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Published on: January 26, 2024
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Hardware Acceleration of the STRIKE String Kernel Algorithm for Estimating Protein to Protein Interactions
Summary
Hardware accelerators significantly speed up the STRIKE algorithm for protein-protein interaction (PPI) prediction. Developed accelerators achieve orders of magnitude performance improvement over traditional computing, enabling faster disease research.
Area of Science:
- Bioinformatics
- Computational Biology
- Biotechnology
Background:
- Protein-protein interaction (PPI) is crucial for understanding diseases and developing therapies.
- The STRIKE algorithm offers improvements in PPI prediction but requires further acceleration due to its computational demands and large datasets.
- Existing methods face challenges with execution time and scalability for massive protein sequence databases.
Purpose of the Study:
- To design and evaluate hardware accelerators for the STRIKE protein-protein interaction prediction algorithm.
- To address the computational intensity and accelerate the execution time of the STRIKE algorithm.
- To improve the efficiency of PPI prediction for large-scale bioinformatics applications.
Main Methods:
- Development of hardware accelerator designs for the STRIKE algorithm.
- Implementation and simulation of weighted and unweighted STRIKE accelerators using Verilog.
- Design of a parallel module accelerator organization for enhanced weighted STRIKE performance.
- Validation through Field-Programmable Gate Array (FPGA) runs and comparisons with multi-core and cluster computers.
Main Results:
- Weighted STRIKE accelerators showed approximately 10x longer execution times compared to unweighted versions.
- A parallel module accelerator organization for weighted STRIKE achieved near-linear speedups for sequences of 100+ characters.
- The weighted STRIKE module accelerator demonstrated a three-orders-of-magnitude speed improvement over multi-core and cluster systems.
- Potential for even greater speedups with the parallel module accelerator design.
Conclusions:
- Hardware acceleration offers a significant performance boost for the STRIKE PPI prediction algorithm.
- The parallel module accelerator design provides substantial speed improvements, particularly for long protein sequences.
- These hardware solutions are critical for accelerating large-scale bioinformatics analyses and advancing disease research.
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