scholarly journals UbiComb: A Hybrid Deep Learning Model for Predicting Plant-Specific Protein Ubiquitylation Sites

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 717
Author(s):  
Arslan Siraj ◽  
Dae Yeong Lim ◽  
Hilal Tayara ◽  
Kil To Chong
Keyword(s):  
Mass Spectrometry ◽  
Deep Learning ◽  
Large Scale ◽  
Critical Role ◽  
Learning Model ◽  
Mass Spectrometry Analysis ◽  
Independent Dataset ◽  
Effective Manner ◽  
Wide Range ◽  
Deep Learning Model

Protein ubiquitylation is an essential post-translational modification process that performs a critical role in a wide range of biological functions, even a degenerative role in certain diseases, and is consequently used as a promising target for the treatment of various diseases. Owing to the significant role of protein ubiquitylation, these sites can be identified by enzymatic approaches, mass spectrometry analysis, and combinations of multidimensional liquid chromatography and tandem mass spectrometry. However, these large-scale experimental screening techniques are time consuming, expensive, and laborious. To overcome the drawbacks of experimental methods, machine learning and deep learning-based predictors were considered for prediction in a timely and cost-effective manner. In the literature, several computational predictors have been published across species; however, predictors are species-specific because of the unclear patterns in different species. In this study, we proposed a novel approach for predicting plant ubiquitylation sites using a hybrid deep learning model by utilizing convolutional neural network and long short-term memory. The proposed method uses the actual protein sequence and physicochemical properties as inputs to the model and provides more robust predictions. The proposed predictor achieved the best result with accuracy values of 80% and 81% and F-scores of 79% and 82% on the 10-fold cross-validation and an independent dataset, respectively. Moreover, we also compared the testing of the independent dataset with popular ubiquitylation predictors; the results demonstrate that our model significantly outperforms the other methods in prediction classification results.

scholarly journals Microwave Dielectric Property Retrieval from Open-Ended Coaxial Probe Response with Deep Learning

2021 ◽  
Author(s):  
Cemanur Aydinalp ◽  
Sulayman Joof ◽  
Mehmet Nuri Akinci ◽  
Ibrahim Akduman ◽  
Tuba Yilmaz
Keyword(s):  
Deep Learning ◽  
Dielectric Property ◽  
Large Scale ◽  
Real Data ◽  
Learning Model ◽  
Data Generation ◽  
Retrieval Technique ◽  
Design Flexibility ◽  
A New Technique ◽  
Deep Learning Model

In the manuscript, we propose a new technique for determination of Debye parameters, representing the dielectric properties of materials, from the reflection coefficient response of open-ended coaxial probes. The method retrieves the Debye parameters using a deep learning model designed through utilization of numerically generated data. Unlike real data, using synthetically generated input and output data for training purposes provides representation of a wide variety of materials with rapid data generation. Furthermore, the proposed method provides design flexibility and can be applied to any desired probe with intended dimensions and material. Next, we experimentally verified the designed deep learning model using measured reflection coefficients when the probe was terminated with five different standard liquids, four mixtures,and a gel-like material.and compared the results with the literature. Obtained mean percent relative error was ranging from 1.21±0.06 to 10.89±0.08. Our work also presents a large-scale statistical verification of the proposed dielectric property retrieval technique.

scholarly journals A Physics-Infused Deep Learning Model for the Prediction of Refractive Indices and Its Use for the Large-Scale Screening of Organic Compound Space

2019 ◽  
Author(s):  
Mojtaba Haghighatlari ◽  
Gaurav Vishwakarma ◽  
Mohammad Atif Faiz Afzal ◽  
Johannes Hachmann
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Large Scale ◽  
Organic Molecules ◽  
Learning Model ◽  
Training Data ◽  
Refractive Indices ◽  
Learning Models ◽  
Deep Learning Model ◽  
Machine Learning Models

