[HTML][HTML] From GPUs to AI and quantum: three waves of acceleration in bioinformatics
B Schmidt, A Hildebrandt - Drug Discovery Today, 2024 - Elsevier
The enormous growth in the amount of data generated by the life sciences is continuously
shifting the field from model-driven science towards data-driven science. The need for …
shifting the field from model-driven science towards data-driven science. The need for …
GPT-Driven Source-to-Source Transformation for Generating Compilable Parallel CUDA Code for Nussinov's Algorithm
M Palkowski, M Gruzewski - Electronics, 2024 - mdpi.com
Designing automatic optimizing compilers is an advanced engineering process requiring a
great deal of expertise, programming, testing, and experimentation. Maintaining the …
great deal of expertise, programming, testing, and experimentation. Maintaining the …
Time and Energy Benefits of Using Automatic Optimization Compilers for NPDP Tasks
M Palkowski, M Gruzewski - Electronics, 2023 - mdpi.com
In this article, we analyze the program codes generated automatically using three advanced
optimizers: Pluto, Traco, and Dapt, which are specifically tailored for the NPDP benchmark …
optimizers: Pluto, Traco, and Dapt, which are specifically tailored for the NPDP benchmark …
Efficiency of Various Tiling Strategies for the Zuker Algorithm Optimization
P Blaszynski, M Palkowski, W Bielecki, M Poliwoda - Mathematics, 2024 - mdpi.com
This paper focuses on optimizing the Zuker RNA folding algorithm, a bioinformatics task with
non-serial polyadic dynamic programming and non-uniform loop dependencies. The …
non-serial polyadic dynamic programming and non-uniform loop dependencies. The …
[PDF][PDF] Polyhedral Tiling Strategies for the Zuker Algorithm Optimization.
W Bielecki, M Palkowski, P Blaszynski… - FedCSIS …, 2023 - annals-csis.org
In this paper, we focus on optimizing the code for computing the Zuker RNA folding
algorithm. This bioinformatics task belongs to the class of non-serial polyadic dynamic …
algorithm. This bioinformatics task belongs to the class of non-serial polyadic dynamic …