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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cholesky-based experimental design for Gaussian process and kernel-based emulation and calibration.

Gaussian processes and other kernel-based methods are used extensively to construct approximations of multivariate data sets. The accuracy of these approximations is dependent on the data used. This paper presents a computationally efficient algorithm to greedily select training samples that minimize the weighted L p error of kernel-based approximations for a given number of data. The method successively generates nested samples, with the goal of minimizing the error in high probability regions of densities specified by users. The algorithm presented is extremely simple and can be implemented using existing pivoted Cholesky factorization methods. Training samples are generated in batches which allows training data to be evaluated (labeled) in parallel. For smooth kernels, the algorithm performs comparably with the greedy integrated variance design but has significantly lower complexity. Numerical experiments demonstrate the efficacy of the approach for bounded, unbounded, multi-modal and non-tensor product densities. We also show how to use the proposed algorithm to efficiently generate surrogates for inferring unknown model parameters from data using Bayesian inference.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

On-the-fly autonomous control of neutron diffraction via physics-informed Bayesian active learning

We demonstrate the first live, autonomous control over neutron diffraction experiments by developing and deploying ANDiE: the autonomous neutron diffraction explorer. Neutron scattering is a unique and versatile characterization technique for probing the magnetic structure and behavior of materials. However, instruments at neutron scattering facilities in the world is limited, and instruments at such facilities are perennially oversubscribed. We demonstrate a significant reduction in experimental time required for neutron diffraction experiments by implementation of autonomous navigation of measurement parameter space through machine learning. Prior scientific knowledge and Bayesian active learning are used to dynamically steer the sequence of measurements. We show that ANDiE can experimentally determine the magnetic ordering transition of both MnO and Fe 1.09 Te all while providing a fivefold enhancement in measurement efficiency. Furthermore, in a hypothesis testing post-processing step, ANDiE can determine transition behavior from a set of possible physical models. ANDiE's active learning approach is broadly applicable to a variety of neutron-based experiments and can open the door for neutron scattering as a tool of accelerated materials discovery.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Snowmass Computational Frontier: Topical Group Report on Experimental Algorithm Parallelization

The substantial increase in data volume and complexity expected from future experiments will require significant investment to prepare experimental algorithms. These algorithms include physics object reconstruction, calibrations, and processing of observational data. In addition, the changing computing architecture landscape, which will be primarily composed of heterogeneous resources, will continue to pose major challenges with regard to algorithmic migration. Portable tools need to be developed that can be shared among the frontiers (e.g., for code execution on different platforms) and opportunities, such as forums or cross-experimental working groups, need to be provided where experiences and lessons learned can be shared between experiments and frontiers. At the same time, individual experiments also need to invest considerable resources to develop algorithms unique to their needs (e.g., for facilities dedicated to the experiment), and ensure that their specific algorithms will be able to efficiently exploit external heterogeneous computing facilities. Common software tools represent a cost-effective solution, providing ready-to-use software solutions as well as a platform for R&D work. These are particularly important for small experiments which typically do not have dedicated resources needed to face the challenges imposed by the evolving computing technologies. Workforce development is a key concern across frontiers and experiments, and additional support is needed to provide career opportunities for researchers working in the field of experimental algorithm development. Finally, cross-discipline collaborations going beyond high-energy physics are a key ingredient to address the challenges ahead and more support for such collaborations needs to be created. This report targets future experiments, observations and experimental algorithm development for the next 10-15 years.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Deep learning of electrochemical CO 2 conversion literature reveals research trends and directions

