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Proceedings ArticleDOI
07 Dec 2015
TL;DR: A novel deep learning framework for attribute prediction in the wild that cascades two CNNs, LNet and ANet, which are fine-tuned jointly with attribute tags, but pre-trained differently.
Abstract: Predicting face attributes in the wild is challenging due to complex face variations. We propose a novel deep learning framework for attribute prediction in the wild. It cascades two CNNs, LNet and ANet, which are fine-tuned jointly with attribute tags, but pre-trained differently. LNet is pre-trained by massive general object categories for face localization, while ANet is pre-trained by massive face identities for attribute prediction. This framework not only outperforms the state-of-the-art with a large margin, but also reveals valuable facts on learning face representation. (1) It shows how the performances of face localization (LNet) and attribute prediction (ANet) can be improved by different pre-training strategies. (2) It reveals that although the filters of LNet are fine-tuned only with image-level attribute tags, their response maps over entire images have strong indication of face locations. This fact enables training LNet for face localization with only image-level annotations, but without face bounding boxes or landmarks, which are required by all attribute recognition works. (3) It also demonstrates that the high-level hidden neurons of ANet automatically discover semantic concepts after pre-training with massive face identities, and such concepts are significantly enriched after fine-tuning with attribute tags. Each attribute can be well explained with a sparse linear combination of these concepts.

6,273 citations


Journal ArticleDOI
Heng Li1
TL;DR: Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database and is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mapper at higher accuracy, surpassing most aligners specialized in one type of alignment.
Abstract: Motivation Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Results Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. Availability and implementation https://github.com/lh3/minimap2. Supplementary information Supplementary data are available at Bioinformatics online.

6,264 citations


Journal ArticleDOI
TL;DR: An emphasis is placed on low muscle strength as a key characteristic of sarcopenia, uses detection of low muscle quantity and quality to confirm the sarc Openia diagnosis, and provides clear cut-off points for measurements of variables that identify and characterise sarc openia.
Abstract: Background in 2010, the European Working Group on Sarcopenia in Older People (EWGSOP) published a sarcopenia definition that aimed to foster advances in identifying and caring for people with sarcopenia. In early 2018, the Working Group met again (EWGSOP2) to update the original definition in order to reflect scientific and clinical evidence that has built over the last decade. This paper presents our updated findings. Objectives to increase consistency of research design, clinical diagnoses and ultimately, care for people with sarcopenia. Recommendations sarcopenia is a muscle disease (muscle failure) rooted in adverse muscle changes that accrue across a lifetime; sarcopenia is common among adults of older age but can also occur earlier in life. In this updated consensus paper on sarcopenia, EWGSOP2: (1) focuses on low muscle strength as a key characteristic of sarcopenia, uses detection of low muscle quantity and quality to confirm the sarcopenia diagnosis, and identifies poor physical performance as indicative of severe sarcopenia; (2) updates the clinical algorithm that can be used for sarcopenia case-finding, diagnosis and confirmation, and severity determination and (3) provides clear cut-off points for measurements of variables that identify and characterise sarcopenia. Conclusions EWGSOP2's updated recommendations aim to increase awareness of sarcopenia and its risk. With these new recommendations, EWGSOP2 calls for healthcare professionals who treat patients at risk for sarcopenia to take actions that will promote early detection and treatment. We also encourage more research in the field of sarcopenia in order to prevent or delay adverse health outcomes that incur a heavy burden for patients and healthcare systems.

6,250 citations


Journal ArticleDOI
TL;DR: SciPy as discussed by the authors is an open-source scientific computing library for the Python programming language, which has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year.
Abstract: SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

6,244 citations


Journal ArticleDOI
TL;DR: A validated diagnostic workflow for 2019-nCoV is presented, its design relying on close genetic relatedness of 2019- nCoV with SARS coronavirus, making use of synthetic nucleic acid technology.
Abstract: Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. Aim We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. Methods Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. Results The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project. Conclusion The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

