cancer site classifier to quantify race information encoded in document embeddings. We then evaluated how performance changes when race-correlated embedding dimensions are removed in a post-training sensitivity analysis. Methods The cancer site classifier was trained using 3.5 million electronic cancer pathology reports from six of the National Cancer Institute's SEER registries. We trained a hierarchical self-attention network to generate 400-dimensional document embeddings. These embeddings were used to train two downstream, gradient-boosted decision tree classifiers: one to classify the cancer sites and another to predict racial categories. We identified overlapping features by intersecting the top 50 feature-importance rankings from the site and race models and computed their cumulative feature importance in each model. As a post hoc sensitivity analysis, we progressively pruned these overlapping dimensions, retrained the site model, and compared overall macro-F1 and accuracy, race-stratified macro-F1, and group fairness metrics on the basis of demographic parity and equalized odds before and after pruning. Results The analysis revealed minimal feature overlap between the cancer site and race prediction models, and the cumulative importance scores indicated a negligible influence of racial information on clinical predictions. Post-training pruning of overlapping features did not compromise the models' diagnostic accuracy, with a 0.07% loss in accuracy. Conclusion Our findings demonstrate that HiSAN-generated embeddings from SEER data can be used effectively in cancer site classification without significant demographic bias influencing the outcomes. Post-training pruning therefore functions as a practical audit and sensitivity check.

Shivanna, Abhishek [ORNL] (ORCID:0009000665228593)↗

DOE OSTI2021

ESS-DIVE guidelines for archiving terrestrial model data

This dataset contains supporting documents and images for ESS-DIVE terrestrial model data archiving guidelines.Terrestrial models are broadly defined as numerical models that couple both land dynamics and energy, water, carbon, or nutrient fluxes. We created these guidelines based on input from the U.S. Department of Energy’s Biological and Environmental Research land modeling community. The guidelines are intended to help modelers determine which components of their terrestrial model data associated with publication should be archived. Based on input from the land modeling community, the guidelines recommend archiving both model input and testing data, as well as code, script, and metadata. The guidelines also recommend archiving model data output, depending on the limitations set by data repositories. Lastly, we provide recommendations for bundling data files for publication as well as a discussion about tools that can facilitate model data archiving and reuse.This dataset is an archive of the associated GitHub repository for our model archiving guidelines (https://github.com/ess-dive-community/essdive-model-data-archiving-guidelines). The ‘README.pdf’ file gives a general introduction to the guidelines, and the ‘instructions.pdf’ file provides more detailed steps for following the guidelines. We also provide 2 figures in this data package: 1) a decision tree (model_data_guidelines_decision_tree.png) that can help users determine which components of their model data to archive. and 2) the ‘model_data_guidelines_flmd.png’ file depicts the different files that can be archived in addition to the model data itself. Lastly, we include 3 digitized tables from our associated manuscript and 3 CSV files with anonymized input from DOE scientists about the importance of different aspects of model data archiving from which we developed the guidelines.Dataset updates for v1.1.0: We updated this data package on 2021-11-22 in response to review comments on our related manuscript. In this update we removed one figure so that the model archiving guidelines are conveyed in text rather than an image. We updated the file-level metadata (FLMD) figure to be in accord with the most recent FLMD recommendations. We made minor edits to the README file to update the recommended citation and added two co-authors. We also added 6 new data files (3 are anonymized input from DOE scientists that helped to inform guidelines, and 3 are digitized tables from our manuscript.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Simultaneous prediction of structural properties in epitaxially–grown GaN with quantum and conventional multi–output learning algorithms

Hundreds of GaN thin film crystal plasma–assisted molecular beam epitaxy synthesis experiment records spanning two decades were organized into a dataset correlating the growth experiment design parameters with discrete, binary determinations of crystallinity and surface morphology. Conventional data science techniques as well as both quantum and classical multi–output supervised machine learning algorithms were implemented to investigate the relationships between the operating parameter data and the structural figures of merit. Correlation coefficients, decision tree nodes, p–values, and SHAP values all support substrate temperature and gallium effusion cell conditions as being statistically significant for simultaneously influencing GaN crystallinity and surface morphology. Here, a conventional deep neural network learned best from the data, followed by a quantum–classical hybrid gradient boosting algorithm. When combined with calculations of uncertainty intervals based on VennAbers predictors, machine learning predictions of both structural properties show good agreement with results reported in published experimental literature.

36 MATERIALS SCIENCE↗

DOE OSTI2020

A Detailed Vehicle Simulation Process to Support CAFE and CO 2 Standards (MY 2021–2026 Final Rule Analysis)

In 1975, Congress passed the Energy Policy and Conservation Act (EPCA), requiring standards for corporate average fuel economy (CAFE), and charging the U.S. Department of Transportation (DOT) with the establishment and enforcement of these standards. The Secretary of Transportation has delegated these responsibilities to the National Highway Traffic Safety Administration (NHTSA). NHTSA has contracted the DOT Volpe National Transportation Systems Center (Volpe Center) to provide analytical support for NHTSA’s regulatory and analytical activities related to fuel economy standards. Unlike long-standing safety and criteria pollutant emissions standards, fuel economy standards apply to manufacturers’ overall fleets rather than to individual vehicle models. In developing the standards, NHTSA made use of the CAFE Compliance and Effects Modeling System (the “CAFE model”), which was developed by DOT’s Volpe Center for the 2005-2007 CAFE rulemaking and has been continually updated since. The model is the primary tool used by the agency to evaluate potential CAFE stringency levels by applying technologies incrementally to each manufacturer’s fleet until the requirements under consideration are met. The CAFE model relies on numerous technology-related and economic inputs such as market forecasts and technology cost and effectiveness estimates; these inputs are categorized by vehicle classification, technology synergies, phase-in rates, cost learning curve adjustments, and technology “decision trees.” The Volpe Center assists NHTSA in the development of the engineering and economic inputs to the CAFE model by analyzing the application of potential technologies to the current automotive industry vehicle fleet to determine the feasibility of future CAFE standards, the associated costs, and the benefits of the standards.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