Large-scale and openly available material science databases are mainly composed of computer simulation results rather than experimental data. Some examples include the Materials Project, Open Quantum Materials Database, and Open Catalyst 2022. Unfortunately, building large-scale experimental databases remains challenging due to the difficulties in consolidating locally distributed datasets. In this work, focusing on the catalysis literature of CO 2 reduction reactions (CO 2 RRs), we present a machine learning (ML)-based protocol for selecting highly relevant papers and extracting important experimental data. First, we report a document embedding method (Doc2Vec) for collecting papers of greatest relevance to the specific target domain, which yielded 3154 CO 2 RR-related papers from six publishers. Next, we developed named entity recognition (NER) models to extract twelve entities related to material names (catalyst, electrolyte, etc.) and catalytic performance (Faradaic efficiency, current density, etc.). Further, among several tested models, the MatBERT-based approach achieved the highest accuracy, with an average F1-score of 90.4% and an F1-score of 95.2% in a boundary relaxation evaluation scheme. The accurate and accelerated NER-based data extraction from a large volume of catalysis literature enables temporal trend analyses of the CO 2 RR catalysts, products, and performances, revealing the potentially effective material space in CO 2 RRs. While this work demonstrates the effectiveness of our ML-based text mining methods for specifically CO 2 RR literature, the methods and approach are applicable to and may be used to accelerate the development of other catalytic chemical reactions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Bayesian experimental design and parameter estimation for ultrafast spin dynamics

Abstract Advanced experimental measurements are crucial for driving theoretical developments and unveiling novel phenomena in condensed matter and materials physics, which often suffer from the scarcity of large-scale facility resources, such as x-ray or neutron scattering centers. To address these limitations, we introduce a methodology that leverages the Bayesian optimal experimental design paradigm to efficiently uncover key quantum spin fluctuation parameters from x-ray photon fluctuation spectroscopy (XPFS) data. Our method is compatible with existing theoretical simulation pipelines and can also be used in combination with fast machine learning surrogate models in the event that real-time simulations are unfeasible. Our numerical benchmarks demonstrate the superior performance in predicting model parameters and in delivering more informative measurements within limited experimental time. Our method can be adapted to many different types of experiments beyond XPFS and spin fluctuation studies, facilitating more efficient data collection and accelerating scientific discoveries.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Parameters, Properties, and Process: Conditional Neural Generation of Realistic SEM Imagery Toward ML-Assisted Advanced Manufacturing

Abstract The research and development cycle of advanced manufacturing processes traditionally requires a large investment of time and resources. Experiments can be expensive and are hence conducted on relatively small scales. This poses problems for typically data-hungry machine learning tools which could otherwise expedite the development cycle. We build upon prior work by applying conditional generative adversarial networks (GANs) to scanning electron microscope (SEM) imagery from an emerging advanced manufacturing process, shear-assisted processing and extrusion (ShAPE). We generate realistic images conditioned on temper and either experimental parameters or material properties. In doing so, we are able to integrate machine learning into the development cycle, by allowing a user to immediately visualize the microstructure that would arise from particular process parameters or properties. This work forms a technical backbone for a fundamentally new approach for understanding manufacturing processes in the absence of first-principle models. By characterizing microstructure from a topological perspective, we are able to evaluate our models’ ability to capture the breadth and diversity of experimental scanning electron microscope (SEM) samples. Our method is successful in capturing the visual and general microstructural features arising from the considered process, with analysis highlighting directions to further improve the topological realism of our synthetic imagery.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Discovery of multi-functional polyimides through high-throughput screening using explainable machine learning

Polyimides have been widely used in modern industries because of their excellent mechanical and thermal properties, e.g., high-temperature fuel cells, displays, and aerospace composites. However, it usually takes decades of experimental efforts to develop a successful product. Aiming to expedite the discovery of high-performance polyimides, we utilize computational methods of machine learning (ML) and molecular dynamics (MD) simulations. Our study provides compelling evidence for the effectiveness of a data-driven approach in discovering novel polyimides. We first build a comprehensive library of more than 8 million hypothetical polyimides based on the polycondensation of existing dianhydride and diamine/diisocyanate molecules. Then we establish multiple ML models for the thermal and mechanical properties of polyimides based on their experimentally reported values, including glass transition temperature, Young’s modulus, and tensile yield strength. The obtained ML models demonstrate excellent predictive performance in identifying the key chemical substructures influencing the thermal and mechanical properties of polyimides. The use of explainable machine learning describes the effect of chemical substructures on individual properties, from which human experts can understand the cause of the ML model decision. Applying the well-trained ML models, we obtain property predictions of the 8 million hypothetical polyimides. Then, we screen the whole hypothetical dataset and identify three (3) best-performing novel polyimides that have better-combined properties than existing ones through Pareto frontier analysis. For an easy query of the discovered high-performing polyimides, we also create an online platform https://polyimide-explorer.herokuapp.com/ that embeds the developed ML model with interactive visualization. Furthermore, we validate the ML predictions through all-atom MD simulations and examine their synthesizability. The MD simulations are in good agreement with the ML predictions and the three novel polyimides are predicted to be easy to synthesize via Schuffenhauer’s synthetic accessibility score. Following the proposed ML guidance, we successfully synthesized a novel polyimide and the experimentally obtained high glass transition/thermal decomposition temperature demonstrated its excellent thermal stability. Here our study demonstrates an efficient way to expedite the discovery of novel polymers using ML prediction and MD validation. The high-throughput screening of a large computational dataset can serve as a general approach for new material discovery in other polymeric material exploration problems, such as organic photovoltaics, polymer membranes, and dielectrics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Machine Learning Analysis of Direct Dynamics Trajectory Outcomes for Thermal Deazetization of 2,3-Diazabicyclo[2.2.1]hept-2-ene