6,229 citations


Posted Content
Mingxing Tan1, Quoc V. Le1
TL;DR: A new scaling method is proposed that uniformly scales all dimensions of depth/width/resolution using a simple yet highly effective compound coefficient and is demonstrated the effectiveness of this method on scaling up MobileNets and ResNet.
Abstract: Convolutional Neural Networks (ConvNets) are commonly developed at a fixed resource budget, and then scaled up for better accuracy if more resources are available. In this paper, we systematically study model scaling and identify that carefully balancing network depth, width, and resolution can lead to better performance. Based on this observation, we propose a new scaling method that uniformly scales all dimensions of depth/width/resolution using a simple yet highly effective compound coefficient. We demonstrate the effectiveness of this method on scaling up MobileNets and ResNet. To go even further, we use neural architecture search to design a new baseline network and scale it up to obtain a family of models, called EfficientNets, which achieve much better accuracy and efficiency than previous ConvNets. In particular, our EfficientNet-B7 achieves state-of-the-art 84.3% top-1 accuracy on ImageNet, while being 8.4x smaller and 6.1x faster on inference than the best existing ConvNet. Our EfficientNets also transfer well and achieve state-of-the-art accuracy on CIFAR-100 (91.7%), Flowers (98.8%), and 3 other transfer learning datasets, with an order of magnitude fewer parameters. Source code is at this https URL.

6,222 citations


Journal ArticleDOI
TL;DR: A comprehensive overview of the considerations and metrics required for partial least squares structural equation modeling (PLS-SEM) analysis and result reporting can be found in this paper, where the authors provide an overview of previously and recently proposed metrics as well as rules of thumb for evaluating the research results based on the application of PLSSEM.
Abstract: The purpose of this paper is to provide a comprehensive, yet concise, overview of the considerations and metrics required for partial least squares structural equation modeling (PLS-SEM) analysis and result reporting. Preliminary considerations are summarized first, including reasons for choosing PLS-SEM, recommended sample size in selected contexts, distributional assumptions, use of secondary data, statistical power and the need for goodness-of-fit testing. Next, the metrics as well as the rules of thumb that should be applied to assess the PLS-SEM results are covered. Besides presenting established PLS-SEM evaluation criteria, the overview includes the following new guidelines: PLSpredict (i.e., a novel approach for assessing a model’s out-of-sample prediction), metrics for model comparisons, and several complementary methods for checking the results’ robustness.,This paper provides an overview of previously and recently proposed metrics as well as rules of thumb for evaluating the research results based on the application of PLS-SEM.,Most of the previously applied metrics for evaluating PLS-SEM results are still relevant. Nevertheless, scholars need to be knowledgeable about recently proposed metrics (e.g. model comparison criteria) and methods (e.g. endogeneity assessment, latent class analysis and PLSpredict), and when and how to apply them to extend their analyses.,Methodological developments associated with PLS-SEM are rapidly emerging. The metrics reported in this paper are useful for current applications, but must always be up to date with the latest developments in the PLS-SEM method.,In light of more recent research and methodological developments in the PLS-SEM domain, guidelines for the method’s use need to be continuously extended and updated. This paper is the most current and comprehensive summary of the PLS-SEM method and the metrics applied to assess its solutions.

6,220 citations


Journal ArticleDOI
03 Apr 2015-Science
TL;DR: Treatment efficacy was associated with a higher number of mutations in the tumors, and a tumor-specific T cell response paralleled tumor regression in one patient, suggesting that the genomic landscape of lung cancers shapes response to anti–PD-1 therapy.
Abstract: Immune checkpoint inhibitors, which unleash a patient’s own T cells to kill tumors, are revolutionizing cancer treatment. To unravel the genomic determinants of response to this therapy, we used whole-exome sequencing of non–small cell lung cancers treated with pembrolizumab, an antibody targeting programmed cell death-1 (PD-1). In two independent cohorts, higher nonsynonymous mutation burden in tumors was associated with improved objective response, durable clinical benefit, and progression-free survival. Efficacy also correlated with the molecular smoking signature, higher neoantigen burden, and DNA repair pathway mutations; each factor was also associated with mutation burden. In one responder, neoantigen-specific CD8+ T cell responses paralleled tumor regression, suggesting that anti–PD-1 therapy enhances neoantigen-specific T cell reactivity. Our results suggest that the genomic landscape of lung cancers shapes response to anti–PD-1 therapy.

