Accelerating Viterbi algorithm on graphics processing units

DOI10.1007/s00607-017-0557-6zbMath1430.68434OpenAlexW2616045668WikidataQ60204442 ScholiaQ60204442MaRDI QIDQ1700985

Karl-Heinz Zimmermann, Muhammad Kashif Hanif

Publication date: 22 February 2018

Published in: Computing (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s00607-017-0557-6

zbMATH Keywords

hidden Markov modelmatrix productViterbi algorithmgraphics processing unit

Mathematics Subject Classification ID

Dynamic programming (90C39) Parallel algorithms in computer science (68W10) Parallel numerical computation (65Y05) Complexity and performance of numerical algorithms (65Y20)

Uses Software

• Matlab
• CUDA
• ClawHMMER
• Btas
• CuHMM
• zipHMMlib

Cites Work

• Unnamed Item
• Speeding up HMM decoding and training by exploiting sequence repetitions
• Matrix multiplication via arithmetic progressions
• Gaussian elimination is not optimal
• Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions
• More algorithms for all-pairs shortest paths in weighted graphs
• Biological Sequence Analysis
• Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
• Algebraic Statistics for Computational Biology

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