Experimentally, the thermal gas-phase deazetization of 2,3-diazabicyclo[2.2.1]hept-2-ene (1) results in the loss of N2 and the formation of bicyclo products 3 (exo) and 4 (endo) in a nonstatistical ratio, with preference for the exo product. Here, we report unrestricted M06-2X quasiclassical trajectories initialized from the concerted N2 ejection transition state that were able to replicate the experimental preference to form 3. We found that the 3:4 ratio results from the relative amounts of very fast (ballistic) exotype trajectories versus trajectories that lead to the 1,3-diradical intermediate 2. These quasiclassical trajectories provided a set of transition-state vibrational, velocity, momenta, and geometric features for the machine learning analysis. Additionally, a selection of popular supervised classification algorithms (e.g., random forest) provided poor prediction of trajectory outcomes based on only transition-state vibrational quanta and energy features. However, these machine learning models provided more accurate predictions using atomic velocities and atomic positions, attaining ~70% accuracy using initial conditions and between 85 and 95% accuracy at later reaction time steps. This increased accuracy allowed the feature importance analysis to reveal that, at the later-time analysis, the methylene bridge out-of-plane bending is correlated with trajectory outcomes for the formation of either the exo product or toward the diradical intermediate. Possible reasons for the struggle of machine learning algorithms to classify trajectories based on transition-state features is the heavily overlapping feature values, the finite but very large possible vibrational mode combinations, and the possibility of chaos as trajectories propagate. We examined this chaos by comparing a set of nearly identical trajectories that differed by only a very small scaling of the kinetic energies resulting from the transition-state reaction coordinate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Real-time tracking of structural evolution in 2D MXenes using theory-enhanced machine learning

In situ Electron Energy Loss Spectroscopy (EELS) combined with Transmission Electron Microscopy (TEM) has traditionally been pivotal for understanding how material processing choices affect local structure and composition. However, the ability to monitor and respond to ultrafast transient changes, now achievable with EELS and TEM, necessitates innovative analytical frameworks. Here, we introduce a machine learning (ML) framework tailored for the real-time assessment and characterization of in operando EELS Spectrum Images (EELS-SI). We focus on 2D MXenes as the sample material system, specifically targeting the understanding and control of their atomic-scale structural transformations that critically influence their electronic and optical properties. This approach requires fewer labeled training data points than typical deep learning classification methods. By integrating computationally generated structures of MXenes and experimental datasets into a unified latent space using Variational Autoencoders (VAE) in a unique training method, our framework accurately predicts structural evolutions at latencies pertinent to closed-loop processing within the TEM. This study presents a critical advancement in enabling automated, on-the-fly synthesis and characterization, significantly enhancing capabilities for materials discovery and the precision engineering of functional materials at the atomic scale.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Inverse design of hypoeutectoid pearlite steel microstructures using a deep learning and genetic algorithm optimization framework

