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Background High-throughput sequencing technologies have led to an unprecedented explosion in the amounts of sequencing data available, which are typically stored using FASTA and FASTQ files. We can find in the literature several tools to process and manipulate those type of files with the aim of transforming sequence data into biological knowledge. However, none of them are well fitted for processing efficiently very large files, likely in the order of terabytes in the following years, since they are based on sequential processing. Only some routines of the well-known seqkit tool are partly parallelized. In any case, its scalability is limited to use few threads on a single computing node. Results Our approach, BigSeqKit , takes advantage of a high-performance computing–Big Data framework to parallelize and optimize the commands included in seqkit with the aim of speeding up the manipulation of FASTA/FASTQ files. In this way, in most cases, it is from tens to hundreds of times faster than several state-of-the-art tools. At the same time, our toolkit is easy to use and install on any kind of hardware platform (local server or cluster), and its routines can be used as a bioinformatics library or from the command line. Conclusions BigSeqKit is a very complete and ultra-fast toolkit to process and manipulate large FASTA and FASTQ files. It is publicly available at https://github.com/citiususc/BigSeqKit. [ABSTRACT FROM AUTHOR]

The integration of quantum processing units (QPUs) in a heterogeneous high-performance computing environment requires solutions that facilitate hybrid classical–quantum programming. Standards such as OpenCL facilitate the programming of heterogeneous environments, consisting of CPUs and hardware accelerators. This study presents an innovative method that incorporates QPU functionality into OpenCL, standardizing quantum processes within classical environments. By leveraging QPUs within OpenCL, hybrid quantum–classical computations can be sped up, impacting domains like cryptography, optimization problems, and quantum chemistry simulations. Using Portable Computing Language (Jääskeläinen et al. in Int J Parallel Program 43(5):752–785, 2014. https://doi.org/10.1007/s10766-014-0320-y) and the Qulacs library (Suzuki et al. in Quantum 5:559, 2021. https://doi.org/10.22331/q-2021-10-06-559), results demonstrate, for instance, the successful execution of Shor's algorithm (Nielsen and Chuang in Quantum computation and quantum information, 10th anniversary edn. Cambridge University Press, Cambridge, 2010), serving as a proof of concept for extending the approach to larger qubit systems and other hybrid quantum–classical algorithms. This integration approach bridges the gap between quantum and classical computing paradigms, paving the way for further optimization and application to a wide range of computational problems. [ABSTRACT FROM AUTHOR]

Next-generation sequencing (NGS) technologies have led to a huge amount of genomic data that need to be analyzed and interpreted. This fact has a huge impact on the DNA sequence alignment process, which nowadays requires the mapping of billions of small DNA sequences onto a reference genome. In this way, sequence alignment remains the most time-consuming stage in the sequence analysis workflow. To deal with this issue, state of the art aligners take advantage of parallelization strategies. However, the existent solutions show limited scalability and have a complex implementation. In this work we introduce SparkBWA, a new tool that exploits the capabilities of a big data technology as Spark to boost the performance of one of the most widely adopted aligner, the Burrows-Wheeler Aligner (BWA). The design of SparkBWA uses two independent software layers in such a way that no modifications to the original BWA source code are required, which assures its compatibility with any BWA version (future or legacy). SparkBWA is evaluated in different scenarios showing noticeable results in terms of performance and scalability. A comparison to other parallel BWA-based aligners validates the benefits of our approach. Finally, an intuitive and flexible API is provided to NGS professionals in order to facilitate the acceptance and adoption of the new tool. The source code of the software described in this paper is publicly available at , with a GPL3 license. [ABSTRACT FROM AUTHOR]

Abstract: The microprocessor industry has responded to memory, power and ILP walls by turning to many-core processors, increasing parallelism as the primary method to improve processor performance. These processors are expected to consist of tens or even hundreds of cores. One of these future processors is the 48-core experimental processor Single-Chip Cloud Computer (SCC). The SCC was created by Intel Labs as a platform for many-core software research. In this work we study the behavior of an important irregular application such as the Sparse Matrix–Vector multiplication (SpMV) on the SCC processor in terms of performance and power efficiency. In addition, some of the most successful optimization techniques for this kernel are evaluated. In particular, reordering, blocking and data compression techniques have been considered. Our experiments give some key insights that can serve as guidelines for the understanding and optimization of the SpMV kernel on this architecture. Furthermore, an architectural comparison of the SCC processor with several leading multicore processors and GPUs is performed, including the new Intel Xeon Phi coprocessor. The SCC only outperforms the Itanium2 multicore processor. Best performance results are observed for the high-end GPUs and the Phi, while reaching low values with respect to their peak performance. In terms of power efficiency, we must highlight the good behavior of the ATI GPUs. [Copyright &y& Elsevier]