6,215 citations


Journal ArticleDOI
TL;DR: The compelling combination of enhanced optical properties and chemical robustness makes CsPbX3 nanocrystals appealing for optoelectronic applications, particularly for blue and green spectral regions (410–530 nm), where typical metal chalcogenide-based quantum dots suffer from photodegradation.
Abstract: Metal halides perovskites, such as hybrid organic–inorganic CH3NH3PbI3, are newcomer optoelectronic materials that have attracted enormous attention as solution-deposited absorbing layers in solar cells with power conversion efficiencies reaching 20%. Herein we demonstrate a new avenue for halide perovskites by designing highly luminescent perovskite-based colloidal quantum dot materials. We have synthesized monodisperse colloidal nanocubes (4–15 nm edge lengths) of fully inorganic cesium lead halide perovskites (CsPbX3, X = Cl, Br, and I or mixed halide systems Cl/Br and Br/I) using inexpensive commercial precursors. Through compositional modulations and quantum size-effects, the bandgap energies and emission spectra are readily tunable over the entire visible spectral region of 410–700 nm. The photoluminescence of CsPbX3 nanocrystals is characterized by narrow emission line-widths of 12–42 nm, wide color gamut covering up to 140% of the NTSC color standard, high quantum yields of up to 90%, and radiativ...

6,170 citations


Proceedings Article
07 Dec 2015
TL;DR: This work introduces a new learnable module, the Spatial Transformer, which explicitly allows the spatial manipulation of data within the network, and can be inserted into existing convolutional architectures, giving neural networks the ability to actively spatially transform feature maps.
Abstract: Convolutional Neural Networks define an exceptionally powerful class of models, but are still limited by the lack of ability to be spatially invariant to the input data in a computationally and parameter efficient manner. In this work we introduce a new learnable module, the Spatial Transformer, which explicitly allows the spatial manipulation of data within the network. This differentiable module can be inserted into existing convolutional architectures, giving neural networks the ability to actively spatially transform feature maps, conditional on the feature map itself, without any extra training supervision or modification to the optimisation process. We show that the use of spatial transformers results in models which learn invariance to translation, scale, rotation and more generic warping, resulting in state-of-the-art performance on several benchmarks, and for a number of classes of transformations.

6,150 citations


Journal ArticleDOI
TL;DR: The UK Biobank is described, a large population-based prospective study, established to allow investigation of the genetic and non-genetic determinants of the diseases of middle and old age.
Abstract: Cathie Sudlow and colleagues describe the UK Biobank, a large population-based prospective study, established to allow investigation of the genetic and non-genetic determinants of the diseases of middle and old age.

Journal ArticleDOI
TL;DR: A combination of automated approaches and expert curation is used to develop a collection of "hallmark" gene sets, derived from multiple "founder" sets, that conveys a specific biological state or process and displays coherent expression in MSigDB.
Abstract: The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of “hallmark” gene sets as part of MSigDB. Each hallmark in this collection consists of a “refined” gene set, derived from multiple “founder” sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis.

Journal ArticleDOI
TL;DR: A review of the Pascal Visual Object Classes challenge from 2008-2012 and an appraisal of the aspects of the challenge that worked well, and those that could be improved in future challenges.
Abstract: The Pascal Visual Object Classes (VOC) challenge consists of two components: (i) a publicly available dataset of images together with ground truth annotation and standardised evaluation software; and (ii) an annual competition and workshop. There are five challenges: classification, detection, segmentation, action classification, and person layout. In this paper we provide a review of the challenge from 2008---2012. The paper is intended for two audiences: algorithm designers, researchers who want to see what the state of the art is, as measured by performance on the VOC datasets, along with the limitations and weak points of the current generation of algorithms; and, challenge designers, who want to see what we as organisers have learnt from the process and our recommendations for the organisation of future challenges. To analyse the performance of submitted algorithms on the VOC datasets we introduce a number of novel evaluation methods: a bootstrapping method for determining whether differences in the performance of two algorithms are significant or not; a normalised average precision so that performance can be compared across classes with different proportions of positive instances; a clustering method for visualising the performance across multiple algorithms so that the hard and easy images can be identified; and the use of a joint classifier over the submitted algorithms in order to measure their complementarity and combined performance. We also analyse the community's progress through time using the methods of Hoiem et al. (Proceedings of European Conference on Computer Vision, 2012) to identify the types of occurring errors. We conclude the paper with an appraisal of the aspects of the challenge that worked well, and those that could be improved in future challenges.