Goal-oriented microstructure design in metallic materials is a challenging task due to complex structure-property relationships. Traditional experimental and computational approaches are time-intensive and economically inefficient, limiting their applicability for large-scale design space exploration. Here, in this work, we propose an end-to-end framework that integrates deep learning models with genetic optimization to design microstructures with targeted mechanical properties. Deep learning models enable accurate forward design, while their integration with genetic optimization enables efficient inverse design within a few hours, compared to days or weeks using conventional finite element simulations. The framework combines experimental characterization and finite element modeling to analyze the influence of microstructural features on the mechanical behavior of hypoeutectoid steels. Data from both experiments and simulations are used to train the deep learning models. To demonstrate its effectiveness, we apply the framework to 0.63% carbon steel with proeutectoid ferrite and pearlite phases, commonly used in industrial applications. In this study, 2D microstructures were used for modeling, selected primarily for computational efficiency and to establish proof of concept. The framework successfully optimizes microstructures for targeted yield strength, ultimate strength, and stress concentration factors while significantly reducing computational time. Beyond hypoeutectoid steels, this scalable framework can be extended to other material systems and integrated with additive manufacturing, offering an efficient approach for accelerating microstructure design for specific engineering applications.

ConvLSTM↗
DOE OSTI2021

Three-dimensional coherent X-ray diffraction imaging via deep convolutional neural networks

Abstract As a critical component of coherent X-ray diffraction imaging (CDI), phase retrieval has been extensively applied in X-ray structural science to recover the 3D morphological information inside measured particles. Despite meeting all the oversampling requirements of Sayre and Shannon, current phase retrieval approaches still have trouble achieving a unique inversion of experimental data in the presence of noise. Here, we propose to overcome this limitation by incorporating a 3D Machine Learning (ML) model combining (optional) supervised learning with transfer learning. The trained ML model can rapidly provide an immediate result with high accuracy which could benefit real-time experiments, and the predicted result can be further refined with transfer learning. More significantly, the proposed ML model can be used without any prior training to learn the missing phases of an image based on minimization of an appropriate ‘loss function’ alone. We demonstrate significantly improved performance with experimental Bragg CDI data over traditional iterative phase retrieval algorithms.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

CRCNS22 Learning Rules in the Hippocampus and their Mapping to Neuromorphic Systems (Final Technical Report)

Large scale biologically-realistic computational models are key to investigating the interplay between structure and function in nervous systems, thus paving the way to new clinical methods and neuro-inspired computing solutions. This project focuses on the hippocampus, in particular the CA3-CA1 regions, due to their role in associative learning and memory, pattern separation and completion, and spatial navigation. Investigations into the neuronal organization and learning rule(s) of this circuit can shed light into how declarative memories are formed, stored, recalled and forgotten and inform computational, experimental and clinical neuroscience work. Our project aims at developing a novel data-driven methodology supported by a broad heterogeneous base of neuroscience experimental knowledge and inspired from advances in computer science and engineering. Specifically, this work will benchmark existing and new learning rules within a full-scale spiking neural network simulation of the CA3-CA1 region. The model will be based on an open-source repository, called the Hippocampome, which contains neuronal morphologies, firing patterns, synapse probabilities, and most other required parameters for all known neuron types in the rodent hippocampal formation. The model will be first trained in a supervised fashion for associative memory tasks using backpropagation through time traditionally used in computer science, enhanced with a new technique called the surrogate gradient method. This optimization method will be used to obtain a global loss minimization, but it is not biologically inspired as it assumes the use of data not locally available to the synapses. However, we propose its use as a benchmarking tool, to compare the training performance of local biologically plausible and hardware-mappable learning rules at scale. New rules or combinations will be proposed and tested as needed, based on the obtained results. Progress in this area will also drive the development of novel hardware-mappable algorithms for continual lifelong learning and categorization of new events from few presented examples. This project goes beyond the existing state-of-the-art by looking at large scale realistic neuronal circuits as networks trainable via global optimization methods such as surrogate gradient descent. The objective function of the brain that supports learning is largely unknown, but it is likely that it operates through local learning rules. Studying network trajectories around local minima as proposed in this work represents a useful strategy for understanding whether a network is training by using a specific (set of) learning rule(s). Starting from a completely untrained network is a challenging test since it is difficult to determine how the learning rule affects the trajectory of the network. This interdisciplinary project will help understand what rule governs learning in these regions or if multiple learning rules are involved. The work will develop a robust methodology to measure if the network is converging to the target solution, oscillating around it, or diverging away.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Accelerating the discovery of novel magnetic materials using machine learning–guided adaptive feedback

