Running FeatureSpacePlot[mols] gives me an interesting plot and I would like to understand the method.
Does anyone know or can point me to a reference page on how features are extracted for molecules?
$\begingroup$ $\endgroup$
Add a comment |
1 Answer
$\begingroup$
$\endgroup$
Default feature extraction for molecules is the extended connectivity fingerprint, also known as "circular fingerprint" or "Morgan fingerprint". You can access it via undocumented function:
Chemistry`MoleculeFeatureVector[Molecule["glucose"], "ExtendedConnectivity-v1"] (* NumericArray[...] *) or via MoleculeFingerprints Paclet:
PacletInstall["WolframChemistry/MoleculeFingerprints"]; Needs["WolframChemistry`MoleculeFingerprints`"]; WolframChemistry`MoleculeFingerprints`ExtendedConnectivityFingerprint[ Molecule["glucose"]] (* NumericArray[...] *) and the resulting output is a bit vector. It is expected that in version 15.0, this function will be incorporated in the system as MoleculeFingerprint.
Here is a recreation of FeatureSpacePlot for molecules via several underlying steps. Unfortunately, I don't think this is very well documented.
Needs["WolframChemistry`MoleculeFingerprints`"] mols = Molecule /@ {"decane", "L-glucose", "D-glucose", "L-galactose", "D-galactose", "L-fructose", "D-fructose", "nitrogen monoxide", "nitrogen dioxide", "nitric acid"}; (* Calculate molecular fingerprints *) fingerprints = WolframChemistry`MoleculeFingerprints`ExtendedConnectivityFingerprint /@ mols // Normal; (* Standardize features *) standardized = Transpose[Quiet[Check[Standardize[#, Mean, Max], ConstantArray[0., Length[#]]]] & /@ Transpose@N@fingerprints]; (* tSNE reduction *) res = DimensionReduce[standardized, 2, Method -> "TSNE", PerformanceGoal -> "Quality"]; (* Plotting *) Show[FeatureSpacePlot[Legended[mols, "FeatureSpacePlot"], PlotStyle -> GrayLevel[0.8], LabelingFunction -> Function[mol, mol["MolecularFormula"]], PlotMarkers -> {Automatic, Large}], ListPlot[Legended[res, "ExtendedConnectivityFingerprint \[Rule] DimensionReduce"]]] 