scholarly journals Data Set Augmentation Allows Deep Learning-Based Virtual Screening to Better Generalize to Unseen Target Classes and Highlight Important Binding Interactions

2020 ◽  
Vol 60 (8) ◽  
pp. 3722-3730
Author(s):  
Jack Scantlebury ◽  
Nathan Brown ◽  
Frank Von Delft ◽  
Charlotte M. Deane
Keyword(s):  
Deep Learning ◽  
Virtual Screening ◽  
Data Set ◽  
Binding Interactions

Deep Learning Approaches for Whiteboard Image Quality Enhancement

2019 ◽  
Vol 2019 (1) ◽  
pp. 360-368
Author(s):  
Mekides Assefa Abebe ◽  
Jon Yngve Hardeberg
Keyword(s):  
Deep Learning ◽  
Image Quality ◽  
Image Data ◽  
Quality Enhancement ◽  
Network Architectures ◽  
Learning Approaches ◽  
Data Set ◽  
Image Quality Enhancement ◽  
Processing Techniques ◽  
White Balancing

Different whiteboard image degradations highly reduce the legibility of pen-stroke content as well as the overall quality of the images. Consequently, different researchers addressed the problem through different image enhancement techniques. Most of the state-of-the-art approaches applied common image processing techniques such as background foreground segmentation, text extraction, contrast and color enhancements and white balancing. However, such types of conventional enhancement methods are incapable of recovering severely degraded pen-stroke contents and produce artifacts in the presence of complex pen-stroke illustrations. In order to surmount such problems, the authors have proposed a deep learning based solution. They have contributed a new whiteboard image data set and adopted two deep convolutional neural network architectures for whiteboard image quality enhancement applications. Their different evaluations of the trained models demonstrated their superior performances over the conventional methods.

A Deep Learning based Arabic Script Recognition System: Benchmark on KHAT

2020 ◽  
Vol 17 (3) ◽  
pp. 299-305 ◽  
Author(s):  
Riaz Ahmad ◽  
Saeeda Naz ◽  
Muhammad Afzal ◽  
Sheikh Rashid ◽  
Marcus Liwicki ◽  
...  
Keyword(s):  
Deep Learning ◽  
Character Recognition ◽  
Data Augmentation ◽  
Short Term Memory ◽  
Recognition System ◽  
Learning Approach ◽  
Arabic Text ◽  
Data Set ◽  
Processing Step ◽  
Handwritten Arabic

This paper presents a deep learning benchmark on a complex dataset known as KFUPM Handwritten Arabic TexT (KHATT). The KHATT data-set consists of complex patterns of handwritten Arabic text-lines. This paper contributes mainly in three aspects i.e., (1) pre-processing, (2) deep learning based approach, and (3) data-augmentation. The pre-processing step includes pruning of white extra spaces plus de-skewing the skewed text-lines. We deploy a deep learning approach based on Multi-Dimensional Long Short-Term Memory (MDLSTM) networks and Connectionist Temporal Classification (CTC). The MDLSTM has the advantage of scanning the Arabic text-lines in all directions (horizontal and vertical) to cover dots, diacritics, strokes and fine inflammation. The data-augmentation with a deep learning approach proves to achieve better and promising improvement in results by gaining 80.02% Character Recognition (CR) over 75.08% as baseline.

Virtual Screening Meets Deep Learning

2018 ◽  
Vol 15 (1) ◽  
pp. 6-28 ◽  
Author(s):  
Javier Pérez-Sianes ◽  
Horacio Pérez-Sánchez ◽  
Fernando Díaz
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Deep Learning ◽  
Virtual Screening ◽  
Great Increase ◽  
New Drugs ◽  
Learning Approach ◽  
Screening Strategies ◽  
Computer Aided ◽  
Recent Developments

Background: Automated compound testing is currently the de facto standard method for drug screening, but it has not brought the great increase in the number of new drugs that was expected. Computer- aided compounds search, known as Virtual Screening, has shown the benefits to this field as a complement or even alternative to the robotic drug discovery. There are different methods and approaches to address this problem and most of them are often included in one of the main screening strategies. Machine learning, however, has established itself as a virtual screening methodology in its own right and it may grow in popularity with the new trends on artificial intelligence. Objective: This paper will attempt to provide a comprehensive and structured review that collects the most important proposals made so far in this area of research. Particular attention is given to some recent developments carried out in the machine learning field: the deep learning approach, which is pointed out as a future key player in the virtual screening landscape.

