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At least 181 records · Page 10

Automatic Organ Segmentation for CT Scans Based on Super-Pixel and Convolutional Neural Networks

Accurate segmentation of specific organ from computed tomography (CT) scans is a basic and crucial task for accurate diagnosis and treatment. To avoid time-consuming manual optimization and to help physicians distinguish diseases, an automatic organ segmentation framework is presented. The framework utilized convolution neural networks (CNN) to classify pixels. To reduce the redundant inputs, the simple linear iterative clustering (SLIC) of super-pixels and the support vector machine (SVM) classifier are introduced. To establish the perfect boundary of organs in one-pixel-level, the pixels need to be classified step-by-step. First, the SLIC is used to cut an image into grids and extract respective digital signatures. Next, the signature is classified by the SVM, and the rough edges are acquired. Finally, a precise boundary is obtained by the CNN, which is based on patches around each pixel-point. The framework is applied to abdominal CT scans of livers and high-resolution computed tomography (HRCT) scans of lungs. The experimental CT scans are derived from two public datasets (Sliver 07 and a Chinese local dataset). Experimental results show that the proposed method can precisely and efficiently detect the organs. This method consumes 38 s/slice for liver segmentation. The Dice coefficient of the liver segmentation results reaches to 97.43%. For lung segmentation, the Dice coefficient is 97.93%. This finding demonstrates that the proposed framework is a favorable method for lung segmentation of HRCT scans.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Charge-density based convolutional neural networks for stacking fault energy prediction in concentrated alloys

A descriptor-less machine learning (ML) model based only on charge density images extracted from density functional theory (DFT) is developed to predict stacking fault energies (SFE) in concentrated alloys. The model is based on convolutional neural networks (CNNs) as one of the promising ML techniques for dealing with complex images and data. Identification of correct descriptors is a key bottleneck to develop ML models for predicting materials properties. Often, in most ML models, textbook physical descriptors such as atomic radius, valence charge and electronegativity are used as descriptors which have limitations because these properties change in concentrated alloys when multiple elements are mixed to form a solid solution. Here, we illustrate that, within the scope of DFT, the search for descriptors can be circumvented by electronic charge density, which is the backbone of the Kohn-Sham DFT and describes the system completely. The performance of our model is demonstrated by predicting SFE of concentrated alloys with an RMSE and R 2 of 6.18 mJ/m 2 and 0.87, respectively, validating the accuracy of the proposed approach.

36 MATERIALS SCIENCE↗

Multi-Task Convolutional Neural Networks for Natural Text Classification

Information extraction and coding of free-text pathology reports is an important activity for cancer registries to support national cancer surveillance. Cancer registrars must process high volumes of pathology reports on an annual basis. We investigated an automated approach using a convolutional neural networks (CNNs) for extracting the primary site, laterality, histology, behavior, and histological grade from unstructured cancer pathology text reports. Our multi-task learning (MTL) with hard parameter sharing approach is used to train a multi-task MT-CNN model for all the tasks. The performance of our proposed approach was compared against a state of-the-art CNN and the commonly used SVM classifier. We observed that the proposed model consistently outperformed the baseline models, especially for the less prevalent classes. Also, the results demonstrate the potential of the proposed method for handling class imbalance within each task.

Yoon, HongJun↗

Modeling Cell Migration with Convolutional Neural Network and Deep Reinforcement Learning

Cell migration modeling is a longstanding biological challenge, which is regulated by a highly complex set of regulatory mechanisms at multiple scales in a developmental system. This study presents a generic framework for regulatory mechanisms discovery during cell migration. This framework uses convolutional neural networks and reinforcement learning to better study navigation rules and mechanisms during cell migration. This framework adopts a flexible model-free approach that directly takes raw images as the sensory input. It can better handle simulation scenarios that involve cell division during embryogenesis. Computational experiments also prove that this model achieves better performance than a previous model with a fully connected neural network.

