Second-generation PLINK: rising to the challenge of larger and richer datasets

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information. The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.Comment: 2 figures, 1 additional fil

Will SDN be part of 5G?

For many, this is no longer a valid question and the case is considered settled with SDN/NFV (Software Defined Networking/Network Function Virtualization) providing the inevitable innovation enablers solving many outstanding management issues regarding 5G. However, given the monumental task of softwarization of radio access network (RAN) while 5G is just around the corner and some companies have started unveiling their 5G equipment already, the concern is very realistic that we may only see some point solutions involving SDN technology instead of a fully SDN-enabled RAN. This survey paper identifies all important obstacles in the way and looks at the state of the art of the relevant solutions. This survey is different from the previous surveys on SDN-based RAN as it focuses on the salient problems and discusses solutions proposed within and outside SDN literature. Our main focus is on fronthaul, backward compatibility, supposedly disruptive nature of SDN deployment, business cases and monetization of SDN related upgrades, latency of general purpose processors (GPP), and additional security vulnerabilities, softwarization brings along to the RAN. We have also provided a summary of the architectural developments in SDN-based RAN landscape as not all work can be covered under the focused issues. This paper provides a comprehensive survey on the state of the art of SDN-based RAN and clearly points out the gaps in the technology.Comment: 33 pages, 10 figure

Robo-line storage: Low latency, high capacity storage systems over geographically distributed networks

Rapid advances in high performance computing are making possible more complete and accurate computer-based modeling of complex physical phenomena, such as weather front interactions, dynamics of chemical reactions, numerical aerodynamic analysis of airframes, and ocean-land-atmosphere interactions. Many of these 'grand challenge' applications are as demanding of the underlying storage system, in terms of their capacity and bandwidth requirements, as they are on the computational power of the processor. A global view of the Earth's ocean chlorophyll and land vegetation requires over 2 terabytes of raw satellite image data. In this paper, we describe our planned research program in high capacity, high bandwidth storage systems. The project has four overall goals. First, we will examine new methods for high capacity storage systems, made possible by low cost, small form factor magnetic and optical tape systems. Second, access to the storage system will be low latency and high bandwidth. To achieve this, we must interleave data transfer at all levels of the storage system, including devices, controllers, servers, and communications links. Latency will be reduced by extensive caching throughout the storage hierarchy. Third, we will provide effective management of a storage hierarchy, extending the techniques already developed for the Log Structured File System. Finally, we will construct a protototype high capacity file server, suitable for use on the National Research and Education Network (NREN). Such research must be a Cornerstone of any coherent program in high performance computing and communications

Water vapor sorption dynamics in different compressions of eelgrass insulation

Eelgrass shows potential in meeting the rising demands towards new, sustainable materials. It hosts a range of characteristics that benefits its application as a building material, such as thermal and acoustic insulating properties that can compete with conventional mineral wool insulation. However, as a porous bio-based building material, the moisture performance of eelgrass must be assessed to ensure its practical application. In this study, experimental investigations are conducted by a new automated vapor sorption analyzer (VSA) to measure adsorption and desorption of water vapor on different compressions of eelgrass insulation, ranging from loose strands to densely compacted insulation batts. Overall, higher sorption dynamics are observed in eelgrass insulation compared to conventional mineral wool insulation. Loose strands of eelgrass depict higher dynamics (including hysteresis) for the full range of relative humidity in comparison to insulation batts, potentially due to additional binder. Increasing the compression of eelgrass insulation batts results in lower sorption dynamics in the >70% relative humidity range. A Guggenheim-Anderson-deBoer model is applied that shows good fit with the experimental data and may be applied in moisture transfer calculations. This study furthers the potential of compressing eelgrass for application in passive design strategies through its moisture buffering capabilities

Accurate Neural Network Pruning Requires Rethinking Sparse Optimization

Obtaining versions of deep neural networks that are both highly-accurate and highly-sparse is one of the main challenges in the area of model compression, and several high-performance pruning techniques have been investigated by the community. Yet, much less is known about the interaction between sparsity and the standard stochastic optimization techniques used for training sparse networks, and most existing work uses standard dense schedules and hyperparameters for training sparse networks. In this work, we examine the impact of high sparsity on model training using the standard computer vision and natural language processing sparsity benchmarks. We begin by showing that using standard dense training recipes for sparse training is suboptimal, and results in under-training. We provide new approaches for mitigating this issue for both sparse pre-training of vision models (e.g. ResNet50/ImageNet) and sparse fine-tuning of language models (e.g. BERT/GLUE), achieving state-of-the-art results in both settings in the high-sparsity regime, and providing detailed analyses for the difficulty of sparse training in both scenarios. Our work sets a new threshold in terms of the accuracies that can be achieved under high sparsity, and should inspire further research into improving sparse model training, to reach higher accuracies under high sparsity, but also to do so efficiently

National Educators' Workshop: Update 1991. Standard Experiments in Engineering Materials Science and Technology

Given here is a collection of experiments presented and demonstrated at the National Educators' Workshop: Update 91, held at the Oak Ridge National Laboratory on November 12-14, 1991. The experiments related to the nature and properties of engineering materials and provided information to assist in teaching about materials in the education community