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DOE OSTI2021

Optimal dimensionality selection for independent component analysis of transcriptomic data

Independent component analysis is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expression datasets, independent component analysis effectively reveals both the source signals of the transcriptome as co-regulated gene sets, and the activity levels of the underlying regulators across diverse experimental conditions. Two major variables that affect the final gene sets are the diversity of the expression profiles contained in the underlying data, and the user-defined number of independent components, or dimensionality, to compute. Availability of high-quality transcriptomic datasets has grown exponentially as high-throughput technologies have advanced; however, optimal dimensionality selection remains an open question. We computed independent components across a range of dimensionalities for four gene expression datasets with varying dimensions (both in terms of number of genes and number of samples). We computed the correlation between independent components across different dimensionalities to understand how the overall structure evolves as the number of user-defined components increases. We then measured how well the resulting gene clusters reflected known regulatory mechanisms, and developed a set of metrics to assess the accuracy of the decomposition at a given dimension. We found that over-decomposition results in many independent components dominated by a single gene, whereas under-decomposition results in independent components that poorly capture the known regulatory structure. From these results, we developed a new method, called OptICA, for finding the optimal dimensionality that controls for both over- and under-decomposition. Specifically, OptICA selects the highest dimension that produces a low number of components that are dominated by a single gene. We show that OptICA outperforms two previously proposed methods for selecting the number of independent components across four transcriptomic databases of varying sizes. OptICA avoids both over-decomposition and under-decomposition of transcriptomic datasets resulting in the best representation of the organism’s underlying transcriptional regulatory network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Transfer Learning-Based Independent Component Analysis

Understanding the underlying component structure is crucial for multivariate signal analysis. Among all the techniques that try to learn the latent structure, independent component analysis (ICA) is one of the most important and popular methods, which aims to extract independent components from multivariate signals and enables further analysis. For example, in electroencephalogram (EEG) analysis, artifacts filtering and disease detection are conducted based on the independent components of the signals. One critical challenge in existing ICA approaches is that the component extraction accuracy may degrade when the available data of a unit are limited. To address this issue, this paper proposes a transfer learning-based ICA method by innovatively transferring component distribution from a source domain, so that accurate component extraction results can be achieved even when only limited data are available in the target domain. To the best of our knowledge, this is the first work that leverages transfer learning to improve ICA accuracy with limited available data. In particular, we first extract all the independent components from the source domain by maximizing the log-likelihood function with a Newton-like method on a smooth manifold. Then for the target domain, the component with the largest negentropy is extracted in each round. To effectively leverage the knowledge from the source domain and to prevent the negative transfer, we try to find a component in the source domain that matches the component we are extracting. The probability density function of the matched component will then be used to improve the component extraction accuracy if such matched component can be found; otherwise, no knowledge will be transferred. Finally, numerical simulations and a case study with electrocardiogram (ECG) data are conducted, showing the effectiveness of the proposed method in transferring knowledge and reducing negative transfer.

42 ENGINEERING↗

DOE OSTI2020

Neural Learning Based Blind Source Separation for Detection of Material Defects in Pulsed Thermography Images

In this paper, we introduce a neural learning-based approach to blind source separation for detection of material flaws in pulsed thermography (PT) images. This approach can be used to detect internal defects (pores) in metallic Additively Manufactured (AM) materials. Such defects occur in high-strength alloys produced with direct laser sintering AM method for nuclear energy applications. Pulsed thermal imaging system utilizes a high intensity flash lamp to rapidly heat surface of sample, a high sensitivity infrared camera to capture data of surface temperature variations. The data cube obtained with PT (stack of surface temperature images at different times) can be analyzed with image processing algorithms to detect material defects. Compared with conventional nondestructive evaluation (NDE) methods, such as digital radiography and ultrasonic testing, the PT pulsed infrared thermal detection technique has advantages of one-sided non-contact measurements, fast processing of large sample areas captured in one image. Detection of small material defects requires finding features in thermal images, which have signal contrast levels approaching sensitivity limit of IR camera. In this study, an optimized Neural Learning based Blind Source Separation (NLBSS) algorithm, including Principal Component Analysis (PCA), and Independent Component Analysis (ICA) is demonstrated to automatically extract principal temporal and spatial features of thermography frames to enhance flaw detection. By using the NLBSS algorithm, material internal defects can be automatically detected. Furthermore, this processing approach compensates for experimental thermal imaging artifacts, such as noise and uneven heating. By merging artificial intelligence with the photothermic, the NDE system detects internal calibrated defects of various sizes and depths in AM nuclear-grade metallic alloys.