Wang, Zi↗

Data-Driven Validation of NOvA's Convolutional Neural Network for Electron (Anti)Neutrino Selection

NOvA is a long-baseline neutrino oscillation experiment, designed to make measurements of several oscillation parameters using muon neutrino disappearance and electron neutrino appearance. It consists of two functionally equivalent detectors and utilizes the Fermilab NuMI neutrino beam. NOvA uses a convolutional neural network for particle identification of electron neutrino events with a validation process that includes several data-driven techniques. These Muon Removed studies ensure that our classifier performs the same on data as it does on simulation. In particular, Muon Removed Electron-Added studies involve selecting muon neutrino charged current events from both data and simulation and replacing the muon with a simulated electron of similar energy. For Muon Removed Bremsstrahlung and Muon Removed Decay-in-Flight studies, we remove muonic hits from cosmic muons that have either experienced Bremsstrahlung radiation or decayed in flight, producing samples of pure electromagnetic showers. Each of these electron neutrino-like samples are then evaluated by our classifier to obtain selection efficiencies. Our most recent analysis showed good agreement in the electron selection efficiency between data and simulation using these techniques. Furthermore, these cross-checks can be extended to corrections to our predicted electron neutrino signal. The impact of one such set of corrections on the overall analysis results were also evaluated in thesis.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Predicting Mechanical Properties from Microstructure Images in Fiber-Reinforced Polymers Using Convolutional Neural Networks

Evaluating the mechanical response of fiber-reinforced composites can be extremely time-consuming and expensive. Machine learning (ML) techniques offer a means for faster predictions via models trained on existing input–output pairs and have exhibited success in composite research. This paper explores a fully convolutional neural network modified from StressNet, which was originally used for linear elastic materials, and extended here for a non-linear finite element (FE) simulation to predict the stress field in 2D slices of segmented tomography images of a fiber-reinforced polymer specimen. The network was trained and evaluated on data generated from the FE simulations of the exact microstructure. The testing results show that the trained network accurately captures the characteristics of the stress distribution, especially on fibers, solely from the segmented microstructure images. The trained model can make predictions within seconds in a single forward pass on an ordinary laptop, given the input microstructure, compared to 92.5 h to run the full FE simulation on a high-performance computing cluster. These results show promise in using ML techniques to conduct fast structural analysis for fiber-reinforced composites and suggest a corollary that the trained model can be used to identify the location of potential damage sites in fiber-reinforced polymers.

Sun, Yixuan (ORCID:0000000311093380)↗

Convolutional neural networks for intra-hour solar forecasting based on sky image sequences

Accurate and timely solar forecasts play an increasingly critical role in power systems. Compared to longer forecasting timescales, very short-term solar forecasting has lagged behind in both research and practice. In this paper, we propose deep convolutional neural networks (CNNs) to provide operational intra-hour (10-minute-ahead to 60-minute-ahead) solar forecasts. We develop two CNN structures inspired by a widely-used CNN architecture. The CNNs are tailored to our solar forecasting regression tasks and rely solely on sky image sequences. Case studies based on six years of data (over 150,000 data points) demonstrate that the best CNN model has forecast skill scores of 20%-39% over the naive persistence of cloudiness benchmark, even at these very short timescales. The CNNs also have consistently superior performance when compared to shallow machine learning models with meteorological predictors, where the improvement averages around 7%. The sensitivity analyses show that the sky image length, resolution, and weather conditions have impacts on the deep learning model accuracy. In our intra-hour problem with specific setups, two sky images with a 10-minute 128 x 128 resolution yield the most accurate forecasts. Current limitations, future work, and deployment challenges and solutions are also discussed.