Journal ArticleDOI
Clotilde Théry1, Kenneth W. Witwer2, Elena Aikawa3, María José Alcaraz4  +414 moreInstitutions (209)
TL;DR: The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities, and a checklist is provided with summaries of key points.
Abstract: The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

Proceedings ArticleDOI
27 Jun 2016
TL;DR: This work revisits the global average pooling layer proposed in [13], and sheds light on how it explicitly enables the convolutional neural network (CNN) to have remarkable localization ability despite being trained on imagelevel labels.
Abstract: In this work, we revisit the global average pooling layer proposed in [13], and shed light on how it explicitly enables the convolutional neural network (CNN) to have remarkable localization ability despite being trained on imagelevel labels. While this technique was previously proposed as a means for regularizing training, we find that it actually builds a generic localizable deep representation that exposes the implicit attention of CNNs on an image. Despite the apparent simplicity of global average pooling, we are able to achieve 37.1% top-5 error for object localization on ILSVRC 2014 without training on any bounding box annotation. We demonstrate in a variety of experiments that our network is able to localize the discriminative image regions despite just being trained for solving classification task1.

Posted Content
H. Brendan McMahan1, Eider Moore1, Daniel Ramage1, Seth Hampson, Blaise Aguera y Arcas1 
TL;DR: This work presents a practical method for the federated learning of deep networks based on iterative model averaging, and conducts an extensive empirical evaluation, considering five different model architectures and four datasets.
Abstract: Modern mobile devices have access to a wealth of data suitable for learning models, which in turn can greatly improve the user experience on the device. For example, language models can improve speech recognition and text entry, and image models can automatically select good photos. However, this rich data is often privacy sensitive, large in quantity, or both, which may preclude logging to the data center and training there using conventional approaches. We advocate an alternative that leaves the training data distributed on the mobile devices, and learns a shared model by aggregating locally-computed updates. We term this decentralized approach Federated Learning. We present a practical method for the federated learning of deep networks based on iterative model averaging, and conduct an extensive empirical evaluation, considering five different model architectures and four datasets. These experiments demonstrate the approach is robust to the unbalanced and non-IID data distributions that are a defining characteristic of this setting. Communication costs are the principal constraint, and we show a reduction in required communication rounds by 10-100x as compared to synchronized stochastic gradient descent.

Journal ArticleDOI
TL;DR: This work equips the networks with another pooling strategy, "spatial pyramid pooling", to eliminate the above requirement, and develops a new network structure, called SPP-net, which can generate a fixed-length representation regardless of image size/scale.
Abstract: Existing deep convolutional neural networks (CNNs) require a fixed-size (e.g., 224 $\times$ 224) input image. This requirement is “artificial” and may reduce the recognition accuracy for the images or sub-images of an arbitrary size/scale. In this work, we equip the networks with another pooling strategy, “spatial pyramid pooling”, to eliminate the above requirement. The new network structure, called SPP-net, can generate a fixed-length representation regardless of image size/scale. Pyramid pooling is also robust to object deformations. With these advantages, SPP-net should in general improve all CNN-based image classification methods. On the ImageNet 2012 dataset, we demonstrate that SPP-net boosts the accuracy of a variety of CNN architectures despite their different designs. On the Pascal VOC 2007 and Caltech101 datasets, SPP-net achieves state-of-the-art classification results using a single full-image representation and no fine-tuning. The power of SPP-net is also significant in object detection. Using SPP-net, we compute the feature maps from the entire image only once, and then pool features in arbitrary regions (sub-images) to generate fixed-length representations for training the detectors. This method avoids repeatedly computing the convolutional features. In processing test images, our method is 24-102 $\times$ faster than the R-CNN method, while achieving better or comparable accuracy on Pascal VOC 2007. In ImageNet Large Scale Visual Recognition Challenge (ILSVRC) 2014, our methods rank #2 in object detection and #3 in image classification among all 38 teams. This manuscript also introduces the improvement made for this competition.