Zhang, Xin↗

DOE OSTI2020

Imaging of Calibrated Defects in Additively Manufactured Materials: Pulsed Thermal Tomography Nondestructive Examination of Additively Manufactured Reactor Materials and Components

Additive manufacturing (AM, or 3D printing) for commercial nuclear energy applications is an emerging method for cost-efficient manufacturing aimed at replacing aging nuclear reactor parts and reducing costs for new construction. Known material flaws in AM include low-density regions consisting of non-sintered powder, which have to be detected to ensure the safety of long-term performance nuclear reactor components. Currently, limited options are available for nondestructive evaluation (NDE), either during or post manufacturing. As a solution to NDE of AM, we are developing pulsed thermal imaging which is non-contact, one-sided, and scalable to arbitrary size and shape of the AM parts. Pulsed thermography (PT) system utilizes a high intensity flash lamp to rapidly heat surface of sample, and a high sensitivity fast-frame megapixel infrared (IR) camera to capture data of surface temperature variations. The acquired data cube consists of a stack of surface temperature images taken at different times. Information about material internal defects is extracted by analyzing the data cube. This report provides results of preliminary performance evaluation of pulsed thermal imaging capability in detection of imprinted flaws in AM metallic structures. The flaws were introduced into AM parts as imprinted hemispherical low density regions, consisting of trapped un-sintered metallic powder. Specimens for developed for this study consisted of AM stainless steel 316 and Inconel 718 plates. The diameters of imprinted defects varied from 1mm to 8mm, and their depths below the plate flat surface varied between 1mm and 6mm. Pulsed thermal tomography (PTT) processes the measured data cube to obtain 3D reconstructions of material effusivity using a unique inversion algorithm developed at Argonne. PTT has been previously used in imaging of similar size flat bottom hole (FBH) simulated defects in stainless steel 316 and Inconel 718 specimens. In the study involving AM specimens, PTT imaging results have shown that 1mm-diameter defects located 1mm and 2mm below the surface of specimens were detectable. Larger size defects were detectable at greater depth. We also explored an alternative approach to detection of material flaws in PT data cube, which is using neural learning-based approach to blind source separation. Detection of small material defects requires finding features in the data cube which have signal contrast levels approaching sensitivity limit of IR camera. In this study, an optimized Neural Learning based Blind Source Separation (NLBSS) algorithm, including Principal Component Analysis (PCA), and Independent Component Analysis (ICA) is demonstrated to automatically extract principal temporal and spatial features of thermography frames to enhance flaw detection. By using the NLBSS algorithm, material internal defects can be automatically detected. Furthermore, this processing approach compensates for experimental thermal imaging artifacts, such as noise and uneven heating. By merging artificial intelligence with phtotothermics, the NDE system detects internal calibrated defects of various sizes and depths in AM nuclear-grade metallic alloys.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Performance of Compact Pulsed Thermal Imaging System for In-Service Applications. Pulsed thermal tomography nondestructive examination of additively manufactured reactor materials and components