<div><div><div><p>We present a multitask, physics-infused deep learning model to accurately and efficiently predict refractive indices (RIs) of organic molecules, and we apply it to a library of 1.5 million compounds. We show that it outperforms earlier machine learning models by a significant margin, and that incorporating known physics into data-derived models provides valuable guardrails. Using a transfer learning approach, we augment the model to reproduce results consistent with higher-level computational chemistry training data, but with a considerably reduced number of corresponding calculations. Prediction errors of machine learning models are typically smallest for commonly observed target property values, consistent with the distribution of the training data. However, since our goal is to identify candidates with unusually large RI values, we propose a strategy to boost the performance of our model in the remoter areas of the RI distribution: We bias the model with respect to the under-represented classes of molecules that have values in the high-RI regime. By adopting a metric popular in web search engines, we evaluate our effectiveness in ranking top candidates. We confirm that the models developed in this study can reliably predict the RIs of the top 1,000 compounds, and are thus able to capture their ranking. We believe that this is the first study to develop a data-derived model that ensures the reliability of RI predictions by model augmentation in the extrapolation region on such a large scale. These results underscore the tremendous potential of machine learning in facilitating molecular (hyper)screening approaches on a massive scale and in accelerating the discovery of new compounds and materials, such as organic molecules with high-RI for applications in opto-electronics.</p></div></div></div>

scholarly journals Deep Learning Based Ethiopian Car’s License Plate Detection and Recognition

2020 ◽  
Vol 8 (6) ◽  
pp. 5730-5737
Keyword(s):  
Image Processing ◽  
Deep Learning ◽  
Learning Model ◽  
Motor Vehicles ◽  
License Plate ◽  
License Plate Recognition ◽  
Computer Algorithms ◽  
Wide Range ◽  
Processing Techniques ◽  
Deep Learning Model

Digital Image Processing is application of computer algorithms to process, manipulate and interpret images. As a field it is playing an increasingly important role in many aspects of people’s daily life. Even though Image Processing has accomplished a great deal on its own, nowadays researches are being conducted in using it with Deep Learning (which is part of a broader family, Machine Learning) to achieve better performance in detecting and classifying objects in an image. Car’s License Plate Recognition is one of the hottest research topics in the domain of Image Processing (Computer Vision). It is having wide range of applications since license number is the primary and mandatory identifier of motor vehicles. When it comes to license plates in Ethiopia, they have unique features like Amharic characters, differing dimensions and plate formats. Although there is a research conducted on ELPR, it was attempted using the conventional image processing techniques but never with deep learning. In this proposed research an attempt is going to be made in tackling the problem of ELPR with deep learning and image processing. Tensorflow is going to be used in building the deep learning model and all the image processing is going to be done with OpenCV-Python. So, at the end of this research a deep learning model that recognizes Ethiopian license plates with better accuracy is going to be built.

scholarly journals Spatio-temporal deep learning model for distortion classification in laparoscopic video

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 1010
Author(s):  
Nouar AlDahoul ◽  
Hezerul Abdul Karim ◽  
Abdulaziz Saleh Ba Wazir ◽  
Myles Joshua Toledo Tan ◽  
Mohammad Faizal Ahmad Fauzi
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Spatial Information ◽  
Short Term Memory ◽  
Learning Model ◽  
Motion Blur ◽  
Video Frame ◽  
Video Enhancement ◽  
Deep Learning Model ◽  
Laparoscopic Videos

Background: Laparoscopy is a surgery performed in the abdomen without making large incisions in the skin and with the aid of a video camera, resulting in laparoscopic videos. The laparoscopic video is prone to various distortions such as noise, smoke, uneven illumination, defocus blur, and motion blur. One of the main components in the feedback loop of video enhancement systems is distortion identification, which automatically classifies the distortions affecting the videos and selects the video enhancement algorithm accordingly. This paper aims to address the laparoscopic video distortion identification problem by developing fast and accurate multi-label distortion classification using a deep learning model. Current deep learning solutions based on convolutional neural networks (CNNs) can address laparoscopic video distortion classification, but they learn only spatial information. Methods: In this paper, utilization of both spatial and temporal features in a CNN-long short-term memory (CNN-LSTM) model is proposed as a novel solution to enhance the classification. First, pre-trained ResNet50 CNN was used to extract spatial features from each video frame by transferring representation from large-scale natural images to laparoscopic images. Next, LSTM was utilized to consider the temporal relation between the features extracted from the laparoscopic video frames to produce multi-label categories. A novel laparoscopic video dataset proposed in the ICIP2020 challenge was used for training and evaluation of the proposed method. Results: The experiments conducted show that the proposed CNN-LSTM outperforms the existing solutions in terms of accuracy (85%), and F1-score (94.2%). Additionally, the proposed distortion identification model is able to run in real-time with low inference time (0.15 sec). Conclusions: The proposed CNN-LSTM model is a feasible solution to be utilized in laparoscopic videos for distortion identification.

