Merge with develop

README.md

@@ -20,7 +20,44 @@ Each such a stream can consist of several components, including one problem inst
 
 As a result, the training & testing mechanisms are no longer pinned to a specific model or problem, and built-in mechanisms for compatibility checking (handshaking), configuration management & statistics collection facilitate running diverse experiments.
 
-## Mainainers
+## Installation
+
+PTP relies on [PyTorch](https://github.com/pytorch/pytorch), so you need to install it first.
+Refer to the official installation [guide](https://github.com/pytorch/pytorch#installation) for its installation.
+It is easily installable via conda_, or you can compile it from source to optimize it for your machine.
+
+PTP is not (yet) available as a [pip](https://pip.pypa.io/en/stable/quickstart/) package, or on [conda](https://anaconda.org/pytorch/pytorch).
+However, we provide the `setup.py` script and recommend to use it for installation.
+First please clone the project repository::
+
+```console
+git clone git@github.com:IBM/pytorchpipe.git
+cd pytorchpipe/
+```
+
+Then, install the dependencies by running::
+
+```console
+python setup.py install
+```
+
+This command will install all dependencies via pip_.
+
+---
+**NOTE**
+
+If you plan to develop and introduce changes, please call the following command instead::
+
+```console
+  python setup.py develop
+```
+
+This will enable you to change the code of the existing components/workers and still be able to run them by calling the associated ``ptp-*`` commands.
+More in that subject can be found in the following blog post on [dev_mode](https://setuptools.readthedocs.io/en/latest/setuptools.html#development-mode).
+
+---
+
+## Maintainers
 
 A project of the Machine Intelligence team, IBM Research, Almaden.
 

configs/default/components/losses/nll_loss.yml

@@ -12,6 +12,9 @@ num_targets_dims: 1
 # Options: NLLLoss | CrossEntropyLoss (NOT OPERATIONAL YET!)
 # loss_function: NLLLoss
 
+# When set to True, performs masking of selected samples from batch (LOADED)
+use_masking: False
+
 streams: 
   ####################################################################
   # 2. Keymappings associated with INPUT and OUTPUT streams.
@@ -23,6 +26,9 @@ streams:
   # Stream containing batch of predictions (INPUT)
   predictions: predictions
 
+  # Stream containing masks used for masking of selected samples from batch (INPUT)
+  masks: masks
+
   # Stream containing loss (OUTPUT)
   loss: loss
 

configs/default/components/masking/join_masked_predictions.yml

@@ -0,0 +1,44 @@
+# This file defines the default values for the Join Masked Predictions component.
+
+####################################################################
+# 1. CONFIGURATION PARAMETERS that will be LOADED by the component.
+####################################################################
+
+# List of input stream names, each containing batch of predictions (LOADED)
+input_prediction_streams: ''
+
+# List of input stream names, each containing batch of masks (LOADED)
+input_mask_streams: ''
+
+# List of word mapping names - those will be loaded from globals (LOADED)
+input_word_mappings: ''
+
+streams: 
+  ####################################################################
+  # 2. Keymappings associated with INPUT and OUTPUT streams.
+  ####################################################################
+
+  # Stream containing batch of output strings (OUTPUT)
+  output_strings: output_strings
+
+  # Stream containing batch of output indices (OUTPUT)
+  # WARNING: As performed operations are not differentiable,
+  # those indices cannot be used for e.g. calculation of loss!!
+  output_indices: output_indices
+
+globals:
+  ####################################################################
+  # 3. Keymappings of variables that will be RETRIEVED from GLOBALS.
+  ####################################################################
+
+  # Vocabulary used to produce output strings (RETRIEVED)
+  output_word_mappings: output_word_mappings
+
+  ####################################################################
+  # 4. Keymappings associated with GLOBAL variables that will be SET.
+  ####################################################################
+
+  ####################################################################
+  # 5. Keymappings associated with statistics that will be ADDED.
+  ####################################################################
+