Additive manufacturing (AM) is an emerging method for cost-efficient fabrication of complex topology nuclear reactor parts from high-strength corrosion resistance alloys, such as stainless steel and Inconel. AM of metallic structures for nuclear energy applications is currently based on laser powder bed fusion (LPBF) process, which has the capability of melting metallic powder and net shaping the structures with relatively high precision. Some of the challenges with using LPBF method for nuclear manufacturing include the possibility of introducing pores into metallic structures. Integrity of AM structures needs to be evaluated nondestructively because material flaws could lead to premature failures due to creep in high temperature nuclear reactor environment. Currently, there exist limited capabilities to evaluate actual AM structures nondestructively. Pulsed Thermography (PT) imaging provides a capability for non-destructive evaluation (NDE) of sub-surface defects in arbitrary size structures. The PT method is based on recording material surface temperature transients with infrared (IR) camera following thermal pulse delivered on material surface with flash light. The PT method has advantages for NDE of actual AM structures because the method involves one-sided non-contact measurements and fast processing of large sample areas captured in one image. The data cube of PT measurements consists of surface temperature taken at sequential time intervals T(x,y,t). Material defects can be detected either by analyzing the thermograms T(x,y,t) data cube, or by using thermal tomography (TT) algorithm to obtain 3D spatial reconstruction of thermal effusivity e(x,y,z). To reduce the cost and enable in-service NDE in spatially constrained environment, it is highly desirable to develop PT with compact and inexpensive IR camera. Following initial qualification of an AM component for deployment in a nuclear reactor, a compact PT system can also be used for in-service nondestructive evaluation (NDE) applications. However, data cube obtained with PT based on compact IR camera suffers from strong thermal noises and loss of features due to relatively low sampling rate. In this report we describe two unsupervised machine learning (ML) algorithms for enhancement of PT images obtained with compact IR camera. In one approach, we introduce Sparse Coding Discrete Cosine Transform (SC/DCT) algorithm to remove additive white Gaussian noise (AWGN) from spatial thermal effusivity reconstructions. In another approach we introduce a Spatial Temporal Denoised Thermal Source Separation (STDTSS) ML algorithm to process thermograms. The STDTSS algorithm consists of spatial and temporal denoising using Gaussian and Savitzky–Golay filtering, followed by the matrix decomposition using Principal Component Analysis (PCA), and Independent Component Analysis (ICA) to automatically detect flaws. In the work described in this report, we constructed a compact PT system using a relatively small and low-cost FLIR A65 camera, consisting on uncooled microbolometer detector. Performance of SC/DCT algorithm was demonstrated on enhancing TT images of Inconel 718 AM plate. Performance of the STDTSS methods was investigated using thermography data obtained from imaging stainless steel 316L specimens produced with LPBF method with imprinted calibrated porosity defects.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

ABSTRACT There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (“functional modules”), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida . Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

09 BIOMASS FUELS↗

DOE OSTI2025

Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase

ABSTRACT The composition of bacterial transcriptomes is determined by the transcriptional regulatory network (TRN). The TRN regulates the transition from one physiological state to another. Here, we use independent component analysis to monitor the composition of the transcriptome during the transition from the exponential growth phase to the stationary phase. With Escherichia coli K-12 MG1655 as a model strain, we trigger the transition using carbon, nitrogen, and sulfur starvation. We find that (i) the transition to the stationary phase accompanies common transcriptome changes, including increased stringent responses and reduced production of cellular building blocks and energy regardless of the limiting element; (ii) condition-specific changes are strongly associated with transcriptional regulators ( e.g. , Crp, NtrC, CysB, Cbl) responsible for metabolizing the limiting element; and (iii) the shortage of each limiting element differentially affects the production of amino acids and extracellular polymers. This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria. IMPORTANCE Nutrient limitations are critical environmental perturbations in bacterial physiology. Despite its importance, a detailed understanding of how bacterial transcriptomes are adjusted has been limited. By utilizing independent component analysis (ICA) to decompose transcriptome data, this study reveals key regulatory events that enable bacteria to adapt to nutrient limitations. The findings not only highlight common responses, such as the stringent response, but also condition-specific regulatory shifts associated with carbon, nitrogen, and sulfur starvation. The insights gained from this work advance our knowledge of bacterial physiology, gene regulation, and metabolic adaptation.

