scholarly journals HELLO: improved neural network architectures and methodologies for small variant calling

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anand Ramachandran ◽  
Steven S. Lumetta ◽  
Eric W. Klee ◽  
Deming Chen
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Image Recognition ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Method Development ◽  
Variant Calling ◽  
Network Architectures ◽  
Sequencing Data ◽  
Neural Network Architectures

Abstract Background Modern Next Generation- and Third Generation- Sequencing methods such as Illumina and PacBio Circular Consensus Sequencing platforms provide accurate sequencing data. Parallel developments in Deep Learning have enabled the application of Deep Neural Networks to variant calling, surpassing the accuracy of classical approaches in many settings. DeepVariant, arguably the most popular among such methods, transforms the problem of variant calling into one of image recognition where a Deep Neural Network analyzes sequencing data that is formatted as images, achieving high accuracy. In this paper, we explore an alternative approach to designing Deep Neural Networks for variant calling, where we use meticulously designed Deep Neural Network architectures and customized variant inference functions that account for the underlying nature of sequencing data instead of converting the problem to one of image recognition. Results Results from 27 whole-genome variant calling experiments spanning Illumina, PacBio and hybrid Illumina-PacBio settings suggest that our method allows vastly smaller Deep Neural Networks to outperform the Inception-v3 architecture used in DeepVariant for indel and substitution-type variant calls. For example, our method reduces the number of indel call errors by up to 18%, 55% and 65% for Illumina, PacBio and hybrid Illumina-PacBio variant calling respectively, compared to a similarly trained DeepVariant pipeline. In these cases, our models are between 7 and 14 times smaller. Conclusions We believe that the improved accuracy and problem-specific customization of our models will enable more accurate pipelines and further method development in the field. HELLO is available at https://github.com/anands-repo/hello

scholarly journals Analysis of the possibilities of using a deep neural networks as an image recognition technology to solve the problem of automating attendance tracking

2020 ◽  
pp. 15-26
Author(s):  
Anna Ilina ◽  
Vladimir Korenkov
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Quality Assessment ◽  
Image Recognition ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Facial Recognition ◽  
Manual Counting

The task of counting the number of people is relevant when conducting various types of events, which may include seminars, lectures, conferences, meetings, etc. Instead of monotonous manual counting of participants, it is much more effective to use facial recognition technology, which makes it possible not only to quickly count those present, but also to recognize each of them, which makes it possible to conduct further analysis of this data, identify patterns in them and predict. The research conducted in this paper determines the quality assessment of the use of facial recognition technology in images andvideo streams, based on the use of a deep neural network, to solve the problem of automating attendance tracking.

scholarly journals Classification of Fermi-LAT sources with deep learning using energy and time spectra

2021 ◽  
Vol 507 (3) ◽  
pp. 4061-4073
Author(s):  
Thorben Finke ◽  
Michael Krämer ◽  
Silvia Manconi
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Active Galactic Nuclei ◽  
Photon Energy ◽  
Deep Neural Network ◽  
Gamma Ray ◽  
Galactic Nuclei ◽  
Network Architectures ◽  
Neural Network Architectures

ABSTRACT Despite the growing number of gamma-ray sources detected by the Fermi-Large Area Telescope (LAT), about one-third of the sources in each survey remains of uncertain type. We present a new deep neural network approach for the classification of unidentified or unassociated gamma-ray sources in the last release of the Fermi-LAT catalogue (4FGL-DR2) obtained with 10 yr of data. In contrast to previous work, our method directly uses the measurements of the photon energy spectrum and time series as input for the classification, instead of specific, human-crafted features. Dense neural networks, and for the first time in the context of gamma-ray source classification recurrent neural networks, are studied in depth. We focus on the separation between extragalactic sources, i.e. active galactic nuclei, and Galactic pulsars, and on the further classification of pulsars into young and millisecond pulsars. Our neural network architectures provide powerful classifiers, with a performance that is comparable to previous analyses based on human-crafted features. Our benchmark neural network predicts that of the sources of uncertain type in the 4FGL-DR2 catalogue, 1050 are active galactic nuclei and 78 are Galactic pulsars, with both classes following the expected sky distribution and the clustering in the variability–curvature plane. We investigate the problem of sample selection bias by testing our architectures against a cross-match test data set using an older catalogue, and propose a feature selection algorithm using autoencoders. Our list of high-confidence candidate sources labelled by the neural networks provides a set of targets for further multiwavelength observations addressed to identify their nature. The deep neural network architectures we develop can be easily extended to include specific features, as well as multiwavelength data on the source photon energy and time spectra coming from different instruments.

scholarly journals Interaffection of Multiple Datasets with Neural Networks in Speech Emotion Recognition

