Remove deprecated solr_root keywords

Author: jmohdyusof

Pilot1/Uno/README.AUC.md

@@ -72,7 +72,6 @@ Params:
  'scaling': 'std',
  'shuffle': False,
  'single': True,
- 'solr_root': '',
  'tb': False,
  'tb_prefix': 'tb',
  'test_sources': ['train'],

Pilot1/Uno/README.md

@@ -7,7 +7,7 @@ Uno can be trained with a subset of dose response data sources. Here is an comma
 uno_baseline_keras2.py --train_sources all --cache cache/all --use_landmark_genes True --preprocess_rnaseq source_scale --no_feature_source True --no_response_source True
 Using TensorFlow backend.
 Params: {'activation': 'relu', 'batch_size': 32, 'dense': [1000, 1000, 1000], 'dense_feature_layers': [1000, 1000, 1000], 'drop': 0, 'epochs': 10, 'learning_rate': None, 'loss':
-'mse', 'optimizer': 'adam', 'residual': False, 'rng_seed': 2018, 'save': 'save/uno', 'scaling': 'std', 'feature_subsample': 0, 'validation_split': 0.2, 'solr_root': '', 'timeout'
+'mse', 'optimizer': 'adam', 'residual': False, 'rng_seed': 2018, 'save': 'save/uno', 'scaling': 'std', 'feature_subsample': 0, 'validation_split': 0.2, 'timeout'
 : -1, 'train_sources': ['all'], 'test_sources': ['train'], 'cell_types': None, 'cell_features': ['rnaseq'], 'drug_features': ['descriptors', 'fingerprints'], 'cv': 1, 'max_val_lo
 ss': 1.0, 'base_lr': None, 'reduce_lr': False, 'warmup_lr': False, 'batch_normalization': False, 'no_gen': False, 'config_file': '/raid/fangfang/Benchmarks/Pilot1/Uno/uno_default
 _model.txt', 'verbose': False, 'logfile': None, 'train_bool': True, 'shuffle': True, 'alpha_dropout': False, 'gpus': [], 'experiment_id': 'EXP.000', 'run_id': 'RUN.000', 'by_cell

Pilot1/Uno/uno_auc_clr_model.txt

@@ -38,9 +38,9 @@ cp=True
 save_path='save/uno'
 
 single=True
-timeout=-1
 
 [Monitor_Params]
+timeout=-1
 
 [CLR_Params]
 clr_flag = True

Pilot1/Uno/uno_auc_model.txt

@@ -38,7 +38,6 @@ cp=True
 save_path='save/uno'
 
 single=True
-timeout=-1
 
 [Monitor_Params]
-solr_root=''
+timeout=-1

Pilot1/Uno/uno_by_drug_example.txt

@@ -36,5 +36,4 @@ by_drug='paclitaxel'
 cache='cache.pac'
 
 [Monitor_Params]
-solr_root=''
 timeout=3600

Pilot1/Uno/uno_clr_model.txt

@@ -0,0 +1,39 @@
+[Global_Params]
+train_sources=['GDSC', 'CTRP', 'ALMANAC']
+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'
+dropout=0
+epochs=10
+batch_size=32
+val_split=0.2
+cv=1
+max_val_loss=1.0
+learning_rate=None
+base_lr=None
+residual=False
+reduce_lr=True
+warmup_lr=True
+batch_normalization=False
+feature_subsample=0
+rng_seed=2018
+save_path='save/uno'
+no_gen=False
+verbose = False
+
+[Monitor_Params]
+timeout=3600
+
+[CLR_Params]
+clr_flag = False
+clr_mode = 'trng1'
+clr_base_lr = 0.00001
+clr_max_lr = 0.001
+clr_gamma = 0.999

Pilot1/Uno/uno_default_model.txt

@@ -29,5 +29,4 @@ no_gen=False
 verbose = False
 
 [Monitor_Params]
-solr_root=''
 timeout=3600

Pilot1/Uno/uno_fom_model.txt

@@ -34,5 +34,4 @@ no_response_source=True
 single=True
 
 [Monitor_Params]
-solr_root=''
 timeout=-1

Pilot1/Uno/uno_perf_bench_model.txt

@@ -30,5 +30,4 @@ verbose = False
 use_landmark_genes=True
 
 [Monitor_Params]
-solr_root=''
 timeout=3600