Lim, Hyun Gyu (ORCID:0000000204692388)↗

DOE OSTI2023

An ICA-Based HVAC Load Disaggregation Method Using Smart Meter Data

This paper presents an independent component analysis (ICA) based unsupervised-learning method for heat, ventilation, and air-conditioning (HVAC) load disaggregation using row-resolution (i.e., 15 minutes) smart meter data. We first demonstrate that the electricity consumption profiles on mild-temperature days can be used to approximate the base load on hot days. A residual load profile can then be calculated by subtracting the mild-day load profile from the hot-day load profile. The residual load profiles are processed using ICA for HVAC load extraction. An optimization-based algorithm is proposed for post-adjustment of the ICA results, considering two bounding factors for enhancing the robustness of the ICA algorithm. First, we use the hourly HVAC energy bounds computed from the relationship between HVAC load and temperature to remove unrealistic HVAC load spikes. Second, we exploit the dependency between the daily nocturnal and diurnal loads extracted from historical meter data to smooth the base load profile. Pecan Street data with sub-metered HVAC data were used to test and verify the proposed methods. Simulation results demonstrated that the proposed method is computationally efficient and robust across multiple customers.

Kim, Hyeonjin↗

DOE OSTI2024

Unsupervised learning-enabled pulsed infrared thermographic microscopy of subsurface defects in stainless steel

Metallic structures produced with laser powder bed fusion (LPBF) additive manufacturing method (AM) frequently contain microscopic porosity defects, with typical approximate size distribution from one to 100 microns. Presence of such defects could lead to premature failure of the structure. In principle, structural integrity assessment of LPBF metals can be accomplished with nondestructive evaluation (NDE). Pulsed infrared thermography (PIT) is a non-contact, one-sided NDE method that allows for imaging of internal defects in arbitrary size and shape metallic structures using heat transfer. PIT imaging is performed using compact instrumentation consisting of a flash lamp for deposition of a heat pulse, and a fast frame infrared (IR) camera for measuring surface temperature transients. However, limitations of imaging resolution with PIT include blurring due to heat diffusion, sensitivity limit of the IR camera. We demonstrate enhancement of PIT imaging capability with unsupervised learning (UL), which enables PIT microscopy of subsurface defects in high strength corrosion resistant stainless steel 316 alloy. PIT images were processed with UL spatial–temporal separation-based clustering segmentation (STSCS) algorithm, refined by morphology image processing methods to enhance visibility of defects. The STSCS algorithm starts with wavelet decomposition to spatially de-noise thermograms, followed by UL principal component analysis (PCA), fine-tuning optimization, and neural learning-based independent component analysis (ICA) algorithms to temporally compress de-noised thermograms. The compressed thermograms were further processed with UL-based graph thresholding K-means clustering algorithm for defects segmentation. The STSCS algorithm also includes online learning feature for efficient re-training of the model with new data. For this study, metallic specimens with calibrated microscopic flat bottom hole defects, with diameters in the range from 203 to 76 µm, were produced using electro discharge machining (EDM) drilling. While the raw thermograms do not show any material defects, using STSCS algorithm to process PIT images reveals defects as small as 101 µm in diameter. To the best of our knowledge, this is the smallest reported size of a sub-surface defect in a metal imaged with PIT, which demonstrates the PIT capability of detecting defects in the size range relevant to quality control requirements of LPBF-printed high-strength metals.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network

Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida KT2440, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida KT2440 and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.

