scholarly journals DeepCentering: fully automated crystal centering using deep learning for macromolecular crystallography

2019 ◽  
Vol 26 (4) ◽  
pp. 1361-1366 ◽  
Author(s):  
Sho Ito ◽  
Go Ueno ◽  
Masaki Yamamoto
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Drug Discovery ◽  
Data Collection ◽  
High Throughput ◽  
Macromolecular Crystallography ◽  
Automated Data Collection ◽  
Important Method ◽  
X Ray ◽  
Synchrotron Light

High-throughput protein crystallography using a synchrotron light source is an important method used in drug discovery. Beamline components for automated experiments including automatic sample changers have been utilized to accelerate the measurement of a number of macromolecular crystals. However, unlike cryo-loop centering, crystal centering involving automated crystal detection is a difficult process to automate fully. Here, DeepCentering, a new automated crystal centering system, is presented. DeepCentering works using a convolutional neural network, which is a deep learning operation. This system achieves fully automated accurate crystal centering without using X-ray irradiation of crystals, and can be used for fully automated data collection in high-throughput macromolecular crystallography.

Convolutional Neural Network of Atomic Surface Structures to Predict Binding Energies for High-Throughput Screening of Catalysts

2019 ◽  
Author(s):  
Seoin Back ◽  
Junwoong Yoon ◽  
Nianhan Tian ◽  
Wen Zhong ◽  
Kevin Tran ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
High Throughput ◽  
High Throughput Screening ◽  
Binding Energies ◽  
Surface Structures ◽  
Voronoi Polyhedra ◽  
Atomic Surface

We present an application of deep-learning convolutional neural network of atomic surface structures using atomic and Voronoi polyhedra-based neighbor information to predict adsorbate binding energies for the application in catalysis.

scholarly journals A drug discovery-oriented non-invasive protocol for protein crystal cryoprotection by dehydration, with application for crystallization screening.

2021 ◽  
Author(s):  
Dom Bellini
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Protein Crystal ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Water Fraction ◽  
Non Invasive ◽  
Vapour Diffusion ◽  
Large Compound ◽  
Fragment Libraries

In X-ray macromolecular crystallography, cryoprotection of crystals mounted on harvesting loops is achieved when the water in the sample solvent transitions to vitreous ice before crystalline ice forms. This is achieved by rapid cooling in liquid nitrogen or propane. Protocols for protein crystal cryoprotection are based on either increasing environmental pressure or reducing the water fraction in the solvent. This study presents a new protocol for cryoprotecting crystals. It is based on vapour diffusion dehydration of the crystal drop to reduce the water fraction in the solvent by adding a highly concentrated salt solution, 13 M potassium formate (KF13), directly to the reservoir. Cryoprotection by the KF13 protocol is non-invasive to the crystal, high throughput, not labour intensive, can benefit diffraction resolution and ligand binding, and is very useful in cases with high redundancy such as drug discovery projects which utilize very large compound or fragment libraries. Moreover, an application of KF13 to discover new crystal hits from clear drops of equilibrated crystallization screening plates is also shown.

scholarly journals MFDNN: Multi-channel feature deep neural network algorithm to identify Covid19 chest X-ray images

2021 ◽  
Author(s):  
Liangrui Pan ◽  
boya ji ◽  
Xiaoqi wang ◽  
shaoliang peng
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
Test Accuracy ◽  
Learning Networks ◽  
X Ray ◽  
Network Algorithm ◽  
Life Saving ◽  
Chest X Ray ◽  
Neural Network Algorithm

The use of chest X-ray images (CXI) to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) caused by Coronavirus Disease 2019 (COVID-19) is life-saving important for both patients and doctors. This research proposed a multi-channel feature deep neural network algorithm to screen people infected with COVID-19. The algorithm integrates data oversampling technology and a multi-channel feature deep neural network model to carry out the training process in an end-to-end manner. In the experiment, we used a publicly available CXI database with 10,192 Normal, 6012 Lung Opacity (Non-COVID lung infection), and 1345 Viral Pneumonia images. Compared with traditional deep learning models (Densenet201, ResNet50, VGG19, GoogLeNet), the MFDNN model obtains an average test accuracy of 93.19% in all data. Furthermore, in each type of screening, the precision, recall, and F1 Score of the MFDNN model are also better than traditional deep learning networks. Secondly, compared with the latest CoroDet model, the MFDNN algorithm is 1.91% higher than the CoroDet model in the experiment of detecting the four categories of COVID19 infected persons. Finally, our experimental code will be placed at https://github.com/panliangrui/covid19.

Using Convolutional Neural Networks for the Detection of Spinal Transverse Processes

2019 ◽  
Author(s):  
Victoria Wu
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Transverse Process ◽  
Classification Model ◽  
Ultrasound Images ◽  
Ultrasound Scan ◽  
X Ray ◽  
Scoliosis Screening

