diff --git a/assets/MassSpecGym_infrastructure.pdf b/assets/MassSpecGym_infrastructure.pdf new file mode 100644 index 0000000..220cabf Binary files /dev/null and b/assets/MassSpecGym_infrastructure.pdf differ diff --git a/assets/MassSpecGym_infrastructure.svg b/assets/MassSpecGym_infrastructure.svg index c33c67a..ef4dfa7 100644 --- a/assets/MassSpecGym_infrastructure.svg +++ b/assets/MassSpecGym_infrastructure.svg @@ -1,3461 +1,4 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Intensity -m/z - - -N -N -O -N -O -N - - - - - - - - - - - - - - - - - - - - - -Mass spectrum -(MS/MS) -2D molecular - -graph - - -SpecTransforms - - -MolTransforms - - -MassSpecDataset - - - - - - - -MassSpecGymModel - - -Metric -Callback -'s - - - - - - - - MyModel( ): - - - - - - - - def forward(...): - - - - - - - - - - # -TODO - - - - - - - - def step(...): - - - - - - - - - - # -TODO - - - - - - - - - - -Hidden test results -from cloud -Data -pre-processing -Dataset - -initialization -and splitting -Model definition and -training -Evaluation - -on pre- -defined metrics - - -DeNovo - - -Retrieval - - -Simulation - - - - - -231K labeled -pairs -40M unlabeled -spectra - - -MassSpecDataModule -4M unlabeled -molecules -Local validation -results -Curated and -standardized data - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -MassSpecGym - - - + + + +
Intensity
m/z
 N N O N O N
Mass spectrum
(MS/MS)
2D molecular graph
SpecTransforms
MolTransforms
MassSpecDataset
MassSpecGymModel
Metric Callback's
      MyModel( ):
        def forward(...):
          # TODO
        def step(...):
          # TODO
Test results and leaderboard
Data
pre-processing
Dataset initialization and pre-defined splitting
Model definition and training
Evaluation on pre-defined metrics
DeNovo
Retrieval
Simulation
231K labeled pairs
24M unlabeled spectra
MassSpecDataModule
4M unlabeled molecules
Validation results
Curated and standardized data
MassSpecGym
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