pip install biofilm
conda install -c conda-forge biofilm
go to biofilm and run python biofilm-features.py -h
# options for feature selection:
--method str lasso or svm or all or corr or variance
--out str numpycompressdumpgoeshere
--plot bool False
--svmparamrange float+ 0.01 0.15 0.001
# theese are the options for reading data
--infile str myNumpyDump
--randinit int -1
--folds int 5
--subsample int -1
--Z bool False
a) tools.ndumpfile([X,y, featurenames, instancenames],fname) where feature and instancenames are optional or b) provide --loader whose read function will be called (examples/npzloader)
defaultformat: X,y in a npz dump, features and instances get enumerated a custom dataloader: X,y, features, instances loadfoldsreturns: (X,Y,x,y) features namesOfTestInstances
optimize: out.model: {score:score, modelparams:modelparams} out.csv: instanceId, reallabel, predicted label, probability feature selection: out: featuremask, featureproba, featureId