Add methods for easy development and benchmarking of method variants#3
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niekdejonge wants to merge 48 commits intochange_ms2deepscore_versionfrom
Closed
Add methods for easy development and benchmarking of method variants#3niekdejonge wants to merge 48 commits intochange_ms2deepscore_versionfrom
niekdejonge wants to merge 48 commits intochange_ms2deepscore_versionfrom
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Fix umap-learn requirement
… and exact match searches
… current code base)
…r and to select top k highest ms2deepscores
…correct types of output)
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This is all included in #4, so this PR can now be closed |
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This was initially developed in chemical space exploration but moved here now.
Here we implement benchmarking methods for easy testing of different variants for an analogue search.
There is some overlap in functionality with ms2query_library and MS2Query_database. I looked into merging these directly, but this was not very straightforward, so I propose to first merge it separately in the code base. Some benchmarking methods can be developed without using the sqlite library (like cosine score matching). But it would be nice to create a mapping from sqlite library to SpectrumDataSet, so we can in that way merge both into one.
The reason why it is not very easy to merge right now is that the benchmarking method requires many different library + query pairs, to test exact matching benchmarking. I have set this up to be fast, but for an sqlite library it would require recreating the sqlite library many times and rebuilding the ANN method.