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3D convolutional neural network approach to multi-scale stress/strain relationships in crystallized materials
While there is a growing appreciation of three-dimensional (3D) neural tissues (i.e., hydrogel-based, organoids, and spheroids), shown to improve cellular health and network activity to mirror brain-like activity in vivo , functional assessment using current electrophysiology techniques (e.g., planar multi-electrode arrays or patch clamp) has been technically challenging and limited to surface measurements at the bottom or top of the 3D tissue. As next-generation MEAs, specifically 3D MEAs, are being developed to increase the spatial precision across all three dimensions (X, Y, Z), development of improved computational analytical tools to discern region-specific changes within the Z dimension of the 3D tissue is needed. In the present study, we introduce a novel computational analytical pipeline to analyze 3D neural network activity recorded from a “bottom-up” 3D MEA integrated with a 3D hydrogel-based tissue containing human iPSC-derived neurons and primary astrocytes. Over a period of ~6.5 weeks, we describe the development and maturation of 3D neural activity (i.e., features of spiking and bursting activity) within cross sections of the 3D tissue, based on the vertical position of the electrode on the 3D MEA probe, in addition to network activity (identified using synchrony analysis) within and between cross sections. Then, using the sequential addition of postsynaptic receptor antagonists, bicuculline (BIC), 2-amino-5-phosphonovaleric acid (AP-5), and 6-cyano-5-nitroquinoxaline-2,3-dione (CNQX), we demonstrate that networks within and between cross sections of the 3D hydrogel-based tissue show a preference for GABA and/or glutamate synaptic transmission, suggesting differences in the network composition throughout the neural tissue. The ability to monitor the functional dynamics of the entire 3D reconstructed neural tissue is a critical bottleneck; here we demonstrate a computational pipeline that can be implemented in studies to better interpret network activity within an engineered 3D neural tissue and have a better understanding of the modeled organ tissue.
From quantum chemical and experimental NMR data, a 3D graph neural network, CASCADE, has been developed to predict carbon and proton chemical shifts. Stereoisomers and conformers of organic molecules can be correctly distinguished.
Zeolites are one of the most widely used materials in the chemical industry due to their nanometer-sized pores that can adsorb and react upon molecules selectively. With hundreds of known framework topologies and hundreds of thousands of computationally predicted structures, the ability to rapidly predict zeolite performance allows researchers to prioritize their efforts on the most promising structures for a given application. Although the accuracy of forcefield-based atomistic simulations has advanced significantly in the past two decades, these simulations can be computationally expensive, especially for long-chain, complex molecules. Here, we present ZeoNet, a representation learning framework using convolutional neural networks (ConvNets) and 3D volumetric representations for predicting adsorption in zeolites. ZeoNet was trained on the task of predicting Henry's constants for adsorption, k H , of n-octadecane in more than 330 000 known and predicted zeolite materials. Employing a 3D grid based on the distances to solvent-accessible surfaces, a volumetric representation that can be generated efficiently, the best-performing ZeoNet achieved a correlation coefficient r 2 = 0.977 and a mean-squared error MSE = 3.8 in ln k H , which corresponds to an error of 9.3 kJ mol -1 in adsorption free energy. In comparison, a model based on hand-designed geometric features has values of r 2 = 0.783 and MSE = 35.7. ZeoNet is also relatively efficient and can process ≈8 structures per second on an Nvidia RTX 2080TI GPU, orders of magnitude faster than forcefield-based simulations. A systematic analysis was conducted to investigate how the choice of ConvNet architectures, the linear dimension (L) and spatial resolution (Δd) of the distance grids, batch size, optimizer, and learning rate impact the model performance. We found that ConvNets based on the ResNet architecture offer the best tradeoff between expressiveness and efficiency. The performance for all models reaches a plateau at L = 30–45 Å and depends less sensitively on grid resolution, with a small benefit around Δd = 0.30–0.45 Å. Finally, saliency maps were visualized to identify which regions of the materials contributed the most to model predictions. It was found, interestingly, that the predictions are driven primarily by the accessible pore volume rather than the region occupied by the framework atoms.
Here we present a novel neural network architecture called AutoAtlas for fully unsupervised partitioning and representation learning of 3D brain Magnetic Resonance Imaging (MRI) volumes. AutoAtlas consists of two neural network components: one neural network to perform multi-label partitioning based on local texture in the volume, and a second neural network to compress the information contained within each partition. We train both of these components simultaneously by optimizing a loss function that is designed to promote accurate reconstruction of each partition, while encouraging spatially smooth and contiguous partitioning, and discouraging relatively small partitions. We show that the partitions adapt to the subject specific structural variations of brain tissue while consistently appearing at similar spatial locations across subjects. AutoAtlas also produces very low dimensional features that represent local texture of each partition. We demonstrate prediction of metadata associated with each subject using the derived feature representations and compare the results to prediction using features derived from FreeSurfer anatomical parcellation. Since our features are intrinsically linked to distinct partitions, we can then map values of interest, such as partition-specific feature importance scores onto the brain for visualization.