14 SOLAR ENERGY↗

Automated species-level identification of planktic foraminifera using convolutional neural networks, with comparison to human performance

Picking foraminifera from sediment samples is an essential, but repetitive and low-reward task that is well-suited for automation. The first step toward building a picking robot is the development of an automated identification system. We use machine learning techniques to train convolutional neural networks (CNNs) to identify six species of extant planktic foraminifera that are widely used by paleoceanographers, and to distinguish the six species from other taxa. We employ CNNs that were previously built and trained for image classification. Foraminiferal training and identification use reflected light microscope digital images taken at 16 different illumination angles using a light-emitting diode (LED) ring. Overall machine accuracy, as a combination of precision and recall, is better than 80% even with limited training. We compare machine performance to that of human pickers (six experts and five novices) by tasking each with the identification of 540 specimens based on images. Experts achieved comparable precision but poorer recall relative to the machine, with an average accuracy of 63%. Novices scored lower than experts on both precision and recall, for an overall accuracy of 53%. The machine achieved fairly uniform performance across the six species, while participants' scores were strongly species-dependent, commensurate with their past experience and expertise. The machine was also less sensitive to specimen orientation (umbilical versus spiral views) than the humans. Finally, these results demonstrate that our approach can provide a versatile ‘brain’ for an eventual automated robotic picking system.

58 GEOSCIENCES↗

A Convolutional Neural Network Model for Battery Capacity Fade Curve Prediction using Early Life Data

Herein, early prediction of battery performance degradation trends can facilitate research of new materials and cell designs, rapid deployment of batteries in real-world applications, timely replacement of batteries in critical applications, and even the secondary use market. In this study, we design a convolutional neural network model to predict the entire battery capacity fade curve - a critical indicator of battery performance degradation - using first 100 cycles of data (~ three weeks of testing). We use the discharge voltage-capacity curves as input to the model and automate the feature extraction process through the convolutional layers of the network. Our approach can predict the per cycle capacity fade rate and rollover cycle (knee point) in the capacity fade curve, which indicate the onset of rapid capacity decay. On the publicly available graphite/LiFePO 4 battery dataset, optimized networks predict the capacity fade curves, rollover cycle, and end of life with 3.7% (worst-case), 19%, and 17% mean absolute percentage errors, respectively.

25 ENERGY STORAGE↗

Predicting path-dependent diffusion barrier spectra in vast compositional space of multi-principal element alloys via convolutional neural networks

The emergent multi-principal element alloys (MPEAs) provide a vast compositional space to search for novel materials for technological advances. How to screen promising compositions from such an ample design space for targeted properties is a grand challenge. In this report, we demonstrate the state-of-the-art deep learning technology—convolutional neural network (CNN)—in predicting path-dependent vacancy migration energy barrier spectra, which are critical to diffusion behavior and many high-temperature properties, in the hyperdimensional composition space of MPEAs. The developed CNN model, fully capturing local chemical features surrounding each vacancy, accurately and efficiently predicts migration energy barrier of MPEAs with different degrees of chemical short-range order and at any unseen compositions. By varying the size of the local region encapsulating vacancy in the CNN model, we reveal that the length scale influencing vacancy migration is surprisingly extensive, up to its six nearest neighboring shells. The efforts of the CNN model make it promising for developing a database of diffusion barriers for various MPEA systems, which would have profound implications for accelerating alloy screening and discovering new compositions with desirable properties.

36 MATERIALS SCIENCE↗

Identification and denoising of radio signals from cosmic-ray air showers using convolutional neural networks

Radio pulses generated by cosmic-ray air showers can be used to reconstruct key properties like the energy and depth of the electromagnetic component of cosmic-ray air showers. Radio detection threshold, influenced by natural and anthropogenic radio background, can be reduced through various techniques. In this work, we demonstrate that convolutional neural networks (CNNs) are an effective way to lower the threshold. We developed two CNNs: a classifier to distinguish radio signal waveforms from background noise and a denoiser to clean contaminated radio signals. Following the training and testing phases, we applied the networks to air-shower data triggered by scintillation detectors of the prototype station for the enhancement of IceTop, IceCube’s surface array at the South Pole. Over a four-month period, we identified 554 cosmic-ray events in coincidence with IceTop, approximately five times more compared to a reference method based on a cut on the signal-to-noise ratio. Comparisons with IceTop measurements of the same air showers confirmed that the CNNs reliably identified cosmic-ray radio pulses and outperformed the reference method. Additionally, we find that CNNs reduce the false-positive rate of air-shower candidates and effectively denoise radio waveforms, thereby improving the accuracy of the power and arrival time reconstruction of radio pulses.

