scholarly journals Feature selection may improve deep neural networks for the bioinformatics problems

2019 ◽  
Author(s):  
Zheng Chen ◽  
Meng Pang ◽  
Zixin Zhao ◽  
Shuainan Li ◽  
Rui Miao ◽  
...  
Keyword(s):  
Neural Network ◽  
Feature Selection ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Binary Classification ◽  
Supplementary Information ◽  
Good Prediction ◽  
Programming Environment ◽  
Data Types ◽  
Selection Algorithms

Abstract Motivation Deep neural network (DNN) algorithms were utilized in predicting various biomedical phenotypes recently, and demonstrated very good prediction performances without selecting features. This study proposed a hypothesis that the DNN models may be further improved by feature selection algorithms. Results A comprehensive comparative study was carried out by evaluating 11 feature selection algorithms on three conventional DNN algorithms, i.e. convolution neural network (CNN), deep belief network (DBN) and recurrent neural network (RNN), and three recent DNNs, i.e. MobilenetV2, ShufflenetV2 and Squeezenet. Five binary classification methylomic datasets were chosen to calculate the prediction performances of CNN/DBN/RNN models using feature selected by the 11 feature selection algorithms. Seventeen binary classification transcriptome and two multi-class transcriptome datasets were also utilized to evaluate how the hypothesis may generalize to different data types. The experimental data supported our hypothesis that feature selection algorithms may improve DNN models, and the DBN models using features selected by SVM-RFE usually achieved the best prediction accuracies on the five methylomic datasets. Availability and implementation All the algorithms were implemented and tested under the programming environment Python version 3.6.6. Supplementary information Supplementary data are available at Bioinformatics online.

Explainable Deep Learning Reproduces a ‘Professional Eye’ on the Diagnosis of Internal Disorders in Persimmon Fruit

2020 ◽  
Vol 61 (11) ◽  
pp. 1967-1973
Author(s):  
Takashi Akagi ◽  
Masanori Onishi ◽  
Kanae Masuda ◽  
Ryohei Kuroki ◽  
Kohei Baba ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Binary Classification ◽  
Network Models ◽  
Plant Biology ◽  
Neural Network Models ◽  
Persimmon Fruit

Abstract Recent rapid progress in deep neural network techniques has allowed recognition and classification of various objects, often exceeding the performance of the human eye. In plant biology and crop sciences, some deep neural network frameworks have been applied mainly for effective and rapid phenotyping. In this study, beyond simple optimizations of phenotyping, we propose an application of deep neural networks to make an image-based internal disorder diagnosis that is hard even for experts, and to visualize the reasons behind each diagnosis to provide biological interpretations. Here, we exemplified classification of calyx-end cracking in persimmon fruit by using five convolutional neural network models with various layer structures and examined potential analytical options involved in the diagnostic qualities. With 3,173 visible RGB images from the fruit apex side, the neural networks successfully made the binary classification of each degree of disorder, with up to 90% accuracy. Furthermore, feature visualizations, such as Grad-CAM and LRP, visualize the regions of the image that contribute to the diagnosis. They suggest that specific patterns of color unevenness, such as in the fruit peripheral area, can be indexes of calyx-end cracking. These results not only provided novel insights into indexes of fruit internal disorders but also proposed the potential applicability of deep neural networks in plant biology.

Method of determination of the text direction on the image with the use of convolutional neural network

2020 ◽  
pp. 96-99
Author(s):  
P.L. Nikolaev
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Deep Neural Network ◽  
Binary Classification ◽  
Synthetic Data ◽  
Real Data ◽  
Method Of Determination ◽  
Classification Of Images

This article deals with method of binary classification of images with small text on them Classification is based on the fact that the text can have 2 directions – it can be positioned horizontally and read from left to right or it can be turned 180 degrees so the image must be rotated to read the sign. This type of text can be found on the covers of a variety of books, so in case of recognizing the covers, it is necessary first to determine the direction of the text before we will directly recognize it. The article suggests the development of a deep neural network for determination of the text position in the context of book covers recognizing. The results of training and testing of a convolutional neural network on synthetic data as well as the examples of the network functioning on the real data are presented.

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 Single-cell conventional pap smear image classification using pre-trained deep neural network architectures

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Mohammed Aliy Mohammed ◽  
Fetulhak Abdurahman ◽  
Yodit Abebe Ayalew
Keyword(s):  
Neural Network ◽  
Cervical Cancer ◽  
Computer Vision ◽  
Single Cell ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Pap Smear ◽  
Experimental Result ◽  
Network Architectures ◽  
Average Accuracy

Abstract Background Automating cytology-based cervical cancer screening could alleviate the shortage of skilled pathologists in developing countries. Up until now, computer vision experts have attempted numerous semi and fully automated approaches to address the need. Yet, these days, leveraging the astonishing accuracy and reproducibility of deep neural networks has become common among computer vision experts. In this regard, the purpose of this study is to classify single-cell Pap smear (cytology) images using pre-trained deep convolutional neural network (DCNN) image classifiers. We have fine-tuned the top ten pre-trained DCNN image classifiers and evaluated them using five class single-cell Pap smear images from SIPaKMeD dataset. The pre-trained DCNN image classifiers were selected from Keras Applications based on their top 1% accuracy. Results Our experimental result demonstrated that from the selected top-ten pre-trained DCNN image classifiers DenseNet169 outperformed with an average accuracy, precision, recall, and F1-score of 0.990, 0.974, 0.974, and 0.974, respectively. Moreover, it dashed the benchmark accuracy proposed by the creators of the dataset with 3.70%. Conclusions Even though the size of DenseNet169 is small compared to the experimented pre-trained DCNN image classifiers, yet, it is not suitable for mobile or edge devices. Further experimentation with mobile or small-size DCNN image classifiers is required to extend the applicability of the models in real-world demands. In addition, since all experiments used the SIPaKMeD dataset, additional experiments will be needed using new datasets to enhance the generalizability of the models.

scholarly journals Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Li-Hsin Cheng ◽  
Te-Cheng Hsu ◽  
Che Lin
Keyword(s):  
Breast Cancer ◽  
Neural Network ◽  
Feature Selection ◽  
Systems Biology ◽  
Ensemble Learning ◽  
Microarray Data ◽  
Deep Neural Network ◽  
Prediction Models ◽  
Biological Knowledge ◽  
Prognosis Prediction

AbstractBreast cancer is a heterogeneous disease. To guide proper treatment decisions for each patient, robust prognostic biomarkers, which allow reliable prognosis prediction, are necessary. Gene feature selection based on microarray data is an approach to discover potential biomarkers systematically. However, standard pure-statistical feature selection approaches often fail to incorporate prior biological knowledge and select genes that lack biological insights. Besides, due to the high dimensionality and low sample size properties of microarray data, selecting robust gene features is an intrinsically challenging problem. We hence combined systems biology feature selection with ensemble learning in this study, aiming to select genes with biological insights and robust prognostic predictive power. Moreover, to capture breast cancer's complex molecular processes, we adopted a multi-gene approach to predict the prognosis status using deep learning classifiers. We found that all ensemble approaches could improve feature selection robustness, wherein the hybrid ensemble approach led to the most robust result. Among all prognosis prediction models, the bimodal deep neural network (DNN) achieved the highest test performance, further verified by survival analysis. In summary, this study demonstrated the potential of combining ensemble learning and bimodal DNN in guiding precision medicine.

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.

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