scholarly journals ME-ACP: Multi-view Neural Networks with Ensemble Model for Identification of Anticancer Peptides

2021 ◽  
Author(s):  
Guanwen Feng ◽  
Hang Yao ◽  
Chaoneng Li ◽  
Ruyi Liu ◽  
Rungen Huang ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Neural Network ◽  
Protein Sequences ◽  
Residue Level ◽  
Ensemble Model ◽  
Cancer Treatments ◽  
Anticancer Peptides ◽  
Peptide Level ◽  
Independent Test ◽  
Promising Perspective

Cancer remains one of the most threatening diseases, which kills millions of lives every year. As a promising perspective for cancer treatments, anticancer peptides (ACPs) overcome a lot of disadvantages of traditional treatments. However, it is time-consuming and expensive to identify ACPs through conventional experiments. Hence, it is urgent and necessary to develop highly effective approaches to accurately identify ACPs in large amounts of protein sequences. In this work, we proposed a novel and effective method named ME-ACP which employed multi-view neural networks with ensemble model to identify ACPs. Firstly, we employed residue level and peptide level features preliminarily with ensemble models based on lightGBMs. Then, the outputs of lightGBM classifiers were fed into a hybrid deep neural network (HDNN) to identify ACPs. The experiments on independent test datasets demonstrated that ME-ACP achieved competitive performance on common evaluation metrics.

scholarly journals Deep neural networks using a single neuron: folded-in-time architecture using feedback-modulated delay loops

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Florian Stelzer ◽  
André Röhm ◽  
Raul Vicente ◽  
Ingo Fischer ◽  
Serhiy Yanchuk
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Neural Network ◽  
Single Neuron ◽  
Deep Neural Networks ◽  
Back Propagation ◽  
Local Network ◽  
Multiple Time ◽  
Learning Tools ◽  
Back Propagation Algorithm

AbstractDeep neural networks are among the most widely applied machine learning tools showing outstanding performance in a broad range of tasks. We present a method for folding a deep neural network of arbitrary size into a single neuron with multiple time-delayed feedback loops. This single-neuron deep neural network comprises only a single nonlinearity and appropriately adjusted modulations of the feedback signals. The network states emerge in time as a temporal unfolding of the neuron’s dynamics. By adjusting the feedback-modulation within the loops, we adapt the network’s connection weights. These connection weights are determined via a back-propagation algorithm, where both the delay-induced and local network connections must be taken into account. Our approach can fully represent standard Deep Neural Networks (DNN), encompasses sparse DNNs, and extends the DNN concept toward dynamical systems implementations. The new method, which we call Folded-in-time DNN (Fit-DNN), exhibits promising performance in a set of benchmark tasks.

scholarly journals Deep neural network analysis of nanoparticle ordering to identify defects in layered carbon materials

2021 ◽  
Author(s):  
Daniil A. Boiko ◽  
Evgeniy O. Pentsak ◽  
Vera A. Cherepanova ◽  
Evgeniy G. Gordeev ◽  
Valentine P. Ananikov
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Network Analysis ◽  
Carbon Material ◽  
Deep Neural Network ◽  
Carbon Materials ◽  
Material Surface ◽  
Neural Network Analysis ◽  
Pd Nanoparticle ◽  
Sem Imaging

Defectiveness of carbon material surface is a key issue for many applications. Pd-nanoparticle SEM imaging was used to highlight “hidden” defects and analyzed by neural networks to solve order/disorder classification and defect segmentation tasks.

Inclusion of Multiple Cycling of the Potential into Deep Neural Network Classification of Voltammetric Reaction Mechanisms

2021 ◽  
Author(s):  
Luke Gundry ◽  
Gareth Kennedy ◽  
Alan Bond ◽  
Jie Zhang
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Reaction Mechanisms ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Neural Network Classification ◽  
Initial Cycle

The use of Deep Neural Networks (DNNs) for the classification of electrochemical mechanisms based on training with simulations of the initial cycle of potential have been reported. In this paper,...

Automated vessel segmentation in lung CT and CTA images via deep neural networks

2021 ◽  
pp. 1-15
Author(s):  
Wenjun Tan ◽  
Luyu Zhou ◽  
Xiaoshuo Li ◽  
Xiaoyu Yang ◽  
Yufei Chen ◽  
...  
Keyword(s):  
Neural Network ◽  
Computed Tomography ◽  
Neural Networks ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Vessel Segmentation ◽  
Multi Scale ◽  
Vascular Segmentation ◽  
Study Results ◽  
Lung Ct

