26,981 research outputs found

    JigsawNet: Shredded Image Reassembly using Convolutional Neural Network and Loop-based Composition

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    This paper proposes a novel algorithm to reassemble an arbitrarily shredded image to its original status. Existing reassembly pipelines commonly consist of a local matching stage and a global compositions stage. In the local stage, a key challenge in fragment reassembly is to reliably compute and identify correct pairwise matching, for which most existing algorithms use handcrafted features, and hence, cannot reliably handle complicated puzzles. We build a deep convolutional neural network to detect the compatibility of a pairwise stitching, and use it to prune computed pairwise matches. To improve the network efficiency and accuracy, we transfer the calculation of CNN to the stitching region and apply a boost training strategy. In the global composition stage, we modify the commonly adopted greedy edge selection strategies to two new loop closure based searching algorithms. Extensive experiments show that our algorithm significantly outperforms existing methods on solving various puzzles, especially those challenging ones with many fragment pieces

    Extreme Scale De Novo Metagenome Assembly

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    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
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