Abstract: It is well-known that reordering techniques applied to sparse matrices are common strategies to improve the performance of sparse matrix operations, and particularly, the sparse matrix vector multiplication (SpMV) on CPUs. In this paper, we have evaluated some of the most successful reordering techniques on two different GPUs. In addition, in our study a number of sparse matrix storage formats were considered. Executions for both single and double precision arithmetics were also performed. We have found that SpMV is very sensitive to the application of reordering techniques on GPUs. In particular, several characteristics of the reordered matrices that have a big impact on the SpMV performance have been detected. In most of the cases, reordered matrices outperform the original ones, showing noticeable speedups up to 2.6×. We have also observed that there is no one storage format preferred over the others. [Copyright &y& Elsevier]

BigBWA is a new tool that uses the Big Data technology Hadoop to boost the performance of the Burrows-Wheeler aligner (BWA). Important reductions in the execution times were observed when using this tool. In addition, BigBWA is fault tolerant and it does not require any modification of the original BWA source code. [ABSTRACT FROM AUTHOR]

Abstract: In this paper a heuristic segmentation algorithm is presented based on the oversegmentation of an image. The method uses a set of different segmentations of the image produced previously by standard techniques. These segmentations are combined to create the oversegmented image. They can be performed using different techniques or even the same technique with different initial conditions. Based on this oversegmentation a new method of region merging is proposed. The merging process is guided using only information about the behavior of each pixel in the input segmentations. Therefore, the results are an adequate combination of the features of these segmentations, allowing to mask the negative particularities of individual segmentations. In this work, the quality of the proposal is analyzed with both artificial and real images using a evaluation function as case of study. The results show that our algorithm produces high quality global segmentations from a set of low quality segmentations with reduced execution times. [Copyright &y& Elsevier]

The performance and reliability of semiconductor devices scaled down to the sub-nanometer regime are being seriously affected by process-induced variability. To properly assess the impact of the different sources of fluctuations, such as line edge roughness (LER), statistical analyses involving large samples of device configurations are needed. The computational cost of such studies can be very high if 3D advanced simulation tools (TCAD) that include quantum effects are used. In this work, we present a machine learning approach to model the impact of LER on two gate-all-around nanowire FETs that is able to dramatically decrease the computational effort, thus reducing the carbon footprint of the study, while obtaining great accuracy. Finally, we demonstrate that transfer learning techniques can decrease the computing cost even further, being the carbon footprint of the study just 0.18 g of CO2 (whereas a single device TCAD study can produce up to 2.6 kg of CO2), while obtaining coefficient of determination values larger than 0.985 when using only a 10% of the input samples. [ABSTRACT FROM AUTHOR]

Web search is widely used to find online medical advice. As such, health-related information access requires retrieval algorithms capable of promoting reliable documents and filtering out unreliable ones. To this end, different types of components, such as query-document matching features, passage relevance estimation and AI-based reliability estimators, need to be combined. In this paper, we propose an entire pipeline for misinformation detection, based on the fusion of multiple content-based features. We present experiments which study the influence of each pipeline stage for the target task. Our technological solution incorporates signals from technologies derived from diverse research fields, including search, deep learning for natural language processing, as well as advanced supervised and unsupervised learning. To combine evidence, different score fusion strategies are compared, including unsupervised rank fusion techniques and learning-to-rank methods. The reference framework for empirically validating our solution is the TREC Health Misinformation Track, which provides several challenging subtasks that foster research on the identification of reliable and correct information for health-related decision making tasks. More specifically, we address a total recall task, the goal of which is to identify all the documents conveying incorrect information for a specific set of topics, and an ad-hoc retrieval task, aiming to rank credible and correct information over incorrect information. All variants are evaluated with an assorted set of effectiveness metrics, which includes standard search measures, such as R-Precision, Average Precision or Normalised Discounted Cumulative Gain, and innovative metrics based on the compatibility between the ranked output and two reference rankings composed of helpful and harmful documents, respectively. Our experiments demonstrate the effectiveness of the proposed pipeline stages and indicate that sophisticated supervised fusion methods do not fare better than simpler fusion alternatives. Additionally, for reliability estimation, unsupervised textual similarity performs better than textual classification based on supervised learning. The results also show that the presented approach is highly competitive when compared with state-of-the-art solutions for the same problem. • A complete system for health misinformation detection is proposed. • Several content-based features are proposed for identifying health misinformation. • The performance of the different features and against external baselines is reported. • New metrics considering harmfulness and helpfulness of retrieved documents are used. • The technology developed is freely available for other researchers or stakeholders. [ABSTRACT FROM AUTHOR]