Human Activity Recognition using Fourier Transform Inspired Deep Learning Combination Model

2019 ◽  
Vol 9 (1) ◽  
pp. 16-31
Author(s):  
Kyungkoo Jun
Keyword(s):  
Fourier Transform ◽  
Deep Learning ◽  
Short Term Memory ◽  
Window Size ◽  
Sensor Data ◽  
Data Sets ◽  
Data Set ◽  
Proposed Model ◽  
Testing Data ◽  
Labeling Scheme

Background & Objective: This paper proposes a Fourier transform inspired method to classify human activities from time series sensor data. Methods: Our method begins by decomposing 1D input signal into 2D patterns, which is motivated by the Fourier conversion. The decomposition is helped by Long Short-Term Memory (LSTM) which captures the temporal dependency from the signal and then produces encoded sequences. The sequences, once arranged into the 2D array, can represent the fingerprints of the signals. The benefit of such transformation is that we can exploit the recent advances of the deep learning models for the image classification such as Convolutional Neural Network (CNN). Results: The proposed model, as a result, is the combination of LSTM and CNN. We evaluate the model over two data sets. For the first data set, which is more standardized than the other, our model outperforms previous works or at least equal. In the case of the second data set, we devise the schemes to generate training and testing data by changing the parameters of the window size, the sliding size, and the labeling scheme. Conclusion: The evaluation results show that the accuracy is over 95% for some cases. We also analyze the effect of the parameters on the performance.

scholarly journals Investigating the impact of pre-processing techniques and pre-trained word embeddings in detecting Arabic health information on social media

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yahya Albalawi ◽  
Jim Buckley ◽  
Nikola S. Nikolov
Keyword(s):  
Social Media ◽  
Deep Learning ◽  
Comprehensive Evaluation ◽  
Classification Problem ◽  
Data Sets ◽  
Word Embeddings ◽  
Data Set ◽  
Lower Accuracy ◽  
Health Related ◽  
The Impact

AbstractThis paper presents a comprehensive evaluation of data pre-processing and word embedding techniques in the context of Arabic document classification in the domain of health-related communication on social media. We evaluate 26 text pre-processings applied to Arabic tweets within the process of training a classifier to identify health-related tweets. For this task we use the (traditional) machine learning classifiers KNN, SVM, Multinomial NB and Logistic Regression. Furthermore, we report experimental results with the deep learning architectures BLSTM and CNN for the same text classification problem. Since word embeddings are more typically used as the input layer in deep networks, in the deep learning experiments we evaluate several state-of-the-art pre-trained word embeddings with the same text pre-processing applied. To achieve these goals, we use two data sets: one for both training and testing, and another for testing the generality of our models only. Our results point to the conclusion that only four out of the 26 pre-processings improve the classification accuracy significantly. For the first data set of Arabic tweets, we found that Mazajak CBOW pre-trained word embeddings as the input to a BLSTM deep network led to the most accurate classifier with F1 score of 89.7%. For the second data set, Mazajak Skip-Gram pre-trained word embeddings as the input to BLSTM led to the most accurate model with F1 score of 75.2% and accuracy of 90.7% compared to F1 score of 90.8% achieved by Mazajak CBOW for the same architecture but with lower accuracy of 70.89%. Our results also show that the performance of the best of the traditional classifier we trained is comparable to the deep learning methods on the first dataset, but significantly worse on the second dataset.

scholarly journals Training and deploying a deep learning model for endoscopic severity grading in ulcerative colitis using multicenter clinical trial data

2021 ◽  
Vol 14 ◽  
pp. 263177452199062
Author(s):  
Benjamin Gutierrez Becker ◽  
Filippo Arcadu ◽  
Andreas Thalhammer ◽  
Citlalli Gamez Serna ◽  
Owen Feehan ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Ulcerative Colitis ◽  
Clinical Trials ◽  
Deep Learning ◽  
Mayo Clinic ◽  
Automated System ◽  
Phase Iii ◽  
Plain Language ◽  
Data Set ◽  
Endoscopic Videos