Decades of drug development research have explored a vast chemical space for highly active compounds. The exponential growth of virtual libraries enables easy access to billions of synthesizable molecules. Computational modeling, particularly molecular docking, utilizes physics-based calculations to prioritize molecules for synthesis and testing. Nevertheless, the molecular docking process often yields docking poses with favorable scores that prove to be inaccurate with experimental testing. To address these issues, several approaches using machine learning (ML) have been proposed to filter incorrect poses based on the crystal structures. However, most of the methods are limited by the availability of structure data. Here, we propose a new pose classification approach, PECAN2 (Pose Classification with 3D Atomic Network 2), without the need for crystal structures, based on a 3D atomic neural network with Point Cloud Network (PCN). The new approach uses the correlation between docking scores and experimental data to assign labels, instead of relying on the crystal structures. We validate the proposed classifier on multiple datasets including human mu, delta, and kappa opioid receptors and SARS-CoV-2 Mpro. Our results demonstrate that leveraging the correlation between docking scores and experimental data alone enhances molecular docking performance by filtering out false positives and false negatives.
Dendritic microstructures are ubiquitous in nature and are the primary solidification morphologies in metallic materials. Techniques such as X-ray computed tomography (XCT) have provided new insights into dendritic phase transformation phenomena. However, manual identification of dendritic morphologies in microscopy data can be both labor intensive and potentially ambiguous. The analysis of 3D datasets is particularly challenging due to their large sizes (terabytes) and the presence of artifacts scattered within the imaged volumes. Here, in this study, we trained 3D convolutional neural networks (CNNs) to segment 3D datasets. Three CNN architectures were investigated, including a new version of FCDenseNet which we extended to 3D. We show that using hyperparameter optimization (HPO) and fine-tuning techniques, both 2D and 3D CNN architectures outperform the previous state of the art. The 3D U-Net architecture trained in this study produced the best segmentations according to quantitative metrics (intersection-over-union of 95.56% and a boundary displacement error of 0.58 pixels), while 3D FCDense produced the smoothest boundaries and best segmentations according to visual inspection. The trained 3D CNNs are able to segment entire 852 × 852 × 250 voxel 3D volumes in only ~60 s, thus hastening the progress towards a deeper understanding of phase transformation phenomena such as dendritic solidification.
We present a novel adaptive machine-learning based approach for reconstructing three-dimensional (3D) crystals from coherent diffraction imaging. We represent the crystals using spherical harmonics (SH) and generate the corresponding synthetic diffraction patterns. We utilize 3D convolutional neural networks (CNNs) to learn a mapping between 3D diffraction volumes and the SH, which describe the boundary of the physical volumes from which they were generated. We use the 3D CNN-predicted SH coefficients as the initial guesses, which are then fine-tuned using adaptive model-independent feedback for improved accuracy. We also adaptively tune the locations, intensities, and decay rates of collections of radial basis functions in order to reproduce the non-uniform internal structure of 3D objects and demonstrate the method for a synthetic volume that has an internal void and a density ramp.
The 2x2 Demonstrator is a prototype detector for the Deep Underground Neutrino Experiment (DUNE)'s Near Detector. Both the 2x2 Demonstrator and the Near Detector itself will have inactive regions wherein there is no sensitivity to charge deposition and light signals that arise from charged particle interactions with liquid argon. In the 2x2, these inactive regions are positioned in-between the active detector modules, which introduces the challenge of inferring what charge signals ought to look like in these regions. This study explores the use of a Sparse 3D Convolutional Neural Network (ConvNet) to infer missing regions in charged particle tracks. Hits corresponding to energy depositions are voxelized into a three-dimensional (3D) grid for each track. Inactive regions within the tracks are replaced with a dense, rectangular 3D grid of voxels, ensuring consistent step sizes in X, Y, and Z directions. Voxels in these dense regions are initialized with an energy value of -1, indicating nonphysical energy or charge. The model is trained to predict which voxels should activate as part of the track and which should not, with the goal of eventually inferring the missing charge or energy values in these voxels. Results indicate that the model accurately predicts track voxels within ±1 unit in X, Y, or Z directions and effectively identifies non-track voxels, despite some overprediction. The approach shows promise in prediction of missing track regions with some accuracy.
