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Merge branch 'release_05'
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‎common/parsing_utils.py‎

Lines changed: 49 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -19,48 +19,48 @@
1919
"name": "config_file",
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"type": str,
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"default": argparse.SUPPRESS,
22-
"help": "specify model configuration file",
22+
"help": "Specify alternate model configuration file",
2323
},
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{
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"name": "data_type",
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"abv": "d",
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"type": str,
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"default": argparse.SUPPRESS,
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"choices": ["f16", "f32", "f64"],
30-
"help": "default floating point.",
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"help": "Specify default floating points precision",
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},
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{
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"name": "rng_seed",
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"abv": "r",
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"type": int,
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"default": argparse.SUPPRESS,
37-
"help": "random number generator seed.",
37+
"help": "Random number generator seed",
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},
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{
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"name": "train_bool",
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"type": hutils.str2bool,
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"default": True,
43-
"help": "train model.",
43+
"help": "Flag to toggle model training",
4444
},
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{
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"name": "eval_bool",
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"type": hutils.str2bool,
4848
"default": argparse.SUPPRESS,
49-
"help": "evaluate model (use it for inference).",
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"help": "Flag to evaluate model (use it for inference).",
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},
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{
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"name": "timeout",
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"action": "store",
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"type": int,
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"default": argparse.SUPPRESS,
56-
"help": "seconds allowed to train model (default: no timeout).",
56+
"help": "Maximum time in seconds allowed to train model (default: no timeout).",
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},
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{
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"name": "gpus",
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"nargs": "+",
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"type": int,
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"default": argparse.SUPPRESS,
63-
"help": "set IDs of GPUs to use.",
63+
"help": "Set IDs of GPUs to use.",
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},
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{
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"name": "profiling",
@@ -77,64 +77,64 @@
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"abv": "s",
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"type": str,
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"default": argparse.SUPPRESS,
80-
"help": "file path to save model snapshots.",
80+
"help": "File path to save model snapshots.",
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},
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{
8383
"name": "model_name",
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"type": str,
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"default": argparse.SUPPRESS,
86-
"help": "specify model name to use when building filenames for saving.",
86+
"help": "Specify model name to use when building filenames for saving.",
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},
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{
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"name": "home_dir",
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"type": str,
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"default": argparse.SUPPRESS,
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"help": "set home directory.",
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"help": "Set home directory.",
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},
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{
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"name": "train_data",
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"action": "store",
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"type": str,
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"default": argparse.SUPPRESS,
99-
"help": "training data filename.",
99+
"help": "Training data filename.",
100100
},
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{
102102
"name": "val_data",
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"action": "store",
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"type": str,
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"default": argparse.SUPPRESS,
106-
"help": "validation data filename.",
106+
"help": "Validation data filename.",
107107
},
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{
109109
"name": "test_data",
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"type": str,
111111
"action": "store",
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"default": argparse.SUPPRESS,
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"help": "testing data filename.",
113+
"help": "Testing data filename.",
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},
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{
116116
"name": "output_dir",
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"type": str,
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"default": argparse.SUPPRESS,
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"help": "output directory.",
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"help": "Set output directory.",
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},
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{
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"name": "data_url",
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"type": str,
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"default": argparse.SUPPRESS,
125-
"help": "set data source url.",
125+
"help": "Set data source url.",
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},
127127
{
128128
"name": "experiment_id",
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"type": str,
130130
"default": "EXP000",
131-
"help": "set the experiment unique identifier.",
131+
"help": "Set the experiment unique identifier.",
132132
},
133133
{
134134
"name": "run_id",
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"type": str,
136136
"default": "RUN000",
137-
"help": "set the run unique identifier.",
137+
"help": "Set the run unique identifier.",
138138
},
139139
]
140140

