scholarly journals CRISPRLearner: A Deep Learning-Based System to Predict CRISPR/Cas9 sgRNA On-Target Cleavage Efficiency

Electronics ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 1478 ◽  
Author(s):  
Giovanni Dimauro ◽  
Pierpasquale Colagrande ◽  
Roberto Carlucci ◽  
Mario Ventura ◽  
Vitoantonio Bevilacqua ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Data Augmentation ◽  
Its Sequence ◽  
Target Genome ◽  
Spearman Correlation ◽  
Design Task ◽  
Cleavage Efficiency ◽  
Sgrna Design

CRISPRLearner, the system presented in this paper, makes it possible to predict the on-target cleavage efficiency (also called on-target knockout efficiency) of a given sgRNA sequence, specifying the target genome that this sequence is designed for. After efficiency prediction, the researcher can evaluate its sequence and design a new one if the predicted efficiency is low. CRISPRLearner uses a deep convolutional neural network to automatically learn sequence determinants and predict the efficiency, using pre-trained models or using a model trained on a custom dataset. The convolutional neural network uses linear regression to predict efficiency based on efficiencies used to train the model. Ten different models were trained using ten different gene datasets. The efficiency prediction task attained an average Spearman correlation higher than 0.40. This result was obtained using a data augmentation technique that generates mutations of a sgRNA sequence, maintaining the efficiency value. CRISPRLearner supports researchers in sgRNA design task, predicting a sgRNA on-target knockout efficiency.

Oversampling Based on Data Augmentation in Convolutional Neural Network for Silicon Wafer Defect Classification

2020 ◽  
Author(s):  
Uzma Batool ◽  
Mohd Ibrahim Shapiai ◽  
Nordinah Ismail ◽  
Hilman Fauzi ◽  
Syahrizal Salleh
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Silicon Wafer ◽  
Data Augmentation ◽  
Imbalanced Data ◽  
Training Data ◽  
Defect Classification ◽  
Learning Method ◽  
Test Set

Silicon wafer defect data collected from fabrication facilities is intrinsically imbalanced because of the variable frequencies of defect types. Frequently occurring types will have more influence on the classification predictions if a model gets trained on such skewed data. A fair classifier for such imbalanced data requires a mechanism to deal with type imbalance in order to avoid biased results. This study has proposed a convolutional neural network for wafer map defect classification, employing oversampling as an imbalance addressing technique. To have an equal participation of all classes in the classifier’s training, data augmentation has been employed, generating more samples in minor classes. The proposed deep learning method has been evaluated on a real wafer map defect dataset and its classification results on the test set returned a 97.91% accuracy. The results were compared with another deep learning based auto-encoder model demonstrating the proposed method, a potential approach for silicon wafer defect classification that needs to be investigated further for its robustness.

scholarly journals An Efficient Deep Learning Approach to Pneumonia Classification in Healthcare

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Okeke Stephen ◽  
Mangal Sain ◽  
Uchenna Joseph Maduh ◽  
Do-Un Jeong
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Data Augmentation ◽  
Classification Performance ◽  
Learning Approaches ◽  
X Ray ◽  
Chest X Ray

This study proposes a convolutional neural network model trained from scratch to classify and detect the presence of pneumonia from a collection of chest X-ray image samples. Unlike other methods that rely solely on transfer learning approaches or traditional handcrafted techniques to achieve a remarkable classification performance, we constructed a convolutional neural network model from scratch to extract features from a given chest X-ray image and classify it to determine if a person is infected with pneumonia. This model could help mitigate the reliability and interpretability challenges often faced when dealing with medical imagery. Unlike other deep learning classification tasks with sufficient image repository, it is difficult to obtain a large amount of pneumonia dataset for this classification task; therefore, we deployed several data augmentation algorithms to improve the validation and classification accuracy of the CNN model and achieved remarkable validation accuracy.

scholarly journals Plastic Gasket Defect Detection Based on Transfer Learning

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Xieyi Chen ◽  
Dongyun Wang ◽  
Jinjun Shao ◽  
Jun Fan
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Transfer Learning ◽  
Defect Detection ◽  
Data Augmentation ◽  
Surface Defects ◽  
Visual Detection ◽  
Training Data

