scholarly journals DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout

2019 ◽  
Vol 36 (2) ◽  
pp. 470-477 ◽  
Author(s):  
Badri Adhikari
Keyword(s):  
Neural Networks ◽  
Long Range ◽  
Convolutional Neural Networks ◽  
High Throughput Sequencing ◽  
State Of The Art ◽  
Deep Convolutional Neural Networks ◽  
Contact Prediction ◽  
Learning Techniques ◽  
Medium Range ◽  
Art Methods

Abstract Motivation Exciting new opportunities have arisen to solve the protein contact prediction problem from the progress in neural networks and the availability of a large number of homologous sequences through high-throughput sequencing. In this work, we study how deep convolutional neural networks (ConvNets) may be best designed and developed to solve this long-standing problem. Results With publicly available datasets, we designed and trained various ConvNet architectures. We tested several recent deep learning techniques including wide residual networks, dropouts and dilated convolutions. We studied the improvements in the precision of medium-range and long-range contacts, and compared the performance of our best architectures with the ones used in existing state-of-the-art methods. The proposed ConvNet architectures predict contacts with significantly more precision than the architectures used in several state-of-the-art methods. When trained using the DeepCov dataset consisting of 3456 proteins and tested on PSICOV dataset of 150 proteins, our architectures achieve up to 15% higher precision when L/2 long-range contacts are evaluated. Similarly, when trained using the DNCON2 dataset consisting of 1426 proteins and tested on 84 protein domains in the CASP12 dataset, our single network achieves 4.8% higher precision than the ensembled DNCON2 method when top L long-range contacts are evaluated. Availability and implementation DEEPCON is available at https://github.com/badriadhikari/DEEPCON/.

scholarly journals DEEPCON: Protein Contact Prediction using Dilated Convolutional Neural Networks with Dropout

2019 ◽  
Author(s):  
Badri Adhikari
Keyword(s):  
Neural Networks ◽  
Long Range ◽  
High Throughput Sequencing ◽  
State Of The Art ◽  
Contact Prediction ◽  
Homologous Sequences ◽  
Learning Techniques ◽  
Network Methods ◽  
Medium Range ◽  
Art Methods

AbstractBackgroundExciting new opportunities have arisen to solve the protein contact prediction problem from the progress in neural networks and the availability of a large number of homologous sequences through high-throughput sequencing. In this work, we study how deep convolutional neural network methods (ConvNets) may be best designed and developed to solve this long-standing problem.MethodWith publicly available datasets, we designed and trained various ConvNet architectures. We tested several recent deep learning techniques including wide residual networks, dropouts, and dilated convolutions. We studied the improvements in the precision of medium-range and long-range contacts, and compared the performance of our best architectures with the ones used in existing state-of-the-art methods.ResultsThe proposed ConvNet architectures predict contacts with significantly more precision than the architectures used in several state-of-the-art methods. When trained using the DeepCov dataset consisting of 3,456 proteins and tested on PSICOV dataset of 150 proteins, our architectures achieve up to 15% higher precision when L/2 long-range contacts are evaluated. Similarly, when trained using the DNCON2 dataset consisting of 1,426 proteins and tested on 84 protein domains in the CASP12 dataset, our single network achieves 4.8% higher precision than the ensembled DNCON2 method when top L long-range contacts are evaluated. DEEPCON will be made publicly available athttps://github.com/badriadhikari/DEEPCON/.

scholarly journals Handwritten Bangla Character Recognition Using the State-of-the-Art Deep Convolutional Neural Networks

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Md Zahangir Alom ◽  
Paheding Sidike ◽  
Mahmudul Hasan ◽  
Tarek M. Taha ◽  
Vijayan K. Asari
Keyword(s):  
Neural Networks ◽  
Object Recognition ◽  
Convolutional Neural Networks ◽  
Character Recognition ◽  
State Of The Art ◽  
The State ◽  
Superior Performance ◽  
Deep Convolutional Neural Networks ◽  
Practical Applications ◽  
High Degree

In spite of advances in object recognition technology, handwritten Bangla character recognition (HBCR) remains largely unsolved due to the presence of many ambiguous handwritten characters and excessively cursive Bangla handwritings. Even many advanced existing methods do not lead to satisfactory performance in practice that related to HBCR. In this paper, a set of the state-of-the-art deep convolutional neural networks (DCNNs) is discussed and their performance on the application of HBCR is systematically evaluated. The main advantage of DCNN approaches is that they can extract discriminative features from raw data and represent them with a high degree of invariance to object distortions. The experimental results show the superior performance of DCNN models compared with the other popular object recognition approaches, which implies DCNN can be a good candidate for building an automatic HBCR system for practical applications.

scholarly journals Graph Attention Based Proposal 3D ConvNets for Action Detection