scholarly journals Hierarchical Graph Transformer-Based Deep Learning Model for Large-Scale Multi-Label Text Classification

IEEE Access ◽  
2020 ◽  
Vol 8 ◽  
pp. 30885-30896 ◽  
Author(s):  
Jibing Gong ◽  
Hongyuan Ma ◽  
Zhiyong Teng ◽  
Qi Teng ◽  
Hekai Zhang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Text Classification ◽  
Large Scale ◽  
Learning Model ◽  
Hierarchical Graph ◽  
Deep Learning Model

scholarly journals A Joint Deep Learning Model for Simultaneous Batch Effect Correction, Denoising and Clustering in Single-Cell Transcriptomics

2020 ◽  
Author(s):  
Justin Lakkis ◽  
David Wang ◽  
Yuanchao Zhang ◽  
Gang Hu ◽  
Kui Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Deep Learning ◽  
Single Cell ◽  
Large Scale ◽  
Nearest Neighbor ◽  
Learning Model ◽  
Batch Effect ◽  
Marker Genes ◽  
Deep Learning Model ◽  
Variable Genes

AbstractRecent development of single-cell RNA-seq (scRNA-seq) technologies has led to enormous biological discoveries. As the scale of scRNA-seq studies increases, a major challenge in analysis is batch effect, which is inevitable in studies involving human tissues. Most existing methods remove batch effect in a low-dimensional embedding space. Although useful for clustering, batch effect is still present in the gene expression space, leaving downstream gene-level analysis susceptible to batch effect. Recent studies have shown that batch effect correction in the gene expression space is much harder than in the embedding space. Popular methods such as Seurat3.0 rely on the mutual nearest neighbor (MNN) approach to remove batch effect in the gene expression space, but MNN can only analyze two batches at a time and it becomes computationally infeasible when the number of batches is large. Here we present CarDEC, a joint deep learning model that simultaneously clusters and denoises scRNA-seq data, while correcting batch effect both in the embedding and the gene expression space. Comprehensive evaluations spanning different species and tissues showed that CarDEC consistently outperforms scVI, DCA, and MNN. With CarDEC denoising, those non-highly variable genes offer as much signal for clustering as the highly variable genes, suggesting that CarDEC substantially boosted information content in scRNA-seq. We also showed that trajectory analysis using CarDEC’s denoised and batch corrected expression as input revealed marker genes and transcription factors that are otherwise obscured in the presence of batch effect. CarDEC is computationally fast, making it a desirable tool for large-scale scRNA-seq studies.

scholarly journals DiPLIP: Distributed Parallel Processing Platform for Stream Image Processing Based on Deep Learning Model Inference

Electronics ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1664
Author(s):  
Yoon-Ki Kim ◽  
Yongsung Kim
Keyword(s):  
Image Processing ◽  
Deep Learning ◽  
Parallel Processing ◽  
Real Time ◽  
Large Scale ◽  
Learning Model ◽  
Streaming Data ◽  
Model Inference ◽  
Processing Platform ◽  
Deep Learning Model

Recently, as the amount of real-time video streaming data has increased, distributed parallel processing systems have rapidly evolved to process large-scale data. In addition, with an increase in the scale of computing resources constituting the distributed parallel processing system, the orchestration of technology has become crucial for proper management of computing resources, in terms of allocating computing resources, setting up a programming environment, and deploying user applications. In this paper, we present a new distributed parallel processing platform for real-time large-scale image processing based on deep learning model inference, called DiPLIP. It provides a scheme for large-scale real-time image inference using buffer layer and a scalable parallel processing environment according to the size of the stream image. It allows users to easily process trained deep learning models for processing real-time images in a distributed parallel processing environment at high speeds, through the distribution of the virtual machine container.