The 2x2 Demonstrator is a prototype detector for the Deep Underground Neutrino Experiment (DUNE)'s Near Detector. Both the 2x2 Demonstrator and the Near Detector itself will have inactive regions wherein there is no sensitivity to charge deposition and light signals that arise from charged particle interactions with liquid argon. In the 2x2, these inactive regions are positioned in-between the active detector modules, which introduces the challenge of inferring what charge signals ought to look like in these regions. This study explores the use of a Sparse 3D Convolutional Neural Network (ConvNet) to infer missing regions in charged particle tracks. Hits corresponding to energy depositions are voxelized into a three-dimensional (3D) grid for each track. Inactive regions within the tracks are replaced with a dense, rectangular 3D grid of voxels, ensuring consistent step sizes in X, Y, and Z directions. Voxels in these dense regions are initialized with an energy value of -1, indicating nonphysical energy or charge. The model is trained to predict which voxels should activate as part of the track and which should not, with the goal of eventually inferring the missing charge or energy values in these voxels. Results indicate that the model accurately predicts track voxels within 1 unit in X, Y, or Z directions and effectively identifies non-track voxels, despite some overprediction. The approach shows promise in prediction of missing track regions with some accuracy.
In recent decades, spaceborne microwave and hyperspectral infrared sounding instruments have significantly benefited weather forecasting and climate science. However, existing retrievals of lower troposphere temperature and humidity profiles have limitations in vertical resolution, and often cannot accurately represent key features such as the mixed layer thermodynamic structure and the inversion at the planetary boundary layer (PBL) top. Because of the existing limitations in PBL remote sensing from space, there is a compelling need to improve routine, global observations of the PBL and enable advances in scientific understanding and weather and climate prediction. To address this, we have developed a new 3D deep neural network (DNN) which enhances detail and reduces noise in Level 2 granules of temperature and humidity profiles from the Atmospheric Infrared Sounder (AIRS)/Advanced Microwave Sounding Unit (AMSU) sounder instruments aboard NASA’s Aqua spacecraft. We show that the enhancement improves accuracy and detail including key features such as capping inversions at the top of the PBL over land, resulting in improved accuracy in estimations of PBL height.
The 2x2 Demonstrator is a prototype of ND-LAr, the liquid argon time-projection chamber of the Deep Underground Neutrino Experiment’s Near Detector complex. Both the 2x2 Demonstrator and ND-LAr are modular detectors that will have pixelated charge readouts and inactive regions wherein there is no sensitivity to charge deposition and light signals that arise from charged particle interactions with liquid argon. In the 2x2, these inactive regions are located in between the active detector modules, which introduces the challenge of inferring what charge signals ought to look like in these regions. This study explores the use of a Sparse 3D Convolutional Neural Network (ConvNet) to infer missing regions in charged particle tracks. Hits corresponding to energy depositions are voxelized into a three-dimensional grid for each track. Voxels that fall into predefined inactive regions are removed to simulate the lack of detector output. The model is trained to infer the topology of the missing track voxels, with the ultimate goal of inferring the missing charge or energy values in these voxels as well. Results indicate that this approach shows promise in prediction of missing track regions with some accuracy.
Unmanned aerial vehicle (UAV)-based remote sensing is gaining momentum in a variety of agricultural and environmental applications. Very-high-resolution remote sensing image sets collected repeatedly throughout a crop growing season are becoming increasingly common. Analytical methods able to learn from both spatial and time dimensions of the data may allow for an improved estimation of crop traits, as well as the effects of genetics and the environment on these traits. Multispectral and geometric time series imagery was collected by UAV on 11 dates, along with ground-truth data, in a field trial of 866 genetically diverse biomass sorghum accessions. We compared the performance of Convolution Neural Network (CNN) architectures that used image data from single dates (two spatial dimensions, 2D) versus multiple dates (two spatial dimensions + temporal dimension, 3D) to estimate lodging detection and severity. Lodging was detected with 3D-CNN analysis of time series imagery with 0.88 accuracy, 0.92 Precision, and 0.83 Recall. This outperformed the best 2D-CNN on a single date with 0.85 accuracy, 0.84 Precision, and 0.76 Recall. The variation in lodging severity was estimated by the best 3D-CNN analysis with 9.4% mean absolute error (MAE), 11.9% root mean square error (RMSE), and goodness-of-fit (R2) of 0.76. This was a significant improvement over the best 2D-CNN analysis with 11.84% MAE, 14.91% RMSE, and 0.63 R2. The success of the improved 3D-CNN analysis approach depended on the inclusion of “before and after” data, i.e., images collected on dates before and after the lodging event. The integration of geometric and spectral features with 3D-CNN architecture was also key to the improved assessment of lodging severity, which is an important and difficult-to-assess phenomenon in bioenergy feedstocks such as biomass sorghum. This demonstrates that spatio-temporal CNN architectures based on UAV time series imagery have significant potential to enhance plant phenotyping capabilities in crop breeding and Precision agriculture applications.
