scholarly journals Recursive Convolutional Neural Networks for Epigenomics

2020 ◽  
Author(s):  
Aikaterini Symeonidi ◽  
Anguelos Nicolaou ◽  
Frank Johannes ◽  
Vincent Christlein
Keyword(s):  
Gene Expression ◽  
Neural Networks ◽  
Deep Learning ◽  
Functional Genomics ◽  
Convolutional Neural Networks ◽  
Histone Modifications ◽  
State Of The Art ◽  
Learning Methods ◽  
Arbitrary Size

AbstractDeep learning methods have proved to be powerful classification tools in the fields of structural and functional genomics. In this paper, we introduce a Recursive Convolutional Neural Networks (RCNN) for the analysis of epigenomic data. We focus on the task of predicting gene expression from the intensity of histone modifications. The proposed RCNN architecture can be applied to data of an arbitrary size, and has a single meta-parameter that quantifies the models capacity, thus making it flexible for experimenting. The proposed architecture outperforms state-of-the-art systems, while having several orders of magnitude fewer parameters.

scholarly journals Single-Cell Phenotype Classification Using Deep Convolutional Neural Networks

2016 ◽  
Vol 21 (9) ◽  
pp. 998-1003 ◽  
Author(s):  
Oliver Dürr ◽  
Beate Sick
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Single Cell ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Misclassification Rate ◽  
Support Vector ◽  
Learning Methods ◽  
Phenotype Classification

Deep learning methods are currently outperforming traditional state-of-the-art computer vision algorithms in diverse applications and recently even surpassed human performance in object recognition. Here we demonstrate the potential of deep learning methods to high-content screening–based phenotype classification. We trained a deep learning classifier in the form of convolutional neural networks with approximately 40,000 publicly available single-cell images from samples treated with compounds from four classes known to lead to different phenotypes. The input data consisted of multichannel images. The construction of appropriate feature definitions was part of the training and carried out by the convolutional network, without the need for expert knowledge or handcrafted features. We compare our results against the recent state-of-the-art pipeline in which predefined features are extracted from each cell using specialized software and then fed into various machine learning algorithms (support vector machine, Fisher linear discriminant, random forest) for classification. The performance of all classification approaches is evaluated on an untouched test image set with known phenotype classes. Compared to the best reference machine learning algorithm, the misclassification rate is reduced from 8.9% to 6.6%.

scholarly journals Explaining decisions of Graph Convolutional Neural Networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer

2020 ◽  
Author(s):  
Hryhorii Chereda ◽  
Annalen Bleckmann ◽  
Kerstin Menck ◽  
Júlia Perera-Bel ◽  
Philip Stegmaier ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Gene Expression Data ◽  
Molecular Network ◽  
Patient Specific ◽  
Expression Data ◽  
Learning Methods

AbstractMotivationContemporary deep learning approaches show cutting-edge performance in a variety of complex prediction tasks. Nonetheless, the application of deep learning in healthcare remains limited since deep learning methods are often considered as non-interpretable black-box models. Layer-wise Relevance Propagation (LRP) is a technique to explain decisions of deep learning methods. It is widely used to interpret Convolutional Neural Networks (CNNs) applied on image data. Recently, CNNs started to extend towards non-euclidean domains like graphs. Molecular networks are commonly represented as graphs detailing interactions between molecules. Gene expression data can be assigned to the vertices of these graphs. In other words, gene expression data can be structured by utilizing molecular network information as prior knowledge. Graph-CNNs can be applied to structured gene expression data, for example, to predict metastatic events in breast cancer. Therefore, there is a need for explanations showing which part of a molecular network is relevant for predicting an event, e.g. distant metastasis in cancer, for each individual patient.ResultsWe extended the procedure of LRP to make it available for Graph-CNN and tested its applicability on a large breast cancer dataset. We present Graph Layer-wise Relevance Propagation (GLRP) as a new method to explain the decisions made by Graph-CNNs. We demonstrate a sanity check of the developed GLRP on a hand-written digits dataset, and then applied the method on gene expression data. We show that GLRP provides patient-specific molecular subnetworks that largely agree with clinical knowledge and identify common as well as novel, and potentially druggable, drivers of tumor progression. As a result this method could be potentially highly useful on interpreting classification results on the individual patient level, as for example in precision medicine approaches or a molecular tumor board.Availabilityhttps://gitlab.gwdg.de/UKEBpublic/graph-lrphttps://frankkramer-lab.github.io/MetaRelSubNetVis/[email protected]

scholarly journals 3D Convolutional Neural Networks Initialized from Pretrained 2D Convolutional Neural Networks for Classification of Industrial Parts

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1078
Author(s):  
Ibon Merino ◽  
Jon Azpiazu ◽  
Anthony Remazeilles ◽  
Basilio Sierra
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Learning Methods ◽  
Depth Cameras ◽  
Convolutional Networks ◽  
Vision Sensors ◽  
Industrial Object

