Search Results - Performance Keywords Parallel Array Processing*

A High-Performance Non-Indexed Text Search System by Kieu-Do-Nguyen, Binh, Dang, Tuan-Kiet, The Binh, Nguyen, Pham-Quoc, Cuong, Phuc Nghi, Huynh, Tran, Ngoc-Thinh, Inoue, Katsumi, Pham, Cong-Kha, Hoang, Trong-Thuc

“…Full-text search has a wide range of applications, including tracking systems, computer vision, and natural language processing…”
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Learning-based parallel acceleration for HaplotypeCaller by Lai, Xiangxing, Xiao, Minguang, Weng, Lingling, Chen, Zhiguang

“…) and insertions/deletions (Indels) in samples. However, when processing large-scale datasets, HaplotypeCaller often faces the challenge of excessively long runtime…”
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GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies by Kim, Jeremie S., Senol Cali, Damla, Xin, Hongyi, Lee, Donghyuk, Ghose, Saugata, Alser, Mohammed, Hassan, Hasan, Ergin, Oguz, Alkan, Can, Mutlu, Onur

“…Background Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a…”
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A Survey on Graph Processing Accelerators: Challenges and Opportunities by Gui, Chuang-Yi, Zheng, Long, He, Bingsheng, Liu, Cheng, Chen, Xin-Yu, Liao, Xiao-Fei, Jin, Hai

“…, data science and machine learning. Despite a wealth of existing efforts on developing graph processing systems for improving the performance and/or energy efficiency on traditional architectures, dedicated hardware solutions, also…”
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MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data by Shahryary, Yadollah, Hazarika, Rashmi R., Johannes, Frank

“… The efficient pre-processing of these large amounts of data poses major computational challenges and creates unnecessary bottlenecks for downstream analysis and biological interpretation…”
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Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing by Galanti, Lior, Shasha, Dennis, Gunsalus, Kristin C.

“…Background Systems biology increasingly relies on deep sequencing with combinatorial index tags to associate biological sequences with their sample, cell, or…”
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SparkBLAST: scalable BLAST processing using in-memory operations by de Castro, Marcelo Rodrigo, Tostes, Catherine dos Santos, Dávila, Alberto M. R., Senger, Hermes, da Silva, Fabricio A. B.

“…Background The demand for processing ever increasing amounts of genomic data has raised new challenges for the implementation of highly scalable and efficient computational systems…”
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P-TransUNet: an improved parallel network for medical image segmentation by Chong, Yanwen, Xie, Ningdi, Liu, Xin, Pan, Shaoming

“…Deep learning-based medical image segmentation has made great progress over the past decades. Scholars have proposed many novel transformer-based segmentation…”
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Fast noisy long read alignment with multi-level parallelism by Xia, Zeyu, Yang, Canqun, Peng, Chenchen, Guo, Yifei, Guo, Yufei, Tang, Tao, Cui, Yingbo

“… Additionally, a single CPU’s performance bottleneck restricts the effectiveness of alignment algorithms for SMRT sequencing…”
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HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation by Arcioni, Lorenzo, Arcieri, Manuel, Martino, Jessica Di, Liberati, Franco, Bottoni, Paolo, Castrignanò, Tiziana

“… Results To mitigate the computational burden, we introduce HPC-T-Annotator, a tool for de novo transcriptome homology annotation on high performance…”
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An Efficient Indexing Approach for Continuous Spatial Approximate Keyword Queries over Geo-Textual Streaming Data by Deng, Ze, Wang, Meng, Wang, Lizhe, Huang, Xiaohui, Han, Wei, Chu, Junde, Zomaya, Albert Y.

“… The state-of-the-art continuous spatial-keyword query indexing approaches generally lack both support for approximate keyword matching and high-performance processing for geo-textual streaming data…”
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Impact of concurrency on the performance of a whole exome sequencing pipeline by Dall’Olio, Daniele, Curti, Nico, Fonzi, Eugenio, Sala, Claudia, Remondini, Daniel, Castellani, Gastone, Giampieri, Enrico

“…’ pipeline at a time. We refer to this approach as naive parallel strategy (NPS). Here, we discuss an alternative approach, which we refer to as concurrent execution strategy (CES…”
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DNEA: an R package for fast and versatile data-driven network analysis of metabolomics data by Patsalis, Christopher, Iyer, Gayatri, Brandenburg, Marci, Karnovsky, Alla, Michailidis, George

“… Analysis of metabolomics data is a multi-step process that involves data processing, quality control and normalization, followed by statistical and bioinformatics analysis…”
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Multiple k −opt evaluation multiple k −opt moves with GPU high performance local search to large-scale traveling salesman problems by Qiao, Wen-Bao, Créput, Jean-Charles

“… (Graphics Processing Unit) parallel 2-/3-opt evaluation with characteristic of “data parallelism, decentralized control and O (1…”
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Variable-order reference-free variant discovery with the Burrows-Wheeler Transform by Prezza, Nicola, Pisanti, Nadia, Sciortino, Marinella, Rosone, Giovanna

“…) bad performance in repeated regions longer than k bases. The preliminary tool, however, was able to identify only SNPs and it was too slow and memory consuming due to the use of additional heavy data structures…”
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High throughput automatic muscle image segmentation using parallel framework by Cui, Lei, Feng, Jun, Zhang, Zizhao, Yang, Lin

“… Methods In this paper, we propose a novel distributed computing approach, which adopts both data and model parallel, for fast muscle cell segmentation…”
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transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation by Fallon, Timothy R., Čalounová, Tereza, Mokrejš, Martin, Weng, Jing-Ke, Pluskal, Tomáš

“…Background RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data…”
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Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers by Ito, Satoshi, Yadome, Masaaki, Nishiki, Tatsuo, Ishiduki, Shigeru, Inoue, Hikaru, Yamaguchi, Rui, Miyano, Satoru

“… However, their use is still limited in the bioinformatics field due to the fundamental fact that the asynchronous parallel processing service of Grid Engine is not provided…”
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ASAP-FE: Energy-Efficient Feature Extraction Enabling Multi-Channel Keyword Spotting on Edge Processors by Choi, Jongin, Park, Jina, Lee, Jae-Jin, Pedram, Massoud, Lee, Woojoo

“…Multi-channel keyword spotting (KWS) has become crucial for voice-based applications in edge environments…”
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An analog-AI chip for energy-efficient speech recognition and transcription by Ambrogio, S., Narayanan, P., Okazaki, A., Fasoli, A., Mackin, C., Hosokawa, K., Nomura, A., Yasuda, T., Chen, A., Friz, A., Ishii, M., Luquin, J., Kohda, Y., Saulnier, N., Brew, K., Choi, S., Ok, I., Philip, T., Chan, V., Silvestre, C., Ahsan, I., Narayanan, V., Tsai, H., Burr, G. W.

“… processing units or central processing units. Analog in-memory computing (analog-AI) 3 – 7 can provide better energy efficiency by performing matrix…”
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