Introduction: Scoliosis, an excessive curvature of the spine, affects approximately 1 in 1,000 individuals. As a result, there have formerly been implementations of mandatory scoliosis screening procedures. Screening programs are no longer widely used as the harms often outweigh the benefits; it causes many adolescents to undergo frequent diagnosis X-ray procedure This makes spinal ultrasounds an ideal substitute for scoliosis screening in patients, as it does not expose them to those levels of radiation. Spinal curvatures can be accurately computed from the location of spinal transverse processes, by measuring the vertebral angle from a reference line [1]. However, ultrasound images are less clear than x-ray images, making it difficult to identify the spinal processes. To overcome this, we employ deep learning using a convolutional neural network, which is a powerful tool for computer vision and image classification [2]. Method: A total of 2,752 ultrasound images were recorded from a spine phantom to train a convolutional neural network. Subsequently, we took another recording of 747 images to be used for testing. All the ultrasound images from the scans were then segmented manually, using the 3D Slicer (www.slicer.org) software. Next, the dataset was fed through a convolutional neural network. The network used was a modified version of GoogLeNet (Inception v1), with 2 linearly stacked inception models. This network was chosen because it provided a balance between accurate performance, and time efficient computations. Results: Deep learning classification using the Inception model achieved an accuracy of 84% for the phantom scan.  Conclusion: The classification model performs with considerable accuracy. Better accuracy needs to be achieved, possibly with more available data and improvements in the classification model.  Acknowledgements: G. Fichtinger is supported as a Canada Research Chair in Computer-Integrated Surgery. This work was funded, in part, by NIH/NIBIB and NIH/NIGMS (via grant 1R01EB021396-01A1 - Slicer+PLUS: Point-of-Care Ultrasound) and by CANARIE’s Research Software Program.    Figure 1: Ultrasound scan containing a transverse process (left), and ultrasound scan containing no transverse process (right).                                Figure 2: Accuracy of classification for training (red) and validation (blue). References:           Ungi T, King F, Kempston M, Keri Z, Lasso A, Mousavi P, Rudan J, Borschneck DP, Fichtinger G. Spinal Curvature Measurement by Tracked Ultrasound Snapshots. Ultrasound in Medicine and Biology, 40(2):447-54, Feb 2014.           Krizhevsky A, Sutskeyer I, Hinton GE. (2012). ImageNet Classification with Deep Convolutional Neural Networks. Advances in Neural Information Processing Systems 25:1097-1105. 

scholarly journals Automated harvesting and processing of protein crystals through laser photoablation

2016 ◽  
Vol 72 (4) ◽  
pp. 454-466 ◽  
Author(s):  
Ulrich Zander ◽  
Guillaume Hoffmann ◽  
Irina Cornaciu ◽  
Jean-Pierre Marquette ◽  
Gergely Papp ◽  
...  
Keyword(s):  
Data Collection ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
New Methods ◽  
Repeated Sample ◽  
Sample Recovery ◽  
Through Diffusion ◽  
X Ray Background ◽  
Low X

Currently, macromolecular crystallography projects often require the use of highly automated facilities for crystallization and X-ray data collection. However, crystal harvesting and processing largely depend on manual operations. Here, a series of new methods are presented based on the use of a low X-ray-background film as a crystallization support and a photoablation laser that enable the automation of major operations required for the preparation of crystals for X-ray diffraction experiments. In this approach, the controlled removal of the mother liquor before crystal mounting simplifies the cryocooling process, in many cases eliminating the use of cryoprotectant agents, while crystal-soaking experiments are performed through diffusion, precluding the need for repeated sample-recovery and transfer operations. Moreover, the high-precision laser enables new mounting strategies that are not accessible through other methods. This approach bridges an important gap in automation and can contribute to expanding the capabilities of modern macromolecular crystallography facilities.

scholarly journals An Efficient Deep Learning Approach to Pneumonia Classification in Healthcare

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Okeke Stephen ◽  
Mangal Sain ◽  
Uchenna Joseph Maduh ◽  
Do-Un Jeong
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Data Augmentation ◽  
Classification Performance ◽  
Learning Approaches ◽  
X Ray ◽  
Chest X Ray

This study proposes a convolutional neural network model trained from scratch to classify and detect the presence of pneumonia from a collection of chest X-ray image samples. Unlike other methods that rely solely on transfer learning approaches or traditional handcrafted techniques to achieve a remarkable classification performance, we constructed a convolutional neural network model from scratch to extract features from a given chest X-ray image and classify it to determine if a person is infected with pneumonia. This model could help mitigate the reliability and interpretability challenges often faced when dealing with medical imagery. Unlike other deep learning classification tasks with sufficient image repository, it is difficult to obtain a large amount of pneumonia dataset for this classification task; therefore, we deployed several data augmentation algorithms to improve the validation and classification accuracy of the CNN model and achieved remarkable validation accuracy.

scholarly journals A deep-learning technique for phase identification in multiphase inorganic compounds using synthetic XRD powder patterns

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jin-Woong Lee ◽  
Woon Bae Park ◽  
Jin Hee Lee ◽  
Satendra Pal Singh ◽  
Kee-Sun Sohn
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Inorganic Compounds ◽  
Phase Identification ◽  
X Ray Diffraction ◽  
X Ray ◽  
Learning Techniques ◽  
Learning Technique ◽  
Xrd Patterns

AbstractHere we report a facile, prompt protocol based on deep-learning techniques to sort out intricate phase identification and quantification problems in complex multiphase inorganic compounds. We simulate plausible powder X-ray diffraction (XRD) patterns for 170 inorganic compounds in the Sr-Li-Al-O quaternary compositional pool, wherein promising LED phosphors have been recently discovered. Finally, 1,785,405 synthetic XRD patterns are prepared by combinatorically mixing the simulated powder XRD patterns of 170 inorganic compounds. Convolutional neural network (CNN) models are built and eventually trained using this large prepared dataset. The fully trained CNN model promptly and accurately identifies the constituent phases in complex multiphase inorganic compounds. Although the CNN is trained using the simulated XRD data, a test with real experimental XRD data returns an accuracy of nearly 100% for phase identification and 86% for three-step-phase-fraction quantification.

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