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At least 145 records · Page 8

Machine learning and deep learning tools for the automated capture of cancer surveillance data

The National Cancer Institute and the Department of Energy strategic partnership applies advanced computing and predictive machine learning and deep learning models to automate the capture of information from unstructured clinical text for inclusion in cancer registries. Applications include extraction of key data elements from pathology reports, determination of whether a pathology or radiology report is related to cancer, extraction of relevant biomarker information, and identification of recurrence. With the growing complexity of cancer diagnosis and treatment, capturing essential information with purely manual methods is increasingly difficult. These new methods for applying advanced computational capabilities to automate data extraction represent an opportunity to close critical information gaps and create a nimble, flexible platform on which new information sources, such as genomics, can be added. This will ultimately provide a deeper understanding of the drivers of cancer and outcomes in the population and increase the timeliness of reporting. These advances will enable better understanding of how real-world patients are treated and the outcomes associated with those treatments in the context of our complex medical and social environment.

60 APPLIED LIFE SCIENCES↗

Effect of Zn Addition on Phase Evolution in AlCrFeCoNiZn High–Entropy Alloy

The addition of Zn to AlCrFeCoNi high-entropy alloy (HEA) poses intriguing questions as to how it would affect phase evolution. Herein, the phase evolution in AlCrFeCoNiZn is studied using a combination of experimental techniques (X-ray diffraction, scanning electron microscopy, energy-dispersive spectroscopy, and differential scanning calorimetry) and computational (density-functional theory [DFT], calculation of phase diagrams, and machine-learning) methods. Mechanically alloyed and spark-plasma-sintered AlCrFeCoNiZn assumes a metastable single-phase, body-centered-cubic (BCC) structure that undergoes diffusion-controlled phase separation upon subsequent heat treatment to form separate (Al, Cr)-rich, (Fe, Co)-rich, and (Zn, Ni)-rich phases. The formation of (Al, Cr)-rich phase, not reported previously in AlCrFeCoNi-based HEAs, is attributed to strong clustering tendency of Cr–Zn and Cr–Ni pairs, combined with the strong ordering of Zn–Ni pair, driving out Cr that in turn combines with Al to form a (Al, Cr)-rich phase. In the DFT results, the formation of thermodynamically stable L1 2 phase is shown wherein Cr–Fe–Zn [Al–Ni-Co] preferably occupy1a (000) [3c (0 ½ ½)] positions. Furthermore, the sluggish diffusional transformation to L1 2 phase from BCC precursors is attributed to the small stacking-fault energy of AlCrFeCoNiZn. The equilibrated HEA exhibits a high microhardness of 8.24 GPa with an elastic modulus of 184 GPa.

36 MATERIALS SCIENCE↗

Macro-micro multiscale modeling to assist the design of HPDC Al castings microstructure and alloys for EV super-large body structures (Phase 1)

Implementation of High Pressure Die Casting (HPDC) Aluminum (Al) body structures for high volume electrified vehicles (EV) to improve electric efficiency remains a key strategy within many original equipment manufacturer (OEM)s. In addition to high strength for safety requirements, superior Self-Piercing Riveting (SPR) performance is demanded for HPDC Al alloys to be compatible with high volume SPR joining. In this work, it is proposed to extend and validate an existing Contractor finite element multiscale macro-micro modeling approach to quantify the influence of the microstructure of HPDC alloys on the fracture strain/displacement under 3-point bend and clinch testing. The success of this work will allow to replace solution treatment stage with low energy consumption heat treatment (HT) processes, or to design new non heat treatable (NHT) HPDC Al alloys to eliminate HT requirements. Ultimately, this project will facilitate the application of HPDC Al alloys for super-large vehicle structures to significantly reduce vehicle weight, and thus improving energy efficiency. The purpose of this project is to extend and validate an existing finite element code, which is based on the Contractor developed macro-micro multi-scale modeling approach, to numerically simulate the three-point bending and clinch test and study the influences of material microstructural characteristics and phase properties on the rivetability. The macro-micro modeling approach begins with a sample scale model and identify the location, which is mostly prone to failure, the deformation history of the boundaries of that location calculated will be used to drive a microstructure-based sub-models where the material microstructure and microscale properties are considered. Using this approach, the wrap-bending failure for two Al alloys are correctly predicted for the first time. This will start with phase I effort of building a framework of macro-micro three point bending test and clinch test of Al10SiMgMn HPDC alloy in the as-cast and T7 heat treated conditions. Those results will then be validated with experimental test results. The phase II effort will involve the utilization of the knowledge learned in phase I to establish the quantitative correlation between the microstructure characteristics and the riveting performance, which will be further used to guide the optimization of HPDC Al alloy microstructure using heat treatment process to achieve sufficient rivetability to join large thin-wall HPDC alloys.