2020 ◽  
Vol 34 (04) ◽  
pp. 4626-4633 ◽  
Author(s):  
Jin Li ◽  
Xianglong Liu ◽  
Zhuofan Zong ◽  
Wanru Zhao ◽  
Mingyuan Zhang ◽  
...  
Keyword(s):  
Neural Networks ◽  
Long Range ◽  
Convolutional Neural Networks ◽  
Adjacency Matrix ◽  
State Of The Art ◽  
Original Model ◽  
Action Detection ◽  
Model Experiments ◽  
Temporal And Spatial ◽  
Temporal Action

The recent advances in 3D Convolutional Neural Networks (3D CNNs) have shown promising performance for untrimmed video action detection, employing the popular detection framework that heavily relies on the temporal action proposal generations as the input of the action detector and localization regressor. In practice the proposals usually contain strong intra and inter relations among them, mainly stemming from the temporal and spatial variations in the video actions. However, most of existing 3D CNNs ignore the relations and thus suffer from the redundant proposals degenerating the detection performance and efficiency. To address this problem, we propose graph attention based proposal 3D ConvNets (AGCN-P-3DCNNs) for video action detection. Specifically, our proposed graph attention is composed of intra attention based GCN and inter attention based GCN. We use intra attention to learn the intra long-range dependencies inside each action proposal and update node matrix of Intra Attention based GCN, and use inter attention to learn the inter dependencies between different action proposals as adjacency matrix of Inter Attention based GCN. Afterwards, we fuse intra and inter attention to model intra long-range dependencies and inter dependencies simultaneously. Another contribution is that we propose a simple and effective framewise classifier, which enhances the feature presentation capabilities of backbone model. Experiments on two proposal 3D ConvNets based models (P-C3D and P-ResNet) and two popular action detection benchmarks (THUMOS 2014, ActivityNet v1.3) demonstrate the state-of-the-art performance achieved by our method. Particularly, P-C3D embedded with our module achieves average mAP 3.7% improvement on THUMOS 2014 dataset compared to original model.

Early and Late Level Fusion of Deep Convolutional Neural Networks for Visual Concept Recognition

2016 ◽  
Vol 10 (03) ◽  
pp. 379-397 ◽  
Author(s):  
Hilal Ergun ◽  
Yusuf Caglar Akyuz ◽  
Mustafa Sert ◽  
Jianquan Liu
Keyword(s):  
Neural Networks ◽  
Best Practices ◽  
Convolutional Neural Networks ◽  
Network Architecture ◽  
Data Augmentation ◽  
State Of The Art ◽  
Great Promise ◽  
Visual Concept ◽  
Deep Convolutional Neural Networks ◽  
Concept Recognition

Visual concept recognition is an active research field in the last decade. Related to this attention, deep learning architectures are showing great promise in various computer vision domains including image classification, object detection, event detection and action recognition in videos. In this study, we investigate various aspects of convolutional neural networks for visual concept recognition. We analyze recent studies and different network architectures both in terms of running time and accuracy. In our proposed visual concept recognition system, we first discuss various important properties of popular convolutional network architecture under consideration. Then we describe our method for feature extraction at different levels of abstraction. We present extensive empirical information along with best practices for big data practitioners. Using these best practices we propose efficient fusion mechanisms both for single and multiple network models. We present state-of-the-art results on benchmark datasets while keeping computational costs at low level. Our results show that these state-of-the-art results can be reached without using extensive data augmentation techniques.

scholarly journals iEnhancer-ECNN: identifying enhancers and their strength using ensembles of convolutional neural networks

BMC Genomics ◽  
2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Quang H. Nguyen ◽  
Thanh-Hoang Nguyen-Vo ◽  
Nguyen Quoc Khanh Le ◽  
Trang T.T. Do ◽  
Susanto Rahardja ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Dna Sequences ◽  
State Of The Art ◽  
Characteristic Curve ◽  
Learning Models ◽  
In Silico Studies ◽  
Layer 2 ◽  
Art Methods ◽  
Enhancer Identification

Abstract Background Enhancers are non-coding DNA fragments which are crucial in gene regulation (e.g. transcription and translation). Having high locational variation and free scattering in 98% of non-encoding genomes, enhancer identification is, therefore, more complicated than other genetic factors. To address this biological issue, several in silico studies have been done to identify and classify enhancer sequences among a myriad of DNA sequences using computational advances. Although recent studies have come up with improved performance, shortfalls in these learning models still remain. To overcome limitations of existing learning models, we introduce iEnhancer-ECNN, an efficient prediction framework using one-hot encoding and k-mers for data transformation and ensembles of convolutional neural networks for model construction, to identify enhancers and classify their strength. The benchmark dataset from Liu et al.’s study was used to develop and evaluate the ensemble models. A comparative analysis between iEnhancer-ECNN and existing state-of-the-art methods was done to fairly assess the model performance. Results Our experimental results demonstrates that iEnhancer-ECNN has better performance compared to other state-of-the-art methods using the same dataset. The accuracy of the ensemble model for enhancer identification (layer 1) and enhancer classification (layer 2) are 0.769 and 0.678, respectively. Compared to other related studies, improvements in the Area Under the Receiver Operating Characteristic Curve (AUC), sensitivity, and Matthews’s correlation coefficient (MCC) of our models are remarkable, especially for the model of layer 2 with about 11.0%, 46.5%, and 65.0%, respectively. Conclusions iEnhancer-ECNN outperforms other previously proposed methods with significant improvement in most of the evaluation metrics. Strong growths in the MCC of both layers are highly meaningful in assuring the stability of our models.