@@ -144,7 +144,7 @@
144144
"abv": "v",
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"type": hutils.str2bool,
146146
"default": False,
147-
"help": "increase output verbosity.",
147+
"help": "Increase output verbosity.",
148148
},
149149
{"name": "logfile", "abv": "l", "type": str, "default": None, "help": "log file"},
150150
]
@@ -155,19 +155,19 @@
155155
"type": str,
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"default": argparse.SUPPRESS,
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"choices": ["minabs", "minmax", "std", "none"],
158-
"help": "type of feature scaling; 'minabs': to [-1,1]; 'minmax': to [0,1], 'std': standard unit normalization; 'none': no normalization.",
158+
"help": "Type of feature scaling; 'minabs': to [-1,1]; 'minmax': to [0,1], 'std': standard unit normalization; 'none': no normalization.",
159159
},
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{
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"name": "shuffle",
162162
"type": hutils.str2bool,
163163
"default": False,
164-
"help": "randomly shuffle data set (produces different training and testing partitions each run depending on the seed)",
164+
"help": "Randomly shuffle data set (produces different training and testing partitions each run depending on the seed)",
165165
},
166166
{
167167
"name": "feature_subsample",
168168
"type": int,
169169
"default": argparse.SUPPRESS,
170-
"help": "number of features to randomly sample from each category (cellline expression, drug descriptors, etc), 0 means using all features",
170+
"help": "Number of features to randomly sample from each category (cellline expression, drug descriptors, etc), 0 means using all features",
171171
},
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]
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@@ -176,83 +176,83 @@
176176
"name": "dense",
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"nargs": "+",
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"type": int,
179-
"help": "number of units in fully connected layers in an integer array.",
179+
"help": "Number of units in fully connected layers in an integer array.",
180180
},
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{
182182
"name": "conv",
183183
"nargs": "+",
184184
"type": int,
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"default": argparse.SUPPRESS,
186-
"help": "integer array describing convolution layers: conv1_filters, conv1_filter_len, conv1_stride, conv2_filters, conv2_filter_len, conv2_stride ....",
186+
"help": "Integer array describing convolution layers: conv1_filters, conv1_filter_len, conv1_stride, conv2_filters, conv2_filter_len, conv2_stride ....",
187187
},
188188
{
189189
"name": "locally_connected",
190190
"type": hutils.str2bool,
191191
"default": argparse.SUPPRESS,
192-
"help": "use locally connected layers instead of convolution layers.",
192+
"help": "Use locally connected layers instead of convolution layers.",
193193
},
194194
{
195195
"name": "activation",
196196
"abv": "a",
197197
"type": str,
198198
"default": argparse.SUPPRESS,
199-
"help": "keras activation function to use in inner layers: relu, tanh, sigmoid...",
199+
"help": "Activation function to use in inner layers: relu, tanh, sigmoid...",
200200
},
201201
{
202202
"name": "out_activation",
203203
"type": str,
204204
"default": argparse.SUPPRESS,
205-
"help": "keras activation function to use in out layer: softmax, linear, ...",
205+
"help": "Activation function to use in out layer: softmax, linear, ...",
206206
},
207207
{
208208
"name": "lstm_size",
209209
"nargs": "+",
210210
"type": int,
211211
"default": argparse.SUPPRESS,
212-
"help": "integer array describing size of LSTM internal state per layer.",
212+
"help": "Integer array describing size of LSTM internal state per layer.",
213213
},
214214
{
215215
"name": "recurrent_dropout",
216216
"action": "store",
217217
"type": float,
218218
"default": argparse.SUPPRESS,
219-
"help": "ratio of recurrent dropout.",
219+
"help": "Ratio of recurrent dropout.",
220220
},
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{
222222
"name": "dropout",
223223
"type": float,
224224
"default": argparse.SUPPRESS,
225-
"help": "ratio of dropout used in fully connected layers.",
225+
"help": "Ratio of dropout used in fully connected layers.",
226226
},
227227
{
228228
"name": "pool",
229229
"type": int,
230230
"default": argparse.SUPPRESS,
231-
"help": "pooling layer length.",
231+
"help": "Pooling layer length.",
232232
},
233233
{
234234
"name": "batch_normalization",
235235
"type": hutils.str2bool,
236236
"default": argparse.SUPPRESS,
237-
"help": "use batch normalization.",
237+
"help": "Use batch normalization.",
238238
},
239239
{
240240
"name": "loss",
241241
"type": str,
242242
"default": argparse.SUPPRESS,
243-
"help": "keras loss function to use: mse, ...",
243+
"help": "Loss function to use: mse, ...",
244244
},
245245
{
246246
"name": "optimizer",
247247
"type": str,
248248
"default": argparse.SUPPRESS,
249-
"help": "keras optimizer to use: sgd, rmsprop, ...",
249+
"help": "Optimizer to use: sgd, rmsprop, ...",
250250
},
251251
{
252252
"name": "metrics",
253253
"type": str,
254254
"default": argparse.SUPPRESS,
255-
"help": "metrics to evaluate performance: accuracy, ...",
255+
"help": "Metrics to evaluate performance: accuracy, ...",
256256
},
257257
]
258258