Abbasi, R↗

Recurrent and convolutional neural networks for sequential multispectral optoacoustic tomography ( MSOT ) imaging

Abstract Multispectral optoacoustic tomography (MSOT) is a beneficial technique for diagnosing and analyzing biological samples since it provides meticulous details in anatomy and physiology. However, acquiring high through‐plane resolution volumetric MSOT is time‐consuming. Here, we propose a deep learning model based on hybrid recurrent and convolutional neural networks to generate sequential cross‐sectional images for an MSOT system. This system provides three modalities (MSOT, ultrasound, and optoacoustic imaging of a specific exogenous contrast agent) in a single scan. This study used ICG‐conjugated nanoworms particles (NWs‐ICG) as the contrast agent. Instead of acquiring seven images with a step size of 0.1 mm, we can receive two images with a step size of 0.6 mm as input for the proposed deep learning model. The deep learning model can generate five other images with a step size of 0.1 mm between these two input images meaning we can reduce acquisition time by approximately 71%.

Juhong, Aniwat↗

Complementing Dynamical Downscaling With Super‐Resolution Convolutional Neural Networks

Despite advancements in Artificial Intelligence (AI) methods for climate downscaling, significant challenges remain for their practicality in climate research. Current AI-methods exhibit notable limitations, such as limited application in downscaling Global Climate Models (GCMs), and accurately representing extremes. To address these challenges, we implement an AI-based methodology using super-resolution convolutional neural networks (SRCNN), trained and evaluated on 40 years of daily precipitation data from a reanalysis and a high-resolution dynamically downscaled counterpart. The dynamical downscaled simulations, constrained using spectral nudging, enable the replication of historical events at a higher resolution. This allows the SRCNN to emulate dynamical downscaling effectively. Modifications, such as incorporating elevation data and data pre-processing enhances overall model performance, while using exponential and quantile loss functions improve the simulation of extremes. Our findings show SRCNN models efficiently and skillfully downscale precipitation from GCMs. Future work will expand this methodology to downscale additional variables for future climate projections.

54 ENVIRONMENTAL SCIENCES↗

Low-dose x-ray tomography through a deep convolutional neural network

Synchrotron-based X-ray tomography offers the potential of rapid large-scale reconstructions of the interiors of materials and biological tissue at fine resolution. However, for radiation sensitive samples, there remain fundamental trade-offs between damaging samples during longer acquisition times and reducing signals with shorter acquisition times. We present a deep convolutional neural network (CNN) method that increases the acquired X-ray tomographic signal by at least a factor of 10 during low-dose fast acquisition by improving the quality of recorded projections. Short exposure time projections enhanced with CNN show similar signal to noise ratios as compared with long exposure time projections and much lower noise and more structural information than low-dose fats acquisition without CNN. We optimized this approach using simulated samples and further validated on experimental nano-computed tomography data of radiation sensitive mouse brains acquired with a transmission X-ray microscopy. We demonstrate that automated algorithms can reliably trace brain structures in datasets collected with low dose-CNN. As a result, this method can be applied to other tomographic or scanning based X-ray imaging techniques and has great potential for studying faster dynamics in specimens.

60 APPLIED LIFE SCIENCES↗

Defect Recognition for Eddy Current Testing of Spent Nuclear Fuel Canister using Convolutional Neural Network

This paper proposes an accurate and robust defect detection solution for 304L and 306L stainless steel (SS) weld. In the proposed solution, Eddy current testing (ECT) is employed to generate 2-dimensional (2D) data for samples under test with defects. The 2D data can be treated as images for deep learning-based defect detection. Since convolutional neural networks (CNNs) are powerful in processing images, CNN is employed in this study for defect detection. Experiments are conducted on a submerged arc welding (SAW) 304L SS weld sample with an artificial crack generated by waterjet cutting. The ECT data on this seeded fault sample is utilized to verify the proposed solution. For this purpose, the ECT measurement are separated as from Fault area and Normal area, which are used for CNN training. After training, the testing data is used for verification. Experimental results demonstrate the feasibility and effectiveness of the proposed solution.

