scholarly journals 6mA-Pred: identifying DNA N6-methyladenine sites based on deep learning

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10813
Author(s):  
Qianfei Huang ◽  
Wenyang Zhou ◽  
Fei Guo ◽  
Lei Xu ◽  
Lichao Zhang
Keyword(s):  
Deep Learning ◽  
Mus Musculus ◽  
Source Code ◽  
Experimental Results ◽  
Individual Species ◽  
Identification Method ◽  
Excellent Method ◽  
Multiple Species ◽  
Site Recognition

With the accumulation of data on 6mA modification sites, an increasing number of scholars have begun to focus on the identification of 6mA sites. Despite the recognized importance of 6mA sites, methods for their identification remain lacking, with most existing methods being aimed at their identification in individual species. In the present study, we aimed to develop an identification method suitable for multiple species. Based on previous research, we propose a method for 6mA site recognition. Our experiments prove that the proposed 6mA-Pred method is effective for identifying 6mA sites in genes from taxa such as rice, Mus musculus, and human. A series of experimental results show that 6mA-Pred is an excellent method. We provide the source code used in the study, which can be obtained from http://39.100.246.211:5004/6mA_Pred/.

scholarly journals pDeep3: Towards More Accurate Spectrum Prediction with Fast Few-Shot Learning

2020 ◽  
Author(s):  
Ching Tarn ◽  
Wen-Feng Zeng ◽  
Zhengcong Fei ◽  
Si-Min He
Keyword(s):  
Deep Learning ◽  
Data Quality ◽  
Prediction Accuracy ◽  
Source Code ◽  
Experimental Results ◽  
Collision Induced Dissociation ◽  
Learning Method ◽  
Energy Collision ◽  
Spectrum Prediction ◽  
The Difference

AbstractSpectrum prediction using deep learning has attracted a lot of attention in recent years. Although existing deep learning methods have dramatically increased the prediction accuracy, there is still considerable space for improvement, which is presently limited by the difference of fragmentation types or instrument settings. In this work, we use the few-shot learning method to fit the data online to make up for the shortcoming. The method is evaluated using ten datasets, where the instruments includes Velos, QE, Lumos, and Sciex, with collision energies being differently set. Experimental results show that few-shot learning can achieve higher prediction accuracy with almost negligible computing resources. For example, on the dataset from a untrained instrument Sciex-6600, within about 10 seconds, the prediction accuracy is increased from 69.7% to 86.4%; on the CID (collision-induced dissociation) dataset, the prediction accuracy of the model trained by HCD (higher energy collision dissociation) spectra is increased from 48.0% to 83.9%. It is also shown that, the method is not critical to data quality and is sufficiently efficient to fill the accuracy gap. The source code of pDeep3 is available at http://pfind.ict.ac.cn/software/pdeep3.

scholarly journals On the Reproducibility and Replicability of Deep Learning in Software Engineering

2022 ◽  
Vol 31 (1) ◽  
pp. 1-46
Author(s):  
Chao Liu ◽  
Cuiyun Gao ◽  
Xin Xia ◽  
David Lo ◽  
John Grundy ◽  
...  
Keyword(s):  
Deep Learning ◽  
Software Engineering ◽  
Source Code ◽  
Experimental Results ◽  
Supervised Machine Learning ◽  
Optimization Process ◽  
Experimental Result ◽  
Experimental Setup ◽  
High Quality ◽  
Two Factors