scholarly journals Detecting prodromal Alzheimer’s disease with MRI through deep learning

2019 ◽  
Author(s):  
Xinyang Feng ◽  
Frank A. Provenzano ◽  
Scott A. Small ◽  
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Data Augmentation ◽  
Hippocampal Formation ◽  
Mechanistic Explanation ◽  
Learning Model ◽  
Tau Pathology ◽  
Cross Sectional ◽  
And Performance ◽  
Deep Learning Model

ABSTRACTDeep learning applied to MRI for Alzheimer’s classification is hypothesized to improve if the deep learning model implicates disease’s pathophysiology. The challenge in testing this hypothesis is that large-scale data are required to train this type of model. Here, we overcome this challenge by using a novel data augmentation strategy and show that our MRI-based deep learning model classifies Alzheimer’s dementia with high accuracy. Moreover, a class activation map was found dominated by signal from the hippocampal formation, a site where Alzheimer’s pathophysiology begins. Next, we tested the model’s performance in prodromal Alzheimer’s when patients present with mild cognitive impairment (MCI). We retroactively dichotomized a large cohort of MCI patients who were followed for up to 10 years into those with and without prodromal Alzheimer’s at baseline and used the dementia-derived model to generate individual ‘deep learning MRI’ scores. We compared the two groups on these scores, and on other biomarkers of amyloid pathology, tau pathology, and neurodegeneration. The deep learning MRI scores outperformed nearly all other biomarkers, including—unexpectedly—biomarkers of amyloid or tau pathology, in classifying prodromal disease and in predicting clinical progression. Providing a mechanistic explanation, the deep learning MRI scores were found to be linked to regional tau pathology, through investigations using cross-sectional, longitudinal, premortem and postmortem data. Our findings validate that a disease’s known pathophysiology can improve the design and performance of deep learning models. Moreover, by showing that deep learning can extract useful biomarker information from conventional MRIs, the advantages of this model extend practically, potentially reducing patient burden, risk, and cost.

scholarly journals A Large-Scale Dataset and Deep Learning Model for Detecting and Counting Olive Trees in Satellite Imagery

2022 ◽  
Vol 2022 ◽  
pp. 1-8
Author(s):  
Amr Abozeid ◽  
Rayan Alanazi ◽  
Ahmed Elhadad ◽  
Ahmed I. Taloba ◽  
Rasha M. Abd El-Aziz
Keyword(s):  
Deep Learning ◽  
Satellite Imagery ◽  
Large Scale ◽  
Estimation Error ◽  
Satellite Image ◽  
Olive Tree ◽  
Learning Model ◽  
Large Area ◽  
Olive Trees ◽  
Deep Learning Model

Since the Pre-Roman era, olive trees have a significant economic and cultural value. In 2019, the Al-Jouf region, in the north of the Kingdom of Saudi Arabia, gained a global presence by entering the Guinness World Records, with the largest number of olive trees in the world. Olive tree detecting and counting from a given satellite image are a significant and difficult computer vision problem. Because olive farms are spread out over a large area, manually counting the trees is impossible. Moreover, accurate automatic detection and counting of olive trees in satellite images have many challenges such as scale variations, weather changes, perspective distortions, and orientation changes. Another problem is the lack of a standard database of olive trees available for deep learning applications. To address these problems, we first build a large-scale olive dataset dedicated to deep learning research and applications. The dataset consists of 230 RGB images collected over the territory of Al-Jouf, KSA. We then propose an efficient deep learning model (SwinTUnet) for detecting and counting olive trees from satellite imagery. The proposed SwinTUnet is a Unet-like network which consists of an encoder, a decoder, and skip connections. Swin Transformer block is the fundamental unit of SwinTUnet to learn local and global semantic information. The results of an experimental study on the proposed dataset show that the SwinTUnet model outperforms the related studies in terms of overall detection with a 0.94% estimation error.

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