36 MATERIALS SCIENCE↗

GeN-ROM—An OpenFOAM®-based multiphysics reduced-order modeling framework for the analysis of Molten Salt Reactors

This work presents a projection-based multiphysics Model Order Reduction (MOR) framework for the analysis of nuclear systems and its application to parametric simulations of Molten Salt Reactors (MSR). The framework, named GeN-ROM, is developed using OpenFOAM® and employs a Proper Orthogonal Decomposition aided Reduced-Basis technique (POD-RB). It can be used to reduce steady-state and transient multiphysics problems involving parametric fluid dynamics, heat exchange, and neutronics phenomena. For the treatment of structural elements in the hydraulic systems, a porous medium approach has been adopted. The reduction process is data-driven and snapshot information is extracted via POD to learn the solution manifold and to build global spatial basis functions. At the data collection phase, GeN-ROM makes use of the solvers available in GeN-Foam, a similarly OpenFOAM®-based multiphysics framework developed for the analysis of nuclear reactors. The global bases are used both to approximate the solution fields and to project the full-order equations onto lower-dimensional subspaces, thus considerably reducing the number of unknowns in a numerical system. This reduction leads to significant computational speedups, which is ideal for multi-query applications such as uncertainty quantification or design optimization. The developed tool has been tested using a 2D multiphysics model of the Molten Salt Fast Reactor (MSFR) with steady-state and transient scenarios, with speedups on the order of 10 – 10 5 .

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Criticality analysis of nuclear binding energy neural networks

Machine learning methods, in particular deep learning methods such as artificial neural networks (ANNs) with many layers, have become widespread and useful tools in nuclear physics. However, these ANNs are typically treated as ‘black boxes’, with their architecture (width, depth, and weight/bias initialization) and the training algorithm and parameters chosen empirically by optimizing learning based on limited exploration. We test a non-empirical approach to understanding and optimizing nuclear physics ANNs by adapting a criticality analysis based on renormalization group flows in terms of the hyperparameters for weight/bias initialization, training rates, and the ratio of depth to width. This treatment utilizes the statistical properties of neural network initialization to find a generating functional for network outputs at any layer, allowing for a path integral formulation of the ANN outputs as a Euclidean statistical field theory. We use a prototypical example to test the applicability of this approach: a simple ANN for nuclear binding energies. We find that with training using a stochastic gradient descent optimizer, the predicted criticality behavior is realized, and optimal performance is found with critical tuning. However, the use of an adaptive learning algorithm leads to somewhat superior results without concern for tuning and thus obscures the analysis. Nevertheless, the criticality analysis offers a way to look within the black box of ANNs, which is a first step towards potential improvements in network performance beyond using adaptive optimizers.

artificial neural network↗

AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2

Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic’s evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (M pro ), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. Here, this work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic “warhead” to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of M pro with micromolar affinities (K I of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.