Niu, Guangxing↗

Event Selection and Background Rejection in Time Projection Chambers Using Convolutional Neural Networks and a Specific Application to the AdEPT Gamma-ray Polarimeter Mission

The Advanced Energetic Pair Telescope gamma-ray polarimeter uses a time projection chamber for measuring pair production events and is expected to generate a raw instrument data rate four orders of magnitude greater than is transmittable with typical satellite data communications. GammaNet, a convolutional neural network, proposes to solve this problem by performing event classification on-board for pair production and background events, reducing the data rate to a level that can be accommodated by typical satellite communication systems. In order to train GammaNet, a set of 1.1 × 10(exp 6) pair production events and 10(exp 6) background events were simulated for the Advanced Energetic Pair Telescope using the Geant4 Monte Carlo code. An additional set of 10(exp 6) pair production and 10 background events were simulated to test GammaNet’s capability for background discrimination. With optimization, GammaNet has achieved the proposed background rejection requirements for Galactic Cosmic Ray proton events. Given the best case assumption for downlink speeds, signal sensitivity for pair production ranged between 1.1 ± 0.5% to 69 ± 2% for 5 and 250 MeV incident gamma rays. This range became 0.1 ± 0.1% to 17 ± 2% for the worst case scenario of downlink speeds. The application of a feature visualization algorithm to GammaNet demonstrated decreased response to electronic noise and events exiting or entering the frame and increased response to parallel tracks that are close in proximity. GammaNet has been successfully implemented and shows promising results.

Richard L. Garnett↗

Noise reduction in X-ray photon correlation spectroscopy with convolutional neural networks encoder–decoder models

Abstract Like other experimental techniques, X-ray photon correlation spectroscopy is subject to various kinds of noise. Random and correlated fluctuations and heterogeneities can be present in a two-time correlation function and obscure the information about the intrinsic dynamics of a sample. Simultaneously addressing the disparate origins of noise in the experimental data is challenging. We propose a computational approach for improving the signal-to-noise ratio in two-time correlation functions that is based on convolutional neural network encoder–decoder (CNN-ED) models. Such models extract features from an image via convolutional layers, project them to a low dimensional space and then reconstruct a clean image from this reduced representation via transposed convolutional layers. Not only are ED models a general tool for random noise removal, but their application to low signal-to-noise data can enhance the data’s quantitative usage since they are able to learn the functional form of the signal. We demonstrate that the CNN-ED models trained on real-world experimental data help to effectively extract equilibrium dynamics’ parameters from two-time correlation functions, containing statistical noise and dynamic heterogeneities. Strategies for optimizing the models’ performance and their applicability limits are discussed.

36 MATERIALS SCIENCE↗

DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network

Abstract Background Estimation of the accuracy (quality) of protein structural models is important for both prediction and use of protein structural models. Deep learning methods have been used to integrate protein structure features to predict the quality of protein models. Inter-residue distances are key information for predicting protein’s tertiary structures and therefore have good potentials to predict the quality of protein structural models. However, few methods have been developed to fully take advantage of predicted inter-residue distance maps to estimate the accuracy of a single protein structural model. Result We developed an attentive 2D convolutional neural network (CNN) with channel-wise attention to take only a raw difference map between the inter-residue distance map calculated from a single protein model and the distance map predicted from the protein sequence as input to predict the quality of the model. The network comprises multiple convolutional layers, batch normalization layers, dense layers, and Squeeze-and-Excitation blocks with attention to automatically extract features relevant to protein model quality from the raw input without using any expert-curated features. We evaluated DISTEMA’s capability of selecting the best models for CASP13 targets in terms of ranking loss of GDT-TS score. The ranking loss of DISTEMA is 0.079, lower than several state-of-the-art single-model quality assessment methods. Conclusion This work demonstrates that using raw inter-residue distance information with deep learning can predict the quality of protein structural models reasonably well. DISTEMA is freely at https://github.com/jianlin-cheng/DISTEMA

59 BASIC BIOLOGICAL SCIENCES↗