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gao-lab / GLUE

Graph-linked unified embedding for single-cell multi-omics data integration
MIT License
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CLUE paper reproducibility code #84

Closed valentinwust closed 1 year ago

valentinwust commented 1 year ago

In the supplementary material to the CLUE paper, you mention a .zip file with all the relevant code; however I can't find this anywhere. Did you use the exact same setup as published on the competition git? I'm trying to run some benchmarks and want to stay as close to your paper as possible.

Greetings Valentin

Jeff1995 commented 1 year ago

Hi @valentinwust! Yes that's the identical setup as the competition git.

valentinwust commented 1 year ago

Thank you, then I'll probably just use that. That being said, this uses scclue 0.1.1, and I've noticed some slight changes in the code of CLUE since then. Do they meaningfully affect the preformance?

Jeff1995 commented 1 year ago

Actually that was not 0.1.1, but a version between 0.1.1 and 0.2.0. We didn't tag it as a dedicated public release. To exactly reproduce the CLUE model in the competition, I'd suggest using the whl file in the competition repo to install scglue. Apologies for the inconvenience.

valentinwust commented 1 year ago

No problem, this is indeed what I am currently doing. I was just wondering whether the current release (0.3.2) would perform better or similar, if it has a relevant performance increase it might make sense to use the most current version instead.

Jeff1995 commented 1 year ago

Great! There shouldn't be a noticeable performance difference. You may just use the whl version to avoid needing to change some of the function calls due to API changes along the way.

valentinwust commented 1 year ago

Thanks, then I'll do that.