60 APPLIED LIFE SCIENCES↗

Lessons Learned—Fluoride Exposure and Response

Laboratory research can expose workers to a wide variety of chemical hazards. Researchers must not only take personal responsibility for their safety but also inevitably rely on coworkers to also work safely. The foundations for protocols, requirements, and behaviors come from our history and lessons learned from others. For that reason, here, a recent incident is examined in which a researcher suffered hydrofluoric acid (HF) burns while working with an inorganic digestion mixture of aqueous HF (8%) and nitric acid (HNO 3 , 58%). HF education is critical for workers because delays in treatment, improper treatment, and delay of symptoms are all factors in unfavorable outcomes in case reports. Furthermore, while the potential severity of the incident was elevated due to bypassed engineered controls and lack of proper personal protective equipment, only minor injuries were sustained. We discuss the results of a causal analysis of the incident that revealed areas of improvement in protocols, personal protective equipment, and emergency response that could help prevent similar accidents from occurring. We also present simple improvements that anyone can implement to reduce the potential consequences of an accident, based upon our lessons learned.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modeling inter‐reader variability in clinical target volume delineation for soft tissue sarcomas using diffusion model

Abstract Background Accurate delineation of the clinical target volume (CTV) is essential in the radiotherapy treatment of soft tissue sarcomas. However, this process is subject to inter‐reader variability due to the need for clinical assessment of risk and extent of potential microscopic spread. This can lead to inconsistencies in treatment planning, potentially impacting treatment outcomes. Most existing automatic CTV delineation methods do not account for this variability and can only generate a single CTV for each case. Purpose This study aims to develop a deep learning‐based technique to generate multiple CTV contours for each case, simulating the inter‐reader variability in the clinical practice. Methods We employed a publicly available dataset consisting of fluorodeoxyglucose positron emission tomography (FDG‐PET), x‐ray computed tomography (CT), and pre‐contrast T1‐weighted magnetic resonance imaging (MRI) scans from 51 patients with soft tissue sarcoma, along with an independent validation set containing five additional patients. An experienced reader drew a contour of the gross tumor volume (GTV) for each patient based on multi‐modality images. Subsequently, two additional readers, together with the first one, were responsible for contouring three CTVs in total based on the GTV. We developed a diffusion model‐based deep learning method that is capable of generating arbitrary number of different and plausible CTVs to mimic the inter‐reader variability in CTV delineation. The proposed model incorporates a separate encoder to extract features from the GTV masks, leveraging the critical role of GTV information in accurate CTV delineation. Results The proposed diffusion model demonstrated superior performance with the highest Dice Index (0.902 compared to values below 0.881 for state‐of‐the‐art models) and the best generalized energy distance (GED) (0.209 compared to values exceeding 0.221 for state‐of‐the‐art models). It also achieved the second‐highest recall and precision metrics among the compared ambiguous image segmentation models. Results from both datasets exhibited consistent trends, reinforcing the reliability of our findings. Additionally, ablation studies exploring different model structures and input configurations highlighted the significance of incorporating prior GTV information for accurate CTV delineation. Conclusions The proposed diffusion model successfully generates multiple plausible CTV contours for soft tissue sarcomas, effectively capturing inter‐reader variability in CTV delineation.

Dong, Yafei [Yale Biomedical Imaging Institute Yal↗

Prediction of condition-specific regulatory genes using machine learning

Recent advances in genomic technologies have generated data on large-scale protein–DNA interactions and open chromatin regions for many eukaryotic species. How to identify condition-specific functions of transcription factors using these data has become a major challenge in genomic research. To solve this problem, we have developed a method called ConSReg, which provides a novel approach to integrate regulatory genomic data into predictive machine learning models of key regulatory genes. Using Arabidopsis as a model system, we tested our approach to identify regulatory genes in data sets from single cell gene expression and from abiotic stress treatments. Our results showed that ConSReg accurately predicted transcription factors that regulate differentially expressed genes with an average auROC of 0.84, which is 23.5–25% better than enrichment-based approaches. To further validate the performance of ConSReg, we analyzed an independent data set related to plant nitrogen responses. ConSReg provided better rankings of the correct transcription factors in 61.7% of cases, which is three times better than other plant tools. We applied ConSReg to Arabidopsis single cell RNA-seq data, successfully identifying candidate regulatory genes that control cell wall formation. Our methods provide a new approach to define candidate regulatory genes using integrated genomic data in plants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Neural chaos: A spectral stochastic neural operator

