scholarly journals Scalable Graph Neural Network Training

2021 ◽  
Vol 55 (1) ◽  
pp. 68-76
Author(s):  
Marco Serafini

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.

2021 ◽  
Vol 507 (3) ◽  
pp. 4061-4073
Author(s):  
Thorben Finke ◽  
Michael Krämer ◽  
Silvia Manconi

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.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anand Ramachandran ◽  
Steven S. Lumetta ◽  
Eric W. Klee ◽  
Deming Chen

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


2014 ◽  
Vol 10 (S306) ◽  
pp. 279-287 ◽  
Author(s):  
Michael Hobson ◽  
Philip Graff ◽  
Farhan Feroz ◽  
Anthony Lasenby

AbstractMachine-learning methods may be used to perform many tasks required in the analysis of astronomical data, including: data description and interpretation, pattern recognition, prediction, classification, compression, inference and many more. An intuitive and well-established approach to machine learning is the use of artificial neural networks (NNs), which consist of a group of interconnected nodes, each of which processes information that it receives and then passes this product on to other nodes via weighted connections. In particular, I discuss the first public release of the generic neural network training algorithm, calledSkyNet, and demonstrate its application to astronomical problems focusing on its use in the BAMBI package for accelerated Bayesian inference in cosmology, and the identification of gamma-ray bursters. TheSkyNetand BAMBI packages, which are fully parallelised using MPI, are available athttp://www.mrao.cam.ac.uk/software/.


2017 ◽  
Vol 109 (1) ◽  
pp. 29-38 ◽  
Author(s):  
Valentin Deyringer ◽  
Alexander Fraser ◽  
Helmut Schmid ◽  
Tsuyoshi Okita

Abstract Neural Networks are prevalent in todays NLP research. Despite their success for different tasks, training time is relatively long. We use Hogwild! to counteract this phenomenon and show that it is a suitable method to speed up training Neural Networks of different architectures and complexity. For POS tagging and translation we report considerable speedups of training, especially for the latter. We show that Hogwild! can be an important tool for training complex NLP architectures.


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