Motivation: One basic step in many bioinformatics analyses is the multiple sequence alignment. One of the state-of-the-art tools to perform multiple sequence alignment is PASTA (Practical Alignments using SATe' and TrAnsitivity). PASTA supports multithreading but it is limited to process datasets on shared memory systems. In this work we introduce PASTASpark, a tool that uses the Big Data engine Apache Spark to boost the performance of the alignment phase of PASTA, which is the most expensive task in terms of time consumption. Results: Speedups up to 10° with respect to single-threaded PASTA were observed, which allows to process an ultra-large dataset of 200 000 sequences within the 24-h limit. [ABSTRACT FROM AUTHOR]

Motivation FastTree-2 is one of the most successful tools for inferring large phylogenies. With speed at the core of its design, there are still important issues in the FastTree-2 implementation that harm its performance and scalability. To deal with these limitations, we introduce VeryFastTree, a highly tuned implementation of the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to boost performance. Results VeryFastTree is able to construct a tree on a standard server using double-precision arithmetic from an ultra-large 330k alignment in only 4.5 h, which is 7.8× and 3.5× faster than the sequential and best parallel FastTree-2 times, respectively. Availability and implementation VeryFastTree is available at the GitHub repository: https://github.com/citiususc/veryfasttree. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Background: All-Food-Sequencing (AFS) is an untargeted metagenomic sequencing method that allows for the detection and quantification of food ingredients including animals, plants, and microbiota. While this approach avoids some of the shortcomings of targeted PCR-based methods, it requires the comparison of sequence reads to large collections of reference genomes. The steadily increasing amount of available reference genomes establishes the need for efficient big data approaches. Results: We introduce an alignment-free k-mer based method for detection and quantification of species composition in food and other complex biological matters. It is orders-of-magnitude faster than our previous alignment-based AFS pipeline. In comparison to the established tools CLARK, Kraken2, and Kraken2+Bracken it is superior in terms of false-positive rate and quantification accuracy. Furthermore, the usage of an efficient database partitioning scheme allows for the processing of massive collections of reference genomes with reduced memory requirements on a workstation (AFS-MetaCache) or on a Spark-based compute cluster (MetaCacheSpark). Conclusions: We present a fast yet accurate screening method for whole genome shotgun sequencing-based biosurveillance applications such as food testing. By relying on a big data approach it can scale efficiently towards large-scale collections of complex eukaryotic and bacterial reference genomes. AFS-MetaCache and MetaCacheSpark are suitable tools for broad-scale metagenomic screening applications. They are available at https://muellan.github.io/metacache/afs.html (C++ version for a workstation) and https://github.com/jmabuin/MetaCacheSpark (Spark version for big data clusters). [ABSTRACT FROM AUTHOR]

In this work, we present a machine learning neural network model to predict the impact of realistic metal grain granularity (MGG) variability on the threshold voltage V T h and on the I D − V G characteristics of a silicon-based 12 nm gate length nanosheet FET. This model is based on the multi-layer perceptron (MLP) machine learning architecture. As realistic MGG maps consist of the distribution of grains on the gate with different work-function values, it is relevant to apply algorithms such as the principal component analysis to reduce these features to the most representative ones. Once the realistic MGG features are correctly reduced without losing information, we train two different neural networks with the neurons in the output layer as the only difference, to predict the V T h and the I D − V G characteristics, respectively. The comparison between TCAD results and the model, shows excellent agreement for the mean and standard deviation of V T h distributions for different average grain sizes values (from 3 nm to 10 nm) demonstrating the accuracy of the machine learning model. Also, we study the amount of data needed to accurately train the MLPs, leading to results that allow us to drastically reduce the computational time required to perform variability studies for state-of-art nano FET devices. • Machine learning model to predict the impact of variability on state-of-the-art semiconductor devices. • Prediction of the impact of metal grain granularity on the Vth and on the I-V characteristics of a 12 nm gate length Si-based nanosheet FET. • Model that reduces the computational cost of variability statistical studies. • Comparison of the model performance against TCAD simulations. [ABSTRACT FROM AUTHOR]