Magnetic materials are essential for energy generation and information devices, and they play an important role in advanced technologies and green energy economies. Currently, the most widely used magnets contain rare earth (RE) elements. An outstanding challenge of notable scientific interest is the discovery and synthesis of novel magnetic materials without RE elements that meet the performance and cost goals for advanced electromagnetic devices. Here, we report our discovery and synthesis of an RE-free magnetic compound, Fe 3 CoB 2 , through an efficient feedback framework by integrating machine learning (ML), an adaptive genetic algorithm, first-principles calculations, and experimental synthesis. Magnetic measurements show that Fe 3 CoB 2 exhibits a high magnetic anisotropy ( K 1 = 1.2 MJ/m 3 ) and saturation magnetic polarization ( J s = 1.39 T), which is suitable for RE-free permanent-magnet applications. Our ML-guided approach presents a promising paradigm for efficient materials design and discovery and can also be applied to the search for other functional materials.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Integrated Computational Materials and Mechanical Modeling for Additive Manufacturing of Alloys with Graded Structure Used in Fossil Fuel Power Plants

Wire-arc additive manufacturing (WAAM) has demonstrated its unique capability of producing large-size alloy components with a significantly reduced fabrication time and enhanced geometry design freedom. In this project, the team has developed an ICME (Integrated Computational Materials Engineering) modeling framework, which supports the WAAM of the AUSC (Advanced Ultra-Supercritical) power plant components. The manufacturing design has been applied to Inconel 740H, steel P91, as well as the dissimilar alloy components between steel P91 and Inconel 740H. The ICME model framework is developed by considering two types of modeling. First, mechanistic modeling has been applied to control the printing quality and understand the sequence of the dissimilar printing of the wall structure. The following models have been included in the developed ICME framework: finite element thermal model, grain structure model, residual stress simulation, crystal plasticity model, CALPHAD-based precipitation kinetic model, phase stability prediction, thermal expansion predictive model, and heuristic creep model. Secondary, a physics-based machine learning model has also been developed based on the ICME model structure. The machine learning model development is based on the ICME model prediction with calibration of the experiments. In addition, the WAAM has been utilized as a high-throughput experimental tool rapidly generating a gradient of alloy composition to facilitate experimental database generation for process-structure-property relationships. Such a database directly supported the ICME-enhanced machine learning, which further assisted in intermediate composition block design between P91 and 740H. A high-throughput screening study of the oxidation resistance has been performed based on such high-throughput experimentation. Based on the computational design, several dissimilar alloy manufacturing with post-heat treatment have been performed with a comprehensive evaluation of mechanical performance, including hardness mapping, yield strength, creep resistance. In this project, the single component of P91 and 740H processed by WAAM after heat treatment designed by ICME has demonstrated higher performance in yield strength and creep resistance than the wrought materials. The P91 sample prepared by WAAM with ICME-designed heat treatment performs better than P92 in creep resistance. The designed graded alloy printing with intermediate block shows a promising performance that exceeds the traditional welding. Moreover, the current research indicates the high need for location-specific design analysis with uncertainty quantification, an important topic that deserves more dedicated research. The achievement of this project demonstrated the promising future of WAAM in structural alloy manufacturing for energy power plant development. Successful printing requires synergetic efforts made by manufacturing, mechanical, and materials sciences.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2022

Bridging Nano- and Microscale X-Ray Tomography for Battery Research by Leveraging Artificial Intelligence

X-ray computed tomography (CT) is a non-destructive imaging technique in which contrast originates from the materials' absorption coefficient. The recent development of laboratory nanoscale CT (nano-CT) systems has pushed the spatial resolution for battery material imaging to voxel sizes of 50 nm, a limit previously achievable only with synchrotron facilities. Given the non-destructive nature of CT, in situ and operando studies have emerged as powerful methods to quantify morphological parameters, such as tortuosity factor, porosity, surface area and volume expansion, during battery operation or cycling. Combined with artificial intelligence and machine learning analysis techniques, nano-CT has enabled the development of predictive models to analyse the impact of the electrode microstructure on cell performances or the influence of material heterogeneities on electrochemical responses. In this Review, we discuss the role of X-ray CT and nano-CT experimentation in the battery field, discuss the incorporation of artificial intelligence and machine learning analyses and provide a perspective on how the combination of multiscale CT imaging techniques can expand the development of predictive multiscale battery behavioural models.