Three-dimensional (3D) cloud retrievals are critical for understanding their impact on climate and other applications such as aviation safety, weather prediction, and remote sensing. However, obtaining high-resolution and accurate vertical representation of clouds remains unsolved due to the limitations imposed by satellite instrumentation, viewing conditions, and the complexity of cloud dynamics. Cloud masks are essential for comprehending various cloud vertical properties, but deriving accurate 3D cloud masks from 2D satellite imagery data is a challenging task. To tackle these challenges, we introduce a physics-informed loss function for training deep learning models that can extend 2D cloud images into 3D cloud masks. The proposed loss, called CloudMask Loss, is composed of two domain knowledge-informed loss terms: one for evaluating cloud position and thickness, and the other for measuring the number of layers. By combining these loss terms, we improve the trainability of the deep learning models for more accurate and meaningful results. We apply the proposed loss function to different neural networks and demonstrate significant improvements in multi-layer cloud mask reconstruction. Utilizing the same neural network architecture, our proposed loss outperforms standard binary crossentropy loss in terms of multi-layer cloud classification accuracy, number of layers accuracy, and thickness mean absolute error (MAE). The proposed loss function can be readily integrated into various neural network architectures, resulting in substantial performance gains in 3D cloud mask generation.
In inertial confinement fusion (ICF), x-ray radiography is a critical diagnostic for measuring implosion dynamics, which contain rich three-dimensional (3D) information. Traditional methods for reconstructing 3D volumes from 2D radiographs, such as filtered backprojection, require radiographs from at least two different angles or lines of sight (LOS). In ICF experiments, the space for diagnostics is limited, and cameras that can operate on fast timescales are expensive to implement, limiting the number of projections that can be acquired. To improve the imaging quality as a result of this limitation, convolutional neural networks (CNNs) have recently been shown to be capable of producing 3D models from visible light images or medical x-ray images rendered by volumetric computed tomography. Here, we propose a CNN to reconstruct 3D ICF spherical shells from single radiographs. We also examine the sensitivity of the 3D reconstruction to different illumination models using preprocessing techniques such as pseudo-flatfielding. To resolve the issue of the lack of 3D supervision, we show that training the CNN utilizing synthetic radiographs produced by known simulation methods allows for reconstruction of experimental data as long as the experimental data are similar to the synthetic data. We also show that the CNN allows for 3D reconstruction of shells that possess low mode asymmetries. Further comparisons of the 3D reconstructions with direct multiple LOS measurements are justified.
We present a physics-constrained neural network (PCNN) approach to solving Maxwell’s equations for the electromagnetic fields of intense relativistic charged particle beams. We create a 3D convolutional PCNN to map time-varying current and charge densities J(r, t) and ρ(r, t) to vector and scalar potentials A(r, t) and φ(r, t) from which we generate electromagnetic fields according to Maxwell’s equations: B = ∇ × A and E = −∇φ − ∂A/∂t. Our PCNNs satisfy hard constraints, such as ∇ · B = 0, by construction. Soft constraints push A and φ toward satisfying the Lorenz gauge.
Additive manufacturing (AM), while commonly used for rapid prototyping and creating components with complex geometries, has not been widely adopted for critical applications across the aerospace, automotive, defense, energy, and medical industries. This is, in part, due to the challenges of controlling flaws and uncertainty in the mechanical behavior of additively manufactured components. In recent years, there has been an increase in research aimed at predicting the final mechanical properties of additively manufactured components during the printing process. To address these issues, a 3D-CNN model was trained using low-cost in situ visible-light camera data, anomaly classifications, and the chosen process parameters to predict the ultimate tensile strength (UTS), yield strength (YS), total elongation (TE), and uniform elongation (UE). The 3D-CNN layers of the model employed attention mechanisms to prioritize features in the data, thereby improving prediction accuracy. Furthermore, the effect of each process parameter and anomaly class is investigated using attention-based dynamic sigmoid weighted gates to interpret the influence each class has on the final prediction. Different combinations of the in situ data were fed into the 3D-CNN, with varying amounts of image layers, to determine the ideal combination for predicting mechanical properties in situ. Here, the 3D-CNN model achieved mean absolute percentage errors (MAPE) below 5% for both UTS and YS while using only a single camera input and under half of the available image layers.
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