2020 ◽  
Author(s):  
Ronnypetson Da Silva ◽  
Valter M. Filho ◽  
Mario Souza
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Emotion Recognition ◽  
Deep Neural Networks ◽  
Speech Emotion Recognition ◽  
Network Architectures ◽  
Shared Representations ◽  
Multiple Datasets ◽  
Neural Network Architectures

Many works that apply Deep Neural Networks (DNNs) to Speech Emotion Recognition (SER) use single datasets or train and evaluate the models separately when using multiple datasets. Those datasets are constructed with specific guidelines and the subjective nature of the labels for SER makes it difficult to obtain robust and general models. We investigate how DNNs learn shared representations for different datasets in both multi-task and unified setups. We also analyse how each dataset benefits from others in different combinations of datasets and popular neural network architectures. We show that the longstanding belief of more data resulting in more general models doesn’t always hold for SER, as different dataset and meta-parameter combinations hold the best result for each of the analysed datasets.

scholarly journals Scalable Graph Neural Network Training

2021 ◽  
Vol 55 (1) ◽  
pp. 68-76
Author(s):  
Marco Serafini
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Neural Network ◽  
Network Architectures ◽  
Neural Network Training ◽  
Large Graphs ◽  
Graph Data ◽  
Network Training ◽  
Neural Network Architectures ◽  
Graph Neural Networks

Graph Neural Networks (GNNs) are a new and increasingly popular family of deep neural network architectures to perform learning on graphs. Training them efficiently is challenging due to the irregular nature of graph data. The problem becomes even more challenging when scaling to large graphs that exceed the capacity of single devices. Standard approaches to distributed DNN training, like data and model parallelism, do not directly apply to GNNs. Instead, two different approaches have emerged in the literature: whole-graph and sample-based training. In this paper, we review and compare the two approaches. Scalability is challenging with both approaches, but we make a case that research should focus on sample-based training since it is a more promising approach. Finally, we review recent systems supporting sample-based training.

scholarly journals StochasticNet in StochasticNet

2016 ◽  
Vol 2 (1) ◽  
Author(s):  
Mohammad Javad Shafiee ◽  
Paul Fieguth ◽  
Alexander Wong
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
High Performance ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Low Cost ◽  
Network Architectures ◽  
Modeling Accuracy ◽  
Random Graph Theory ◽  
Performance Computing

Deep neural networks have been shown to outperform conventionalstate-of-the-art approaches in several structured predictionapplications. While high-performance computing devices such asGPUs has made developing very powerful deep neural networkspossible, it is not feasible to run these networks on low-cost, lowpowercomputing devices such as embedded CPUs or even embeddedGPUs. As such, there has been a lot of recent interestto produce efficient deep neural network architectures that can berun on small computing devices. Motivated by this, the idea ofStochasticNets was introduced, where deep neural networks areformed by leveraging random graph theory. It has been shownthat StochasticNet can form new networks with 2X or 3X architecturalefficiency while maintaining modeling accuracy. Motivated bythese promising results, here we investigate the idea of Stochastic-Net in StochasticNet (SiS), where highly-efficient deep neural networkswith Network in Network (NiN) architectures are formed ina stochastic manner. Such networks have an intertwining structurecomposed of convolutional layers and micro neural networksto boost the modeling accuracy. The experimental results showthat SiS can form deep neural networks with NiN architectures thathave 4X greater architectural efficiency with only a 2% dropin accuracy for the CIFAR10 dataset. The results are even morepromising for the SVHN dataset, where SiS formed deep neuralnetworks with NiN architectures that have 11.5X greater architecturalefficiency with only a 1% decrease in modeling accuracy.

scholarly journals Book spine recognition with the use of deep neural networks

2020 ◽  
Vol 44 (6) ◽  
pp. 968-977
Author(s):  
M.O. Kalinina ◽  
P.L. Nikolaev
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Network Performance ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Original Data ◽  
Network Architectures ◽  
Data Set ◽  
The Neural Network ◽  
Processing Information

Nowadays deep neural networks play a significant part in various fields of human activity. Especially they benefit spheres dealing with large amounts of data and lengthy operations on obtaining and processing information from the visual environment. This article deals with the development of a convolutional neural network based on the YOLO architecture, intended for real-time book recognition. The creation of an original data set and the training of the deep neural network are described. The structure of the neural network obtained is presented and the most frequently used metrics for estimating the quality of the network performance are considered. A brief review of the existing types of neural network architectures is also made. YOLO architecture possesses a number of advantages that allow it to successfully compete with other models and make it the most suitable variant for creating an object detection network since it enables some of the common disadvantages of such networks to be significantly mitigated (such as recognition of similarly looking, same-color book coves or slanted books). The results obtained in the course of training the deep neural network allow us to use it as a basis for the development of the software for book spine recognition.