To automatically detect plastic gasket defects, a set of plastic gasket defect visual detection devices based on GoogLeNet Inception-V2 transfer learning was designed and established in this study. The GoogLeNet Inception-V2 deep convolutional neural network (DCNN) was adopted to extract and classify the defect features of plastic gaskets to solve the problem of their numerous surface defects and difficulty in extracting and classifying the features. Deep learning applications require a large amount of training data to avoid model overfitting, but there are few datasets of plastic gasket defects. To address this issue, data augmentation was applied to our dataset. Finally, the performance of the three convolutional neural networks was comprehensively compared. The results showed that the GoogLeNet Inception-V2 transfer learning model had a better performance in less time. It means it had higher accuracy, reliability, and efficiency on the dataset used in this paper.

scholarly journals Face Image Age Estimation Based on Data Augmentation and Lightweight Convolutional Neural Network

Symmetry ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 146 ◽  
Author(s):  
Xinhua Liu ◽  
Yao Zou ◽  
Hailan Kuang ◽  
Xiaolin Ma
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Convolutional Neural Networks ◽  
Age Estimation ◽  
Data Augmentation ◽  
Rapid Development ◽  
Estimation Methods ◽  
Face Images

Face images contain many important biological characteristics. The research directions of face images mainly include face age estimation, gender judgment, and facial expression recognition. Taking face age estimation as an example, the estimation of face age images through algorithms can be widely used in the fields of biometrics, intelligent monitoring, human-computer interaction, and personalized services. With the rapid development of computer technology, the processing speed of electronic devices has greatly increased, and the storage capacity has been greatly increased, allowing deep learning to dominate the field of artificial intelligence. Traditional age estimation methods first design features manually, then extract features, and perform age estimation. Convolutional neural networks (CNN) in deep learning have incomparable advantages in processing image features. Practice has proven that the accuracy of using convolutional neural networks to estimate the age of face images is far superior to traditional methods. However, as neural networks are designed to be deeper, and networks are becoming larger and more complex, this makes it difficult to deploy models on mobile terminals. Based on a lightweight convolutional neural network, an improved ShuffleNetV2 network based on the mixed attention mechanism (MA-SFV2: Mixed Attention-ShuffleNetV2) is proposed in this paper by transforming the output layer, merging classification and regression age estimation methods, and highlighting important features by preprocessing images and data augmentation methods. The influence of noise vectors such as the environmental information unrelated to faces in the image is reduced, so that the final age estimation accuracy can be comparable to the state-of-the-art.

scholarly journals Bearing Fault Diagnosis Based on Multiscale Convolutional Neural Network Using Data Augmentation

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Seungmin Han ◽  
Seokju Oh ◽  
Jongpil Jeong
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Fault Diagnosis ◽  
Convolutional Neural Network ◽  
Data Augmentation ◽  
Feature Learning ◽  
Learning Technology ◽  
Financial Loss ◽  
Training Time ◽  
Imbalance Problem

Bearings are one of the most important parts of a rotating machine. Bearing failure can lead to mechanical failure, financial loss, and even personal injury. In recent years, various deep learning techniques have been used to diagnose bearing faults in rotating machines. However, deep learning technology has a data imbalance problem because it requires huge amounts of data. To solve this problem, we used data augmentation techniques. In addition, Convolutional Neural Network, one of the deep learning models, is a method capable of performing feature learning without prior knowledge. However, since conventional fault diagnosis based on CNN can only extract single-scale features, not only useful information may be lost but also domain shift problems may occur. In this paper, we proposed a Multiscale Convolutional Neural Network (MSCNN) to extract more powerful and differentiated features from raw signals. MSCNN can learn more powerful feature expression than conventional CNN through multiscale convolution operation and reduce the number of parameters and training time. The proposed model proved better results and validated the effectiveness of the model compared to 2D-CNN and 1D-CNN.

scholarly journals Toward a Highly Accurate Classification of Underwater Cable Images via Deep Convolutional Neural Network

2020 ◽  
Vol 8 (11) ◽  
pp. 924
Author(s):  
Guan Wei Thum ◽  
Sai Hong Tang ◽  
Siti Azfanizam Ahmad ◽  
Moath Alrifaey
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Data Augmentation ◽  
Power Transmission ◽  
Vision System ◽  
Autonomous Underwater Vehicles ◽  
Deep Convolutional Neural Network ◽  
Computational Time ◽  
Learning Method