Posted Content
TL;DR: This work proposes a small DNN architecture called SqueezeNet, which achieves AlexNet-level accuracy on ImageNet with 50x fewer parameters and is able to compress to less than 0.5MB (510x smaller than AlexNet).
Abstract: Recent research on deep neural networks has focused primarily on improving accuracy. For a given accuracy level, it is typically possible to identify multiple DNN architectures that achieve that accuracy level. With equivalent accuracy, smaller DNN architectures offer at least three advantages: (1) Smaller DNNs require less communication across servers during distributed training. (2) Smaller DNNs require less bandwidth to export a new model from the cloud to an autonomous car. (3) Smaller DNNs are more feasible to deploy on FPGAs and other hardware with limited memory. To provide all of these advantages, we propose a small DNN architecture called SqueezeNet. SqueezeNet achieves AlexNet-level accuracy on ImageNet with 50x fewer parameters. Additionally, with model compression techniques we are able to compress SqueezeNet to less than 0.5MB (510x smaller than AlexNet). The SqueezeNet architecture is available for download here: this https URL

Posted Content
TL;DR: This paper proposed an attention-based model that automatically learns to describe the content of images by focusing on salient objects while generating corresponding words in the output sequence, which achieved state-of-the-art performance on three benchmark datasets: Flickr8k, Flickr30k and MS COCO.
Abstract: Inspired by recent work in machine translation and object detection, we introduce an attention based model that automatically learns to describe the content of images. We describe how we can train this model in a deterministic manner using standard backpropagation techniques and stochastically by maximizing a variational lower bound. We also show through visualization how the model is able to automatically learn to fix its gaze on salient objects while generating the corresponding words in the output sequence. We validate the use of attention with state-of-the-art performance on three benchmark datasets: Flickr8k, Flickr30k and MS COCO.

Journal ArticleDOI
18 Oct 2016-PeerJ
TL;DR: VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with US EARCH for paired-ends read merging and dereplication.
Abstract: Background: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. Methods: When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. Results: VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. Discussion: VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.

Journal ArticleDOI
Theo Vos1, Theo Vos2, Theo Vos3, Stephen S Lim  +2416 moreInstitutions (246)
TL;DR: Global health has steadily improved over the past 30 years as measured by age-standardised DALY rates, and there has been a marked shift towards a greater proportion of burden due to YLDs from non-communicable diseases and injuries.

Journal ArticleDOI
Mohsen Naghavi1, Haidong Wang1, Rafael Lozano1, Adrian Davis2  +728 moreInstitutions (294)
TL;DR: In the Global Burden of Disease Study 2013 (GBD 2013) as discussed by the authors, the authors used the GBD 2010 methods with some refinements to improve accuracy applied to an updated database of vital registration, survey, and census data.

Posted Content
TL;DR: This work studies the adversarial robustness of neural networks through the lens of robust optimization, and suggests the notion of security against a first-order adversary as a natural and broad security guarantee.
Abstract: Recent work has demonstrated that deep neural networks are vulnerable to adversarial examples---inputs that are almost indistinguishable from natural data and yet classified incorrectly by the network. In fact, some of the latest findings suggest that the existence of adversarial attacks may be an inherent weakness of deep learning models. To address this problem, we study the adversarial robustness of neural networks through the lens of robust optimization. This approach provides us with a broad and unifying view on much of the prior work on this topic. Its principled nature also enables us to identify methods for both training and attacking neural networks that are reliable and, in a certain sense, universal. In particular, they specify a concrete security guarantee that would protect against any adversary. These methods let us train networks with significantly improved resistance to a wide range of adversarial attacks. They also suggest the notion of security against a first-order adversary as a natural and broad security guarantee. We believe that robustness against such well-defined classes of adversaries is an important stepping stone towards fully resistant deep learning models. Code and pre-trained models are available at this https URL and this https URL.