Building surrogate models for operators with uncertainty quantification capabilities is essential for many engineering applications where randomness–such as variability in material properties, boundary conditions, and initial conditions–is unavoidable. Polynomial Chaos Expansion (PCE) is widely recognized as a go-to method for constructing stochastic surrogates in both intrusive and non-intrusive ways, and it has recently been used in the context of operator learning. However, its application becomes challenging for complex or high-dimensional processes, as achieving accuracy requires higher-order polynomials, which can increase computational demand and/or the risk of overfitting. Furthermore, PCE requires specialized treatments to manage random variables that are not independent, and these treatments may be problem-dependent or may fail with increasing complexity. Here, in this work, we adopt the same formalism as the spectral expansion used in PCE; however, we replace the classical polynomial basis functions with neural network (NN) basis functions to leverage their expressivity. To achieve this, we propose an algorithm that identifies NN-parameterized basis functions in a purely data-driven manner, without any prior assumptions about the joint distribution of the random variables involved, whether independent or dependent, or about their marginal distributions. The proposed algorithm identifies each NN-parameterized basis function sequentially, ensuring they are orthogonal with respect to the data distribution. The basis functions are constructed directly on the joint stochastic variables without requiring a tensor product structure or assuming independence of the random variables. This approach may offer greater flexibility for complex stochastic models, while simplifying implementation compared to the tensor product structures typically used in PCE to handle random vectors. This is particularly advantageous given the current state of open-source packages, where building and training neural networks can be done with just a few lines of code and extensive community support. We demonstrate the effectiveness of the proposed scheme through several numerical examples of varying complexity and provide comparisons with classical PCE.

Polynomial chaos expansion↗

Nonlocal Kernel Network (NKN): a Stable and Resolution-Independent Deep Neural Network.

Neural operators have recently become popular tools for designing solution maps between function spaces in the form of neural networks. Differently from classical scientific machine learning approaches that learn parameters of a known partial differential equation (PDE) for a single instance of the input parameters at a fixed resolution, neural operators approximate the solution map of a family of PDEs [6, 7]. Despite their success, the uses of neural operators are so far restricted to relatively shallow neural networks and confined to learning hidden governing laws. In this work, we propose a novel nonlocal neural operator, which we refer to as nonlocal kernel network (NKN), that is resolution independent, characterized by deep neural networks, and capable of handling a variety of tasks such as learning governing equations and classifying images. Our NKN stems from the interpretation of the neural network as a discrete nonlocal diffusion reaction equation that, in the limit of infinite layers, is equivalent to a parabolic nonlocal equation, whose stability is analyzed via nonlocal vector calculus. The resemblance with integral forms of neural operators allows NKNs to capture long-range dependencies in the feature space, while the continuous treatment of node-to-node interactions makes NKNs resolution independent. The resemblance with neural ODEs, reinterpreted in a nonlocal sense, and the stable network dynamics between layers allow for generalization of NKN’s optimal parameters from shallow to deep networks. This fact enables the use of shallow-to-deep initialization techniques [8]. Our tests show that NKNs outperform baseline methods in both learning governing equations and image classification tasks and generalize well to different resolutions and depths.

