diff --git a/common/parsing_utils.py b/common/parsing_utils.py index 9606e6f4..9a2bb3b1 100644 --- a/common/parsing_utils.py +++ b/common/parsing_utils.py @@ -19,7 +19,7 @@ "name": "config_file", "type": str, "default": argparse.SUPPRESS, - "help": "specify model configuration file", + "help": "Specify alternate model configuration file", }, { "name": "data_type", @@ -27,40 +27,40 @@ "type": str, "default": argparse.SUPPRESS, "choices": ["f16", "f32", "f64"], - "help": "default floating point.", + "help": "Specify default floating points precision", }, { "name": "rng_seed", "abv": "r", "type": int, "default": argparse.SUPPRESS, - "help": "random number generator seed.", + "help": "Random number generator seed", }, { "name": "train_bool", "type": hutils.str2bool, "default": True, - "help": "train model.", + "help": "Flag to toggle model training", }, { "name": "eval_bool", "type": hutils.str2bool, "default": argparse.SUPPRESS, - "help": "evaluate model (use it for inference).", + "help": "Flag to evaluate model (use it for inference).", }, { "name": "timeout", "action": "store", "type": int, "default": argparse.SUPPRESS, - "help": "seconds allowed to train model (default: no timeout).", + "help": "Maximum time in seconds allowed to train model (default: no timeout).", }, { "name": "gpus", "nargs": "+", "type": int, "default": argparse.SUPPRESS, - "help": "set IDs of GPUs to use.", + "help": "Set IDs of GPUs to use.", }, { "name": "profiling", @@ -77,64 +77,64 @@ "abv": "s", "type": str, "default": argparse.SUPPRESS, - "help": "file path to save model snapshots.", + "help": "File path to save model snapshots.", }, { "name": "model_name", "type": str, "default": argparse.SUPPRESS, - "help": "specify model name to use when building filenames for saving.", + "help": "Specify model name to use when building filenames for saving.", }, { "name": "home_dir", "type": str, "default": argparse.SUPPRESS, - "help": "set home directory.", + "help": "Set home directory.", }, { "name": "train_data", "action": "store", "type": str, "default": argparse.SUPPRESS, - "help": "training data filename.", + "help": "Training data filename.", }, { "name": "val_data", "action": "store", "type": str, "default": argparse.SUPPRESS, - "help": "validation data filename.", + "help": "Validation data filename.", }, { "name": "test_data", "type": str, "action": "store", "default": argparse.SUPPRESS, - "help": "testing data filename.", + "help": "Testing data filename.", }, { "name": "output_dir", "type": str, "default": argparse.SUPPRESS, - "help": "output directory.", + "help": "Set output directory.", }, { "name": "data_url", "type": str, "default": argparse.SUPPRESS, - "help": "set data source url.", + "help": "Set data source url.", }, { "name": "experiment_id", "type": str, "default": "EXP000", - "help": "set the experiment unique identifier.", + "help": "Set the experiment unique identifier.", }, { "name": "run_id", "type": str, "default": "RUN000", - "help": "set the run unique identifier.", + "help": "Set the run unique identifier.", }, ] @@ -144,7 +144,7 @@ "abv": "v", "type": hutils.str2bool, "default": False, - "help": "increase output verbosity.", + "help": "Increase output verbosity.", }, {"name": "logfile", "abv": "l", "type": str, "default": None, "help": "log file"}, ] @@ -155,19 +155,19 @@ "type": str, "default": argparse.SUPPRESS, "choices": ["minabs", "minmax", "std", "none"], - "help": "type of feature scaling; 'minabs': to [-1,1]; 'minmax': to [0,1], 'std': standard unit normalization; 'none': no normalization.", + "help": "Type of feature scaling; 'minabs': to [-1,1]; 'minmax': to [0,1], 'std': standard unit normalization; 'none': no normalization.", }, { "name": "shuffle", "type": hutils.str2bool, "default": False, - "help": "randomly shuffle data set (produces different training and testing partitions each run depending on the seed)", + "help": "Randomly shuffle data set (produces different training and testing partitions each run depending on the seed)", }, { "name": "feature_subsample", "type": int, "default": argparse.SUPPRESS, - "help": "number of features to randomly sample from each category (cellline expression, drug descriptors, etc), 0 means using all features", + "help": "Number of features to randomly sample from each category (cellline expression, drug descriptors, etc), 0 means using all features", }, ] @@ -176,83 +176,83 @@ "name": "dense", "nargs": "+", "type": int, - "help": "number of units in fully connected layers in an integer array.", + "help": "Number of units in fully connected layers in an integer array.", }, { "name": "conv", "nargs": "+", "type": int, "default": argparse.SUPPRESS, - "help": "integer array describing convolution layers: conv1_filters, conv1_filter_len, conv1_stride, conv2_filters, conv2_filter_len, conv2_stride ....", + "help": "Integer array describing convolution layers: conv1_filters, conv1_filter_len, conv1_stride, conv2_filters, conv2_filter_len, conv2_stride ....", }, { "name": "locally_connected", "type": hutils.str2bool, "default": argparse.SUPPRESS, - "help": "use