09 BIOMASS FUELS↗

DOE OSTI2021

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

In vitro antibiotic susceptibility testing often fails to accurately predict in vivo drug efficacies, in part due to differences in the molecular composition between standardized bacteriologic media and physiological environments within the body. Here, we investigate the interrelationship between antibiotic susceptibility and medium composition in Escherichia coli K-12 MG1655 as contextualized through machine learning of transcriptomics data. Application of independent component analysis, a signal separation algorithm, shows that complex phenotypic changes induced by environmental conditions or antibiotic treatment are directly traced to the action of a few key transcriptional regulators, including RpoS, Fur, and Fnr. Integrating machine learning results with biochemical knowledge of transcription factor activation reveals medium-dependent shifts in respiration and iron availability that drive differential antibiotic susceptibility. By extension, the data generation and data analytics workflow used here can interrogate the regulatory state of a pathogen under any measured condition and can be applied to any strain or organism for which sufficient transcriptomics data are available.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Implementing nonlinear optics from Off-Energy closed orbit at NSLS-II

To characterize the second-order (chromatic sextupole) magnet lattice with high precision, we implemented nonlinear optics from off-energy closed orbit (NOECO) tool based on the linear optics from closed orbit modulation (LOCOM) method, named LOCOM-NOECO. The preliminary numerical study indicates that 1–2% precision can be achieved for the calibration of chromatic sextupoles. Further, this accuracy could potentially help in resolving some long-standing challenges of NSLS-II (e.g., the discrepancy between the designed and measured dynamic apertures) if such high precision can be fulfilled. As an independent crosscheck, we also implemented NOECO based on the independent component analysis (ICA) method using turn-by-turn (TBT) BPM data, named ICA-NOECO. Both ICA-NOECO and LOCOM-NOECO have been successfully applied to identify the pre-dialed random errors of a chromatic sextupole family including five power supplies, and achieved the root mean square (RMS) residual error of 1% and peak error less than 2%. Moreover, to mitigate the chromatic sextupole error effect, we applied the correction and achieved significant improvements in the injection efficiency as well as the dynamic apertures.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2026

Unbiased primordial gravitational wave inference from the CMB with SMICA

The detection of primordial gravitational waves in Cosmic Microwave Background B-mode polarization observations requires accurate and robust subtraction of astrophysical contamination. We show, using a blind Spectral Matching Independent Component Analysis, that it is possible to infer unbiased estimates of the primordial B-mode signal from ground-based observations of a small patch of sky even for highly complex foreground contamination. This work, originally performed in the context of configuration studies for a future CMB-S4 observatory, is highly relevant for the analysis of observations by the current generation of CMB experiments.

cosmological parameters from CMBR↗

DOE OSTI2020

Flow-based likelihoods for non-Gaussian inference

We investigate the use of data-driven likelihoods to bypass a key assumption made in many scientific analyses, which is that the true likelihood of the data is Gaussian. In particular, we suggest using the optimization targets of flow-based generative models, a class of models that can capture complex distributions by transforming a simple base distribution through layers of nonlinearities. We call these flow-based likelihoods (FBL). We analyze the accuracy and precision of the reconstructed likelihoods on mock Gaussian data, and show that simply gauging the quality of samples drawn from the trained model is not a sufficient indicator that the true likelihood has been learned. We nevertheless demonstrate that the likelihood can be reconstructed to a precision equal to that of sampling error due to a finite sample size. We then apply FBLs to mock weak lensing convergence power spectra, a cosmological observable that is significantly non-Gaussian (NG). We find that the FBL captures the NG signatures in the data extremely well, while other commonly used data-driven likelihoods, such as Gaussian mixture models and independent component analysis, fail to do so. This suggests that works that have found small posterior shifts in NG data with data-driven likelihoods such as these could be underestimating the impact of non-Gaussianity in parameter constraints. By introducing a suite of tests that can capture different levels of NG in the data, we show that the success or failure of traditional data-driven likelihoods can be tied back to the structure of the NG in the data. Here, unlike other methods, the flexibility of the FBL makes it successful at tackling different types of NG simultaneously. Because of this, and consequently their likely applicability across datasets and domains, we encourage their use for inference when sufficient mock data are available for training.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Impulsive Magnetic Anomaly Detection At the 100-m Scale With an Array of Induction Coil Magnetometers