scholarly journals What is this Article about? Extreme Summarization with Topic-aware Convolutional Neural Networks

2019 ◽  
Vol 66 ◽  
pp. 243-278
Author(s):  
Shashi Narayan ◽  
Shay B. Cohen ◽  
Mirella Lapata
Keyword(s):  
Neural Networks ◽  
Long Range ◽  
Convolutional Neural Networks ◽  
Real World ◽  
Large Scale ◽  
State Of The Art ◽  
British Broadcasting Corporation ◽  
Document Summarization ◽  
Modeling Approach ◽  
Large Scale Dataset

We introduce "extreme summarization," a new single-document summarization task which aims at creating a short, one-sentence news summary answering the question "What is the article about?". We argue that extreme summarization, by nature, is not amenable to extractive strategies and requires an abstractive modeling approach. In the hope of driving research on this task further: (a) we collect a real-world, large scale dataset by harvesting online articles from the British Broadcasting Corporation (BBC); and (b) propose a novel abstractive model which is conditioned on the article's topics and based entirely on convolutional neural networks. We demonstrate experimentally that this architecture captures long-range dependencies in a document and recognizes pertinent content, outperforming an oracle extractive system and state-of-the-art abstractive approaches when evaluated automatically and by humans on the extreme summarization dataset.

scholarly journals Direct Quantization for Training Highly Accurate Low Bit-width Deep Neural Networks

2020 ◽  
Author(s):  
Tuan Hoang ◽  
Thanh-Toan Do ◽  
Tam V. Nguyen ◽  
Ngai-Man Cheung
Keyword(s):  
Neural Networks ◽  
Cost Function ◽  
Image Classification ◽  
Convolutional Neural Networks ◽  
Gradient Descent ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Deep Convolutional Neural Networks ◽  
Novel Method ◽  
The Cost

This paper proposes two novel techniques to train deep convolutional neural networks with low bit-width weights and activations. First, to obtain low bit-width weights, most existing methods obtain the quantized weights by performing quantization on the full-precision network weights. However, this approach would result in some mismatch: the gradient descent updates full-precision weights, but it does not update the quantized weights. To address this issue, we propose a novel method that enables direct updating of quantized weights with learnable quantization levels to minimize the cost function using gradient descent. Second, to obtain low bit-width activations, existing works consider all channels equally. However, the activation quantizers could be biased toward a few channels with high-variance. To address this issue, we propose a method to take into account the quantization errors of individual channels. With this approach, we can learn activation quantizers that minimize the quantization errors in the majority of channels. Experimental results demonstrate that our proposed method achieves state-of-the-art performance on the image classification task, using AlexNet, ResNet and MobileNetV2 architectures on CIFAR-100 and ImageNet datasets.

scholarly journals An automatic nuclei segmentation method based on deep convolutional neural networks for histopathology images

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Hwejin Jung ◽  
Bilal Lodhi ◽  
Jaewoo Kang
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Gaussian Mixture ◽  
Color Variation ◽  
Post Processing ◽  
Segmentation Method ◽  
Deep Convolutional Neural Networks ◽  
Nuclei Segmentation ◽  
Histopathology Images

Abstract Background Since nuclei segmentation in histopathology images can provide key information for identifying the presence or stage of a disease, the images need to be assessed carefully. However, color variation in histopathology images, and various structures of nuclei are two major obstacles in accurately segmenting and analyzing histopathology images. Several machine learning methods heavily rely on hand-crafted features which have limitations due to manual thresholding. Results To obtain robust results, deep learning based methods have been proposed. Deep convolutional neural networks (DCNN) used for automatically extracting features from raw image data have been proven to achieve great performance. Inspired by such achievements, we propose a nuclei segmentation method based on DCNNs. To normalize the color of histopathology images, we use a deep convolutional Gaussian mixture color normalization model which is able to cluster pixels while considering the structures of nuclei. To segment nuclei, we use Mask R-CNN which achieves state-of-the-art object segmentation performance in the field of computer vision. In addition, we perform multiple inference as a post-processing step to boost segmentation performance. We evaluate our segmentation method on two different datasets. The first dataset consists of histopathology images of various organ while the other consists histopathology images of the same organ. Performance of our segmentation method is measured in various experimental setups at the object-level and the pixel-level. In addition, we compare the performance of our method with that of existing state-of-the-art methods. The experimental results show that our nuclei segmentation method outperforms the existing methods. Conclusions We propose a nuclei segmentation method based on DCNNs for histopathology images. The proposed method which uses Mask R-CNN with color normalization and multiple inference post-processing provides robust nuclei segmentation results. Our method also can facilitate downstream nuclei morphological analyses as it provides high-quality features extracted from histopathology images.

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