97 MATHEMATICS AND COMPUTING↗

Social Learning and Solar Photovoltaic Adoption

Growing literature points to the effectiveness of leveraging social interactions and nudges to spur adoption of prosocial behaviors. This study investigates a large-scale behavioral intervention designed to actively leverage social learning and peer interactions to encourage adoption of residential solar photovoltaic systems. Municipalities choose a solar installer offering group pricing and undertake an informational campaign driven by volunteer ambassadors. We find a causal treatment effect of 37 installations per municipality from the campaigns and no evidence of harvesting or persistence. The intervention also lowers installation prices. Randomized controlled trials based on the intervention show that selection into the program is important, whereas group pricing is not. Our results suggest that the program provided economies of scale and lowered consumer acquisition costs, leading to low-cost emission reductions. This paper was accepted by Matthew Shum, marketing.

Business & Economics↗

Optimizing Patient-Specific Medication Regimen Policies Using Wearable Sensors in Parkinson’s Disease

Effective treatment of Parkinson’s disease (PD) is a continual challenge for healthcare providers, and providers can benefit from leveraging emerging technologies to supplement traditional clinic care. We develop a data-driven reinforcement learning (RL) framework to optimize PD medication regimens through wearable sensors. We leverage a data set of n = 26 PD patients who wore wrist-mounted movement trackers for two separate six-day periods. Using these data, we first build and validate a simulation model of how individual patients’ movement symptoms respond to medication administration. We then pair this simulation model with an on-policy RL algorithm that recommends optimal medication types, timing, and dosages during the day while incorporating human-in-the-loop considerations on medication administration. The results show that the RL-prescribed medication regimens outperform physicians’ medication regimens, despite physicians having access to the same data as the RL agent. To validate our results, we assess our wearable-based RL medication regimens using n = 399 PD patients from the Parkinson’s Progression Markers Initiative data set. We show that the wearable-based RL medication regimens would lead to significant symptom improvement for these patients, even more so than training RL policies directly from this data set. In doing so, we show that RL models from even small data sets of wearable data can offer novel, generalizable clinical insights and medication strategies, which may outperform those derived from larger data sets without wearable data.

60 APPLIED LIFE SCIENCES↗

Developments in algal processing

Macroalgae and microalgae, including cyanobacteria, are primarily photosynthetic organisms grown for the production of renewable biomass for foods, feedstocks, and high-value specialty chemicals. While there are differences in cultivating and harvesting macro- and microalgae due to scale, many of the same downstream techniques can be used for processing algal biomass. This chapter will outline various developments in processing technologies used for the treatment of algal biomass with discussion of scalability, cost, time, and efficacy. Topics will cover methods for harvesting and dewatering algae, drying algal biomass, biomass disruption, and nutrient recovery, including case studies with lessons learned. Here, the final section presents biomass applications and product considerations. While there is no universally-adopted approach for processing algal biomass, these studies provide the foundation for making informed decisions, considering the unique properties of the algae and the integrity of the desired end products.

09 BIOMASS FUELS↗

Periodic GFN1-xTB Tight Binding: A Generalized Ewald Partitioning Scheme for the Klopman–Ohno Function

A novel formulation is presented for the treatment of electrostatics in the periodic GFN1-xTB tight-binding model. Periodic GFN1-xTB is hindered by the functional form of the second-order electrostatics, which only recovers Coulombic behavior at large interatomic distances and lacks a closed-form solution for its Fourier transform. We address this by introducing a binomial expansion of the Klopman–Ohno function to partition short- and long-range interactions, enabling the use of a generalized Ewald summation for the solution of the electrostatic energy. This approach is general and is applicable to any damped potential of the form |R n + c| –m . Benchmarks on the X23 molecular crystal dataset and a range of prototypical bulk semiconductors demonstrate that this systematic treatment of the electrostatics eliminates unphysical behavior in the equation of state curves. In the bulk systems studied, we observe a mean absolute error in total energy of 35 meV/atom, comparable to the machine-learned universal force field, M3GNet, and sufficiently precise for structure relaxation. These results highlight the promising potential of GFN1-xTB as a universal tight-binding parametrization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Contrastive Machine Learning with Gamma Spectroscopy Data Augmentations for Detecting Shielded Radiological Material Transfers