We demonstrate magnetic anomaly detection (MAD) using an array of 24 commercial induction coil magnetometers with stand-off distances from a pulsed 99.8(3) kA·m 2 magnetic dipole source of 260–1200 m. The sparse array is used to estimate the magnetic dipole location, magnitude, and orientation. We demonstrate how independent component analysis (ICA) improves the accuracy and precision of the magnetometer array when estimating the dipole parameters. Using sensor responses recorded from individual source pulses, we estimate the dipole location to within 29 ± 2 m, the magnitude to within 3 ± 3 kA·m 2 , and dipole orientation error to within 19 ± 0.6°.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Report on PTT Imaging of Defects in AM Metallic Materials-Part 2

36 MATERIALS SCIENCE↗

DOE OSTI2022

Pulsed Thermal Tomography Nondestructive Examination of Additively Manufactured Reactor Materials and Components (Final Technical Report)

Metal Additive Manufacturing (AM) is a promising method for cost-efficient fabrication of complex shape structures for applications in harsh environment, such as in a nuclear reactor. However, internal defects (pores) occur in high-strength AM alloys, which are manufactured with Laser Powder Bed Fusion (LPBF) AM method. Pulsed Infrared Thermography (PIT) is an efficient nondestructive evaluation (NDE) method to examine actual structures, because this method offers one-sided non-contact measurements, and fast processing of large sample areas. However, imaging of material defects, particularly defects with sizes at microscopic level, is challenging. In this report, we benchmark the performance of several Unsupervised Learning (UL) algorithms designed to enhance imaging of microscopic defects in metals with PIT. UL aims to learn the latent principal patterns (dictionaries) in PIT data to detect defects with minimal human supervision. Performance of Independent Component Analysis (ICA), Sparse Coding (SC), Principal Component Analysis (PCA) and Exploratory Factor Analysis (EFA) was compared using F-score, UL model training time and defects reconstruction time. We obtained the average F-score of 0.75, and a highest F-score of 0.89 for the EFA algorithm. Overall, EFA outperforms other UL algorithms considered in this study. In another approach, we investigate Thermal Tomography (TT), which is a computational method for reconstruction of depth profile of internal material defects from PIT nondestructive evaluation (NDE). TT algorithm obtains depth reconstructions of thermal effusivity, which has been shown to provide visualization of subsurface internals defects in metals. In many applications, one needs to determine the defect shape and orientation from reconstructed effusivity images. Interpretation of TT images is non-trivial because of blurring, which increases with depth due to heat diffusion-based nature of image formation. We have developed a deep learning convolutional neural network (CNN) to classify size and orientation of subsurface material defects in TT images. CNN was trained with TT images produced with computer simulations of 2D metallic structures (thin plates) containing elliptical subsurface voids. Performance of CNN was investigated using test TT images developed with computer simulations of plates containing elliptical defects, and defects with shape imported from scanning electron microscopy (SEM) images. CNN demonstrated the ability to classify radii and angular orientation of elliptical defects in previously unseen test TT images. We have also demonstrated that CNN trained on TT images of elliptical defects is capable of classifying shape and orientation of irregular defects. Training the CNN on irregular defect shapes instead of on elliptical shapes would make the resulting classifications more descriptive of actual defect shapes. However, this requires a much higher volume of SEM images of material defects, which are difficult to obtain because of random occurrence of defects in LPBF. To address this challenge, we developed a generative adversarial network (GAN) to augment the existing dataset of SEM defect images. The GAN model is demonstrated to create novel yet realistic defect shapes that can be used as input for simulated PTT images to train CNN. We also investigate several approaches based on Gaussian Random Circle and Bezier Curves for constructing parametric models of irregular-shape defects.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

59 BASIC BIOLOGICAL SCIENCES↗