Optimizing Classifiers for Radionuclide Identification

Identifying threat nuclear materials is a critical for the prevention of acts of nuclear terrorism on the homeland. For this purpose, many radionuclide identification devices are deployed in the field. However, these will not necessarily be in the hands of non-experts, therefore these devices need to provide ready-made answers for the personnel in the field. This is where advanced algorithms are employed to both interpret the data and provide the identification of the nuclear material being interrogated. We took a machine learning approach to identification, by using training and validation data sets to create and optimize classifiers which determine which radionuclide is consistent with the data. The classifiers investigated were the Random Forest, Decision Tree, Support Vector Machine, and XG Boost and their performance was judged using the F1 Score for both hyperparameter tuning and comparison. In the end, we found out that the Random Forest Classifier worked the best based off the F1 Score they got which was 0.98.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2021

The Application of Machine Learning Techniques to Meteorological Forecasting

Fog and inland-penetrating sea-breezes occur often at SRS and have a strong impact on site operations. Site personnel therefore require accurate forecasts of these events, but both are difficult to forecast using traditional techniques. Our goal is to apply machine learning (ML) techniques to the problem of forecasting fog and the sea breeze at the Savannah River Site. We apply several such techniques - decision trees, regression, and a series of classification/regression techniques – and train them using the large datasets collected by our group at SRS and from external organizations that maintain databases of regional meteorological variables.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Low-Cost Aero Technology Demonstrations

The main focus of this work was to demonstrate the use of polymeric additive manufacturing (AM) to create tooling for both preforming and consolidation. Polymeric tooling was utilized where both modest and higher pressures are used for part consolidation. The key focus for the AM tooling development was for fabrication of complex structures such as ducting, C-channel stiffened skins, and airfoils where conventional male tooling would typically be trapped in the cured part. The AM tooling was evaluated for use as a tool master used to fabricate and re-shape deformable/re-formable mandrels based on SpinTech’s shape memory composite technology known as Smart Tooling. The AM tooling was also evaluated for use as a mold for composite infusion and consolidation. Key performance parameters were tracked for project schedule completion with each step comprising of “art to part” cycle time, cost, and model fidelity for dimensions, performance, and cost. The primary focus of this demonstration was to determine if a 50% cost reduction was achievable, for each AM tooling-set, as compared to conventional processes. UDRI leveraged project partner SpinTech, who manufactures tools and parts in these categories and thus provided a baseline regarding current best practices and provided valuable feedback during the entirety of this demonstration. This demonstration primarily focused on the use of AM tooling for fabrication of three composite component structures which are typically utilized in aircraft and comprise salient geometric features of broad interest. These components are often tooling intensive and have features requiring extraction of male tools which are usually trapped by the geometry. The three structures selected by the team included: 1) A one-piece airfoil shell comprised of compound contours where male tooling would be trapped unless the part were manufactured in two halves as is typically the case. 2) A one-piece duct used for air handling, comprised of compound contours where male tooling would be trapped unless the part were manufactured in two halves, or a washout mandrel were to be used. 3) A co-cured C-channel stiffened skin where typically C-channels would be individually manufactured and then bonded to a cured skin. The demonstration was comprised of three main tasks: • Task 1: AM Tool Feasibility Study – ensure the AM tooling meets the performance requirements as specified by SpinTech to match baseline performance. • Task 2: Complex Tool Demonstration – Fabricate tooling, preforms, and parts representative of an airfoil and duct. • Task 3: Large Aerostructure Fabrication Demonstration – Fabricate tooling, preforms, and part representative of a C-channel stiffened skin. With the conclusion of this project, a decision tree was developed to determine the key considerations necessary to determine if use of AM tooling for the three selected structures was able to attain the same quality as historically achieved on metallic tooling, while providing a significant cost reduction.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Data Science and Machine Learning for Genome Security

This report describes research conducted to use data science and machine learning methods to distinguish targeted genome editing versus natural mutation and sequencer machine noise. Genome editing capabilities have been around for more than 20 years, and the efficiencies of these techniques has improved dramatically in the last 5+ years, notably with the rise of CRISPR-Cas technology. Whether or not a specific genome has been the target of an edit is concern for U.S. national security. The research detailed in this report provides first steps to address this concern. A large amount of data is necessary in our research, thus we invested considerable time collecting and processing it. We use an ensemble of decision tree and deep neural network machine learning methods as well as anomaly detection to detect genome edits given either whole exome or genome DNA reads. The edit detection results we obtained with our algorithms tested against samples held out during training of our methods are significantly better than random guessing, achieving high F1 and recall scores as well as with precision overall.

59 BASIC BIOLOGICAL SCIENCES↗