BACKGROUND: The distribution of pulmonary vessels in computed tomography (CT) and computed tomography angiography (CTA) images of lung is important for diagnosing disease, formulating surgical plans and pulmonary research. PURPOSE: Based on the pulmonary vascular segmentation task of International Symposium on Image Computing and Digital Medicine 2020 challenge, this paper reviews 12 different pulmonary vascular segmentation algorithms of lung CT and CTA images and then objectively evaluates and compares their performances. METHODS: First, we present the annotated reference dataset of lung CT and CTA images. A subset of the dataset consisting 7,307 slices for training and 3,888 slices for testing was made available for participants. Second, by analyzing the performance comparison of different convolutional neural networks from 12 different institutions for pulmonary vascular segmentation, the reasons for some defects and improvements are summarized. The models are mainly based on U-Net, Attention, GAN, and multi-scale fusion network. The performance is measured in terms of Dice coefficient, over segmentation ratio and under segmentation rate. Finally, we discuss several proposed methods to improve the pulmonary vessel segmentation results using deep neural networks. RESULTS: By comparing with the annotated ground truth from both lung CT and CTA images, most of 12 deep neural network algorithms do an admirable job in pulmonary vascular extraction and segmentation with the dice coefficients ranging from 0.70 to 0.85. The dice coefficients for the top three algorithms are about 0.80. CONCLUSIONS: Study results show that integrating methods that consider spatial information, fuse multi-scale feature map, or have an excellent post-processing to deep neural network training and optimization process are significant for further improving the accuracy of pulmonary vascular segmentation.

Identification of motifs with insertions and deletions in protein sequences using self-organizing neural networks

2005 ◽  
Vol 18 (5-6) ◽  
pp. 835-842 ◽  
Author(s):  
Derong Liu ◽  
Xiaoxu Xiong ◽  
Zeng-Guang Hou ◽  
Bhaskar DasGupta
Keyword(s):  
Neural Networks ◽  
Protein Sequences ◽  
Insertions And Deletions ◽  
Self Organizing

Web application to support evidence of individual emotional impact evoked by COVID-19 pandemic restrictions (Preprint)

2021 ◽  
Author(s):  
Hugo Mitre-Hernandez ◽  
Rodolfo Ferro-Perez ◽  
Francisco Gonzalez-Hernandez
Keyword(s):  
Neural Network ◽  
Mental Health ◽  
Neural Networks ◽  
Emotion Recognition ◽  
Web Application ◽  
Deep Neural Network ◽  
Data Transfer ◽  
Computational Cost ◽  
Low Computational Cost ◽  
The Web

BACKGROUND Mental health effects during COVID-19 quarantine need to be handled because patients, relatives, and healthcare workers are living with negative emotional behaviors. The clinical disorders of depression and anxiety are evoking anger, fear, sadness, disgust, and reducing happiness. Therefore, track emotions with the help of psychologists on online consultations –to reduce the risk of contagion– will go a long way in assisting with mental health. The human micro-expressions can describe genuine emotions of people and can be captured by Deep Neural Networks (DNNs) models. But the challenge is to implement it under the poor performance of a part of society's computers and the low speed of internet connection. OBJECTIVE This study aimed to create a useful and usable web application to record emotions in a patient’s card in real-time, achieving a small data transfer, and a Convolutional Neural Networks (CNN) model with a low computational cost. METHODS To validate the low computational cost premise, firstly, we compare DNN architectures results, collecting the floating-point operations per second (FLOPS), the Number of Parameters (NP) and accuracy from the MobileNet, PeleeNet, Extended Deep Neural Network (EDNN), Inception- Based Deep Neural Network (IDNN) and our proposed Residual mobile-based Network (ResmoNet) model. Secondly, we compare the trained models' results in terms of Main Memory Utilization (MMU) and Response Time to complete the Emotion recognition (RTE). Finally, we design a data transfer that includes the raw data of emotions and the basic text information of the patient. The web application was evaluated with the System Usability Scale (SUS) and a utility questionnaire by psychologists and psychiatrists (experts). RESULTS All CNN models were set up using 150 epochs for training and testing comparing the results for each variable in ResmoNet with the best model. It was obtained that ResmoNet has 115,976 NP less than MobileNet, 243,901 FLOPS less than MobileNet, and 5% less accuracy than EDNN (95%). Moreover, ResmoNet used less MMU than any model, only EDNN overcomes ResmoNet in 0.01 seconds for RTE. Finally, with our model, we develop a web application to collect emotions in real-time during a psychological consultation. For data transfer, the patient’s card and raw emotional data have 2 kb with a UTF-8 encoding approximately. Finally, according to the experts, the web application has good usability (73.8 of 100) and utility (3.94 of 5). CONCLUSIONS A usable and useful web application for psychologists and psychiatrists is presented. This tool includes an efficient and light facial emotion recognition model. Its purpose is to be a complementary tool for diagnostic processes.

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