configs/default/components/masking/string_to_mask.yml

@@ -0,0 +1,40 @@
+# This file defines the default values for the String To Mask component.
+
+####################################################################
+# 1. CONFIGURATION PARAMETERS that will be LOADED by the component.
+####################################################################
+
+# Value that will be used when word is out of vocavbulary (LOADED)
+# (Mask for that element will be 0 as well)
+out_of_vocabulary_value: -1
+
+streams: 
+  ####################################################################
+  # 2. Keymappings associated with INPUT and OUTPUT streams.
+  ####################################################################
+
+  # Stream containing input strings (INPUT)
+  strings: strings
+
+  # Stream containing output masks (OUTPUT)
+  masks: masks
+
+  # Stream containing output indices (OUTPUT)
+  string_indices: string_indices
+
+globals:
+  ####################################################################
+  # 3. Keymappings of variables that will be RETRIEVED from GLOBALS.
+  ####################################################################
+
+  # Vocabulary used to produce masks and indices (RETRIEVED)
+  word_mappings: word_mappings
+
+  ####################################################################
+  # 4. Keymappings associated with GLOBAL variables that will be SET.
+  ####################################################################
+
+  ####################################################################
+  # 5. Keymappings associated with statistics that will be ADDED.
+  ####################################################################
+

configs/default/components/publishers/accuracy_statistics.yml

@@ -4,6 +4,14 @@
 # 1. CONFIGURATION PARAMETERS that will be LOADED by the component.
 ####################################################################
 
+# Flag indicating whether prediction are represented as distributions or indices (LOADED)
+# Options: True (expects distribution for each preditions)
+#          False (expects indices (max args))
+use_prediction_distributions: True
+
+# When set to True, performs masking of selected samples from batch (LOADED)
+use_masking: False
+
 streams: 
   ####################################################################
   # 2. Keymappings associated with INPUT and OUTPUT streams.
@@ -15,6 +23,9 @@ streams:
   # Stream containing batch of predictions (INPUT)
   predictions: predictions
 
+  # Stream containing masks used for masking of selected samples from batch (INPUT)
+  masks: masks
+
 globals:
   ####################################################################
   # 3. Keymappings of variables that will be RETRIEVED from GLOBALS.

configs/default/components/publishers/precision_recall_statistics.yml

@@ -4,6 +4,11 @@
 # 1. CONFIGURATION PARAMETERS that will be LOADED by the component.
 ####################################################################
 
+# Flag indicating whether prediction are represented as distributions or indices (LOADED)
+# Options: True (expects distribution for each preditions)
+#          False (expects indices (max args))
+use_prediction_distributions: True
+
 # Flag indicating whether confusion matrix will be shown (LOADED)
 show_confusion_matrix: False
 
@@ -13,6 +18,9 @@ show_class_scores: False
 # When set to true, will use the provided word mappings as labels (LOADED)
 use_word_mappings: False
 
+# When set to True, performs masking of selected samples from batch (LOADED)
+use_masking: False
+
 streams: 
   ####################################################################
   # 2. Keymappings associated with INPUT and OUTPUT streams.
@@ -24,6 +32,9 @@ streams:
   # Stream containing batch of predictions (INPUT)
   predictions: predictions
 
+  # Stream containing masks used for masking of selected samples from batch (INPUT)
+  masks: masks
+
 globals:
   ####################################################################
   # 3. Keymappings of variables that will be RETRIEVED from GLOBALS.

configs/mnist/default_mnist.yml

@@ -12,10 +12,10 @@ training:
   # optimizer parameters:
   optimizer:
     name: Adam
-    lr: 0.01
+    lr: 0.0001
   # settings parameters
   terminal_conditions:
-    loss_stop: 1.0e-2
+    loss_stop: 0.05
     episode_limit: 10000
     epoch_limit: 10
 
@@ -45,20 +45,16 @@ pipeline:
   # Loss
   nllloss:
     type: NLLLoss
-    priority: 10
+    priority: 10.0
 
   # Statistics.
   batch_size:
     type: BatchSizeStatistics
-    priority: 100.1
-
-  accuracy:
-    type: AccuracyStatistics
-    priority: 100.2
+    priority: 100.0
 
   precision_recall:
     type: PrecisionRecallStatistics
-    priority: 100.3
+    priority: 100.1
     use_word_mappings: True
     show_class_scores: True
     globals:

configs/mnist/mnist_classification_convnet_softmax.yml

@@ -23,7 +23,7 @@ pipeline:
 
   # Image classifier.
   classifier:
-    type: SoftmaxClassifier 
+    type: FeedForwardNetwork 
     priority: 3
     streams:
       inputs: reshaped_maps