Prediction of subcellular location of proteins
(http://brain.cs.unr.edu/publications/NevProp.zip)
(http://brain.cs.unr.edu/publications/NevPropManual.pdf)
FileFormat 3.0
# NP FILE SETTINGS
ResultsFile prot.res
# ReadWeightsFile prot.wts
SaveWeightsFile prot.wts
SaveTrainPrdFile prot.ptr
# SaveTrainImputFile prot.itr
# SaveTestImputFile prot.its
# SaveTestPrdFile prot.pts
# DATA FILE SETTINGS
ReadTrainFile prot.trn
# ReadTestFile prot.tst
NHeaders 1 IDColumn YES
StandardizeInputs 1 SaveStandWts NO ImputeMissing median
InputColumns 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
OutputColumns 22 23
NVars 23 ShuffleData YES
# REPORTING SETTINGS
DescribeVars YES MinCasesPerBin 25
NBoots 0 NEffectBoots 0
CalccIndex YES ScoreThreshold 0.5
OutputStatVars 0
# CONNECT CALLS
Connect 1 21 22 24
Connect 22 24 25 26
# CONFIGURATION SETTINGS
Ninputs 21 Nhidden 3 Noutputs 2
kNN 0 1ofN NO
HiddenUnitType 1 OutputUnitType 3
WeightRange 0.001
# TRAINING SETTINGS
TrainCriterion 3 BiasPenalty NO WeightDecay -0.001
OptimizeMethod 1 SigmoidPrimeOffset 0
QPMaxFactor 1.75 QPModeSwitchThreshold 0
Stochastic NO LearnRate 0.01 SplitLearnRate NO Momentum 0.0
# BEST-BY-HOLDOUT SETTINGS
PercentHoldout 50
AutoTrain YES MinEpochs 50 BeyondBestEpoch 1.5
NSplits 10 SepBootXVal YES
# AUTOMATIC RELEVANCE DETERMINATION SETTINGS
UseARD NO WhenARD auto ARDTolerance 0.05 ARDFreq 25
GroupSelection Input BiasRelevance NO ARDFactor 1
Reinhardt a, Hubbard T. Using neural networks for prediction of the subcellular location of proteins. Nucleic acids research. 1998;26(9):2230-6. [PDF]
Rey S, Acab M, Gardy JL, et al. PSORTdb: a protein subcellular localization database for bacteria. Nucleic acids research. 2005;33(Database issue):D164-8. [PDF]