Journal ArticleDOI
TL;DR: An objective measure of genome quality is proposed that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities and is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches.
Abstract: Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.

Journal ArticleDOI
TL;DR: This survey will present existing methods for Data Augmentation, promising developments, and meta-level decisions for implementing DataAugmentation, a data-space solution to the problem of limited data.
Abstract: Deep convolutional neural networks have performed remarkably well on many Computer Vision tasks. However, these networks are heavily reliant on big data to avoid overfitting. Overfitting refers to the phenomenon when a network learns a function with very high variance such as to perfectly model the training data. Unfortunately, many application domains do not have access to big data, such as medical image analysis. This survey focuses on Data Augmentation, a data-space solution to the problem of limited data. Data Augmentation encompasses a suite of techniques that enhance the size and quality of training datasets such that better Deep Learning models can be built using them. The image augmentation algorithms discussed in this survey include geometric transformations, color space augmentations, kernel filters, mixing images, random erasing, feature space augmentation, adversarial training, generative adversarial networks, neural style transfer, and meta-learning. The application of augmentation methods based on GANs are heavily covered in this survey. In addition to augmentation techniques, this paper will briefly discuss other characteristics of Data Augmentation such as test-time augmentation, resolution impact, final dataset size, and curriculum learning. This survey will present existing methods for Data Augmentation, promising developments, and meta-level decisions for implementing Data Augmentation. Readers will understand how Data Augmentation can improve the performance of their models and expand limited datasets to take advantage of the capabilities of big data.

Posted Content
TL;DR: The proposed Convolutional Block Attention Module (CBAM), a simple yet effective attention module for feed-forward convolutional neural networks, can be integrated into any CNN architectures seamlessly with negligible overheads and is end-to-end trainable along with base CNNs.
Abstract: We propose Convolutional Block Attention Module (CBAM), a simple yet effective attention module for feed-forward convolutional neural networks. Given an intermediate feature map, our module sequentially infers attention maps along two separate dimensions, channel and spatial, then the attention maps are multiplied to the input feature map for adaptive feature refinement. Because CBAM is a lightweight and general module, it can be integrated into any CNN architectures seamlessly with negligible overheads and is end-to-end trainable along with base CNNs. We validate our CBAM through extensive experiments on ImageNet-1K, MS~COCO detection, and VOC~2007 detection datasets. Our experiments show consistent improvements in classification and detection performances with various models, demonstrating the wide applicability of CBAM. The code and models will be publicly available.

Journal ArticleDOI
Minoru Kanehisa1, Miho Furumichi1, Mao Tanabe1, Yoko Sato2, Kanae Morishima1 
TL;DR: The content has been expanded and the quality improved irrespective of whether or not the KOs appear in the three molecular network databases, and the newly introduced addendum category of the GENES database is a collection of individual proteins whose functions are experimentally characterized and from which an increasing number of KOs are defined.
Abstract: KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an encyclopedia of genes and genomes. Assigning functional meanings to genes and genomes both at the molecular and higher levels is the primary objective of the KEGG database project. Molecular-level functions are stored in the KO (KEGG Orthology) database, where each KO is defined as a functional ortholog of genes and proteins. Higher-level functions are represented by networks of molecular interactions, reactions and relations in the forms of KEGG pathway maps, BRITE hierarchies and KEGG modules. In the past the KO database was developed for the purpose of defining nodes of molecular networks, but now the content has been expanded and the quality improved irrespective of whether or not the KOs appear in the three molecular network databases. The newly introduced addendum category of the GENES database is a collection of individual proteins whose functions are experimentally characterized and from which an increasing number of KOs are defined. Furthermore, the DISEASE and DRUG databases have been improved by systematic analysis of drug labels for better integration of diseases and drugs with the KEGG molecular networks. KEGG is moving towards becoming a comprehensive knowledge base for both functional interpretation and practical application of genomic information.