Underwater cables or pipelines are commonly utilized elements in ocean research, marine engineering, power transmission, and communication-based activities. Their performance necessitates regularly conducted inspection for maintenance purposes. A vision system is commonly used by autonomous underwater vehicles (AUVs) to track and search for underwater cable. Its traditional methods are characteristically applicable in AUVs, wherein they are equipped with handcrafted features and shallow trainable architectures. However, such methods are subpar or even incapable of tracking underwater cable in fast-changing and complex underwater conditions. In contrast to this, the deep learning method is linked with the capacity to learn semantic, high-level, and deeper features, thus rendering it recommended for performing underwater cable tracking. In this study, several deep Convolutional Neural Network (CNN) models were proposed to classify underwater cable images obtained from a set of underwater images, whereby transfer learning and data augmentation were applied to enhance the classification accuracy. Following a comparison and discussion regarding the performance of these models, MobileNetV2 outperformed among other models and yielded lower computational time and the highest accuracy for classifying underwater cable images at 93.5%. Hence, the main contribution of this study is geared toward developing a deep learning method for underwater cable image classification.

scholarly journals Identifikasi Foto Wanita Berhijab dari Majalah Untuk Pembuatan Katalog Busana Muslim Otomatis Memanfaatkan Convolutional Neural Network

2019 ◽  
Vol 1 (2) ◽  
pp. 85-91
Author(s):  
M. Najamudin Ridha ◽  
Endang Setyati ◽  
Yosi Kristian
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Image Classification ◽  
Large Scale ◽  
Data Augmentation ◽  
Rectified Linear Unit

Abstrak—Perkembangan Fashion Muslim di Indonesia terus meningkat, disisi lain terobosan baru pada Deep Learning dengan memadukan arsitektur seperti dropout regularizations dan Rectified Linear Unit (ReLU) sebagai fungsi aktivasi dan data augmentation, mampu mencapai terobosan pada large scale image classification. Penelitian ini menggunakan metode deteksi objek wajah dengan Haar Cascades Classification untuk mendapatkan sample dataset wajah dan preprocessing data testing untuk dilanjutkan pada metode machine learning untuk klasifikasi citra dengan Convolutional Neural Network. Dataset yang digunakan adalah kumpulan katalog busana online, dataset yang sudah di preprocessing dibagi menjadi dua kategori, yaitu Hijab untuk semua citra wanita berhijab, dan Non Hijab untuk citra yang bukan wanita berhijab. selanjutnya klasifikasi citra menggunakan data ujicoba majalah digital terbitan Hijabella, Joy Indonesia dan Scarf Indonesia. Semakin besar resolusi citra input untuk preprocessing pada majalah digital, maka akan semakin banyak objek citra yang terdeteksi, dengan meningkatkan jumlah dataset untuk training dan validasi, mampu menambah hasil akurasi yang didapatkan, terjadi peningkatan akurasi pada dataset 2.500 wajah perkategori ke 5.000 wajah perkategori dengan resolusi 720p meningkat dari rata-rata 81.30% menjadi 82.31%, peningkatan rata-rata 1.01% dan tertinggi 2.14%, sedangkan resolusi 1080p meningkat dari rata-rata 83.03% menjadi 83.68%, peningkatan rata-rata 0.65% dan tertinggi 1.73%, akurasi tertinggi adalah sebesar 84.72% menggunakan model dataset 5.000 secara acak perkategori.

scholarly journals Data Augmentation using Adversarial Networks for Tea Diseases Detection

2020 ◽  
Vol 20 (1) ◽  
pp. 29
Author(s):  
R. Sandra Yuwana ◽  
Fani Fauziah ◽  
Ana Heryana ◽  
Dikdik Krisnandi ◽  
R. Budiarianto Suryo Kusumo ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Data Augmentation ◽  
Original Data ◽  
The Other ◽  
Generative Adversarial Networks ◽  
Learning Technology ◽  
Limited Data ◽  
Adversarial Networks

Deep learning technology has a better result when trained using an abundant amount of data. However, collecting such data is expensive and time consuming.  On the other hand, limited data often be the inevitable condition. To increase the number of data, data augmentation is usually implemented.  By using it, the original data are transformed, by rotating, shifting, or both, to generate new data artificially. In this paper, generative adversarial networks (GAN) and deep convolutional GAN (DCGAN) are used for data augmentation. Both approaches are applied for diseases detection. The performance of the tea diseases detection on the augmented data is evaluated using various deep convolutional neural network (DCNN) including AlexNet, DenseNet, ResNet, and Xception.  The experimental results indicate that the highest GAN accuracy is obtained by DenseNet architecture, which is 88.84%, baselines accuracy on the same architecture is 86.30%. The results of DCGAN accuracy on the use of the same architecture show a similar trend, which is 88.86%. 

Sign in / Sign up

Export Citation Format

Share Document