Context: Deep learning (DL) techniques have gained significant popularity among software engineering (SE) researchers in recent years. This is because they can often solve many SE challenges without enormous manual feature engineering effort and complex domain knowledge. Objective: Although many DL studies have reported substantial advantages over other state-of-the-art models on effectiveness, they often ignore two factors: (1) reproducibility —whether the reported experimental results can be obtained by other researchers using authors’ artifacts (i.e., source code and datasets) with the same experimental setup; and (2) replicability —whether the reported experimental result can be obtained by other researchers using their re-implemented artifacts with a different experimental setup. We observed that DL studies commonly overlook these two factors and declare them as minor threats or leave them for future work. This is mainly due to high model complexity with many manually set parameters and the time-consuming optimization process, unlike classical supervised machine learning (ML) methods (e.g., random forest). This study aims to investigate the urgency and importance of reproducibility and replicability for DL studies on SE tasks. Method: In this study, we conducted a literature review on 147 DL studies recently published in 20 SE venues and 20 AI (Artificial Intelligence) venues to investigate these issues. We also re-ran four representative DL models in SE to investigate important factors that may strongly affect the reproducibility and replicability of a study. Results: Our statistics show the urgency of investigating these two factors in SE, where only 10.2% of the studies investigate any research question to show that their models can address at least one issue of replicability and/or reproducibility. More than 62.6% of the studies do not even share high-quality source code or complete data to support the reproducibility of their complex models. Meanwhile, our experimental results show the importance of reproducibility and replicability, where the reported performance of a DL model could not be reproduced for an unstable optimization process. Replicability could be substantially compromised if the model training is not convergent, or if performance is sensitive to the size of vocabulary and testing data. Conclusion: It is urgent for the SE community to provide a long-lasting link to a high-quality reproduction package, enhance DL-based solution stability and convergence, and avoid performance sensitivity on different sampled data.

Literature survey of deep learning-based vulnerability analysis on source code

IET Software ◽  
2020 ◽  
Vol 14 (6) ◽  
pp. 654-664
Author(s):  
Abubakar Omari Abdallah Semasaba ◽  
Wei Zheng ◽  
Xiaoxue Wu ◽  
Samuel Akwasi Agyemang
Keyword(s):  
Deep Learning ◽  
Source Code ◽  
Vulnerability Analysis ◽  
Literature Survey

scholarly journals PyConvU-Net: a lightweight and multiscale network for biomedical image segmentation

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Changyong Li ◽  
Yongxian Fan ◽  
Xiaodong Cai
Keyword(s):  
Image Segmentation ◽  
Deep Learning ◽  
State Of The Art ◽  
Experimental Results ◽  
Actual Situation ◽  
Controlled Experiments ◽  
Biomedical Image ◽  
Segmentation Methods ◽  
Art Performance

Abstract Background With the development of deep learning (DL), more and more methods based on deep learning are proposed and achieve state-of-the-art performance in biomedical image segmentation. However, these methods are usually complex and require the support of powerful computing resources. According to the actual situation, it is impractical that we use huge computing resources in clinical situations. Thus, it is significant to develop accurate DL based biomedical image segmentation methods which depend on resources-constraint computing. Results A lightweight and multiscale network called PyConvU-Net is proposed to potentially work with low-resources computing. Through strictly controlled experiments, PyConvU-Net predictions have a good performance on three biomedical image segmentation tasks with the fewest parameters. Conclusions Our experimental results preliminarily demonstrate the potential of proposed PyConvU-Net in biomedical image segmentation with resources-constraint computing.

scholarly journals Deep Learning Based Pavement Inspection Using Self-Reconfigurable Robot

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2595
Author(s):  
Balakrishnan Ramalingam ◽  
Abdullah Aamir Hayat ◽  
Mohan Rajesh Elara ◽  
Braulio Félix Gómez ◽  
Lim Yi ◽  
...  
Keyword(s):  
Deep Learning ◽  
Semantic Segmentation ◽  
High Accuracy ◽  
Experimental Results ◽  
Mobile Mapping ◽  
Mapping System ◽  
Mobile Mapping System ◽  
Reconfigurable Robot ◽  
Nvidia Gpu ◽  
Inspection Task

