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Add benchmarks #23

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michabirklbauer opened this issue Dec 4, 2023 · 8 comments · Fixed by #38
Closed

Add benchmarks #23

michabirklbauer opened this issue Dec 4, 2023 · 8 comments · Fixed by #38
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documentation Improvements or additions to documentation

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Compare CPU_DV and GPU_DV on HPC with peptides and peptidoforms -> plot
Add system info
Update doxygen docs once completed!
@michabirklbauer michabirklbauer self-assigned this Dec 4, 2023
@michabirklbauer michabirklbauer added the documentation Improvements or additions to documentation label Dec 4, 2023
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datasets for benchmarking:

  • hela
  • beveridge xl
  • maybe one with tmt mods (maybe from the ms2rescore paper?)

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benchmarks should also include normalize vs not normalize, gaussian vs not gaussian

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Also don't forget to document all parameters for searches!

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datasets for benchmarking:

  • hela
  • beveridge xl
  • maybe one with tmt mods (maybe from the ms2rescore paper?)

@michabirklbauer
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Compare CPU_DV and GPU_DV on HPC with peptides and peptidoforms -> plot Add system info Update doxygen docs once completed!

Actually need to re-think which methods to benchmark, it appears that CPU_SM is maybe the fastest?

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Last dataset -> because tmt is a fixed modification it's not good for testing since we consider those

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Probably these two datasets are enough anyway, crosslinked peptides have enough modifications anyway

@michabirklbauer michabirklbauer mentioned this issue May 11, 2024
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@michabirklbauer michabirklbauer linked a pull request May 11, 2024 that will close this issue
Add Benchmarks and Results for v1.1.2 #38
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Add links to raw files into readme as there seems to be a problem with pcloud with them

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Add Benchmarks and Results for v1.1.2 hgb-bin-proteomics/CandidateSearch
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