Data analysis techniques can be powerful tools for rapidly analyzing data and extracting information that can be used in a latent space for categorizing observations between classes of data. Machine learning models that exploit learned data relationships can address a variety of nuclear nonproliferation challenges like the detection and tracking of shielded radiological material transfers. The high resource cost of manually labeling radiation spectra is a hindrance to the rapid analysis of data collected from persistent monitoring and to the adoption of supervised machine learning methods that require large volumes of curated training data. Instead, contrastive self-supervised learning on unlabeled spectra can enhance models that are built on limited labeled radiation datasets. This work demonstrates that contrastive machine learning is an effective technique for leveraging unlabeled data in detecting and characterizing nuclear material transfers demonstrated on radiation measurements collected at an Oak Ridge National Laboratory testbed, where sodium iodide detectors measure gamma radiation emitted by material transfers between the High Flux Isotope Reactor and the Radiochemical Engineering Development Center. Label-invariant data augmentations tailored for gamma radiation detection physics are used on unlabeled spectra to contrastively train an encoder, learning a complex, embedded state space with self-supervision. A linear classifier is then trained on a limited set of labeled data to distinguish transfer spectra between byproducts and tracked nuclear material using representations from the contrastively trained encoder. The optimized hyperparameter model achieves a balanced accuracy score of 80.30%. Any given model—that is, a trained encoder and classifier—shows preferential treatment for specific subclasses of transfer types. Regardless of the classifier complexity, a supervised classifier using contrastively trained representations achieves higher accuracy than using spectra when trained and tested on limited labeled data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Improving the reliability of machine learned potentials for modeling inhomogeneous liquids

The atomic-scale response of inhomogeneous fluids at interfaces and surrounding solute particles plays a critical role in governing chemical, electrochemical, and biological processes. Classical molecular dynamics simulations have been applied extensively to simulate the response of fluids to inhomogeneities directly, but are limited by the accuracy of the underlying interatomic potentials. Here, we use neural network potentials (NNPs) trained to ab initio simulations to accurately predict the inhomogeneous responses of two distinct fluids: liquid water and molten NaCl. Although NNPs can be readily trained to model complex bulk systems across a range of state points, we show that to appropriately model a fluid's response at an interface, relevant inhomogeneous configurations must be included in the training data. In order to sufficiently sample appropriate configurations of such inhomogeneous fluids, we develop protocols based on molecular dynamics simulations in the presence of external potentials. We demonstrate that NNPs trained on inhomogeneous fluid configurations can more accurately predict several key properties of fluids—including the density response, surface tension and size-dependent cavitation free energies—for liquid water and molten NaCl, compared to both empirical interatomic potentials and NNPs that are not trained on such inhomogeneous configurations. This work therefore provides a first demonstration and framework to extract the response of inhomogeneous fluids from first principles for classical density-functional treatment of fluids free from empirical potentials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Application of Machine Learning to Improve Biobased Glucaric Acid Production (CRADA 504)

The Agile Biofoundry (ABF) is a multi-national lab consortium funded by the DOE Bioenergy Technologies Office that has developed a biofoundry that enables the rapid deployment of bioproducts into the market. Working with four ABF laboratory members (National Renewable Energy Laboratory (NREL), Pacific Northwest National Laboratory (PNNL), Lawrence Berkeley National Laboratory (LBNL), and Argonne National Laboratory (ANL)), Kalion will use advanced high throughput techniques, advanced analytics, and machine learning to optimize the production environment for glucaric acid. Low-cost, high-purity glucaric acid enables products in a wide range of fields to improve the chemical properties of products and applications ranging from water treatment, polymers & textiles, coatings, detergents, and pharmaceuticals. With its broad range of applications, glucaric acid has the potential to demonstrate how such bio-based materials offer great benefit to the US economy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