Deep learning methods have been successfully applied to image processing, mainly using 2D vision sensors. Recently, the rise of depth cameras and other similar 3D sensors has opened the field for new perception techniques. Nevertheless, 3D convolutional neural networks perform slightly worse than other 3D deep learning methods, and even worse than their 2D version. In this paper, we propose to improve 3D deep learning results by transferring the pretrained weights learned in 2D networks to their corresponding 3D version. Using an industrial object recognition context, we have analyzed different combinations of 3D convolutional networks (VGG16, ResNet, Inception ResNet, and EfficientNet), comparing the recognition accuracy. The highest accuracy is obtained with EfficientNetB0 using extrusion with an accuracy of 0.9217, which gives comparable results to state-of-the art methods. We also observed that the transfer approach enabled to improve the accuracy of the Inception ResNet 3D version up to 18% with respect to the score of the 3D approach alone.

scholarly journals Fusion High-Resolution Network for Diagnosing ChestX-ray Images

Electronics ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 190 ◽  
Author(s):  
Zhiwei Huang ◽  
Jinzhao Lin ◽  
Liming Xu ◽  
Huiqian Wang ◽  
Tong Bai ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
High Resolution ◽  
Convolutional Neural Networks ◽  
Characteristic Curve ◽  
Area Under The Curve ◽  
Disease Classification ◽  
Deep Convolutional Neural Networks ◽  
Learning Methods ◽  
Global And Local

The application of deep convolutional neural networks (CNN) in the field of medical image processing has attracted extensive attention and demonstrated remarkable progress. An increasing number of deep learning methods have been devoted to classifying ChestX-ray (CXR) images, and most of the existing deep learning methods are based on classic pretrained models, trained by global ChestX-ray images. In this paper, we are interested in diagnosing ChestX-ray images using our proposed Fusion High-Resolution Network (FHRNet). The FHRNet concatenates the global average pooling layers of the global and local feature extractors—it consists of three branch convolutional neural networks and is fine-tuned for thorax disease classification. Compared with the results of other available methods, our experimental results showed that the proposed model yields a better disease classification performance for the ChestX-ray 14 dataset, according to the receiver operating characteristic curve and area-under-the-curve score. An ablation study further confirmed the effectiveness of the global and local branch networks in improving the classification accuracy of thorax diseases.

scholarly journals A convolutional neural network for predicting transcriptional regulators of genes in Arabidopsis transcriptome data reveals classification based on positive regulatory interactions

2019 ◽  
Author(s):  
Dan MacLean
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Convolutional Neural Networks ◽  
Expression Profiles ◽  
Biological Data ◽  
Expression Data ◽  
Data Set

AbstractGene Regulatory networks that control gene expression are widely studied yet the interactions that make them up are difficult to predict from high throughput data. Deep Learning methods such as convolutional neural networks can perform surprisingly good classifications on a variety of data types and the matrix-like gene expression profiles would seem to be ideal input data for deep learning approaches. In this short study I compiled training sets of expression data using the Arabidopsis AtGenExpress global stress expression data set and known transcription factor-target interactions from the Arabidopsis PLACE database. I built and optimised convolutional neural networks with a best model providing 95 % accuracy of classification on a held-out validation set. Investigation of the activations within this model revealed that classification was based on positive correlation of expression profiles in short sections. This result shows that a convolutional neural network can be used to make classifications and reveal the basis of those calssifications for gene expression data sets, indicating that a convolutional neural network is a useful and interpretable tool for exploratory classification of biological data. The final model is available for download and as a web application.

scholarly journals GraphProt2: A novel deep learning-based method for predicting binding sites of RNA-binding proteins

2019 ◽  
Author(s):  
Michael Uhl ◽  
Van Dinh Tran ◽  
Rolf Backofen
Keyword(s):  
Gene Expression ◽  
Neural Networks ◽  
Deep Learning ◽  
Binding Sites ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
State Of The Art ◽  
Prediction Method ◽  
Superior Performance

AbstractCLIP-seq is the state-of-the-art technique to experimentally determine transcriptome-wide binding sites of RNA-binding proteins (RBPs). However, it relies on gene expression which can be highly variable between conditions, and thus cannot provide a complete picture of the RBP binding landscape. This necessitates the use of computational methods to predict missing binding sites. Here we present GraphProt2, a computational RBP binding site prediction method based on graph convolutional neural networks (GCN). In contrast to current CNN methods, GraphProt2 supports variable length input as well as the possibility to accurately predict nucleotide-wise binding profiles. We demonstrate its superior performance compared to GraphProt and a CNN-based method on single as well as combined CLIP-seq datasets.