scholarly journals Using Summary Layers to Probe Neural Network Behaviour

2020 ◽  
Vol 32 (2) ◽  
Author(s):  
Marelie Hattingh Davel
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Neural Networks ◽  
Network Architectures ◽  
Feedforward Networks ◽  
Empirical Results ◽  
Analysis Process ◽  
Generalisation Ability ◽  
Neural Network Architectures ◽  
Fully Connected

No framework exists that can explain and predict the generalisation ability of deep neural networks in general circumstances. In fact, this question has not been answered for some of the least complicated of neural network architectures: fully-connected feedforward networks with rectified linear activations and a limited number of hidden layers. For such an architecture, we show how adding a summary layer to the network makes it more amenable to analysis, and allows us to define the conditions that are required to guarantee that a set of samples will all be classified correctly. This process does not describe the generalisation behaviour of these networks, but produces a number of metrics that are useful for probing their learning and generalisation behaviour. We support the analytical conclusions with empirical results, both to confirm that the mathematical guarantees hold in practice, and to demonstrate the use of the analysis process.

scholarly journals Identifying Skeletal Maturity from X-rays using Deep Neural Networks

2021 ◽  
Vol 15 (1) ◽  
pp. 141-148
Author(s):  
Suprava Patnaik ◽  
Sourodip Ghosh ◽  
Richik Ghosh ◽  
Shreya Sahay
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
Skeletal Maturity ◽  
Bone Age ◽  
Network Architectures ◽  
X Rays ◽  
X Ray ◽  
Regression Techniques

Skeletal maturity estimation is routinely evaluated by pediatrics and radiologists to assess growth and hormonal disorders. Methods integrated with regression techniques are incompatible with low-resolution digital samples and generate bias, when the evaluation protocols are implemented for feature assessment on coarse X-Ray hand images. This paper proposes a comparative analysis between two deep neural network architectures, with the base models such as Inception-ResNet-V2 and Xception-pre-trained networks. Based on 12,611 hand X-Ray images of RSNA Bone Age database, Inception-ResNet-V2 and Xception models have achieved R-Squared value of 0.935 and 0.942 respectively. Further, in the same order, the MAE accomplished by the two models are 12.583 and 13.299 respectively, when subjected to very few training instances with negligible chances of overfitting.

scholarly journals Dropout with Tabu Strategy for Regularizing Deep Neural Networks

2019 ◽  
Vol 63 (7) ◽  
pp. 1031-1038
Author(s):  
Zongjie Ma ◽  
Abdul Sattar ◽  
Jun Zhou ◽  
Qingliang Chen ◽  
Kaile Su
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Neural Networks ◽  
Network Architectures ◽  
Computationally Efficient ◽  
Diversification Strategy ◽  
Working Mechanism ◽  
Training Stage ◽  
Neural Network Architectures ◽  
Public Datasets

Abstract Dropout has been proven to be an effective technique for regularizing and preventing the co-adaptation of neurons in deep neural networks (DNN). It randomly drops units with a probability of p during the training stage of DNN to avoid overfitting. The working mechanism of dropout can be interpreted as approximately and exponentially combining many different neural network architectures efficiently, leading to a powerful ensemble. In this work, we propose a novel diversification strategy for dropout, which aims at generating more different neural network architectures in less numbers of iterations. The dropped units in the last forward propagation will be marked. Then the selected units for dropping in the current forward propagation will be retained if they have been marked in the last forward propagation, i.e., we only mark the units from the last forward propagation. We call this new regularization scheme Tabu dropout, whose significance lies in that it does not have extra parameters compared with the standard dropout strategy and is computationally efficient as well. Experiments conducted on four public datasets show that Tabu dropout improves the performance of the standard dropout, yielding better generalization capability.

scholarly journals SURVEY ON EVOLVING DEEP LEARNING NEURAL NETWORK ARCHITECTURES

2019 ◽  
Vol 2019 (2) ◽  
pp. 73-82 ◽  
Author(s):  
Dr. Abul Bashar
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Feature Extraction ◽  
Deep Learning ◽  
Human Performance ◽  
Deep Neural Networks ◽  
Network Architectures ◽  
Neural Network Architectures ◽  
Deep Learning Neural Network

The deep learning being a subcategory of the machine learning follows the human instincts of learning by example to produce accurate results. The deep learning performs training to the computer frame work to directly classify the tasks from the documents available either in the form of the text, image, or the sound. Most often the deep learning utilizes the neural network to perform the accurate classification and is referred as the deep neural networks; one of the most common deep neural networks used in a broader range of applications is the convolution neural network that provides an automated way of feature extraction by learning the features directly from the images or the text unlike the machine learning that extracts the features manually. This enables the deep learning neural networks to have a state of art accuracy that mostly expels even the human performance. So the paper is to present the survey on the deep learning neural network architectures utilized in various applications for having an accurate classification with an automated feature extraction.

Sign in / Sign up

Export Citation Format

Share Document