InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/
OutFilePrefix /cse/faculty/karplus/dna/predict-2nd/testing/

ReadNeuralNet networks/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded-stride-trained.net
NameNet overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net

ReadParams params/2-feb-00-fast

# Note: the following includes read the training set(s),
# and, in doing so, reset the InFilePrefix

ReadToSet train
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include overrep-2500.t99-stride

SetOverhang

ReportTrainByChain quality-reports/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.by-chain
ReportQvsPhatTo quality-reports/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.q-vs-phat
ReportUnitUsageTo quality-reports/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.unit-usage

TestNet

ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo



ReportNetQualityForTrainTo quality-reports/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-t.quality
ReportNetQualityForCrossTrainTo quality-reports/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride.quality



unfreeze 0
unfreeze 1
unfreeze 2
unfreeze 3
TrainNet 50
ReportNeuralNet networks/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net

TrainNet 100
ReportNeuralNet networks/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net

TrainNet 100
ReportNeuralNet networks/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net
TrainNet 100
ReportNeuralNet networks/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net


ReportTrainByChain quality-reports/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.by-chain
ReportQvsPhatTo quality-reports/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.q-vs-phat
ReportUnitUsageTo quality-reports/overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.unit-usage

TestNet