The pavement inspection task, which mainly includes crack and garbage detection, is essential and carried out frequently. The human-based or dedicated system approach for inspection can be easily carried out by integrating with the pavement sweeping machines. This work proposes a deep learning-based pavement inspection framework for self-reconfigurable robot named Panthera. Semantic segmentation framework SegNet was adopted to segment the pavement region from other objects. Deep Convolutional Neural Network (DCNN) based object detection is used to detect and localize pavement defects and garbage. Furthermore, Mobile Mapping System (MMS) was adopted for the geotagging of the defects. The proposed system was implemented and tested with the Panthera robot having NVIDIA GPU cards. The experimental results showed that the proposed technique identifies the pavement defects and litters or garbage detection with high accuracy. The experimental results on the crack and garbage detection are presented. It is found that the proposed technique is suitable for deployment in real-time for garbage detection and, eventually, sweeping or cleaning tasks.

Real-Time Identification and Tracking of Infrared Markers Based on Kalman Filter

2012 ◽  
Vol 249-250 ◽  
pp. 1147-1153
Author(s):  
Qiao Na Xing ◽  
Da Yuan Yan ◽  
Xiao Ming Hu ◽  
Jun Qin Lin ◽  
Bo Yang
Keyword(s):  
Kalman Filter ◽  
Visible Light ◽  
Real Time ◽  
Complex Terrain ◽  
Experimental Results ◽  
Identification Method ◽  
In The Wild ◽  
Real Time Identification

Automatic equipmenttransportation in the wild complex terrain circumstances is very important in rescue or military. In this paper, an accompanying system based on the identification and tracking of infrared LEDmarkers is proposed. This system avoidsthe defect that visible-light identification method has. In addition, this paper presents a Kalman filter to predict where infraredmarkers may appear in the nextframe imageto reduce the searchingarea of infrared markers, which remarkablyimproves the identificationspeed of infrared markers. The experimental results show that the algorithm proposed in this paper is effective and feasible.

Wavelets as activation functions in Neural Networks

2021 ◽  
pp. 1-11
Author(s):  
Oscar Herrera ◽  
Belém Priego
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
High Performance ◽  
Research Area ◽  
Experimental Results ◽  
Activation Functions ◽  
Hyperbolic Tangent ◽  
Open Research ◽  
Bounded Functions

Traditionally, a few activation functions have been considered in neural networks, including bounded functions such as threshold, sigmoidal and hyperbolic-tangent, as well as unbounded ReLU, GELU, and Soft-plus, among other functions for deep learning, but the search for new activation functions still being an open research area. In this paper, wavelets are reconsidered as activation functions in neural networks and the performance of Gaussian family wavelets (first, second and third derivatives) are studied together with other functions available in Keras-Tensorflow. Experimental results show how the combination of these activation functions can improve the performance and supports the idea of extending the list of activation functions to wavelets which can be available in high performance platforms.

The Development of an Identification Photo Booth System based on a Deep Learning Automatic Image Capturing Method

2020 ◽  
Author(s):  
Yu-Xiang Zhao ◽  
Yi-Zeng Hsieh ◽  
Shih-Syun Lin
Keyword(s):  
Deep Learning ◽  
Experimental Results ◽  
Automatic Annotation ◽  
Learning Method ◽  
Facial Region ◽  
Facial Landmarks ◽  
Image Capturing ◽  
The Face ◽  
Facial Contours

With advances in technology, photo booths equipped with automatic capturing systems have gradually replaced the identification (ID) photo service provided by photography studios, thereby enabling consumers to save a considerable amount of time and money. Common automatic capturing systems employ text and voice instructions to guide users in capturing their ID photos; however, the capturing results may not conform to ID photo specifications. To address this issue, this study proposes an ID photo capturing algorithm that can automatically detect facial contours and adjust the size of captured images. The authors adopted a deep learning method (You Only Look Once) to detect the face and applied a semi-automatic annotation technique of facial landmarks to find the lip and chin regions from the facial region. In the experiments, subjects were seated at various distances and heights for testing the performance of the proposed algorithm. The experimental results show that the proposed algorithm can effectively and accurately capture ID photos that satisfy the required specifications.

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