SUMMARY: The PacBio High-Fidelity (HiFi) sequencing technology produces long reads of >99% in accuracy. It has enabled the development of a new generation of de novo sequence assemblers, which all have sequencing error correction (EC) as the first step. As HiFi is a new data type, this critical step has not been evaluated before. Here, we introduced hifieval, a new command-line tool for measuring over- and under-corrections produced by EC algorithms. We assessed the accuracy of the EC components of existing HiFi assemblers on the CHM13 and the HG002 datasets and further investigated the performance of EC methods in challenging regions such as homopolymer regions, centromeric regions, and segmental duplications. Hifieval will help HiFi assemblers to improve EC and assembly quality in the long run. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/magspho/hifieval.

With the rapid growth of data, near-duplicate documents bearing high similarity are abundant. Elimination of near-duplicates can reduce storage cost and improve the quality of search indexes in data mining. A challenging problem is to find near-duplicate records in large-scale collections efficiently. There have already been several efforts on implementing near-duplicate detection on different architectures. In this paper, a new implementation, using a special hash function namely simhash, is proposed to identify near-duplicate documents on CUDA enabled devices. Two mechanisms are designed to achieve higher performance, including swapping and dynamic allocating. Experimental results show that our parallel implementation outperforms the serial CPU version, achieving up to 18 times.

SUMMARY The challenge forSparse Matrix–Vector multiplication(SpMV) performance is memory bandwidth, which mostly depends on input matrices and underlying computing platforms. To solve this challenge, many researchers have explored a variety of optimization techniques. One of the most promising aspects focuses on designing storage formats to represent sparse matrices. However, lots of prior storage formats cannot fully take advantage of the underlying computing platforms, resulting in unsatisfactory performance and large memory footprint. Therefore, a novel storage format, calledSegmented Hybrid ELL + Compressed Sparse Row (CSR)(SHEC for short), is proposed to further improve the throughput and lessen memory footprint onGraphics Processing Unit(GPU). SHEC format employs an interleaved combination pattern, which combines certain amount of compressed rows to form a new SHEC row. Segmentation is brought in to balance load and reduce memory footprint. According to the empirical data, an automatic SHEC‐based SpMV is developed to fit for all the matrices. Experimental results show that SHEC approach outperforms the best results of NVIDIA SpMV library and exhibits a comparable performance with state‐of‐the‐art storage formats on the standard dataset. Copyright © 2012 John Wiley & Sons, Ltd.

Inspired by the success of bag‐of‐words in text retrieval, bag‐of‐visual‐words and its variants are widely used in content‐based image retrieval to describe visual content. Various weighting schemes have also been proposed to integrate different yet complementary visual‐words. However, most of these weighting schemes tend to use fixed weight for every visual‐word extracted from the query image, which may lose the discriminative information. This study presents a novel combining method which captures query‐specific weights for visual‐words in query image. The method mainly contains two stages. Firstly, in offline weight learning, the authors introduce a linear classifier to build a query‐category mapping table, and max‐margin learning to build category‐weight mapping table. Query‐category mapping table is used to map the query image to the most likely image class, and category‐weight mapping table is used to map image class to the weights of visual‐words. Secondly, in online weight mapping, the weights of visual‐words are determined efficiently by looking into the pre‐learned mapping tables. Experimental results on WANG database and Caltech 101 demonstrate that the proposed weighting scheme can effectively weight visual‐words of query image according to their discriminative information. In addition, comparative experiments demonstrate the proposed weighting scheme can obtain higher retrieval performance than other weighting schemes.

With Graphics Processing Units (GPUs) becoming more and more popular in general purpose computing, more attentions have been paid on building a framework to provide convenient interfaces for GPU programming. MapReduce can greatly simplify the programming for data-parallel applications in cloud computing environment, and it is also naturally suitable for GPUs. However, there are some problems in recent reduction-based MapReduce implementation on GPUs. Its performance is dramatically degraded when handling massive distinct keys because the massive data cannot be stored in tiny shared memory entirely.

Sparse Matrix-Vector multiplication (SpMV) is one of the most significant yet challenging issues in computational science area. It is a memory-bound application whose performance mostly depends on the input matrix and the underlying architecture. Many researchers have paid more attentions on exploring a variety of optimization techniques to SpMV. One of the most promising respects is how to adapt the storage format to satisfy the underlying architecture. Alterative storage formats can largely lessen memory pressure, however, the computational resources are often underutilized. Therefore, a new storage format, which is called Compressed Sparse Row with Segmented Interleave Combination (SIC), is proposed. Stemming from Compressed Sparse Row format (CSR), SIC format employs an interleave combination pattern that combines certain amount of CSR rows to form a new SIC row. In order to further improve performance, segmented processing is also brought in. According to the empirical data, we also develop an automatic SIC-based SpMV suitable for all the matrices. Experimental results show that our approach outperforms the NVIDIA CSR vector kernel, achieving up to 12.6 × speedup. It also demonstrates a comparable performance with the Hybrid format, even with the highest 2.89 × speedup.