@@ -262,33 +262,33 @@
262262
"type": int,
263263
"abv": "e",
264264
"default": argparse.SUPPRESS,
265-
"help": "number of training epochs.",
265+
"help": "Number of training epochs.",
266266
},
267267
{
268268
"name": "batch_size",
269269
"type": int,
270270
"abv": "z",
271271
"default": argparse.SUPPRESS,
272-
"help": "batch size.",
272+
"help": "Batch size.",
273273
},
274274
{
275275
"name": "learning_rate",
276276
"abv": "lr",
277277
"type": float,
278278
"default": argparse.SUPPRESS,
279-
"help": "overrides the learning rate for training.",
279+
"help": "Overrides the default learning rate for training.",
280280
},
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{
282282
"name": "early_stop",
283283
"type": hutils.str2bool,
284284
"default": argparse.SUPPRESS,
285-
"help": "activates keras callback for early stopping of training in function of the monitored variable specified.",
285+
"help": "Activates keras callback for early stopping of training in function of the monitored variable specified.",
286286
},
287287
{
288288
"name": "momentum",
289289
"type": float,
290290
"default": argparse.SUPPRESS,
291-
"help": "overrides the momentum to use in the SGD optimizer when training.",
291+
"help": "Overrides the default momentum to use in the SGD optimizer when training.",
292292
},
293293
{
294294
"name": "initialization",
@@ -303,43 +303,43 @@
303303
"lecun_uniform",
304304
"he_normal",
305305
],
306-
"help": "type of weight initialization; 'constant': to 0; 'uniform': to [-0.05,0.05], 'normal': mean 0, stddev 0.05; 'glorot_uniform': [-lim,lim] with lim = sqrt(6/(fan_in+fan_out)); 'lecun_uniform' : [-lim,lim] with lim = sqrt(3/fan_in); 'he_normal' : mean 0, stddev sqrt(2/fan_in).",
306+
"help": "Type of weight initialization; 'constant': to 0; 'uniform': to [-0.05,0.05], 'normal': mean 0, stddev 0.05; 'glorot_uniform': [-lim,lim] with lim = sqrt(6/(fan_in+fan_out)); 'lecun_uniform' : [-lim,lim] with lim = sqrt(3/fan_in); 'he_normal' : mean 0, stddev sqrt(2/fan_in).",
307307
},
308308
{
309309
"name": "val_split",
310310
"type": float,
311311
"default": argparse.SUPPRESS,
312-
"help": "fraction of data to use in validation.",
312+
"help": "Fraction of data to use in validation.",
313313
},
314314
{
315315
"name": "train_steps",
316316
"type": int,
317317
"default": argparse.SUPPRESS,
318-
"help": "overrides the number of training batches per epoch if set to nonzero.",
318+
"help": "Overrides the number of training batches per epoch if set to nonzero.",
319319
},
320320
{
321321
"name": "val_steps",
322322
"type": int,
323323
"default": argparse.SUPPRESS,
324-
"help": "overrides the number of validation batches per epoch if set to nonzero.",
324+
"help": "Overrides the number of validation batches per epoch if set to nonzero.",
325325
},
326326
{
327327
"name": "test_steps",
328328
"type": int,
329329
"default": argparse.SUPPRESS,
330-
"help": "overrides the number of test batches per epoch if set to nonzero.",
330+
"help": "Overrides the number of test batches per epoch if set to nonzero.",
331331
},
332332
{
333333
"name": "train_samples",
334334
"type": int,
335335
"default": argparse.SUPPRESS,
336-
"help": "overrides the number of training samples if set to nonzero.",
336+
"help": "Overrides the number of training samples if set to nonzero.",
337337
},
338338
{
339339
"name": "val_samples",
340340
"type": int,
341341
"default": argparse.SUPPRESS,
342-
"help": "overrides the number of validation samples if set to nonzero.",
342+
"help": "Overrides the number of validation samples if set to nonzero.",
343343
},
344344
]
345345

@@ -362,19 +362,19 @@
362362
"name": "clr_base_lr",
363363
"type": float,
364364
"default": argparse.SUPPRESS,
365-
"help": "Base lr for cycle lr.",
365+
"help": "Base lr for cyclic lr.",
366366
},
367367
{
368368
"name": "clr_max_lr",
369369
"type": float,
370370
"default": argparse.SUPPRESS,
371-
"help": "Max lr for cycle lr.",
371+
"help": "Max lr for cyclic lr.",
372372
},
373373
{
374374
"name": "clr_gamma",
375375
"type": float,
376376
"default": argparse.SUPPRESS,
377-
"help": "Gamma parameter for learning cycle LR.",
377+
"help": "Gamma parameter for cyclic LR.",
378378
},
379379
]
380380

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