Merge remote-tracking branch 'origin/master'

models/somatic-variation/pair_exome-1481155294032/bestAUC-perf-log.tsv

@@ -0,0 +1,12 @@
+numExamplesUsed	epoch	AUC	score	condition
+2861327	0	0.994160	0.374068	fullset
+5722654	1	0.994788	0.593242	fullset
+8583981	2	0.995150	0.475541	fullset
+11445308	3	0.995258	0.413675	fullset
+17167962	5	0.995427	0.510989	fullset
+20029289	6	0.995744	0.245182	fullset
+22890616	7	0.995768	0.467109	fullset
+28613270	9	0.995794	0.576796	fullset
+31474597	10	0.996010	0.425386	fullset
+37197251	12	0.996067	0.364467	fullset
+57226540	19	0.996102	0.545729	fullset

models/somatic-variation/pair_exome-1481155294032/bestScore

@@ -0,0 +1 @@
+1.7976931348623157E308

models/somatic-variation/pair_exome-1481155294032/config.properties

@@ -0,0 +1,34 @@
+#total testRecords added other settings, for use in statistics
+#Thu Dec 08 22:27:08 EST 2016
+numRecords=2861327
+randomSeed=1478360241635
+stats.readMappingQuality.reverse.min=40.0
+stats.readMappingQuality.reverse.max=40.0
+dropoutRate=0.9
+time=1481155294032
+stats.baseQuality.reverse.min=0.0
+earlyStopCondition=10
+stats.insertSizes.min=0.0
+stats.baseQuality.reverse.max=235.0
+stats.readMappingQuality.forward.min=40.0
+stats.insertSizes.max=0.0
+goby.version=
+numTrainingSets=1
+domainDescriptor=org.campagnelab.dl.somatic.learning.domains.SomaticMutationDomainDescriptor
+testRecordCount=3233836
+stats.readMappingQuality.forward.max=40.0
+regularizationRate=1.0E-9
+miniBatchSize=512
+stats.baseQuality.forward.min=0.0
+allArguments=--auc-clip-max-observations 10000 --dropout-rate 0.9 --early-stopping-measure AUC --early-stopping-num-epochs 10 --error-enrichment false --experimental-condition fullset --feature-mapper org.campagnelab.dl.somatic.mappers.FeatureMapperV25 --gpu-device 3 --ignore-cache false --learning-rate 5.0 --max-epochs 2147483647 --memory-cache false --mini-batch-size 512 --model-conditions ./model-conditions.txt --net-architecture org.campagnelab.dl.somatic.learning.architecture.graphs.SixDenseLayersNarrower2WithFrequencyAndBase --num-errors-added 16 --num-training 2147483647 --num-validation 10000 --parallel false --parameter-precision FP32 --previous-model-name bestAUC --previous-model-path null --random-seed 1478360241635 --regularization-rate 1.0E-9 --training-sets [../exome/exome_pair_train_q5c/WXAQEBF-mutated-randomized.sbi] --trio false --validate-every 1 --validation-set ../exome/exome_duo_val_qtt1/ENQOAZV-mutated-randomized.sbi 
+stats.genomicContextSize.min=21.0
+stats.baseQuality.forward.max=235.0
+mapper=org.campagnelab.dl.somatic.mappers.FeatureMapperV25
+precision=FP32
+stats.genomicContextSize.max=21.0
+stats.numVariationsInRead.min=0.0
+hiddenNodes=0
+learningRate=5.0
+numEpochs=2147483647
+stats.numVariationsInRead.max=14.0
+tag=9D21O2

models/somatic-variation/pair_exome-1481155294032/domain.properties

@@ -0,0 +1,11 @@
+#Domain properties created with org.campagnelab.dl.somatic.learning.domains.SomaticMutationDomainDescriptor
+#Thu Dec 08 00:46:39 EST 2016
+net.architecture.classname=org.campagnelab.dl.somatic.learning.architecture.graphs.SixDenseLayersNarrower2WithFrequencyAndBase
+isBaseMutated.predictionInterpreter=org.campagnelab.dl.somatic.learning.domains.IsBaseMutatedInterpreter
+input.featureMapper.numFeatures=280
+isBaseMutated.labelMapper.numLabels=6
+somaticFrequency.predictionInterpreter=org.campagnelab.dl.somatic.learning.domains.SomaticFrequencyInterpreter
+isBaseMutated.labelMapper=org.campagnelab.dl.somatic.mappers.IsBaseMutatedMapper
+somaticFrequency.labelMapper.numLabels=1
+somaticFrequency.labelMapper=org.campagnelab.dl.somatic.mappers.SomaticFrequencyLabelMapper
+input.featureMapper=org.campagnelab.dl.somatic.mappers.FeatureMapperV25

models/somatic-variation/pair_exome-1481155294032/epochs-perf-log.tsv

@@ -0,0 +1,32 @@
+numExamplesUsed	epoch	AUC	score	condition
+2861327	0	0.994160	0.374068	fullset
+5722654	1	0.994788	0.593242	fullset
+8583981	2	0.995150	0.475541	fullset
+11445308	3	0.995258	0.413675	fullset
+14306635	4	0.995127	0.637889	fullset
+17167962	5	0.995427	0.510989	fullset
+20029289	6	0.995744	0.245182	fullset
+22890616	7	0.995768	0.467109	fullset
+25751943	8	0.995726	0.436410	fullset
+28613270	9	0.995794	0.576796	fullset
+31474597	10	0.996010	0.425386	fullset
+34335924	11	0.995886	0.543662	fullset
+37197251	12	0.996067	0.364467	fullset
+40058578	13	0.996023	0.263937	fullset
+42919905	14	0.995976	0.526979	fullset
+45781232	15	0.995993	0.403771	fullset
+48642559	16	0.995894	0.574370	fullset
+51503886	17	0.995950	0.298926	fullset
+54365213	18	0.996025	0.252709	fullset
+57226540	19	0.996102	0.545729	fullset
+60087867	20	0.996043	0.281790	fullset
+62949194	21	0.996015	0.489378	fullset
+65810521	22	0.996041	0.406756	fullset
+68671848	23	0.995870	0.438424	fullset
+71533175	24	0.995927	0.270874	fullset
+74394502	25	0.996018	0.314095	fullset
+77255829	26	0.995969	0.505824	fullset
+80117156	27	0.995895	0.268865	fullset
+82978483	28	0.995967	0.246807	fullset
+85839810	29	0.995868	0.253776	fullset
+88701137	30	0.995944	0.076157	fullset