Introduction: The Mayo Clinic Endoscopic Subscore is a commonly used grading system to assess the severity of ulcerative colitis. Correctly grading colonoscopies using the Mayo Clinic Endoscopic Subscore is a challenging task, with suboptimal rates of interrater and intrarater variability observed even among experienced and sufficiently trained experts. In recent years, several machine learning algorithms have been proposed in an effort to improve the standardization and reproducibility of Mayo Clinic Endoscopic Subscore grading. Methods: Here we propose an end-to-end fully automated system based on deep learning to predict a binary version of the Mayo Clinic Endoscopic Subscore directly from raw colonoscopy videos. Differently from previous studies, the proposed method mimics the assessment done in practice by a gastroenterologist, that is, traversing the whole colonoscopy video, identifying visually informative regions and computing an overall Mayo Clinic Endoscopic Subscore. The proposed deep learning–based system has been trained and deployed on raw colonoscopies using Mayo Clinic Endoscopic Subscore ground truth provided only at the colon section level, without manually selecting frames driving the severity scoring of ulcerative colitis. Results and Conclusion: Our evaluation on 1672 endoscopic videos obtained from a multisite data set obtained from the etrolizumab Phase II Eucalyptus and Phase III Hickory and Laurel clinical trials, show that our proposed methodology can grade endoscopic videos with a high degree of accuracy and robustness (Area Under the Receiver Operating Characteristic Curve = 0.84 for Mayo Clinic Endoscopic Subscore ⩾ 1, 0.85 for Mayo Clinic Endoscopic Subscore ⩾ 2 and 0.85 for Mayo Clinic Endoscopic Subscore ⩾ 3) and reduced amounts of manual annotation. Plain language summary Patient, caregiver and provider thoughts on educational materials about prescribing and medication safety Artificial intelligence can be used to automatically assess full endoscopic videos and estimate the severity of ulcerative colitis. In this work, we present an artificial intelligence algorithm for the automatic grading of ulcerative colitis in full endoscopic videos. Our artificial intelligence models were trained and evaluated on a large and diverse set of colonoscopy videos obtained from concluded clinical trials. We demonstrate not only that artificial intelligence is able to accurately grade full endoscopic videos, but also that using diverse data sets obtained from multiple sites is critical to train robust AI models that could potentially be deployed on real-world data.

scholarly journals Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods

2010 ◽  
Vol 50 (12) ◽  
pp. 2079-2093 ◽  
Author(s):  
Vishwesh Venkatraman ◽  
Violeta I. Pérez-Nueno ◽  
Lazaros Mavridis ◽  
David W. Ritchie
Keyword(s):  
Virtual Screening ◽  
Screening Tools ◽  
Data Set ◽  
Comprehensive Comparison ◽  
3D Methods

scholarly journals RISC-V Virtual Platform-Based Convolutional Neural Network Accelerator Implemented in SystemC

Electronics ◽  
2021 ◽  
Vol 10 (13) ◽  
pp. 1514
Author(s):  
Seung-Ho Lim ◽  
WoonSik William Suh ◽  
Jin-Young Kim ◽  
Sang-Young Cho
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Network Model ◽  
Neural Network Model ◽  
Deep Neural Network ◽  
System Level ◽  
Neural Network Models ◽  
Data Set ◽  
Embedded Device ◽  
Virtual Platform

The optimization for hardware processor and system for performing deep learning operations such as Convolutional Neural Networks (CNN) in resource limited embedded devices are recent active research area. In order to perform an optimized deep neural network model using the limited computational unit and memory of an embedded device, it is necessary to quickly apply various configurations of hardware modules to various deep neural network models and find the optimal combination. The Electronic System Level (ESL) Simulator based on SystemC is very useful for rapid hardware modeling and verification. In this paper, we designed and implemented a Deep Learning Accelerator (DLA) that performs Deep Neural Network (DNN) operation based on the RISC-V Virtual Platform implemented in SystemC in order to enable rapid and diverse analysis of deep learning operations in an embedded device based on the RISC-V processor, which is a recently emerging embedded processor. The developed RISC-V based DLA prototype can analyze the hardware requirements according to the CNN data set through the configuration of the CNN DLA architecture, and it is possible to run RISC-V compiled software on the platform, can perform a real neural network model like Darknet. We performed the Darknet CNN model on the developed DLA prototype, and confirmed that computational overhead and inference errors can be analyzed with the DLA prototype developed by analyzing the DLA architecture for various data sets.

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