Identifying Emotion on Indonesian Tweets using Convolutional Neural Networks

2021 ◽  
Vol 5 (3) ◽  
pp. 584-593
Author(s):  
Naufal Hilmiaji ◽  
Kemas Muslim Lhaksmana ◽  
Mahendra Dwifebri Purbolaksono
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Performance Evaluation ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Convolutional Neural Networks ◽  
Text Classification ◽  
Classification Model ◽  
Learning Methods ◽  
Expected Performance

especially with the advancement of deep learning methods for text classification. Despite some effort to identify emotion on Indonesian tweets, its performance evaluation results have not achieved acceptable numbers. To solve this problem, this paper implements a classification model using a convolutional neural network (CNN), which has demonstrated expected performance in text classification. To easily compare with the previous research, this classification is performed on the same dataset, which consists of 4,403 tweets in Indonesian that were labeled using five different emotion classes: anger, fear, joy, love, and sadness. The performance evaluation results achieve the precision, recall, and F1-score at respectively 90.1%, 90.3%, and 90.2%, while the highest accuracy achieves 89.8%. These results outperform previous research that classifies the same classification on the same dataset.

Sanitizing hidden activations for improving adversarial robustness of convolutional neural networks

2021 ◽  
pp. 1-11
Author(s):  
Tianshi Mu ◽  
Kequan Lin ◽  
Huabing Zhang ◽  
Jian Wang
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Black Box ◽  
Experimental Results ◽  
Amplification Effect ◽  
Wide Range ◽  
Adversarial Examples

Deep learning is gaining significant traction in a wide range of areas. Whereas, recent studies have demonstrated that deep learning exhibits the fatal weakness on adversarial examples. Due to the black-box nature and un-transparency problem of deep learning, it is difficult to explain the reason for the existence of adversarial examples and also hard to defend against them. This study focuses on improving the adversarial robustness of convolutional neural networks. We first explore how adversarial examples behave inside the network through visualization. We find that adversarial examples produce perturbations in hidden activations, which forms an amplification effect to fool the network. Motivated by this observation, we propose an approach, termed as sanitizing hidden activations, to help the network correctly recognize adversarial examples by eliminating or reducing the perturbations in hidden activations. To demonstrate the effectiveness of our approach, we conduct experiments on three widely used datasets: MNIST, CIFAR-10 and ImageNet, and also compare with state-of-the-art defense techniques. The experimental results show that our sanitizing approach is more generalized to defend against different kinds of attacks and can effectively improve the adversarial robustness of convolutional neural networks.

scholarly journals Multiscale Convolutional Neural Networks for Hand Detection

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Shiyang Yan ◽  
Yizhang Xia ◽  
Jeremy S. Smith ◽  
Wenjin Lu ◽  
Bailing Zhang
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Hand Tracking ◽  
Language Recognition ◽  
Hand Detection ◽  
Still Images ◽  
Detection Scheme ◽  
Gesture Analysis

Unconstrained hand detection in still images plays an important role in many hand-related vision problems, for example, hand tracking, gesture analysis, human action recognition and human-machine interaction, and sign language recognition. Although hand detection has been extensively studied for decades, it is still a challenging task with many problems to be tackled. The contributing factors for this complexity include heavy occlusion, low resolution, varying illumination conditions, different hand gestures, and the complex interactions between hands and objects or other hands. In this paper, we propose a multiscale deep learning model for unconstrained hand detection in still images. Deep learning models, and deep convolutional neural networks (CNNs) in particular, have achieved state-of-the-art performances in many vision benchmarks. Developed from the region-based CNN (R-CNN) model, we propose a hand detection scheme based on candidate regions generated by a generic region proposal algorithm, followed by multiscale information fusion from the popular VGG16 model. Two benchmark datasets were applied to validate the proposed method, namely, the Oxford Hand Detection Dataset and the VIVA Hand Detection Challenge. We achieved state-of-the-art results on the Oxford Hand Detection Dataset and had satisfactory performance in the VIVA Hand Detection Challenge.

scholarly journals Image Steganalysis via Diverse Filters and Squeeze-and-Excitation Convolutional Neural Network

Mathematics ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 189
Author(s):  
Feng Liu ◽  
Xuan Zhou ◽  
Xuehu Yan ◽  
Yuliang Lu ◽  
Shudong Wang
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Image Steganalysis ◽  
Process Information ◽  
Effective Network ◽  
Convolution Filters

Steganalysis is a method to detect whether the objects contain secret messages. With the popularity of deep learning, using convolutional neural networks (CNNs), steganalytic schemes have become the chief method of combating steganography in recent years. However, the diversity of filters has not been fully utilized in the current research. This paper constructs a new effective network with diverse filter modules (DFMs) and squeeze-and-excitation modules (SEMs), which can better capture the embedding artifacts. As the essential parts, combining three different scale convolution filters, DFMs can process information diversely, and the SEMs can enhance the effective channels out from DFMs. The experiments presented that our CNN is effective against content-adaptive steganographic schemes with different payloads, such as S-UNIWARD and WOW algorithms. Moreover, some state-of-the-art methods are compared with our approach to demonstrate the outstanding performance.

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