scholarly journals Identification of Low Population States in Cryo-EM Using Deep Learning

2021 ◽  
Author(s):  
Alec Fraser ◽  
Nikolai S Prokhorov ◽  
John M Miller ◽  
Ekaterina S Knyazhanskaya ◽  
Petr G Leiman

Cryo-EM has made extraordinary headway towards becoming a semi-automated, high-throughput structure determination technique. In the general workflow, high-to-medium population states are grouped into two- and three-dimensional classes, from which structures can be obtained with near-atomic resolution and subsequently analyzed to interpret function. However, low population states, which are also functionally important, are often discarded. Here, we describe a technique whereby low population states can be efficiently identified with minimal human effort via a deep convolutional neural network classifier. We use this deep learning classifier to describe a transient, low population state of bacteriophage A511 in the midst of infecting its bacterial host. This method can be used to further automate data collection and identify other functionally important low population states.

2021 ◽  
Vol 15 ◽  
Author(s):  
Saba Momeni ◽  
Amir Fazlollahi ◽  
Leo Lebrat ◽  
Paul Yates ◽  
Christopher Rowe ◽  
...  

Cerebral microbleeds (CMB) are increasingly present with aging and can reveal vascular pathologies associated with neurodegeneration. Deep learning-based classifiers can detect and quantify CMB from MRI, such as susceptibility imaging, but are challenging to train because of the limited availability of ground truth and many confounding imaging features, such as vessels or infarcts. In this study, we present a novel generative adversarial network (GAN) that has been trained to generate three-dimensional lesions, conditioned by volume and location. This allows one to investigate CMB characteristics and create large training datasets for deep learning-based detectors. We demonstrate the benefit of this approach by achieving state-of-the-art CMB detection of real CMB using a convolutional neural network classifier trained on synthetic CMB. Moreover, we showed that our proposed 3D lesion GAN model can be applied on unseen dataset, with different MRI parameters and diseases, to generate synthetic lesions with high diversity and without needing laboriously marked ground truth.


Author(s):  
BalaAnand Muthu ◽  
Sivaparthipan CB ◽  
Priyan Malarvizhi Kumar ◽  
Seifedine Nimer Kadry ◽  
Ching-Hsien Hsu ◽  
...  

2020 ◽  
Vol 205 ◽  
pp. 03007
Author(s):  
Yejin Kim ◽  
Seong Jun Ha ◽  
Tae sup Yun

Hydraulic stimulation has been a key technique in enhanced geothermal systems (EGS) and the recovery of unconventional hydrocarbon resources to artificially generate fractures in a rock formation. Previous experimental studies present that the pattern and aperture of generated fractures vary as the fracking pressure propagation. The recent development of three-dimensional X-ray computed tomography allows visualizing the fractures for further analysing the morphological features of fractures. However, the generated fracture consists of a few pixels (e.g., 1-3 pixels) so that the accurate and quantitative extract of micro-fracture is highly challenging. Also, the high-frequency noise around the fracture and the weak contrast across the fracture makes the application of conventional segmentation methods limited. In this study, we adopted an encoder-decoder network with a convolutional neural network (CNN) based on deep learning method for the fast and precise detection of micro-fractures. The conventional image processing methods fail to extract the continuous fractures and overestimate the fracture thickness and aperture values while the CNN-based approach successfully detects the barely seen fractures. The reconstruction of the 3D fracture surface and quantitative roughness analysis of fracture surfaces extracted by different methods enables comparison of sensitivity (or robustness) to noise between each method.


2021 ◽  
Author(s):  
Yael Sde-Chen ◽  
Yoav Y. Schechner ◽  
Vadim Holodovsky ◽  
Eshkol Eytan

<p>Clouds are a key factor in Earth's energy budget and thus significantly affect climate and weather predictions. These effects are dominated by shallow warm clouds (shown by Sherwood et al., 2014, Zelinka et al., 2020) which tend to be small and heterogenous. Therefore, remote sensing of clouds and three-dimensional (3D) volumetric reconstruction of their internal properties are of significant importance.</p><p>Recovery of the volumetric information of the clouds relies on 3D radiative transfer, that models 3D multiple scattering. This model is complex and nonlinear. Thus, inverting the model poses a major challenge and typically requires using a simplification. A common relaxation assumes that clouds are horizontally uniform and infinitely broad, leading to one-dimensional modeling. However, generally this assumption is invalid since clouds are naturally highly heterogeneous. A novel alternative is to perform cloud retrieval by developing tools of 3D scattering tomography. Then, multiple satellite images of the clouds are acquired from different points of view. For example, simultaneous multi-view radiometric images of clouds are proposed by the CloudCT project, funded by the ERC. Unfortunately, 3D scattering tomography require high computational resources. This results, in practice, in slow run times and prevents large scale analysis. Moreover, existing scattering tomography is based on iterative optimization, which is sensitive to initialization.</p><p>In this work we introduce a deep neural network for 3D volumetric reconstruction of clouds. In recent years, supervised learning using deep neural networks has led to remarkable results in various fields ranging from computer vision to medical imaging. However, these deep learning techniques have not been extensively studied in the context of volumetric atmospheric science and specifically cloud research.</p><p>We present a convolutional neural network (CNN) whose architecture is inspired by the physical nature of clouds. Due to the lack of real-world datasets, we train the network in a supervised manner using a physics-based simulator that generates realistic volumetric cloud fields. In addition, we propose a hybrid approach, which combines the proposed neural network with an iterative physics-based optimization technique.</p><p>We demonstrate the recovery performance of our proposed method in cloud fields. In a single cloud-scale, our resulting quality is comparable to state-of-the-art methods, while run time improves by orders of magnitude. In contrast to existing physics-based methods, our network offers scalability, which enables the reconstruction of wider cloud fields. Finally, we show that the hybrid approach leads to improved retrieval in a fast process.</p>


PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5429 ◽  
Author(s):  
Kai Wang ◽  
Joshua Hoeksema ◽  
Chun Liang

Piwi-interacting RNAs (piRNAs) are the largest class of small non-coding RNAs discovered in germ cells. Identifying piRNAs from small RNA data is a challenging task due to the lack of conserved sequences and structural features of piRNAs. Many programs have been developed to identify piRNA from small RNA data. However, these programs have limitations. They either rely on extracting complicated features, or only demonstrate strong performance on transposon related piRNAs. Here we proposed a new program called piRNN for piRNA identification. For our software, we applied a convolutional neural network classifier that was trained on the datasets from four different species (Caenorhabditis elegans, Drosophila melanogaster, rat and human). A matrix of k-mer frequency values was used to represent each sequence. piRNN has great usability and shows better performance in comparison with other programs. It is freely available at https://github.com/bioinfolabmu/piRNN.


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