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TL;DR: GNMT, Google's Neural Machine Translation system, is presented, which attempts to address many of the weaknesses of conventional phrase-based translation systems and provides a good balance between the flexibility of "character"-delimited models and the efficiency of "word"-delicited models.
Abstract: Neural Machine Translation (NMT) is an end-to-end learning approach for automated translation, with the potential to overcome many of the weaknesses of conventional phrase-based translation systems. Unfortunately, NMT systems are known to be computationally expensive both in training and in translation inference. Also, most NMT systems have difficulty with rare words. These issues have hindered NMT's use in practical deployments and services, where both accuracy and speed are essential. In this work, we present GNMT, Google's Neural Machine Translation system, which attempts to address many of these issues. Our model consists of a deep LSTM network with 8 encoder and 8 decoder layers using attention and residual connections. To improve parallelism and therefore decrease training time, our attention mechanism connects the bottom layer of the decoder to the top layer of the encoder. To accelerate the final translation speed, we employ low-precision arithmetic during inference computations. To improve handling of rare words, we divide words into a limited set of common sub-word units ("wordpieces") for both input and output. This method provides a good balance between the flexibility of "character"-delimited models and the efficiency of "word"-delimited models, naturally handles translation of rare words, and ultimately improves the overall accuracy of the system. Our beam search technique employs a length-normalization procedure and uses a coverage penalty, which encourages generation of an output sentence that is most likely to cover all the words in the source sentence. On the WMT'14 English-to-French and English-to-German benchmarks, GNMT achieves competitive results to state-of-the-art. Using a human side-by-side evaluation on a set of isolated simple sentences, it reduces translation errors by an average of 60% compared to Google's phrase-based production system.

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TL;DR: In this article, the authors present a variety of new architectural features and training procedures that apply to the generative adversarial networks (GANs) framework and achieve state-of-the-art results in semi-supervised classification on MNIST, CIFAR-10 and SVHN.
Abstract: We present a variety of new architectural features and training procedures that we apply to the generative adversarial networks (GANs) framework. We focus on two applications of GANs: semi-supervised learning, and the generation of images that humans find visually realistic. Unlike most work on generative models, our primary goal is not to train a model that assigns high likelihood to test data, nor do we require the model to be able to learn well without using any labels. Using our new techniques, we achieve state-of-the-art results in semi-supervised classification on MNIST, CIFAR-10 and SVHN. The generated images are of high quality as confirmed by a visual Turing test: our model generates MNIST samples that humans cannot distinguish from real data, and CIFAR-10 samples that yield a human error rate of 21.3%. We also present ImageNet samples with unprecedented resolution and show that our methods enable the model to learn recognizable features of ImageNet classes.

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TL;DR: This work uses new features: WRC, CSP, CmBN, SAT, Mish activation, Mosaic data augmentation, C mBN, DropBlock regularization, and CIoU loss, and combine some of them to achieve state-of-the-art results: 43.5% AP for the MS COCO dataset at a realtime speed of ~65 FPS on Tesla V100.
Abstract: There are a huge number of features which are said to improve Convolutional Neural Network (CNN) accuracy. Practical testing of combinations of such features on large datasets, and theoretical justification of the result, is required. Some features operate on certain models exclusively and for certain problems exclusively, or only for small-scale datasets; while some features, such as batch-normalization and residual-connections, are applicable to the majority of models, tasks, and datasets. We assume that such universal features include Weighted-Residual-Connections (WRC), Cross-Stage-Partial-connections (CSP), Cross mini-Batch Normalization (CmBN), Self-adversarial-training (SAT) and Mish-activation. We use new features: WRC, CSP, CmBN, SAT, Mish activation, Mosaic data augmentation, CmBN, DropBlock regularization, and CIoU loss, and combine some of them to achieve state-of-the-art results: 43.5% AP (65.7% AP50) for the MS COCO dataset at a realtime speed of ~65 FPS on Tesla V100. Source code is at this https URL