locally connected layers instead of convolution layers.", + "help": "Use locally connected layers instead of convolution layers.", }, { "name": "activation", "abv": "a", "type": str, "default": argparse.SUPPRESS, - "help": "keras activation function to use in inner layers: relu, tanh, sigmoid...", + "help": "Activation function to use in inner layers: relu, tanh, sigmoid...", }, { "name": "out_activation", "type": str, "default": argparse.SUPPRESS, - "help": "keras activation function to use in out layer: softmax, linear, ...", + "help": "Activation function to use in out layer: softmax, linear, ...", }, { "name": "lstm_size", "nargs": "+", "type": int, "default": argparse.SUPPRESS, - "help": "integer array describing size of LSTM internal state per layer.", + "help": "Integer array describing size of LSTM internal state per layer.", }, { "name": "recurrent_dropout", "action": "store", "type": float, "default": argparse.SUPPRESS, - "help": "ratio of recurrent dropout.", + "help": "Ratio of recurrent dropout.", }, { "name": "dropout", "type": float, "default": argparse.SUPPRESS, - "help": "ratio of dropout used in fully connected layers.", + "help": "Ratio of dropout used in fully connected layers.", }, { "name": "pool", "type": int, "default": argparse.SUPPRESS, - "help": "pooling layer length.", + "help": "Pooling layer length.", }, { "name": "batch_normalization", "type": hutils.str2bool, "default": argparse.SUPPRESS, - "help": "use batch normalization.", + "help": "Use batch normalization.", }, { "name": "loss", "type": str, "default": argparse.SUPPRESS, - "help": "keras loss function to use: mse, ...", + "help": "Loss function to use: mse, ...", }, { "name": "optimizer", "type": str, "default": argparse.SUPPRESS, - "help": "keras optimizer to use: sgd, rmsprop, ...", + "help": "Optimizer to use: sgd, rmsprop, ...", }, { "name": "metrics", "type": str, "default": argparse.SUPPRESS, - "help": "metrics to evaluate performance: accuracy, ...", + "help": "Metrics to evaluate performance: accuracy, ...", }, ] @@ -262,33 +262,33 @@ "type": int, "abv": "e", "default": argparse.SUPPRESS, - "help": "number of training epochs.", + "help": "Number of training epochs.", }, { "name": "batch_size", "type": int, "abv": "z", "default": argparse.SUPPRESS, - "help": "batch size.", + "help": "Batch size.", }, { "name": "learning_rate", "abv": "lr", "type": float, "default": argparse.SUPPRESS, - "help": "overrides the learning rate for training.", + "help": "Overrides the default learning rate for training.", }, { "name": "early_stop", "type": hutils.str2bool, "default": argparse.SUPPRESS, - "help": "activates keras callback for early stopping of training in function of the monitored variable specified.", + "help": "Activates keras callback for early stopping of training in function of the monitored variable specified.", }, { "name": "momentum", "type": float, "default": argparse.SUPPRESS, - "help": "overrides the momentum to use in the SGD optimizer when training.", + "help": "Overrides the default momentum to use in the SGD optimizer when training.", }, { "name": "initialization", @@ -303,43 +303,43 @@ "lecun_uniform", "he_normal", ], - "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).", + "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).", }, { "name": "val_split", "type": float, "default": argparse.SUPPRESS, - "help": "fraction of data to use in validation.", + "help": "Fraction of data to use in validation.", }, { "name": "train_steps", "type": int, "default": argparse.SUPPRESS, - "help": "overrides the number of training batches per epoch if set to nonzero.", + "help": "Overrides the number of training batches per epoch if set to nonzero.", }, { "name": "val_steps", "type": int, "default": argparse.SUPPRESS, - "help": "overrides the number of validation batches per epoch if set to nonzero.", + "help": "Overrides the number of validation batches per epoch if set to nonzero.", }, { "name": "test_steps", "type": int, "default": argparse.SUPPRESS, - "help": "overrides the number of test batches per epoch if set to nonzero.", + "help": "Overrides the number of test batches per epoch if set to nonzero.", }, { "name": "train_samples", "type": int, "default": argparse.SUPPRESS, - "help": "overrides the number of training samples if set to nonzero.", + "help": "Overrides the number of training samples if set to nonzero.", }, { "name": "val_samples", "type": int, "default": argparse.SUPPRESS, - "help": "overrides the number of validation samples if set to nonzero.", + "help": "Overrides the number of validation samples if set to nonzero.", }, ] @@ -362,19 +362,19 @@ "name": "clr_base_lr", "type": float, "default": argparse.SUPPRESS, - "help": "Base lr for cycle lr.", + "help": "Base lr for cyclic lr.", }, { "name": "clr_max_lr", "type": float, "default": argparse.SUPPRESS, - "help": "Max lr for cycle lr.", + "help": "Max lr for cyclic lr.", }, { "name": "clr_gamma", "type": float, "default": argparse.SUPPRESS, - "help": "Gamma parameter for learning cycle LR.", + "help": "Gamma parameter for cyclic LR.", }, ]