Task-based adaptive multiresolution for time-space multi-scale reaction-diffusion systems on multi-core architectures

A new solver featuring time-space adaptation and error control has been recently introduced to tackle the numerical solution of stiff reaction-diffusion systems. Based on operator splitting, finite volume adaptive multiresolution and high order time integrators with specific stability properties for each operator, this strategy yields high computational efficiency for large multidimensional computations on standard architectures such as powerful workstations. However, the data structure of the original implementation, based on trees of pointers, provides limited opportunities for efficiency enhancements, while posing serious challenges in terms of parallel programming and load balancing. The present contribution proposes a new implementation of the whole set of numerical methods including Radau5 and ROCK4, relying on a fully different data structure together with the use of a specific library, TBB, for shared-memory, task-based parallelism with work-stealing. The performance of our implementation is assessed in a series of test-cases of increasing difficulty in two and three dimensions on multi-core and many-core architectures, demonstrating high scalability

Extreme Scale De Novo Metagenome Assembly

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art tools require big shared memory machines and cannot handle contemporary metagenome datasets that exceed Terabytes in size. In this paper, we introduce the MetaHipMer pipeline, a high-quality and high-performance metagenome assembler that employs an iterative de Bruijn graph approach. MetaHipMer leverages a specialized scaffolding algorithm that produces long scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMer is end-to-end parallelized using the Unified Parallel C language and therefore can run seamlessly on shared and distributed-memory systems. Experimental results show that MetaHipMer matches or outperforms the state-of-the-art tools in terms of accuracy. Moreover, MetaHipMer scales efficiently to large concurrencies and is able to assemble previously intractable grand challenge metagenomes. We demonstrate the unprecedented capability of MetaHipMer by computing the first full assembly of the Twitchell Wetlands dataset, consisting of 7.5 billion reads - size 2.6 TBytes.Comment: Accepted to SC1

Stealing Links from Graph Neural Networks

Graph data, such as chemical networks and social networks, may be deemed confidential/private because the data owner often spends lots of resources collecting the data or the data contains sensitive information, e.g., social relationships. Recently, neural networks were extended to graph data, which are known as graph neural networks (GNNs). Due to their superior performance, GNNs have many applications, such as healthcare analytics, recommender systems, and fraud detection. In this work, we propose the first attacks to steal a graph from the outputs of a GNN model that is trained on the graph. Specifically, given a black-box access to a GNN model, our attacks can infer whether there exists a link between any pair of nodes in the graph used to train the model. We call our attacks link stealing attacks. We propose a threat model to systematically characterize an adversary's background knowledge along three dimensions which in total leads to a comprehensive taxonomy of 8 different link stealing attacks. We propose multiple novel methods to realize these 8 attacks. Extensive experiments on 8 real-world datasets show that our attacks are effective at stealing links, e.g., AUC (area under the ROC curve) is above 0.95 in multiple cases. Our results indicate that the outputs of a GNN model reveal rich information about the structure of the graph used to train the model.Comment: To appear in the 30th Usenix Security Symposium, August 2021, Vancouver, B.C., Canad

QuickCSG: Fast Arbitrary Boolean Combinations of N Solids

QuickCSG computes the result for general N-polyhedron boolean expressions without an intermediate tree of solids. We propose a vertex-centric view of the problem, which simplifies the identification of final geometric contributions, and facilitates its spatial decomposition. The problem is then cast in a single KD-tree exploration, geared toward the result by early pruning of any region of space not contributing to the final surface. We assume strong regularity properties on the input meshes and that they are in general position. This simplifying assumption, in combination with our vertex-centric approach, improves the speed of the approach. Complemented with a task-stealing parallelization, the algorithm achieves breakthrough performance, one to two orders of magnitude speedups with respect to state-of-the-art CPU algorithms, on boolean operations over two to dozens of polyhedra. The algorithm also outperforms GPU implementations with approximate discretizations, while producing an output without redundant facets. Despite the restrictive assumptions on the input, we show the usefulness of QuickCSG for applications with large CSG problems and strong temporal constraints, e.g. modeling for 3D printers, reconstruction from visual hulls and collision detection

The Heterogeneity of MNC' Subsidiaries and Technology Spillovers: Explaining positive and negative effects in emerging economies

Conventional models of multinational corporation (MNC) related spillovers in host economies assume that they derive from the technological assets created at the headquarters. Subsidiaries' activities in the host economy are not given any role in this process. In this paper, drawing on recent advances in MNC literature, we propose an alternative model. In this alternative model the local innovative activity of subsidiaries plays a critical role in accounting for both the possibility of positive or negative effects. More specifically, we distinguish between three types of subsidiaries: "competence creating", "competence exploiting" and passive; and explore conceptually and empirically the spillover effects of each type. Our results confirm our predictions that, in less advanced contexts such as India, only creative subsidiaries have a positive effect on host country firms; that competence exploiting subsidiaries generate negative effects when domestic firms are more advanced; and passive subsidiaries have no effects. The implications for theory and policy are discussed.Technological spillovers, MNCs, emerging economies, subsidiaries heterogeneity