add parameter model for performance benchmark

Author: hyoo

Pilot1/Combo/combo_perf_bench_model.txt

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+[Global_Params]
+cell_features=['expression']
+drug_features=['descriptors']
+dense=[1000, 1000, 1000]
+dense_feature_layers=[1000, 1000, 1000]
+activation='relu'
+loss='mse'
+optimizer='adam'
+scaling='std'
+drop=0
+epochs=10
+batch_size=32
+validation_split=0.2
+cv=1
+cv_partition='overlapping'
+max_val_loss=1.0
+learning_rate=None
+base_lr=None
+residual=False
+reduce_lr=False
+warmup_lr=False
+batch_normalization=False
+feature_subsample=0
+rng_seed=2017
+save='save/combo'
+gen=False
+use_combo_score=False
+verbose=False
+use_landmark_genes=True
+
+[Monitor_Params]
+solr_root=''
+timeout=3600

Pilot1/NT3/nt3_perf_bench_model.txt

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+[Global_Params]
+data_url = 'ftp://ftp.mcs.anl.gov/pub/candle/public/benchmarks/Pilot1/normal-tumor/'
+train_data = 'nt_train2.csv'
+test_data = 'nt_test2.csv'
+model_name = 'nt3'
+conv = [128, 20, 1, 128, 10, 1]
+dense = [200,20]
+activation = 'relu'
+out_act = 'softmax'
+loss = 'categorical_crossentropy'
+optimizer = 'sgd'
+metrics = 'accuracy'
+epochs = 50
+batch_size = 20
+learning_rate = 0.001
+drop = 0.1
+classes = 2
+pool = [1, 10]
+save = '.'
+timeout = 3600

Pilot1/P1B3/p1b3_perf_bench_model.txt

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+[Global_Params]
+dense=[1000, 500, 100, 50]
+batch_size=100
+epochs=3
+activation='relu'
+loss='mse'
+optimizer='sgd'
+learning_rate=0.001
+scaling='std'
+drop=0.1
+feature_subsample=500
+validation_split=0.1
+rng_seed=2017
+initialization='normal'
+min_logconc=-5.
+max_logconc=-4.
+category_cutoffs=[0.]
+test_cell_split=0.15
+cell_features=['expression']
+drug_features=['descriptors']
+subsample='naive_balancing'
+batch_normalization=False
+cell_noise_sigma=0.
+output_dir='save'

Pilot1/Uno/uno_perf_bench_model.txt

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+[Global_Params]
+train_sources=['CCLE']
+test_sources=['train']
+cell_types=None
+cell_features=['rnaseq']
+drug_features=['descriptors', 'fingerprints']
+dense=[1000, 1000, 1000]
+dense_feature_layers=[1000, 1000, 1000]
+activation='relu'
+loss='mse'
+optimizer='adam'
+scaling='std'
+drop=0
+epochs=3
+batch_size=32
+validation_split=0.2
+cv=1
+max_val_loss=1.0
+learning_rate=None
+base_lr=None
+residual=False
+reduce_lr=False
+warmup_lr=False
+batch_normalization=False
+feature_subsample=0
+rng_seed=2018
+save='save/uno'
+no_gen=False
+verbose = False
+use_landmark_genes=True
+
+[Monitor_Params]
+solr_root=''
+timeout=3600