diagnostics↗
DOE OSTI2025

Deep potential molecular dynamics simulations of ion-enhanced etching of silicon by atomic chlorine

The continued development of plasma-assisted processing techniques requires a fundamental understanding of plasma-surface interactions. Molecular dynamics (MD) simulations have been employed to complement experimental studies and better understand the properties of such systems. Recently, machine learning (ML) methods have enabled the development of ab initio-based interatomic potentials, which can be generalized to complex combinations of multiple atom types. In this work, we use ML potentials developed using the Deep Potential Molecular Dynamics (DeepMD) framework to provide a model of ion-enhanced etching of Si by Cl atoms. We demonstrate the importance of proper selection of the training data set to the accuracy of the DeepMD model and compare our results to MD results using empirical potentials, as well as to experimental measurements. Exposure of undoped Si at 300 K to thermal Cl atoms yields a steady-state Cl coverage of 1.25 monolayers, which is slightly lower than the value obtained in previous experimental studies. Predictions of Si etch yields by simultaneous Cl atom and Ar + ion impacts as a function of ion energy, neutral to ion flux ratio, and angle of incidence of the ions are in reasonably good agreement with classical MD results and experimental measurements. Finally, etch yields and SiCl x mixed layer thicknesses during simultaneous bombardment of the Si(100) surface by Cl atoms and Cl + ions are in good agreement with experimental data. In conclusion, the present work is a necessary condition for the extension of the DeepMD procedure to more complex systems of interest in plasma-surface interactions.

Artificial neural networks↗
DOE OSTI2020

LANL's Contribution to the Design and Preparation of the ANL Bubble Experiment #2

In collaboration with Argonne National Laboratory (ANL), Los Alamos National Laboratory (LANL) is assisting in the design and development of portions of the second ANL Bubble Experiment to be performed in late 2020 at ANL. The ANL Bubble Experiment, as called in this report, is a series of direct electron irradiations of a uranyl sulfate solution to produce radiolysis-induced gas bubbles of hydrogen and oxygen. The gas bubbles formed in the solution enhance mixing and heat transfer. The study of the dynamics, shape, and size of radiolysis-induced gas bubbles is of great importance to understand and characterize the thermal and fluid behavior of the solution, especially for the solution based, neutron-induced fission production technique for Mo-99. During the first experiment performed in 2014, ANL’s 35 MeV electron linear accelerator provided average powers of 6, 12, and 15 kW using a rastered beam to homogeneously heat the 15 x 15 x 80-cm uranyl-sulfate solution. Gas bubble size, shape, velocity, solution temperature, and hydrogen and oxygen concentrations were recorded during the irradiations. The details of the experimental setup and results for the first experiment are described in the ANL reports, Design and Construction of Experiment for Direct Electron Irradiation of a Uranyl Sulfate Solution: Bubble Formation and Thermal Hydraulics Studies and Experimental Results for Direct Electron Irradiation of a Uranyl Sulfate Solution: Bubble Formation and Thermal Hydraulics Studies. The purpose of this report is to describe the issues and lessons learned associated with the first experiment and elaborate on designs to improve and obtain more accurate experimental results for the upcoming experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Learning protein fitness models from evolutionary and assay-labeled data

Machine learning-based models of protein fitness typically learn from either unlabeled, evolutionarily related sequences or variant sequences with experimentally measured labels. For regimes where only limited experimental data are available, recent work has suggested methods for combining both sources of information. Toward that goal, we propose a simple combination approach that is competitive with, and on average outperforms more sophisticated methods. Our approach uses ridge regression on site-specific amino acid features combined with one probability density feature from modeling the evolutionary data. Within this approach, we find that a variational autoencoder-based probability density model showed the best overall performance, although any evolutionary density model can be used. Moreover, our analysis highlights the importance of systematic evaluations and sufficient baselines.

59 BASIC BIOLOGICAL SCIENCES↗