Open questions regarding implementation details

aalto-ics-kepaco / msms_rt_ssvm

Implementation of the LC-MS²Struct model published in the manuscript "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data" by Bach et al.

MIT License

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Open questions regarding implementation details #1

Open bachi55 opened 3 years ago

bachi55 commented 3 years ago

If two MS-features, e.g. within one sequence, have them same candidate sets, should the randomly sub-sampled candidate sets, e.g. used during training, be identical for both features?
Is it sufficient to calculate the average, e.g. top-k, accuracy over the sequences in the sample? Thereby we first calculate the average, e.g. top-k, accuracy over the sequence and subsequently average over the samples.

bachi55 commented 3 years ago

Answer to first question: I think it does not really matter. My experiments showed that we can even have different random candidate subsets each time a specific spectrum re-appears in a training sequence. Only in during testing this matters, but that we anyway do not randomly sub-sample.